From f87dfb9828e33f9703729b76cd0f5b064cd40b11 Mon Sep 17 00:00:00 2001 From: Howard Pritchard Date: Tue, 10 Mar 2020 02:01:02 -0600 Subject: [PATCH 001/377] openmpi: add version 4.0.3 (#15414) Signed-off-by: Howard Pritchard --- var/spack/repos/builtin/packages/openmpi/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index efb7198444a..a2b75bd67ee 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -80,9 +80,10 @@ class Openmpi(AutotoolsPackage): version('develop', branch='master') # Current - version('4.0.2', sha256='900bf751be72eccf06de9d186f7b1c4b5c2fa9fa66458e53b77778dffdfe4057') # libmpi.so.40.20.2 + version('4.0.3', sha256='1402feced8c3847b3ab8252165b90f7d1fa28c23b6b2ca4632b6e4971267fd03') # libmpi.so.40.20.3 # Still supported + version('4.0.2', sha256='900bf751be72eccf06de9d186f7b1c4b5c2fa9fa66458e53b77778dffdfe4057') # libmpi.so.40.20.2 version('4.0.1', sha256='cce7b6d20522849301727f81282201d609553103ac0b09162cf28d102efb9709') # libmpi.so.40.20.1 version('4.0.0', sha256='2f0b8a36cfeb7354b45dda3c5425ef8393c9b04115570b615213faaa3f97366b') # libmpi.so.40.20.0 version('3.1.5', preferred=True, sha256='fbf0075b4579685eec8d56d34d4d9c963e6667825548554f5bf308610af72133') # libmpi.so.40.10.4 @@ -193,7 +194,7 @@ class Openmpi(AutotoolsPackage): patch('llnl-platforms.patch', when="@1.6.5") patch('configure.patch', when="@1.10.1") patch('fix_multidef_pmi_class.patch', when="@2.0.0:2.0.1") - patch('fix-ucx-1.7.0-api-instability.patch', when='@4.0.0:4.0.3') + patch('fix-ucx-1.7.0-api-instability.patch', when='@4.0.0:4.0.2') # Vader Bug: https://github.com/open-mpi/ompi/issues/5375 # Haven't release fix for 2.1.x From 65b131f3739fdcb3412e510cd3d175542eb97706 Mon Sep 17 00:00:00 2001 From: Tim Haines Date: Tue, 10 Mar 2020 03:58:40 -0500 Subject: [PATCH 002/377] Ignore Eclipse files and folders (#15413) --- .gitignore | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.gitignore b/.gitignore index f5169a54058..0c79893369d 100644 --- a/.gitignore +++ b/.gitignore @@ -27,3 +27,8 @@ lib/spack/spack/test/.cache *.in.log *.out.log *.orig + +# Eclipse files +.project +.cproject +.pydevproject From b86aa4ec187121f2386924a58e4b1e1ff65df00a Mon Sep 17 00:00:00 2001 From: Justin S <3630356+codeandkey@users.noreply.github.com> Date: Tue, 10 Mar 2020 04:05:34 -0500 Subject: [PATCH 003/377] eagle: new package at v1.1.2 (#15409) --- .../repos/builtin/packages/eagle/package.py | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 var/spack/repos/builtin/packages/eagle/package.py diff --git a/var/spack/repos/builtin/packages/eagle/package.py b/var/spack/repos/builtin/packages/eagle/package.py new file mode 100644 index 00000000000..81e0be6f903 --- /dev/null +++ b/var/spack/repos/builtin/packages/eagle/package.py @@ -0,0 +1,46 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Eagle(MakefilePackage): + """EAGLE: Explicit Alternative Genome Likelihood Evaluator""" + + homepage = "https://github.com/tony-kuo/eagle" + url = "https://github.com/tony-kuo/eagle/archive/v1.1.2.tar.gz" + + version('1.1.2', sha256='afe967560d1f8fdbd0caf4b93b5f2a86830e9e4d399fee4a526140431343045e') + + depends_on('curl') + depends_on('zlib') + depends_on('lzma') + depends_on('htslib') + + def edit(self, spec, prefix): + # remove unused gcc flags + filter_file('$(LFLAGS) $(INCLUDES)', '', 'Makefile', string=True) + + # drop static link to htslib + filter_file('$(LIBS)', '', 'Makefile', string=True) + + # don't try to build htslib. + filter_file('all: UTIL HTSLIB', 'all: UTIL', + 'Makefile', string=True) + + # add htslib link to ldflags + filter_file('-lcurl', '-lcurl -lhts', 'Makefile', string=True) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + + bins = [ + 'eagle', + 'eagle-rc', + 'eagle-nm', + ] + + for b in bins: + install(b, prefix.bin) From da677b3cb801cca408f73b46d188d2be0689a09b Mon Sep 17 00:00:00 2001 From: Mathias Anselmann Date: Tue, 10 Mar 2020 10:15:31 +0100 Subject: [PATCH 004/377] update binutils to 2.34 (#15401) --- var/spack/repos/builtin/packages/binutils/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index d84dd32bc58..1f4a675546b 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -14,6 +14,7 @@ class Binutils(AutotoolsPackage, GNUMirrorPackage): homepage = "http://www.gnu.org/software/binutils/" gnu_mirror_path = "binutils/binutils-2.28.tar.bz2" + version('2.34', sha256='89f010078b6cf69c23c27897d686055ab89b198dddf819efb0a4f2c38a0b36e6') version('2.33.1', sha256='0cb4843da15a65a953907c96bad658283f3c4419d6bcc56bf2789db16306adb2') version('2.32', sha256='de38b15c902eb2725eac6af21183a5f34ea4634cb0bcef19612b50e5ed31072d') version('2.31.1', sha256='ffcc382695bf947da6135e7436b8ed52d991cf270db897190f19d6f9838564d0') From ebe7590310c30d6860a7596eea639091e195f210 Mon Sep 17 00:00:00 2001 From: Melven Roehrig-Zoellner Date: Tue, 10 Mar 2020 10:18:29 +0100 Subject: [PATCH 005/377] bazel: add missing dependency on zip (#15402) --- var/spack/repos/builtin/packages/bazel/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/bazel/package.py b/var/spack/repos/builtin/packages/bazel/package.py index 655c9151781..26d79616dd9 100644 --- a/var/spack/repos/builtin/packages/bazel/package.py +++ b/var/spack/repos/builtin/packages/bazel/package.py @@ -92,6 +92,7 @@ class Bazel(Package): # https://docs.bazel.build/versions/master/install-compile-source.html#bootstrap-unix-prereq depends_on('jdk@1.8.0:1.8.999', type=('build', 'run')) depends_on('python', type=('build', 'run')) + depends_on('zip', type=('build', 'run')) # Pass Spack environment variables to the build patch('bazelruleclassprovider-0.25.patch', when='@0.25:') From 48f8f0ec58bd80a25b8e278fbcc1687ddd5585d9 Mon Sep 17 00:00:00 2001 From: TZ Date: Tue, 10 Mar 2020 16:03:14 +0100 Subject: [PATCH 006/377] likwid: added v5.0.1 (#15421) includes fixes for likwid-mpirun, better support for ARM and POWER, other bugfixes. For full support of ARM and POWER, #14183 has to be merged, too. Added TomTheBear as maintainer. He is the current main developer of LIKWID. --- var/spack/repos/builtin/packages/likwid/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/likwid/package.py b/var/spack/repos/builtin/packages/likwid/package.py index c24d5e720a8..c121b1ef35a 100644 --- a/var/spack/repos/builtin/packages/likwid/package.py +++ b/var/spack/repos/builtin/packages/likwid/package.py @@ -19,7 +19,9 @@ class Likwid(Package): homepage = "https://github.com/RRZE-HPC/likwid" url = "https://github.com/RRZE-HPC/likwid/archive/v5.0.0.tar.gz" git = "https://github.com/RRZE-HPC/likwid.git" + maintainers = ['TomTheBear'] + version('5.0.1', sha256='3757b0cb66e8af0116f9288c7f90543acbd8e2af8f72f77aef447ca2b3e76453') version('5.0.0', sha256='26623f5a1a5fec19d798f0114774a5293d1c93a148538b9591a13e50930fa41e') version('4.3.4', sha256='5c0d1c66b25dac8292a02232f06454067f031a238f010c62f40ef913c6609a83') version('4.3.3', sha256='a681378cd66c1679ca840fb5fac3136bfec93c01b3d78cc1d00a641db325a9a3') From 774407078728faee465addc48f825a7da330d40a Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Tue, 10 Mar 2020 09:08:10 -0600 Subject: [PATCH 007/377] gromacs: remove simd variants (#13636) --- .../repos/builtin/packages/gromacs/package.py | 48 +++++++++++++------ 1 file changed, 34 insertions(+), 14 deletions(-) diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py index 72aca3e5f03..037b25721b1 100644 --- a/var/spack/repos/builtin/packages/gromacs/package.py +++ b/var/spack/repos/builtin/packages/gromacs/package.py @@ -2,8 +2,7 @@ # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * +import llnl.util.cpu class Gromacs(CMakePackage): @@ -62,12 +61,6 @@ class Gromacs(CMakePackage): description='The build type to build', values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel', 'Reference', 'RelWithAssert', 'Profile')) - variant('simd', default='auto', - description='The SIMD instruction set to use', - values=('auto', 'none', 'SSE2', 'SSE4.1', 'AVX_128_FMA', 'AVX_256', - 'AVX2_128', 'AVX2_256', 'AVX_512', 'AVX_512_KNL', - 'IBM_QPX', 'Sparc64_HPC_ACE', 'IBM_VMX', 'IBM_VSX', - 'ARM_NEON', 'ARM_NEON_ASIMD')) variant('rdtscp', default=True, description='Enable RDTSCP instruction usage') variant('mdrun_only', default=False, description='Enables the build of a cut-down version' @@ -119,13 +112,40 @@ def cmake_args(self): else: options.append('-DGMX_GPU:BOOL=OFF') - simd_value = self.spec.variants['simd'].value - if simd_value == 'auto': - pass - elif simd_value == 'none': - options.append('-DGMX_SIMD:STRING=None') + # Activate SIMD based on properties of the target + target = self.spec.target + if target >= llnl.util.cpu.targets['bulldozer']: + # AMD Family 15h + options.append('-DGMX_SIMD=AVX_128_FMA') + elif target >= llnl.util.cpu.targets['zen']: + # AMD Family 17h + options.append('-DGMX_SIMD=AVX2_128') + elif target >= llnl.util.cpu.targets['power7']: + # IBM Power 7 and beyond + options.append('-DGMX_SIMD=IBM_VSX') + elif target.family == llnl.util.cpu.targets['aarch64']: + # ARMv8 + options.append('-DGMX_SIMD=ARM_NEON_ASIMD') + elif target == llnl.util.cpu.targets['mic_knl']: + # Intel KNL + options.append('-DGMX_SIMD=AVX_512_KNL') + elif target.vendor == 'GenuineIntel': + # Other Intel architectures + simd_features = [ + ('sse2', 'SSE2'), + ('sse4_1', 'SSE4.1'), + ('avx', 'AVX_256'), + ('axv128', 'AVX2_128'), + ('avx2', 'AVX2_256'), + ('avx512', 'AVX_512'), + ] + for feature, flag in reversed(simd_features): + if feature in target: + options.append('-DGMX_SIMD:STRING={0}'.format(flag)) + break else: - options.append('-DGMX_SIMD:STRING=' + simd_value) + # Fall back to this for unknown microarchitectures + options.append('-DGMX_SIMD:STRING=None') if '-rdtscp' in self.spec: options.append('-DGMX_USE_RDTSCP:BOOL=OFF') From 21634e805ef61b4e503f25a681003a9ef19e68c0 Mon Sep 17 00:00:00 2001 From: "Seth R. Johnson" Date: Tue, 10 Mar 2020 12:09:46 -0400 Subject: [PATCH 008/377] libfabric: added v1.9.1 (#15405) --- var/spack/repos/builtin/packages/libfabric/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/libfabric/package.py b/var/spack/repos/builtin/packages/libfabric/package.py index bb1730993f3..927dd24d551 100644 --- a/var/spack/repos/builtin/packages/libfabric/package.py +++ b/var/spack/repos/builtin/packages/libfabric/package.py @@ -16,9 +16,9 @@ class Libfabric(AutotoolsPackage): git = "https://github.com/ofiwg/libfabric.git" version('master', branch='master') - version('1.9.1rc1', sha256='fdf89a0797f0d923aaef2c41cc70be45716e4d07dc5d318365b9c17795eb49ab') + version('1.9.1', sha256='c305c6035c992523e08c7591a6a3707225ba3e72de40443eaed837a10df6771a') version('1.9.0', sha256='559bfb7376c38253c936d0b104591c3394880376d676894895706c4f5f88597c') - version('1.8.1', sha256='3c560b997f9eafd89f961dd8e8a29a81aad3e39aee888e3f3822da419047dc88', preferred=True) + version('1.8.1', sha256='3c560b997f9eafd89f961dd8e8a29a81aad3e39aee888e3f3822da419047dc88') version('1.8.0', sha256='c4763383a96af4af52cd81b3b094227f5cf8e91662f861670965994539b7ee37') version('1.7.1', sha256='f4e9cc48319763cff4943de96bf527b737c9f1d6ac3088b8b5c75d07bd719569') version('1.7.0', sha256='b3dd9cc0fa36fe8c3b9997ba279ec831a905704816c25fe3c4c09fc7eeceaac4') From 7118e24664a62f193fb86c2178e02033a219e834 Mon Sep 17 00:00:00 2001 From: Sergey Kosukhin Date: Tue, 10 Mar 2020 17:29:57 +0100 Subject: [PATCH 009/377] Parallel-netcdf: update package. (#15359) * Parallel-netcdf: update package. * Add a temporary patch for version 'develop'. * Rename version 'develop' to 'master'. * Drop the patch for 'master'. --- .../parallel-netcdf/nag_libtool.patch | 69 +++++++++++++++ .../packages/parallel-netcdf/package.py | 86 +++++++++++++------ 2 files changed, 128 insertions(+), 27 deletions(-) create mode 100644 var/spack/repos/builtin/packages/parallel-netcdf/nag_libtool.patch diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/nag_libtool.patch b/var/spack/repos/builtin/packages/parallel-netcdf/nag_libtool.patch new file mode 100644 index 00000000000..f391c1dc5ef --- /dev/null +++ b/var/spack/repos/builtin/packages/parallel-netcdf/nag_libtool.patch @@ -0,0 +1,69 @@ +--- a/configure ++++ b/configure +@@ -11745,6 +11745,8 @@ _LT_EOF + whole_archive_flag_spec= + tmp_sharedflag='--shared' ;; + nagfor*) # NAGFOR 5.3 ++ whole_archive_flag_spec='$wl--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive' ++ compiler_needs_object=yes + tmp_sharedflag='-Wl,-shared' ;; + xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' +@@ -21030,6 +21032,8 @@ _LT_EOF + whole_archive_flag_spec_F77= + tmp_sharedflag='--shared' ;; + nagfor*) # NAGFOR 5.3 ++ whole_archive_flag_spec_F77='$wl--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive' ++ compiler_needs_object_F77=yes + tmp_sharedflag='-Wl,-shared' ;; + xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' +@@ -24765,6 +24769,8 @@ _LT_EOF + whole_archive_flag_spec_FC= + tmp_sharedflag='--shared' ;; + nagfor*) # NAGFOR 5.3 ++ whole_archive_flag_spec_FC='$wl--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive' ++ compiler_needs_object_FC=yes + tmp_sharedflag='-Wl,-shared' ;; + xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' +--- a/scripts/ltmain.sh ++++ b/scripts/ltmain.sh +@@ -7862,6 +7862,13 @@ func_mode_link () + # Convert "-framework foo" to "foo.ltframework" + if test -n "$inherited_linker_flags"; then + tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'` ++ ++ # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor ++ func_cc_basename $CC ++ case $func_cc_basename_result in ++ nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;; ++ esac ++ + for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do + case " $new_inherited_linker_flags " in + *" $tmp_inherited_linker_flag "*) ;; +@@ -8881,7 +8888,8 @@ func_mode_link () + xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision" + verstring="-compatibility_version $minor_current -current_version $minor_current.$revision" + # On Darwin other compilers +- case $CC in ++ func_cc_basename $CC ++ case $func_cc_basename_result in + nagfor*) + verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision" + ;; +@@ -9493,6 +9501,13 @@ EOF + ;; + esac + ++ # Time to revert the changes made for nagfor. ++ func_cc_basename $CC ++ case $func_cc_basename_result in ++ nagfor*) ++ new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;; ++ esac ++ + # move library search paths that coincide with paths to not yet + # installed libraries to the beginning of the library search list + new_libs= diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py index 34a1af59845..384717d05ef 100644 --- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py +++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py @@ -25,7 +25,6 @@ def url_for_version(self, version): return url.format(version.dotted) - version('develop', branch='develop') version('master', branch='master') version('1.12.1', sha256='56f5afaa0ddc256791c405719b6436a83b92dcd5be37fe860dea103aee8250a2') version('1.11.2', sha256='d2c18601b364c35b5acb0a0b46cd6e14cae456e0eb854e5c789cf65f3cd6a2a7') @@ -42,41 +41,74 @@ def url_for_version(self, version): variant('fortran', default=True, description='Build the Fortran Interface') variant('pic', default=True, description='Produce position-independent code (for shared libs)') + variant('shared', default=True, description='Enable shared library') depends_on('mpi') depends_on('m4', type='build') + depends_on('autoconf', when='@master', type='build') + depends_on('automake', when='@master', type='build') + depends_on('libtool', when='@master', type='build') + + conflicts('+shared', when='@:1.9%nag+fortran') + conflicts('+shared', when='@:1.8') + + patch('nag_libtool.patch', when='@1.9:1.12.1%nag') + + @property + def libs(self): + libraries = ['libpnetcdf'] + + query_parameters = self.spec.last_query.extra_parameters + + if 'shared' in query_parameters: + shared = True + elif 'static' in query_parameters: + shared = False + else: + shared = '+shared' in self.spec + + libs = find_libraries( + libraries, root=self.prefix, shared=shared, recursive=True + ) + + if libs: + return libs + + msg = 'Unable to recursively locate {0} {1} libraries in {2}' + raise spack.error.NoLibrariesError( + msg.format('shared' if shared else 'static', + self.spec.name, + self.spec.prefix)) + + @when('@master') + def autoreconf(self, spec, prefix): + with working_dir(self.configure_directory): + # We do not specify '-f' because we need to use libtool files from + # the repository. + autoreconf('-iv') - # See: - # https://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/INSTALL def configure_args(self): - spec = self.spec + args = ['--with-mpi=%s' % self.spec['mpi'].prefix, + 'SEQ_CC=%s' % spack_cc] - args = ['--with-mpi={0}'.format(spec['mpi'].prefix)] - args.append('MPICC={0}'.format(spec['mpi'].mpicc)) - args.append('MPICXX={0}'.format(spec['mpi'].mpicxx)) - args.append('MPIF77={0}'.format(spec['mpi'].mpifc)) - args.append('MPIF90={0}'.format(spec['mpi'].mpifc)) - args.append('SEQ_CC={0}'.format(spack_cc)) + args += self.enable_or_disable('cxx') + args += self.enable_or_disable('fortran') - if '+pic' in spec: - args.extend([ - 'CFLAGS={0}'.format(self.compiler.pic_flag), - 'CXXFLAGS={0}'.format(self.compiler.pic_flag), - 'FFLAGS={0}'.format(self.compiler.pic_flag) - ]) + if '+pic' in self.spec: + args.extend(['{0}FLAGS={1}'.format(lang, self.compiler.pic_flag) + for lang in ['C', 'CXX', 'F', 'FC']]) - if '~cxx' in spec: - args.append('--disable-cxx') - - if '~fortran' in spec: - args.append('--disable-fortran') - - if spec.satisfies('@1.8.0:'): + if self.version >= Version('1.8'): args.append('--enable-relax-coord-bound') - return args + if self.version >= Version('1.9'): + args += self.enable_or_disable('shared') + args.extend(['--enable-static', + '--disable-silent-rules']) - def install(self, spec, prefix): - # Installation fails in parallel - make('install', parallel=False) + if self.spec.satisfies('%nag+fortran+shared'): + args.extend(['ac_cv_prog_fc_v=-Wl,-v', + 'ac_cv_prog_f77_v=-Wl,-v']) + + return args From 577860761b1425c231ed6091d35d2047e5a2a34f Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Tue, 10 Mar 2020 10:46:45 -0600 Subject: [PATCH 010/377] decompressor: add support for bz2 (#15424) --- lib/spack/spack/util/compression.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/lib/spack/spack/util/compression.py b/lib/spack/spack/util/compression.py index d617954ab17..1688b49f1b1 100644 --- a/lib/spack/spack/util/compression.py +++ b/lib/spack/spack/util/compression.py @@ -32,6 +32,9 @@ def decompressor_for(path, extension=None): if extension and re.match(r'gz', extension): gunzip = which('gunzip', required=True) return gunzip + if extension and re.match(r'bz2', extension): + bunzip2 = which('bunzip2', required=True) + return bunzip2 tar = which('tar', required=True) tar.add_default_arg('-xf') return tar From bbbee6700bfea23ac36c0715db72e426c8995f26 Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Tue, 10 Mar 2020 10:35:20 -0700 Subject: [PATCH 011/377] bugfix: fix install_missing_compilers option bug from v0.14.0 (#15416) * bugfix: ensure bootstrapped compilers built before packages using the compiler --- lib/spack/spack/installer.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py index bd38d11ea2e..f226429f6a3 100644 --- a/lib/spack/spack/installer.py +++ b/lib/spack/spack/installer.py @@ -182,6 +182,9 @@ def _packages_needed_to_bootstrap_compiler(pkg): # concrete CompilerSpec has less info than concrete Spec # concretize as Spec to add that information dep.concretize() + # mark compiler as depended-on by the package that uses it + dep._dependents[pkg.name] = spack.spec.DependencySpec( + pkg.spec, dep, ('build',)) packages = [(s.package, False) for s in dep.traverse(order='post', root=False)] packages.append((dep.package, True)) @@ -1608,6 +1611,21 @@ def __init__(self, pkg, compiler, start, attempts, status, installed): self.spec.dependencies() if package_id(d.package) != self.pkg_id) + # Handle bootstrapped compiler + # + # The bootstrapped compiler is not a dependency in the spec, but it is + # a dependency of the build task. Here we add it to self.dependencies + compiler_spec = self.spec.compiler + arch_spec = self.spec.architecture + if not spack.compilers.compilers_for_spec(compiler_spec, + arch_spec=arch_spec): + # The compiler is in the queue, identify it as dependency + dep = spack.compilers.pkg_spec_for_compiler(compiler_spec) + dep.architecture = arch_spec + dep.concretize() + dep_id = package_id(dep.package) + self.dependencies.add(dep_id) + # List of uninstalled dependencies, which is used to establish # the priority of the build task. # From c4c6accace0cbbf4907dca8d65038664bda27484 Mon Sep 17 00:00:00 2001 From: broderickpt <50112491+broderickpt@users.noreply.github.com> Date: Tue, 10 Mar 2020 14:07:53 -0400 Subject: [PATCH 012/377] =?UTF-8?q?contrib-spiral:=20submit=20SPIRAL=20pac?= =?UTF-8?q?kage=20recipe=20and=20HCOL=20package=20recipe=20=E2=80=A6=20(#1?= =?UTF-8?q?5188)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * contrib-spiral: submit SPIRAL package recipe and HCOL package recipe (extension package for SPIRAL) to spack * contrib-spiral: fix flake8 complaints for spiral & hcol * contrib-spiral: Revisions to package recipes to address comments * contrib-spiral: remove unecessary 'test' function * contrib-spiral: update hcol package to install in /namespaces/packages/hcol * contrib-spiral: don't import os to hcol * contrib-spiral: tweak hcol package recipe --- .../repos/builtin/packages/hcol/package.py | 25 +++++++ .../repos/builtin/packages/spiral/package.py | 65 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 var/spack/repos/builtin/packages/hcol/package.py create mode 100644 var/spack/repos/builtin/packages/spiral/package.py diff --git a/var/spack/repos/builtin/packages/hcol/package.py b/var/spack/repos/builtin/packages/hcol/package.py new file mode 100644 index 00000000000..70278eba930 --- /dev/null +++ b/var/spack/repos/builtin/packages/hcol/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Hcol(Package): + """This is the SPIRAL package for the Hybrid Control Operator Language + (HCOL).""" + + homepage = "https://https://spiral.net" + url = "https://github.com/spiral-software/spiral-package-hcol/archive/1.0.0.zip" + + maintainers = ['spiralgen'] + extends('spiral') + + version('1.0.0', sha256='9a95574e2b061d03d264c32dbf733e893017d1644b6486c7a8a55a3b24783f58') + + # HCOL package is an extension for Spiral. Install the files in their own + # prefix, in "namespaces/packages/hcol". This allows 'spack activate' to + # symlink hcol at the right location for spiral packages. + def install(self, spec, prefix): + install_tree('.', prefix.namespaces.packages.hcol) diff --git a/var/spack/repos/builtin/packages/spiral/package.py b/var/spack/repos/builtin/packages/spiral/package.py new file mode 100644 index 00000000000..5011875e131 --- /dev/null +++ b/var/spack/repos/builtin/packages/spiral/package.py @@ -0,0 +1,65 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Spiral(CMakePackage): + """SPIRAL is a program generation system for linear transforms and other + mathematical functions that produces very high performance code for a wide + spectrum of hardware platforms.""" + + homepage = "https://spiral.net" + url = "https://github.com/spiral-software/spiral-software/archive/8.1.2.tar.gz" + + maintainers = ['spiralgen'] + + version('8.1.2', sha256='506f1dbf923aa1c9f19f05444fa947085715eef37c9d2494d133fcaaa1dd50bc') + + extendable = True + + # No dependencies. + + def build(self, spec, prefix): + with working_dir(self.build_directory): + make('all') + make('install/local') + + # For some reason the make install/local doesn't seem to install + # the gap exe...though it does work if run manually + gapfil = join_path(self.build_directory, 'gap/src/gap') + dest = join_path(self.stage.source_path, 'gap/bin') + install(gapfil, dest) + + def install(self, spec, prefix): + mkdirp(prefix.gap.bin) + gapfil = join_path(self.build_directory, 'gap/src/gap') + install(gapfil, prefix.gap.bin) + with working_dir(join_path(self.build_directory, 'gap')): + files = ('spiral', 'spirald', '_spiral.g') + for fil in files: + install(fil, prefix) + set_executable(join_path(prefix, fil)) + + with working_dir(self.stage.source_path): + files = ('LICENSE', 'README.md', 'ReleaseNotes.md') + for fil in files: + install(fil, prefix) + + mkdirp(prefix.gap.lib) + mkdirp(prefix.gap.grp) + mkdirp(prefix.namespaces) + mkdirp(prefix.profiler) + mkdirp(prefix.tests) + + print("self.stage.source_path = " + self.stage.source_path) + with working_dir(self.stage.source_path): + install_tree('namespaces', prefix.namespaces) + install_tree('profiler', prefix.profiler) + install_tree('tests', prefix.tests) + + with working_dir(join_path(self.stage.source_path, 'gap')): + install_tree('lib', prefix.gap.lib) + install_tree('grp', prefix.gap.grp) From 9debb7e1b6e565320a9d9095acaf8253e2473d39 Mon Sep 17 00:00:00 2001 From: "Elsa Gonsiorowski, PhD" Date: Tue, 10 Mar 2020 13:27:41 -0700 Subject: [PATCH 013/377] SCR: build with components (#14931) * scr: add develop, legacy branches; version 2.0.0 squash! scr: add develop and legacy versions * filo: package for SCR component * spath: package for SCR component * axl: update for versions 0.3 and 0.2 * scr: build with components * spath: structure of +mpi if/else * :ok_hand: capitalization of ecp-veloc * scr: branches are always greater than any version --- .../repos/builtin/packages/axl/package.py | 6 ++-- .../repos/builtin/packages/er/package.py | 4 +-- .../repos/builtin/packages/filo/package.py | 32 +++++++++++++++++ .../repos/builtin/packages/kvtree/package.py | 4 +-- .../repos/builtin/packages/rankstr/package.py | 4 +-- .../repos/builtin/packages/redset/package.py | 4 +-- .../repos/builtin/packages/scr/package.py | 13 ++++++- .../builtin/packages/shuffile/package.py | 4 +-- .../repos/builtin/packages/spath/package.py | 34 +++++++++++++++++++ 9 files changed, 92 insertions(+), 13 deletions(-) create mode 100644 var/spack/repos/builtin/packages/filo/package.py create mode 100644 var/spack/repos/builtin/packages/spath/package.py diff --git a/var/spack/repos/builtin/packages/axl/package.py b/var/spack/repos/builtin/packages/axl/package.py index 1725a2751cf..73eb5acdcd7 100644 --- a/var/spack/repos/builtin/packages/axl/package.py +++ b/var/spack/repos/builtin/packages/axl/package.py @@ -19,13 +19,15 @@ def async_api_validator(pkg_name, variant_name, values): class Axl(CMakePackage): """Asynchronous transfer library""" - homepage = "https://github.com/ECP-VeloC/AXL" - url = "https://github.com/ECP-VeloC/AXL/archive/v0.1.1.zip" + homepage = "https://github.com/ecp-veloc/AXL" + url = "https://github.com/ecp-veloc/AXL/archive/v0.1.1.zip" git = "https://github.com/ecp-veloc/axl.git" tags = ['ecp'] version('master', branch='master') + version('0.3.0', sha256='3f5efff87be700a5792a0ee9a7aeae45c640e2936623b024e8bc1056f7952a46') + version('0.2.0', sha256='a0babe3576da30919f89df2f83c76bd01d06345919f2e54d4dddcd6f73faedcc') version('0.1.1', sha256='ebbf231bb542a6c91efb79fce05d4c8a346d5506d88ae1899fb670be52e81933') variant('async_api', default='daemon', diff --git a/var/spack/repos/builtin/packages/er/package.py b/var/spack/repos/builtin/packages/er/package.py index 55e5067f129..343a08ff919 100644 --- a/var/spack/repos/builtin/packages/er/package.py +++ b/var/spack/repos/builtin/packages/er/package.py @@ -9,8 +9,8 @@ class Er(CMakePackage): """Encoding and redundancy on a file set""" - homepage = "https://github.com/ECP-VeloC/er" - url = "https://github.com/ECP-VeloC/er/archive/v0.0.3.zip" + homepage = "https://github.com/ecp-veloc/er" + url = "https://github.com/ecp-veloc/er/archive/v0.0.3.zip" git = "https://github.com/ecp-veloc/er.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/filo/package.py b/var/spack/repos/builtin/packages/filo/package.py new file mode 100644 index 00000000000..aeba476c041 --- /dev/null +++ b/var/spack/repos/builtin/packages/filo/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Filo(CMakePackage): + """File flush and fetch, with MPI""" + + homepage = "https://github.com/ecp-veloc/filo" + git = "https://github.com/ecp-veloc/filo.git" + + tags = ['ecp'] + + version('master', branch='master') + + depends_on('mpi') + depends_on('axl') + depends_on('kvtree') + depends_on('spath') + + def cmake_args(self): + args = [] + args.append("-DMPI_C_COMPILER=%s" % self.spec['mpi'].mpicc) + if self.spec.satisfies('platform=cray'): + args.append("-DFILO_LINK_STATIC=ON") + args.append("-DWITH_AXL_PREFIX=%s" % self.spec['axl'].prefix) + args.append("-DWITH_KVTREE_PREFIX=%s" % self.spec['kvtree'].prefix) + args.append("-DWITH_SPATH_PREFIX=%s" % self.spec['spath'].prefix) + return args diff --git a/var/spack/repos/builtin/packages/kvtree/package.py b/var/spack/repos/builtin/packages/kvtree/package.py index be265f5ecdc..40e57ed0ee6 100644 --- a/var/spack/repos/builtin/packages/kvtree/package.py +++ b/var/spack/repos/builtin/packages/kvtree/package.py @@ -10,8 +10,8 @@ class Kvtree(CMakePackage): """KVTree provides a fully extensible C datastructure modeled after perl hashes.""" - homepage = "https://github.com/ECP-VeloC/KVTree" - url = "https://github.com/ECP-VeloC/KVTree/archive/v1.0.2.zip" + homepage = "https://github.com/ecp-veloc/KVTree" + url = "https://github.com/ecp-veloc/KVTree/archive/v1.0.2.zip" git = "https://github.com/ecp-veloc/kvtree.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/rankstr/package.py b/var/spack/repos/builtin/packages/rankstr/package.py index 6cf2dc42f9f..98d7aea87fd 100644 --- a/var/spack/repos/builtin/packages/rankstr/package.py +++ b/var/spack/repos/builtin/packages/rankstr/package.py @@ -9,8 +9,8 @@ class Rankstr(CMakePackage): """Assign one-to-one mapping of MPI ranks to strings""" - homepage = "https://github.com/ECP-VeloC/rankstr" - url = "https://github.com/ECP-VeloC/rankstr/archive/v0.0.2.zip" + homepage = "https://github.com/ecp-veloc/rankstr" + url = "https://github.com/ecp-veloc/rankstr/archive/v0.0.2.zip" git = "https://github.com/ecp-veloc/rankstr.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/redset/package.py b/var/spack/repos/builtin/packages/redset/package.py index d06eaca1087..88ea8b92d49 100644 --- a/var/spack/repos/builtin/packages/redset/package.py +++ b/var/spack/repos/builtin/packages/redset/package.py @@ -9,8 +9,8 @@ class Redset(CMakePackage): """Create MPI communicators for disparate redundancy sets""" - homepage = "https://github.com/ECP-VeloC/redset" - url = "https://github.com/ECP-VeloC/redset/archive/v0.0.3.zip" + homepage = "https://github.com/ecp-veloc/redset" + url = "https://github.com/ecp-veloc/redset/archive/v0.0.3.zip" git = "https://github.com/ecp-veloc/redset.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/scr/package.py b/var/spack/repos/builtin/packages/scr/package.py index 63d0af34eb8..3e0e1456cdd 100644 --- a/var/spack/repos/builtin/packages/scr/package.py +++ b/var/spack/repos/builtin/packages/scr/package.py @@ -17,7 +17,10 @@ class Scr(CMakePackage): url = "https://github.com/LLNL/scr/archive/v1.2.0.tar.gz" git = "https://github.com/llnl/scr.git" - version('master', branch='master') + version('develop', branch='develop') + version('legacy', branch='legacy') + + version('2.0.0', sha256='471978ae0afb56a20847d3989b994fbd680d1dea21e77a5a46a964b6e3deed6b') version('1.2.2', sha256='764a85638a9e8762667ec1f39fa5f7da7496fca78de379a22198607b3e027847') version('1.2.1', sha256='23acab2dc7203e9514455a5168f2fd57bc590affb7a1876912b58201513628fe') version('1.2.0', sha256='e3338ab2fa6e9332d2326c59092b584949a083a876adf5a19d4d5c7a1bbae047') @@ -26,6 +29,14 @@ class Scr(CMakePackage): depends_on('zlib') depends_on('mpi') + # SCR legacy is anything 2.x.x or earlier + # SCR components is anything 3.x.x or later + depends_on('er', when="@3:") + depends_on('kvtree', when="@3:") + depends_on('rankstr', when="@3:") + depends_on('filo', when="@3:") + depends_on('spath', when="@3:") + variant('dtcmp', default=True, description="Build with DTCMP. " "Necessary to enable user directory naming at runtime") diff --git a/var/spack/repos/builtin/packages/shuffile/package.py b/var/spack/repos/builtin/packages/shuffile/package.py index 1dc23f1a2c3..e7a8da2c0e8 100644 --- a/var/spack/repos/builtin/packages/shuffile/package.py +++ b/var/spack/repos/builtin/packages/shuffile/package.py @@ -9,8 +9,8 @@ class Shuffile(CMakePackage): """Shuffle files between MPI ranks""" - homepage = "https://github.com/ECP-VeloC/shuffile" - url = "https://github.com/ECP-VeloC/shuffile/archive/v0.0.3.zip" + homepage = "https://github.com/ecp-veloc/shuffile" + url = "https://github.com/ecp-veloc/shuffile/archive/v0.0.3.zip" git = "https://github.com/ecp-veloc/shuffile.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/spath/package.py b/var/spack/repos/builtin/packages/spath/package.py new file mode 100644 index 00000000000..5ccd259f485 --- /dev/null +++ b/var/spack/repos/builtin/packages/spath/package.py @@ -0,0 +1,34 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Spath(CMakePackage): + """Represent and manipulate file system paths""" + + homepage = "https://github.com/ecp-veloc/spath" + git = "https://github.com/ecp-veloc/spath.git" + + tags = ['ecp'] + + version('master', branch='master') + + variant('mpi', default=True, description="Build with MPI support.") + depends_on('mpi', when='+mpi') + + def cmake_args(self): + args = [] + + if self.spec.satisfies('platform=cray'): + args.append("-DSPATH_LINK_STATIC=ON") + + if "+mpi" in self.spec: + args.append('-DMPI=ON') + args.append("-DMPI_C_COMPILER=%s" % self.spec['mpi'].mpicc) + else: + args.append('-DMPI=OFF') + + return args From 6993a82cb401489195d09005de46bf6ae911f1ea Mon Sep 17 00:00:00 2001 From: "Dr. Christian Tacke" <58549698+ChristianTackeGSI@users.noreply.github.com> Date: Tue, 10 Mar 2020 22:18:59 +0100 Subject: [PATCH 014/377] cryptsetup: Add pkgconfig dependency (#15422) --- var/spack/repos/builtin/packages/cryptsetup/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/cryptsetup/package.py b/var/spack/repos/builtin/packages/cryptsetup/package.py index 10519100ee8..ccde594c84f 100644 --- a/var/spack/repos/builtin/packages/cryptsetup/package.py +++ b/var/spack/repos/builtin/packages/cryptsetup/package.py @@ -25,6 +25,7 @@ class Cryptsetup(AutotoolsPackage): depends_on('util-linux~libuuid', type=('build', 'link')) depends_on('gettext', type=('build', 'link')) + depends_on('pkgconfig', type='build') depends_on('autoconf', type='build') depends_on('automake', type='build') depends_on('libtool', type='build') From 03c684954e8d48b5845b3a80723dc55890b6ad69 Mon Sep 17 00:00:00 2001 From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com> Date: Wed, 11 Mar 2020 06:21:14 +0900 Subject: [PATCH 015/377] r: Lower optimization level when using Fujitsu compiler@4.1.0. (#15418) --- .../packages/r/change_optflags_tmp.patch | 67 +++++++++++++++++++ var/spack/repos/builtin/packages/r/package.py | 6 ++ 2 files changed, 73 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r/change_optflags_tmp.patch diff --git a/var/spack/repos/builtin/packages/r/change_optflags_tmp.patch b/var/spack/repos/builtin/packages/r/change_optflags_tmp.patch new file mode 100644 index 00000000000..4e39b02be74 --- /dev/null +++ b/var/spack/repos/builtin/packages/r/change_optflags_tmp.patch @@ -0,0 +1,67 @@ +diff -ur R-3.6.3.org/configure R-3.6.3/configure +--- R-3.6.3.org/configure 2020-03-09 11:09:16.060825352 +0900 ++++ R-3.6.3/configure 2020-03-09 11:10:47.011280195 +0900 +@@ -6470,13 +6470,13 @@ + CFLAGS=$ac_save_CFLAGS + elif test $ac_cv_prog_cc_g = yes; then + if test "$GCC" = yes; then +- CFLAGS="-g -O2" ++ CFLAGS="-g -O1" + else + CFLAGS="-g" + fi + else + if test "$GCC" = yes; then +- CFLAGS="-O2" ++ CFLAGS="-O1" + else + CFLAGS= + fi +@@ -7445,13 +7445,13 @@ + FCFLAGS=$ac_save_FCFLAGS + elif test $ac_cv_prog_fc_g = yes; then + if test "x$ac_cv_fc_compiler_gnu" = xyes; then +- FCFLAGS="-g -O2" ++ FCFLAGS="-g -O1" + else + FCFLAGS="-g" + fi + else + if test "x$ac_cv_fc_compiler_gnu" = xyes; then +- FCFLAGS="-O2" ++ FCFLAGS="-O1" + else + FCFLAGS= + fi +@@ -7717,13 +7717,13 @@ + CXXFLAGS=$ac_save_CXXFLAGS + elif test $ac_cv_prog_cxx_g = yes; then + if test "$GXX" = yes; then +- CXXFLAGS="-g -O2" ++ CXXFLAGS="-g -O1" + else + CXXFLAGS="-g" + fi + else + if test "$GXX" = yes; then +- CXXFLAGS="-O2" ++ CXXFLAGS="-O1" + else + CXXFLAGS= + fi +@@ -8336,13 +8336,13 @@ + OBJCFLAGS=$ac_save_OBJCFLAGS + elif test $ac_cv_prog_objc_g = yes; then + if test "$GOBJC" = yes; then +- OBJCFLAGS="-g -O2" ++ OBJCFLAGS="-g -O1" + else + OBJCFLAGS="-g" + fi + else + if test "$GOBJC" = yes; then +- OBJCFLAGS="-O2" ++ OBJCFLAGS="-O1" + else + OBJCFLAGS= + fi diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py index 9257c5e733d..1893aca9ac3 100644 --- a/var/spack/repos/builtin/packages/r/package.py +++ b/var/spack/repos/builtin/packages/r/package.py @@ -86,6 +86,12 @@ class R(AutotoolsPackage): patch('zlib.patch', when='@:3.3.2') + # R cannot be built with '-O2' optimization + # with Fujitsu Compiler @4.1.0 now. + # Until the Fujitsu compiler resolves this problem, + # temporary fix to lower the optimization level. + patch('change_optflags_tmp.patch', when='%fj@4.1.0') + filter_compiler_wrappers( 'Makeconf', relative_root=os.path.join('rlib', 'R', 'etc') ) From 9fba110372c01912e8854687db57b3f4bce84707 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Wed, 11 Mar 2020 06:22:04 +0900 Subject: [PATCH 016/377] libxpresent: Add some dependencies. (#15417) * libxpresent: Add some dependencies. * Change *proto dependency type from build to link. --- .../repos/builtin/packages/libxpresent/package.py | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/libxpresent/package.py b/var/spack/repos/builtin/packages/libxpresent/package.py index 0fddba389a1..1305623472c 100644 --- a/var/spack/repos/builtin/packages/libxpresent/package.py +++ b/var/spack/repos/builtin/packages/libxpresent/package.py @@ -15,10 +15,15 @@ class Libxpresent(AutotoolsPackage): version('1.0.0', sha256='92f1bdfb67ae2ffcdb25ad72c02cac5e4912dc9bc792858240df1d7f105946fa') - depends_on('libx11') + depends_on('libx11', type='link') + depends_on('libxext', type='link') + depends_on('libxfixes', type='link') + depends_on('libxrandr', type='link') - depends_on('xproto', type='build') - depends_on('presentproto@1.0:', type='build') - depends_on('xextproto', type='build') + depends_on('xproto', type='link') + depends_on('presentproto@1.0:', type='link') + depends_on('xextproto', type='link') + depends_on('fixesproto', type='link') + depends_on('randrproto', type='link') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') From 94b686e32bbcd125a30c5a20d64b0c414defa00d Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Wed, 11 Mar 2020 06:22:24 +0900 Subject: [PATCH 017/377] libxpresent: Add some dependencies. (#15417) * libxpresent: Add some dependencies. * Change *proto dependency type from build to link. From 4ef0442a017841922ea58381080380ba29cfe118 Mon Sep 17 00:00:00 2001 From: Nisarg Patel <33021055+hpcnpatel@users.noreply.github.com> Date: Tue, 10 Mar 2020 22:23:41 +0100 Subject: [PATCH 018/377] fix static mumps build error - Added a space at the end of ar vr for the static build to run successfully (#15407) --- var/spack/repos/builtin/packages/mumps/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py index a56bc111e29..de34b6aa190 100644 --- a/var/spack/repos/builtin/packages/mumps/package.py +++ b/var/spack/repos/builtin/packages/mumps/package.py @@ -241,7 +241,7 @@ def write_makefile_inc(self): else: makefile_conf.extend([ 'LIBEXT = .a', - 'AR = ar vr', + 'AR = ar vr ', 'RANLIB = ranlib' ]) From fc78456547fa99a14b1e40e3d8af75f9cd72966d Mon Sep 17 00:00:00 2001 From: Mathias Anselmann Date: Tue, 10 Mar 2020 22:27:07 +0100 Subject: [PATCH 019/377] gcc: backporting fix for glibc 2.31 (#15403) * backporting fix for building gcc >= 8.1.0 and gcc <= 9.2.0 with binutils 2.31 * removed trailing whitespace --- .../gcc/glibc-2.31-libsanitizer-1.patch | 37 ++++++++++ .../gcc/glibc-2.31-libsanitizer-2.patch | 73 +++++++++++++++++++ .../repos/builtin/packages/gcc/package.py | 4 + 3 files changed, 114 insertions(+) create mode 100644 var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-1.patch create mode 100644 var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-2.patch diff --git a/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-1.patch b/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-1.patch new file mode 100644 index 00000000000..96037707d3c --- /dev/null +++ b/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-1.patch @@ -0,0 +1,37 @@ +From ce9568e9e9cf6094be30e748821421e703754ffc Mon Sep 17 00:00:00 2001 +From: Jakub Jelinek +Date: Fri, 8 Nov 2019 19:53:18 +0100 +Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm + bootstrap due to libsanitizer) + + Backported from mainline + 2019-10-22 Tamar Christina + + PR sanitizer/92154 + * sanitizer_common/sanitizer_platform_limits_posix.cc: + Cherry-pick compiler-rt revision r375220. + +From-SVN: r277981 +--- + libsanitizer/ChangeLog | 9 +++++++++ + .../sanitizer_common/sanitizer_platform_limits_posix.cc | 6 +++++- + 2 files changed, 14 insertions(+), 1 deletion(-) + +diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc +index 6cd4a5bac8b0..06a605ff4670 100644 +--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc ++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc +@@ -1156,8 +1156,12 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid); + CHECK_SIZE_AND_OFFSET(ipc_perm, gid); + CHECK_SIZE_AND_OFFSET(ipc_perm, cuid); + CHECK_SIZE_AND_OFFSET(ipc_perm, cgid); +-#if !defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21) ++#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \ ++ !defined(__arm__) + /* On aarch64 glibc 2.20 and earlier provided incorrect mode field. */ ++/* On Arm glibc 2.31 and later provide a different mode field, this field is ++ never used by libsanitizer so we can simply ignore this assert for all glibc ++ versions. */ + CHECK_SIZE_AND_OFFSET(ipc_perm, mode); + #endif + diff --git a/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-2.patch b/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-2.patch new file mode 100644 index 00000000000..75234436e8e --- /dev/null +++ b/var/spack/repos/builtin/packages/gcc/glibc-2.31-libsanitizer-2.patch @@ -0,0 +1,73 @@ +From 75003cdd23c310ec385344e8040d490e8dd6d2be Mon Sep 17 00:00:00 2001 +From: Jakub Jelinek +Date: Fri, 20 Dec 2019 17:58:35 +0100 +Subject: [PATCH] backport: re PR sanitizer/92154 (new glibc breaks arm + bootstrap due to libsanitizer) + + Backported from mainline + 2019-11-26 Jakub Jelinek + + PR sanitizer/92154 + * sanitizer_common/sanitizer_platform_limits_posix.h: Cherry-pick + llvm-project revision 947f9692440836dcb8d88b74b69dd379d85974ce. + * sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise. + +From-SVN: r279653 +--- + libsanitizer/ChangeLog | 10 ++++++++++ + .../sanitizer_platform_limits_posix.cc | 9 +++------ + .../sanitizer_platform_limits_posix.h | 15 +-------------- + 3 files changed, 14 insertions(+), 20 deletions(-) + +diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc +index 06a605ff4670..d823a12190c0 100644 +--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc ++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc +@@ -1156,12 +1156,9 @@ CHECK_SIZE_AND_OFFSET(ipc_perm, uid); + CHECK_SIZE_AND_OFFSET(ipc_perm, gid); + CHECK_SIZE_AND_OFFSET(ipc_perm, cuid); + CHECK_SIZE_AND_OFFSET(ipc_perm, cgid); +-#if (!defined(__aarch64__) || !SANITIZER_LINUX || __GLIBC_PREREQ (2, 21)) && \ +- !defined(__arm__) +-/* On aarch64 glibc 2.20 and earlier provided incorrect mode field. */ +-/* On Arm glibc 2.31 and later provide a different mode field, this field is +- never used by libsanitizer so we can simply ignore this assert for all glibc +- versions. */ ++#if !SANITIZER_LINUX || __GLIBC_PREREQ (2, 31) ++/* glibc 2.30 and earlier provided 16-bit mode field instead of 32-bit ++ on many architectures. */ + CHECK_SIZE_AND_OFFSET(ipc_perm, mode); + #endif + +diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h +index 73af92af1e8f..6a673a7c9959 100644 +--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h ++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h +@@ -211,26 +211,13 @@ namespace __sanitizer { + u64 __unused1; + u64 __unused2; + #elif defined(__sparc__) +-#if defined(__arch64__) + unsigned mode; +- unsigned short __pad1; +-#else +- unsigned short __pad1; +- unsigned short mode; + unsigned short __pad2; +-#endif + unsigned short __seq; + unsigned long long __unused1; + unsigned long long __unused2; +-#elif defined(__mips__) || defined(__aarch64__) || defined(__s390x__) +- unsigned int mode; +- unsigned short __seq; +- unsigned short __pad1; +- unsigned long __unused1; +- unsigned long __unused2; + #else +- unsigned short mode; +- unsigned short __pad1; ++ unsigned int mode; + unsigned short __seq; + unsigned short __pad2; + #if defined(__x86_64__) && !defined(_LP64) diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 4b47217c9a6..eb1c65630f7 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -230,6 +230,10 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage): patch('piclibs.patch', when='+piclibs') patch('gcc-backport.patch', when='@4.7:4.9.2,5:5.3') + # Backport libsanitizer patch for glibc >= 2.31 and 8.1.0 <= gcc <= 9.2.0 + # https://bugs.gentoo.org/708346 + patch('glibc-2.31-libsanitizer-1.patch', when='@8.1.0:9.2.0') + patch('glibc-2.31-libsanitizer-2.patch', when='@8.1.0:9.2.0') # Older versions do not compile with newer versions of glibc # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81712 patch('ucontext_t.patch', when='@4.9,5.1:5.4,6.1:6.4,7.1') From 8ac06ece3d6a1cb700d7f2dd2da58a3f7f995233 Mon Sep 17 00:00:00 2001 From: "Seth R. Johnson" Date: Tue, 10 Mar 2020 17:40:03 -0400 Subject: [PATCH 020/377] Fix OpenBLAS 0.2 build, 0.38+ Intel builds, and variant name (#15419) * Remove ARCH argument in OpenBLAS < 0.3.0 * Fix Intel OpenBLAS that uses lapack 0.3.9 * Improve variant name consistency see https://github.com/spack/spack/issues/15239 --- .../openblas/lapack-0.3.9-xerbl.patch | 14 ++++++ .../builtin/packages/openblas/package.py | 49 ++++++++++++------- 2 files changed, 44 insertions(+), 19 deletions(-) create mode 100644 var/spack/repos/builtin/packages/openblas/lapack-0.3.9-xerbl.patch diff --git a/var/spack/repos/builtin/packages/openblas/lapack-0.3.9-xerbl.patch b/var/spack/repos/builtin/packages/openblas/lapack-0.3.9-xerbl.patch new file mode 100644 index 00000000000..a61f3b3c009 --- /dev/null +++ b/var/spack/repos/builtin/packages/openblas/lapack-0.3.9-xerbl.patch @@ -0,0 +1,14 @@ +diff --git a/lapack-netlib/SRC/sorhr_col.f b/lapack-netlib/SRC/sorhr_col.f +index 38976245..600c19fb 100644 +--- a/lapack-netlib/SRC/sorhr_col.f ++++ b/lapack-netlib/SRC/sorhr_col.f +@@ -282,7 +282,8 @@ + $ NPLUSONE + * .. + * .. External Subroutines .. +- EXTERNAL SCOPY, SLAORHR_COL_GETRFNP, SSCAL, STRSM, XERBLA ++ EXTERNAL SCOPY, SLAORHR_COL_GETRFNP, SSCAL, STRSM, ++ $ XERBLA + * .. + * .. Intrinsic Functions .. + INTRINSIC MAX, MIN diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index b98085c19c1..71d2ec4a6bd 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -38,7 +38,7 @@ class Openblas(MakefilePackage): variant('ilp64', default=False, description='Force 64-bit Fortran native integers') variant('pic', default=True, description='Build position independent code') variant('shared', default=True, description='Build shared libraries') - variant('consistentFPCSR', default=False, description='Synchronize FP CSR between threads (x86/x86_64 only)') + variant('consistent_fpcsr', default=False, description='Synchronize FP CSR between threads (x86/x86_64 only)') variant( 'threads', default='none', @@ -60,6 +60,8 @@ class Openblas(MakefilePackage): patch('openblas_icc_openmp.patch', when='@:0.2.20%intel@16.0:') patch('openblas_icc_fortran.patch', when='%intel@16.0:') patch('openblas_icc_fortran2.patch', when='%intel@18.0:') + # See https://github.com/spack/spack/issues/15385 + patch('lapack-0.3.9-xerbl.patch', when='@0.3.8: %intel') # Fixes compilation error on POWER8 with GCC 7 # https://github.com/xianyi/OpenBLAS/pull/1098 @@ -94,7 +96,10 @@ class Openblas(MakefilePackage): # Add conditions to f_check to determine the Fujitsu compiler patch('openblas_fujitsu.patch', when='%fj') + # See https://github.com/spack/spack/issues/3036 conflicts('%intel@16', when='@0.2.15:0.2.19') + conflicts('+consistent_fpcsr', when='threads=none', + msg='FPCSR consistency only applies to multithreading') @property def parallel(self): @@ -137,12 +142,23 @@ def _read_targets(target_file): return micros - @staticmethod - def _microarch_target_args(microarch, available_targets): + def _microarch_target_args(self): """Given a spack microarchitecture and a list of targets found in OpenBLAS' TargetList.txt, determine the best command-line arguments. """ - args = [] # Return value + # Read available openblas targets + targetlist_name = join_path(self.stage.source_path, "TargetList.txt") + if os.path.exists(targetlist_name): + with open(targetlist_name) as f: + available_targets = self._read_targets(f) + else: + available_targets = [] + + # Get our build microarchitecture + microarch = self.spec.target + + # List of arguments returned by this function + args = [] # List of available architectures, and possible aliases openblas_arch = set(['alpha', 'arm', 'ia64', 'mips', 'mips64', @@ -166,11 +182,14 @@ def _microarch_target_args(microarch, available_targets): if microarch.name in available_targets: break - arch_name = microarch.family.name - if arch_name in openblas_arch: - # Apply possible spack->openblas arch name mapping - arch_name = openblas_arch_map.get(arch_name, arch_name) - args.append('ARCH=' + arch_name) + if self.version >= Version("0.3"): + # 'ARCH' argument causes build errors in older OpenBLAS + # see https://github.com/spack/spack/issues/15385 + arch_name = microarch.family.name + if arch_name in openblas_arch: + # Apply possible spack->openblas arch name mapping + arch_name = openblas_arch_map.get(arch_name, arch_name) + args.append('ARCH=' + arch_name) if microarch.vendor == 'generic': # User requested a generic platform, or we couldn't find a good @@ -190,8 +209,6 @@ def _microarch_target_args(microarch, available_targets): @property def make_defs(self): - spec = self.spec - # Configure fails to pick up fortran from FC=/abs/path/to/fc, but # works fine with FC=/abs/path/to/gfortran. # When mixing compilers make sure that @@ -209,13 +226,7 @@ def make_defs(self): make_defs.append('MAKE_NB_JOBS=0') # flag provided by OpenBLAS # Add target and architecture flags - targetlist_name = join_path(self.stage.source_path, "TargetList.txt") - if os.path.exists(targetlist_name): - with open(targetlist_name) as f: - avail_targets = self._read_targets(f) - else: - avail_targets = [] - make_defs += self._microarch_target_args(spec.target, avail_targets) + make_defs += self._microarch_target_args() if '~shared' in self.spec: if '+pic' in self.spec: @@ -242,7 +253,7 @@ def make_defs(self): # Synchronize floating-point control and status register (FPCSR) # between threads (x86/x86_64 only). - if '+consistentFPCSR' in self.spec: + if '+consistent_fpcsr' in self.spec: make_defs += ['CONSISTENT_FPCSR=1'] # Prevent errors in `as` assembler from newer instructions From 6d8cd446c5c7cba12b82bf1f297e86bfa9104156 Mon Sep 17 00:00:00 2001 From: Hector <10837193+he-b@users.noreply.github.com> Date: Tue, 10 Mar 2020 20:41:00 -0500 Subject: [PATCH 021/377] Add valgrind variant to petsc (#15427) * Add PETSc valgrind dependency * Remove +debug on valgrind dependency * enh variant description --- var/spack/repos/builtin/packages/petsc/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 88332caec98..ddee34e1872 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -99,6 +99,8 @@ class Petsc(Package): description='Activate X support') variant('batch', default=False, description='Enable when mpiexec is not available to run binaries') + variant('valgrind', default=False, + description='Enable Valgrind Client Request mechanism') # 3.8.0 has a build issue with MKL - so list this conflict explicitly conflicts('^intel-mkl', when='@3.8.0') @@ -146,6 +148,7 @@ class Petsc(Package): depends_on('hdf5+mpi+hl+fortran', when='+hdf5+mpi') depends_on('zlib', when='+hdf5') depends_on('parmetis', when='+metis+mpi') + depends_on('valgrind', when='+valgrind') # Hypre does not support complex numbers. # Also PETSc prefer to build it without internal superlu, likely due to # conflict in headers see @@ -280,7 +283,7 @@ def install(self, spec, prefix): # Activates library support if needed for library in ('metis', 'hdf5', 'hypre', 'parmetis', - 'mumps', 'trilinos', 'fftw'): + 'mumps', 'trilinos', 'fftw', 'valgrind'): options.append( '--with-{library}={value}'.format( library=library, value=('1' if library in spec else '0')) From 9b114c486f4f2bddfb3471382bc65de53f3bf3a9 Mon Sep 17 00:00:00 2001 From: Neil Flood Date: Wed, 11 Mar 2020 20:06:18 +1000 Subject: [PATCH 022/377] kealib: moved to github, added v1.4.12 (#15436) --- var/spack/repos/builtin/packages/kealib/package.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/kealib/package.py b/var/spack/repos/builtin/packages/kealib/package.py index e164dac4b4a..3e050a213cb 100644 --- a/var/spack/repos/builtin/packages/kealib/package.py +++ b/var/spack/repos/builtin/packages/kealib/package.py @@ -23,12 +23,13 @@ class Kealib(CMakePackage): Development work on this project has been funded by Landcare Research. """ homepage = "http://www.kealib.org/" - url = "https://bitbucket.org/chchrsc/kealib/downloads/kealib-1.4.11.tar.gz" - hg = "https://bitbucket.org/chchrsc/kealib" + url = "https://github.com/ubarsc/kealib/releases/download/kealib-1.4.12/kealib-1.4.12.tar.gz" + git = "https://github.com/ubarsc/kealib" maintainers = ['gillins'] - version('develop', hg=hg) + version('develop', git=git) + version('1.4.12', sha256='0b100e36b3e25e57487aa197d7be47f22e1b30afb16a57fdaa5f877696ec321e') version('1.4.11', sha256='3d64cdec560c7a338ccb38e3a456db4e3b176ac62f945daa6e332e60fe4eca90') version('1.4.10', sha256='b1bd2d6834d2fe09ba456fce77f7a9452b406dbe302f7ef1aabe924e45e6bb5e') version('1.4.9', sha256='1c80489f17114a229097c2e8c61d5e4c82ea63ae631c81a817fef95cfd527174') From 299fa6b5ca8072743b30379266459bbc0a53f10c Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Wed, 11 Mar 2020 03:24:38 -0700 Subject: [PATCH 023/377] fetch_strategy: remove vestigial code (#15431) --- lib/spack/spack/fetch_strategy.py | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index d923e2b58e7..f4d46b5f8c1 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -29,7 +29,6 @@ import re import shutil import sys -import xml.etree.ElementTree import llnl.util.tty as tty import six @@ -773,13 +772,6 @@ def mirror_id(self): result = os.path.sep.join(['git', repo_path, repo_ref]) return result - def get_source_id(self): - if not self.branch: - return - output = self.git('ls-remote', self.url, self.branch, output=str) - if output: - return output.split()[0] - def _repo_info(self): args = '' @@ -957,11 +949,6 @@ def cachable(self): def source_id(self): return self.revision - def get_source_id(self): - output = self.svn('info', '--xml', self.url, output=str) - info = xml.etree.ElementTree.fromstring(output) - return info.find('entry/commit').get('revision') - def mirror_id(self): if self.revision: repo_path = url_util.parse(self.url).path @@ -1077,11 +1064,6 @@ def mirror_id(self): result = os.path.sep.join(['hg', repo_path, self.revision]) return result - def get_source_id(self): - output = self.hg('id', self.url, output=str) - if output: - return output.strip() - @_needs_stage def fetch(self): if self.stage.expanded: From 20c77cade532844c758290c242536436cecfe922 Mon Sep 17 00:00:00 2001 From: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Date: Wed, 11 Mar 2020 03:39:23 -0700 Subject: [PATCH 024/377] bugfix: resolve undefined source_pkg_dir failure (#15339) --- lib/spack/spack/installer.py | 11 +++-- lib/spack/spack/test/installer.py | 71 +++++++++++++++++++++++++++++-- 2 files changed, 74 insertions(+), 8 deletions(-) diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py index f226429f6a3..78405e37f09 100644 --- a/lib/spack/spack/installer.py +++ b/lib/spack/spack/installer.py @@ -410,7 +410,10 @@ def dump_packages(spec, path): source_repo = spack.repo.Repo(source_repo_root) source_pkg_dir = source_repo.dirname_for_package_name( node.name) - except spack.repo.RepoError: + except spack.repo.RepoError as err: + tty.debug('Failed to create source repo for {0}: {1}' + .format(node.name, str(err))) + source_pkg_dir = None tty.warn("Warning: Couldn't copy in provenance for {0}" .format(node.name)) @@ -422,10 +425,10 @@ def dump_packages(spec, path): # Get the location of the package in the dest repo. dest_pkg_dir = repo.dirname_for_package_name(node.name) - if node is not spec: - install_tree(source_pkg_dir, dest_pkg_dir) - else: + if node is spec: spack.repo.path.dump_provenance(node, dest_pkg_dir) + elif source_pkg_dir: + install_tree(source_pkg_dir, dest_pkg_dir) def install_msg(name, pid): diff --git a/lib/spack/spack/test/installer.py b/lib/spack/spack/test/installer.py index 8c3a232f19f..b9730c31657 100644 --- a/lib/spack/spack/test/installer.py +++ b/lib/spack/spack/test/installer.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) import os +import py import pytest import llnl.util.tty as tty @@ -17,6 +18,22 @@ import spack.spec +def _mock_repo(root, namespace): + """Create an empty repository at the specified root + + Args: + root (str): path to the mock repository root + namespace (str): mock repo's namespace + """ + repodir = py.path.local(root) if isinstance(root, str) else root + repodir.ensure(spack.repo.packages_dir_name, dir=True) + yaml = repodir.join('repo.yaml') + yaml.write(""" +repo: + namespace: {0} +""".format(namespace)) + + def _noop(*args, **kwargs): """Generic monkeypatch no-op routine.""" pass @@ -284,11 +301,57 @@ def _no_compilers(pkg, arch_spec): inst._packages_needed_to_bootstrap_compiler(spec.package) -def test_dump_packages_deps(install_mockery, tmpdir): - """Test to add coverage to dump_packages.""" +def test_dump_packages_deps_ok(install_mockery, tmpdir, mock_repo_path): + """Test to add coverage to dump_packages with dependencies happy path.""" + + spec_name = 'simple-inheritance' + spec = spack.spec.Spec(spec_name).concretized() + inst.dump_packages(spec, str(tmpdir)) + + repo = mock_repo_path.repos[0] + dest_pkg = repo.filename_for_package_name(spec_name) + assert os.path.isfile(dest_pkg) + + +def test_dump_packages_deps_errs(install_mockery, tmpdir, monkeypatch, capsys): + """Test to add coverage to dump_packages with dependencies.""" + orig_bpp = spack.store.layout.build_packages_path + orig_dirname = spack.repo.Repo.dirname_for_package_name + repo_err_msg = "Mock dirname_for_package_name" + + def bpp_path(spec): + # Perform the original function + source = orig_bpp(spec) + # Mock the required directory structure for the repository + _mock_repo(os.path.join(source, spec.namespace), spec.namespace) + return source + + def _repoerr(repo, name): + if name == 'cmake': + raise spack.repo.RepoError(repo_err_msg) + else: + return orig_dirname(repo, name) + + # Now mock the creation of the required directory structure to cover + # the try-except block + monkeypatch.setattr(spack.store.layout, 'build_packages_path', bpp_path) + spec = spack.spec.Spec('simple-inheritance').concretized() - with tmpdir.as_cwd(): - inst.dump_packages(spec, '.') + path = str(tmpdir) + + # The call to install_tree will raise the exception since not mocking + # creation of dependency package files within *install* directories. + with pytest.raises(IOError, match=path): + inst.dump_packages(spec, path) + + # Now try the error path, which requires the mock directory structure + # above + monkeypatch.setattr(spack.repo.Repo, 'dirname_for_package_name', _repoerr) + with pytest.raises(spack.repo.RepoError, match=repo_err_msg): + inst.dump_packages(spec, path) + + out = str(capsys.readouterr()[1]) + assert "Couldn't copy in provenance for cmake" in out @pytest.mark.tld From 87e69eed1c4864730aa221aa014c234e4ac3f83f Mon Sep 17 00:00:00 2001 From: rvinaybharadwaj Date: Wed, 11 Mar 2020 12:00:02 -0600 Subject: [PATCH 025/377] Horovod (#15380) --- .../repos/builtin/packages/minigan/package.py | 28 +++++++++ .../builtin/packages/py-horovod/package.py | 60 +++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 var/spack/repos/builtin/packages/minigan/package.py create mode 100644 var/spack/repos/builtin/packages/py-horovod/package.py diff --git a/var/spack/repos/builtin/packages/minigan/package.py b/var/spack/repos/builtin/packages/minigan/package.py new file mode 100644 index 00000000000..5d3b553bcf1 --- /dev/null +++ b/var/spack/repos/builtin/packages/minigan/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Minigan(Package): + """miniGAN is a generative adversarial network code developed as part of the + Exascale Computing Project's (ECP) ExaLearn project at + Sandia National Laboratories.""" + + homepage = "https://github.com/SandiaMLMiniApps/miniGAN" + url = "https://github.com/SandiaMLMiniApps/miniGAN/archive/1.0.0.tar.gz" + + version('1.0.0', sha256='ef6d5def9c7040af520acc64b7a8b6c8ec4b7901721b11b0cb25a583ea0c8ae3') + + depends_on('python', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-torch', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-horovod@master', type=('build', 'run')) + depends_on('py-torchvision', type=('build', 'run')) + depends_on('py-matplotlib@3.0.0', type=('build', 'run')) + + def install(self, spec, prefix): + install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/py-horovod/package.py b/var/spack/repos/builtin/packages/py-horovod/package.py new file mode 100644 index 00000000000..884721b286f --- /dev/null +++ b/var/spack/repos/builtin/packages/py-horovod/package.py @@ -0,0 +1,60 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import fnmatch +import os + + +class PyHorovod(PythonPackage): + """Horovod is a distributed deep learning training framework for + TensorFlow, Keras, PyTorch, and Apache MXNet.""" + + homepage = "https://github.com/horovod" + git = "https://github.com/horovod/horovod.git" + url = "https://github.com/horovod/horovod/archive/v0.19.0.tar.gz" + + version('master', branch='master', submodules='True') + version('0.19.0', sha256='0e9fec11cd7f5f39a09f0785d1097cb51c44537ae14c9b4b2578b5cdd21efb9b') + version('0.18.2', sha256='a073e08cec65474afdb2d011486b4cb6c7ac8fcb1eca3e02b169e1e7b4a66da6') + version('0.18.1', sha256='26e236d1f60955e9dd12b9f0a836f0691296a010fcd1ac72295970a780f4e4fb') + version('0.18.0', sha256='94f13e7110c5f3fd1aa194b9d886b5bb91c9bc02ade31bcb84fc6e7f9c043455') + version('0.17.1', sha256='14eea5744eda9c62988ffa278a9a5472cebbc6a287eca9ed48cacfcd177e8978') + version('0.17.0.post1', sha256='220b230611e22dc69777f1be4d9788a07e73a0722e511091fa156cdf68ca798b') + version('0.17.0', sha256='4bb121dda6cdaa1677535470adc1836493a9c4930ab19f6b491254ea47a12a4f') + version('0.16.4', sha256='c0168dfeb31a56ede52eae115f43fa2d06a5db55a37201064ef901c8000d708d') + version('0.16.3', sha256='1857cf1b335723366cc71e4bcd0583f2dde0c821212cda0e1b6bddfe4ba1ea0d') + version('0.16.2', sha256='baa9754e59ab0ee72d3b5769cf77e06a2c7b0a2d9626e0e14ca2ab131934ce74') + + variant('pytorch', default=True, description='Enables PyTorch') + variant('mxnet', default=False, description='Enables mxnet') + variant('mpi', default=True, description='Enables MPI build') + variant('gloo', default=False, description='Enables features related to distributed support') + variant('cuda', default=True, description='Enables CUDA build') + + depends_on('python', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-cloudpickle', type=('build', 'run')) + depends_on('py-psutil', type=('build', 'run')) + depends_on('py-pyyaml', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) + depends_on('py-torch', type=('build', 'run')) + depends_on('py-pip', type=('build')) + + # Optional dependencies + depends_on('cuda', when='+cuda') + depends_on('nccl', when='+nccl') + depends_on('gloo', when='+gloo') + depends_on('mpi', when='+mpi') + depends_on('py-torch', type=('build', 'run'), when='+pytorch') + depends_on('mxnet', when='+mxnet') + + phases = ['clean', 'sdist', 'install'] + + def install(self, spec, prefix): + pip = which('pip') + for file in os.listdir(prefix): + if fnmatch.fnmatch(file, 'horovod-*.tar.gz'): + pip('install', file, '--prefix={0}'.format(prefix)) From 83584afa35fcde93de98976b12909f7c19f69529 Mon Sep 17 00:00:00 2001 From: Anthony Scemama Date: Wed, 11 Mar 2020 20:44:36 +0100 Subject: [PATCH 026/377] Package for the resultsFile Python module (#15088) * Added resultsFile package * Added comments * Fixed PEP8 * Added Python3 package * Removed py-setuptools --- .../packages/py-resultsfile/package.py | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-resultsfile/package.py diff --git a/var/spack/repos/builtin/packages/py-resultsfile/package.py b/var/spack/repos/builtin/packages/py-resultsfile/package.py new file mode 100644 index 00000000000..6f00a3ab1d7 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-resultsfile/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyResultsfile(PythonPackage): + """Python module to read output files of quantum chemistry programs""" + + homepage = "https://gitlab.com/scemama/resultsFile" + url = "https://gitlab.com/scemama/resultsFile/-/archive/v1.0/resultsFile-v1.0.tar.gz" + git = "https://gitlab.com/scemama/resultsFile.git" + + maintainers = ['scemama'] + + version('2.0', sha256='2a34208254e4bea155695690437f6a59bf5f7b0ddb421d6c1a2d377510f018f7') + version('1.0', sha256='e029054b2727131da9684fa2ec9fb8b6a3225dc7f648216a9390267b2d5d60c3') + + depends_on('python@2.7:2.8.999', type=('build', 'run'), when='@1.0:1.999') + depends_on('python@3:', type=('build', 'run'), when='@2.0:') From 12940f344850805d37279111ec799eb838f31f0c Mon Sep 17 00:00:00 2001 From: "Dr. Christian Tacke" <58549698+ChristianTackeGSI@users.noreply.github.com> Date: Wed, 11 Mar 2020 20:51:35 +0100 Subject: [PATCH 027/377] libfabric@1.9.1: Add fabtests (#15440) The test utils for the new version 1.9.1 are missing. Add them. --- var/spack/repos/builtin/packages/libfabric/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/libfabric/package.py b/var/spack/repos/builtin/packages/libfabric/package.py index 927dd24d551..f2f21570f73 100644 --- a/var/spack/repos/builtin/packages/libfabric/package.py +++ b/var/spack/repos/builtin/packages/libfabric/package.py @@ -74,6 +74,10 @@ class Libfabric(AutotoolsPackage): depends_on('automake', when='@develop', type='build') depends_on('libtool', when='@develop', type='build') + resource(name='fabtests', + url='https://github.com/ofiwg/libfabric/releases/download/v1.9.1/fabtests-1.9.1.tar.bz2', + sha256='6f8ced2c6b3514759a0e177c8b2a19125e4ef0714d4cc0fe0386b33bd6cd5585', + placement='fabtests', when='@1.9.1') resource(name='fabtests', url='https://github.com/ofiwg/libfabric/releases/download/v1.9.0/fabtests-1.9.0.tar.bz2', sha256='60cc21db7092334904cbdafd142b2403572976018a22218e7c453195caef366e', From 6af8e19b2d96700ae9699f0e0568037f51b0d9e9 Mon Sep 17 00:00:00 2001 From: Stephanie Brink Date: Wed, 11 Mar 2020 17:23:32 -0700 Subject: [PATCH 028/377] add hatchet python package (#15428) --- .../builtin/packages/py-hatchet/package.py | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-hatchet/package.py diff --git a/var/spack/repos/builtin/packages/py-hatchet/package.py b/var/spack/repos/builtin/packages/py-hatchet/package.py new file mode 100644 index 00000000000..91df70b61b3 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-hatchet/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyHatchet(PythonPackage): + """Hatchet is an analysis tool for structured tree or graph performance data + using an indexed Pandas dataframe.""" + + homepage = "https://github.com/LLNL/hatchet" + url = "https://github.com/LLNL/hatchet/archive/v1.0.0.tar.gz" + + maintainers = ["slabasan", "bhatele", "tgamblin"] + + version('1.0.0', sha256='efd218bc9152abde0a8006489a2c432742f00283a114c1eeb6d25abc10f5862d') + + depends_on('python@2.7,3:', type=('build', 'run')) + + depends_on('py-setuptools', type='build') + depends_on('py-matplotlib', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-pandas', type=('build', 'run')) + depends_on('py-pydot', type=('build', 'run')) + depends_on('py-pyyaml', type=('build', 'run')) From a9a59ea3b41cac6e8ed638e0cd23700c7e94a232 Mon Sep 17 00:00:00 2001 From: darmac Date: Thu, 12 Mar 2020 08:29:31 +0800 Subject: [PATCH 029/377] add new package: keyutils (#15433) --- .../builtin/packages/keyutils/package.py | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 var/spack/repos/builtin/packages/keyutils/package.py diff --git a/var/spack/repos/builtin/packages/keyutils/package.py b/var/spack/repos/builtin/packages/keyutils/package.py new file mode 100644 index 00000000000..049dbb1c228 --- /dev/null +++ b/var/spack/repos/builtin/packages/keyutils/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import glob + + +class Keyutils(MakefilePackage): + """These tools are used to control the key management system built + into the Linux kernel.""" + + homepage = "https://git.kernel.org/pub/scm/linux/kernel/git/dhowells/keyutils.git/" + url = "https://git.kernel.org/pub/scm/linux/kernel/git/dhowells/keyutils.git/snapshot/keyutils-1.6.1.tar.gz" + + version('1.6.1', sha256='3c71dcfc6900d07b02f4e061d8fb218a4ae6519c1d283d6a57b8e27718e2f557') + version('1.6', sha256='c6a27b4e3d0122d921f3dcea4b1f02a8616ca844535960d6af76ef67d015b5cf') + version('1.5.10', sha256='e1fdbde234c786b65609a4cf080a2c5fbdb57f049249c139160c85fc3dfa7da9') + version('1.5.9', sha256='2dc0bdb099ab8331e02e5dbbce320359bef76eda0a4ddbd2ba1d1b9d3a8cdff8') + + def install(self, spec, prefix): + install_tree('.', prefix) + mkdirp(prefix.include) + headers = glob.glob(join_path(prefix, '*.h')) + for h in headers: + install(h, prefix.include) From e01817cb1571f0cbf0b8810adb7e4cd84f208176 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Thu, 12 Mar 2020 01:34:24 +0100 Subject: [PATCH 030/377] binutils: Add missing texinfo dependency (#15444) --- var/spack/repos/builtin/packages/binutils/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index 1f4a675546b..4a647e7e888 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -47,6 +47,10 @@ class Binutils(AutotoolsPackage, GNUMirrorPackage): depends_on('m4', type='build', when='@:2.29.99 +gold') depends_on('bison', type='build', when='@:2.29.99 +gold') + # 2.34 needs makeinfo due to a bug, see: + # https://sourceware.org/bugzilla/show_bug.cgi?id=25491 + depends_on('texinfo', type='build', when='@2.34') + conflicts('+gold', when='platform=darwin', msg="Binutils cannot build linkers on macOS") From 3e8f873b03a6f696ddf999990466fa6e38fc3b85 Mon Sep 17 00:00:00 2001 From: "Daryl W. Grunau" Date: Wed, 11 Mar 2020 18:35:10 -0600 Subject: [PATCH 031/377] cpio: icc -no-gcc (#15446) Co-authored-by: Daryl W. Grunau --- var/spack/repos/builtin/packages/cpio/package.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/var/spack/repos/builtin/packages/cpio/package.py b/var/spack/repos/builtin/packages/cpio/package.py index ae6b429ccc6..2381a824997 100644 --- a/var/spack/repos/builtin/packages/cpio/package.py +++ b/var/spack/repos/builtin/packages/cpio/package.py @@ -16,3 +16,8 @@ class Cpio(AutotoolsPackage, GNUMirrorPackage): version('2.13', sha256='e87470d9c984317f658567c03bfefb6b0c829ff17dbf6b0de48d71a4c8f3db88') build_directory = 'spack-build' + + def flag_handler(self, name, flags): + if self.spec.satisfies('%intel') and name == 'cflags': + flags.append('-no-gcc') + return (flags, None, None) From 77434c24a850f8ef04c828f730352056fdbd8be2 Mon Sep 17 00:00:00 2001 From: darmac Date: Thu, 12 Mar 2020 08:36:23 +0800 Subject: [PATCH 032/377] add new package: php (#15435) --- .../repos/builtin/packages/php/package.py | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 var/spack/repos/builtin/packages/php/package.py diff --git a/var/spack/repos/builtin/packages/php/package.py b/var/spack/repos/builtin/packages/php/package.py new file mode 100644 index 00000000000..714bfb0e8f6 --- /dev/null +++ b/var/spack/repos/builtin/packages/php/package.py @@ -0,0 +1,41 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Php(AutotoolsPackage): + """ + PHP is a popular general-purpose scripting language that is especially + suited to web development. Fast, flexible and pragmatic, PHP powers + everything from your blog to the most popular websites in the world. + """ + + homepage = "https://php.net/" + url = "https://github.com/php/php-src/archive/php-7.3.13.tar.gz" + + version('7.4.1', sha256='4d9d7c5681bec3af38a935d033657dce09a9913498f8022d7ca163a7f2f493a7') + version('7.4.0', sha256='91d34b48025ab9789216df89e247b6904912eeeaeff38c300ef314bdda8920b0') + version('7.3.13', sha256='e68b8d9e659f2993eee912f05860e546fdc18e459f31cd2771f404df21285f0b') + version('7.3.12', sha256='d0672ea84c0ab184f636acff3230d376d89a2067d59a87a2f1842361ee1f97d6') + version('7.3.11', sha256='4d861b2f3bc640ded8b591ce87250161392a6244a3c84042da0c06fd8c500eb2') + version('7.2.26', sha256='da132a836cec8021c00f22952e6044d91628ee3d2ef92a95d65cf91bad810600') + version('7.2.25', sha256='049b2d291c45cb889d15fcd2bac6da7d15ca5d535d272d2f8879fb834bbf276e') + version('7.2.24', sha256='334c9915733f6a29e1462f64038b1b4b1b21cb18f4f5f980add86792b5550ab3') + version('7.1.33', sha256='f80a795a09328a9441bae4a8a60fa0d6d43ec5adc98f5aa5f51d06f4522c07fe') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + depends_on('pkgconfig', type='build') + depends_on('bison', type='build') + depends_on('re2c', type='build') + depends_on('libxml2') + depends_on('sqlite') + + def autoreconf(self, spec, prefix): + bash = which('bash') + bash('./buildconf', '--force') From 99e465663aee43d244efc29542f2cd43e90dfda1 Mon Sep 17 00:00:00 2001 From: Les Kurz Date: Wed, 11 Mar 2020 20:08:49 -0500 Subject: [PATCH 033/377] Update package.py for HDF5 1.12.0 release (#15430) * Update package.py * Update package.py * add upper bounds to production config_option * fix config_options * Fix mistaken changes. --- var/spack/repos/builtin/packages/hdf5/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index 3c62d46f0d6..e560c23f44c 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -23,6 +23,8 @@ class Hdf5(AutotoolsPackage): version('develop', branch='develop') + version('1.12.0', sha256='a62dcb276658cb78e6795dd29bf926ed7a9bc4edf6e77025cd2c689a8f97c17a') + version('1.10.6', sha256='5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa') version('1.10.5', sha256='6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8') version('1.10.4', sha256='8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2') From 8bdbd96e68dabe63d136fa9a11df09474311e327 Mon Sep 17 00:00:00 2001 From: Nick Booher Date: Wed, 11 Mar 2020 22:04:59 -0500 Subject: [PATCH 034/377] revbayes: Update URLs and hashes for old archives (#15451) * revbayes: Update URLs and hashes for old archives * Switch to url_for_version * Fix whitespace --- .../repos/builtin/packages/revbayes/package.py | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/revbayes/package.py b/var/spack/repos/builtin/packages/revbayes/package.py index 7cf707a72eb..5f556683924 100644 --- a/var/spack/repos/builtin/packages/revbayes/package.py +++ b/var/spack/repos/builtin/packages/revbayes/package.py @@ -15,10 +15,10 @@ class Revbayes(CMakePackage): git = "https://github.com/revbayes/revbayes.git" version('develop', branch='development') - version('1.0.13', sha256='472b4ccc44d813c1ff1b8d27e8ccf3d96388de79aa1688b3714f683ba65038fa') - version('1.0.12', sha256='d79f3a9bc72305cab35009d11e1f027fcaacde7329a4c49b5b8285588a8d3588') - version('1.0.11', sha256='7e81b1952e3a63cb84617fa632f4ccdf246b4d79e7d537a423540de047dadf50') - version('1.0.10', sha256='95e9affe8ca8d62880cf46778b6ec9dd8726e62a185670ebcbadf2eb2bb79f93') + version('1.0.13', sha256='e85e2e1fe182fe9f504900150d936a06d252a362c591b9d3d8272dd085aa85d9') + version('1.0.12', sha256='80c926bb6b37288d02e36e07b44e4663841cd1fe541e2cc0b0e44c89ca929759') + version('1.0.11', sha256='03052194baa220dde7e622a739f09f34393f67ea00a0b163b409d313d7fc7c02') + version('1.0.10', sha256='6a3cf303e7224b0b32637bd8e2c3c2cf2621f5dbe599cd74ce4b0c215d0fcd2d') variant('mpi', default=True, description='Enable MPI parallel support') @@ -27,6 +27,12 @@ class Revbayes(CMakePackage): conflicts('%gcc@7.1.0:', when='@:1.0.12') + def url_for_version(self, version): + if version > Version('1.0.13'): + return 'https://github.com/revbayes/revbayes/archive/v{0}.tar.gz'.format(version) + else: + return 'https://github.com/revbayes/revbayes.archive/archive/v{0}.tar.gz'.format(version) + @property def root_cmakelists_dir(self): if self.spec.version > Version('1.0.13') and '+mpi' in self.spec: From f4a5eb2b6d90c0f0fe7a888cc94a72c13301d29b Mon Sep 17 00:00:00 2001 From: darmac Date: Thu, 12 Mar 2020 11:49:22 +0800 Subject: [PATCH 035/377] add new package: lmbench (#15457) * add new package: lmbench * refine LDFLAGS append call --- .../repos/builtin/packages/lmbench/package.py | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 var/spack/repos/builtin/packages/lmbench/package.py diff --git a/var/spack/repos/builtin/packages/lmbench/package.py b/var/spack/repos/builtin/packages/lmbench/package.py new file mode 100644 index 00000000000..e38ca29e242 --- /dev/null +++ b/var/spack/repos/builtin/packages/lmbench/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Lmbench(MakefilePackage): + """lmbench is a suite of simple, portable, ANSI/C microbenchmarks for + UNIX/POSIX. In general, it measures two key features: latency and + bandwidth. lmbench is intended to give system developers insight into + basic costs of key operations.""" + + homepage = "http://lmbench.sourceforge.net/" + git = "https://github.com/intel/lmbench.git" + + version('master', branch='master') + + depends_on('libtirpc') + + def setup_build_environment(self, env): + env.prepend_path('CPATH', self.spec['libtirpc'].prefix.include.tirpc) + env.append_flags('LDFLAGS', '-ltirpc') + + def build(self, spec, prefix): + make('build') + + def install(self, spec, prefix): + install_tree('.', prefix) From a22d52a67dffa8dbf1632ce17129de32ca39c591 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 12 Mar 2020 08:19:42 +0100 Subject: [PATCH 036/377] Minor updates to CI configuration (#15458) * Check on Python versions uses action/checkout@v2 * Update the apt cache before installing system packages --- .github/workflows/linux_build_tests.yaml | 1 + .github/workflows/minimum_python_versions.yaml | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/linux_build_tests.yaml b/.github/workflows/linux_build_tests.yaml index 68c60c08edf..04119c5c6ed 100644 --- a/.github/workflows/linux_build_tests.yaml +++ b/.github/workflows/linux_build_tests.yaml @@ -42,6 +42,7 @@ jobs: python-version: 3.8 - name: Install System Packages run: | + sudo apt-get update sudo apt-get -yqq install ccache gfortran perl perl-base r-base r-base-core r-base-dev findutils openssl libssl-dev libpciaccess-dev R --version perl --version diff --git a/.github/workflows/minimum_python_versions.yaml b/.github/workflows/minimum_python_versions.yaml index c55042ffa11..95bc9af3582 100644 --- a/.github/workflows/minimum_python_versions.yaml +++ b/.github/workflows/minimum_python_versions.yaml @@ -15,7 +15,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v2 - name: Setup Python uses: actions/setup-python@v1 with: From 59b6822a4749af28417541981f160d4a1766bd46 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 12 Mar 2020 09:21:19 +0100 Subject: [PATCH 037/377] Creating versions from urls doesn't modify class attributes (#15452) fixes #15449 Before this PR a call to pkg.url_for_version was modifying class attributes determining different results for subsequents calls and an error when the urls was empty. --- lib/spack/spack/fetch_strategy.py | 2 +- lib/spack/spack/package.py | 2 +- lib/spack/spack/test/url_fetch.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index f4d46b5f8c1..85e93164a85 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -1261,7 +1261,7 @@ def _from_merged_attrs(fetcher, pkg, version): # TODO: refactor this logic into its own method or function # TODO: to avoid duplication mirrors = [spack.url.substitute_version(u, version) - for u in getattr(pkg, 'urls', [])] + for u in getattr(pkg, 'urls', [])[1:]] attrs = {fetcher.url_attr: url, 'mirrors': mirrors} else: url = getattr(pkg, fetcher.url_attr) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 56bdab22c17..ff45355055a 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -763,7 +763,7 @@ def url_for_version(self, version): # If no specific URL, use the default, class-level URL url = getattr(self, 'url', None) urls = getattr(self, 'urls', [None]) - default_url = url or urls.pop(0) + default_url = url or urls[0] # if no exact match AND no class-level default, use the nearest URL if not default_url: diff --git a/lib/spack/spack/test/url_fetch.py b/lib/spack/spack/test/url_fetch.py index 71a122455f7..679240049d9 100644 --- a/lib/spack/spack/test/url_fetch.py +++ b/lib/spack/spack/test/url_fetch.py @@ -32,7 +32,7 @@ def pkg_factory(): def factory(url, urls): def fn(v): - main_url = url or urls.pop(0) + main_url = url or urls[0] return spack.url.substitute_version(main_url, v) return Pkg( From ad1a28ee48a46ef8400b43f3f21c33ec8c5f2311 Mon Sep 17 00:00:00 2001 From: Jeffrey Salmond Date: Thu, 12 Mar 2020 11:01:52 +0000 Subject: [PATCH 038/377] plumed: add cython as dependency (#15460) --- var/spack/repos/builtin/packages/plumed/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index c8b1f8e9b96..a3f62ac38a3 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -68,6 +68,7 @@ class Plumed(AutotoolsPackage): depends_on('autoconf', type='build') depends_on('automake', type='build') depends_on('libtool', type='build') + depends_on('py-cython', type='build', when='@2.5:') force_autoreconf = True From e916a9424ca6195e0685071f3bf3a8f532cb22fe Mon Sep 17 00:00:00 2001 From: Thomas Gruber Date: Thu, 12 Mar 2020 14:44:43 +0100 Subject: [PATCH 039/377] likwid: add compiler selection for ARM and POWER architecture (#14183) Co-Authored-By: Massimiliano Culpo --- var/spack/repos/builtin/packages/likwid/package.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/likwid/package.py b/var/spack/repos/builtin/packages/likwid/package.py index c121b1ef35a..8556fb0d8e9 100644 --- a/var/spack/repos/builtin/packages/likwid/package.py +++ b/var/spack/repos/builtin/packages/likwid/package.py @@ -42,8 +42,6 @@ class Likwid(Package): depends_on('perl', type=('build', 'run')) - supported_compilers = {'clang': 'CLANG', 'gcc': 'GCC', 'intel': 'ICC'} - def patch(self): files = glob.glob('perl/*.*') + glob.glob('bench/perl/*.*') @@ -61,13 +59,18 @@ def filter_sbang(self): *files) def install(self, spec, prefix): - if self.compiler.name not in self.supported_compilers: + supported_compilers = {'clang': 'CLANG', 'gcc': 'GCC', 'intel': 'ICC'} + if spec.target.family == 'aarch64': + supported_compilers = {'gcc': 'GCCARMv8', 'clang': 'ARMCLANG'} + elif spec.target.family == 'ppc64' or spec.target.family == 'ppc64le': + supported_compilers = {'gcc': 'GCCPOWER'} + if self.compiler.name not in supported_compilers: raise RuntimeError('{0} is not a supported compiler \ to compile Likwid'.format(self.compiler.name)) filter_file('^COMPILER .*', 'COMPILER = ' + - self.supported_compilers[self.compiler.name], + supported_compilers[self.compiler.name], 'config.mk') filter_file('^PREFIX .*', 'PREFIX = ' + From d95766756c979461a0f98bd26284dc1af78ffe14 Mon Sep 17 00:00:00 2001 From: Zhiyi Wu Date: Thu, 12 Mar 2020 16:47:26 +0000 Subject: [PATCH 040/377] Update plumed 2.5.4 and 2.6.0 (#15462) Co-authored-by: zhiyiwu --- var/spack/repos/builtin/packages/plumed/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index a3f62ac38a3..b51d3c12c2d 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -25,8 +25,9 @@ class Plumed(AutotoolsPackage): git = 'https://github.com/plumed/plumed2.git' version('master', branch='master') - version('2.6b', sha256='3ecda9d46967c8ddd08e820aed974794d926cffb78b262f9d42cdbece3b15677') - version('2.5.3', preferred=True, sha256='543288be667dc4201fc461ecd2dd4878ddfbeac682d0c021c99ea8e501c7c9dc') + version('2.6.0', sha256='3d57ae460607a49547ef38a52c4ac93493a3966857c352280a9c05f5dcdb1820') + version('2.5.4', preferred=True, sha256='a1647e598191f261e75d06351e607475d395af481315052a4c28563ac9989a7f') + version('2.5.3', sha256='543288be667dc4201fc461ecd2dd4878ddfbeac682d0c021c99ea8e501c7c9dc') version('2.5.2', sha256='85d10cc46e2e37c7719cf51c0931278f56c2c8f8a9d86188b2bf97c2535a2ab4') version('2.5.1', sha256='de309980dcfd6f6e0e70e138856f4bd9eb4d8a513906a5e6389f18a5af7f2eba') version('2.5.0', sha256='53e08187ec9f8af2326fa84407e34644a7c51d2af93034309fb70675eee5e4f7') From 6887cb3da49e12308655d7aed1098985a4eb6ef4 Mon Sep 17 00:00:00 2001 From: Bryce Allen Date: Thu, 12 Mar 2020 12:58:18 -0400 Subject: [PATCH 041/377] pfunit: add max_array_rank=(int) variant (#15348) * pfunit: add max_array_rank=(int) variant * pfunit: flake8 line length fixes --- var/spack/repos/builtin/packages/pfunit/package.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/pfunit/package.py b/var/spack/repos/builtin/packages/pfunit/package.py index 30704ac62ed..ab6bc53d2c5 100644 --- a/var/spack/repos/builtin/packages/pfunit/package.py +++ b/var/spack/repos/builtin/packages/pfunit/package.py @@ -30,10 +30,14 @@ class Pfunit(CMakePackage): variant('shared', default=True, description='Build shared library in addition to static') variant('mpi', default=False, description='Enable MPI') - variant('use_comm_world', default=False, description='Enable MPI_COMM_WORLD for testing') + variant('use_comm_world', default=False, + description='Enable MPI_COMM_WORLD for testing') variant('openmp', default=False, description='Enable OpenMP') variant('docs', default=False, description='Build docs') + variant('max_array_rank', values=int, default=5, + description='Max number of Fortran dimensions of array asserts') + depends_on('python@2.7:', type=('build', 'run')) # python3 too! depends_on('mpi', when='+mpi') @@ -53,7 +57,8 @@ def cmake_args(self): '-DBUILD_SHARED=%s' % ('YES' if '+shared' in spec else 'NO'), '-DCMAKE_Fortran_MODULE_DIRECTORY=%s' % spec.prefix.include, '-DBUILD_DOCS=%s' % ('YES' if '+docs' in spec else 'NO'), - '-DOPENMP=%s' % ('YES' if '+openmp' in spec else 'NO')] + '-DOPENMP=%s' % ('YES' if '+openmp' in spec else 'NO'), + '-DMAX_RANK=%s' % spec.variants['max_array_rank'].value] if spec.satisfies('+mpi'): args.extend(['-DMPI=YES', '-DMPI_USE_MPIEXEC=YES', From d87f09cc5edd0127561786011f3ad5e50ac079d1 Mon Sep 17 00:00:00 2001 From: Joe Koning Date: Thu, 12 Mar 2020 11:27:02 -0700 Subject: [PATCH 042/377] Change py-merlinwf to py-merlin (#15453) * Change py-merlinwf to py-merlin to match PyPi. Change py-merlin to py-merlin-info. Move to py-merlin_info. Add py-merlin-info back in. * Update dependent packages for the new merlin name. * Remove non-working pyre and the associated packages, exchanger, py-pythia and py-mlerin-info from citcoms. * Remove blank line. --- .../repos/builtin/packages/citcoms/package.py | 18 +-------- .../builtin/packages/exchanger/package.py | 21 ---------- .../builtin/packages/py-merlin/package.py | 31 +++++++++++---- .../builtin/packages/py-merlinwf/package.py | 38 ------------------- .../builtin/packages/py-pythia/package.py | 20 ---------- 5 files changed, 25 insertions(+), 103 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/exchanger/package.py delete mode 100644 var/spack/repos/builtin/packages/py-merlinwf/package.py delete mode 100644 var/spack/repos/builtin/packages/py-pythia/package.py diff --git a/var/spack/repos/builtin/packages/citcoms/package.py b/var/spack/repos/builtin/packages/citcoms/package.py index 2529e544f64..f05c3d7cd60 100644 --- a/var/spack/repos/builtin/packages/citcoms/package.py +++ b/var/spack/repos/builtin/packages/citcoms/package.py @@ -16,8 +16,6 @@ class Citcoms(AutotoolsPackage): version('3.3.1', sha256='e3520e0a933e4699d31e86fe309b8c154ea6ecb0f42a1cf6f25e8d13d825a4b3') version('3.2.0', sha256='773a14d91ecbb4a4d1e04317635fab79819d83c57b47f19380ff30b9b19cb07a') - variant('pyre', default=False, description='build Pyre modules') - variant('exchanger', default=False, description='use Exchanger') variant('ggrd', default=False, description='use GGRD file support') variant('cuda', default=False, description='use CUDA') variant('hdf5', default=False, description='add HDF5 support') @@ -27,15 +25,10 @@ class Citcoms(AutotoolsPackage): depends_on('zlib') # Optional dependencies - depends_on('exchanger', when='+exchanger') - depends_on('py-pythia', type=('build', 'run'), when='+pyre') depends_on('hc', when='+ggrd') depends_on('cuda', when='+cuda') depends_on('hdf5+mpi', when='+hdf5') - conflicts('+pyre', when='@3.3:', msg='Pyre support was removed from 3.3+') - conflicts('+exchanger', when='@3.3:', msg='Exchanger support was removed from 3.3+') - def setup_build_environment(self, env): if '+ggrd' in self.spec: env.set('HC_HOME', self.spec['hc'].prefix) @@ -45,15 +38,8 @@ def configure_args(self): # Flags only valid in 3.2 if self.spec.satisfies('@:3.2'): - if '+pyre' in self.spec: - args.append('--with-pyre') - else: - args.append('--without-pyre') - - if '+exchanger' in self.spec: - args.append('--with-exchanger') - else: - args.append('--without-exchanger') + args.append('--without-pyre') + args.append('--without-exchanger') if '+ggrd' in self.spec: args.append('--with-ggrd') diff --git a/var/spack/repos/builtin/packages/exchanger/package.py b/var/spack/repos/builtin/packages/exchanger/package.py deleted file mode 100644 index 018459d8c32..00000000000 --- a/var/spack/repos/builtin/packages/exchanger/package.py +++ /dev/null @@ -1,21 +0,0 @@ -# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Exchanger(AutotoolsPackage): - """Exchanger is a package containing several C++ base classes. These - classes, when customized for a solver, can provide communication channels - between solvers. This packaged is used by CitcomS for solver coupling.""" - - homepage = "https://geodynamics.org/cig/software/exchanger/" - url = "https://geodynamics.org/cig/software/exchanger/Exchanger-1.0.1.tar.gz" - - version('1.0.1', sha256='1e6c8311db96582bcf2c9aee16a863a5730c1aa54cb3aa7d0249239c6e0b68ee') - - depends_on('python', type=('build', 'run')) - depends_on('py-merlin', type='build') - depends_on('py-pythia@0.8.1.0:0.8.1.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-merlin/package.py b/var/spack/repos/builtin/packages/py-merlin/package.py index 7ae05a8014c..c4185e9193c 100644 --- a/var/spack/repos/builtin/packages/py-merlin/package.py +++ b/var/spack/repos/builtin/packages/py-merlin/package.py @@ -7,15 +7,30 @@ class PyMerlin(PythonPackage): - """A custom version of Phillip J. Eby's setuptools.""" + """Merlin Workflow for HPC.""" - homepage = "https://pypi.org/project/merlin/" - url = "https://pypi.io/packages/source/m/merlin/merlin-1.8.tar.gz" + homepage = "https://github.com/LLNL/merlin" + url = "https://pypi.io/packages/source/m/merlin/merlin-1.4.1.tar.gz" + git = "https://github.com/LLNL/merlin.git" - version('1.8', sha256='a1ba9c13c74daa1724dd3820f1c241d7594d487b11f35347606986028c1881fd') + version('1.4.1', sha256='9d515cfdbcde2443892afd92b78dbc5bf2aed2060ed3a336e683188e015bca7c') + version('master', branch='master') + version('develop', branch='develop') - depends_on('python@:2', type=('build', 'run')) + depends_on('python@3.6:', type=('build', 'run')) + depends_on('py-setuptools', type=('build', 'run')) - def test(self): - # Unit tests are missing from tarball - pass + depends_on('py-pytest', type='test') + + depends_on('py-cached-property', type=('build', 'run')) + depends_on('py-celery@4.3.0:+redis', type=('build', 'run')) + depends_on('py-coloredlogs@10.0:', type=('build', 'run')) + depends_on('py-cryptography', type=('build', 'run')) + depends_on('py-importlib-resources', when="^python@3.0:3.6.99", type=('build', 'run')) + depends_on('py-maestrowf@1.1.7dev0:', when="@1.2.0:", type=('build', 'run')) + depends_on('py-maestrowf@1.1.6:', when="@:1.1.99", type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-parse', type=('build', 'run')) + depends_on('py-psutil@5.1.0:', type=('build', 'run')) + depends_on('py-pyyaml@5.1.2:', type=('build', 'run')) + depends_on('py-tabulate', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-merlinwf/package.py b/var/spack/repos/builtin/packages/py-merlinwf/package.py deleted file mode 100644 index 2082e779978..00000000000 --- a/var/spack/repos/builtin/packages/py-merlinwf/package.py +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class PyMerlinwf(PythonPackage): - """Merlin Workflow for HPC.""" - - homepage = "https://github.com/LLNL/merlin" - url = "https://pypi.io/packages/source/m/merlinwf/merlinwf-1.2.3.tar.gz" - git = "https://github.com/LLNL/merlin.git" - - version('1.2.3', sha256='6b13a315f3e8e2894ea05d9cc072639f02eaf71ae0fdbd2bafebd1c20c8470ab') - version('1.1.1', sha256='306055a987e42a79ce348a3f9d71293ed8a9b7f5909c26b6fd233d6a176fff6d') - version('1.0.5', sha256='d66f50eac84ff9d7aa484f2d9655dc60f0352196d333284d81b6623a6f0aa180') - version('master', branch='master') - version('develop', branch='develop') - - depends_on('python@3.6:', type=('build', 'run')) - depends_on('py-setuptools', type=('build', 'run')) - - depends_on('py-pytest', type='test') - - depends_on('py-cached-property', type=('build', 'run')) - depends_on('py-celery@4.3.0:+redis', type=('build', 'run')) - depends_on('py-coloredlogs@10.0:', type=('build', 'run')) - depends_on('py-cryptography', type=('build', 'run')) - depends_on('py-importlib-resources', when="^python@3.0:3.6.99", type=('build', 'run')) - depends_on('py-maestrowf@1.1.7dev0:', when="@1.2.0:", type=('build', 'run')) - depends_on('py-maestrowf@1.1.6:', when="@:1.1.99", type=('build', 'run')) - depends_on('py-numpy', type=('build', 'run')) - depends_on('py-parse', type=('build', 'run')) - depends_on('py-psutil@5.1.0:', type=('build', 'run')) - depends_on('py-pyyaml@5.1.2:', type=('build', 'run')) - depends_on('py-tabulate', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pythia/package.py b/var/spack/repos/builtin/packages/py-pythia/package.py deleted file mode 100644 index 721d7470faf..00000000000 --- a/var/spack/repos/builtin/packages/py-pythia/package.py +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class PyPythia(PythonPackage): - """Pythia refers to the Pyre framework and a collection of packages that - interact with it, such as an interface to the ACIS solid modelling package. - """ - - homepage = "https://geodynamics.org/cig/software/pythia/" - url = "https://geodynamics.org/cig/software/github/pythia/v0.8.1.18/pythia-0.8.1.18.tar.gz" - - version('0.8.1.18', sha256='f6025e6d70046dc71e375eded3d731506f8dd79e2e53b7e1436754439dcdef1e') - - depends_on('python@:2', type=('build', 'run')) - depends_on('py-merlin', type='build') From ed5b10d11fd7fead20703106a0423fc3138e8efe Mon Sep 17 00:00:00 2001 From: Amjad Kotobi Date: Thu, 12 Mar 2020 19:35:30 +0100 Subject: [PATCH 043/377] Add package jblob-3.0 (#15400) --- .../repos/builtin/packages/jblob/package.py | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 var/spack/repos/builtin/packages/jblob/package.py diff --git a/var/spack/repos/builtin/packages/jblob/package.py b/var/spack/repos/builtin/packages/jblob/package.py new file mode 100644 index 00000000000..1aa1738230a --- /dev/null +++ b/var/spack/repos/builtin/packages/jblob/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Jblob(Package): + """ + The German Climate Computing Center + (DKRZ: Deutsches Klimarechenzentrum GmbH) + provides a Long Term Archiving Service for large research + data sets which are relevant for climate or Earth system research. + """ + + homepage = "https://cera-www.dkrz.de/WDCC/ui/cerasearch" + url = "https://cera-www.dkrz.de/jblob/jblob-3.0.zip" + + maintainers = ['ajkotobi'] + + version('3.0', sha256='576b5956358386a8832c6d1d13c410705e54888354a10cfd4f094513458067e4') + + depends_on('java@8:', type='run') + + def setup_run_environment(self, env): + env.set('JAVA_HOME', self.spec['java'].prefix) + + def install(self, spec, prefix): + filter_file('/opt/jblob-' + self.version, prefix, 'jblob') + + mkdir(prefix.bin) + install('jblob', prefix.bin) + install_tree('lib', prefix.lib) + install_tree('docs', prefix.docs) From b8064df495889b329771208c18584adaeb334691 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?David=20B=C3=B6hme?= Date: Thu, 12 Mar 2020 11:37:15 -0700 Subject: [PATCH 044/377] Add Caliper v2.3.0 (#15468) --- var/spack/repos/builtin/packages/caliper/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/caliper/package.py b/var/spack/repos/builtin/packages/caliper/package.py index 53b34dd04dd..fb12a787045 100644 --- a/var/spack/repos/builtin/packages/caliper/package.py +++ b/var/spack/repos/builtin/packages/caliper/package.py @@ -19,6 +19,7 @@ class Caliper(CMakePackage): git = "https://github.com/LLNL/Caliper.git" version('master') + version('2.3.0', tag='v2.3.0') version('2.2.0', tag='v2.2.0') version('2.1.1', tag='v2.1.1') version('2.0.1', tag='v2.0.1') @@ -72,7 +73,7 @@ class Caliper(CMakePackage): depends_on('python@3:', type='build') # sosflow support not yet in 2.0 - conflicts('+sosflow', '@2.0.0:2.2.99') + conflicts('+sosflow', '@2.0.0:2.3.99') conflicts('+adiak', '@:2.1.99') def cmake_args(self): From f2a13af43e505495473354f258e216ebb4632d43 Mon Sep 17 00:00:00 2001 From: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Date: Thu, 12 Mar 2020 13:20:20 -0700 Subject: [PATCH 045/377] testing: increase installer coverage (#15237) --- lib/spack/spack/installer.py | 51 +++--- lib/spack/spack/test/install.py | 69 ++++++-- lib/spack/spack/test/installer.py | 269 ++++++++++++++++++++++-------- 3 files changed, 280 insertions(+), 109 deletions(-) diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py index 78405e37f09..a9965c91141 100644 --- a/lib/spack/spack/installer.py +++ b/lib/spack/spack/installer.py @@ -36,6 +36,7 @@ import sys import time +import llnl.util.filesystem as fs import llnl.util.lock as lk import llnl.util.tty as tty import spack.binary_distribution as binary_distribution @@ -43,14 +44,12 @@ import spack.error import spack.hooks import spack.package +import spack.package_prefs as prefs import spack.repo import spack.store -from llnl.util.filesystem import \ - chgrp, install, install_tree, mkdirp, touch, working_dir from llnl.util.tty.color import colorize, cwrite from llnl.util.tty.log import log_output -from spack.package_prefs import get_package_dir_permissions, get_package_group from spack.util.environment import dump_environment from spack.util.executable import which @@ -133,21 +132,21 @@ def _do_fake_install(pkg): chmod = which('chmod') # Install fake command - mkdirp(pkg.prefix.bin) - touch(os.path.join(pkg.prefix.bin, command)) + fs.mkdirp(pkg.prefix.bin) + fs.touch(os.path.join(pkg.prefix.bin, command)) chmod('+x', os.path.join(pkg.prefix.bin, command)) # Install fake header file - mkdirp(pkg.prefix.include) - touch(os.path.join(pkg.prefix.include, header + '.h')) + fs.mkdirp(pkg.prefix.include) + fs.touch(os.path.join(pkg.prefix.include, header + '.h')) # Install fake shared and static libraries - mkdirp(pkg.prefix.lib) + fs.mkdirp(pkg.prefix.lib) for suffix in [dso_suffix, '.a']: - touch(os.path.join(pkg.prefix.lib, library + suffix)) + fs.touch(os.path.join(pkg.prefix.lib, library + suffix)) # Install fake man page - mkdirp(pkg.prefix.man.man1) + fs.mkdirp(pkg.prefix.man.man1) packages_dir = spack.store.layout.build_packages_path(pkg.spec) dump_packages(pkg.spec, packages_dir) @@ -380,14 +379,14 @@ def dump_packages(spec, path): Dump all package information for a spec and its dependencies. This creates a package repository within path for every namespace in the - spec DAG, and fills the repos wtih package files and patch files for every + spec DAG, and fills the repos with package files and patch files for every node in the DAG. Args: spec (Spec): the Spack spec whose package information is to be dumped path (str): the path to the build packages directory """ - mkdirp(path) + fs.mkdirp(path) # Copy in package.py files from any dependencies. # Note that we copy them in as they are in the *install* directory @@ -428,7 +427,7 @@ def dump_packages(spec, path): if node is spec: spack.repo.path.dump_provenance(node, dest_pkg_dir) elif source_pkg_dir: - install_tree(source_pkg_dir, dest_pkg_dir) + fs.install_tree(source_pkg_dir, dest_pkg_dir) def install_msg(name, pid): @@ -464,17 +463,17 @@ def log(pkg): tty.debug(e) # Archive the whole stdout + stderr for the package - install(pkg.log_path, pkg.install_log_path) + fs.install(pkg.log_path, pkg.install_log_path) # Archive the environment used for the build - install(pkg.env_path, pkg.install_env_path) + fs.install(pkg.env_path, pkg.install_env_path) if os.path.exists(pkg.configure_args_path): # Archive the args used for the build - install(pkg.configure_args_path, pkg.install_configure_args_path) + fs.install(pkg.configure_args_path, pkg.install_configure_args_path) # Finally, archive files that are specific to each package - with working_dir(pkg.stage.path): + with fs.working_dir(pkg.stage.path): errors = six.StringIO() target_dir = os.path.join( spack.store.layout.metadata_path(pkg.spec), 'archived-files') @@ -496,8 +495,8 @@ def log(pkg): target = os.path.join(target_dir, f) # We must ensure that the directory exists before # copying a file in - mkdirp(os.path.dirname(target)) - install(f, target) + fs.mkdirp(os.path.dirname(target)) + fs.install(f, target) except Exception as e: tty.debug(e) @@ -508,7 +507,7 @@ def log(pkg): if errors.getvalue(): error_file = os.path.join(target_dir, 'errors.txt') - mkdirp(target_dir) + fs.mkdirp(target_dir) with open(error_file, 'w') as err: err.write(errors.getvalue()) tty.warn('Errors occurred when archiving files.\n\t' @@ -1074,10 +1073,10 @@ def build_process(): pkg.name, 'src') tty.msg('{0} Copying source to {1}' .format(pre, src_target)) - install_tree(pkg.stage.source_path, src_target) + fs.install_tree(pkg.stage.source_path, src_target) # Do the real install in the source directory. - with working_dir(pkg.stage.source_path): + with fs.working_dir(pkg.stage.source_path): # Save the build environment in a file before building. dump_environment(pkg.env_path) @@ -1289,20 +1288,20 @@ def _setup_install_dir(self, pkg): spack.store.layout.create_install_directory(pkg.spec) else: # Set the proper group for the prefix - group = get_package_group(pkg.spec) + group = prefs.get_package_group(pkg.spec) if group: - chgrp(pkg.spec.prefix, group) + fs.chgrp(pkg.spec.prefix, group) # Set the proper permissions. # This has to be done after group because changing groups blows # away the sticky group bit on the directory mode = os.stat(pkg.spec.prefix).st_mode - perms = get_package_dir_permissions(pkg.spec) + perms = prefs.get_package_dir_permissions(pkg.spec) if mode != perms: os.chmod(pkg.spec.prefix, perms) # Ensure the metadata path exists as well - mkdirp(spack.store.layout.metadata_path(pkg.spec), mode=perms) + fs.mkdirp(spack.store.layout.metadata_path(pkg.spec), mode=perms) def _update_failed(self, task, mark=False, exc=None): """ diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py index ff7f5a33556..2f779c6a5f3 100644 --- a/lib/spack/spack/test/install.py +++ b/lib/spack/spack/test/install.py @@ -7,7 +7,7 @@ import pytest import shutil -from llnl.util.filesystem import mkdirp, touch, working_dir +import llnl.util.filesystem as fs from spack.package import InstallError, PackageBase, PackageStillNeededError import spack.error @@ -380,11 +380,11 @@ def test_pkg_build_paths(install_mockery): # Backward compatibility checks log_dir = os.path.dirname(log_path) - mkdirp(log_dir) - with working_dir(log_dir): + fs.mkdirp(log_dir) + with fs.working_dir(log_dir): # Start with the older of the previous log filenames older_log = 'spack-build.out' - touch(older_log) + fs.touch(older_log) assert spec.package.log_path.endswith(older_log) # Now check the newer log filename @@ -416,11 +416,11 @@ def test_pkg_install_paths(install_mockery): # Backward compatibility checks log_dir = os.path.dirname(log_path) - mkdirp(log_dir) - with working_dir(log_dir): + fs.mkdirp(log_dir) + with fs.working_dir(log_dir): # Start with the older of the previous install log filenames older_log = 'build.out' - touch(older_log) + fs.touch(older_log) assert spec.package.install_log_path.endswith(older_log) # Now check the newer install log filename @@ -437,7 +437,8 @@ def test_pkg_install_paths(install_mockery): shutil.rmtree(log_dir) -def test_pkg_install_log(install_mockery): +def test_log_install_without_build_files(install_mockery): + """Test the installer log function when no build files are present.""" # Get a basic concrete spec for the trivial install package. spec = Spec('trivial-install-test-package').concretized() @@ -445,17 +446,40 @@ def test_pkg_install_log(install_mockery): with pytest.raises(IOError, match="No such file or directory"): spack.installer.log(spec.package) - # Set up mock build files and try again + +def test_log_install_with_build_files(install_mockery, monkeypatch): + """Test the installer's log function when have build files.""" + config_log = 'config.log' + + # Retain the original function for use in the monkey patch that is used + # to raise an exception under the desired condition for test coverage. + orig_install_fn = fs.install + + def _install(src, dest): + orig_install_fn(src, dest) + if src.endswith(config_log): + raise Exception('Mock log install error') + + monkeypatch.setattr(fs, 'install', _install) + + spec = Spec('trivial-install-test-package').concretized() + + # Set up mock build files and try again to include archive failure log_path = spec.package.log_path log_dir = os.path.dirname(log_path) - mkdirp(log_dir) - with working_dir(log_dir): - touch(log_path) - touch(spec.package.env_path) - touch(spec.package.configure_args_path) + fs.mkdirp(log_dir) + with fs.working_dir(log_dir): + fs.touch(log_path) + fs.touch(spec.package.env_path) + fs.touch(spec.package.configure_args_path) install_path = os.path.dirname(spec.package.install_log_path) - mkdirp(install_path) + fs.mkdirp(install_path) + + source = spec.package.stage.source_path + config = os.path.join(source, 'config.log') + fs.touchp(config) + spec.package.archive_files = ['missing', '..', config] spack.installer.log(spec.package) @@ -463,6 +487,21 @@ def test_pkg_install_log(install_mockery): assert os.path.exists(spec.package.install_env_path) assert os.path.exists(spec.package.install_configure_args_path) + archive_dir = os.path.join(install_path, 'archived-files') + source_dir = os.path.dirname(source) + rel_config = os.path.relpath(config, source_dir) + + assert os.path.exists(os.path.join(archive_dir, rel_config)) + assert not os.path.exists(os.path.join(archive_dir, 'missing')) + + expected_errs = [ + 'OUTSIDE SOURCE PATH', # for '..' + 'FAILED TO ARCHIVE' # for rel_config + ] + with open(os.path.join(archive_dir, 'errors.txt'), 'r') as fd: + for ln, expected in zip(fd, expected_errs): + assert expected in ln + # Cleanup shutil.rmtree(log_dir) diff --git a/lib/spack/spack/test/installer.py b/lib/spack/spack/test/installer.py index b9730c31657..0be4bc78c02 100644 --- a/lib/spack/spack/test/installer.py +++ b/lib/spack/spack/test/installer.py @@ -7,15 +7,19 @@ import py import pytest +import llnl.util.filesystem as fs import llnl.util.tty as tty +import llnl.util.lock as ulk import spack.binary_distribution import spack.compilers import spack.directory_layout as dl import spack.installer as inst -import spack.util.lock as lk +import spack.package_prefs as prefs import spack.repo import spack.spec +import spack.store +import spack.util.lock as lk def _mock_repo(root, namespace): @@ -152,7 +156,7 @@ def test_process_external_package_module(install_mockery, monkeypatch, capfd): def test_process_binary_cache_tarball_none(install_mockery, monkeypatch, capfd): - """Tests to cover _process_binary_cache_tarball when no tarball.""" + """Tests of _process_binary_cache_tarball when no tarball.""" monkeypatch.setattr(spack.binary_distribution, 'download_tarball', _none) pkg = spack.repo.get('trivial-install-test-package') @@ -162,7 +166,7 @@ def test_process_binary_cache_tarball_none(install_mockery, monkeypatch, def test_process_binary_cache_tarball_tar(install_mockery, monkeypatch, capfd): - """Tests to cover _process_binary_cache_tarball with a tar file.""" + """Tests of _process_binary_cache_tarball with a tar file.""" def _spec(spec): return spec @@ -179,6 +183,25 @@ def _spec(spec): assert 'Installing a from binary cache' in capfd.readouterr()[0] +def test_try_install_from_binary_cache(install_mockery, mock_packages, + monkeypatch, capsys): + """Tests SystemExit path for_try_install_from_binary_cache.""" + def _spec(spec, force): + spec = spack.spec.Spec('mpi').concretized() + return {spec: None} + + spec = spack.spec.Spec('mpich') + spec.concretize() + + monkeypatch.setattr(spack.binary_distribution, 'get_spec', _spec) + + with pytest.raises(SystemExit): + inst._try_install_from_binary_cache(spec.package, False, False) + + captured = capsys.readouterr() + assert 'add a spack mirror to allow download' in str(captured) + + def test_installer_init_errors(install_mockery): """Test to ensure cover installer constructor errors.""" with pytest.raises(ValueError, match='must be a package'): @@ -189,17 +212,18 @@ def test_installer_init_errors(install_mockery): inst.PackageInstaller(pkg) -def test_installer_strings(install_mockery): - """Tests of installer repr and str for coverage purposes.""" +def test_installer_repr(install_mockery): spec, installer = create_installer('trivial-install-test-package') - # Cover __repr__ irep = installer.__repr__() assert irep.startswith(installer.__class__.__name__) assert "installed=" in irep assert "failed=" in irep - # Cover __str__ + +def test_installer_str(install_mockery): + spec, installer = create_installer('trivial-install-test-package') + istr = str(installer) assert "#tasks=0" in istr assert "installed (0)" in istr @@ -207,7 +231,6 @@ def test_installer_strings(install_mockery): def test_installer_last_phase_error(install_mockery, capsys): - """Test to cover last phase error.""" spec = spack.spec.Spec('trivial-install-test-package') spec.concretize() assert spec.concrete @@ -220,7 +243,6 @@ def test_installer_last_phase_error(install_mockery, capsys): def test_installer_ensure_ready_errors(install_mockery): - """Test to cover _ensure_ready errors.""" spec, installer = create_installer('trivial-install-test-package') fmt = r'cannot be installed locally.*{0}' @@ -247,24 +269,102 @@ def test_installer_ensure_ready_errors(install_mockery): installer._ensure_install_ready(spec.package) -def test_ensure_locked_have(install_mockery, tmpdir): - """Test to cover _ensure_locked when already have lock.""" +def test_ensure_locked_err(install_mockery, monkeypatch, tmpdir, capsys): + """Test _ensure_locked when a non-lock exception is raised.""" + mock_err_msg = 'Mock exception error' + + def _raise(lock, timeout): + raise RuntimeError(mock_err_msg) + + spec, installer = create_installer('trivial-install-test-package') + + monkeypatch.setattr(ulk.Lock, 'acquire_read', _raise) + with tmpdir.as_cwd(): + with pytest.raises(RuntimeError): + installer._ensure_locked('read', spec.package) + + out = str(capsys.readouterr()[1]) + assert 'Failed to acquire a read lock' in out + assert mock_err_msg in out + + +def test_ensure_locked_have(install_mockery, tmpdir, capsys): + """Test _ensure_locked when already have lock.""" spec, installer = create_installer('trivial-install-test-package') with tmpdir.as_cwd(): + # Test "downgrade" of a read lock (to a read lock) lock = lk.Lock('./test', default_timeout=1e-9, desc='test') lock_type = 'read' tpl = (lock_type, lock) installer.locks[installer.pkg_id] = tpl assert installer._ensure_locked(lock_type, spec.package) == tpl + # Test "upgrade" of a read lock without read count to a write + lock_type = 'write' + err = 'Cannot upgrade lock' + with pytest.raises(ulk.LockUpgradeError, match=err): + installer._ensure_locked(lock_type, spec.package) -def test_package_id(install_mockery): - """Test to cover package_id functionality.""" + out = str(capsys.readouterr()[1]) + assert 'Failed to upgrade to a write lock' in out + assert 'exception when releasing read lock' in out + + # Test "upgrade" of the read lock *with* read count to a write + lock._reads = 1 + tpl = (lock_type, lock) + assert installer._ensure_locked(lock_type, spec.package) == tpl + + # Test "downgrade" of the write lock to a read lock + lock_type = 'read' + tpl = (lock_type, lock) + assert installer._ensure_locked(lock_type, spec.package) == tpl + + +@pytest.mark.parametrize('lock_type,reads,writes', [ + ('read', 1, 0), + ('write', 0, 1)]) +def test_ensure_locked_new_lock( + install_mockery, tmpdir, lock_type, reads, writes): + pkg_id = 'a' + spec, installer = create_installer(pkg_id) + with tmpdir.as_cwd(): + ltype, lock = installer._ensure_locked(lock_type, spec.package) + assert ltype == lock_type + assert lock is not None + assert lock._reads == reads + assert lock._writes == writes + + +def test_ensure_locked_new_warn(install_mockery, monkeypatch, tmpdir, capsys): + orig_pl = spack.database.Database.prefix_lock + + def _pl(db, spec, timeout): + lock = orig_pl(db, spec, timeout) + lock.default_timeout = 1e-9 if timeout is None else None + return lock + + pkg_id = 'a' + spec, installer = create_installer(pkg_id) + + monkeypatch.setattr(spack.database.Database, 'prefix_lock', _pl) + + lock_type = 'read' + ltype, lock = installer._ensure_locked(lock_type, spec.package) + assert ltype == lock_type + assert lock is not None + + out = str(capsys.readouterr()[1]) + assert 'Expected prefix lock timeout' in out + + +def test_package_id_err(install_mockery): pkg = spack.repo.get('trivial-install-test-package') with pytest.raises(ValueError, match='spec is not concretized'): inst.package_id(pkg) + +def test_package_id_ok(install_mockery): spec = spack.spec.Spec('trivial-install-test-package') spec.concretize() assert spec.concrete @@ -273,36 +373,44 @@ def test_package_id(install_mockery): def test_fake_install(install_mockery): - """Test to cover fake install basics.""" spec = spack.spec.Spec('trivial-install-test-package') spec.concretize() assert spec.concrete + pkg = spec.package inst._do_fake_install(pkg) assert os.path.isdir(pkg.prefix.lib) -def test_packages_needed_to_bootstrap_compiler(install_mockery, monkeypatch): - """Test to cover most of _packages_needed_to_boostrap_compiler.""" - # TODO: More work is needed to go beyond the dependency check - def _no_compilers(pkg, arch_spec): - return [] - - # Test path where no compiler packages returned +def test_packages_needed_to_bootstrap_compiler_none(install_mockery): spec = spack.spec.Spec('trivial-install-test-package') spec.concretize() assert spec.concrete + packages = inst._packages_needed_to_bootstrap_compiler(spec.package) assert not packages - # Test up to the dependency check - monkeypatch.setattr(spack.compilers, 'compilers_for_spec', _no_compilers) - with pytest.raises(spack.repo.UnknownPackageError, match='not found'): - inst._packages_needed_to_bootstrap_compiler(spec.package) + +def test_packages_needed_to_bootstrap_compiler_packages(install_mockery, + monkeypatch): + spec = spack.spec.Spec('trivial-install-test-package') + spec.concretize() + + def _conc_spec(compiler): + return spack.spec.Spec('a').concretized() + + # Ensure we can get past functions that are precluding obtaining + # packages. + monkeypatch.setattr(spack.compilers, 'compilers_for_spec', _none) + monkeypatch.setattr(spack.compilers, 'pkg_spec_for_compiler', _conc_spec) + monkeypatch.setattr(spack.spec.Spec, 'concretize', _noop) + + packages = inst._packages_needed_to_bootstrap_compiler(spec.package) + assert packages def test_dump_packages_deps_ok(install_mockery, tmpdir, mock_repo_path): - """Test to add coverage to dump_packages with dependencies happy path.""" + """Test happy path for dump_packages with dependencies.""" spec_name = 'simple-inheritance' spec = spack.spec.Spec(spec_name).concretized() @@ -314,7 +422,7 @@ def test_dump_packages_deps_ok(install_mockery, tmpdir, mock_repo_path): def test_dump_packages_deps_errs(install_mockery, tmpdir, monkeypatch, capsys): - """Test to add coverage to dump_packages with dependencies.""" + """Test error paths for dump_packages with dependencies.""" orig_bpp = spack.store.layout.build_packages_path orig_dirname = spack.repo.Repo.dirname_for_package_name repo_err_msg = "Mock dirname_for_package_name" @@ -354,59 +462,45 @@ def _repoerr(repo, name): assert "Couldn't copy in provenance for cmake" in out -@pytest.mark.tld -def test_check_deps_status_errs(install_mockery, monkeypatch): - """Test to cover _check_deps_status failures.""" +def test_check_deps_status_install_failure(install_mockery, monkeypatch): spec, installer = create_installer('a') # Make sure the package is identified as failed - orig_fn = spack.database.Database.prefix_failed monkeypatch.setattr(spack.database.Database, 'prefix_failed', _true) with pytest.raises(inst.InstallError, match='install failure'): installer._check_deps_status() - monkeypatch.setattr(spack.database.Database, 'prefix_failed', orig_fn) - # Ensure do not acquire the lock +def test_check_deps_status_write_locked(install_mockery, monkeypatch): + spec, installer = create_installer('a') + + # Ensure the lock is not acquired monkeypatch.setattr(inst.PackageInstaller, '_ensure_locked', _not_locked) with pytest.raises(inst.InstallError, match='write locked by another'): installer._check_deps_status() -@pytest.mark.tld def test_check_deps_status_external(install_mockery, monkeypatch): - """Test to cover _check_deps_status for external.""" spec, installer = create_installer('a') - deps = spec.dependencies() - assert len(deps) > 0 - dep_id = 'b' - - # Ensure the known dependent is installed if flagged as external + # Mock the known dependent, b, as external so assumed to be installed monkeypatch.setattr(spack.spec.Spec, 'external', True) installer._check_deps_status() - assert dep_id in installer.installed + assert 'b' in installer.installed -@pytest.mark.tld def test_check_deps_status_upstream(install_mockery, monkeypatch): - """Test to cover _check_deps_status for upstream.""" spec, installer = create_installer('a') - deps = spec.dependencies() - assert len(deps) > 0 - dep_id = 'b' - - # Ensure the known dependent, b, is installed if flagged as upstream + # Mock the known dependent, b, as installed upstream monkeypatch.setattr(spack.package.PackageBase, 'installed_upstream', True) installer._check_deps_status() - assert dep_id in installer.installed + assert 'b' in installer.installed def test_add_bootstrap_compilers(install_mockery, monkeypatch): - """Test to cover _add_bootstrap_compilers.""" def _pkgs(pkg): spec = spack.spec.Spec('mpi').concretized() return [(spec.package, True)] @@ -445,7 +539,6 @@ def test_installer_init_queue(install_mockery): def test_install_task_use_cache(install_mockery, monkeypatch): - """Test _install_task to cover use_cache path.""" spec, installer = create_installer('trivial-install-test-package') task = create_build_task(spec.package) @@ -454,25 +547,27 @@ def test_install_task_use_cache(install_mockery, monkeypatch): assert spec.package.name in installer.installed -def test_install_task_stop_iter(install_mockery, monkeypatch, capfd): - """Test _install_task to cover the StopIteration exception.""" - mock_err_msg = 'mock stop iteration' +def test_install_task_add_compiler(install_mockery, monkeypatch, capfd): + config_msg = 'mock add_compilers_to_config' - def _raise(installer, pkg): - raise StopIteration(mock_err_msg) + def _add(_compilers): + tty.msg(config_msg) spec, installer = create_installer('a') task = create_build_task(spec.package) + task.compiler = True + # Preclude any meaningful side-effects monkeypatch.setattr(spack.package.PackageBase, 'unit_test_check', _true) - monkeypatch.setattr(inst.PackageInstaller, '_setup_install_dir', _raise) + monkeypatch.setattr(inst.PackageInstaller, '_setup_install_dir', _noop) + monkeypatch.setattr(spack.build_environment, 'fork', _noop) + monkeypatch.setattr(spack.database.Database, 'add', _noop) + monkeypatch.setattr(spack.compilers, 'add_compilers_to_config', _add) installer._install_task(task) - out = capfd.readouterr()[0] - assert mock_err_msg in out - assert 'Package stage directory' in out - assert spec.package.stage.source_path in out + out = capfd.readouterr()[0] + assert config_msg in out def test_release_lock_write_n_exception(install_mockery, tmpdir, capsys): @@ -529,8 +624,36 @@ def _rmtask(installer, pkg_id): assert len(installer.build_tasks) == 1 -def test_cleanup_failed(install_mockery, tmpdir, monkeypatch, capsys): - """Test to increase coverage of _cleanup_failed.""" +def test_setup_install_dir_grp(install_mockery, monkeypatch, capfd): + """Test _setup_install_dir's group change.""" + mock_group = 'mockgroup' + mock_chgrp_msg = 'Changing group for {0} to {1}' + + def _get_group(spec): + return mock_group + + def _chgrp(path, group): + tty.msg(mock_chgrp_msg.format(path, group)) + + monkeypatch.setattr(prefs, 'get_package_group', _get_group) + monkeypatch.setattr(fs, 'chgrp', _chgrp) + + spec, installer = create_installer('trivial-install-test-package') + + fs.touchp(spec.prefix) + metadatadir = spack.store.layout.metadata_path(spec) + # Should fail with a "not a directory" error + with pytest.raises(OSError, match=metadatadir): + installer._setup_install_dir(spec.package) + + out = str(capfd.readouterr()[0]) + + expected_msg = mock_chgrp_msg.format(spec.prefix, mock_group) + assert expected_msg in out + + +def test_cleanup_failed_err(install_mockery, tmpdir, monkeypatch, capsys): + """Test _cleanup_failed exception path.""" msg = 'Fake release_write exception' def _raise_except(lock): @@ -550,13 +673,14 @@ def _raise_except(lock): assert msg in out -def test_update_failed_no_mark(install_mockery): - """Test of _update_failed sans mark and dependent build tasks.""" +def test_update_failed_no_dependent_task(install_mockery): + """Test _update_failed with missing dependent build tasks.""" spec, installer = create_installer('dependent-install') - task = create_build_task(spec.package) - installer._update_failed(task) - assert installer.failed['dependent-install'] is None + for dep in spec.traverse(root=False): + task = create_build_task(dep.package) + installer._update_failed(task, mark=False) + assert installer.failed[task.pkg_id] is None def test_install_uninstalled_deps(install_mockery, monkeypatch, capsys): @@ -710,3 +834,12 @@ def _install(installer, task, **kwargs): installer.install() assert 'b' in installer.installed + + +def test_install_skip_patch(install_mockery, mock_fetch): + """Test the path skip_patch install path.""" + spec, installer = create_installer('b') + + installer.install(fake=False, skip_patch=True) + + assert 'b' in installer.installed From fddca6312c17d9eab1d7484cb1a594511b2ab57e Mon Sep 17 00:00:00 2001 From: noguchi-k <55966120+noguchi-k@users.noreply.github.com> Date: Fri, 13 Mar 2020 06:09:07 +0900 Subject: [PATCH 046/377] cpprestsdk: fix common error and, use boost@1.69.0 or lower (#15463) --- .../builtin/packages/cpprestsdk/Release.patch | 45 +++++++++++++++++++ .../builtin/packages/cpprestsdk/package.py | 7 ++- 2 files changed, 51 insertions(+), 1 deletion(-) create mode 100644 var/spack/repos/builtin/packages/cpprestsdk/Release.patch diff --git a/var/spack/repos/builtin/packages/cpprestsdk/Release.patch b/var/spack/repos/builtin/packages/cpprestsdk/Release.patch new file mode 100644 index 00000000000..e860b85f18c --- /dev/null +++ b/var/spack/repos/builtin/packages/cpprestsdk/Release.patch @@ -0,0 +1,45 @@ +diff -ur spack-src/Release.org/include/pplx/pplxlinux.h spack-src/Release/include/pplx/pplxlinux.h +--- spack-src/Release.org/include/pplx/pplxlinux.h 2020-03-12 13:52:40.161917503 +0900 ++++ spack-src/Release/include/pplx/pplxlinux.h 2020-03-12 14:05:50.834896829 +0900 +@@ -240,6 +240,11 @@ + { + public: + _PPLXIMP virtual void schedule( TaskProc_t proc, _In_ void* param); ++#if defined(__APPLE__) ++ virtual ~apple_scheduler() {} ++#else ++ virtual ~linux_scheduler() {} ++#endif + }; + + } // namespace details +diff -ur spack-src/Release.org/libs/websocketpp/websocketpp/transport/asio/connection.hpp spack-src/Release/libs/websocketpp/websocketpp/transport/asio/connection.hpp +--- spack-src/Release.org/libs/websocketpp/websocketpp/transport/asio/connection.hpp 2020-03-12 13:52:40.201921703 +0900 ++++ spack-src/Release/libs/websocketpp/websocketpp/transport/asio/connection.hpp 2020-03-12 14:09:13.586186467 +0900 +@@ -422,7 +422,7 @@ + m_io_service = io_service; + + if (config::enable_multithreading) { +- m_strand = lib::make_shared( ++ m_strand = lib::make_shared( + lib::ref(*io_service)); + + m_async_read_handler = m_strand->wrap(lib::bind( +diff -ur spack-src/Release.org/src/uri/uri.cpp spack-src/Release/src/uri/uri.cpp +--- spack-src/Release.org/src/uri/uri.cpp 2020-03-12 13:52:40.241925902 +0900 ++++ spack-src/Release/src/uri/uri.cpp 2020-03-12 13:53:58.610152210 +0900 +@@ -22,12 +22,12 @@ + // canonicalize components first + + // convert scheme to lowercase +- std::transform(m_scheme.begin(), m_scheme.end(), m_scheme.begin(), [this](utility::char_t c) { ++ std::transform(m_scheme.begin(), m_scheme.end(), m_scheme.begin(), [](utility::char_t c) { + return (utility::char_t)tolower(c); + }); + + // convert host to lowercase +- std::transform(m_host.begin(), m_host.end(), m_host.begin(), [this](utility::char_t c) { ++ std::transform(m_host.begin(), m_host.end(), m_host.begin(), [](utility::char_t c) { + return (utility::char_t)tolower(c); + }); + diff --git a/var/spack/repos/builtin/packages/cpprestsdk/package.py b/var/spack/repos/builtin/packages/cpprestsdk/package.py index 51acc882b6d..3bfbf52c292 100644 --- a/var/spack/repos/builtin/packages/cpprestsdk/package.py +++ b/var/spack/repos/builtin/packages/cpprestsdk/package.py @@ -17,6 +17,11 @@ class Cpprestsdk(CMakePackage): version('2.9.1', sha256='537358760acd782f4d2ed3a85d92247b4fc423aff9c85347dc31dbb0ab9bab16') - depends_on('boost') + depends_on('boost@:1.69.0') + + # Ref: https://github.com/microsoft/cpprestsdk/commit/f9f518e4ad84577eb684ad8235181e4495299af4 + # Ref: https://github.com/Microsoft/cpprestsdk/commit/6b2e0480018530b616f61d5cdc786c92ba148bb7 + # Ref: https://github.com/microsoft/cpprestsdk/commit/70c1b14f39f5d47984fdd8a31fc357ebb5a37851 + patch('Release.patch') root_cmakelists_dir = 'Release' From 9806149145b6b92887649366bf2bea6cb32db994 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Thu, 12 Mar 2020 22:10:21 +0100 Subject: [PATCH 047/377] gcc: Add 9.3.0 (#15469) --- var/spack/repos/builtin/packages/gcc/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index eb1c65630f7..c5b98286b2c 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -25,6 +25,7 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage): version('develop', svn=svn + 'trunk') + version('9.3.0', sha256='71e197867611f6054aa1119b13a0c0abac12834765fe2d81f35ac57f84f742d1') version('9.2.0', sha256='ea6ef08f121239da5695f76c9b33637a118dcf63e24164422231917fa61fb206') version('9.1.0', sha256='79a66834e96a6050d8fe78db2c3b32fb285b230b855d0a66288235bc04b327a0') From 7ddd84ac147e779a9836f5f83b87f9657b9ea012 Mon Sep 17 00:00:00 2001 From: Hector <10837193+he-b@users.noreply.github.com> Date: Thu, 12 Mar 2020 19:26:45 -0500 Subject: [PATCH 048/377] Add source highlight package (#15473) * add GNU source-highlight package * fix flake8 * Allows the package to download from GNU mirrors --- .../packages/source-highlight/package.py | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 var/spack/repos/builtin/packages/source-highlight/package.py diff --git a/var/spack/repos/builtin/packages/source-highlight/package.py b/var/spack/repos/builtin/packages/source-highlight/package.py new file mode 100644 index 00000000000..eee706518a6 --- /dev/null +++ b/var/spack/repos/builtin/packages/source-highlight/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class SourceHighlight(AutotoolsPackage, GNUMirrorPackage): + """This program, given a source file, produces a document with syntax + highlighting. It also provides a C++ highlight library + (since version 3.0). """ + + homepage = "https://www.gnu.org/software/src-highlite/" + gnu_mirror_path = "src-highlite/source-highlight-3.1.8.tar.gz" + + version('3.1.9', sha256='3a7fd28378cb5416f8de2c9e77196ec915145d44e30ff4e0ee8beb3fe6211c91') + version('3.1.8', sha256='01336a7ea1d1ccc374201f7b81ffa94d0aecb33afc7d6903ebf9fbf33a55ada3') + + depends_on('boost') From d1bf433d199419a275306e636b930ceabab82538 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 13 Mar 2020 03:39:34 -0500 Subject: [PATCH 049/377] gitignore: pytest cache directory (#15476) --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 0c79893369d..da05b2bcf04 100644 --- a/.gitignore +++ b/.gitignore @@ -22,6 +22,7 @@ .coverage \#* .#* +.cache lib/spack/spack/test/.cache /bin/spackc *.in.log From a3c319979bef91374aa35dff56396fe5e1e2a5c2 Mon Sep 17 00:00:00 2001 From: Hadrien G Date: Fri, 13 Mar 2020 13:57:32 +0100 Subject: [PATCH 050/377] Add new ACTS version (#15479) --- var/spack/repos/builtin/packages/acts-core/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/acts-core/package.py b/var/spack/repos/builtin/packages/acts-core/package.py index 1cd9fe63758..78edad95ab9 100644 --- a/var/spack/repos/builtin/packages/acts-core/package.py +++ b/var/spack/repos/builtin/packages/acts-core/package.py @@ -34,6 +34,7 @@ class ActsCore(CMakePackage): maintainers = ['HadrienG2'] version('develop', branch='master') + version('0.17.0', commit='0789f654ff484b013fd27e5023cf342785ea8d97') version('0.16.0', commit='b3d965fe0b8ae335909d79114ef261c6b996773a') version('0.15.0', commit='267c28f69c561e64369661a6235b03b5a610d6da') version('0.14.0', commit='38d678fcb205b77d60326eae913fbb1b054acea1') From 27bd4a5cdd478dd5d05706cbb634d18c4e96cd54 Mon Sep 17 00:00:00 2001 From: Thomas Kluyver Date: Fri, 13 Mar 2020 14:05:31 +0100 Subject: [PATCH 051/377] Add py-h5glance versions 0.5 & 0.6 (#15461) * Add py-h5glance versions 0.5 & 0.6 * List versions newest to oldest --- var/spack/repos/builtin/packages/py-h5glance/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-h5glance/package.py b/var/spack/repos/builtin/packages/py-h5glance/package.py index 93a1be40289..9d3c3c91716 100644 --- a/var/spack/repos/builtin/packages/py-h5glance/package.py +++ b/var/spack/repos/builtin/packages/py-h5glance/package.py @@ -15,7 +15,9 @@ class PyH5glance(PythonPackage): homepage = "https://github.com/European-XFEL/h5glance" url = "https://pypi.io/packages/source/h/h5glance/h5glance-0.4.tar.gz" - version('0.4', sha256='03babaee0d481991062842796126bc9e6b11e2e6e7daba57c26f2b58bf3bbd32') + version('0.6', sha256='203369ab614273aaad3419f151e234609bb8390b201b65f678d7e17c57633e35') + version('0.5', sha256='bc34ee42429f0440b329083e3f67fbf3d7016a4aed9e8b30911e5905217bc8d9') + version('0.4', sha256='03babaee0d481991062842796126bc9e6b11e2e6e7daba57c26f2b58bf3bbd32') depends_on('python@3.5:', type=('build', 'run')) depends_on('py-h5py', type=('build', 'run')) From 7b00712fff44a6ef0c09ab09025f2b4efaac5e65 Mon Sep 17 00:00:00 2001 From: Melven Roehrig-Zoellner Date: Fri, 13 Mar 2020 19:07:35 +0100 Subject: [PATCH 052/377] pgi: add missing paths in setup_run_environment (#15480) --- var/spack/repos/builtin/packages/pgi/package.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py index 5be94303355..aa6e60ddcc4 100644 --- a/var/spack/repos/builtin/packages/pgi/package.py +++ b/var/spack/repos/builtin/packages/pgi/package.py @@ -91,6 +91,9 @@ def install(self, spec, prefix): def setup_run_environment(self, env): prefix = Prefix(join_path(self.prefix, 'linux86-64', self.version)) + env.prepend_path('PATH', prefix.bin) + env.prepend_path('MANPATH', prefix.man) + env.prepend_path('LD_LIBRARY_PATH', prefix.lib) env.set('CC', join_path(prefix.bin, 'pgcc')) env.set('CXX', join_path(prefix.bin, 'pgc++')) env.set('F77', join_path(prefix.bin, 'pgfortran')) From 14441e00dc1c04df40d361ca46fd63c7446ac2ae Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Fri, 13 Mar 2020 19:41:19 +0100 Subject: [PATCH 053/377] package: Add fetch_options variable (#15317) PR #15212 added a new connect_timeout option that can be overridden using fetch_options but had to specified per-version. This adds a new per-package variable that can be used to override fetch_options for all versions in the package. This includes connect_timeout as well as 'cookie' (e.g. for the jdk package). Packages can combine package-level fetch_options with per-version fetch_options, in which case the version fetch_options completely override the package-level fetch_options. This commit includes tests for the added behavior. --- lib/spack/spack/fetch_strategy.py | 13 ++++++--- lib/spack/spack/package.py | 3 ++ lib/spack/spack/test/packages.py | 21 ++++++++++++++ lib/spack/spack/test/url_fetch.py | 19 +++++++++++-- .../packages/fetch-options/package.py | 22 +++++++++++++++ .../repos/builtin/packages/bzip2/package.py | 6 ++-- .../packages/eclipse-gcj-parser/package.py | 3 ++ .../builtin/packages/elfutils/package.py | 20 ++++++------- .../repos/builtin/packages/gcc/package.py | 6 +++- .../repos/builtin/packages/jdk/package.py | 28 +++++++++---------- .../repos/builtin/packages/libffi/package.py | 3 +- .../repos/builtin/packages/lvm2/package.py | 3 ++ .../builtin/packages/valgrind/package.py | 3 ++ .../repos/builtin/packages/verrou/package.py | 12 ++++++-- 14 files changed, 121 insertions(+), 41 deletions(-) create mode 100644 var/spack/repos/builtin.mock/packages/fetch-options/package.py diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index 85e93164a85..d7613ae58af 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -256,7 +256,7 @@ def __init__(self, url=None, checksum=None, **kwargs): self.digest = kwargs[h] self.expand_archive = kwargs.get('expand', True) - self.extra_options = kwargs.get('fetch_options', []) + self.extra_options = kwargs.get('fetch_options', {}) self._curl = None self.extension = kwargs.get('extension', None) @@ -1247,7 +1247,8 @@ def _check_version_attributes(fetcher, pkg, version): def _extrapolate(pkg, version): """Create a fetcher from an extrapolated URL for this version.""" try: - return URLFetchStrategy(pkg.url_for_version(version)) + return URLFetchStrategy(pkg.url_for_version(version), + fetch_options=pkg.fetch_options) except spack.package.NoURLError: msg = ("Can't extrapolate a URL for version %s " "because package %s defines no URLs") @@ -1267,6 +1268,7 @@ def _from_merged_attrs(fetcher, pkg, version): url = getattr(pkg, fetcher.url_attr) attrs = {fetcher.url_attr: url} + attrs['fetch_options'] = pkg.fetch_options attrs.update(pkg.versions[version]) return fetcher(**attrs) @@ -1289,8 +1291,10 @@ def for_package_version(pkg, version): if version not in pkg.versions: return _extrapolate(pkg, version) + # Set package args first so version args can override them + args = {'fetch_options': pkg.fetch_options} # Grab a dict of args out of the package version dict - args = pkg.versions[version] + args.update(pkg.versions[version]) # If the version specifies a `url_attr` directly, use that. for fetcher in all_strategies: @@ -1370,7 +1374,8 @@ def from_list_url(pkg): args.get('checksum')) # construct a fetcher - return URLFetchStrategy(url_from_list, checksum) + return URLFetchStrategy(url_from_list, checksum, + fetch_options=pkg.fetch_options) except KeyError as e: tty.debug(e) tty.msg("Cannot find version %s in url_list" % pkg.version) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index ff45355055a..2c8917a9aca 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -477,6 +477,9 @@ class PackageBase(with_metaclass(PackageMeta, PackageViewMixin, object)): #: This is currently only used by package sanity tests. manual_download = False + #: Set of additional options used when fetching package versions. + fetch_options = {} + # # Set default licensing information # diff --git a/lib/spack/spack/test/packages.py b/lib/spack/spack/test/packages.py index 299c56481e4..ffaad396c18 100644 --- a/lib/spack/spack/test/packages.py +++ b/lib/spack/spack/test/packages.py @@ -402,3 +402,24 @@ def test_bundle_patch_directive(mock_directive_bundle, match="Patches are not allowed"): patch = spack.directives.patch('mock/patch.txt') patch(mock_directive_bundle) + + +def test_fetch_options(mock_packages, config): + """Test fetch options inference.""" + + pkg = spack.repo.get('fetch-options') + + fetcher = spack.fetch_strategy.for_package_version(pkg, '1.0') + assert isinstance(fetcher, spack.fetch_strategy.URLFetchStrategy) + assert fetcher.digest == 'abc10' + assert fetcher.extra_options == {'timeout': 42, 'cookie': 'foobar'} + + fetcher = spack.fetch_strategy.for_package_version(pkg, '1.1') + assert isinstance(fetcher, spack.fetch_strategy.URLFetchStrategy) + assert fetcher.digest == 'abc11' + assert fetcher.extra_options == {'timeout': 65} + + fetcher = spack.fetch_strategy.for_package_version(pkg, '1.2') + assert isinstance(fetcher, spack.fetch_strategy.URLFetchStrategy) + assert fetcher.digest == 'abc12' + assert fetcher.extra_options == {'cookie': 'baz'} diff --git a/lib/spack/spack/test/url_fetch.py b/lib/spack/spack/test/url_fetch.py index 679240049d9..20648b47666 100644 --- a/lib/spack/spack/test/url_fetch.py +++ b/lib/spack/spack/test/url_fetch.py @@ -26,10 +26,10 @@ def checksum_type(request): @pytest.fixture def pkg_factory(): Pkg = collections.namedtuple( - 'Pkg', ['url_for_version', 'urls', 'url', 'versions'] + 'Pkg', ['url_for_version', 'urls', 'url', 'versions', 'fetch_options'] ) - def factory(url, urls): + def factory(url, urls, fetch_options={}): def fn(v): main_url = url or urls[0] @@ -37,7 +37,8 @@ def fn(v): return Pkg( url_for_version=fn, url=url, urls=urls, - versions=collections.defaultdict(dict) + versions=collections.defaultdict(dict), + fetch_options=fetch_options ) return factory @@ -130,6 +131,10 @@ def test_from_list_url(mock_packages, config, spec, url, digest): assert isinstance(fetch_strategy, fs.URLFetchStrategy) assert os.path.basename(fetch_strategy.url) == url assert fetch_strategy.digest == digest + assert fetch_strategy.extra_options == {} + pkg.fetch_options = {'timeout': 60} + fetch_strategy = fs.from_list_url(pkg) + assert fetch_strategy.extra_options == {'timeout': 60} def test_from_list_url_unspecified(mock_packages, config): @@ -142,6 +147,10 @@ def test_from_list_url_unspecified(mock_packages, config): assert isinstance(fetch_strategy, fs.URLFetchStrategy) assert os.path.basename(fetch_strategy.url) == 'foo-2.0.0.tar.gz' assert fetch_strategy.digest is None + assert fetch_strategy.extra_options == {} + pkg.fetch_options = {'timeout': 60} + fetch_strategy = fs.from_list_url(pkg) + assert fetch_strategy.extra_options == {'timeout': 60} def test_nosource_from_list_url(mock_packages, config): @@ -191,3 +200,7 @@ def test_candidate_urls(pkg_factory, url, urls, version, expected): pkg = pkg_factory(url, urls) f = fs._from_merged_attrs(fs.URLFetchStrategy, pkg, version) assert f.candidate_urls == expected + assert f.extra_options == {} + pkg = pkg_factory(url, urls, fetch_options={'timeout': 60}) + f = fs._from_merged_attrs(fs.URLFetchStrategy, pkg, version) + assert f.extra_options == {'timeout': 60} diff --git a/var/spack/repos/builtin.mock/packages/fetch-options/package.py b/var/spack/repos/builtin.mock/packages/fetch-options/package.py new file mode 100644 index 00000000000..1a31a535e13 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/fetch-options/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class FetchOptions(Package): + """Mock package with fetch_options.""" + + homepage = "http://www.fetch-options-example.com" + + url = 'https://example.com/some/tarball-1.0.tar.gz' + + fetch_options = {'timeout': 42, 'cookie': 'foobar'} + timeout = {'timeout': 65} + cookie = {'cookie': 'baz'} + + version('1.2', 'abc12', fetch_options=cookie) + version('1.1', 'abc11', fetch_options=timeout) + version('1.0', 'abc10') diff --git a/var/spack/repos/builtin/packages/bzip2/package.py b/var/spack/repos/builtin/packages/bzip2/package.py index 87e616d76cd..08d5978a63d 100644 --- a/var/spack/repos/builtin/packages/bzip2/package.py +++ b/var/spack/repos/builtin/packages/bzip2/package.py @@ -19,9 +19,9 @@ class Bzip2(Package): # The server is sometimes a bit slow to respond fetch_options = {'timeout': 60} - version('1.0.8', sha256='ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', fetch_options=fetch_options) - version('1.0.7', sha256='e768a87c5b1a79511499beb41500bcc4caf203726fff46a6f5f9ad27fe08ab2b', fetch_options=fetch_options) - version('1.0.6', sha256='a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', fetch_options=fetch_options) + version('1.0.8', sha256='ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269') + version('1.0.7', sha256='e768a87c5b1a79511499beb41500bcc4caf203726fff46a6f5f9ad27fe08ab2b') + version('1.0.6', sha256='a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd') variant('shared', default=True, description='Enables the build of shared libraries.') diff --git a/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py b/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py index 11054b409c1..13100d89a86 100644 --- a/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py +++ b/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py @@ -19,6 +19,9 @@ class EclipseGcjParser(Package): maintainers = ['citibeth'] + # The server is sometimes a bit slow to respond + fetch_options = {'timeout': 60} + version('4.8', sha256='98fd128f1d374d9e42fd9d4836bdd249c6d511ebc6c0df17fbc1b9df96c3d781', expand=False) phases = ('build', 'install') diff --git a/var/spack/repos/builtin/packages/elfutils/package.py b/var/spack/repos/builtin/packages/elfutils/package.py index 8dd2980c3d3..e1ffdc0e3b6 100644 --- a/var/spack/repos/builtin/packages/elfutils/package.py +++ b/var/spack/repos/builtin/packages/elfutils/package.py @@ -22,17 +22,17 @@ class Elfutils(AutotoolsPackage): list_depth = 1 # Sourceware is often slow to respond. - timeout = {'timeout': 60} + fetch_options = {'timeout': 60} - version('0.178', sha256='31e7a00e96d4e9c4bda452e1f2cdac4daf8abd24f5e154dee232131899f3a0f2', fetch_options=timeout) - version('0.177', sha256='fa489deccbcae7d8c920f60d85906124c1989c591196d90e0fd668e3dc05042e', fetch_options=timeout) - version('0.176', sha256='eb5747c371b0af0f71e86215a5ebb88728533c3a104a43d4231963f308cd1023', fetch_options=timeout) - version('0.175', sha256='f7ef925541ee32c6d15ae5cb27da5f119e01a5ccdbe9fe57bf836730d7b7a65b', fetch_options=timeout) - version('0.174', sha256='cdf27e70076e10a29539d89e367101d516bc4aa11b0d7777fe52139e3fcad08a', fetch_options=timeout) - version('0.173', sha256='b76d8c133f68dad46250f5c223482c8299d454a69430d9aa5c19123345a000ff', fetch_options=timeout) - version('0.170', sha256='1f844775576b79bdc9f9c717a50058d08620323c1e935458223a12f249c9e066', fetch_options=timeout) - version('0.168', sha256='b88d07893ba1373c7dd69a7855974706d05377766568a7d9002706d5de72c276', fetch_options=timeout) - version('0.163', sha256='7c774f1eef329309f3b05e730bdac50013155d437518a2ec0e24871d312f2e23', fetch_options=timeout) + version('0.178', sha256='31e7a00e96d4e9c4bda452e1f2cdac4daf8abd24f5e154dee232131899f3a0f2') + version('0.177', sha256='fa489deccbcae7d8c920f60d85906124c1989c591196d90e0fd668e3dc05042e') + version('0.176', sha256='eb5747c371b0af0f71e86215a5ebb88728533c3a104a43d4231963f308cd1023') + version('0.175', sha256='f7ef925541ee32c6d15ae5cb27da5f119e01a5ccdbe9fe57bf836730d7b7a65b') + version('0.174', sha256='cdf27e70076e10a29539d89e367101d516bc4aa11b0d7777fe52139e3fcad08a') + version('0.173', sha256='b76d8c133f68dad46250f5c223482c8299d454a69430d9aa5c19123345a000ff') + version('0.170', sha256='1f844775576b79bdc9f9c717a50058d08620323c1e935458223a12f249c9e066') + version('0.168', sha256='b88d07893ba1373c7dd69a7855974706d05377766568a7d9002706d5de72c276') + version('0.163', sha256='7c774f1eef329309f3b05e730bdac50013155d437518a2ec0e24871d312f2e23') # Libraries for reading compressed DWARF sections. variant('bzip2', default=False, diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index c5b98286b2c..d167bc78cb9 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -109,12 +109,16 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage): depends_on('zip', type='build', when='languages=java') depends_on('cuda', when='+nvptx') + # The server is sometimes a bit slow to respond + timeout = {'timeout': 60} + resource( name='newlib', url='ftp://sourceware.org/pub/newlib/newlib-3.0.0.20180831.tar.gz', sha256='3ad3664f227357df15ff34e954bfd9f501009a647667cd307bf0658aefd6eb5b', destination='newlibsource', - when='+nvptx' + when='+nvptx', + fetch_options=timeout ) # nvptx-tools does not seem to work as a dependency, diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py index 6e9c0329dc3..025d12be659 100644 --- a/var/spack/repos/builtin/packages/jdk/package.py +++ b/var/spack/repos/builtin/packages/jdk/package.py @@ -24,9 +24,7 @@ class Jdk(Package): # automate this process, we need to utilize these additional curl # command-line options. See: # http://stackoverflow.com/questions/10268583/how-to-automate-download-and-installation-of-java-jdk-on-linux - fetch_options = { - 'cookie': 'oraclelicense=accept-securebackup-cookie' - } + fetch_options = {'cookie': 'oraclelicense=accept-securebackup-cookie'} # To add the latest version, go to the homepage listed above, # click "JDK Download", click "Accept License Agreement", right-click the @@ -34,29 +32,29 @@ class Jdk(Package): # found in a link above. The build number can be deciphered from the URL. # Alternatively, run `bin/java -version` after extracting. Replace '+' # symbol in version with '_', otherwise it will be interpreted as a variant - version('12.0.2_10', sha256='2dde6fda89a4ec6e6560ed464e917861c9e40bf576e7a64856dafc55abaaff51', fetch_options=fetch_options, + version('12.0.2_10', sha256='2dde6fda89a4ec6e6560ed464e917861c9e40bf576e7a64856dafc55abaaff51', url='https://download.oracle.com/otn-pub/java/jdk/12.0.2+10/e482c34c86bd4bf8b56c0b35558996b9/jdk-12.0.2_linux-x64_bin.tar.gz') - version('12.0.1_12', sha256='9fd6dcdaf2cfca7da59e39b009a0f5bcd53bec2fb16105f7ca8d689cdab68d75', fetch_options=fetch_options, + version('12.0.1_12', sha256='9fd6dcdaf2cfca7da59e39b009a0f5bcd53bec2fb16105f7ca8d689cdab68d75', url='https://download.oracle.com/otn-pub/java/jdk/12.0.1+12/69cfe15208a647278a19ef0990eea691/jdk-12.0.1_linux-x64_bin.tar.gz') - version('11.0.2_9', sha256='7b4fd8ffcf53e9ff699d964a80e4abf9706b5bdb5644a765c2b96f99e3a2cdc8', fetch_options=fetch_options, + version('11.0.2_9', sha256='7b4fd8ffcf53e9ff699d964a80e4abf9706b5bdb5644a765c2b96f99e3a2cdc8', url='https://download.oracle.com/otn-pub/java/jdk/11.0.2+9/f51449fcd52f4d52b93a989c5c56ed3c/jdk-11.0.2_linux-x64_bin.tar.gz') - version('11.0.1_13', sha256='e7fd856bacad04b6dbf3606094b6a81fa9930d6dbb044bbd787be7ea93abc885', fetch_options=fetch_options, + version('11.0.1_13', sha256='e7fd856bacad04b6dbf3606094b6a81fa9930d6dbb044bbd787be7ea93abc885', url='https://download.oracle.com/otn-pub/java/jdk/11.0.1+13/90cf5d8f270a4347a95050320eef3fb7/jdk-11.0.1_linux-x64_bin.tar.gz') - version('10.0.2_13', sha256='6633c20d53c50c20835364d0f3e172e0cbbce78fff81867488f22a6298fa372b', fetch_options=fetch_options, + version('10.0.2_13', sha256='6633c20d53c50c20835364d0f3e172e0cbbce78fff81867488f22a6298fa372b', url='https://download.oracle.com/otn-pub/java/jdk/10.0.2+13/19aef61b38124481863b1413dce1855f/jdk-10.0.2_linux-x64_bin.tar.gz') - version('10.0.1_10', sha256='ae8ed645e6af38432a56a847597ac61d4283b7536688dbab44ab536199d1e5a4', fetch_options=fetch_options, + version('10.0.1_10', sha256='ae8ed645e6af38432a56a847597ac61d4283b7536688dbab44ab536199d1e5a4', url='https://download.oracle.com/otn-pub/java/jdk/10.0.1+10/fb4372174a714e6b8c52526dc134031e/jdk-10.0.1_linux-x64_bin.tar.gz') - version('1.8.0_241-b07', sha256='419d32677855f676076a25aed58e79432969142bbd778ff8eb57cb618c69e8cb', fetch_options=fetch_options, + version('1.8.0_241-b07', sha256='419d32677855f676076a25aed58e79432969142bbd778ff8eb57cb618c69e8cb', url='https://download.oracle.com/otn-pub/java/jdk/8u241-b07/1f5b5a70bf22433b84d0e960903adac8/jdk-8u241-linux-x64.tar.gz') - version('1.8.0_231-b11', sha256='a011584a2c9378bf70c6903ef5fbf101b30b08937441dc2ec67932fb3620b2cf', fetch_options=fetch_options, + version('1.8.0_231-b11', sha256='a011584a2c9378bf70c6903ef5fbf101b30b08937441dc2ec67932fb3620b2cf', url='https://download.oracle.com/otn-pub/java/jdk/8u231-b11/5b13a193868b4bf28bcb45c792fce896/jdk-8u231-linux-x64.tar.gz') - version('1.8.0_212-b10', sha256='3160c50aa8d8e081c8c7fe0f859ea452922eca5d2ae8f8ef22011ae87e6fedfb', fetch_options=fetch_options, + version('1.8.0_212-b10', sha256='3160c50aa8d8e081c8c7fe0f859ea452922eca5d2ae8f8ef22011ae87e6fedfb', url='https://download.oracle.com/otn-pub/java/jdk/8u212-b10/59066701cf1a433da9770636fbc4c9aa/jdk-8u212-linux-x64.tar.gz') - version('1.8.0_202-b08', sha256='9a5c32411a6a06e22b69c495b7975034409fa1652d03aeb8eb5b6f59fd4594e0', fetch_options=fetch_options, + version('1.8.0_202-b08', sha256='9a5c32411a6a06e22b69c495b7975034409fa1652d03aeb8eb5b6f59fd4594e0', url='https://download.oracle.com/otn-pub/java/jdk/8u202-b08/1961070e4c9b4e26a04e7f5a083f551e/jdk-8u202-linux-x64.tar.gz') - version('1.8.0_141-b15', sha256='041d5218fbea6cd7e81c8c15e51d0d32911573af2ed69e066787a8dc8a39ba4f', fetch_options=fetch_options, + version('1.8.0_141-b15', sha256='041d5218fbea6cd7e81c8c15e51d0d32911573af2ed69e066787a8dc8a39ba4f', url='https://download.oracle.com/otn-pub/java/jdk/8u141-b15/336fa29ff2bb4ef291e347e091f7f4a7/jdk-8u141-linux-x64.tar.gz') - version('1.8.0_131-b11', sha256='62b215bdfb48bace523723cdbb2157c665e6a25429c73828a32f00e587301236', fetch_options=fetch_options, + version('1.8.0_131-b11', sha256='62b215bdfb48bace523723cdbb2157c665e6a25429c73828a32f00e587301236', url='https://download.oracle.com/otn-pub/java/jdk/8u131-b11/d54c1d3a095b4ff2b6607d096fa80163/jdk-8u131-linux-x64.tar.gz') provides('java@12', when='@12.0:12.999') diff --git a/var/spack/repos/builtin/packages/libffi/package.py b/var/spack/repos/builtin/packages/libffi/package.py index 028c5913550..07ec319fb82 100644 --- a/var/spack/repos/builtin/packages/libffi/package.py +++ b/var/spack/repos/builtin/packages/libffi/package.py @@ -17,8 +17,7 @@ class Libffi(AutotoolsPackage): fetch_options = {'timeout': 60} version('3.2.1', sha256='d06ebb8e1d9a22d19e38d63fdb83954253f39bedc5d46232a05645685722ca37', - url="https://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz", - fetch_options=fetch_options) + url="https://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz") @property def headers(self): diff --git a/var/spack/repos/builtin/packages/lvm2/package.py b/var/spack/repos/builtin/packages/lvm2/package.py index c552fe3ef59..55fa1f1d39e 100644 --- a/var/spack/repos/builtin/packages/lvm2/package.py +++ b/var/spack/repos/builtin/packages/lvm2/package.py @@ -20,6 +20,9 @@ class Lvm2(AutotoolsPackage): homepage = "https://www.sourceware.org/lvm2" url = "https://sourceware.org/pub/lvm2/releases/LVM2.2.03.05.tgz" + # The server is sometimes a bit slow to respond + fetch_options = {'timeout': 60} + version('2.03.05', sha256='ca52815c999b20c6d25e3192f142f081b93d01f07b9d787e99664b169dba2700') version('2.03.04', sha256='f151f36fc0039997d2d9369b607b9262568b1a268afe19fd1535807355402142') version('2.03.03', sha256='cedefa63ec5ae1b62fedbfddfc30706c095be0fc7c6aaed6fd1c50bc8c840dde') diff --git a/var/spack/repos/builtin/packages/valgrind/package.py b/var/spack/repos/builtin/packages/valgrind/package.py index 684a5bdfa8f..3f759efeac9 100644 --- a/var/spack/repos/builtin/packages/valgrind/package.py +++ b/var/spack/repos/builtin/packages/valgrind/package.py @@ -22,6 +22,9 @@ class Valgrind(AutotoolsPackage): url = "https://sourceware.org/pub/valgrind/valgrind-3.13.0.tar.bz2" git = "git://sourceware.org/git/valgrind.git" + # The server is sometimes a bit slow to respond + fetch_options = {'timeout': 60} + version('develop', branch='master') version('3.15.0', sha256='417c7a9da8f60dd05698b3a7bc6002e4ef996f14c13f0ff96679a16873e78ab1') version('3.14.0', sha256='037c11bfefd477cc6e9ebe8f193bb237fe397f7ce791b4a4ce3fa1c6a520baa5') diff --git a/var/spack/repos/builtin/packages/verrou/package.py b/var/spack/repos/builtin/packages/verrou/package.py index 265ee2b0963..f92443d1441 100644 --- a/var/spack/repos/builtin/packages/verrou/package.py +++ b/var/spack/repos/builtin/packages/verrou/package.py @@ -32,18 +32,24 @@ class Verrou(AutotoolsPackage): version('2.0.0', sha256='798df6e426ec57646a2a626d756b72f0171647ae5b07c982952dae2d71e26045') version('1.1.0', sha256='b5105f61c65680f31551199cd143b2e15f412c34c821537998a7165e315dde2d') + # The server is sometimes a bit slow to respond + timeout = {'timeout': 60} + resource(name='valgrind-3.15.0', url='https://sourceware.org/pub/valgrind/valgrind-3.15.0.tar.bz2', sha256='417c7a9da8f60dd05698b3a7bc6002e4ef996f14c13f0ff96679a16873e78ab1', - when='@2.2.0:') + when='@2.2.0:', + fetch_options=timeout) resource(name='valgrind-3.14.0', url='https://sourceware.org/pub/valgrind/valgrind-3.14.0.tar.bz2', sha256='037c11bfefd477cc6e9ebe8f193bb237fe397f7ce791b4a4ce3fa1c6a520baa5', - when='@2.1.0:2.1.99') + when='@2.1.0:2.1.99', + fetch_options=timeout) resource(name='valgrind-3.13.0', url='https://sourceware.org/pub/valgrind/valgrind-3.13.0.tar.bz2', sha256='d76680ef03f00cd5e970bbdcd4e57fb1f6df7d2e2c071635ef2be74790190c3b', - when='@1.1.0:2.0.99') + when='@1.1.0:2.0.99', + fetch_options=timeout) variant('fma', default=True, description='Activates fused multiply-add support for Verrou') From 262a69c0a9b6ad6c2e197a068958b0e2976cff72 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 13 Mar 2020 14:40:58 -0500 Subject: [PATCH 054/377] py-astpretty: add new package (#15484) * py-astpretty: add new package * pkg_resources needed at run-time --- .../builtin/packages/py-astpretty/package.py | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-astpretty/package.py diff --git a/var/spack/repos/builtin/packages/py-astpretty/package.py b/var/spack/repos/builtin/packages/py-astpretty/package.py new file mode 100644 index 00000000000..b6b4e9855fa --- /dev/null +++ b/var/spack/repos/builtin/packages/py-astpretty/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyAstpretty(PythonPackage): + """Pretty print the output of python stdlib `ast.parse`.""" + + homepage = "https://github.com/asottile/astpretty" + url = "https://pypi.io/packages/source/a/astpretty/astpretty-2.0.0.tar.gz" + + version('2.0.0', sha256='e4724bfd753636ba4a84384702e9796e5356969f40af2596d846ce64addde086') + + variant('typed', default=False, description='Add support for typed comments') + + depends_on('python@3.6.1:', type=('build', 'run')) + depends_on('py-setuptools', type=('build', 'run')) + depends_on('py-typed-ast', type=('build', 'run'), when='+typed') From 38d04e29ebe481bcc6d344e669ffca4ebb79bb9f Mon Sep 17 00:00:00 2001 From: Hans Pabst Date: Fri, 13 Mar 2020 20:44:26 +0100 Subject: [PATCH 055/377] LIBXSMM 1.15 (#15482) * LIBXSMM 1.15 * LIBXSMM: renamed development version according to the related branch on GitHub. --- var/spack/repos/builtin/packages/libxsmm/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/libxsmm/package.py b/var/spack/repos/builtin/packages/libxsmm/package.py index 070b24396f4..12cfc32dfd2 100644 --- a/var/spack/repos/builtin/packages/libxsmm/package.py +++ b/var/spack/repos/builtin/packages/libxsmm/package.py @@ -14,10 +14,11 @@ class Libxsmm(MakefilePackage): and deep learning primitives.""" homepage = 'https://github.com/hfp/libxsmm' - url = 'https://github.com/hfp/libxsmm/archive/1.14.tar.gz' + url = 'https://github.com/hfp/libxsmm/archive/1.15.tar.gz' git = 'https://github.com/hfp/libxsmm.git' - version('develop', branch='master') + version('master', branch='master') + version('1.15', sha256='499e5adfbf90cd3673309243c2b56b237d54f86db2437e1ac06c8746b55ab91c') version('1.14', sha256='9c0af4509ea341d1ee2c6c19fc6f19289318c3bd4b17844efeb9e7f9691abf76') version('1.13', sha256='47c034e169820a9633770eece0e0fdd8d4a744e09b81da2af8c2608a4625811e') version('1.12.1', sha256='3687fb98da00ba92cd50b5f0d18b39912c7886dad3856843573aee0cb34e9791') From 471f23e456e3b26aff75c17e8e97497087fd7fd3 Mon Sep 17 00:00:00 2001 From: Tim Haines Date: Sat, 14 Mar 2020 07:45:00 -0500 Subject: [PATCH 056/377] Limit binutils to <= 2.33.1 (#15470) HPCToolKit <= 2020.03.01 does not build with binutils 2.34. --- var/spack/repos/builtin/packages/hpctoolkit/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/hpctoolkit/package.py b/var/spack/repos/builtin/packages/hpctoolkit/package.py index 9a965502de2..a8c489f87d4 100644 --- a/var/spack/repos/builtin/packages/hpctoolkit/package.py +++ b/var/spack/repos/builtin/packages/hpctoolkit/package.py @@ -60,7 +60,7 @@ class Hpctoolkit(AutotoolsPackage): ' +graph +regex +shared +multithreaded visibility=global' ) - depends_on('binutils+libiberty~nls', type='link') + depends_on('binutils@:2.33.1+libiberty~nls', type='link') depends_on('boost' + boost_libs) depends_on('bzip2+shared', type='link') depends_on('dyninst@9.3.2:') From 96a037adf7910b550784ec92e6c889ac093e3a97 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Sun, 15 Mar 2020 18:43:23 -0400 Subject: [PATCH 057/377] gcc: Don't apply macOS 9.2.0 patch for 9.3.0 (#15493) The patch neither applies nor is necessary. --- var/spack/repos/builtin/packages/gcc/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index d167bc78cb9..f3891161a2b 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -223,7 +223,7 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage): # Fix system headers for Catalina SDK # (otherwise __OSX_AVAILABLE_STARTING ends up undefined) patch('https://raw.githubusercontent.com/Homebrew/formula-patches/b8b8e65e/gcc/9.2.0-catalina.patch', - sha256='0b8d14a7f3c6a2f0d2498526e86e088926671b5da50a554ffa6b7f73ac4f132b', when='@9.2.0:') + sha256='0b8d14a7f3c6a2f0d2498526e86e088926671b5da50a554ffa6b7f73ac4f132b', when='@9.2.0') # Use -headerpad_max_install_names in the build, # otherwise updated load commands won't fit in the Mach-O header. # This is needed because `gcc` avoids the superenv shim. From d24c64c9364780d69967c33f7af2bde126caff6e Mon Sep 17 00:00:00 2001 From: Matthieu Dorier Date: Mon, 16 Mar 2020 07:33:42 +0000 Subject: [PATCH 058/377] unqlite: added package at v1.1.9 (#15501) --- .../repos/builtin/packages/unqlite/package.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 var/spack/repos/builtin/packages/unqlite/package.py diff --git a/var/spack/repos/builtin/packages/unqlite/package.py b/var/spack/repos/builtin/packages/unqlite/package.py new file mode 100644 index 00000000000..84c3b5575e4 --- /dev/null +++ b/var/spack/repos/builtin/packages/unqlite/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Unqlite(CMakePackage): + """UnQLite is a in-process software library which implements a self-contained, + serverless, zero-configuration, transactional NoSQL database engine.""" + + homepage = "https://unqlite.org/" + url = "https://github.com/symisc/unqlite/archive/v1.1.9.tar.gz" + git = 'https://github.com/symisc/unqlite.git' + + version('master', branch='master') + version('1.1.9', sha256='33d5b5e7b2ca223942e77d31112d2e20512bc507808414451c8a98a7be5e15c0') From 410ad0b1589001c39182c05588ee475154200682 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Mon, 16 Mar 2020 03:42:49 -0400 Subject: [PATCH 059/377] cmake: added v3.16.5 (#15492) --- var/spack/repos/builtin/packages/cmake/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index fdfa46af426..994ed42392e 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -13,6 +13,7 @@ class Cmake(Package): url = 'https://github.com/Kitware/CMake/releases/download/v3.15.5/cmake-3.15.5.tar.gz' maintainers = ['chuckatkins'] + version('3.16.5', sha256='5f760b50b8ecc9c0c37135fae5fbf00a2fef617059aa9d61c1bb91653e5a8bfc') version('3.16.2', sha256='8c09786ec60ca2be354c29829072c38113de9184f29928eb9da8446a5f2ce6a9') version('3.16.1', sha256='a275b3168fa8626eca4465da7bb159ff07c8c6cb0fb7179be59e12cbdfa725fd') version('3.16.0', sha256='6da56556c63cab6e9a3e1656e8763ed4a841ac9859fefb63cbe79472e67e8c5f') From 1e547f58ab21423ec9f4be68f51c522958a736cd Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Mon, 16 Mar 2020 03:43:21 -0400 Subject: [PATCH 060/377] ncurses: added v6.2 (#15494) --- var/spack/repos/builtin/packages/ncurses/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py index bee4fd655ce..9df2de49b76 100644 --- a/var/spack/repos/builtin/packages/ncurses/package.py +++ b/var/spack/repos/builtin/packages/ncurses/package.py @@ -20,6 +20,7 @@ class Ncurses(AutotoolsPackage, GNUMirrorPackage): # URL must remain http:// so Spack can bootstrap curl gnu_mirror_path = "ncurses/ncurses-6.1.tar.gz" + version('6.2', sha256='30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d') version('6.1', sha256='aa057eeeb4a14d470101eff4597d5833dcef5965331be3528c08d99cebaa0d17') version('6.0', sha256='f551c24b30ce8bfb6e96d9f59b42fbea30fa3a6123384172f9e7284bcf647260') version('5.9', sha256='9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b') From 77e845d53cec7b12009b404ab128805195c69739 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Mon, 16 Mar 2020 03:45:25 -0400 Subject: [PATCH 061/377] swig: added v4.0.1 (#15496) --- var/spack/repos/builtin/packages/swig/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py index ac48fb12464..ebc04dd077d 100644 --- a/var/spack/repos/builtin/packages/swig/package.py +++ b/var/spack/repos/builtin/packages/swig/package.py @@ -23,6 +23,7 @@ class Swig(AutotoolsPackage): url = "http://prdownloads.sourceforge.net/swig/swig-3.0.12.tar.gz" version('master', git='https://github.com/swig/swig.git') + version('4.0.1', sha256='7a00b4d0d53ad97a14316135e2d702091cd5f193bb58bcfcd8bc59d41e7887a9') version('4.0.0', sha256='e8a39cd6437e342cdcbd5af27a9bf11b62dc9efec9248065debcb8276fcbb925') version('3.0.12', sha256='7cf9f447ae7ed1c51722efc45e7f14418d15d7a1e143ac9f09a668999f4fc94d') version('3.0.11', sha256='d9031d531d7418829a54d0d51c4ed9007016b213657ec70be44031951810566e') From 0301ec32b42d46ffb1f497112be71e3406eb4ce6 Mon Sep 17 00:00:00 2001 From: Melven Roehrig-Zoellner Date: Mon, 16 Mar 2020 09:02:10 +0100 Subject: [PATCH 062/377] tixi: added package at v3.0.3 (#15490) --- .../repos/builtin/packages/tixi/package.py | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 var/spack/repos/builtin/packages/tixi/package.py diff --git a/var/spack/repos/builtin/packages/tixi/package.py b/var/spack/repos/builtin/packages/tixi/package.py new file mode 100644 index 00000000000..74a7ed7c656 --- /dev/null +++ b/var/spack/repos/builtin/packages/tixi/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Tixi(CMakePackage): + """TiXI is a fast and simple XML interface library and could be used + from applications written in C, C++, Fortran, JAVA and Python. """ + + homepage = "https://github.com/DLR-SC/tixi" + url = "https://github.com/DLR-SC/tixi/archive/v3.0.3.tar.gz" + git = "https://github.com/DLR-SC/tixi.git" + + version('3.0.3', sha256='3584e0cec6ab811d74fb311a9af0663736b1d7f11b81015fcb378efaf5ad3589') + version('2.2.4', sha256='9080d2a617b7c411b9b4086de23998ce86e261b88075f38c73d3ce25da94b21c') + + depends_on('python', type='build') + depends_on('expat') + depends_on('curl') + depends_on('libxml2') + depends_on('libxslt') From 17e4df1e41998c1f5f777127c1157cdd7c61fe90 Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Mon, 16 Mar 2020 08:42:23 -0500 Subject: [PATCH 063/377] Buildcache: Install into non-default directory layouts (#13797) * Buildcache: Install into non-default directory layouts Store a dictionary mapping of original dependency prefixes to dependency hashes Use the loaded spec to grab the new dependency prefixes in the new directory layout. Map the original dependency prefixes to the new dependency prefixes using the dependency hashes. Use the dependency prefixes map to replace original rpaths with new rpaths preserving the order. For mach-o binaries, use the dependency prefixes map to replace the dependency library entires for libraries and executables and the replace the library id for libraries. On Linux, patchelf is used to replace the rpaths of elf binaries. On macOS, install_name_tool is used to replace the rpaths and dependency libraries of mach-o binaries and the id of mach-o libraries. On Linux, macholib is used to replace the dependency libraries of mach-o binaries and the id of mach-o libraries. Binary text with padding replacement is attempted for all binaries for the following paths: spack layout root spack prefix sbang script location dependency prefixes package prefix Text replacement is attempted for all text files using the paths above. Symbolic links to the absolute path of the package install prefix are replaced, all others produce warnings. --- lib/spack/external/altgraph/__init__.py | 9 +- lib/spack/spack/binary_distribution.py | 252 ++++++--- lib/spack/spack/relocate.py | 687 +++++++++++++----------- lib/spack/spack/test/packaging.py | 515 +++++++++++------- 4 files changed, 887 insertions(+), 576 deletions(-) diff --git a/lib/spack/external/altgraph/__init__.py b/lib/spack/external/altgraph/__init__.py index 289c6408d11..ee70a9c91bf 100644 --- a/lib/spack/external/altgraph/__init__.py +++ b/lib/spack/external/altgraph/__init__.py @@ -139,9 +139,12 @@ @contributor: U{Reka Albert } ''' -import pkg_resources -__version__ = pkg_resources.require('altgraph')[0].version - +# import pkg_resources +# __version__ = pkg_resources.require('altgraph')[0].version +# pkg_resources is not finding the altgraph import despite the fact that it is in sys.path +# there is no .dist-info or .egg-info for pkg_resources to query the version from +# so it must be set manually +__version__ = '0.16.1' class GraphError(ValueError): pass diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py index 0569bcc665f..7902e5fc584 100644 --- a/lib/spack/spack/binary_distribution.py +++ b/lib/spack/spack/binary_distribution.py @@ -10,6 +10,9 @@ import shutil import tempfile import hashlib +import glob +import platform + from contextlib import closing import ruamel.yaml as yaml @@ -53,7 +56,7 @@ BUILD_CACHE_INDEX_ENTRY_TEMPLATE = '
  • {path}
    • ' -class NoOverwriteException(Exception): +class NoOverwriteException(spack.error.SpackError): """ Raised when a file exists and must be overwritten. """ @@ -68,14 +71,18 @@ class NoGpgException(spack.error.SpackError): """ Raised when gpg2 is not in PATH """ - pass + + def __init__(self, msg): + super(NoGpgException, self).__init__(msg) class NoKeyException(spack.error.SpackError): """ Raised when gpg has no default key added. """ - pass + + def __init__(self, msg): + super(NoKeyException, self).__init__(msg) class PickKeyException(spack.error.SpackError): @@ -84,7 +91,7 @@ class PickKeyException(spack.error.SpackError): """ def __init__(self, keys): - err_msg = "Multi keys available for signing\n%s\n" % keys + err_msg = "Multiple keys available for signing\n%s\n" % keys err_msg += "Use spack buildcache create -k to pick a key." super(PickKeyException, self).__init__(err_msg) @@ -107,7 +114,9 @@ class NewLayoutException(spack.error.SpackError): """ Raised if directory layout is different from buildcache. """ - pass + + def __init__(self, msg): + super(NewLayoutException, self).__init__(msg) def build_cache_relative_path(): @@ -137,15 +146,21 @@ def read_buildinfo_file(prefix): return buildinfo -def write_buildinfo_file(prefix, workdir, rel=False): +def write_buildinfo_file(spec, workdir, rel=False): """ Create a cache file containing information required for the relocation """ + prefix = spec.prefix text_to_relocate = [] binary_to_relocate = [] link_to_relocate = [] blacklist = (".spack", "man") + prefix_to_hash = dict() + prefix_to_hash[str(spec.package.prefix)] = spec.dag_hash() + deps = spack.build_environment.get_rpath_deps(spec.package) + for d in deps: + prefix_to_hash[str(d.prefix)] = d.dag_hash() # Do this at during tarball creation to save time when tarball unpacked. # Used by make_package_relative to determine binaries to change. for root, dirs, files in os.walk(prefix, topdown=True): @@ -162,8 +177,8 @@ def write_buildinfo_file(prefix, workdir, rel=False): link_to_relocate.append(rel_path_name) else: msg = 'Absolute link %s to %s ' % (path_name, link) - msg += 'outside of stage %s ' % prefix - msg += 'cannot be relocated.' + msg += 'outside of prefix %s ' % prefix + msg += 'should not be relocated.' tty.warn(msg) if relocate.needs_binary_relocation(m_type, m_subtype): @@ -184,6 +199,7 @@ def write_buildinfo_file(prefix, workdir, rel=False): buildinfo['relocate_textfiles'] = text_to_relocate buildinfo['relocate_binaries'] = binary_to_relocate buildinfo['relocate_links'] = link_to_relocate + buildinfo['prefix_to_hash'] = prefix_to_hash filename = buildinfo_file_name(workdir) with open(filename, 'w') as outfile: outfile.write(syaml.dump(buildinfo, default_flow_style=True)) @@ -356,7 +372,7 @@ def build_tarball(spec, outdir, force=False, rel=False, unsigned=False, os.remove(temp_tarfile_path) # create info for later relocation and create tar - write_buildinfo_file(spec.prefix, workdir, rel=rel) + write_buildinfo_file(spec, workdir, rel) # optionally make the paths in the binaries relative to each other # in the spack install tree before creating tarball @@ -370,7 +386,7 @@ def build_tarball(spec, outdir, force=False, rel=False, unsigned=False, tty.die(e) else: try: - make_package_placeholder(workdir, spec, allow_root) + check_package_relocatable(workdir, spec, allow_root) except Exception as e: shutil.rmtree(workdir) shutil.rmtree(tarfile_dir) @@ -400,6 +416,7 @@ def build_tarball(spec, outdir, force=False, rel=False, unsigned=False, buildinfo = {} buildinfo['relative_prefix'] = os.path.relpath( spec.prefix, spack.store.layout.root) + buildinfo['relative_rpaths'] = rel spec_dict['buildinfo'] = buildinfo spec_dict['full_hash'] = spec.full_hash() @@ -481,100 +498,149 @@ def make_package_relative(workdir, spec, allow_root): """ prefix = spec.prefix buildinfo = read_buildinfo_file(workdir) - old_path = buildinfo['buildpath'] + old_layout_root = buildinfo['buildpath'] orig_path_names = list() cur_path_names = list() for filename in buildinfo['relocate_binaries']: orig_path_names.append(os.path.join(prefix, filename)) cur_path_names.append(os.path.join(workdir, filename)) - if spec.architecture.platform == 'darwin': + if (spec.architecture.platform == 'darwin' or + spec.architecture.platform == 'test' and + platform.system().lower() == 'darwin'): relocate.make_macho_binaries_relative(cur_path_names, orig_path_names, - old_path, allow_root) - else: + old_layout_root) + if (spec.architecture.platform == 'linux' or + spec.architecture.platform == 'test' and + platform.system().lower() == 'linux'): relocate.make_elf_binaries_relative(cur_path_names, orig_path_names, - old_path, allow_root) + old_layout_root) + relocate.check_files_relocatable(cur_path_names, allow_root) orig_path_names = list() cur_path_names = list() - for filename in buildinfo.get('relocate_links', []): - orig_path_names.append(os.path.join(prefix, filename)) - cur_path_names.append(os.path.join(workdir, filename)) + for linkname in buildinfo.get('relocate_links', []): + orig_path_names.append(os.path.join(prefix, linkname)) + cur_path_names.append(os.path.join(workdir, linkname)) relocate.make_link_relative(cur_path_names, orig_path_names) -def make_package_placeholder(workdir, spec, allow_root): +def check_package_relocatable(workdir, spec, allow_root): """ Check if package binaries are relocatable. Change links to placeholder links. """ - prefix = spec.prefix buildinfo = read_buildinfo_file(workdir) cur_path_names = list() for filename in buildinfo['relocate_binaries']: cur_path_names.append(os.path.join(workdir, filename)) relocate.check_files_relocatable(cur_path_names, allow_root) - cur_path_names = list() - for filename in buildinfo.get('relocate_links', []): - cur_path_names.append(os.path.join(workdir, filename)) - relocate.make_link_placeholder(cur_path_names, workdir, prefix) - -def relocate_package(workdir, spec, allow_root): +def relocate_package(spec, allow_root): """ Relocate the given package """ + workdir = str(spec.prefix) buildinfo = read_buildinfo_file(workdir) - new_path = str(spack.store.layout.root) - new_prefix = str(spack.paths.prefix) - old_path = str(buildinfo['buildpath']) - old_prefix = str(buildinfo.get('spackprefix', - '/not/in/buildinfo/dictionary')) - rel = buildinfo.get('relative_rpaths', False) + new_layout_root = str(spack.store.layout.root) + new_prefix = str(spec.prefix) + new_rel_prefix = str(os.path.relpath(new_prefix, new_layout_root)) + new_spack_prefix = str(spack.paths.prefix) + old_layout_root = str(buildinfo['buildpath']) + old_spack_prefix = str(buildinfo.get('spackprefix')) + old_rel_prefix = buildinfo.get('relative_prefix') + old_prefix = os.path.join(old_layout_root, old_rel_prefix) + rel = buildinfo.get('relative_rpaths') + prefix_to_hash = buildinfo.get('prefix_to_hash', None) + if (old_rel_prefix != new_rel_prefix and not prefix_to_hash): + msg = "Package tarball was created from an install " + msg += "prefix with a different directory layout and an older " + msg += "buildcache create implementation. It cannot be relocated." + raise NewLayoutException(msg) + # older buildcaches do not have the prefix_to_hash dictionary + # need to set an empty dictionary and add one entry to + # prefix_to_prefix to reproduce the old behavior + if not prefix_to_hash: + prefix_to_hash = dict() + hash_to_prefix = dict() + hash_to_prefix[spec.format('{hash}')] = str(spec.package.prefix) + new_deps = spack.build_environment.get_rpath_deps(spec.package) + for d in new_deps: + hash_to_prefix[d.format('{hash}')] = str(d.prefix) + prefix_to_prefix = dict() + for orig_prefix, hash in prefix_to_hash.items(): + prefix_to_prefix[orig_prefix] = hash_to_prefix.get(hash, None) + prefix_to_prefix[old_prefix] = new_prefix + prefix_to_prefix[old_layout_root] = new_layout_root - tty.msg("Relocating package from", - "%s to %s." % (old_path, new_path)) - path_names = set() + tty.debug("Relocating package from", + "%s to %s." % (old_layout_root, new_layout_root)) + + def is_backup_file(file): + return file.endswith('~') + + # Text files containing the prefix text + text_names = list() for filename in buildinfo['relocate_textfiles']: - path_name = os.path.join(workdir, filename) + text_name = os.path.join(workdir, filename) # Don't add backup files generated by filter_file during install step. - if not path_name.endswith('~'): - path_names.add(path_name) - relocate.relocate_text(path_names, oldpath=old_path, - newpath=new_path, oldprefix=old_prefix, - newprefix=new_prefix) - # If the binary files in the package were not edited to use - # relative RPATHs, then the RPATHs need to be relocated - if rel: - if old_path != new_path: - files_to_relocate = list(filter( - lambda pathname: not relocate.file_is_relocatable( - pathname, paths_to_relocate=[old_path, old_prefix]), - map(lambda filename: os.path.join(workdir, filename), - buildinfo['relocate_binaries']))) + if not is_backup_file(text_name): + text_names.append(text_name) - if len(old_path) < len(new_path) and files_to_relocate: - tty.debug('Cannot do a binary string replacement with padding ' - 'for package because %s is longer than %s.' % - (new_path, old_path)) - else: - for path_name in files_to_relocate: - relocate.replace_prefix_bin(path_name, old_path, new_path) - else: - path_names = set() - for filename in buildinfo['relocate_binaries']: - path_name = os.path.join(workdir, filename) - path_names.add(path_name) - if spec.architecture.platform == 'darwin': - relocate.relocate_macho_binaries(path_names, old_path, - new_path, allow_root) - else: - relocate.relocate_elf_binaries(path_names, old_path, - new_path, allow_root) - path_names = set() - for filename in buildinfo.get('relocate_links', []): - path_name = os.path.join(workdir, filename) - path_names.add(path_name) - relocate.relocate_links(path_names, old_path, new_path) +# If we are installing back to the same location don't replace anything + if old_layout_root != new_layout_root: + paths_to_relocate = [old_spack_prefix, old_layout_root] + paths_to_relocate.extend(prefix_to_hash.keys()) + files_to_relocate = list(filter( + lambda pathname: not relocate.file_is_relocatable( + pathname, paths_to_relocate=paths_to_relocate), + map(lambda filename: os.path.join(workdir, filename), + buildinfo['relocate_binaries']))) + # If the buildcache was not created with relativized rpaths + # do the relocation of path in binaries + if (spec.architecture.platform == 'darwin' or + spec.architecture.platform == 'test' and + platform.system().lower() == 'darwin'): + relocate.relocate_macho_binaries(files_to_relocate, + old_layout_root, + new_layout_root, + prefix_to_prefix, rel, + old_prefix, + new_prefix) + if (spec.architecture.platform == 'linux' or + spec.architecture.platform == 'test' and + platform.system().lower() == 'linux'): + relocate.relocate_elf_binaries(files_to_relocate, + old_layout_root, + new_layout_root, + prefix_to_prefix, rel, + old_prefix, + new_prefix) + # Relocate links to the new install prefix + link_names = [linkname + for linkname in buildinfo.get('relocate_links', [])] + relocate.relocate_links(link_names, + old_layout_root, + new_layout_root, + old_prefix, + new_prefix, + prefix_to_prefix) + + # For all buildcaches + # relocate the install prefixes in text files including dependencies + relocate.relocate_text(text_names, + old_layout_root, new_layout_root, + old_prefix, new_prefix, + old_spack_prefix, + new_spack_prefix, + prefix_to_prefix) + + # relocate the install prefixes in binary files including dependencies + relocate.relocate_text_bin(files_to_relocate, + old_layout_root, new_layout_root, + old_prefix, new_prefix, + old_spack_prefix, + new_spack_prefix, + prefix_to_prefix) def extract_tarball(spec, filename, allow_root=False, unsigned=False, @@ -610,7 +676,7 @@ def extract_tarball(spec, filename, allow_root=False, unsigned=False, Gpg.verify('%s.asc' % specfile_path, specfile_path, suppress) except Exception as e: shutil.rmtree(tmpdir) - tty.die(e) + raise e else: shutil.rmtree(tmpdir) raise NoVerifyException( @@ -639,22 +705,30 @@ def extract_tarball(spec, filename, allow_root=False, unsigned=False, # if the original relative prefix is in the spec file use it buildinfo = spec_dict.get('buildinfo', {}) old_relative_prefix = buildinfo.get('relative_prefix', new_relative_prefix) + rel = buildinfo.get('relative_rpaths') # if the original relative prefix and new relative prefix differ the # directory layout has changed and the buildcache cannot be installed - if old_relative_prefix != new_relative_prefix: - shutil.rmtree(tmpdir) - msg = "Package tarball was created from an install " - msg += "prefix with a different directory layout.\n" - msg += "It cannot be relocated." - raise NewLayoutException(msg) + # if it was created with relative rpaths + info = 'old relative prefix %s\nnew relative prefix %s\nrelative rpaths %s' + tty.debug(info % + (old_relative_prefix, new_relative_prefix, rel)) +# if (old_relative_prefix != new_relative_prefix and (rel)): +# shutil.rmtree(tmpdir) +# msg = "Package tarball was created from an install " +# msg += "prefix with a different directory layout. " +# msg += "It cannot be relocated because it " +# msg += "uses relative rpaths." +# raise NewLayoutException(msg) # extract the tarball in a temp directory with closing(tarfile.open(tarfile_path, 'r')) as tar: tar.extractall(path=tmpdir) - # the base of the install prefix is used when creating the tarball - # so the pathname should be the same now that the directory layout - # is confirmed - workdir = os.path.join(tmpdir, os.path.basename(spec.prefix)) + # get the parent directory of the file .spack/binary_distribution + # this should the directory unpacked from the tarball whose + # name is unknown because the prefix naming is unknown + bindist_file = glob.glob('%s/*/.spack/binary_distribution' % tmpdir)[0] + workdir = re.sub('/.spack/binary_distribution$', '', bindist_file) + tty.debug('workdir %s' % workdir) # install_tree copies hardlinks # create a temporary tarfile from prefix and exract it to workdir # tarfile preserves hardlinks @@ -672,10 +746,10 @@ def extract_tarball(spec, filename, allow_root=False, unsigned=False, os.remove(specfile_path) try: - relocate_package(spec.prefix, spec, allow_root) + relocate_package(spec, allow_root) except Exception as e: shutil.rmtree(spec.prefix) - tty.die(e) + raise e else: manifest_file = os.path.join(spec.prefix, spack.store.layout.metadata_dir, @@ -685,6 +759,8 @@ def extract_tarball(spec, filename, allow_root=False, unsigned=False, tty.warn('No manifest file in tarball for spec %s' % spec_id) finally: shutil.rmtree(tmpdir) + if os.path.exists(filename): + os.remove(filename) # Internal cache for downloaded specs @@ -732,7 +808,7 @@ def get_spec(spec=None, force=False): tty.debug("No Spack mirrors are currently configured") return {} - if spec in _cached_specs: + if _cached_specs and spec in _cached_specs: return _cached_specs for mirror in spack.mirror.MirrorCollection().values(): @@ -817,7 +893,7 @@ def get_keys(install=False, trust=False, force=False): mirror_dir = url_util.local_file_path(fetch_url_build_cache) if mirror_dir: tty.msg("Finding public keys in %s" % mirror_dir) - files = os.listdir(mirror_dir) + files = os.listdir(str(mirror_dir)) for file in files: if re.search(r'\.key', file) or re.search(r'\.pub', file): link = url_util.join(fetch_url_build_cache, file) diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py index c8c7947f9c3..7a364347367 100644 --- a/lib/spack/spack/relocate.py +++ b/lib/spack/spack/relocate.py @@ -13,6 +13,9 @@ import llnl.util.lang from spack.util.executable import Executable, ProcessError import llnl.util.tty as tty +from macholib.MachO import MachO +from spack.spec import Spec +import macholib.mach_o class InstallRootStringException(spack.error.SpackError): @@ -41,45 +44,56 @@ def __init__(self, file_path, old_len, new_len): (file_path, old_len, new_len)) -class MissingMacholibException(spack.error.SpackError): +class BinaryTextReplaceException(spack.error.SpackError): """ - Raised when the size of the file changes after binary path substitution. + Raised when the new install path is shorter than the old install path + so binary text replacement cannot occur. + """ + + def __init__(self, old_path, new_path): + msg = "New path longer than old path: binary text" + msg += " replacement not possible." + err_msg = "The new path %s" % new_path + err_msg += " is longer than the old path %s.\n" % old_path + err_msg += "Text replacement in binaries will not work.\n" + err_msg += "Create buildcache from an install path " + err_msg += "longer than new path." + super(BinaryTextReplaceException, self).__init__(msg, err_msg) + + +class PatchelfError(spack.error.SpackError): + """ + Raised when patchelf command returns a ProcessError. """ def __init__(self, error): - super(MissingMacholibException, self).__init__( - "%s\n" - "Python package macholib needs to be avaiable to list\n" - "and modify a mach-o binary's rpaths, deps and id.\n" - "Use virtualenv with pip install macholib or\n" - "use spack to install the py-macholib package\n" - "spack install py-macholib\n" - "spack activate py-macholib\n" - "spack load python\n" - % error) + super(PatchelfError, self).__init__(error) def get_patchelf(): """ + Returns the full patchelf binary path if available in $PATH. Builds and installs spack patchelf package on linux platforms - using the first concretized spec. - Returns the full patchelf binary path. + using the first concretized spec if it is not installed and + returns the full patchelf binary path. """ # as we may need patchelf, find out where it is patchelf = spack.util.executable.which('patchelf') if patchelf is not None: return patchelf.path - else: - if str(spack.architecture.platform()) == 'test': - return None - if str(spack.architecture.platform()) == 'darwin': - return None - patchelf_spec = spack.cmd.parse_specs("patchelf", concretize=True)[0] - patchelf = spack.repo.get(patchelf_spec) - if not patchelf.installed: - patchelf.do_install(use_cache=False) + patchelf_spec = Spec('patchelf').concretized() + patchelf = patchelf_spec.package + if patchelf.installed: patchelf_executable = os.path.join(patchelf.prefix.bin, "patchelf") return patchelf_executable + else: + if (str(spack.architecture.platform()) == 'test' or + str(spack.architecture.platform()) == 'darwin'): + return None + else: + patchelf.do_install() + patchelf_executable = os.path.join(patchelf.prefix.bin, "patchelf") + return patchelf_executable def get_existing_elf_rpaths(path_name): @@ -95,33 +109,53 @@ def get_existing_elf_rpaths(path_name): else: patchelf = Executable(get_patchelf()) + rpaths = list() try: output = patchelf('--print-rpath', '%s' % path_name, output=str, error=str) - return output.rstrip('\n').split(':') + rpaths = output.rstrip('\n').split(':') except ProcessError as e: - tty.debug('patchelf --print-rpath produced an error on %s' % - path_name, e) - return [] - return + msg = 'patchelf --print-rpath %s produced an error %s' % (path_name, e) + raise PatchelfError(msg) + return rpaths -def get_relative_rpaths(path_name, orig_dir, orig_rpaths): +def get_relative_elf_rpaths(path_name, orig_layout_root, orig_rpaths): """ - Replaces orig_dir with relative path from dirname(path_name) if an rpath - in orig_rpaths contains orig_path. Prefixes $ORIGIN + Replaces orig rpath with relative path from dirname(path_name) if an rpath + in orig_rpaths contains orig_layout_root. Prefixes $ORIGIN to relative paths and returns replacement rpaths. """ rel_rpaths = [] for rpath in orig_rpaths: - if re.match(orig_dir, rpath): + if re.match(orig_layout_root, rpath): rel = os.path.relpath(rpath, start=os.path.dirname(path_name)) - rel_rpaths.append('$ORIGIN/%s' % rel) + rel_rpaths.append(os.path.join('$ORIGIN', '%s' % rel)) else: rel_rpaths.append(rpath) return rel_rpaths +def get_normalized_elf_rpaths(orig_path_name, rel_rpaths): + """ + Normalize the relative rpaths with respect to the original path name + of the file. If the rpath starts with $ORIGIN replace $ORIGIN with the + dirname of the original path name and then normalize the rpath. + A dictionary mapping relativized rpaths to normalized rpaths is returned. + """ + norm_rpaths = list() + for rpath in rel_rpaths: + if rpath.startswith('$ORIGIN'): + sub = re.sub('$ORIGIN', + os.path.dirname(orig_path_name), + rpath) + norm = os.path.normpath(sub) + norm_rpaths.append(norm) + else: + norm_rpaths.append(rpath) + return norm_rpaths + + def set_placeholder(dirname): """ return string of @'s with same length @@ -129,183 +163,157 @@ def set_placeholder(dirname): return '@' * len(dirname) -def get_placeholder_rpaths(path_name, orig_rpaths): +def macho_make_paths_relative(path_name, old_layout_root, + rpaths, deps, idpath): """ - Replaces original layout root dir with a placeholder string in all rpaths. + Return a dictionary mapping the original rpaths to the relativized rpaths. + This dictionary is used to replace paths in mach-o binaries. + Replace old_dir with relative path from dirname of path name + in rpaths and deps; idpath is replaced with @rpath/libname. """ - rel_rpaths = [] - orig_dir = spack.store.layout.root - for rpath in orig_rpaths: - if re.match(orig_dir, rpath): - placeholder = set_placeholder(orig_dir) - rel = re.sub(orig_dir, placeholder, rpath) - rel_rpaths.append('%s' % rel) - else: - rel_rpaths.append(rpath) - return rel_rpaths - - -def macho_get_paths(path_name): - """ - Examines the output of otool -l path_name for these three fields: - LC_ID_DYLIB, LC_LOAD_DYLIB, LC_RPATH and parses out the rpaths, - dependiencies and library id. - Returns these values. - """ - otool = Executable('otool') - output = otool("-l", path_name, output=str, err=str) - last_cmd = None - idpath = None - rpaths = [] - deps = [] - for line in output.split('\n'): - match = re.search('( *[a-zA-Z]+ )(.*)', line) - if match: - lhs = match.group(1).lstrip().rstrip() - rhs = match.group(2) - match2 = re.search(r'(.*) \(.*\)', rhs) - if match2: - rhs = match2.group(1) - if lhs == 'cmd': - last_cmd = rhs - if lhs == 'path' and last_cmd == 'LC_RPATH': - rpaths.append(rhs) - if lhs == 'name' and last_cmd == 'LC_ID_DYLIB': - idpath = rhs - if lhs == 'name' and last_cmd == 'LC_LOAD_DYLIB': - deps.append(rhs) - return rpaths, deps, idpath - - -def macho_make_paths_relative(path_name, old_dir, rpaths, deps, idpath): - """ - Replace old_dir with relative path from dirname(path_name) - in rpaths and deps; idpaths are replaced with @rpath/libname as needed; - replacement are returned. - """ - new_idpath = None + paths_to_paths = dict() if idpath: - new_idpath = '@rpath/%s' % os.path.basename(idpath) - new_rpaths = list() - new_deps = list() + paths_to_paths[idpath] = os.path.join( + '@rpath', '%s' % os.path.basename(idpath)) for rpath in rpaths: - if re.match(old_dir, rpath): + if re.match(old_layout_root, rpath): rel = os.path.relpath(rpath, start=os.path.dirname(path_name)) - new_rpaths.append('@loader_path/%s' % rel) + paths_to_paths[rpath] = os.path.join('@loader_path', '%s' % rel) else: - new_rpaths.append(rpath) + paths_to_paths[rpath] = rpath for dep in deps: - if re.match(old_dir, dep): + if re.match(old_layout_root, dep): rel = os.path.relpath(dep, start=os.path.dirname(path_name)) - new_deps.append('@loader_path/%s' % rel) + paths_to_paths[dep] = os.path.join('@loader_path', '%s' % rel) else: - new_deps.append(dep) - return (new_rpaths, new_deps, new_idpath) + paths_to_paths[dep] = dep + return paths_to_paths -def macho_make_paths_placeholder(rpaths, deps, idpath): +def macho_make_paths_normal(orig_path_name, rpaths, deps, idpath): """ - Replace old_dir with a placeholder of the same length - in rpaths and deps and idpaths is needed. - replacement are returned. + Return a dictionary mapping the relativized rpaths to the original rpaths. + This dictionary is used to replace paths in mach-o binaries. + Replace '@loader_path' with the dirname of the origname path name + in rpaths and deps; idpath is replaced with the original path name """ - new_idpath = None - old_dir = spack.store.layout.root - placeholder = set_placeholder(old_dir) + rel_to_orig = dict() if idpath: - new_idpath = re.sub(old_dir, placeholder, idpath) - new_rpaths = list() - new_deps = list() + rel_to_orig[idpath] = orig_path_name + for rpath in rpaths: - if re.match(old_dir, rpath): - ph = re.sub(old_dir, placeholder, rpath) - new_rpaths.append('%s' % ph) + if re.match('@loader_path', rpath): + norm = os.path.normpath(re.sub(re.escape('@loader_path'), + os.path.dirname(orig_path_name), + rpath)) + rel_to_orig[rpath] = norm else: - new_rpaths.append(rpath) + rel_to_orig[rpath] = rpath for dep in deps: - if re.match(old_dir, dep): - ph = re.sub(old_dir, placeholder, dep) - new_deps.append('%s' % ph) + if re.match('@loader_path', dep): + norm = os.path.normpath(re.sub(re.escape('@loader_path'), + os.path.dirname(orig_path_name), + dep)) + rel_to_orig[dep] = norm else: - new_deps.append(dep) - return (new_rpaths, new_deps, new_idpath) + rel_to_orig[dep] = dep + return rel_to_orig -def macho_replace_paths(old_dir, new_dir, rpaths, deps, idpath): +def macho_find_paths(orig_rpaths, deps, idpath, + old_layout_root, prefix_to_prefix): """ - Replace old_dir with new_dir in rpaths, deps and idpath - and return replacements + Inputs + original rpaths from mach-o binaries + dependency libraries for mach-o binaries + id path of mach-o libraries + old install directory layout root + prefix_to_prefix dictionary which maps prefixes in the old directory layout + to directories in the new directory layout + Output + paths_to_paths dictionary which maps all of the old paths to new paths """ - new_idpath = None + paths_to_paths = dict() + for orig_rpath in orig_rpaths: + if orig_rpath.startswith(old_layout_root): + for old_prefix, new_prefix in prefix_to_prefix.items(): + if orig_rpath.startswith(old_prefix): + new_rpath = re.sub(re.escape(old_prefix), + new_prefix, orig_rpath) + paths_to_paths[orig_rpath] = new_rpath + else: + paths_to_paths[orig_rpath] = orig_rpath + if idpath: - new_idpath = idpath.replace(old_dir, new_dir) - new_rpaths = list() - new_deps = list() - for rpath in rpaths: - new_rpath = rpath.replace(old_dir, new_dir) - new_rpaths.append(new_rpath) + for old_prefix, new_prefix in prefix_to_prefix.items(): + if idpath.startswith(old_prefix): + paths_to_paths[idpath] = re.sub( + re.escape(old_prefix), new_prefix, idpath) for dep in deps: - new_dep = dep.replace(old_dir, new_dir) - new_deps.append(new_dep) - return new_rpaths, new_deps, new_idpath + for old_prefix, new_prefix in prefix_to_prefix.items(): + if dep.startswith(old_prefix): + paths_to_paths[dep] = re.sub( + re.escape(old_prefix), new_prefix, dep) + if dep.startswith('@'): + paths_to_paths[dep] = dep + + return paths_to_paths def modify_macho_object(cur_path, rpaths, deps, idpath, - new_rpaths, new_deps, new_idpath): + paths_to_paths): """ - Modify MachO binary path_name by replacing old_dir with new_dir - or the relative path to spack install root. - The old install dir in LC_ID_DYLIB is replaced with the new install dir - using install_name_tool -id newid binary - The old install dir in LC_LOAD_DYLIB is replaced with the new install dir - using install_name_tool -change old new binary - The old install dir in LC_RPATH is replaced with the new install dir using - install_name_tool -rpath old new binary + This function is used to make machO buildcaches on macOS by + replacing old paths with new paths using install_name_tool + Inputs: + mach-o binary to be modified + original rpaths + original dependency paths + original id path if a mach-o library + dictionary mapping paths in old install layout to new install layout """ # avoid error message for libgcc_s if 'libgcc_' in cur_path: return install_name_tool = Executable('install_name_tool') - if new_idpath and not idpath == new_idpath: - install_name_tool('-id', new_idpath, str(cur_path)) - if len(deps) == len(new_deps): - for orig, new in zip(deps, new_deps): - if not orig == new: - install_name_tool('-change', orig, new, str(cur_path)) - - if len(rpaths) == len(new_rpaths): - for orig, new in zip(rpaths, new_rpaths): - if not orig == new: - install_name_tool('-rpath', orig, new, str(cur_path)) + if idpath: + new_idpath = paths_to_paths.get(idpath, None) + if new_idpath and not idpath == new_idpath: + install_name_tool('-id', new_idpath, str(cur_path)) + for dep in deps: + new_dep = paths_to_paths.get(dep) + if new_dep and dep != new_dep: + install_name_tool('-change', dep, new_dep, str(cur_path)) + for orig_rpath in rpaths: + new_rpath = paths_to_paths.get(orig_rpath) + if new_rpath and not orig_rpath == new_rpath: + install_name_tool('-rpath', orig_rpath, new_rpath, str(cur_path)) return -def modify_object_macholib(cur_path, old_dir, new_dir): +def modify_object_macholib(cur_path, paths_to_paths): """ - Modify MachO binary path_name by replacing old_dir with new_dir - or the relative path to spack install root. - The old install dir in LC_ID_DYLIB is replaced with the new install dir - using py-macholib - The old install dir in LC_LOAD_DYLIB is replaced with the new install dir - using py-macholib - The old install dir in LC_RPATH is replaced with the new install dir using - using py-macholib + This function is used when install machO buildcaches on linux by + rewriting mach-o loader commands for dependency library paths of + mach-o binaries and the id path for mach-o libraries. + Rewritting of rpaths is handled by replace_prefix_bin. + Inputs + mach-o binary to be modified + dictionary mapping paths in old install layout to new install layout """ - if cur_path.endswith('.o'): - return - try: - from macholib.MachO import MachO - except ImportError as e: - raise MissingMacholibException(e) - - def match_func(cpath): - rpath = cpath.replace(old_dir, new_dir) - return rpath dll = MachO(cur_path) - dll.rewriteLoadCommands(match_func) + + changedict = paths_to_paths + + def changefunc(path): + npath = changedict.get(path, None) + return npath + + dll.rewriteLoadCommands(changefunc) + try: f = open(dll.filename, 'rb+') for header in dll.headers: @@ -320,14 +328,32 @@ def match_func(cpath): return -def strings_contains_installroot(path_name, root_dir): +def macholib_get_paths(cur_path): """ - Check if the file contain the install root string. + Get rpaths, dependencies and id of mach-o objects + using python macholib package """ - strings = Executable('strings') - output = strings('%s' % path_name, - output=str, err=str) - return (root_dir in output or spack.paths.prefix in output) + dll = MachO(cur_path) + + ident = None + rpaths = list() + deps = list() + for header in dll.headers: + rpaths = [data.rstrip(b'\0').decode('utf-8') + for load_command, dylib_command, data in header.commands if + load_command.cmd == macholib.mach_o.LC_RPATH] + deps = [data.rstrip(b'\0').decode('utf-8') + for load_command, dylib_command, data in header.commands if + load_command.cmd == macholib.mach_o.LC_LOAD_DYLIB] + idents = [data.rstrip(b'\0').decode('utf-8') + for load_command, dylib_command, data in header.commands if + load_command.cmd == macholib.mach_o.LC_ID_DYLIB] + if len(idents) == 1: + ident = idents[0] + tty.debug('ident: %s' % ident) + tty.debug('deps: %s' % deps) + tty.debug('rpaths: %s' % rpaths) + return (rpaths, deps, ident) def modify_elf_object(path_name, new_rpaths): @@ -338,9 +364,9 @@ def modify_elf_object(path_name, new_rpaths): new_joined = ':'.join(new_rpaths) # if we're relocating patchelf itself, use it + bak_path = path_name + ".bak" if path_name[-13:] == "/bin/patchelf": - bak_path = path_name + ".bak" shutil.copy(path_name, bak_path) patchelf = Executable(bak_path) else: @@ -350,9 +376,11 @@ def modify_elf_object(path_name, new_rpaths): patchelf('--force-rpath', '--set-rpath', '%s' % new_joined, '%s' % path_name, output=str, error=str) except ProcessError as e: - tty.die('patchelf --set-rpath %s failed' % - path_name, e) + msg = 'patchelf --set-rpath %s failed with error %s' % (path_name, e) + raise PatchelfError(msg) pass + if os.path.exists(bak_path): + os.remove(bak_path) def needs_binary_relocation(m_type, m_subtype): @@ -447,11 +475,15 @@ def replace(match): return data return match.group().replace(old_dir.encode('utf-8'), new_dir.encode('utf-8')) + b'\0' * padding + + if len(new_dir) > len(old_dir): + raise BinaryTextReplaceException(old_dir, new_dir) + with open(path_name, 'rb+') as f: data = f.read() f.seek(0) original_data_len = len(data) - pat = re.compile(old_dir.encode('utf-8') + b'([^\0]*?)\0') + pat = re.compile(re.escape(old_dir).encode('utf-8') + b'([^\0]*?)\0') if not pat.search(data): return ndata = pat.sub(replace, data) @@ -462,80 +494,129 @@ def replace(match): f.truncate() -def relocate_macho_binaries(path_names, old_dir, new_dir, allow_root): +def relocate_macho_binaries(path_names, old_layout_root, new_layout_root, + prefix_to_prefix, rel, old_prefix, new_prefix): """ - Change old_dir to new_dir in LC_RPATH of mach-o files (on macOS) - Change old_dir to new_dir in LC_ID and LC_DEP of mach-o files - Account for the case where old_dir is now a placeholder + Use macholib python package to get the rpaths, depedent libraries + and library identity for libraries from the MachO object. Modify them + with the replacement paths queried from the dictionary mapping old layout + prefixes to hashes and the dictionary mapping hashes to the new layout + prefixes. """ - placeholder = set_placeholder(old_dir) + for path_name in path_names: + # Corner case where macho object file ended up in the path name list if path_name.endswith('.o'): continue - if new_dir == old_dir: - continue - if platform.system().lower() == 'darwin': - rpaths, deps, idpath = macho_get_paths(path_name) - # one pass to replace placeholder - (n_rpaths, - n_deps, - n_idpath) = macho_replace_paths(placeholder, - new_dir, - rpaths, - deps, - idpath) - # another pass to replace old_dir - (new_rpaths, - new_deps, - new_idpath) = macho_replace_paths(old_dir, - new_dir, - n_rpaths, - n_deps, - n_idpath) - modify_macho_object(path_name, - rpaths, deps, idpath, - new_rpaths, new_deps, new_idpath) + if rel: + # get the relativized paths + rpaths, deps, idpath = macholib_get_paths(path_name) + # get the file path name in the original prefix + orig_path_name = re.sub(re.escape(new_prefix), old_prefix, + path_name) + # get the mapping of the relativized paths to the original + # normalized paths + rel_to_orig = macho_make_paths_normal(orig_path_name, + rpaths, deps, + idpath) + # replace the relativized paths with normalized paths + if platform.system().lower() == 'darwin': + modify_macho_object(path_name, rpaths, deps, + idpath, rel_to_orig) + else: + modify_object_macholib(path_name, + rel_to_orig) + # get the normalized paths in the mach-o binary + rpaths, deps, idpath = macholib_get_paths(path_name) + # get the mapping of paths in old prefix to path in new prefix + paths_to_paths = macho_find_paths(rpaths, deps, idpath, + old_layout_root, + prefix_to_prefix) + # replace the old paths with new paths + if platform.system().lower() == 'darwin': + modify_macho_object(path_name, rpaths, deps, + idpath, paths_to_paths) + else: + modify_object_macholib(path_name, + paths_to_paths) + # get the new normalized path in the mach-o binary + rpaths, deps, idpath = macholib_get_paths(path_name) + # get the mapping of paths to relative paths in the new prefix + paths_to_paths = macho_make_paths_relative(path_name, + new_layout_root, + rpaths, deps, idpath) + # replace the new paths with relativized paths in the new prefix + if platform.system().lower() == 'darwin': + modify_macho_object(path_name, rpaths, deps, + idpath, paths_to_paths) + else: + modify_object_macholib(path_name, + paths_to_paths) else: - modify_object_macholib(path_name, placeholder, new_dir) - modify_object_macholib(path_name, old_dir, new_dir) - if len(new_dir) <= len(old_dir): - replace_prefix_nullterm(path_name, old_dir, new_dir) - else: - tty.warn('Cannot do a binary string replacement' - ' with padding for %s' - ' because %s is longer than %s' % - (path_name, new_dir, old_dir)) + # get the paths in the old prefix + rpaths, deps, idpath = macholib_get_paths(path_name) + # get the mapping of paths in the old prerix to the new prefix + paths_to_paths = macho_find_paths(rpaths, deps, idpath, + old_layout_root, + prefix_to_prefix) + # replace the old paths with new paths + if platform.system().lower() == 'darwin': + modify_macho_object(path_name, rpaths, deps, + idpath, paths_to_paths) + else: + modify_object_macholib(path_name, + paths_to_paths) -def relocate_elf_binaries(path_names, old_dir, new_dir, allow_root): +def elf_find_paths(orig_rpaths, old_layout_root, prefix_to_prefix): + new_rpaths = list() + for orig_rpath in orig_rpaths: + if orig_rpath.startswith(old_layout_root): + for old_prefix, new_prefix in prefix_to_prefix.items(): + if orig_rpath.startswith(old_prefix): + new_rpaths.append(re.sub(re.escape(old_prefix), + new_prefix, orig_rpath)) + else: + new_rpaths.append(orig_rpath) + return new_rpaths + + +def relocate_elf_binaries(path_names, old_layout_root, new_layout_root, + prefix_to_prefix, rel, old_prefix, new_prefix): """ - Change old_dir to new_dir in RPATHs of elf binaries - Account for the case where old_dir is now a placeholder + Use patchelf to get the original rpaths and then replace them with + rpaths in the new directory layout. + New rpaths are determined from a dictionary mapping the prefixes in the + old directory layout to the prefixes in the new directory layout if the + rpath was in the old layout root, i.e. system paths are not replaced. """ - placeholder = set_placeholder(old_dir) for path_name in path_names: orig_rpaths = get_existing_elf_rpaths(path_name) - if orig_rpaths: - # one pass to replace placeholder - n_rpaths = substitute_rpath(orig_rpaths, - placeholder, new_dir) - # one pass to replace old_dir - new_rpaths = substitute_rpath(n_rpaths, - old_dir, new_dir) + new_rpaths = list() + if rel: + # get the file path in the old_prefix + orig_path_name = re.sub(re.escape(new_prefix), old_prefix, + path_name) + # get the normalized rpaths in the old prefix using the file path + # in the orig prefix + orig_norm_rpaths = get_normalized_elf_rpaths(orig_path_name, + orig_rpaths) + # get the normalize rpaths in the new prefix + norm_rpaths = elf_find_paths(orig_norm_rpaths, old_layout_root, + prefix_to_prefix) + # get the relativized rpaths in the new prefix + new_rpaths = get_relative_elf_rpaths(path_name, new_layout_root, + norm_rpaths) + modify_elf_object(path_name, new_rpaths) + else: + new_rpaths = elf_find_paths(orig_rpaths, old_layout_root, + prefix_to_prefix) modify_elf_object(path_name, new_rpaths) - if not new_dir == old_dir: - if len(new_dir) <= len(old_dir): - replace_prefix_bin(path_name, old_dir, new_dir) - else: - tty.warn('Cannot do a binary string replacement' - ' with padding for %s' - ' because %s is longer than %s.' % - (path_name, new_dir, old_dir)) def make_link_relative(cur_path_names, orig_path_names): """ - Change absolute links to be relative. + Change absolute links to relative links. """ for cur_path, orig_path in zip(cur_path_names, orig_path_names): target = os.readlink(orig_path) @@ -545,8 +626,8 @@ def make_link_relative(cur_path_names, orig_path_names): os.symlink(relative_target, cur_path) -def make_macho_binaries_relative(cur_path_names, orig_path_names, old_dir, - allow_root): +def make_macho_binaries_relative(cur_path_names, orig_path_names, + old_layout_root): """ Replace old RPATHs with paths relative to old_dir in binary files """ @@ -555,33 +636,26 @@ def make_macho_binaries_relative(cur_path_names, orig_path_names, old_dir, deps = set() idpath = None if platform.system().lower() == 'darwin': - (rpaths, deps, idpath) = macho_get_paths(cur_path) - (new_rpaths, - new_deps, - new_idpath) = macho_make_paths_relative(orig_path, old_dir, - rpaths, deps, idpath) + (rpaths, deps, idpath) = macholib_get_paths(cur_path) + paths_to_paths = macho_make_paths_relative(orig_path, + old_layout_root, + rpaths, deps, idpath) modify_macho_object(cur_path, rpaths, deps, idpath, - new_rpaths, new_deps, new_idpath) - if (not allow_root and - not file_is_relocatable(cur_path)): - raise InstallRootStringException(cur_path, old_dir) + paths_to_paths) -def make_elf_binaries_relative(cur_path_names, orig_path_names, old_dir, - allow_root): +def make_elf_binaries_relative(cur_path_names, orig_path_names, + old_layout_root): """ Replace old RPATHs with paths relative to old_dir in binary files """ for cur_path, orig_path in zip(cur_path_names, orig_path_names): orig_rpaths = get_existing_elf_rpaths(cur_path) if orig_rpaths: - new_rpaths = get_relative_rpaths(orig_path, old_dir, - orig_rpaths) + new_rpaths = get_relative_elf_rpaths(orig_path, old_layout_root, + orig_rpaths) modify_elf_object(cur_path, new_rpaths) - if (not allow_root and - not file_is_relocatable(cur_path)): - raise InstallRootStringException(cur_path, old_dir) def check_files_relocatable(cur_path_names, allow_root): @@ -595,63 +669,74 @@ def check_files_relocatable(cur_path_names, allow_root): cur_path, spack.store.layout.root) -def make_link_placeholder(cur_path_names, cur_dir, old_dir): +def relocate_links(linknames, old_layout_root, new_layout_root, + old_install_prefix, new_install_prefix, prefix_to_prefix): """ - Replace old install path with placeholder in absolute links. - - Links in ``cur_path_names`` must link to absolute paths. + The symbolic links in filenames are absolute links or placeholder links. + The old link target is read and the placeholder is replaced by the old + layout root. If the old link target is in the old install prefix, the new + link target is create by replacing the old install prefix with the new + install prefix. """ - for cur_path in cur_path_names: - placeholder = set_placeholder(spack.store.layout.root) - placeholder_prefix = old_dir.replace(spack.store.layout.root, - placeholder) - cur_src = os.readlink(cur_path) - rel_src = os.path.relpath(cur_src, cur_dir) - new_src = os.path.join(placeholder_prefix, rel_src) - - os.unlink(cur_path) - os.symlink(new_src, cur_path) + placeholder = set_placeholder(old_layout_root) + link_names = [os.path.join(new_install_prefix, linkname) + for linkname in linknames] + for link_name in link_names: + old_link_target = os.readlink(link_name) + old_link_target = re.sub(placeholder, old_layout_root, old_link_target) + if old_link_target.startswith(old_install_prefix): + new_link_target = re.sub( + old_install_prefix, new_install_prefix, old_link_target) + os.unlink(link_name) + os.symlink(new_link_target, link_name) + else: + msg = 'Old link target %s' % old_link_target + msg += ' for symbolic link %s is outside' % link_name + msg += ' of the old install prefix %s.\n' % old_install_prefix + msg += 'This symbolic link will not be relocated' + msg += ' and might break relocation.' + tty.warn(msg) -def relocate_links(path_names, old_dir, new_dir): +def relocate_text(path_names, old_layout_root, new_layout_root, + old_install_prefix, new_install_prefix, + old_spack_prefix, new_spack_prefix, + prefix_to_prefix): """ - Replace old path with new path in link sources. - - Links in ``path_names`` must link to absolute paths or placeholders. + Replace old paths with new paths in text files + including the path the the spack sbang script """ - placeholder = set_placeholder(old_dir) + sbangre = '#!/bin/bash %s/bin/sbang' % old_spack_prefix + sbangnew = '#!/bin/bash %s/bin/sbang' % new_spack_prefix + for path_name in path_names: - old_src = os.readlink(path_name) - # replace either placeholder or old_dir - new_src = old_src.replace(placeholder, new_dir, 1) - new_src = new_src.replace(old_dir, new_dir, 1) - - os.unlink(path_name) - os.symlink(new_src, path_name) - - -def relocate_text(path_names, oldpath, newpath, oldprefix, newprefix): - """ - Replace old path with new path in text files - including the path the the spack sbang script. - """ - sbangre = '#!/bin/bash %s/bin/sbang' % oldprefix - sbangnew = '#!/bin/bash %s/bin/sbang' % newprefix - for path_name in path_names: - replace_prefix_text(path_name, oldpath, newpath) + replace_prefix_text(path_name, old_install_prefix, new_install_prefix) + for orig_dep_prefix, new_dep_prefix in prefix_to_prefix.items(): + replace_prefix_text(path_name, orig_dep_prefix, new_dep_prefix) + replace_prefix_text(path_name, old_layout_root, new_layout_root) replace_prefix_text(path_name, sbangre, sbangnew) - replace_prefix_text(path_name, oldprefix, newprefix) -def substitute_rpath(orig_rpath, topdir, new_root_path): +def relocate_text_bin(path_names, old_layout_root, new_layout_root, + old_install_prefix, new_install_prefix, + old_spack_prefix, new_spack_prefix, + prefix_to_prefix): """ - Replace topdir with new_root_path RPATH list orig_rpath - """ - new_rpaths = [] - for path in orig_rpath: - new_rpath = path.replace(topdir, new_root_path) - new_rpaths.append(new_rpath) - return new_rpaths + Replace null terminated path strings hard coded into binaries. + Raise an exception when the new path in longer than the old path + because this breaks the binary. + """ + if len(new_install_prefix) <= len(old_install_prefix): + for path_name in path_names: + for old_dep_prefix, new_dep_prefix in prefix_to_prefix.items(): + if len(new_dep_prefix) <= len(old_dep_prefix): + replace_prefix_bin( + path_name, old_dep_prefix, new_dep_prefix) + replace_prefix_bin(path_name, old_spack_prefix, new_spack_prefix) + else: + if len(path_names) > 0: + raise BinaryTextReplaceException( + old_install_prefix, new_install_prefix) def is_relocatable(spec): @@ -729,7 +814,7 @@ def file_is_relocatable(file, paths_to_relocate=None): set_of_strings.discard(rpaths) if platform.system().lower() == 'darwin': if m_subtype == 'x-mach-binary': - rpaths, deps, idpath = macho_get_paths(file) + rpaths, deps, idpath = macholib_get_paths(file) set_of_strings.discard(set(rpaths)) set_of_strings.discard(set(deps)) if idpath is not None: @@ -779,6 +864,8 @@ def mime_type(file): file_cmd = Executable('file') output = file_cmd('-b', '-h', '--mime-type', file, output=str, error=str) tty.debug('[MIME_TYPE] {0} -> {1}'.format(file, output.strip())) + # In corner cases the output does not contain a subtype prefixed with a / + # In those cases add the / so the tuple can be formed. if '/' not in output: output += '/' split_by_slash = output.strip().split('/') diff --git a/lib/spack/spack/test/packaging.py b/lib/spack/spack/test/packaging.py index 39d12df7b71..5d5b2ccf8b0 100644 --- a/lib/spack/spack/test/packaging.py +++ b/lib/spack/spack/test/packaging.py @@ -8,10 +8,11 @@ """ import os import stat -import sys import shutil import pytest import argparse +import re +import platform from llnl.util.filesystem import mkdirp @@ -19,16 +20,15 @@ import spack.store import spack.binary_distribution as bindist import spack.cmd.buildcache as buildcache -import spack.util.gpg from spack.spec import Spec from spack.paths import mock_gpg_keys_path from spack.fetch_strategy import URLFetchStrategy, FetchStrategyComposite from spack.relocate import needs_binary_relocation, needs_text_relocation -from spack.relocate import strings_contains_installroot -from spack.relocate import get_patchelf, relocate_text, relocate_links -from spack.relocate import substitute_rpath, get_relative_rpaths -from spack.relocate import macho_replace_paths, macho_make_paths_relative -from spack.relocate import modify_macho_object, macho_get_paths +from spack.relocate import relocate_text, relocate_links +from spack.relocate import get_relative_elf_rpaths +from spack.relocate import macho_make_paths_relative +from spack.relocate import set_placeholder, macho_find_paths +from spack.relocate import file_is_relocatable def has_gpg(): @@ -50,9 +50,9 @@ def fake_fetchify(url, pkg): @pytest.mark.usefixtures('install_mockery', 'mock_gnupghome') def test_buildcache(mock_archive, tmpdir): # tweak patchelf to only do a download - spec = Spec("patchelf") - spec.concretize() - pkg = spack.repo.get(spec) + pspec = Spec("patchelf") + pspec.concretize() + pkg = spack.repo.get(pspec) fake_fetchify(pkg.fetcher, pkg) mkdirp(os.path.join(pkg.prefix, "bin")) patchelfscr = os.path.join(pkg.prefix, "bin", "patchelf") @@ -71,7 +71,7 @@ def test_buildcache(mock_archive, tmpdir): pkg = spec.package fake_fetchify(mock_archive.url, pkg) pkg.do_install() - pkghash = '/' + spec.dag_hash(7) + pkghash = '/' + str(spec.dag_hash(7)) # Put some non-relocatable file in there filename = os.path.join(spec.prefix, "dummy.txt") @@ -99,88 +99,69 @@ def test_buildcache(mock_archive, tmpdir): parser = argparse.ArgumentParser() buildcache.setup_parser(parser) + create_args = ['create', '-a', '-f', '-d', mirror_path, pkghash] # Create a private key to sign package with if gpg2 available if spack.util.gpg.Gpg.gpg(): spack.util.gpg.Gpg.create(name='test key 1', expires='0', email='spack@googlegroups.com', comment='Spack test key') - # Create build cache with signing - args = parser.parse_args(['create', '-d', mirror_path, str(spec)]) - buildcache.buildcache(parser, args) - - # Uninstall the package - pkg.do_uninstall(force=True) - - # test overwrite install - args = parser.parse_args(['install', '-f', str(pkghash)]) - buildcache.buildcache(parser, args) - - files = os.listdir(spec.prefix) - - # create build cache with relative path and signing - args = parser.parse_args( - ['create', '-d', mirror_path, '-f', '-r', str(spec)]) - buildcache.buildcache(parser, args) - - # Uninstall the package - pkg.do_uninstall(force=True) - - # install build cache with verification - args = parser.parse_args(['install', str(spec)]) - buildcache.install_tarball(spec, args) - - # test overwrite install - args = parser.parse_args(['install', '-f', str(pkghash)]) - buildcache.buildcache(parser, args) - else: - # create build cache without signing - args = parser.parse_args( - ['create', '-d', mirror_path, '-f', '-u', str(spec)]) - buildcache.buildcache(parser, args) + create_args.insert(create_args.index('-a'), '-u') - # Uninstall the package - pkg.do_uninstall(force=True) + args = parser.parse_args(create_args) + buildcache.buildcache(parser, args) + # trigger overwrite warning + buildcache.buildcache(parser, args) - # install build cache without verification - args = parser.parse_args(['install', '-u', str(spec)]) - buildcache.install_tarball(spec, args) + # Uninstall the package + pkg.do_uninstall(force=True) - files = os.listdir(spec.prefix) - assert 'link_to_dummy.txt' in files - assert 'dummy.txt' in files - # test overwrite install without verification - args = parser.parse_args(['install', '-f', '-u', str(pkghash)]) - buildcache.buildcache(parser, args) + install_args = ['install', '-a', '-f', pkghash] + if not spack.util.gpg.Gpg.gpg(): + install_args.insert(install_args.index('-a'), '-u') + args = parser.parse_args(install_args) + # Test install + buildcache.buildcache(parser, args) - # create build cache with relative path - args = parser.parse_args( - ['create', '-d', mirror_path, '-f', '-r', '-u', str(pkghash)]) - buildcache.buildcache(parser, args) + files = os.listdir(spec.prefix) - # Uninstall the package - pkg.do_uninstall(force=True) - - # install build cache - args = parser.parse_args(['install', '-u', str(spec)]) - buildcache.install_tarball(spec, args) - - # test overwrite install - args = parser.parse_args(['install', '-f', '-u', str(pkghash)]) - buildcache.buildcache(parser, args) - - files = os.listdir(spec.prefix) - assert 'link_to_dummy.txt' in files - assert 'dummy.txt' in files - assert os.path.realpath( - os.path.join(spec.prefix, 'link_to_dummy.txt') - ) == os.path.realpath(os.path.join(spec.prefix, 'dummy.txt')) + assert 'link_to_dummy.txt' in files + assert 'dummy.txt' in files # Validate the relocation information buildinfo = bindist.read_buildinfo_file(spec.prefix) assert(buildinfo['relocate_textfiles'] == ['dummy.txt']) assert(buildinfo['relocate_links'] == ['link_to_dummy.txt']) + # create build cache with relative path + create_args.insert(create_args.index('-a'), '-f') + create_args.insert(create_args.index('-a'), '-r') + args = parser.parse_args(create_args) + buildcache.buildcache(parser, args) + + # Uninstall the package + pkg.do_uninstall(force=True) + + if not spack.util.gpg.Gpg.gpg(): + install_args.insert(install_args.index('-a'), '-u') + args = parser.parse_args(install_args) + buildcache.buildcache(parser, args) + + # test overwrite install + install_args.insert(install_args.index('-a'), '-f') + args = parser.parse_args(install_args) + buildcache.buildcache(parser, args) + + files = os.listdir(spec.prefix) + assert 'link_to_dummy.txt' in files + assert 'dummy.txt' in files +# assert os.path.realpath( +# os.path.join(spec.prefix, 'link_to_dummy.txt') +# ) == os.path.realpath(os.path.join(spec.prefix, 'dummy.txt')) + + args = parser.parse_args(['keys']) + buildcache.buildcache(parser, args) + args = parser.parse_args(['list']) buildcache.buildcache(parser, args) @@ -200,6 +181,9 @@ def test_buildcache(mock_archive, tmpdir): args = parser.parse_args(['keys', '-f']) buildcache.buildcache(parser, args) + args = parser.parse_args(['keys', '-i', '-t']) + buildcache.buildcache(parser, args) + # unregister mirror with spack config mirrors = {} spack.config.set('mirrors', mirrors) @@ -210,7 +194,10 @@ def test_buildcache(mock_archive, tmpdir): bindist._cached_specs = set() +@pytest.mark.usefixtures('install_mockery') def test_relocate_text(tmpdir): + spec = Spec('trivial-install-test-package') + spec.concretize() with tmpdir.as_cwd(): # Validate the text path replacement old_dir = '/home/spack/opt/spack' @@ -220,24 +207,46 @@ def test_relocate_text(tmpdir): script.close() filenames = [filename] new_dir = '/opt/rh/devtoolset/' - relocate_text(filenames, oldpath=old_dir, newpath=new_dir, - oldprefix=old_dir, newprefix=new_dir) + relocate_text(filenames, old_dir, new_dir, + old_dir, new_dir, + old_dir, new_dir, + {old_dir: new_dir}) with open(filename, "r")as script: for line in script: assert(new_dir in line) - assert(strings_contains_installroot(filename, old_dir) is False) + assert(file_is_relocatable(os.path.realpath(filename))) + # Remove cached binary specs since we deleted the mirror + bindist._cached_specs = set() def test_relocate_links(tmpdir): with tmpdir.as_cwd(): - old_dir = '/home/spack/opt/spack' - filename = 'link.ln' - old_src = os.path.join(old_dir, filename) - os.symlink(old_src, filename) - filenames = [filename] - new_dir = '/opt/rh/devtoolset' - relocate_links(filenames, old_dir, new_dir) - assert os.path.realpath(filename) == os.path.join(new_dir, filename) + old_layout_root = os.path.join( + '%s' % tmpdir, 'home', 'spack', 'opt', 'spack') + old_install_prefix = os.path.join( + '%s' % old_layout_root, 'debian6', 'test') + old_binname = os.path.join(old_install_prefix, 'binfile') + placeholder = set_placeholder(old_layout_root) + re.sub(old_layout_root, placeholder, old_binname) + filenames = ['link.ln', 'outsideprefix.ln'] + new_layout_root = os.path.join( + '%s' % tmpdir, 'opt', 'rh', 'devtoolset') + new_install_prefix = os.path.join( + '%s' % new_layout_root, 'test', 'debian6') + new_linkname = os.path.join(new_install_prefix, 'link.ln') + new_linkname2 = os.path.join(new_install_prefix, 'outsideprefix.ln') + new_binname = os.path.join(new_install_prefix, 'binfile') + mkdirp(new_install_prefix) + with open(new_binname, 'w') as f: + f.write('\n') + os.utime(new_binname, None) + os.symlink(old_binname, new_linkname) + os.symlink('/usr/lib/libc.so', new_linkname2) + relocate_links(filenames, old_layout_root, new_layout_root, + old_install_prefix, new_install_prefix, + {old_install_prefix: new_install_prefix}) + assert os.readlink(new_linkname) == new_binname + assert os.readlink(new_linkname2) == '/usr/lib/libc.so' def test_needs_relocation(): @@ -246,15 +255,222 @@ def test_needs_relocation(): assert needs_binary_relocation('application', 'x-executable') assert not needs_binary_relocation('application', 'x-octet-stream') assert not needs_binary_relocation('text', 'x-') - assert needs_text_relocation('text', 'x-') assert not needs_text_relocation('symbolic link to', 'x-') assert needs_binary_relocation('application', 'x-mach-binary') -def test_macho_paths(): +def test_replace_paths(tmpdir): + with tmpdir.as_cwd(): + suffix = 'dylib' if platform.system().lower() == 'darwin' else 'so' + hash_a = '53moz6jwnw3xpiztxwhc4us26klribws' + hash_b = 'tk62dzu62kd4oh3h3heelyw23hw2sfee' + hash_c = 'hdkhduizmaddpog6ewdradpobnbjwsjl' + hash_d = 'hukkosc7ahff7o65h6cdhvcoxm57d4bw' + hash_loco = 'zy4oigsc4eovn5yhr2lk4aukwzoespob' + prefix2hash = dict() + + old_spack_dir = os.path.join('%s' % tmpdir, + 'Users', 'developer', 'spack') + mkdirp(old_spack_dir) + + oldprefix_a = os.path.join('%s' % old_spack_dir, 'pkgA-%s' % hash_a) + oldlibdir_a = os.path.join('%s' % oldprefix_a, 'lib') + mkdirp(oldlibdir_a) + prefix2hash[str(oldprefix_a)] = hash_a + + oldprefix_b = os.path.join('%s' % old_spack_dir, 'pkgB-%s' % hash_b) + oldlibdir_b = os.path.join('%s' % oldprefix_b, 'lib') + mkdirp(oldlibdir_b) + prefix2hash[str(oldprefix_b)] = hash_b + + oldprefix_c = os.path.join('%s' % old_spack_dir, 'pkgC-%s' % hash_c) + oldlibdir_c = os.path.join('%s' % oldprefix_c, 'lib') + oldlibdir_cc = os.path.join('%s' % oldlibdir_c, 'C') + mkdirp(oldlibdir_c) + prefix2hash[str(oldprefix_c)] = hash_c + + oldprefix_d = os.path.join('%s' % old_spack_dir, 'pkgD-%s' % hash_d) + oldlibdir_d = os.path.join('%s' % oldprefix_d, 'lib') + mkdirp(oldlibdir_d) + prefix2hash[str(oldprefix_d)] = hash_d + + oldprefix_local = os.path.join('%s' % tmpdir, 'usr', 'local') + oldlibdir_local = os.path.join('%s' % oldprefix_local, 'lib') + mkdirp(oldlibdir_local) + prefix2hash[str(oldprefix_local)] = hash_loco + libfile_a = 'libA.%s' % suffix + libfile_b = 'libB.%s' % suffix + libfile_c = 'libC.%s' % suffix + libfile_d = 'libD.%s' % suffix + libfile_loco = 'libloco.%s' % suffix + old_libnames = [os.path.join(oldlibdir_a, libfile_a), + os.path.join(oldlibdir_b, libfile_b), + os.path.join(oldlibdir_c, libfile_c), + os.path.join(oldlibdir_d, libfile_d), + os.path.join(oldlibdir_local, libfile_loco)] + + for old_libname in old_libnames: + with open(old_libname, 'a'): + os.utime(old_libname, None) + + hash2prefix = dict() + + new_spack_dir = os.path.join('%s' % tmpdir, 'Users', 'Shared', + 'spack') + mkdirp(new_spack_dir) + + prefix_a = os.path.join(new_spack_dir, 'pkgA-%s' % hash_a) + libdir_a = os.path.join(prefix_a, 'lib') + mkdirp(libdir_a) + hash2prefix[hash_a] = str(prefix_a) + + prefix_b = os.path.join(new_spack_dir, 'pkgB-%s' % hash_b) + libdir_b = os.path.join(prefix_b, 'lib') + mkdirp(libdir_b) + hash2prefix[hash_b] = str(prefix_b) + + prefix_c = os.path.join(new_spack_dir, 'pkgC-%s' % hash_c) + libdir_c = os.path.join(prefix_c, 'lib') + libdir_cc = os.path.join(libdir_c, 'C') + mkdirp(libdir_cc) + hash2prefix[hash_c] = str(prefix_c) + + prefix_d = os.path.join(new_spack_dir, 'pkgD-%s' % hash_d) + libdir_d = os.path.join(prefix_d, 'lib') + mkdirp(libdir_d) + hash2prefix[hash_d] = str(prefix_d) + + prefix_local = os.path.join('%s' % tmpdir, 'usr', 'local') + libdir_local = os.path.join(prefix_local, 'lib') + mkdirp(libdir_local) + hash2prefix[hash_loco] = str(prefix_local) + + new_libnames = [os.path.join(libdir_a, libfile_a), + os.path.join(libdir_b, libfile_b), + os.path.join(libdir_cc, libfile_c), + os.path.join(libdir_d, libfile_d), + os.path.join(libdir_local, libfile_loco)] + + for new_libname in new_libnames: + with open(new_libname, 'a'): + os.utime(new_libname, None) + + prefix2prefix = dict() + for prefix, hash in prefix2hash.items(): + prefix2prefix[prefix] = hash2prefix[hash] + + out_dict = macho_find_paths([oldlibdir_a, oldlibdir_b, + oldlibdir_c, + oldlibdir_cc, oldlibdir_local], + [os.path.join(oldlibdir_a, + libfile_a), + os.path.join(oldlibdir_b, + libfile_b), + os.path.join(oldlibdir_local, + libfile_loco)], + os.path.join(oldlibdir_cc, + libfile_c), + old_spack_dir, + prefix2prefix + ) + assert out_dict == {oldlibdir_a: libdir_a, + oldlibdir_b: libdir_b, + oldlibdir_c: libdir_c, + oldlibdir_cc: libdir_cc, + libdir_local: libdir_local, + os.path.join(oldlibdir_a, libfile_a): + os.path.join(libdir_a, libfile_a), + os.path.join(oldlibdir_b, libfile_b): + os.path.join(libdir_b, libfile_b), + os.path.join(oldlibdir_local, libfile_loco): + os.path.join(libdir_local, libfile_loco), + os.path.join(oldlibdir_cc, libfile_c): + os.path.join(libdir_cc, libfile_c)} + + out_dict = macho_find_paths([oldlibdir_a, oldlibdir_b, + oldlibdir_c, + oldlibdir_cc, + oldlibdir_local], + [os.path.join(oldlibdir_a, + libfile_a), + os.path.join(oldlibdir_b, + libfile_b), + os.path.join(oldlibdir_cc, + libfile_c), + os.path.join(oldlibdir_local, + libfile_loco)], + None, + old_spack_dir, + prefix2prefix + ) + assert out_dict == {oldlibdir_a: libdir_a, + oldlibdir_b: libdir_b, + oldlibdir_c: libdir_c, + oldlibdir_cc: libdir_cc, + libdir_local: libdir_local, + os.path.join(oldlibdir_a, libfile_a): + os.path.join(libdir_a, libfile_a), + os.path.join(oldlibdir_b, libfile_b): + os.path.join(libdir_b, libfile_b), + os.path.join(oldlibdir_local, libfile_loco): + os.path.join(libdir_local, libfile_loco), + os.path.join(oldlibdir_cc, libfile_c): + os.path.join(libdir_cc, libfile_c)} + + out_dict = macho_find_paths([oldlibdir_a, oldlibdir_b, + oldlibdir_c, oldlibdir_cc, + oldlibdir_local], + ['@rpath/%s' % libfile_a, + '@rpath/%s' % libfile_b, + '@rpath/%s' % libfile_c, + '@rpath/%s' % libfile_loco], + None, + old_spack_dir, + prefix2prefix + ) + + assert out_dict == {'@rpath/%s' % libfile_a: + '@rpath/%s' % libfile_a, + '@rpath/%s' % libfile_b: + '@rpath/%s' % libfile_b, + '@rpath/%s' % libfile_c: + '@rpath/%s' % libfile_c, + '@rpath/%s' % libfile_loco: + '@rpath/%s' % libfile_loco, + oldlibdir_a: libdir_a, + oldlibdir_b: libdir_b, + oldlibdir_c: libdir_c, + oldlibdir_cc: libdir_cc, + libdir_local: libdir_local, + } + + out_dict = macho_find_paths([oldlibdir_a, + oldlibdir_b, + oldlibdir_d, + oldlibdir_local], + ['@rpath/%s' % libfile_a, + '@rpath/%s' % libfile_b, + '@rpath/%s' % libfile_loco], + None, + old_spack_dir, + prefix2prefix) + assert out_dict == {'@rpath/%s' % libfile_a: + '@rpath/%s' % libfile_a, + '@rpath/%s' % libfile_b: + '@rpath/%s' % libfile_b, + '@rpath/%s' % libfile_loco: + '@rpath/%s' % libfile_loco, + oldlibdir_a: libdir_a, + oldlibdir_b: libdir_b, + oldlibdir_d: libdir_d, + libdir_local: libdir_local, + } + + +def test_macho_make_paths(): out = macho_make_paths_relative('/Users/Shares/spack/pkgC/lib/libC.dylib', '/Users/Shared/spack', ('/Users/Shared/spack/pkgA/lib', @@ -264,13 +480,19 @@ def test_macho_paths(): '/Users/Shared/spack/pkgB/libB.dylib', '/usr/local/lib/libloco.dylib'), '/Users/Shared/spack/pkgC/lib/libC.dylib') - assert out == (['@loader_path/../../../../Shared/spack/pkgA/lib', - '@loader_path/../../../../Shared/spack/pkgB/lib', - '/usr/local/lib'], - ['@loader_path/../../../../Shared/spack/pkgA/libA.dylib', - '@loader_path/../../../../Shared/spack/pkgB/libB.dylib', - '/usr/local/lib/libloco.dylib'], - '@rpath/libC.dylib') + assert out == {'/Users/Shared/spack/pkgA/lib': + '@loader_path/../../../../Shared/spack/pkgA/lib', + '/Users/Shared/spack/pkgB/lib': + '@loader_path/../../../../Shared/spack/pkgB/lib', + '/usr/local/lib': '/usr/local/lib', + '/Users/Shared/spack/pkgA/libA.dylib': + '@loader_path/../../../../Shared/spack/pkgA/libA.dylib', + '/Users/Shared/spack/pkgB/libB.dylib': + '@loader_path/../../../../Shared/spack/pkgB/libB.dylib', + '/usr/local/lib/libloco.dylib': + '/usr/local/lib/libloco.dylib', + '/Users/Shared/spack/pkgC/lib/libC.dylib': + '@rpath/libC.dylib'} out = macho_make_paths_relative('/Users/Shared/spack/pkgC/bin/exeC', '/Users/Shared/spack', @@ -281,98 +503,21 @@ def test_macho_paths(): '/Users/Shared/spack/pkgB/libB.dylib', '/usr/local/lib/libloco.dylib'), None) - assert out == (['@loader_path/../../pkgA/lib', - '@loader_path/../../pkgB/lib', - '/usr/local/lib'], - ['@loader_path/../../pkgA/libA.dylib', - '@loader_path/../../pkgB/libB.dylib', - '/usr/local/lib/libloco.dylib'], None) - - out = macho_replace_paths('/Users/Shared/spack', - '/Applications/spack', - ('/Users/Shared/spack/pkgA/lib', - '/Users/Shared/spack/pkgB/lib', - '/usr/local/lib'), - ('/Users/Shared/spack/pkgA/libA.dylib', - '/Users/Shared/spack/pkgB/libB.dylib', - '/usr/local/lib/libloco.dylib'), - '/Users/Shared/spack/pkgC/lib/libC.dylib') - assert out == (['/Applications/spack/pkgA/lib', - '/Applications/spack/pkgB/lib', - '/usr/local/lib'], - ['/Applications/spack/pkgA/libA.dylib', - '/Applications/spack/pkgB/libB.dylib', - '/usr/local/lib/libloco.dylib'], - '/Applications/spack/pkgC/lib/libC.dylib') - - out = macho_replace_paths('/Users/Shared/spack', - '/Applications/spack', - ('/Users/Shared/spack/pkgA/lib', - '/Users/Shared/spack/pkgB/lib', - '/usr/local/lib'), - ('/Users/Shared/spack/pkgA/libA.dylib', - '/Users/Shared/spack/pkgB/libB.dylib', - '/usr/local/lib/libloco.dylib'), - None) - assert out == (['/Applications/spack/pkgA/lib', - '/Applications/spack/pkgB/lib', - '/usr/local/lib'], - ['/Applications/spack/pkgA/libA.dylib', - '/Applications/spack/pkgB/libB.dylib', - '/usr/local/lib/libloco.dylib'], - None) + assert out == {'/Users/Shared/spack/pkgA/lib': + '@loader_path/../../pkgA/lib', + '/Users/Shared/spack/pkgB/lib': + '@loader_path/../../pkgB/lib', + '/usr/local/lib': '/usr/local/lib', + '/Users/Shared/spack/pkgA/libA.dylib': + '@loader_path/../../pkgA/libA.dylib', + '/Users/Shared/spack/pkgB/libB.dylib': + '@loader_path/../../pkgB/libB.dylib', + '/usr/local/lib/libloco.dylib': + '/usr/local/lib/libloco.dylib'} def test_elf_paths(): - out = get_relative_rpaths( + out = get_relative_elf_rpaths( '/usr/bin/test', '/usr', ('/usr/lib', '/usr/lib64', '/opt/local/lib')) assert out == ['$ORIGIN/../lib', '$ORIGIN/../lib64', '/opt/local/lib'] - - out = substitute_rpath( - ('/usr/lib', '/usr/lib64', '/opt/local/lib'), '/usr', '/opt') - assert out == ['/opt/lib', '/opt/lib64', '/opt/local/lib'] - - -@pytest.mark.skipif(sys.platform != 'darwin', - reason="only works with Mach-o objects") -def test_relocate_macho(tmpdir): - with tmpdir.as_cwd(): - - get_patchelf() # this does nothing on Darwin - - rpaths, deps, idpath = macho_get_paths('/bin/bash') - nrpaths, ndeps, nid = macho_make_paths_relative('/bin/bash', '/usr', - rpaths, deps, idpath) - shutil.copyfile('/bin/bash', 'bash') - modify_macho_object('bash', - rpaths, deps, idpath, - nrpaths, ndeps, nid) - - rpaths, deps, idpath = macho_get_paths('/bin/bash') - nrpaths, ndeps, nid = macho_replace_paths('/usr', '/opt', - rpaths, deps, idpath) - shutil.copyfile('/bin/bash', 'bash') - modify_macho_object('bash', - rpaths, deps, idpath, - nrpaths, ndeps, nid) - - path = '/usr/lib/libncurses.5.4.dylib' - rpaths, deps, idpath = macho_get_paths(path) - nrpaths, ndeps, nid = macho_make_paths_relative(path, '/usr', - rpaths, deps, idpath) - shutil.copyfile( - '/usr/lib/libncurses.5.4.dylib', 'libncurses.5.4.dylib') - modify_macho_object('libncurses.5.4.dylib', - rpaths, deps, idpath, - nrpaths, ndeps, nid) - - rpaths, deps, idpath = macho_get_paths(path) - nrpaths, ndeps, nid = macho_replace_paths('/usr', '/opt', - rpaths, deps, idpath) - shutil.copyfile( - '/usr/lib/libncurses.5.4.dylib', 'libncurses.5.4.dylib') - modify_macho_object( - 'libncurses.5.4.dylib', - rpaths, deps, idpath, - nrpaths, ndeps, nid) From 55d5adfecfdaa097724ca75bdcb4b92251697e97 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Mon, 16 Mar 2020 14:10:06 -0400 Subject: [PATCH 064/377] silo: depends on hdf5@:1.10.999 (#15495) Silo does not build with HDF5 1.12. --- var/spack/repos/builtin/packages/silo/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py index 9b980ba0ac8..98e8b4be155 100644 --- a/var/spack/repos/builtin/packages/silo/package.py +++ b/var/spack/repos/builtin/packages/silo/package.py @@ -28,6 +28,7 @@ class Silo(AutotoolsPackage): variant('mpi', default=True, description='Compile with MPI Compatibility') + depends_on('hdf5@:1.10.999', when='@:4.10.2') depends_on('hdf5~mpi', when='~mpi') depends_on('mpi', when='+mpi') depends_on('hdf5+mpi', when='+mpi') From a8706cc89b49fadadc644cdbb7077743fcc58b4b Mon Sep 17 00:00:00 2001 From: "Seth R. Johnson" Date: Mon, 16 Mar 2020 14:41:19 -0400 Subject: [PATCH 065/377] CMakePackage: convert variants to CMake arguments (#14376) Add a 'define_from_variant` helper function to CMake-based Spack packages to convert package variants into CMake arguments. For example: args.append('-DFOO=%s' % ('ON' if '+foo' in self.spec else 'OFF')) can be replaced with: args.append(self.define_from_variant('foo')) The following conversions are handled automatically: * Flag variants will be converted to CMake booleans * Multivalued variants will be converted to semicolon-separated strings * Other variant values are converted to CMake string arguments This also adds a 'define' helper method to convert any variable to a CMake argument. It has the same conversion rules as 'define_from_variant' (but operates directly on values rather than requiring the user to supply the name of a package variant). --- lib/spack/docs/build_systems/cmakepackage.rst | 17 +-- lib/spack/spack/build_systems/cmake.py | 114 ++++++++++++++++-- lib/spack/spack/test/build_systems.py | 38 ++++++ .../packages/cmake-client/package.py | 8 ++ 4 files changed, 161 insertions(+), 16 deletions(-) diff --git a/lib/spack/docs/build_systems/cmakepackage.rst b/lib/spack/docs/build_systems/cmakepackage.rst index 0a771edad32..76e89c80b1a 100644 --- a/lib/spack/docs/build_systems/cmakepackage.rst +++ b/lib/spack/docs/build_systems/cmakepackage.rst @@ -128,17 +128,20 @@ Adding flags to cmake ^^^^^^^^^^^^^^^^^^^^^ To add additional flags to the ``cmake`` call, simply override the -``cmake_args`` function: +``cmake_args`` function. The following example defines values for the flags +``WHATEVER``, ``ENABLE_BROKEN_FEATURE``, ``DETECT_HDF5``, and ``THREADS`` with +and without the :py:meth:`~.CMakePackage.define` and +:py:meth:`~.CMakePackage.define_from_variant` helper functions: .. code-block:: python def cmake_args(self): - args = [] - - if '+hdf5' in self.spec: - args.append('-DDETECT_HDF5=ON') - else: - args.append('-DDETECT_HDF5=OFF') + args = [ + '-DWHATEVER:STRING=somevalue', + self.define('ENABLE_BROKEN_FEATURE', False), + self.define_from_variant('DETECT_HDF5', 'hdf5'), + self.define_from_variant('THREADS'), # True if +threads + ] return args diff --git a/lib/spack/spack/build_systems/cmake.py b/lib/spack/spack/build_systems/cmake.py index 14f33e94e67..d7da957a9d6 100644 --- a/lib/spack/spack/build_systems/cmake.py +++ b/lib/spack/spack/build_systems/cmake.py @@ -147,33 +147,129 @@ def _std_args(pkg): except KeyError: build_type = 'RelWithDebInfo' + define = CMakePackage.define args = [ '-G', generator, - '-DCMAKE_INSTALL_PREFIX:PATH={0}'.format(pkg.prefix), - '-DCMAKE_BUILD_TYPE:STRING={0}'.format(build_type), + define('CMAKE_INSTALL_PREFIX', pkg.prefix), + define('CMAKE_BUILD_TYPE', build_type), ] if primary_generator == 'Unix Makefiles': - args.append('-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON') + args.append(define('CMAKE_VERBOSE_MAKEFILE', True)) if platform.mac_ver()[0]: args.extend([ - '-DCMAKE_FIND_FRAMEWORK:STRING=LAST', - '-DCMAKE_FIND_APPBUNDLE:STRING=LAST' + define('CMAKE_FIND_FRAMEWORK', "LAST"), + define('CMAKE_FIND_APPBUNDLE', "LAST"), ]) # Set up CMake rpath - args.append('-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE') - rpaths = ';'.join(spack.build_environment.get_rpaths(pkg)) - args.append('-DCMAKE_INSTALL_RPATH:STRING={0}'.format(rpaths)) + args.extend([ + define('CMAKE_INSTALL_RPATH_USE_LINK_PATH', False), + define('CMAKE_INSTALL_RPATH', + spack.build_environment.get_rpaths(pkg)), + ]) # CMake's find_package() looks in CMAKE_PREFIX_PATH first, help CMake # to find immediate link dependencies in right places: deps = [d.prefix for d in pkg.spec.dependencies(deptype=('build', 'link'))] deps = filter_system_paths(deps) - args.append('-DCMAKE_PREFIX_PATH:STRING={0}'.format(';'.join(deps))) + args.append(define('CMAKE_PREFIX_PATH', deps)) return args + @staticmethod + def define(cmake_var, value): + """Return a CMake command line argument that defines a variable. + + The resulting argument will convert boolean values to OFF/ON + and lists/tuples to CMake semicolon-separated string lists. All other + values will be interpreted as strings. + + Examples: + + .. code-block:: python + + [define('BUILD_SHARED_LIBS', True), + define('CMAKE_CXX_STANDARD', 14), + define('swr', ['avx', 'avx2'])] + + will generate the following configuration options: + + .. code-block:: console + + ["-DBUILD_SHARED_LIBS:BOOL=ON", + "-DCMAKE_CXX_STANDARD:STRING=14", + "-DSWR:STRING=avx;avx2] + + """ + # Create a list of pairs. Each pair includes a configuration + # option and whether or not that option is activated + if isinstance(value, bool): + kind = 'BOOL' + value = "ON" if value else "OFF" + else: + kind = 'STRING' + if isinstance(value, (list, tuple)): + value = ";".join(str(v) for v in value) + else: + value = str(value) + + return "".join(["-D", cmake_var, ":", kind, "=", value]) + + def define_from_variant(self, cmake_var, variant=None): + """Return a CMake command line argument from the given variant's value. + + The optional ``variant`` argument defaults to the lower-case transform + of ``cmake_var``. + + This utility function is similar to + :py:meth:`~.AutotoolsPackage.with_or_without`. + + Examples: + + Given a package with: + + .. code-block:: python + + variant('cxxstd', default='11', values=('11', '14'), + multi=False, description='') + variant('shared', default=True, description='') + variant('swr', values=any_combination_of('avx', 'avx2'), + description='') + + calling this function like: + + .. code-block:: python + + [define_from_variant('BUILD_SHARED_LIBS', 'shared'), + define_from_variant('CMAKE_CXX_STANDARD', 'cxxstd'), + define_from_variant('SWR')] + + will generate the following configuration options: + + .. code-block:: console + + ["-DBUILD_SHARED_LIBS:BOOL=ON", + "-DCMAKE_CXX_STANDARD:STRING=14", + "-DSWR:STRING=avx;avx2] + + for `` cxxstd=14 +shared swr=avx,avx2`` + """ + + if variant is None: + variant = cmake_var.lower() + + if variant not in self.variants: + raise KeyError( + '"{0}" is not a variant of "{1}"'.format(variant, self.name)) + + value = self.spec.variants[variant].value + if isinstance(value, (tuple, list)): + # Sort multi-valued variants for reproducibility + value = sorted(value) + + return self.define(cmake_var, value) + def flags_to_build_system_args(self, flags): """Produces a list of all command line arguments to pass the specified compiler flags to cmake. Note CMAKE does not have a cppflags option, diff --git a/lib/spack/spack/test/build_systems.py b/lib/spack/spack/test/build_systems.py index 744821a04e2..7ede78b7a51 100644 --- a/lib/spack/spack/test/build_systems.py +++ b/lib/spack/spack/test/build_systems.py @@ -181,3 +181,41 @@ def test_none_is_allowed(self): assert '--without-bar' in options assert '--without-baz' in options assert '--no-fee' in options + + +@pytest.mark.usefixtures('config', 'mock_packages') +class TestCMakePackage(object): + + def test_define(self): + s = Spec('cmake-client') + s.concretize() + pkg = spack.repo.get(s) + + for cls in (list, tuple): + arg = pkg.define('MULTI', cls(['right', 'up'])) + assert arg == '-DMULTI:STRING=right;up' + + arg = pkg.define('ENABLE_TRUTH', False) + assert arg == '-DENABLE_TRUTH:BOOL=OFF' + arg = pkg.define('ENABLE_TRUTH', True) + assert arg == '-DENABLE_TRUTH:BOOL=ON' + + arg = pkg.define('SINGLE', 'red') + assert arg == '-DSINGLE:STRING=red' + + def test_define_from_variant(self): + s = Spec('cmake-client multi=up,right ~truthy single=red') + s.concretize() + pkg = spack.repo.get(s) + + arg = pkg.define_from_variant('MULTI') + assert arg == '-DMULTI:STRING=right;up' + + arg = pkg.define_from_variant('ENABLE_TRUTH', 'truthy') + assert arg == '-DENABLE_TRUTH:BOOL=OFF' + + arg = pkg.define_from_variant('SINGLE') + assert arg == '-DSINGLE:STRING=red' + + with pytest.raises(KeyError, match="not a variant"): + pkg.define_from_variant('NONEXISTENT') diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py index 286ee080863..2350259b228 100644 --- a/var/spack/repos/builtin.mock/packages/cmake-client/package.py +++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py @@ -21,6 +21,14 @@ class CmakeClient(CMakePackage): version('1.0', '4cb3ff35b2472aae70f542116d616e63') + variant( + 'multi', description='', + values=any_combination_of('up', 'right', 'back').with_default('up') + ) + variant('single', description='', default='blue', + values=('blue', 'red', 'green'), multi=False) + variant('truthy', description='', default=True) + callback_counter = 0 flipped = False From 3029dde7ec96a33769d420f6b1f5c58086795931 Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Mon, 16 Mar 2020 14:49:55 -0500 Subject: [PATCH 066/377] When replacing path text in ELF binaries do not include null byte padding in search string (#15508) --- lib/spack/spack/relocate.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py index 7a364347367..e7c85fa4d90 100644 --- a/lib/spack/spack/relocate.py +++ b/lib/spack/spack/relocate.py @@ -447,7 +447,7 @@ def replace(match): data = f.read() f.seek(0) original_data_len = len(data) - pat = re.compile(old_dir.encode('utf-8') + b'([^\0]*?)\0') + pat = re.compile(old_dir.encode('utf-8')) if not pat.search(data): return ndata = pat.sub(replace, data) From c9a715b190c7ac077ca29143b57ec0b7445bc9c1 Mon Sep 17 00:00:00 2001 From: "Seth R. Johnson" Date: Mon, 16 Mar 2020 15:55:16 -0400 Subject: [PATCH 067/377] veccore: added package at v0.6.0 (#15472) --- .../repos/builtin/packages/veccore/package.py | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 var/spack/repos/builtin/packages/veccore/package.py diff --git a/var/spack/repos/builtin/packages/veccore/package.py b/var/spack/repos/builtin/packages/veccore/package.py new file mode 100644 index 00000000000..a339358a084 --- /dev/null +++ b/var/spack/repos/builtin/packages/veccore/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Veccore(CMakePackage, CudaPackage): + """SIMD Vectorization Library for VecGeom and GeantV""" + + homepage = "https://gitlab.cern.ch/VecGeom/VecCore" + url = "https://gitlab.cern.ch/VecGeom/VecCore/-/archive/v0.6.0/VecCore-v0.6.0.tar.gz" + git = "https://gitlab.cern.ch/VecGeom/VecCore.git" + + maintainers = ['drbenmorgan', 'sethrj'] + + version('master', branch='master') + version('0.6.0', sha256='e7ff874ba2a8201624795cbe11c84634863e4ac7da691a936772d4202ef54413') + version('0.5.2', sha256='0cfaa830b9d10fb9df4ced5208a742623da08520fea5949461fe81637a27db15') + version('0.5.1', sha256='5ef3a8d8692d8f82641aae76b58405b8b3a1539a8f21b23d66a5df8327eeafc4') + version('0.5.0', sha256='aba3e0217c0cd829290c9fe63f1db865838aa25312ae0a09effdcb186f7771be') + version('0.4.2', sha256='4a3bb944bce63dc1dc9757ba53624b822e1aff5ed088d542039a20227ed2b715') + + variant('cxxstd', + default='11', + values=('11', '14', '17'), + multi=False, + description='Use the specified C++ standard when building.') + conflicts('cxxstd=14', when='@:0.5') + conflicts('cxxstd=17', when='@:0.5') + + def cmake_args(self): + define = CMakePackage.define + return [ + define('VC', False), + define('UMESIMD', False), + self.define_from_variant('CMAKE_CXX_STANDARD', 'cxxstd'), + self.define_from_variant('CUDA'), + ] From e48d24ee4591bd94e8fc3c9091d740440cbb9abd Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Mon, 16 Mar 2020 18:43:11 -0500 Subject: [PATCH 068/377] Warn only if link target is not relative and outside of the install prefix (#15512) --- lib/spack/spack/relocate.py | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py index e7c85fa4d90..88b5a36c565 100644 --- a/lib/spack/spack/relocate.py +++ b/lib/spack/spack/relocate.py @@ -682,19 +682,18 @@ def relocate_links(linknames, old_layout_root, new_layout_root, link_names = [os.path.join(new_install_prefix, linkname) for linkname in linknames] for link_name in link_names: - old_link_target = os.readlink(link_name) - old_link_target = re.sub(placeholder, old_layout_root, old_link_target) - if old_link_target.startswith(old_install_prefix): + link_target = os.readlink(link_name) + link_target = re.sub(placeholder, old_layout_root, link_target) + if link_target.startswith(old_install_prefix): new_link_target = re.sub( - old_install_prefix, new_install_prefix, old_link_target) + old_install_prefix, new_install_prefix, link_target) os.unlink(link_name) os.symlink(new_link_target, link_name) - else: - msg = 'Old link target %s' % old_link_target + if (os.path.isabs(link_target) and + not link_target.startswith(new_install_prefix)): + msg = 'Link target %s' % link_target msg += ' for symbolic link %s is outside' % link_name - msg += ' of the old install prefix %s.\n' % old_install_prefix - msg += 'This symbolic link will not be relocated' - msg += ' and might break relocation.' + msg += ' of the newinstall prefix %s.\n' % new_install_prefix tty.warn(msg) From c92847a30c945612658a617bf70d33f794736390 Mon Sep 17 00:00:00 2001 From: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com> Date: Mon, 16 Mar 2020 17:47:24 -0700 Subject: [PATCH 069/377] cap binutils version @:2.33.1 due to build failures with 2.34 (#15504) --- var/spack/repos/builtin/packages/tau/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/tau/package.py b/var/spack/repos/builtin/packages/tau/package.py index e6eaa43bf87..f17b8202d29 100644 --- a/var/spack/repos/builtin/packages/tau/package.py +++ b/var/spack/repos/builtin/packages/tau/package.py @@ -87,7 +87,7 @@ class Tau(Package): depends_on('libdwarf', when='+libdwarf') depends_on('libelf', when='+libdwarf') # TAU requires the ELF header support, libiberty and demangle. - depends_on('binutils+libiberty+headers~nls', when='+binutils') + depends_on('binutils@:2.33.1+libiberty+headers~nls', when='+binutils') depends_on('python@2.7:', when='+python') depends_on('libunwind', when='+libunwind') depends_on('mpi', when='+mpi', type=('build', 'run', 'link')) From e3f97b37e64d4de70baf8e58fcd747b021d8f2f9 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Tue, 17 Mar 2020 08:36:56 +0100 Subject: [PATCH 070/377] Module files won't use CPATH by default, but language specific vars (#14749) fixes #11555 Every path in CPATH is equivalent to a -I path to the compiler, while every path in *_INCLUDE_PATH is equivalent to -isystem. The latter avoids the noise due to warnings coming from 3rd party libraries that a project depends on. Added INCLUDE env variable (Intel Fortran, .mod files) --- etc/spack/defaults/modules.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/etc/spack/defaults/modules.yaml b/etc/spack/defaults/modules.yaml index 77c976510bd..5ae1b50fdad 100644 --- a/etc/spack/defaults/modules.yaml +++ b/etc/spack/defaults/modules.yaml @@ -30,7 +30,11 @@ modules: lib64: - LIBRARY_PATH include: - - CPATH + - C_INCLUDE_PATH + - CPLUS_INCLUDE_PATH + # The INCLUDE env variable specifies paths to look for + # .mod file for Intel Fortran compilers + - INCLUDE lib/pkgconfig: - PKG_CONFIG_PATH lib64/pkgconfig: From 402d89afa26d90f255b91f737cc8fa3a032fecbf Mon Sep 17 00:00:00 2001 From: darmac Date: Tue, 17 Mar 2020 15:49:35 +0800 Subject: [PATCH 071/377] nfs-utils: added package at v2.4.2 (#15491) --- .../builtin/packages/nfs-utils/package.py | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 var/spack/repos/builtin/packages/nfs-utils/package.py diff --git a/var/spack/repos/builtin/packages/nfs-utils/package.py b/var/spack/repos/builtin/packages/nfs-utils/package.py new file mode 100644 index 00000000000..be46c57030b --- /dev/null +++ b/var/spack/repos/builtin/packages/nfs-utils/package.py @@ -0,0 +1,34 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class NfsUtils(AutotoolsPackage): + """The NFS Utilities package contains the userspace server and client tools + necessary to use the kernel's NFS abilities. NFS is a protocol that allows + sharing file systems over the network.""" + + homepage = "http://linux-nfs.org/" + url = "https://sourceforge.net/projects/nfs/files/nfs-utils/2.4.2/nfs-utils-2.4.2.tar.gz/download" + + version('2.4.2', sha256='bb08106cd7bd397c6cc34e2461bc7818a664450d2805da08b07e1ced88e5155f') + version('2.4.1', sha256='c0dda96318af554881f4eb1590bfe91f1aba2fba59ed2ac3ba099f80fdf838e9') + version('2.3.4', sha256='36e70b0a583751ead0034ebe5d8826caf2dcc7ee7c0beefe94d6ee5a3b0b2484') + + depends_on('libtirpc') + depends_on('libevent') + depends_on('libdmx') + depends_on('lvm2') + depends_on('keyutils') + depends_on('sqlite') + depends_on('util-linux') + + def setup_build_environment(self, env): + env.append_flags('LDFLAGS', '-lintl') + + def configure_args(self): + args = ['--disable-gss', '--with-rpcgen=internal'] + return args From 05d0c7b4776ceb3afa5cebdab31dd42b494764bd Mon Sep 17 00:00:00 2001 From: "Seth R. Johnson" Date: Tue, 17 Mar 2020 06:18:40 -0400 Subject: [PATCH 072/377] Update and exetend VecGeom (#14520) * Add new vecgeom versions, add cuda support, automate target options * Add ROOT, GDML, and external VecCore support to VecGeom * Address reviewer comments * Update vecgeom for CUDA * Update versions --- .../repos/builtin/packages/vecgeom/package.py | 111 +++++++++++++----- 1 file changed, 79 insertions(+), 32 deletions(-) diff --git a/var/spack/repos/builtin/packages/vecgeom/package.py b/var/spack/repos/builtin/packages/vecgeom/package.py index ed6e516c8aa..2e28586ef63 100644 --- a/var/spack/repos/builtin/packages/vecgeom/package.py +++ b/var/spack/repos/builtin/packages/vecgeom/package.py @@ -5,49 +5,96 @@ from spack import * -import platform -class Vecgeom(CMakePackage): +class Vecgeom(CMakePackage, CudaPackage): """The vectorized geometry library for particle-detector simulation (toolkits).""" homepage = "https://gitlab.cern.ch/VecGeom/VecGeom" - url = "https://gitlab.cern.ch/api/v4/projects/VecGeom%2FVecGeom/repository/archive.tar.gz?sha=v0.3.rc" + url = "https://gitlab.cern.ch/VecGeom/VecGeom/-/archive/v1.1.6/VecGeom-v1.1.6.tar.gz" + git = "https://gitlab.cern.ch/VecGeom/VecGeom.git" - version('01.01.03', git='https://gitlab.cern.ch/VecGeom/VecGeom.git', tag='v01.01.03', preferred=True) - version('01.00.00', git='https://gitlab.cern.ch/VecGeom/VecGeom.git', tag='v01.00.00') - version('00.05.00', git='https://gitlab.cern.ch/VecGeom/VecGeom.git', tag='v00.05.00') + maintainers = ['drbenmorgan', 'sethrj'] + + version('master', branch='master') + version('1.1.6', sha256='c4806a6b67d01b40074b8cc6865d78574a6a1c573be51696f2ecdf98b9cb954a') + version('1.1.5', sha256='da674f3bbc75c30f56c1a2d251fa8930c899f27fa64b03a36569924030d87b95') + version('1.1.3', sha256='ada09e8b6b2fa6c058290302b2cb5a6c2e644192aab1623c31d18c6a2f4c01c8') + version('1.0.1', sha256='1eae7ac9014c608e8d8db5568058b8c0fea1a1dc7a8f54157a3a1c997b6fd9eb') + version('0.5.2', tag='v00.05.02', + commit='a7e0828c915ff936a79e672d1dd84b087a323b51') version('0.3.rc', sha256='a87a9ea4ab126b59ff9c79182bc0911ead3d76dd197194742e2a35ccd341299d') - variant('cxxstd', - default='17', - values=('11', '14', '17'), - multi=False, - description='Use the specified C++ standard when building.') - variant('vector', - default='native', - values=('sse3', 'sse4.2', 'native'), - multi=False, - description='Specify the instruction set for vectorization.') + _cxxstd_values = ('11', '14', '17') + variant('cxxstd', default='11', values=_cxxstd_values, multi=False, + description='Use the specified C++ standard when building') + variant('gdml', default=True, + description='Support native GDML geometry descriptions') + variant('geant4', default=False, + description='Support Geant4 geometry construction') + variant('root', default=False, + description='Support ROOT geometry construction') + variant('shared', default=True, + description='Build shared libraries') - depends_on('cmake@3.5:', type='build') + depends_on('veccore@0.5.2:', type=('build', 'link'), when='@1.1.0:') + depends_on('veccore@0.4.2', type=('build', 'link'), when='@:1.0') + depends_on('veccore+cuda', type=('build', 'link'), when='+cuda') + + conflicts('+cuda', when='@:1.1.5') + + for std in _cxxstd_values: + depends_on('geant4 cxxstd=' + std, when='+geant4 cxxstd=' + std) + depends_on('root cxxstd=' + std, when='+root cxxstd=' + std) + depends_on('veccore cxxstd=' + std, when='cxxstd=' + std) + depends_on('xerces-c cxxstd=' + std, when='+gdml cxxstd=' + std) def cmake_args(self): - options = [ - '-DBACKEND=Scalar', - '-DGEANT4=OFF', - '-DUSOLIDS=ON', - '-DUSOLIDS_VECGEOM=ON', - '-DROOT=OFF', - '-DNO_SPECIALIZATION=ON', - '-DCMAKE_VERBOSE_MAKEFILE=TRUE'] - options.append('-DCMAKE_CXX_STANDARD={0}'. - format(self.spec.variants['cxxstd'].value)) - arch = platform.machine() - if arch == 'x86_64': - options.append('-DVECGEOM_VECTOR={0}'. - format(self.spec.variants['vector'].value)) + # Possible target options are from the main CMakeLists.txt, assuming + # "best" is last + target = self.spec.target + vecgeom_arch = "sse2 sse3 ssse3 sse4.1 sse4.2 avx avx2".split() + for feature in reversed(vecgeom_arch): + if feature.replace('.', '_') in target: + target_instructions = feature + break else: - options.append('-DVECGEOM_VECTOR=' + arch) + # No features available (could be 'generic' arch) + target_instructions = 'empty' + + define = CMakePackage.define + options = [ + define('BACKEND', 'Scalar'), + define('BUILTIN_VECCORE', False), + define('NO_SPECIALIZATION', True), + define('VECGEOM_VECTOR', target_instructions), + self.define_from_variant('BUILD_SHARED_LIBS', 'shared'), + self.define_from_variant('CMAKE_CXX_STANDARD', 'cxxstd'), + self.define_from_variant('CUDA'), + self.define_from_variant('GDML'), + self.define_from_variant('GEANT4'), + self.define_from_variant('ROOT'), + ] + + # Set testing flags + build_tests = self.run_tests + options.extend([ + define('BUILD_TESTING', build_tests), + define('CTEST', build_tests), + define('GDMLTESTING', build_tests and '+gdml' in self.spec), + ]) + + if '+cuda' in self.spec: + arch = self.spec.variants['cuda_arch'].value + if len(arch) != 1 or arch[0] == 'none': + raise InstallError("Exactly one cuda_arch must be specified") + options.append(define('CUDA_ARCH', arch[0])) + + if self.spec.satisfies("@:0.5.2"): + options.extend([ + define('USOLIDS', True), + define('USOLIDS_VECGEOM', True), + ]) + return options From c2e0ee63830c17493c9d025fa46251b806b0323f Mon Sep 17 00:00:00 2001 From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com> Date: Tue, 17 Mar 2020 19:31:31 +0900 Subject: [PATCH 073/377] geant4: Removed unnecessary definition of xerces-c. (#15513) --- var/spack/repos/builtin/packages/geant4/package.py | 1 - 1 file changed, 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py index 3c87ccdff61..f3bcb121f60 100644 --- a/var/spack/repos/builtin/packages/geant4/package.py +++ b/var/spack/repos/builtin/packages/geant4/package.py @@ -58,7 +58,6 @@ class Geant4(CMakePackage): depends_on("expat") depends_on("zlib") - depends_on("xerces-c") depends_on("gl", when='+opengl') depends_on("glx", when='+opengl+x11') depends_on("libx11", when='+x11') From 304f0e9ef1f0e811225d4cf5cce957d4431bb734 Mon Sep 17 00:00:00 2001 From: wspear Date: Tue, 17 Mar 2020 08:38:53 -0700 Subject: [PATCH 074/377] Corrected compiler filtering for TAU makefiles (#15342) * Implemented working file filtering to replace spack compiler wrapper with real compiler. * Using string=True instead of re.escape. Using self.prefix.lib instead of appending /lib. Co-authored-by: Wyatt Spear --- .../repos/builtin/packages/tau/package.py | 22 +++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/tau/package.py b/var/spack/repos/builtin/packages/tau/package.py index f17b8202d29..4ac71b793f4 100644 --- a/var/spack/repos/builtin/packages/tau/package.py +++ b/var/spack/repos/builtin/packages/tau/package.py @@ -104,8 +104,6 @@ class Tau(Package): conflicts('+adios2', when='@:2.29.1') conflicts('+sqlite', when='@:2.29.1') - filter_compiler_wrappers('tau_cc.sh', 'Makefile.tau', relative_root='bin') - def set_compiler_options(self, spec): useropt = ["-O2 -g", self.rpath_args] @@ -271,11 +269,15 @@ def install(self, spec, prefix): compiler_specific_options = self.set_compiler_options(spec) options.extend(compiler_specific_options) configure(*options) + make("install") # Link arch-specific directories into prefix since there is # only one arch per prefix the way spack installs. self.link_tau_arch_dirs() + # TAU may capture Spack's internal compiler wrapper. Replace + # it with the correct compiler. + self.fix_tau_compilers() def link_tau_arch_dirs(self): for subdir in os.listdir(self.prefix): @@ -285,6 +287,22 @@ def link_tau_arch_dirs(self): if os.path.isdir(src) and not os.path.exists(dest): os.symlink(join_path(subdir, d), dest) + def fix_tau_compilers(self): + filter_file('FULL_CC=' + spack_cc, 'FULL_CC=' + self.compiler.cc, + self.prefix + '/include/Makefile', backup=False, + string=True) + filter_file('FULL_CXX=' + spack_cxx, 'FULL_CXX=' + + self.compiler.cxx, self.prefix + '/include/Makefile', + backup=False, string=True) + for makefile in os.listdir(self.prefix.lib): + if makefile.startswith('Makefile.tau'): + filter_file('FULL_CC=' + spack_cc, 'FULL_CC=' + + self.compiler.cc, self.prefix.lib + "/" + + makefile, backup=False, string=True) + filter_file('FULL_CXX=' + spack_cxx, 'FULL_CXX=' + + self.compiler.cxx, self.prefix.lib + + "/" + makefile, backup=False, string=True) + def setup_run_environment(self, env): pattern = join_path(self.prefix.lib, 'Makefile.*') files = glob.glob(pattern) From be8841cbc5ced1d702fae194193b9029765c1a7e Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Tue, 17 Mar 2020 10:49:24 -0500 Subject: [PATCH 075/377] Remove PatchelfError and change patchelf error message to a warning. (#15518) --- lib/spack/spack/relocate.py | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py index 88b5a36c565..afbae543afb 100644 --- a/lib/spack/spack/relocate.py +++ b/lib/spack/spack/relocate.py @@ -61,15 +61,6 @@ def __init__(self, old_path, new_path): super(BinaryTextReplaceException, self).__init__(msg, err_msg) -class PatchelfError(spack.error.SpackError): - """ - Raised when patchelf command returns a ProcessError. - """ - - def __init__(self, error): - super(PatchelfError, self).__init__(error) - - def get_patchelf(): """ Returns the full patchelf binary path if available in $PATH. @@ -116,7 +107,7 @@ def get_existing_elf_rpaths(path_name): rpaths = output.rstrip('\n').split(':') except ProcessError as e: msg = 'patchelf --print-rpath %s produced an error %s' % (path_name, e) - raise PatchelfError(msg) + tty.warn(msg) return rpaths @@ -376,9 +367,9 @@ def modify_elf_object(path_name, new_rpaths): patchelf('--force-rpath', '--set-rpath', '%s' % new_joined, '%s' % path_name, output=str, error=str) except ProcessError as e: - msg = 'patchelf --set-rpath %s failed with error %s' % (path_name, e) - raise PatchelfError(msg) - pass + msg = 'patchelf --force-rpath --set-rpath %s failed with error %s' % ( + path_name, e) + tty.warn(msg) if os.path.exists(bak_path): os.remove(bak_path) From 06bf93b270382b030e578ebe9534164fbfd9ff0e Mon Sep 17 00:00:00 2001 From: Sergey Kosukhin Date: Tue, 17 Mar 2020 19:41:47 +0100 Subject: [PATCH 076/377] MPICH: optional libxml2 support; NAG patches (#15235) * Add patches when building with NAG * Make libxml2 support optional. Also include conflict for @:3.2~hydra+libxml2 since @:3.2~hydra does not require libxml2 support * Add '--disable-silent-rules' to get more verbose output during the build --- .../packages/mpich/nag_libtool_2.4.2_0.patch | 29 ++++++++ .../packages/mpich/nag_libtool_2.4.2_1.patch | 71 +++++++++++++++++++ .../packages/mpich/nag_libtool_2.4.2_2.patch | 11 +++ .../packages/mpich/nag_libtool_2.4.6.patch | 69 ++++++++++++++++++ .../repos/builtin/packages/mpich/package.py | 44 +++++++++++- 5 files changed, 222 insertions(+), 2 deletions(-) create mode 100644 var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.2_0.patch create mode 100644 var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.2_1.patch create mode 100644 var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.2_2.patch create mode 100644 var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.6.patch diff --git a/var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.2_0.patch b/var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.2_0.patch new file mode 100644 index 00000000000..18d5c2ad657 --- /dev/null +++ b/var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.2_0.patch @@ -0,0 +1,29 @@ +--- a/configure ++++ b/configure +@@ -11563,6 +11563,8 @@ _LT_EOF + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec= + tmp_sharedflag='--shared' ;; ++ nagfor*) # NAGFOR 5.3 ++ tmp_sharedflag='-Wl,-shared' ;; + xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' + tmp_addflag= ;; +@@ -19036,6 +19038,8 @@ _LT_EOF + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec_F77= + tmp_sharedflag='--shared' ;; ++ nagfor*) # NAGFOR 5.3 ++ tmp_sharedflag='-Wl,-shared' ;; + xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' + tmp_addflag= ;; +@@ -22116,6 +22120,8 @@ _LT_EOF + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec_FC= + tmp_sharedflag='--shared' ;; ++ nagfor*) # NAGFOR 5.3 ++ tmp_sharedflag='-Wl,-shared' ;; + xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' + tmp_addflag= ;; diff --git a/var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.2_1.patch b/var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.2_1.patch new file mode 100644 index 00000000000..8fb671093bf --- /dev/null +++ b/var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.2_1.patch @@ -0,0 +1,71 @@ +--- a/confdb/ltmain.sh ++++ b/confdb/ltmain.sh +@@ -180,6 +180,20 @@ func_basename () + func_basename_result=`$ECHO "${1}" | $SED "$basename"` + } # func_basename may be replaced by extended shell implementation + ++# Calculate cc_basename. Skip known compiler wrappers and cross-prefix. ++func_cc_basename () ++{ ++ for cc_temp in $*""; do ++ case $cc_temp in ++ compile | *[\\/]compile | ccache | *[\\/]ccache ) ;; ++ distcc | *[\\/]distcc | purify | *[\\/]purify ) ;; ++ \-*) ;; ++ *) break;; ++ esac ++ done ++ func_cc_basename_result=`$ECHO "$cc_temp" | $SED "s%.*/%%; s%^$host_alias-%%"` ++} ++ + + # func_dirname_and_basename file append nondir_replacement + # perform func_basename and func_dirname in a single function +@@ -6419,6 +6433,13 @@ func_mode_link () + # Convert "-framework foo" to "foo.ltframework" + if test -n "$inherited_linker_flags"; then + tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'` ++ ++ # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor ++ func_cc_basename $CC ++ case $func_cc_basename_result in ++ nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;; ++ esac ++ + for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do + case " $new_inherited_linker_flags " in + *" $tmp_inherited_linker_flag "*) ;; +@@ -8001,6 +8022,13 @@ EOF + ;; + esac + ++ # Time to revert the changes made for nagfor. ++ func_cc_basename $CC ++ case $func_cc_basename_result in ++ nagfor*) ++ new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;; ++ esac ++ + # move library search paths that coincide with paths to not yet + # installed libraries to the beginning of the library search list + new_libs= +--- a/configure ++++ b/configure +@@ -11614,6 +11614,8 @@ _LT_EOF + whole_archive_flag_spec= + tmp_sharedflag='--shared' ;; + nagfor*) # NAGFOR 5.3 ++ whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' ++ compiler_needs_object=yes + tmp_sharedflag='-Wl,-shared' ;; + xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' +@@ -19246,6 +19248,8 @@ _LT_EOF + whole_archive_flag_spec_FC= + tmp_sharedflag='--shared' ;; + nagfor*) # NAGFOR 5.3 ++ whole_archive_flag_spec_FC='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' ++ compiler_needs_object_FC=yes + tmp_sharedflag='-Wl,-shared' ;; + xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' diff --git a/var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.2_2.patch b/var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.2_2.patch new file mode 100644 index 00000000000..871ffe6dd25 --- /dev/null +++ b/var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.2_2.patch @@ -0,0 +1,11 @@ +--- a/configure ++++ b/configure +@@ -22237,6 +22237,8 @@ _LT_EOF + whole_archive_flag_spec_F77= + tmp_sharedflag='--shared' ;; + nagfor*) # NAGFOR 5.3 ++ whole_archive_flag_spec_F77='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' ++ compiler_needs_object_F77=yes + tmp_sharedflag='-Wl,-shared' ;; + xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' diff --git a/var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.6.patch b/var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.6.patch new file mode 100644 index 00000000000..50f73f2dde3 --- /dev/null +++ b/var/spack/repos/builtin/packages/mpich/nag_libtool_2.4.6.patch @@ -0,0 +1,69 @@ +--- a/confdb/ltmain.sh ++++ b/confdb/ltmain.sh +@@ -7867,6 +7867,13 @@ func_mode_link () + # Convert "-framework foo" to "foo.ltframework" + if test -n "$inherited_linker_flags"; then + tmp_inherited_linker_flags=`$ECHO "$inherited_linker_flags" | $SED 's/-framework \([^ $]*\)/\1.ltframework/g'` ++ ++ # Additionally convert " -pthread" to " -Wl,-pthread" for nagfor ++ func_cc_basename $CC ++ case $func_cc_basename_result in ++ nagfor*) tmp_inherited_linker_flags=`$ECHO "$tmp_inherited_linker_flags" | $SED 's/ -pthread/ -Wl,-pthread/g'` ;; ++ esac ++ + for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do + case " $new_inherited_linker_flags " in + *" $tmp_inherited_linker_flag "*) ;; +@@ -8886,7 +8893,8 @@ func_mode_link () + xlcverstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision" + verstring="-compatibility_version $minor_current -current_version $minor_current.$revision" + # On Darwin other compilers +- case $CC in ++ func_cc_basename $CC ++ case $func_cc_basename_result in + nagfor*) + verstring="$wl-compatibility_version $wl$minor_current $wl-current_version $wl$minor_current.$revision" + ;; +@@ -9498,6 +9506,13 @@ EOF + ;; + esac + ++ # Time to revert the changes made for nagfor. ++ func_cc_basename $CC ++ case $func_cc_basename_result in ++ nagfor*) ++ new_inherited_linker_flags=`$ECHO " $new_inherited_linker_flags" | $SED 's% -Wl,-pthread% -pthread%g'` ;; ++ esac ++ + # move library search paths that coincide with paths to not yet + # installed libraries to the beginning of the library search list + new_libs= +--- a/configure ++++ b/configure +@@ -12583,6 +12583,8 @@ _LT_EOF + whole_archive_flag_spec= + tmp_sharedflag='--shared' ;; + nagfor*) # NAGFOR 5.3 ++ whole_archive_flag_spec='$wl--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive' ++ compiler_needs_object=yes + tmp_sharedflag='-Wl,-shared' ;; + xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' +@@ -20684,6 +20686,8 @@ _LT_EOF + whole_archive_flag_spec_FC= + tmp_sharedflag='--shared' ;; + nagfor*) # NAGFOR 5.3 ++ whole_archive_flag_spec_FC='$wl--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive' ++ compiler_needs_object_FC=yes + tmp_sharedflag='-Wl,-shared' ;; + xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' +@@ -23958,6 +23962,8 @@ _LT_EOF + whole_archive_flag_spec_F77= + tmp_sharedflag='--shared' ;; + nagfor*) # NAGFOR 5.3 ++ whole_archive_flag_spec_F77='$wl--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` $wl--no-whole-archive' ++ compiler_needs_object_F77=yes + tmp_sharedflag='-Wl,-shared' ;; + xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) + tmp_sharedflag='-qmkshrobj' diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py index 0980c668185..8360046ab43 100644 --- a/var/spack/repos/builtin/packages/mpich/package.py +++ b/var/spack/repos/builtin/packages/mpich/package.py @@ -63,6 +63,9 @@ class Mpich(AutotoolsPackage): ) variant('pci', default=(sys.platform != 'darwin'), description="Support analyzing devices on PCI bus") + variant('libxml2', default=True, + description='Use libxml2 for XML support instead of the custom ' + 'minimalistic implementation') provides('mpi') provides('mpi@:3.0', when='@3:') @@ -86,6 +89,23 @@ class Mpich(AutotoolsPackage): sha256='c7d4ecf865dccff5b764d9c66b6a470d11b0b1a5b4f7ad1ffa61079ad6b5dede', when='@3.3:3.3.0') + # This patch for Libtool 2.4.2 enables shared libraries for NAG and is + # applied by MPICH starting version 3.1. + patch('nag_libtool_2.4.2_0.patch', when='@:3.0%nag') + + # This patch for Libtool 2.4.2 fixes the problem with '-pthread' flag and + # enables convenience libraries for NAG. Starting version 3.1, the order of + # checks for FC and F77 is changed, therefore we need to apply the patch in + # two steps (the patch files can be merged once the support for versions + # 3.1 and older is dropped). + patch('nag_libtool_2.4.2_1.patch', when='@:3.1.3%nag') + patch('nag_libtool_2.4.2_2.patch', when='@:3.1.3%nag') + + # This patch for Libtool 2.4.6 does the same as the previous two. The + # problem is not fixed upstream yet and the upper version constraint is + # given just to avoid application of the patch to the develop version. + patch('nag_libtool_2.4.6.patch', when='@3.1.4:3.3%nag') + depends_on('findutils', type='build') depends_on('pkgconfig', type='build') @@ -96,8 +116,14 @@ class Mpich(AutotoolsPackage): depends_on('ucx', when='netmod=ucx') - depends_on('libpciaccess', when="+pci") - depends_on('libxml2') + # The dependencies on libpciaccess and libxml2 come from the embedded + # hwloc, which, before version 3.3, was used only for Hydra. + depends_on('libpciaccess', when="@:3.2+hydra+pci") + depends_on('libxml2', when='@:3.2+hydra+libxml2') + + # Starting with version 3.3, MPICH uses hwloc directly. + depends_on('libpciaccess', when="@3.3:+pci") + depends_on('libxml2', when='@3.3:+libxml2') # Starting with version 3.3, Hydra can use libslurm for nodelist parsing depends_on('slurm', when='+slurm') @@ -119,6 +145,12 @@ class Mpich(AutotoolsPackage): conflicts('pmi=pmi2', when='device=ch3 netmod=ofi') conflicts('pmi=pmix', when='device=ch3') + # MPICH does not require libxml2 and libpciaccess for versions before 3.3 + # when ~hydra is set: prevent users from setting +libxml2 and +pci in this + # case to avoid generating an identical MPICH installation. + conflicts('+pci', when='@:3.2~hydra') + conflicts('+libxml2', when='@:3.2~hydra') + def setup_build_environment(self, env): env.unset('F90') env.unset('F90FLAGS') @@ -181,6 +213,7 @@ def die_without_fortran(self): def configure_args(self): spec = self.spec config_args = [ + '--disable-silent-rules', '--enable-shared', '--with-pm={0}'.format('hydra' if '+hydra' in spec else 'no'), '--{0}-romio'.format('enable' if '+romio' in spec else 'disable'), @@ -234,4 +267,11 @@ def configure_args(self): config_args.append('--with-ucx={0}'.format( spec['ucx'].prefix)) + # In other cases the argument is redundant. + if '@:3.2+hydra' in spec or '@3.3:' in spec: + # The root configure script passes the argument to the configure + # scripts of all instances of hwloc (there are three copies of it: + # for hydra, for hydra2, and for MPICH itself). + config_args += self.enable_or_disable('libxml2') + return config_args From 787f89b7db20335704bf17fe81cc3960d39bdda7 Mon Sep 17 00:00:00 2001 From: Greg Sjaardema Date: Tue, 17 Mar 2020 19:02:31 -0600 Subject: [PATCH 077/377] SEACAS: Add versions 2020-03-16 and 2020-01-16 (#15525) --- var/spack/repos/builtin/packages/seacas/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/seacas/package.py b/var/spack/repos/builtin/packages/seacas/package.py index 0e5ac9b72ac..f9790370a07 100644 --- a/var/spack/repos/builtin/packages/seacas/package.py +++ b/var/spack/repos/builtin/packages/seacas/package.py @@ -26,6 +26,8 @@ class Seacas(CMakePackage): # ###################### Versions ########################## version('master', branch='master') + version('2020-03-16', sha256='2eb404f3dcb17c3e7eacf66978372830d40ef3722788207741fcd48417807af6') + version('2020-01-16', sha256='5ae84f61e410a4f3f19153737e0ac0493b144f20feb1bbfe2024f76613d8bff5') version('2019-12-18', sha256='f82cfa276ebc5fe6054852383da16eba7a51c81e6640c73b5f01fc3109487c6f') version('2019-10-14', sha256='ca4cf585cdbc15c25f302140fe1f61ee1a30d72921e032b9a854492b6c61fb91') version('2019-08-20', sha256='a82c1910c2b37427616dc3716ca0b3c1c77410db6723aefb5bea9f47429666e5') From 847d5d345964596c8c11893dfcbe4177adf3f088 Mon Sep 17 00:00:00 2001 From: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com> Date: Tue, 17 Mar 2020 18:45:56 -0700 Subject: [PATCH 078/377] update checksum for intel-tbb@2020.1 (#15528) --- var/spack/repos/builtin/packages/intel-tbb/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/intel-tbb/package.py b/var/spack/repos/builtin/packages/intel-tbb/package.py index 72ed301bd85..6dbb1971f5c 100644 --- a/var/spack/repos/builtin/packages/intel-tbb/package.py +++ b/var/spack/repos/builtin/packages/intel-tbb/package.py @@ -21,7 +21,7 @@ class IntelTbb(Package): # Note: when adding new versions, please check and update the # patches, filters and url_for_version() below as needed. - version('2020.1', sha256='48d51c63b16787af54e1ee4aaf30042087f20564b4eecf9a032d5568bc2f0bf8') + version('2020.1', sha256='7c96a150ed22bc3c6628bc3fef9ed475c00887b26d37bca61518d76a56510971') version('2020.0', sha256='8eed2377ac62e6ac10af5a8303ce861e4525ffe491a061b48e8fe094fc741ce9') version('2019.9', sha256='15652f5328cf00c576f065e5cd3eaf3317422fe82afb67a9bcec0dc065bd2abe') version('2019.8', sha256='7b1fd8caea14be72ae4175896510bf99c809cd7031306a1917565e6de7382fba') From 586609102bde55d495d79ff4c5457a38224e7c8c Mon Sep 17 00:00:00 2001 From: Jim Galarowicz Date: Wed, 18 Mar 2020 08:45:17 -0500 Subject: [PATCH 079/377] Previous qt package file changes broke the openspeedshop gui build. (#15471) * Previous qt changes broke the openspeedshop gui build. This puts back the changes that caused the breakage. * Update the qt version to be more robust. Co-authored-by: Galarowicz, James --- var/spack/repos/builtin/packages/openspeedshop/package.py | 2 +- var/spack/repos/builtin/packages/qt/package.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py index 56f9b0c6891..a0cf6e46cdd 100644 --- a/var/spack/repos/builtin/packages/openspeedshop/package.py +++ b/var/spack/repos/builtin/packages/openspeedshop/package.py @@ -96,7 +96,7 @@ class Openspeedshop(CMakePackage): depends_on("libxml2") - depends_on("qt@3", when='gui=qt3') + depends_on("qt@3:3.9", when='gui=qt3') # Dependencies for the openspeedshop cbtf packages. depends_on("cbtf@develop", when='@develop', type=('build', 'link', 'run')) diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index c07aa5c86eb..1ffb17ceb4d 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -132,9 +132,10 @@ class Qt(Package): depends_on("sqlite+column_metadata", when='+sql%intel', type=('build', 'run')) depends_on("libpng@1.2.57", when='@3') + depends_on("libsm", when='@3') depends_on("pcre+multibyte", when='@5.0:5.8') depends_on("inputproto", when='@:5.8') - depends_on("openssl@:1.0.999", when='@:5.9+ssl') + depends_on("openssl@:1.0.999", when='@4:5.9+ssl') depends_on("glib", when='@4:') depends_on("libpng", when='@4:') From 958f26073efe340d5418e97d01ef82e9a3fbd166 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Wed, 18 Mar 2020 08:47:01 -0500 Subject: [PATCH 080/377] openPMD-api: HDF5 1.12.0 Support (#15530) Fix API breakage in HDF5 1.12.0 for released versions. --- .../packages/openpmd-api/hdf5-1.12.0.patch | 23 +++++++++++++++++++ .../builtin/packages/openpmd-api/package.py | 4 ++++ 2 files changed, 27 insertions(+) create mode 100644 var/spack/repos/builtin/packages/openpmd-api/hdf5-1.12.0.patch diff --git a/var/spack/repos/builtin/packages/openpmd-api/hdf5-1.12.0.patch b/var/spack/repos/builtin/packages/openpmd-api/hdf5-1.12.0.patch new file mode 100644 index 00000000000..f190f12ff1b --- /dev/null +++ b/var/spack/repos/builtin/packages/openpmd-api/hdf5-1.12.0.patch @@ -0,0 +1,23 @@ +From 61ccc18cdd478c6281466f1f77de416559234dd8 Mon Sep 17 00:00:00 2001 +From: Axel Huebl +Date: Tue, 17 Mar 2020 10:51:20 -0700 +Subject: [PATCH] HDF5: H5Oget_info Compatibility + +Update to work with HDF5 1.12.0 signature. +Macro for older releases. +--- + src/IO/HDF5/HDF5IOHandler.cpp | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/src/IO/HDF5/HDF5IOHandler.cpp b/src/IO/HDF5/HDF5IOHandler.cpp +index 7043861b..c125e1f4 100644 +--- a/src/IO/HDF5/HDF5IOHandler.cpp ++++ b/src/IO/HDF5/HDF5IOHandler.cpp +@@ -1535,3 +1535,7 @@ void HDF5IOHandlerImpl::listAttributes(Writable* writable, + H5O_info_t object_info; + herr_t status; ++#if H5_VERSION_GE(1,12,0) ++ status = H5Oget_info(node_id, &object_info, H5O_INFO_NUM_ATTRS); ++#else + status = H5Oget_info(node_id, &object_info); ++#endif diff --git a/var/spack/repos/builtin/packages/openpmd-api/package.py b/var/spack/repos/builtin/packages/openpmd-api/package.py index 0def9bc1f4c..1459a11271e 100644 --- a/var/spack/repos/builtin/packages/openpmd-api/package.py +++ b/var/spack/repos/builtin/packages/openpmd-api/package.py @@ -55,6 +55,10 @@ class OpenpmdApi(CMakePackage): extends('python', when='+python') + # Fix breaking HDF5 1.12.0 API + # https://github.com/openPMD/openPMD-api/pull/696 + patch('hdf5-1.12.0.patch', when='@:0.11.0 +hdf5') + def cmake_args(self): spec = self.spec From e59b506506ec44768fc5372b2cd063138f4ea4e0 Mon Sep 17 00:00:00 2001 From: "Nichols A. Romero" Date: Wed, 18 Mar 2020 11:21:48 -0500 Subject: [PATCH 081/377] QMCPACK Update March 2020 (#15511) * Clean-up description of variants. * Support AFQMC with CUDA. --- .../repos/builtin/packages/qmcpack/package.py | 22 ++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/qmcpack/package.py b/var/spack/repos/builtin/packages/qmcpack/package.py index 64a0e2c2837..ba67282c0c2 100644 --- a/var/spack/repos/builtin/packages/qmcpack/package.py +++ b/var/spack/repos/builtin/packages/qmcpack/package.py @@ -44,11 +44,10 @@ class Qmcpack(CMakePackage, CudaPackage): description='Build the complex (general twist/k-point) version') variant('mixed', default=False, description='Build the mixed precision (mixture of single and ' - 'double precision) version for gpu and cpu') + 'double precision) version') variant('soa', default=True, description='Build with Structure-of-Array instead of ' - 'Array-of-Structure code. Only for CPU code' - 'and only in mixed precision') + 'Array-of-Structure code. Only for CPU code') variant('timers', default=False, description='Build with support for timers') variant('da', default=False, @@ -58,11 +57,19 @@ class Qmcpack(CMakePackage, CudaPackage): variant('qe', default=False, description='Install with patched Quantum Espresso 6.4.1') variant('afqmc', default=False, - description='Install with AFQMC support') + description='Install with AFQMC support. NOTE that if used in ' + 'combination with CUDA, only AFQMC will have CUDA.') + # Notes about CUDA-centric peculiarities: + # # cuda variant implies mixed precision variant by default, but there is # no way to express this in variant syntax, need something like # variant('+mixed', default=True, when='+cuda', description="...") + # + # cuda+afqmc variant will not build the legacy CUDA code in real-space + # QMCPACK. This is due to a conflict in the build system. This is not + # worth fixing since the legacy CUDA code, will be superseded + # by the OpenMP 4.5 code. # high-level variant conflicts conflicts( @@ -251,7 +258,12 @@ def cmake_args(self): # tested. if '+cuda' in spec: - args.append('-DQMC_CUDA=1') + # Cannot support both CUDA builds at the same time, see + # earlier notes in this package. + if '+afqmc' in spec: + args.append('-DENABLE_CUDA=1') + else: + args.append('-DQMC_CUDA=1') cuda_arch_list = spec.variants['cuda_arch'].value cuda_arch = cuda_arch_list[0] if len(cuda_arch_list) > 1: From 57ad02ad43efdd465964a22fcceecaa48ad3d8a5 Mon Sep 17 00:00:00 2001 From: Brian Van Essen Date: Wed, 18 Mar 2020 09:46:49 -0700 Subject: [PATCH 082/377] Added a package for the DiHydrogen distributed linear algebra library. (#15426) * Added a package for the DiHydrogen distributed linear algebra library. * Updated recipe to provide cuda architecture constaints. * Addressed reviewer comments * Fixed flake 8 --- .../builtin/packages/dihydrogen/package.py | 111 ++++++++++++++++++ 1 file changed, 111 insertions(+) create mode 100644 var/spack/repos/builtin/packages/dihydrogen/package.py diff --git a/var/spack/repos/builtin/packages/dihydrogen/package.py b/var/spack/repos/builtin/packages/dihydrogen/package.py new file mode 100644 index 00000000000..6de0cfb5164 --- /dev/null +++ b/var/spack/repos/builtin/packages/dihydrogen/package.py @@ -0,0 +1,111 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Dihydrogen(CMakePackage, CudaPackage): + """DiHydrogen is the second version of the Hydrogen fork of the + well-known distributed linear algebra library, + Elemental. DiHydrogen aims to be a basic distributed + multilinear algebra interface with a particular emphasis on the + needs of the distributed machine learning effort, LBANN.""" + + homepage = "https://github.com/LLNL/DiHydrogen.git" + git = "https://github.com/LLNL/DiHydrogen.git" + + maintainers = ['bvanessen'] + + version('master', branch='master') + + variant('al', default=True, + description='Builds with Aluminum communication library') + variant('developer', default=False, + description='Enable extra warnings and force tests to be enabled.') + variant('half', default=False, + description='Enable FP16 support on the CPU.') + variant('legacy', default=False, + description='Enable the legacy DistConv code branch.') + variant('nvshmem', default=False, + description='Builds with support for NVSHMEM') + variant('openmp', default=False, + description='Enable CPU acceleration with OpenMP threads.') + variant('rocm', default=False, + description='Enable ROCm/HIP language features.') + variant('shared', default=True, + description='Enables the build of shared libraries') + + # Override the default set of CUDA architectures with the relevant + # subset from lib/spack/spack/build_systems/cuda.py + cuda_arch_values = [ + '60', '61', '62', + '70', '72', '75', + ] + variant('cuda_arch', + description='CUDA architecture', + values=spack.variant.auto_or_any_combination_of(*cuda_arch_values)) + + depends_on('mpi') + depends_on('catch2', type='test') + + depends_on('aluminum', when='+al ~cuda') + depends_on('aluminum +gpu +nccl +mpi_cuda', when='+al +cuda') + + depends_on('cuda', when=('+cuda' or '+legacy')) + depends_on('cudnn', when=('+cuda' or '+legacy')) + depends_on('cub', when=('+cuda' or '+legacy')) + + # Legacy builds require cuda + conflicts('~cuda', when='+legacy') + + depends_on('half', when='+half') + + generator = 'Ninja' + depends_on('ninja', type='build') + depends_on('cmake@3.14.0:', type='build') + + illegal_cuda_arch_values = [ + '10', '11', '12', '13', + '20', '21', + '30', '32', '35', '37', + '50', '52', '53', + ] + for value in illegal_cuda_arch_values: + conflicts('cuda_arch=' + value) + + @property + def libs(self): + shared = True if '+shared' in self.spec else False + return find_libraries( + 'libH2Core', root=self.prefix, shared=shared, recursive=True + ) + + def cmake_args(self): + spec = self.spec + + args = [ + '-DCMAKE_INSTALL_MESSAGE:STRING=LAZY', + '-DBUILD_SHARED_LIBS:BOOL=%s' % ('+shared' in spec), + '-DH2_ENABLE_CUDA=%s' % ('+cuda' in spec), + '-DH2_ENABLE_DISTCONV_LEGACY=%s' % ('+legacy' in spec), + '-DH2_ENABLE_OPENMP=%s' % ('+openmp' in spec), + '-DH2_ENABLE_FP16=%s' % ('+half' in spec), + '-DH2_ENABLE_HIP_ROCM=%s' % ('+rocm' in spec), + '-DH2_DEVELOPER_BUILD=%s' % ('+developer' in spec), + ] + + if '+cuda' in spec: + cuda_arch = spec.variants['cuda_arch'].value + if len(cuda_arch) == 1 and cuda_arch[0] == 'auto': + args.append('-DCMAKE_CUDA_FLAGS=-arch=sm_60') + else: + cuda_arch = [x for x in spec.variants['cuda_arch'].value + if x != 'auto'] + if cuda_arch: + args.append('-DCMAKE_CUDA_FLAGS={0}'.format( + ' '.join(self.cuda_flags(cuda_arch)) + )) + + return args From 6993b81bfd7fda08bedc709977d139fc2c9e688d Mon Sep 17 00:00:00 2001 From: Amjad Kotobi Date: Wed, 18 Mar 2020 17:49:50 +0100 Subject: [PATCH 083/377] Add package anaconda3 (#15404) --- .../builtin/packages/anaconda3/package.py | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 var/spack/repos/builtin/packages/anaconda3/package.py diff --git a/var/spack/repos/builtin/packages/anaconda3/package.py b/var/spack/repos/builtin/packages/anaconda3/package.py new file mode 100644 index 00000000000..2925b0a4583 --- /dev/null +++ b/var/spack/repos/builtin/packages/anaconda3/package.py @@ -0,0 +1,53 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +from os.path import split + + +class Anaconda3(Package): + """ + Anaconda is a free and open-source distribution of the Python and R + programming languages for scientific computing, that aims to simplify + package management and deployment. Package versions are managed by + the package management system conda. + """ + homepage = "https://www.anaconda.com" + url = "https://repo.anaconda.com/archive/Anaconda3-2019.10-Linux-x86_64.sh" + + maintainers = ['ajkotobi'] + + version('2019.10', sha256='46d762284d252e51cd58a8ca6c8adc9da2eadc82c342927b2f66ed011d1d8b53', expand=False) + version('2019.07', sha256='69581cf739365ec7fb95608eef694ba959d7d33b36eb961953f2b82cb25bdf5a', expand=False) + version('2019.03', sha256='45c851b7497cc14d5ca060064394569f724b67d9b5f98a926ed49b834a6bb73a', expand=False) + version('2018.12', sha256='1019d0857e5865f8a6861eaf15bfe535b87e92b72ce4f531000dc672be7fce00', expand=False) + version('5.3.1', sha256='d4c4256a8f46173b675dd6a62d12f566ed3487f932bab6bb7058f06c124bcc27', expand=False) + version('5.3.0', sha256='cfbf5fe70dd1b797ec677e63c61f8efc92dad930fd1c94d60390bb07fdc09959', expand=False) + version('5.2.0', sha256='09f53738b0cd3bb96f5b1bac488e5528df9906be2480fe61df40e0e0d19e3d48', expand=False) + version('5.1.0', sha256='7e6785caad25e33930bc03fac4994a434a21bc8401817b7efa28f53619fa9c29', expand=False) + version('5.0.1', sha256='55e4db1919f49c92d5abbf27a4be5986ae157f074bf9f8238963cd4582a4068a', expand=False) + version('5.0.0.1', sha256='092c92427f44687d789a41922ce8426fbdc3c529cc9d6d4ee6de5b62954b93b2', expand=False) + version('5.0.0', sha256='67f5c20232a3e493ea3f19a8e273e0618ab678fa14b03b59b1783613062143e9', expand=False) + version('4.4.0', sha256='3301b37e402f3ff3df216fe0458f1e6a4ccbb7e67b4d626eae9651de5ea3ab63', expand=False) + version('4.3.1', sha256='4447b93d2c779201e5fb50cfc45de0ec96c3804e7ad0fe201ab6b99f73e90302', expand=False) + version('4.3.0', sha256='e9169c3a5029aa820393ac92704eb9ee0701778a085ca7bdc3c57b388ac1beb6', expand=False) + version('4.2.0', sha256='73b51715a12b6382dd4df3dd1905b531bd6792d4aa7273b2377a0436d45f0e78', expand=False) + version('4.1.1', sha256='4f5c95feb0e7efeadd3d348dcef117d7787c799f24b0429e45017008f3534e55', expand=False) + version('4.1.0', sha256='11d32cf4026603d3b327dc4299863be6b815905ff51a80329085e1bb9f96c8bd', expand=False) + version('4.0.0', sha256='36a558a1109868661a5735f5f32607643f6dc05cf581fefb1c10fb8abbe22f39', expand=False) + version('2.5.0', sha256='addadcb927f15cb0b5b6e36890563d3352a8ff6a901ea753d389047d274a29a9', expand=False) + version('2.4.1', sha256='0735e69199fc37135930ea2fd4fb6ad0adef215a2a7ba9fd6b0a0a4daaadb1cf', expand=False) + version('2.4.0', sha256='fb4e480059e991f2fa632b5a9bcdd284c7f0677814cd719c11d524453f96a40d', expand=False) + version('2.3.0', sha256='3be5410b2d9db45882c7de07c554cf4f1034becc274ec9074b23fd37a5c87a6f', expand=False) + version('2.2.0', sha256='4aac68743e7706adb93f042f970373a6e7e087dbf4b02ac467c94ca4ce33d2d1', expand=False) + version('2.1.0', sha256='af3225ccbe8df0ffb918939e009aa57740e35058ebf9dfcf5fec794a77556c3c', expand=False) + version('2.0.1', sha256='3c3b834793e461f3316ad1d9a9178c67859a9d74aaf7bcade076f04134dd1e26', expand=False) + version('2.0.0', sha256='57ce4f97e300cf94c5724f72d992e9eecef708fdaa13bc672ae9779773056540', expand=False) + + def install(self, spec, prefix): + + dir, anaconda_script = split(self.stage.archive_file) + bash = which('bash') + bash(anaconda_script, '-b', '-f', '-p', self.prefix) From 8ad366a978d8a4e209fc19ea110fcb856c4c728d Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 18 Mar 2020 12:50:12 -0400 Subject: [PATCH 084/377] py-numpy: add 1.18.2 (#15546) --- var/spack/repos/builtin/packages/py-numpy/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py index c685a6fb4cc..639ff48d8e5 100644 --- a/var/spack/repos/builtin/packages/py-numpy/package.py +++ b/var/spack/repos/builtin/packages/py-numpy/package.py @@ -16,7 +16,7 @@ class PyNumpy(PythonPackage): number capabilities""" homepage = "https://numpy.org/" - url = "https://pypi.io/packages/source/n/numpy/numpy-1.18.1.zip" + url = "https://pypi.io/packages/source/n/numpy/numpy-1.18.2.zip" git = "https://github.com/numpy/numpy.git" maintainers = ['adamjstewart'] @@ -30,6 +30,7 @@ class PyNumpy(PythonPackage): ] version('master', branch='master') + version('1.18.2', sha256='e7894793e6e8540dbeac77c87b489e331947813511108ae097f1715c018b8f3d') version('1.18.1', sha256='b6ff59cee96b454516e47e7721098e6ceebef435e3e21ac2d6c3b8b02628eb77') version('1.18.0', sha256='a9d72d9abaf65628f0f31bbb573b7d9304e43b1e6bbae43149c17737a42764c4') version('1.17.5', sha256='16507ba6617f62ae3c6ab1725ae6f550331025d4d9a369b83f6d5a470446c342') From 4d449790d04abe77d647903c6722ef9154318ab7 Mon Sep 17 00:00:00 2001 From: Robert Kalescky Date: Wed, 18 Mar 2020 12:59:27 -0500 Subject: [PATCH 085/377] r-openssl requires C99. (#15541) --- var/spack/repos/builtin/packages/r-openssl/package.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py index 36ddd5ed7d6..71f648b480c 100644 --- a/var/spack/repos/builtin/packages/r-openssl/package.py +++ b/var/spack/repos/builtin/packages/r-openssl/package.py @@ -30,3 +30,8 @@ class ROpenssl(RPackage): depends_on('r-askpass', when='@1.2:', type=('build', 'run')) depends_on('openssl@1.0.1:') + + def flag_handler(self, name, flags): + if name == 'cflags': + flags.append(self.compiler.c99_flag) + return (flags, None, None) From 6bb8b92bc303829faac7cc7d715c9fd9b39cc423 Mon Sep 17 00:00:00 2001 From: Robert Kalescky Date: Wed, 18 Mar 2020 12:59:52 -0500 Subject: [PATCH 086/377] Remove trailing newline. (#15539) --- var/spack/repos/builtin/packages/r-sys/package.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/var/spack/repos/builtin/packages/r-sys/package.py b/var/spack/repos/builtin/packages/r-sys/package.py index bd9aff95195..1901e54354b 100644 --- a/var/spack/repos/builtin/packages/r-sys/package.py +++ b/var/spack/repos/builtin/packages/r-sys/package.py @@ -18,3 +18,8 @@ class RSys(RPackage): list_url = "https://cloud.r-project.org/src/contrib/Archive/sys" version('3.2', sha256='2819498461fe2ce83d319d1a47844e86bcea6d01d10861818dba289e7099bbcc') + + def flag_handler(self, name, flags): + if name == 'cflags': + flags.append(self.compiler.c99_flag) + return (flags, None, None) From 209ec03f7e2700b184705007218792d21609e2d9 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Thu, 19 Mar 2020 03:00:28 +0900 Subject: [PATCH 087/377] xts: add some dependencies. (#15537) --- .../repos/builtin/packages/xts/package.py | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/var/spack/repos/builtin/packages/xts/package.py b/var/spack/repos/builtin/packages/xts/package.py index 19149f9ec9f..89dcc96bf76 100644 --- a/var/spack/repos/builtin/packages/xts/package.py +++ b/var/spack/repos/builtin/packages/xts/package.py @@ -15,14 +15,17 @@ class Xts(AutotoolsPackage): version('0.99.1', sha256='d04d987b9a9f8b3921dfe8de8577d0c2a0f21d2c4c3196948fc9805838a352e6') - depends_on('libx11') - depends_on('libxext') - depends_on('libxi') - depends_on('libxtst') - depends_on('libxau') - depends_on('libxt') - depends_on('libxmu') - depends_on('libxaw') + depends_on('libx11', type='link') + depends_on('libxext', type='link') + depends_on('libxi', type='link') + depends_on('libxtst', type='link') + depends_on('libxau', type='link') + depends_on('libxt', type='link') + depends_on('libxmu', type='link') + depends_on('libxaw', type='link') + depends_on('inputproto', type='link') + depends_on('recordproto', type='link') + depends_on('fixesproto', type='link') depends_on('xtrans', type='build') depends_on('bdftopcf', type='build') From cfc5f3caec7436b07581efdb166316d42f3f8477 Mon Sep 17 00:00:00 2001 From: gauthier12 <45069706+gauthier12@users.noreply.github.com> Date: Wed, 18 Mar 2020 19:01:04 +0100 Subject: [PATCH 088/377] adding the fortran option for hdf5 dependency for comptatibility with petsc requirement (#15536) --- var/spack/repos/builtin/packages/mofem-cephas/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/mofem-cephas/package.py b/var/spack/repos/builtin/packages/mofem-cephas/package.py index 28e00565d2f..24e88150841 100644 --- a/var/spack/repos/builtin/packages/mofem-cephas/package.py +++ b/var/spack/repos/builtin/packages/mofem-cephas/package.py @@ -42,7 +42,7 @@ class MofemCephas(CMakePackage): depends_on("parmetis") # Fixed version of hdf5, to remove some problems with dependent # packages, f.e. MED format - depends_on("hdf5@:1.8.19+hl+mpi") + depends_on("hdf5@:1.8.19+hl+mpi+fortran") depends_on("petsc@:3.9.3+mumps+mpi") depends_on('slepc', when='+slepc') depends_on("moab") From 0fce7df1e93830464facd14e9c2bf75a1b1ba7c7 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Thu, 19 Mar 2020 03:02:35 +0900 Subject: [PATCH 089/377] xsetpointer: fix wrong dependency type. (#15534) --- var/spack/repos/builtin/packages/xsetpointer/package.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/xsetpointer/package.py b/var/spack/repos/builtin/packages/xsetpointer/package.py index 57775a6a192..cfd89eb061e 100644 --- a/var/spack/repos/builtin/packages/xsetpointer/package.py +++ b/var/spack/repos/builtin/packages/xsetpointer/package.py @@ -14,9 +14,9 @@ class Xsetpointer(AutotoolsPackage): version('1.0.1', sha256='54be93b20fd6f1deac67246d6e214a60b02dcfbf05295e43751f7a04edb986ac') - depends_on('libxi') - depends_on('libx11') + depends_on('libxi', type='link') + depends_on('libx11', type='link') + depends_on('inputproto@1.4:', type='link') - depends_on('inputproto@1.4:', type='build') depends_on('pkgconfig', type='build') depends_on('util-macros', type='build') From 530e864671397c5cfa9c3fbe62048d046b30ec33 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Thu, 19 Mar 2020 03:03:03 +0900 Subject: [PATCH 090/377] triangle: add X11 dependency. (#15533) --- var/spack/repos/builtin/packages/triangle/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/triangle/package.py b/var/spack/repos/builtin/packages/triangle/package.py index 882b8b472b3..f8703f33b31 100644 --- a/var/spack/repos/builtin/packages/triangle/package.py +++ b/var/spack/repos/builtin/packages/triangle/package.py @@ -18,6 +18,8 @@ class Triangle(Package): version('1.6', sha256='1766327add038495fa3499e9b7cc642179229750f7201b94f8e1b7bee76f8480') + depends_on('libx11', type='link') + def install(self, spec, prefix): make() mkdirp(prefix.bin) From c3434e230a127d6cce7331a0c95d0f4e7f1fb789 Mon Sep 17 00:00:00 2001 From: darmac Date: Thu, 19 Mar 2020 02:04:51 +0800 Subject: [PATCH 091/377] update util-linux to version: 2.33:2.35.1 (#15529) --- var/spack/repos/builtin/packages/util-linux/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/util-linux/package.py b/var/spack/repos/builtin/packages/util-linux/package.py index 49afb16f545..b95f8222e2f 100644 --- a/var/spack/repos/builtin/packages/util-linux/package.py +++ b/var/spack/repos/builtin/packages/util-linux/package.py @@ -14,6 +14,10 @@ class UtilLinux(AutotoolsPackage): list_url = "https://www.kernel.org/pub/linux/utils/util-linux" list_depth = 1 + version('2.35.1', sha256='37ac05d82c6410d89bc05d43cee101fefc8fe6cf6090b3ce7a1409a6f35db606') + version('2.35', sha256='98acab129a8490265052e6c1e033ca96d68758a13bb7fcd232c06bf16cc96238') + version('2.34', sha256='b62c92e5e1629642113cd41cec1ee86d1ee7e36b8ffe8ec3ac89c11797e9ac25') + version('2.33', sha256='952fb0d3498e81bd67b3c48e283c80cb12c719bc2357ec5801e7d420991ad319') version('2.29.2', sha256='29ccdf91d2c3245dc705f0ad3bf729ac41d8adcdbeff914e797c552ecb04a4c7') version('2.29.1', sha256='a6a7adba65a368e6dad9582d9fbedee43126d990df51266eaee089a73c893653') version('2.25', sha256='7e43273a9e2ab99b5a54ac914fddf5d08ba7ab9b114c550e9f03474672bd23a1') From 73321dd3ea81f18ec5430f45916fa8007e83daf7 Mon Sep 17 00:00:00 2001 From: Greg Sjaardema Date: Wed, 18 Mar 2020 12:09:28 -0600 Subject: [PATCH 092/377] CGNS: Version update (#15523) * CGNS: Version update The CGNS library has several new versions. There was a format-changing change in 3.4.0 which was removed for 3.4.1. The change was then added again and released with a change to the major version (4.0.0). Note that 4.0.0 should be close to the functionality of 3.4.0. * CGNS: Add shared variant Added the `shared`variant to make the CMake build correctly pick up the RPATH settings. --- var/spack/repos/builtin/packages/cgns/package.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/cgns/package.py b/var/spack/repos/builtin/packages/cgns/package.py index 4e8a1126346..a4f6aa05826 100644 --- a/var/spack/repos/builtin/packages/cgns/package.py +++ b/var/spack/repos/builtin/packages/cgns/package.py @@ -18,6 +18,10 @@ class Cgns(CMakePackage): version('develop', branch='develop') version('master', branch='master') + version('4.1.1', sha256='055d345c3569df3ae832fb2611cd7e0bc61d56da41b2be1533407e949581e226') + version('4.1.0', sha256='4674de1fac3c47998248725fd670377be497f568312c5903d1bb8090a3cf4da0') + version('4.0.0', sha256='748585a8e52dff4d250d6b603e6b847d05498e4566aba2dc3d7a7d85c4d55849') + version('3.4.1', sha256='d32595e7737b9332243bd3de1eb8c018a272f620f09b289dea8292eba1365994') version('3.4.0', sha256='6372196caf25b27d38cf6f056258cb0bdd45757f49d9c59372b6dbbddb1e05da') version('3.3.1', sha256='81093693b2e21a99c5640b82b267a495625b663d7b8125d5f1e9e7aaa1f8d469') version('3.3.0', sha256='8422c67994f8dc6a2f201523a14f6c7d7e16313bdd404c460c16079dbeafc662') @@ -27,6 +31,7 @@ class Cgns(CMakePackage): variant('scoping', default=True, description='Enable scoping') variant('mpi', default=True, description='Enable parallel cgns') variant('int64', default=False, description='Build with 64-bit integers') + variant('shared', default=True, description='Enable shared library') depends_on('hdf5~mpi', when='+hdf5~mpi') depends_on('hdf5+mpi', when='+hdf5+mpi') @@ -44,7 +49,9 @@ def cmake_args(self): '-DCGNS_ENABLE_PARALLEL:BOOL=%s' % ( 'ON' if '+mpi' in spec else 'OFF'), '-DCGNS_ENABLE_TESTS:BOOL=OFF', - '-DCGNS_BUILD_CGNSTOOLS:BOOL=OFF' + '-DCGNS_BUILD_CGNSTOOLS:BOOL=OFF', + '-DCGNS_BUILD_SHARED:BOOL=%s' % ( + 'ON' if '+shared' in spec else 'OFF') ]) if '+mpi' in spec: From b52b082627bf3a2a3bf8ca15e9229889204197d6 Mon Sep 17 00:00:00 2001 From: darmac Date: Thu, 19 Mar 2020 02:12:02 +0800 Subject: [PATCH 093/377] add new package: userspace-rcu (#15515) --- .../packages/userspace-rcu/examples.patch | 13 ++++++++ .../builtin/packages/userspace-rcu/package.py | 31 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 var/spack/repos/builtin/packages/userspace-rcu/examples.patch create mode 100644 var/spack/repos/builtin/packages/userspace-rcu/package.py diff --git a/var/spack/repos/builtin/packages/userspace-rcu/examples.patch b/var/spack/repos/builtin/packages/userspace-rcu/examples.patch new file mode 100644 index 00000000000..ef65ab4b79a --- /dev/null +++ b/var/spack/repos/builtin/packages/userspace-rcu/examples.patch @@ -0,0 +1,13 @@ +diff --git a/doc/examples/Makefile.am b/doc/examples/Makefile.am +index edf00eb..cd491df 100644 +--- a/doc/examples/Makefile.am ++++ b/doc/examples/Makefile.am +@@ -141,7 +141,7 @@ all-local: + else \ + rel_build_subdir="../"; \ + fi; \ +- $(MAKE) -f dist-files/Makefile CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" AM_CPPFLAGS="$(AM_CPPFLAGS) -I"$${rel_src_subdir}/$(top_srcdir)/include/" -I"$${rel_src_subdir}/$(top_srcdir)/src/" -I"$${rel_build_subdir}$(top_builddir)/include/" -I"$${rel_build_subdir}$(top_builddir)/include/src/"" CFLAGS="$(CFLAGS)" AM_CFLAGS="$(AM_CFLAGS)" LDFLAGS="$(LDFLAGS)" AM_LDFLAGS="$(AM_LDFLAGS) -L../../../src/.libs/ -Wl,-rpath "$(PWD)/../../src/.libs/"" AM_V_P="$(AM_V_P)" AM_V_at="$(AM_V_at)" $(AM_MAKEFLAGS) all; ++ $(MAKE) -f dist-files/Makefile CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" AM_CPPFLAGS="$(AM_CPPFLAGS) -I"$${rel_src_subdir}/$(top_srcdir)/include/" -I"$${rel_src_subdir}/$(top_srcdir)/src/" -I"$${rel_build_subdir}$(top_builddir)/include/" -I"$${rel_build_subdir}$(top_builddir)/include/src/"" CFLAGS="$(CFLAGS)" AM_CFLAGS="$(AM_CFLAGS)" LDFLAGS="$(LDFLAGS)" AM_LDFLAGS="$(AM_LDFLAGS) -L../../../src/.libs/ -Wl,-rpath="$(PWD)/../../src/.libs/"" AM_V_P="$(AM_V_P)" AM_V_at="$(AM_V_at)" $(AM_MAKEFLAGS) all; + + clean-local: + $(AM_V_at)$(MAKE) -f dist-files/Makefile $(AM_MAKEFLAGS) clean; \ diff --git a/var/spack/repos/builtin/packages/userspace-rcu/package.py b/var/spack/repos/builtin/packages/userspace-rcu/package.py new file mode 100644 index 00000000000..be03459d343 --- /dev/null +++ b/var/spack/repos/builtin/packages/userspace-rcu/package.py @@ -0,0 +1,31 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class UserspaceRcu(AutotoolsPackage): + """liburcu is a LGPLv2.1 userspace RCU (read-copy-update) library. This + data synchronization library provides read-side access which scales + linearly with the number of cores.""" + + homepage = "http://liburcu.org/" + url = "https://github.com/urcu/userspace-rcu/archive/v0.11.1.tar.gz" + + version('0.11.1', sha256='a0ed8995edfbeac5f5eb2f152a8f3654040ecfc99a746bfe3da3bccf435b7d5d') + version('0.11.0', sha256='7834e4692565b491b9d2d258095d6c05089c9bae8a1bef280c338d15ba02e9ac') + version('0.10.2', sha256='e117c416fced894e24720cc1b38247074a13020f19d6704b38e554cbcb993d06') + version('0.9.6', sha256='4d9e4ca40c079e0b0e9f912a9092589b97fbaf80eb6537e9ae70d48c09472efa') + + depends_on('m4', type='build') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + + patch('examples.patch', sha256='49aa8fa99d3a1315c639d2a90014079c34a7d0a6dde110b6cbb7b02f87324742') + + def autoreconf(self, spec, prefix): + bash = which('bash') + bash('./bootstrap') From 9372783de679a1efa5215f12cb8b5cbe493397a2 Mon Sep 17 00:00:00 2001 From: darmac Date: Thu, 19 Mar 2020 02:12:40 +0800 Subject: [PATCH 094/377] add new package: acl (#15514) --- .../repos/builtin/packages/acl/package.py | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 var/spack/repos/builtin/packages/acl/package.py diff --git a/var/spack/repos/builtin/packages/acl/package.py b/var/spack/repos/builtin/packages/acl/package.py new file mode 100644 index 00000000000..ea9bf4172f5 --- /dev/null +++ b/var/spack/repos/builtin/packages/acl/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Acl(AutotoolsPackage): + """Commands for Manipulating POSIX Access Control Lists.""" + + homepage = "https://savannah.nongnu.org/projects/acl" + url = "http://git.savannah.nongnu.org/cgit/acl.git/snapshot/acl-2.2.53.tar.gz" + + version('2.2.53', sha256='9e905397ac10d06768c63edd0579c34b8431555f2ea8e8f2cee337b31f856805') + version('2.2.52', sha256='f3f31d2229c903184ff877aa0ee658b87ec20fec8aebb51e65eaa68d7b24e629') + version('2.2.51', sha256='31a43d96a274a39bfcb805fb903d45840515344884d224cef166b482693a9f48') + version('2.2.50', sha256='39e21d623a9f0da8c042cde346c01871b498d51400e92c2ab1490d5ffd724401') + version('2.2.49', sha256='c6e01460cac4e47673dd60a7f57b970b49f6998bb564eff141cca129aa8940d1') + version('2.2.48', sha256='877eaeccc1500baec58391935b46ac7dfc5ffd8c54fbc0385ccd8b2b18ac3fa6') + + depends_on('m4', type='build') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('attr') + + def autoreconf(self, spec, prefix): + bash = which('bash') + bash('./autogen.sh') From 8cdd78cd1d6b9630377d639a71338209fcfd9419 Mon Sep 17 00:00:00 2001 From: Benjamin Tovar Date: Wed, 18 Mar 2020 14:14:45 -0400 Subject: [PATCH 095/377] Cctools 7.1.0 (#15506) * update to 7.1.0 * adds gettext as dependency (needed to link with python) * disable python2 or python3 as needed --- .../repos/builtin/packages/cctools/package.py | 53 ++++++++++++++----- 1 file changed, 41 insertions(+), 12 deletions(-) diff --git a/var/spack/repos/builtin/packages/cctools/package.py b/var/spack/repos/builtin/packages/cctools/package.py index 481e4a47f17..973a6c3d114 100644 --- a/var/spack/repos/builtin/packages/cctools/package.py +++ b/var/spack/repos/builtin/packages/cctools/package.py @@ -13,16 +13,17 @@ class Cctools(AutotoolsPackage): """ homepage = "https://github.com/cooperative-computing-lab/cctools" - url = "https://github.com/cooperative-computing-lab/cctools/archive/release/6.1.1.tar.gz" + url = "https://github.com/cooperative-computing-lab/cctools/archive/release/7.1.0.tar.gz" + version('7.1.0', sha256='84748245db10ff26c0c0a7b9fd3ec20fbbb849dd4aadc5e8531fd1671abe7a81') version('7.0.18', sha256='5b6f3c87ae68dd247534a5c073eb68cb1a60176a7f04d82699fbc05e649a91c2') version('6.1.1', sha256='97f073350c970d6157f80891b3bf6d4f3eedb5f031fea386dc33e22f22b8af9d') depends_on('openssl') depends_on('perl+shared', type=('build', 'run')) - depends_on('python@:2.9', when='@6.1.1', type=('build', 'run')) depends_on('python', type=('build', 'run')) depends_on('readline') + depends_on('gettext') # Corrects python linking of -lintl flag. depends_on('swig') # depends_on('xrootd') depends_on('zlib') @@ -44,21 +45,49 @@ def patch(self): def configure_args(self): args = [] - # For python - if self.spec.satisfies('^python@3:'): - args.append('--with-python-path=no') - args.append( - '--with-python3-path={0}'.format(self.spec['python'].prefix) - ) + + # make sure we do not pick a python outside spack: + if self.spec.satisfies('@6.1.1'): + if self.spec.satisfies('^python@3:'): + args.extend([ + '--with-python3-path', self.spec['python'].prefix, + '--with-python-path', 'no' + ]) + elif self.spec.satisfies('^python@:2.9'): + args.extend([ + '--with-python-path', self.spec['python'].prefix, + '--with-python3-path', 'no' + ]) + else: + args.extend([ + '--with-python-path', 'no', + '--with-python3-path', 'no' + ]) else: - args.append('--with-python3-path=no') - args.append( - '--with-python-path={0}'.format(self.spec['python'].prefix) - ) + # versions 7 and above, where --with-python-path recognized the + # python version: + if self.spec.satisfies('^python@3:'): + args.extend([ + '--with-python-path', self.spec['python'].prefix, + '--with-python2-path', 'no' + ]) + elif self.spec.satisfies('^python@:2.9'): + args.extend([ + '--with-python-path', self.spec['python'].prefix, + '--with-python3-path', 'no' + ]) + else: + args.extend([ + '--with-python2-path', 'no', + '--with-python3-path', 'no' + ]) + # disable these bits for p in ['mysql', 'xrootd']: args.append('--with-{0}-path=no'.format(p)) + # point these bits at the Spack installations for p in ['openssl', 'perl', 'readline', 'swig', 'zlib']: args.append('--with-{0}-path={1}'.format(p, self.spec[p].prefix)) + return args From 156b59c2f1f4ef96f31004a0516eda65ad8f815c Mon Sep 17 00:00:00 2001 From: Nick Booher Date: Wed, 18 Mar 2020 13:18:45 -0500 Subject: [PATCH 096/377] revbayes: Update pre-build process (#15485) --- var/spack/repos/builtin/packages/revbayes/package.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/var/spack/repos/builtin/packages/revbayes/package.py b/var/spack/repos/builtin/packages/revbayes/package.py index 5f556683924..5e02dc974da 100644 --- a/var/spack/repos/builtin/packages/revbayes/package.py +++ b/var/spack/repos/builtin/packages/revbayes/package.py @@ -44,6 +44,11 @@ def root_cmakelists_dir(self): def regenerate(self): with working_dir(join_path('projects', 'cmake')): mkdirp('build') + if self.spec.version > Version('1.0.13'): + generate_version = Executable('./generate_version_number.sh') + generate_version() + dest = join_path('..', '..', 'src', 'revlanguage', 'utils') + install('GitVersion.cpp', dest) edit = FileFilter('regenerate.sh') edit.filter('boost="true"', 'boost="false"') if '+mpi' in self.spec: From 056fc996760a6b0085308848bea5d9d316fb3e56 Mon Sep 17 00:00:00 2001 From: Sinan Date: Wed, 18 Mar 2020 11:19:27 -0700 Subject: [PATCH 097/377] Use python extend_path as pyqt sip fix (#15297) * try extend path to solve PyQt5.sip not found issue * disable private sip installation in sippackage class * undo manual PyQt5 dir creation in py-sip site-packages dir * fix typo * fix typo * also apply fix to PyQt4 * tidy up * flake8 and tidy up * tidy and undo hardcoding of python_include_dir * replace hardcoded python inc dir * fix minor issues * rethink include dir variable name * improve style * add new versions * implement new sip setup to qsci installation * set sip-incdir correctly for the new setup * setup extend_path thing before qsci python bindings * take care of conflict * flake8 * also extend for PyQt4 * improve style * improve style * SipPackage build sys should depend on py-sip * consolidate extend_path fixes into SipPackage * fix typo * fix bugs * flake8 * revert sip doc to pre-resource setup * import os module * flake8 Co-authored-by: Sinan81 --- lib/spack/docs/build_systems/sippackage.rst | 12 ++--- lib/spack/spack/build_systems/sip.py | 48 ++++++++----------- .../builtin/packages/py-pyqt4/package.py | 8 +++- .../builtin/packages/py-pyqt5/package.py | 11 +++-- .../repos/builtin/packages/py-sip/package.py | 15 ++++++ 5 files changed, 53 insertions(+), 41 deletions(-) diff --git a/lib/spack/docs/build_systems/sippackage.rst b/lib/spack/docs/build_systems/sippackage.rst index b8c08ec513e..ddf9a26ab9f 100644 --- a/lib/spack/docs/build_systems/sippackage.rst +++ b/lib/spack/docs/build_systems/sippackage.rst @@ -51,10 +51,8 @@ Build system dependencies ``SIPPackage`` requires several dependencies. Python is needed to run the ``configure.py`` build script, and to run the resulting Python libraries. Qt is needed to provide the ``qmake`` command. SIP is also -needed to build the package. SIP is an unusual dependency in that it -must be installed in the same installation directory as the package, -so instead of a ``depends_on``, we use a ``resource``. All of these -dependencies are automatically added via the base class +needed to build the package. All of these dependencies are automatically +added via the base class .. code-block:: python @@ -62,11 +60,7 @@ dependencies are automatically added via the base class depends_on('qt', type='build') - resource(name='sip', - url='https://www.riverbankcomputing.com/static/Downloads/sip/4.19.18/sip-4.19.18.tar.gz', - sha256='c0bd863800ed9b15dcad477c4017cdb73fa805c25908b0240564add74d697e1e', - destination='.') - + depends_on('py-sip', type='build') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Passing arguments to ``configure.py`` diff --git a/lib/spack/spack/build_systems/sip.py b/lib/spack/spack/build_systems/sip.py index 314f91d5d2c..f814ef1837e 100644 --- a/lib/spack/spack/build_systems/sip.py +++ b/lib/spack/spack/build_systems/sip.py @@ -5,9 +5,10 @@ import inspect -from llnl.util.filesystem import working_dir -from spack.directives import depends_on, extends, resource -from spack.package import PackageBase, run_before, run_after +from llnl.util.filesystem import working_dir, join_path +from spack.directives import depends_on, extends +from spack.package import PackageBase, run_after +import os class SIPPackage(PackageBase): @@ -40,33 +41,12 @@ class SIPPackage(PackageBase): extends('python') depends_on('qt') - - resource(name='sip', - url='https://www.riverbankcomputing.com/static/Downloads/sip/4.19.18/sip-4.19.18.tar.gz', - sha256='c0bd863800ed9b15dcad477c4017cdb73fa805c25908b0240564add74d697e1e', - destination='.') + depends_on('py-sip') def python(self, *args, **kwargs): """The python ``Executable``.""" inspect.getmodule(self).python(*args, **kwargs) - @run_before('configure') - def install_sip(self): - args = [ - '--sip-module={0}'.format(self.sip_module), - '--bindir={0}'.format(self.prefix.bin), - '--destdir={0}'.format(inspect.getmodule(self).site_packages_dir), - '--incdir={0}'.format(inspect.getmodule(self).python_include_dir), - '--sipdir={0}'.format(self.prefix.share.sip), - '--stubsdir={0}'.format(inspect.getmodule(self).site_packages_dir), - ] - - with working_dir('sip-4.19.18'): - self.python('configure.py', *args) - - inspect.getmodule(self).make() - inspect.getmodule(self).make('install') - def configure_file(self): """Returns the name of the configure file to use.""" return 'configure.py' @@ -77,12 +57,15 @@ def configure(self, spec, prefix): args = self.configure_args() + python_include_dir = 'python' + str(spec['python'].version.up_to(2)) + args.extend([ '--verbose', '--confirm-license', '--qmake', spec['qt'].prefix.bin.qmake, - '--sip', prefix.bin.sip, - '--sip-incdir', inspect.getmodule(self).python_include_dir, + '--sip', spec['py-sip'].prefix.bin.sip, + '--sip-incdir', join_path(spec['py-sip'].prefix.include, + python_include_dir), '--bindir', prefix.bin, '--destdir', inspect.getmodule(self).site_packages_dir, ]) @@ -131,3 +114,14 @@ def import_module_test(self): # Check that self.prefix is there after installation run_after('install')(PackageBase.sanity_check_prefix) + + @run_after('install') + def extend_path_setup(self): + # See github issue #14121 and PR #15297 + module = self.spec['py-sip'].variants['module'].value + if module != 'sip': + module = module.split('.')[0] + with working_dir(inspect.getmodule(self).site_packages_dir): + with open(os.path.join(module, '__init__.py'), 'a') as f: + f.write('from pkgutil import extend_path\n') + f.write('__path__ = extend_path(__path__, __name__)\n') diff --git a/var/spack/repos/builtin/packages/py-pyqt4/package.py b/var/spack/repos/builtin/packages/py-pyqt4/package.py index c0e3ae1085b..d1a90042d95 100644 --- a/var/spack/repos/builtin/packages/py-pyqt4/package.py +++ b/var/spack/repos/builtin/packages/py-pyqt4/package.py @@ -34,6 +34,7 @@ class PyPyqt4(SIPPackage): # Supposedly can also be built with Qt 5 compatibility layer depends_on('qt@:4') depends_on('qscintilla', when='+qsci') + depends_on('py-sip module=PyQt4.sip') # For building Qscintilla python bindings resource(name='qscintilla', @@ -68,7 +69,7 @@ def make_qsci(self): pydir = join_path(site_packages_dir, 'PyQt4') python = self.spec['python'].command python('configure.py', - '--sip=' + self.prefix.bin.sip, + '--sip=' + self.spec['py-sip'].prefix.bin.sip, '--qsci-incdir=' + self.spec['qscintilla'].prefix.include, '--qsci-libdir=' + self.spec['qscintilla'].prefix.lib, @@ -76,7 +77,10 @@ def make_qsci(self): '--apidir=' + self.prefix.share.qsci, '--destdir=' + pydir, '--pyqt-sipdir=' + self.prefix.share.sip.PyQt4, - '--sip-incdir=' + python_include_dir, + '--sip-incdir=' + + join_path(self.spec['py-sip'].prefix.include, + 'python' + + str(self.spec['python'].version.up_to(2))), '--stubsdir=' + pydir) # Fix build errors diff --git a/var/spack/repos/builtin/packages/py-pyqt5/package.py b/var/spack/repos/builtin/packages/py-pyqt5/package.py index b91833389b8..bc37d4dcab1 100644 --- a/var/spack/repos/builtin/packages/py-pyqt5/package.py +++ b/var/spack/repos/builtin/packages/py-pyqt5/package.py @@ -26,6 +26,7 @@ class PyPyqt5(SIPPackage): 'PyQt5.QtXmlPatterns' ] + version('5.13.1', sha256='54b7f456341b89eeb3930e786837762ea67f235e886512496c4152ebe106d4af') version('5.13.0', sha256='0cdbffe5135926527b61cc3692dd301cd0328dd87eeaf1313e610787c46faff9') version('5.12.3', sha256='0db0fa37debab147450f9e052286f7a530404e2aaddc438e97a7dcdf56292110') @@ -36,7 +37,8 @@ class PyPyqt5(SIPPackage): depends_on('qt@5:+opengl') depends_on('python@2.6:', type=('build', 'run')) depends_on('py-enum34', type=('build', 'run'), when='^python@:3.3') - + depends_on('py-sip module=PyQt5.sip', type=('build', 'run')) + depends_on('py-sip@:4.19.18 module=PyQt5.sip', type=('build', 'run'), when='@:5.13.0') depends_on('qscintilla', when='+qsci') # For building Qscintilla python bindings @@ -75,7 +77,7 @@ def make_qsci(self): 'PyQt5') python = self.spec['python'].command python('configure.py', '--pyqt=PyQt5', - '--sip=' + self.prefix.bin.sip, + '--sip=' + self.spec['py-sip'].prefix.bin.sip, '--qsci-incdir=' + self.spec['qscintilla'].prefix.include, '--qsci-libdir=' + self.spec['qscintilla'].prefix.lib, @@ -83,7 +85,10 @@ def make_qsci(self): '--apidir=' + self.prefix.share.qsci, '--destdir=' + pydir, '--pyqt-sipdir=' + self.prefix.share.sip.PyQt5, - '--sip-incdir=' + python_include_dir, + '--sip-incdir=' + + join_path(self.spec['py-sip'].prefix.include, + 'python' + + str(self.spec['python'].version.up_to(2))), '--stubsdir=' + pydir) # Fix build errors diff --git a/var/spack/repos/builtin/packages/py-sip/package.py b/var/spack/repos/builtin/packages/py-sip/package.py index 09c6b743b14..d454f05740c 100644 --- a/var/spack/repos/builtin/packages/py-sip/package.py +++ b/var/spack/repos/builtin/packages/py-sip/package.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import os class PySip(Package): @@ -16,6 +17,9 @@ class PySip(Package): hg = "https://www.riverbankcomputing.com/hg/sip" version('develop', hg=hg) # wasn't actually able to clone this + version('4.19.21', sha256='6af9979ab41590e8311b8cc94356718429ef96ba0e3592bdd630da01211200ae') + version('4.19.20', sha256='04cc2f87ac97e8718d8e1ef036e3ec26050ab44c21f9277618d5b67432fcbfd6') + version('4.19.19', sha256='5436b61a78f48c7e8078e93a6b59453ad33780f80c644e5f3af39f94be1ede44') version('4.19.18', sha256='c0bd863800ed9b15dcad477c4017cdb73fa805c25908b0240564add74d697e1e') version('4.19.15', sha256='2b5c0b2c0266b467b365c21376d50dde61a3236722ab87ff1e8dacec283eb610') version('4.19.13', sha256='e353a7056599bf5fbd5d3ff9842a6ab2ea3cf4e0304a0f925ec5862907c0d15e') @@ -53,3 +57,14 @@ def build(self, spec, prefix): def install(self, spec, prefix): make('install') + + @run_after('install') + def extend_path_setup(self): + # See github issue #14121 and PR #15297 + module = self.spec.variants['module'].value + if module != 'sip': + module = module.split('.')[0] + with working_dir(site_packages_dir): + with open(os.path.join(module, '__init__.py'), 'w') as f: + f.write('from pkgutil import extend_path\n') + f.write('__path__ = extend_path(__path__, __name__)\n') From 3bcb5b3a590331b2d1bbdf19fc2d1ca27618357a Mon Sep 17 00:00:00 2001 From: Sinan Date: Wed, 18 Mar 2020 11:19:46 -0700 Subject: [PATCH 098/377] package/QGIS: fix cmake/FindPyqt.py (#15455) * fix cmake/FindPyqt.py * apply patch * generalize patch * rename patch * fix typo Co-authored-by: Sinan81 Co-authored-by: Sinan81 --- .../repos/builtin/packages/qgis/package.py | 2 ++ .../repos/builtin/packages/qgis/pyqt5.patch | 25 +++++++++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 var/spack/repos/builtin/packages/qgis/pyqt5.patch diff --git a/var/spack/repos/builtin/packages/qgis/package.py b/var/spack/repos/builtin/packages/qgis/package.py index af3fe5db3ea..4a6d6a3583b 100644 --- a/var/spack/repos/builtin/packages/qgis/package.py +++ b/var/spack/repos/builtin/packages/qgis/package.py @@ -114,6 +114,8 @@ class Qgis(CMakePackage): depends_on('qtkeychain@:1.5.99', when='^qt@4') depends_on('qt@:4', when='@2') + patch('pyqt5.patch', when='^qt@5') + def cmake_args(self): spec = self.spec args = [] diff --git a/var/spack/repos/builtin/packages/qgis/pyqt5.patch b/var/spack/repos/builtin/packages/qgis/pyqt5.patch new file mode 100644 index 00000000000..1e6b7e6149c --- /dev/null +++ b/var/spack/repos/builtin/packages/qgis/pyqt5.patch @@ -0,0 +1,25 @@ +diff --git a/cmake/FindPyQt5.py b/cmake/FindPyQt5.py +index 6a55a0f801..d6eda1fa1e 100644 +--- a/cmake/FindPyQt5.py ++++ b/cmake/FindPyQt5.py +@@ -40,6 +40,7 @@ except ImportError: + import sys + cfg = sipconfig.Configuration() + sip_dir = cfg.default_sip_dir ++ pyqt_prefix = os.sep.join(PyQt5.QtCore.__file__.split(os.sep)[0:-5]) + if sys.platform.startswith('freebsd'): + py_version = str(sys.version_info.major) + str(sys.version_info.minor) + sip_dir = sip_dir.replace(py_version, '') +@@ -53,9 +54,9 @@ except ImportError: + 'pyqt_version': PyQt5.QtCore.PYQT_VERSION, + 'pyqt_version_str': PyQt5.QtCore.PYQT_VERSION_STR, + 'pyqt_sip_flags': PyQt5.QtCore.PYQT_CONFIGURATION['sip_flags'], +- 'pyqt_mod_dir': os.path.join(cfg.default_mod_dir, "PyQt5"), +- 'pyqt_sip_dir': sip_dir, +- 'pyqt_bin_dir': cfg.default_bin_dir, ++ 'pyqt_mod_dir': os.path.dirname(PyQt5.QtCore.__file__), ++ 'pyqt_sip_dir': os.path.join(pyqt_prefix,'share','sip','PyQt5'), ++ 'pyqt_bin_dir': os.path.join(pyqt_prefix,'bin'), + } + pyqtcfg = sipconfig.Configuration([cfg]) + From ff29599578b669231fad263e7b2e919bfcb974b6 Mon Sep 17 00:00:00 2001 From: gauthier12 <45069706+gauthier12@users.noreply.github.com> Date: Wed, 18 Mar 2020 21:13:57 +0100 Subject: [PATCH 099/377] adol-c:updating sources location (#15532) * adol-c:updating sources location * Update var/spack/repos/builtin/packages/adol-c/package.py Co-Authored-By: Adam J. Stewart Co-authored-by: Adam J. Stewart --- .../repos/builtin/packages/adol-c/package.py | 21 ++++++++++++------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py index 336f1833dba..741b57773b5 100644 --- a/var/spack/repos/builtin/packages/adol-c/package.py +++ b/var/spack/repos/builtin/packages/adol-c/package.py @@ -12,14 +12,19 @@ class AdolC(AutotoolsPackage): overloading.""" homepage = "https://projects.coin-or.org/ADOL-C" - url = "http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.6.1.tgz" - git = "https://gitlab.com/adol-c/adol-c.git" - - version('develop', branch='master') - version('2.6.3', sha256='6ed74580695a0d2c960581e5430ebfcd380eb5da9337daf488bf2e89039e9c21') - version('2.6.2', sha256='f6326e7ba994d02074816132d4461915221069267c31862b31fab7020965c658') - version('2.6.1', sha256='037089e0f64224e5e6255b61af4fe7faac080533fd778b76fe946e52491918b5') - version('2.5.2', sha256='2fa514d9799989d6379738c2bcf75070d9834e4d227eb32a5b278840893b2af9') + url = "https://github.com/coin-or/ADOL-C/archive/releases/2.7.2.tar.gz" + git = "https://github.com/coin-or/ADOL-C.git" + version('master', branch='master') + version('2.7.2', sha256='701e0856baae91b98397960d5e0a87a549988de9d4002d0e9a56fa08f5455f6e') + version('2.7.1', sha256='a05422cc7faff5700e134e113822d1934fb540ad247e63778524d5d6d75bb0ef') + version('2.7.0', sha256='a75cfa6240de8692b2a3e8e782319efefc316f1e595234fcee972ab0e7afa3cd') + version('2.6.3', sha256='9750a0a06dcab9a0dba2010f07872ea9057ed29781e9e7d571691c27aa559b04') + version('2.6.2', sha256='4ef6ff15b4691235c0ea6580917c7eb17d09ded485ac524a0a33ac7e99ab004b') + version('2.6.1', sha256='48b41c40d1c8437fb98eeed4b24deaf3e59da804f34ac9c848da1b049b3b071a') + version('2.6.0', sha256='26a1fcb8561f15781f645d245fc345c83497147ec7bb64d4bfc96e32c34c6c1c') + version('2.5.2', sha256='390edb1513f749b2dbf6fb90db12ce786f6532af80e589f161ff43646b3a78a6') + version('2.5.1', sha256='dedb93c3bb291366d799014b04b6d1ec63ca4e7216edf16167776c07961e3b4a') + version('2.5.0', sha256='9d51c426d831884aac8f418be410c001eb62f3a11cb8f30c66af0b842edffb96') variant('advanced_branching', default=False, description='Enable advanced branching to reduce retaping') From 77b11433b3eecbb0c3555da08d434e8e638536e8 Mon Sep 17 00:00:00 2001 From: ktsai7 <35276356+ktsai7@users.noreply.github.com> Date: Wed, 18 Mar 2020 15:46:29 -0600 Subject: [PATCH 100/377] modified spackage for flecsi and cinch (#15555) --- var/spack/repos/builtin/packages/cinch/package.py | 2 +- var/spack/repos/builtin/packages/flecsi/package.py | 10 ++++++---- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/cinch/package.py b/var/spack/repos/builtin/packages/cinch/package.py index 65281b8455c..f46a801cd4a 100644 --- a/var/spack/repos/builtin/packages/cinch/package.py +++ b/var/spack/repos/builtin/packages/cinch/package.py @@ -16,7 +16,7 @@ class Cinch(Package): url = "https://github.com/laristra/cinch/archive/1.0.zip" git = "https://github.com/laristra/cinch.git" - version('develop', branch='master', submodules=False) + version('master', branch='master', submodules=False) version('1.0', sha256='98b73473829b478191481621d84c3d63c662da6e951321f858a032eae3ca07b7') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/flecsi/package.py b/var/spack/repos/builtin/packages/flecsi/package.py index 59c62e6352e..fccdd686b07 100644 --- a/var/spack/repos/builtin/packages/flecsi/package.py +++ b/var/spack/repos/builtin/packages/flecsi/package.py @@ -20,12 +20,14 @@ class Flecsi(CMakePackage): homepage = 'http://flecsi.org/' git = 'https://github.com/laristra/flecsi.git' - version('master', branch='master', submodules=False, preferred=True) + version('devel', branch='devel', submodules=False, preferred=False) + version('1', branch='1', submodules=False, preferred=True) + version('1.4', branch='1.4', submodules=False, preferred=False) variant('build_type', default='Release', values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel'), description='The build type to build', multi=False) - variant('backend', default='mpi', values=('serial', 'mpi', 'legion', 'hpx'), + variant('backend', default='mpi', values=('serial', 'mpi', 'legion', 'hpx', 'charmpp'), description='Backend to use for distributed memory', multi=False) variant('debug_backend', default=False, description='Build Backend with Debug Mode') @@ -64,8 +66,8 @@ class Flecsi(CMakePackage): depends_on('legion@ctrl-rep+shared+mpi build_type=Debug', when='backend=legion +debug_backend ~hdf5') depends_on('legion@ctrl-rep+shared+mpi+hdf5 build_type=Release', when='backend=legion ~debug_backend +hdf5') depends_on('legion@ctrl-rep+shared+mpi build_type=Release', when='backend=legion ~debug_backend ~hdf5') - depends_on('hpx@1.3.0 cxxstd=14 build_type=Debug', when='backend=hpx +debug_backend') - depends_on('hpx@1.3.0 cxxstd=14 build_type=Release', when='backend=hpx ~debug_backend') + depends_on('hpx@1.3.0 cxxstd=14 malloc=system build_type=Debug', when='backend=hpx +debug_backend') + depends_on('hpx@1.3.0 cxxstd=14 malloc=system build_type=Release', when='backend=hpx ~debug_backend') depends_on('boost@1.70.0: cxxstd=14 +program_options') depends_on('metis@5.1.0:') depends_on('parmetis@4.0.3:') From 51f8744ab77a114fe0e9dd4d99bc957bf5fc39cd Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 18 Mar 2020 18:01:20 -0400 Subject: [PATCH 101/377] py-horovod: set appropriate build env vars (#15548) * py-horovod: set appropriate build env vars * mxnet: add maintainer * py-horovod: fetch git submodules * py-torch: fix CUDA conflicts --- .../repos/builtin/packages/mxnet/package.py | 2 + .../builtin/packages/py-horovod/package.py | 130 +++++++++++++----- .../builtin/packages/py-torch/package.py | 16 +-- 3 files changed, 105 insertions(+), 43 deletions(-) diff --git a/var/spack/repos/builtin/packages/mxnet/package.py b/var/spack/repos/builtin/packages/mxnet/package.py index f3b7cddb23f..492a2573bc1 100644 --- a/var/spack/repos/builtin/packages/mxnet/package.py +++ b/var/spack/repos/builtin/packages/mxnet/package.py @@ -13,6 +13,8 @@ class Mxnet(MakefilePackage): homepage = "http://mxnet.io" url = "https://github.com/apache/incubator-mxnet/releases/download/1.3.0/apache-mxnet-src-1.3.0-incubating.tar.gz" + maintainers = ['adamjstewart'] + version('1.3.0', sha256='c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2') variant('cuda', default=False, description='Enable CUDA support') diff --git a/var/spack/repos/builtin/packages/py-horovod/package.py b/var/spack/repos/builtin/packages/py-horovod/package.py index 884721b286f..598e01c6f91 100644 --- a/var/spack/repos/builtin/packages/py-horovod/package.py +++ b/var/spack/repos/builtin/packages/py-horovod/package.py @@ -3,10 +3,6 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -from spack import * -import fnmatch -import os - class PyHorovod(PythonPackage): """Horovod is a distributed deep learning training framework for @@ -14,47 +10,111 @@ class PyHorovod(PythonPackage): homepage = "https://github.com/horovod" git = "https://github.com/horovod/horovod.git" - url = "https://github.com/horovod/horovod/archive/v0.19.0.tar.gz" - version('master', branch='master', submodules='True') - version('0.19.0', sha256='0e9fec11cd7f5f39a09f0785d1097cb51c44537ae14c9b4b2578b5cdd21efb9b') - version('0.18.2', sha256='a073e08cec65474afdb2d011486b4cb6c7ac8fcb1eca3e02b169e1e7b4a66da6') - version('0.18.1', sha256='26e236d1f60955e9dd12b9f0a836f0691296a010fcd1ac72295970a780f4e4fb') - version('0.18.0', sha256='94f13e7110c5f3fd1aa194b9d886b5bb91c9bc02ade31bcb84fc6e7f9c043455') - version('0.17.1', sha256='14eea5744eda9c62988ffa278a9a5472cebbc6a287eca9ed48cacfcd177e8978') - version('0.17.0.post1', sha256='220b230611e22dc69777f1be4d9788a07e73a0722e511091fa156cdf68ca798b') - version('0.17.0', sha256='4bb121dda6cdaa1677535470adc1836493a9c4930ab19f6b491254ea47a12a4f') - version('0.16.4', sha256='c0168dfeb31a56ede52eae115f43fa2d06a5db55a37201064ef901c8000d708d') - version('0.16.3', sha256='1857cf1b335723366cc71e4bcd0583f2dde0c821212cda0e1b6bddfe4ba1ea0d') - version('0.16.2', sha256='baa9754e59ab0ee72d3b5769cf77e06a2c7b0a2d9626e0e14ca2ab131934ce74') + maintainers = ['adamjstewart'] - variant('pytorch', default=True, description='Enables PyTorch') - variant('mxnet', default=False, description='Enables mxnet') - variant('mpi', default=True, description='Enables MPI build') + version('master', branch='master', submodules=True) + version('0.19.1', tag='v0.19.1', submodules=True) + version('0.19.0', tag='v0.19.0', submodules=True) + version('0.18.2', tag='v0.18.2', submodules=True) + version('0.18.1', tag='v0.18.1', submodules=True) + version('0.18.0', tag='v0.18.0', submodules=True) + version('0.17.1', tag='v0.17.1', submodules=True) + version('0.17.0', tag='v0.17.0', submodules=True) + version('0.16.4', tag='v0.16.4', submodules=True) + version('0.16.3', tag='v0.16.3', submodules=True) + version('0.16.2', tag='v0.16.2', submodules=True) + + # Deep learning frameworks + variant('pytorch', default=True, description='Enables PyTorch') + variant('tensorflow', default=False, description='Enables TensorFlow') + variant('mxnet', default=False, description='Enables Apache MXNet') + + # Distributed support variant('gloo', default=False, description='Enables features related to distributed support') - variant('cuda', default=True, description='Enables CUDA build') + variant('mpi', default=True, description='Enables MPI build') - depends_on('python', type=('build', 'run')) + # GPU support + variant('cuda', default=True, description='Enables CUDA build') + variant('gpu_allreduce', default='mpi', + description='Backend to use for GPU_ALLREDUCE', + values=('mpi', 'nccl'), multi=False) # DDL support is deprecated + variant('gpu_allgather', default='mpi', + description='Backend to use for GPU_ALLGATHER', + values=('mpi',), multi=False) + variant('gpu_broadcast', default='mpi', + description='Backend to use for GPU_BROADCAST', + values=('mpi', 'nccl'), multi=False) + + # Required dependencies depends_on('py-setuptools', type='build') depends_on('py-cloudpickle', type=('build', 'run')) depends_on('py-psutil', type=('build', 'run')) depends_on('py-pyyaml', type=('build', 'run')) depends_on('py-six', type=('build', 'run')) - depends_on('py-torch', type=('build', 'run')) - depends_on('py-pip', type=('build')) - # Optional dependencies - depends_on('cuda', when='+cuda') - depends_on('nccl', when='+nccl') - depends_on('gloo', when='+gloo') + # Deep learning frameworks + depends_on('py-torch@0.4.0:', type=('build', 'run'), when='+pytorch') + depends_on('py-torch+cuda', type=('build', 'run'), when='+pytorch+cuda') + depends_on('py-cffi@1.4.0:', type=('build', 'run'), when='+pytorch') + depends_on('py-tensorflow@1.1.0:', type=('build', 'link', 'run'), when='+tensorflow') + depends_on('mxnet@1.4.0:+python', type=('build', 'link', 'run'), when='+mxnet') + depends_on('mxnet+cuda', type=('build', 'link', 'run'), when='+mxnet+cuda') + + # Distributed support + # There does not appear to be a way to use an external Gloo installation + depends_on('cmake', type='build', when='+gloo') depends_on('mpi', when='+mpi') - depends_on('py-torch', type=('build', 'run'), when='+pytorch') - depends_on('mxnet', when='+mxnet') + depends_on('mpi', when='gpu_allreduce=mpi') + depends_on('mpi', when='gpu_allgather=mpi') + depends_on('mpi', when='gpu_broadcast=mpi') - phases = ['clean', 'sdist', 'install'] + # GPU support + depends_on('cuda', when='+cuda') + depends_on('nccl@2.0:', when='gpu_allreduce=nccl') + depends_on('nccl@2.0:', when='gpu_broadcast=nccl') - def install(self, spec, prefix): - pip = which('pip') - for file in os.listdir(prefix): - if fnmatch.fnmatch(file, 'horovod-*.tar.gz'): - pip('install', file, '--prefix={0}'.format(prefix)) + # Test dependencies + depends_on('py-mock', type='test') + depends_on('py-pytest', type='test') + depends_on('py-pytest-forked', type='test') + + conflicts('+gloo', when='platform=darwin', msg='Gloo cannot be compiled on MacOS') + conflicts('~gloo~mpi', msg='One of Gloo or MPI are required for Horovod to run') + conflicts('~pytorch~tensorflow~mxnet', msg='At least one deep learning backend is required') + + def setup_build_environment(self, env): + # Deep learning frameworks + if '~pytorch' in self.spec: + env.set('HOROVOD_WITHOUT_PYTORCH', 1) + if '~tensorflow' in self.spec: + env.set('HOROVOD_WITHOUT_TENSORFLOW', 1) + if '~mxnet' in self.spec: + env.set('HOROVOD_WITHOUT_MXNET', 1) + + # Distributed support + if '~gloo' in self.spec: + env.set('HOROVOD_WITHOUT_GLOO', 1) + if '+mpi' in self.spec: + env.set('HOROVOD_WITH_MPI', 1) + else: + env.set('HOROVOD_WITHOUT_MPI', 1) + + # GPU support + if '+cuda' in self.spec: + env.set('HOROVOD_CUDA_HOME', self.spec['cuda'].prefix) + env.set('HOROVOD_CUDA_INCLUDE', + self.spec['cuda'].headers.directories[0]) + env.set('HOROVOD_CUDA_LIB', self.spec['cuda'].libs.directories[0]) + if '^nccl' in self.spec: + env.set('HOROVOD_NCCL_HOME', self.spec['nccl'].prefix) + env.set('HOROVOD_NCCL_INCLUDE', + self.spec['nccl'].headers.directories[0]) + env.set('HOROVOD_NCCL_LIB', self.spec['nccl'].libs.directories[0]) + env.set('HOROVOD_GPU_ALLREDUCE', + self.spec.variants['gpu_allreduce'].value.upper()) + env.set('HOROVOD_GPU_ALLGATHER', + self.spec.variants['gpu_allgather'].value.upper()) + env.set('HOROVOD_GPU_BROADCAST', + self.spec.variants['gpu_broadcast'].value.upper()) + env.set('HOROVOD_ALLOW_MIXED_GPU_IMPL', 1) diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py index e40bc840feb..c0be1176e42 100644 --- a/var/spack/repos/builtin/packages/py-torch/package.py +++ b/var/spack/repos/builtin/packages/py-torch/package.py @@ -105,22 +105,22 @@ class PyTorch(PythonPackage, CudaPackage): cuda_arch_conflict = ('This version of Torch/Caffe2 only supports compute ' 'capabilities ') - conflicts('cuda_arch=none', when='+cuda+caffe2', + conflicts('cuda_arch=none', when='+cuda', msg='Must specify CUDA compute capabilities of your GPU, see ' 'https://developer.nvidia.com/cuda-gpus') - conflicts('cuda_arch=52', when='@1.3.0:+cuda+caffe2', + conflicts('cuda_arch=52', when='@1.3.0:+cuda', msg=cuda_arch_conflict + '>=5.3') - conflicts('cuda_arch=50', when='@1.3.0:+cuda+caffe2', + conflicts('cuda_arch=50', when='@1.3.0:+cuda', msg=cuda_arch_conflict + '>=5.3') - conflicts('cuda_arch=35', when='@1.3.0:+cuda+caffe2', + conflicts('cuda_arch=35', when='@1.3.0:+cuda', msg=cuda_arch_conflict + '>=5.3') - conflicts('cuda_arch=32', when='@1.3.0:+cuda+caffe2', + conflicts('cuda_arch=32', when='@1.3.0:+cuda', msg=cuda_arch_conflict + '>=5.3') - conflicts('cuda_arch=30', when='@1.3.0:+cuda+caffe2', + conflicts('cuda_arch=30', when='@1.3.0:+cuda', msg=cuda_arch_conflict + '>=5.3') - conflicts('cuda_arch=30', when='@1.2.0:+cuda+caffe2', + conflicts('cuda_arch=30', when='@1.2.0:+cuda', msg=cuda_arch_conflict + '>=3.2') - conflicts('cuda_arch=20', when='@1.0.0:+cuda+caffe2', + conflicts('cuda_arch=20', when='@1.0.0:+cuda', msg=cuda_arch_conflict + '>=3.0') # Required dependencies From 6a51d540f1de670c817133a47360316782617457 Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Wed, 18 Mar 2020 17:04:38 -0500 Subject: [PATCH 102/377] petsc@3.7 fix dependency of superlu-dist@5.1.3 (#15551) --- var/spack/repos/builtin/packages/petsc/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index ddee34e1872..b58fa0c3c88 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -163,8 +163,8 @@ class Petsc(Package): depends_on('hypre@develop~internal-superlu~int64', when='@develop+hypre+mpi~complex~int64') depends_on('superlu-dist@:4.3~int64', when='@3.4.4:3.6.4+superlu-dist+mpi~int64') depends_on('superlu-dist@:4.3+int64', when='@3.4.4:3.6.4+superlu-dist+mpi+int64') - depends_on('superlu-dist@5.0.0:~int64', when='@3.7:3.7.99+superlu-dist+mpi~int64') - depends_on('superlu-dist@5.0.0:+int64', when='@3.7:3.7.99+superlu-dist+mpi+int64') + depends_on('superlu-dist@5.0.0:5.1.3~int64', when='@3.7:3.7.99+superlu-dist+mpi~int64') + depends_on('superlu-dist@5.0.0:5.1.3+int64', when='@3.7:3.7.99+superlu-dist+mpi+int64') depends_on('superlu-dist@5.2:5.2.99~int64', when='@3.8:3.9.99+superlu-dist+mpi~int64') depends_on('superlu-dist@5.2:5.2.99+int64', when='@3.8:3.9.99+superlu-dist+mpi+int64') depends_on('superlu-dist@5.4:5.4.99~int64', when='@3.10:3.10.2+superlu-dist+mpi~int64') From 432bdeee85edc7fce6b2de100daa2af8d498404f Mon Sep 17 00:00:00 2001 From: Neil Flood Date: Thu, 19 Mar 2020 08:05:05 +1000 Subject: [PATCH 103/377] Tuiview movetogithub (#15498) * py-tuiview: Source has moved to github * py-tuiview: Explicitly require +python on gdal dependency * py-tuiview: Versions up to 1.1.99 are qt4 only * py-tuiview: Add version 1.2.6, which is qt5 only * Explicit version range on gdal dependency --- var/spack/repos/builtin/packages/py-tuiview/package.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py index 95090a26949..9757dd23430 100644 --- a/var/spack/repos/builtin/packages/py-tuiview/package.py +++ b/var/spack/repos/builtin/packages/py-tuiview/package.py @@ -11,11 +11,13 @@ class PyTuiview(PythonPackage): table manipulation abilities. """ - homepage = "https://bitbucket.org/chchrsc/tuiview" - url = "https://bitbucket.org/chchrsc/tuiview/get/tuiview-1.1.7.tar.gz" + homepage = "https://github.com/ubarsc/tuiview" + url = "https://github.com/ubarsc/tuiview/releases/download/tuiview-1.2.6/tuiview-1.2.6.tar.gz" + version('1.2.6', sha256='61b136fa31c949d7a7a4dbf8562e6fc677d5b1845b152ec39e337f4eb2e91662') version('1.1.7', sha256='fbf0bf29cc775357dad4f8a2f0c2ffa98bbf69d603a96353e75b321adef67573') - depends_on("py-pyqt4", type=('build', 'run')) + depends_on("py-pyqt4", type=('build', 'run'), when='@:1.1.99') + depends_on("py-pyqt5", type=('build', 'run'), when='@1.2.0:') depends_on("py-numpy", type=('build', 'run')) - depends_on("gdal") + depends_on("gdal@1.11.0:+python") From 1bcc80ec5d579c733b527bcbca5cad95fa0a3986 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Wed, 18 Mar 2020 16:05:51 -0600 Subject: [PATCH 104/377] Trilinos: Add more variants (~netcdf ~matio ~glm) (#15483) * Trilinos: Add more variants + Provide three new variants to allow building trilinos without netcdf, matio, or glm. + No change to defaults. * Fix style issue. --- .../builtin/packages/trilinos/package.py | 33 ++++++++++++++----- 1 file changed, 25 insertions(+), 8 deletions(-) diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 66e281f28b3..fd623fe8db3 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -86,18 +86,24 @@ class Trilinos(CMakePackage): description='Compile with Boost') variant('cgns', default=False, description='Enable CGNS') - variant('adios2', default=False, + variant('adios2', default=False, description='Enable ADIOS2') + variant('glm', default=True, + description='Compile with GLM') variant('gtest', default=True, description='Compile with Gtest') variant('hdf5', default=True, description='Compile with HDF5') variant('hypre', default=True, description='Compile with Hypre preconditioner') + variant('matio', default=True, + description='Compile with Matio') variant('metis', default=True, description='Compile with METIS and ParMETIS') variant('mumps', default=True, description='Compile with support for MUMPS solvers') + variant('netcdf', default=True, + description='Compile with netcdf') variant('pnetcdf', default=False, description='Compile with parallel-netcdf') variant('suite-sparse', default=True, @@ -312,6 +318,8 @@ class Trilinos(CMakePackage): # ADIOS2 was only added after v12.14.1 conflicts('+adios2', when='@:12.14.1') conflicts('+adios2', when='@xsdk-0.2.0') + conflicts('+pnetcdf', when='~netcdf') + # ###################### Dependencies ########################## # Everything should be compiled position independent (-fpic) @@ -319,17 +327,17 @@ class Trilinos(CMakePackage): depends_on('lapack') depends_on('boost', when='+boost') depends_on('boost', when='+dtk') - depends_on('matio') - depends_on('glm') + depends_on('matio', when='+matio') + depends_on('glm', when='+glm') depends_on('metis@5:', when='+metis') depends_on('suite-sparse', when='+suite-sparse') depends_on('zlib', when="+zlib") # MPI related dependencies depends_on('mpi') - depends_on('netcdf-c+mpi', when="~pnetcdf") - depends_on('netcdf-c+mpi+parallel-netcdf', when="+pnetcdf@master,12.12.1:") - depends_on('parallel-netcdf', when="+pnetcdf@master,12.12.1:") + depends_on('netcdf-c+mpi', when="+netcdf~pnetcdf") + depends_on('netcdf-c+mpi+parallel-netcdf', when="+netcdf+pnetcdf@master,12.12.1:") + depends_on('parallel-netcdf', when="+netcdf+pnetcdf@master,12.12.1:") depends_on('parmetis', when='+metis') depends_on('cgns', when='+cgns') depends_on('adios2', when='+adios2') @@ -537,14 +545,23 @@ def cmake_args(self): '-DTPL_ENABLE_LAPACK=ON', '-DLAPACK_LIBRARY_NAMES=%s' % ';'.join(lapack.names), '-DLAPACK_LIBRARY_DIRS=%s' % ';'.join(lapack.directories), - '-DTPL_ENABLE_Netcdf:BOOL=ON', - '-DNetCDF_ROOT:PATH=%s' % spec['netcdf-c'].prefix, + '-DTPL_ENABLE_GLM:BOOL=%s' % ('ON' if '+glm' in spec else 'OFF'), + '-DTPL_ENABLE_Matio:BOOL=%s' % ( + 'ON' if '+matio' in spec else 'OFF'), '-DTPL_ENABLE_X11:BOOL=%s' % ( 'ON' if '+x11' in spec else 'OFF'), '-DTrilinos_ENABLE_Gtest:BOOL=%s' % ( 'ON' if '+gtest' in spec else 'OFF'), ]) + if '+netcdf' in spec: + options.extend([ + '-DTPL_ENABLE_Netcdf:BOOL=ON', + '-DNetCDF_ROOT:PATH=%s' % spec['netcdf-c'].prefix + ]) + else: + options.extend(['-DTPL_ENABLE_Netcdf:BOOL=OFF']) + if '+hypre' in spec: options.extend([ '-DTPL_ENABLE_HYPRE:BOOL=ON', From 3df712a385ebca05e37dafb7d49ee0f435b5f516 Mon Sep 17 00:00:00 2001 From: Kai Germaschewski Date: Wed, 18 Mar 2020 19:41:18 -0400 Subject: [PATCH 105/377] Upstreams: don't write metadata directory to upstream DB (#15526) When trying to use an upstream Spack repository, as of f2aca86 Spack was attempting to write to the upstream DB based on a new metadata directory added in that commit. Upstream DBs are read-only, so this should not occur. This adds a check to prevent Spack from writing to the upstream DB --- lib/spack/spack/database.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index 5b4d36717c1..4b889da425b 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -311,7 +311,7 @@ def __init__(self, root, db_dir=None, upstream_dbs=None, if not os.path.exists(self._db_dir): mkdirp(self._db_dir) - if not os.path.exists(self._failure_dir): + if not os.path.exists(self._failure_dir) and not is_upstream: mkdirp(self._failure_dir) self.is_upstream = is_upstream From 7bcc41018ff792a26e70f44b4b77722d5d9f042f Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Wed, 18 Mar 2020 20:04:01 -0500 Subject: [PATCH 106/377] Split: Fabtest/libfabric (#15557) Fabtests provides runtime analysis tools and examples of libfabric. As with other projects that are tightly version-bound, e.g. `py-adios` and `adios`, the fact that releases stem from the same repo does not imply they should be the same package. Remove resources, which complicate the libfabric build, and update the fabtests package accordingly. --- .../builtin/packages/fabtests/package.py | 27 ++++++-- .../builtin/packages/libfabric/package.py | 65 ------------------- 2 files changed, 21 insertions(+), 71 deletions(-) diff --git a/var/spack/repos/builtin/packages/fabtests/package.py b/var/spack/repos/builtin/packages/fabtests/package.py index a71a69ab37b..a9f76b5d072 100644 --- a/var/spack/repos/builtin/packages/fabtests/package.py +++ b/var/spack/repos/builtin/packages/fabtests/package.py @@ -7,15 +7,30 @@ class Fabtests(AutotoolsPackage): - """Fabtests provides a set of examples that uses libfabric. - - DEPRECATED. Fabtests has merged with the libfabric git repo.""" + """Fabtests provides a set of runtime analysis tools and examples that use + libfabric.""" homepage = "http://libfabric.org" - url = "https://github.com/ofiwg/fabtests/releases/download/v1.5.3/fabtests-1.5.3.tar.gz" + url = "https://github.com/ofiwg/libfabric/releases/download/v1.9.1/fabtests-1.9.1.tar.bz2" + version('1.9.1', sha256='6f8ced2c6b3514759a0e177c8b2a19125e4ef0714d4cc0fe0386b33bd6cd5585') + version('1.9.0', sha256='60cc21db7092334904cbdafd142b2403572976018a22218e7c453195caef366e') + version('1.8.1', sha256='e9005d8fe73ca3849c872649c29811846bd72a62f897ecab73a08c7a9514f37b') + # old releases, published in a separate repository + version('1.6.2', sha256='37405c6202f5b1aa81f8ea211237a2d87937f06254fa3ed44a9b69ac73b234e8') + version('1.6.1', sha256='d357466b868fdaf1560d89ffac4c4e93a679486f1b4221315644d8d3e21174bf') version('1.6.0', sha256='dc3eeccccb005205017f5af60681ede15782ce202a0103450a6d56a7ff515a67') version('1.5.3', sha256='3835b3bf86cd00d23df0ddba8bf317e4a195e8d5c3c2baa918b373d548f77f29') + version('1.5.0', sha256='1dddd446c3f1df346899f9a8636f1b4265de5b863103ae24876e9f0c1e40a69d') + version('1.4.2', sha256='3b78d0ca1b223ff21b7f5b3627e67e358e3c18b700f86b017e2233fee7e88c2e') - depends_on('libfabric@1.6.0', when='@1.6.0') - depends_on('libfabric@1.5.3', when='@1.5.3') + for v in ['1.4.2', '1.5.0', '1.5.3', '1.6.0', '1.6.1', '1.6.2', + '1.8.1', '1.9.0', '1.9.1']: + depends_on('libfabric@{0}'.format(v), when='@{0}'.format(v)) + + def url_for_version(self, version): + if version >= Version('1.8.1'): + url = "https://github.com/ofiwg/libfabric/releases/download/v{0}/fabtests-{0}.tar.bz2" + else: + url = "https://github.com/ofiwg/fabtests/releases/download/v{0}/fabtests-{0}.tar.gz" + return url.format(version.dotted) diff --git a/var/spack/repos/builtin/packages/libfabric/package.py b/var/spack/repos/builtin/packages/libfabric/package.py index f2f21570f73..cddaee99a73 100644 --- a/var/spack/repos/builtin/packages/libfabric/package.py +++ b/var/spack/repos/builtin/packages/libfabric/package.py @@ -3,7 +3,6 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import os.path from spack import * @@ -74,43 +73,6 @@ class Libfabric(AutotoolsPackage): depends_on('automake', when='@develop', type='build') depends_on('libtool', when='@develop', type='build') - resource(name='fabtests', - url='https://github.com/ofiwg/libfabric/releases/download/v1.9.1/fabtests-1.9.1.tar.bz2', - sha256='6f8ced2c6b3514759a0e177c8b2a19125e4ef0714d4cc0fe0386b33bd6cd5585', - placement='fabtests', when='@1.9.1') - resource(name='fabtests', - url='https://github.com/ofiwg/libfabric/releases/download/v1.9.0/fabtests-1.9.0.tar.bz2', - sha256='60cc21db7092334904cbdafd142b2403572976018a22218e7c453195caef366e', - placement='fabtests', when='@1.9.0') - resource(name='fabtests', - url='https://github.com/ofiwg/libfabric/releases/download/v1.8.0/fabtests-1.8.0.tar.gz', - sha256='4b9af18c9c7c8b28eaeac4e6e9148bd2ea7dc6b6f00f8e31c90a6fc536c5bb6c', - placement='fabtests', when='@1.8.0') - resource(name='fabtests', - url='https://github.com/ofiwg/libfabric/releases/download/v1.7.0/fabtests-1.7.0.tar.gz', - sha256='ebb4129dc69dc0e1f48310ce1abb96673d8ddb18166bc595312ebcb96e803de9', - placement='fabtests', when='@1.7.0') - resource(name='fabtests', - url='https://github.com/ofiwg/fabtests/releases/download/v1.6.1/fabtests-1.6.1.tar.gz', - sha256='d357466b868fdaf1560d89ffac4c4e93a679486f1b4221315644d8d3e21174bf', - placement='fabtests', when='@1.6.1') - resource(name='fabtests', - url='https://github.com/ofiwg/fabtests/releases/download/v1.6.0/fabtests-1.6.0.tar.gz', - sha256='dc3eeccccb005205017f5af60681ede15782ce202a0103450a6d56a7ff515a67', - placement='fabtests', when='@1.6.0') - resource(name='fabtests', - url='https://github.com/ofiwg/fabtests/releases/download/v1.5.3/fabtests-1.5.3.tar.gz', - sha256='3835b3bf86cd00d23df0ddba8bf317e4a195e8d5c3c2baa918b373d548f77f29', - placement='fabtests', when='@1.5.3') - resource(name='fabtests', - url='https://github.com/ofiwg/fabtests/releases/download/v1.5.0/fabtests-1.5.0.tar.gz', - sha256='1dddd446c3f1df346899f9a8636f1b4265de5b863103ae24876e9f0c1e40a69d', - placement='fabtests', when='@1.5.0') - resource(name='fabtests', - url='https://github.com/ofiwg/fabtests/releases/download/v1.4.2/fabtests-1.4.2.tar.gz', - sha256='3b78d0ca1b223ff21b7f5b3627e67e358e3c18b700f86b017e2233fee7e88c2e', - placement='fabtests', when='@1.4.2') - conflicts('@1.9.0', when='platform=darwin', msg='This distribution is missing critical files') @@ -123,10 +85,6 @@ def autoreconf(self, spec, prefix): bash = which('bash') bash('./autogen.sh') - if self.run_tests: - with working_dir('fabtests'): - bash('./autogen.sh') - def configure_args(self): args = [] @@ -143,29 +101,6 @@ def configure_args(self): return args - def install(self, spec, prefix): - # Call main install method - super(Libfabric, self).install(spec, prefix) - - # Build and install fabtests, if available - if not os.path.isdir('fabtests'): - return - with working_dir('fabtests'): - configure = Executable('./configure') - configure('--prefix={0}'.format(self.prefix), - '--with-libfabric={0}'.format(self.prefix)) - make() - make('install') - def installcheck(self): fi_info = Executable(self.prefix.bin.fi_info) fi_info() - - # Run fabtests test suite if available - if not os.path.isdir('fabtests'): - return - if self.spec.satisfies('@1.8.0,1.9.0'): - # make test seems broken. - return - with working_dir('fabtests'): - make('test') From 69231c7d189239df9874b4a4273acf16d64a3dc1 Mon Sep 17 00:00:00 2001 From: "Mark W. Krentel" Date: Wed, 18 Mar 2020 22:19:25 -0500 Subject: [PATCH 107/377] hpctoolkit: restore binutils 2.34 for master (#15556) Hpctoolkit master was recently updated to test for and allow old binutils <= 2.33.1 and/or new binutils 2.34. Older hpctoolkit up to 2030.03.01 will forever require :2.33.1. Adjust the libunwind dependency for safety with the current concretizer. --- var/spack/repos/builtin/packages/hpctoolkit/package.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/hpctoolkit/package.py b/var/spack/repos/builtin/packages/hpctoolkit/package.py index a8c489f87d4..d64ce78fadc 100644 --- a/var/spack/repos/builtin/packages/hpctoolkit/package.py +++ b/var/spack/repos/builtin/packages/hpctoolkit/package.py @@ -60,15 +60,16 @@ class Hpctoolkit(AutotoolsPackage): ' +graph +regex +shared +multithreaded visibility=global' ) - depends_on('binutils@:2.33.1+libiberty~nls', type='link') + depends_on('binutils+libiberty~nls', type='link', when='@master') + depends_on('binutils@:2.33.1+libiberty~nls', type='link', when='@:2020.03.99') depends_on('boost' + boost_libs) depends_on('bzip2+shared', type='link') depends_on('dyninst@9.3.2:') depends_on('elfutils+bzip2+xz~nls', type='link') depends_on('intel-tbb+shared') depends_on('libdwarf') - depends_on('libmonitor+hpctoolkit') - depends_on('libmonitor+bgq', when='+bgq') + depends_on('libmonitor+hpctoolkit+bgq', when='+bgq') + depends_on('libmonitor+hpctoolkit~bgq', when='~bgq') depends_on('libunwind@1.4: +xz') depends_on('mbedtls+pic') depends_on('xerces-c transcoder=iconv') From 8bffa57ac454f4c35fcb53b2dfdcceb15fa01407 Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Wed, 18 Mar 2020 22:37:09 -0500 Subject: [PATCH 108/377] Buildcache: fix relocation of binaries with relative rpaths (#15558) --- lib/spack/spack/relocate.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py index afbae543afb..c7d442a427a 100644 --- a/lib/spack/spack/relocate.py +++ b/lib/spack/spack/relocate.py @@ -137,7 +137,7 @@ def get_normalized_elf_rpaths(orig_path_name, rel_rpaths): norm_rpaths = list() for rpath in rel_rpaths: if rpath.startswith('$ORIGIN'): - sub = re.sub('$ORIGIN', + sub = re.sub(re.escape('$ORIGIN'), os.path.dirname(orig_path_name), rpath) norm = os.path.normpath(sub) From 14e2c42bcef0cf1b233b70eda23a75e269ba8d92 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 18 Mar 2020 23:58:39 -0400 Subject: [PATCH 109/377] py-matplotlib: add 3.2.1 (#15560) --- var/spack/repos/builtin/packages/py-matplotlib/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index e5d898f1df4..4e5dbf91356 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -13,7 +13,7 @@ class PyMatplotlib(PythonPackage): and interactive visualizations in Python.""" homepage = "https://matplotlib.org/" - url = "https://pypi.io/packages/source/m/matplotlib/matplotlib-3.2.0.tar.gz" + url = "https://pypi.io/packages/source/m/matplotlib/matplotlib-3.2.1.tar.gz" maintainers = ['adamjstewart'] @@ -27,6 +27,7 @@ class PyMatplotlib(PythonPackage): 'matplotlib.testing.jpl_units' ] + version('3.2.1', sha256='ffe2f9cdcea1086fc414e82f42271ecf1976700b8edd16ca9d376189c6d93aee') version('3.2.0', sha256='651d76daf9168250370d4befb09f79875daa2224a9096d97dfc3ed764c842be4') version('3.1.3', sha256='db3121f12fb9b99f105d1413aebaeb3d943f269f3d262b45586d12765866f0c6') version('3.1.2', sha256='8e8e2c2fe3d873108735c6ee9884e6f36f467df4a143136209cff303b183bada') From a3cb1b8e7ec66e5f076a6ea31e1f713e34e9c282 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Thu, 19 Mar 2020 20:28:18 +0900 Subject: [PATCH 110/377] amdblis + blis: fix spack info and libs query (#15566) --- var/spack/repos/builtin/packages/amdblis/package.py | 1 + var/spack/repos/builtin/packages/blis/package.py | 4 ++++ 2 files changed, 5 insertions(+) diff --git a/var/spack/repos/builtin/packages/amdblis/package.py b/var/spack/repos/builtin/packages/amdblis/package.py index 5b216bebd7d..706e7f6bd25 100644 --- a/var/spack/repos/builtin/packages/amdblis/package.py +++ b/var/spack/repos/builtin/packages/amdblis/package.py @@ -15,6 +15,7 @@ class Amdblis(BlisBase): computationally intensive operations. """ + _name = 'amdblis' homepage = "https://developer.amd.com/amd-aocl/blas-library/" url = "https://github.com/amd/blis/archive/2.1.tar.gz" git = "https://github.com/amd/blis.git" diff --git a/var/spack/repos/builtin/packages/blis/package.py b/var/spack/repos/builtin/packages/blis/package.py index ea7ca8ff428..c2fc1545a3e 100644 --- a/var/spack/repos/builtin/packages/blis/package.py +++ b/var/spack/repos/builtin/packages/blis/package.py @@ -102,6 +102,10 @@ def darwin_fix(self): if self.spec.satisfies('platform=darwin'): fix_darwin_install_name(self.prefix.lib) + @property + def libs(self): + return find_libraries(['libblis'], root=self.prefix, recursive=True) + class Blis(BlisBase): """BLIS is a portable software framework for instantiating high-performance From 363cf9f9b138cdeaeeecb1cfe7698dcd2dd1a8f4 Mon Sep 17 00:00:00 2001 From: darmac Date: Thu, 19 Mar 2020 22:24:35 +0800 Subject: [PATCH 111/377] update attr version to 2.4.48 (#15535) * update attr version to 2.4.48 * attr: remove redundant make() in install() --- var/spack/repos/builtin/packages/attr/package.py | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/attr/package.py b/var/spack/repos/builtin/packages/attr/package.py index a58dc75f4d0..549909d2097 100644 --- a/var/spack/repos/builtin/packages/attr/package.py +++ b/var/spack/repos/builtin/packages/attr/package.py @@ -12,9 +12,17 @@ class Attr(AutotoolsPackage): homepage = "https://savannah.nongnu.org/projects/attr" url = "http://download.savannah.gnu.org/releases/attr/attr-2.4.47.src.tar.gz" + version('2.4.48', sha256='5ead72b358ec709ed00bbf7a9eaef1654baad937c001c044fe8b74c57f5324e7') version('2.4.47', sha256='25772f653ac5b2e3ceeb89df50e4688891e21f723c460636548971652af0a859') version('2.4.46', sha256='dcd69bdca7ff166bc45141eddbcf21967999a6b66b0544be12a1cc2fd6340e1f') + def url_for_version(self, version): + if version >= Version('2.4.48'): + url = 'http://download.savannah.gnu.org/releases/attr/attr-{0}.tar.gz' + else: + url = 'http://download.savannah.gnu.org/releases/attr/attr-{0}.src.tar.gz' + return url.format(version) + def configure_args(self): args = [] args.append('--disable-static') @@ -22,5 +30,7 @@ def configure_args(self): # Ref. http://www.linuxfromscratch.org/blfs/view/7.5/postlfs/attr.html def install(self, spec, prefix): - make() - make('install', 'install-dev', 'install-lib') + if self.version >= Version('2.4.48'): + make('install') + else: + make('install', 'install-dev', 'install-lib') From 0b1b8c3936ba01767b17b20eb54bfacc8376f2c8 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Thu, 19 Mar 2020 15:34:18 +0100 Subject: [PATCH 112/377] openssl: added v1.1.1e and v1.0.2u (#15568) --- var/spack/repos/builtin/packages/openssl/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 450990c179a..3f8e4647c41 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -25,6 +25,7 @@ class Openssl(Package): # Uses Fake Autotools, should subclass Package # The latest stable version is the 1.1.1 series. This is also our Long Term # Support (LTS) version, supported until 11th September 2023. + version('1.1.1e', sha256='694f61ac11cb51c9bf73f54e771ff6022b0327a43bbdfa1b2f19de1662a6dcbe') version('1.1.1d', sha256='1e3a91bc1f9dfce01af26026f856e064eab4c8ee0a8f457b5ae30b40b8b711f2') version('1.1.1c', sha256='f6fb3079ad15076154eda9413fed42877d668e7069d9b87396d0804fdb3f4c90') version('1.1.1b', sha256='5c557b023230413dfb0756f3137a13e6d726838ccd1430888ad15bfb2b43ea4b') @@ -45,6 +46,7 @@ class Openssl(Package): # Uses Fake Autotools, should subclass Package # Our previous LTS version (1.0.2 series) will continue to be supported # until 31st December 2019 (security fixes only during the last year of # support). + version('1.0.2u', sha256='ecd0c6ffb493dd06707d38b14bb4d8c2288bb7033735606569d8f90f89669d16') version('1.0.2t', sha256='14cb464efe7ac6b54799b34456bd69558a749a4931ecfd9cf9f71d7881cac7bc') version('1.0.2s', sha256='cabd5c9492825ce5bd23f3c3aeed6a97f8142f606d893df216411f07d1abab96') version('1.0.2r', sha256='ae51d08bba8a83958e894946f15303ff894d75c2b8bbd44a852b64e3fe11d0d6') From 7cfa497912d565ae24ae90a8095fde206901a276 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Fri, 3 Jan 2020 23:28:53 -0800 Subject: [PATCH 113/377] bugfix: `spack.package.possible_dependencies()` should return virtuals `spack.package.possible_dependencies()` was forgetting to pass the `visited` dict to recursive calls; this fixes it --- lib/spack/spack/package.py | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 2c8917a9aca..de0f9b3568e 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -2154,11 +2154,6 @@ def possible_dependencies(*pkg_or_spec, **kwargs): See ``PackageBase.possible_dependencies`` for details. """ - transitive = kwargs.get('transitive', True) - expand_virtuals = kwargs.get('expand_virtuals', True) - deptype = kwargs.get('deptype', 'all') - missing = kwargs.get('missing') - packages = [] for pos in pkg_or_spec: if isinstance(pos, PackageMeta): @@ -2172,8 +2167,7 @@ def possible_dependencies(*pkg_or_spec, **kwargs): visited = {} for pkg in packages: - pkg.possible_dependencies( - transitive, expand_virtuals, deptype, visited, missing) + pkg.possible_dependencies(visited=visited, **kwargs) return visited From 3255eaba0dddca0a9e224f9e3e745dc6ff956b1d Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sun, 5 Jan 2020 19:28:23 -0800 Subject: [PATCH 114/377] refactor: `spack.package.possible_dependencies()` handles virtuals - [x] move some logic for handling virtual packages from the `spack dependencies` command into `spack.package.possible_dependencies()` - [x] rework possible dependencies tests so that expected and actual output are on the left/right respectively --- lib/spack/spack/cmd/dependencies.py | 22 +++----- lib/spack/spack/package.py | 27 ++++++---- lib/spack/spack/test/cmd/dependencies.py | 4 +- lib/spack/spack/test/package_class.py | 66 +++++++++++++++++------- 4 files changed, 75 insertions(+), 44 deletions(-) diff --git a/lib/spack/spack/cmd/dependencies.py b/lib/spack/spack/cmd/dependencies.py index e65e050bfac..7f390341ef4 100644 --- a/lib/spack/spack/cmd/dependencies.py +++ b/lib/spack/spack/cmd/dependencies.py @@ -9,6 +9,7 @@ import spack.cmd import spack.cmd.common.arguments as arguments import spack.environment as ev +import spack.package import spack.repo import spack.store @@ -52,22 +53,15 @@ def dependencies(parser, args): else: spec = specs[0] - - if not spec.virtual: - packages = [spec.package] - else: - packages = [ - spack.repo.get(s.name) - for s in spack.repo.path.providers_for(spec)] - - dependencies = set() - for pkg in packages: - possible = pkg.possible_dependencies( - args.transitive, args.expand_virtuals, deptype=args.deptype) - dependencies.update(possible) + dependencies = spack.package.possible_dependencies( + spec, + transitive=args.transitive, + expand_virtuals=args.expand_virtuals, + deptype=args.deptype + ) if spec.name in dependencies: - dependencies.remove(spec.name) + del dependencies[spec.name] if dependencies: colify(sorted(dependencies)) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index de0f9b3568e..9156d7d0dd3 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -605,11 +605,10 @@ def possible_dependencies( """ deptype = spack.dependency.canonical_deptype(deptype) - if visited is None: - visited = {cls.name: set()} + visited = {} if visited is None else visited + missing = {} if missing is None else missing - if missing is None: - missing = {cls.name: set()} + visited.setdefault(cls.name, set()) for name, conditions in cls.dependencies.items(): # check whether this dependency could be of the type asked for @@ -624,6 +623,7 @@ def possible_dependencies( providers = spack.repo.path.providers_for(name) dep_names = [spec.name for spec in providers] else: + visited.setdefault(cls.name, set()).add(name) visited.setdefault(name, set()) continue else: @@ -2157,13 +2157,20 @@ def possible_dependencies(*pkg_or_spec, **kwargs): packages = [] for pos in pkg_or_spec: if isinstance(pos, PackageMeta): - pkg = pos - elif isinstance(pos, spack.spec.Spec): - pkg = pos.package - else: - pkg = spack.spec.Spec(pos).package + packages.append(pos) + continue - packages.append(pkg) + if not isinstance(pos, spack.spec.Spec): + pos = spack.spec.Spec(pos) + + if spack.repo.path.is_virtual(pos.name): + packages.extend( + p.package_class + for p in spack.repo.path.providers_for(pos.name) + ) + continue + else: + packages.append(pos.package_class) visited = {} for pkg in packages: diff --git a/lib/spack/spack/test/cmd/dependencies.py b/lib/spack/spack/test/cmd/dependencies.py index fc470691814..05d05569369 100644 --- a/lib/spack/spack/test/cmd/dependencies.py +++ b/lib/spack/spack/test/cmd/dependencies.py @@ -17,7 +17,7 @@ mpi_deps = ['fake'] -def test_immediate_dependencies(mock_packages): +def test_direct_dependencies(mock_packages): out = dependencies('mpileaks') actual = set(re.split(r'\s+', out.strip())) expected = set(['callpath'] + mpis) @@ -47,7 +47,7 @@ def test_transitive_dependencies_with_deptypes(mock_packages): @pytest.mark.db -def test_immediate_installed_dependencies(mock_packages, database): +def test_direct_installed_dependencies(mock_packages, database): with color_when(False): out = dependencies('--installed', 'mpileaks^mpich') diff --git a/lib/spack/spack/test/package_class.py b/lib/spack/spack/test/package_class.py index b3351ffb491..d540ac663e1 100644 --- a/lib/spack/spack/test/package_class.py +++ b/lib/spack/spack/test/package_class.py @@ -11,12 +11,17 @@ """ import pytest +import spack.package import spack.repo -@pytest.fixture -def mpileaks_possible_deps(mock_packages): - mpi_names = [spec.name for spec in spack.repo.path.providers_for('mpi')] +@pytest.fixture(scope="module") +def mpi_names(mock_repo_path): + return [spec.name for spec in mock_repo_path.providers_for('mpi')] + + +@pytest.fixture() +def mpileaks_possible_deps(mock_packages, mpi_names): possible = { 'callpath': set(['dyninst'] + mpi_names), 'dyninst': set(['libdwarf', 'libelf']), @@ -34,47 +39,72 @@ def mpileaks_possible_deps(mock_packages): def test_possible_dependencies(mock_packages, mpileaks_possible_deps): mpileaks = spack.repo.get('mpileaks') - assert (mpileaks.possible_dependencies(expand_virtuals=True) == - mpileaks_possible_deps) + assert mpileaks_possible_deps == ( + mpileaks.possible_dependencies(expand_virtuals=True)) - assert mpileaks.possible_dependencies(expand_virtuals=False) == { - 'callpath': set(['dyninst']), + assert { + 'callpath': set(['dyninst', 'mpi']), 'dyninst': set(['libdwarf', 'libelf']), 'libdwarf': set(['libelf']), 'libelf': set(), 'mpi': set(), - 'mpileaks': set(['callpath']), - } + 'mpileaks': set(['callpath', 'mpi']), + } == mpileaks.possible_dependencies(expand_virtuals=False) + + +def test_possible_direct_dependencies(mock_packages, mpileaks_possible_deps): + mpileaks = spack.repo.get('mpileaks') + deps = mpileaks.possible_dependencies(transitive=False, + expand_virtuals=False) + + assert { + 'callpath': set(), + 'mpi': set(), + 'mpileaks': set(['callpath', 'mpi']), + } == deps + + +def test_possible_dependencies_virtual(mock_packages, mpi_names): + expected = dict( + (name, set(spack.repo.get(name).dependencies)) + for name in mpi_names + ) + + # only one mock MPI has a dependency + expected['fake'] = set() + + assert expected == spack.package.possible_dependencies( + "mpi", transitive=False) def test_possible_dependencies_missing(mock_packages): md = spack.repo.get("missing-dependency") missing = {} md.possible_dependencies(transitive=True, missing=missing) - assert missing["missing-dependency"] == set([ + assert set([ "this-is-a-missing-dependency" - ]) + ]) == missing["missing-dependency"] def test_possible_dependencies_with_deptypes(mock_packages): dtbuild1 = spack.repo.get('dtbuild1') - assert dtbuild1.possible_dependencies(deptype=('link', 'run')) == { + assert { 'dtbuild1': set(['dtrun2', 'dtlink2']), 'dtlink2': set(), 'dtrun2': set(), - } + } == dtbuild1.possible_dependencies(deptype=('link', 'run')) - assert dtbuild1.possible_dependencies(deptype=('build')) == { + assert { 'dtbuild1': set(['dtbuild2', 'dtlink2']), 'dtbuild2': set(), 'dtlink2': set(), - } + } == dtbuild1.possible_dependencies(deptype=('build')) - assert dtbuild1.possible_dependencies(deptype=('link')) == { + assert { 'dtbuild1': set(['dtlink2']), 'dtlink2': set(), - } + } == dtbuild1.possible_dependencies(deptype=('link')) def test_possible_dependencies_with_multiple_classes( @@ -88,4 +118,4 @@ def test_possible_dependencies_with_multiple_classes( 'dt-diamond-bottom': set(), }) - assert spack.package.possible_dependencies(*pkgs) == expected + assert expected == spack.package.possible_dependencies(*pkgs) From bfa72ed9261ac3df66ce53f92f86ae1548be0731 Mon Sep 17 00:00:00 2001 From: Yannik Stradmann <49203055+ystradmann@users.noreply.github.com> Date: Thu, 19 Mar 2020 17:15:19 +0100 Subject: [PATCH 115/377] Add package: py-deprecated (#15571) https://github.com/tantale/deprecated --- .../builtin/packages/py-deprecated/package.py | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-deprecated/package.py diff --git a/var/spack/repos/builtin/packages/py-deprecated/package.py b/var/spack/repos/builtin/packages/py-deprecated/package.py new file mode 100644 index 00000000000..7d1fe4af933 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-deprecated/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyDeprecated(PythonPackage): + """Python @deprecated decorator to deprecate old python classes, + functions or methods.""" + + homepage = "https://github.com/tantale/deprecated" + url = "https://github.com/tantale/deprecated/archive/v1.2.7.tar.gz" + + version("1.2.7", sha256="7db3c814ddcac9d79c5bae8a0e82a5bba55cb8e46f3d611d0d8611c34a72a783") + + depends_on("python@2.7:2.8,3.4:", type=("build", "run")) + depends_on("py-wrapt@1.10:1.99999", type=("build", "run")) + depends_on("py-setuptools", type="build") From 8142b2dc6b3d74767f69002fdb309e3cc6da58ba Mon Sep 17 00:00:00 2001 From: darmac Date: Fri, 20 Mar 2020 00:21:37 +0800 Subject: [PATCH 116/377] add new package: yarn (#15562) --- .../repos/builtin/packages/yarn/package.py | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 var/spack/repos/builtin/packages/yarn/package.py diff --git a/var/spack/repos/builtin/packages/yarn/package.py b/var/spack/repos/builtin/packages/yarn/package.py new file mode 100644 index 00000000000..c9a5299a10b --- /dev/null +++ b/var/spack/repos/builtin/packages/yarn/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Yarn(Package): + """Fast, reliable, and secure dependency management.""" + + homepage = "https://yarnpkg.com" + url = "https://github.com/yarnpkg/yarn/releases/download/v1.22.4/yarn-v1.22.4.tar.gz" + + version('1.22.4', sha256='bc5316aa110b2f564a71a3d6e235be55b98714660870c5b6b2d2d3f12587fb58') + version('1.22.2', sha256='de4cff575ae7151f8189bf1d747f026695d768d0563e2860df407ab79c70693d') + version('1.22.1', sha256='3af905904932078faa8f485d97c928416b30a86dd09dcd76e746a55c7f533b72') + version('1.22.0', sha256='de8871c4e2822cba80d58c2e72366fb78567ec56e873493c9ca0cca76c60f9a5') + version('1.21.1', sha256='d1d9f4a0f16f5ed484e814afeb98f39b82d4728c6c8beaafb5abc99c02db6674') + + def install(self, spec, prefix): + install_tree('.', prefix) From ef68d1f5dff07a7b80b72f73df3764c869effc3b Mon Sep 17 00:00:00 2001 From: darmac Date: Fri, 20 Mar 2020 00:22:03 +0800 Subject: [PATCH 117/377] add new package: ntirpc (#15561) --- .../repos/builtin/packages/ntirpc/package.py | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ntirpc/package.py diff --git a/var/spack/repos/builtin/packages/ntirpc/package.py b/var/spack/repos/builtin/packages/ntirpc/package.py new file mode 100644 index 00000000000..fa29056e16b --- /dev/null +++ b/var/spack/repos/builtin/packages/ntirpc/package.py @@ -0,0 +1,22 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Ntirpc(CMakePackage): + """New development on tirpc""" + + homepage = "https://github.com/nfs-ganesha/ntirpc" + url = "https://github.com/nfs-ganesha/ntirpc/archive/v3.2.tar.gz" + + version('3.2', sha256='db1639ca2f15df7e30d8c0a820ed9adf4eb623798db03b56a3659eedff49af76') + version('3.1', sha256='280b57db3a37c5b05116a7850460152b1ac53c050fd61ce190f5a5eb55ed3ba1') + version('3.0', sha256='9a6b11c1aa3e7f5f1f491bca0275e759de5bed2d73c8a028af7b6aadb68ac795') + version('1.8.0', sha256='3bb642dccc8f2506b57a03b5d3358654f59f47b33fddfaa5a7330df4cf336f9f') + version('1.7.3', sha256='8713ef095efc44df426bbd2b260ad457e5335bf3008fb97f01b0775c8042e54b') + + depends_on('libnsl') + depends_on('userspace-rcu') From b583b0e112b538530360cb7137f4776999c9b49c Mon Sep 17 00:00:00 2001 From: Kai Germaschewski Date: Thu, 19 Mar 2020 12:42:19 -0400 Subject: [PATCH 118/377] petsc fix hdf5 (#15572) * petsc: add checksum for 3.12.4 * petsc: constrain hdf5 to <= 1.10.x Current petsc will error when being build with hdf5 1.12, so this ensures that a compatible hdf5 will be used. Fix suggested by @balay. --- var/spack/repos/builtin/packages/petsc/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index b58fa0c3c88..577f53a1636 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -24,6 +24,7 @@ class Petsc(Package): version('develop', branch='master') version('xsdk-0.2.0', tag='xsdk-0.2.0') + version('3.12.4', sha256='56a941130da93bbacb3cfa74dcacea1e3cd8e36a0341f9ced09977b1457084c3') version('3.12.3', sha256='91f77d7b0f54056f085b9e27938922db3d9bb1734a2e2a6d26f43d3e6c0cf631') version('3.12.2', sha256='d874b2e198c4cb73551c2eca1d2c5d27da710be4d00517adb8f9eb3d6d0375e8') version('3.12.1', sha256='b72d895d0f4a79acb13ebc782b47b26d10d4e5706d399f533afcd5b3dba13737') @@ -145,7 +146,7 @@ class Petsc(Package): depends_on('metis@5:~int64', when='@3.8:+metis~int64') depends_on('metis@5:+int64', when='@3.8:+metis+int64') - depends_on('hdf5+mpi+hl+fortran', when='+hdf5+mpi') + depends_on('hdf5@:1.10.99+mpi+hl+fortran', when='+hdf5+mpi') depends_on('zlib', when='+hdf5') depends_on('parmetis', when='+metis+mpi') depends_on('valgrind', when='+valgrind') From f9e58a52dad06caee5c7becd4e9025253a2571f4 Mon Sep 17 00:00:00 2001 From: Jordan Ogas Date: Thu, 19 Mar 2020 12:49:11 -0700 Subject: [PATCH 119/377] add charliecloud/0.14; remove umoci/skopeo; remove builder variant (#15573) * add charliecloud/0.14; remove umoci/skopeo; remove builder variant * fix typo * add maintainer; add explicit config doc options; add py-requests as run dependency * add autoconf build dependencies --- .../builtin/packages/charliecloud/package.py | 27 ++++++++++--------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/var/spack/repos/builtin/packages/charliecloud/package.py b/var/spack/repos/builtin/packages/charliecloud/package.py index 9329455d842..e72c71cf860 100644 --- a/var/spack/repos/builtin/packages/charliecloud/package.py +++ b/var/spack/repos/builtin/packages/charliecloud/package.py @@ -9,22 +9,24 @@ class Charliecloud(AutotoolsPackage): """Lightweight user-defined software stacks for HPC.""" + maintainers = ['j-ogas'] homepage = "https://hpc.github.io/charliecloud" - url = "https://github.com/hpc/charliecloud/releases/download/v0.9.10/charliecloud-0.9.10.tar.gz" + url = "https://github.com/hpc/charliecloud/releases/download/v0.14/charliecloud-0.9.10.tar.gz" git = "https://github.com/hpc/charliecloud.git" version('master', branch='master') - version('0.13', sha256='5740bff6e410ca99484c1bdf3dbe834c0f753c846d55c19d6162967a3e2718e0') + version('0.14', sha256='4ae23c2d6442949e16902f9d5604dbd1d6059aeb5dd461b11fc5c74d49dcb194') - depends_on('python@3.4:', type=('build', 'run')) + depends_on('m4', type='build') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') - # experimental builder (ch-grow) - variant('builder', default=False, description='Bundle dependencies for unprivileged builder (ch-grow)') - depends_on('py-lark-parser', type='run', when='+builder') - depends_on('skopeo', type='run', when='+builder') - depends_on('umoci', type='run', when='+builder') + depends_on('python@3.5:', type='run') + depends_on('py-lark-parser', type='run') + depends_on('py-requests', type='run') - # man pages and html docs + # man pages and html docs variant variant('docs', default=False, description='Build man pages and html docs') depends_on('rsync', type='build', when='+docs') depends_on('py-sphinx', type='build', when='+docs') @@ -37,10 +39,9 @@ def configure_args(self): args = [] - if '+docs' not in self.spec: + if '+docs' in self.spec: + args.append('--enable-html') + else: args.append('--disable-html') - if '+builder' not in self.spec: - args.append('--disable-ch-grow') - return args From a61c53a5c96c04d19116673e7c9d2bcc628c889e Mon Sep 17 00:00:00 2001 From: Teodor Nikolov Date: Thu, 19 Mar 2020 21:50:12 +0200 Subject: [PATCH 120/377] cosma: added package at v2.0.2 (#15497) * [new package] COSMA * Use virtual dependencies --- .../repos/builtin/packages/cosma/package.py | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 var/spack/repos/builtin/packages/cosma/package.py diff --git a/var/spack/repos/builtin/packages/cosma/package.py b/var/spack/repos/builtin/packages/cosma/package.py new file mode 100644 index 00000000000..efb81035da9 --- /dev/null +++ b/var/spack/repos/builtin/packages/cosma/package.py @@ -0,0 +1,69 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class Cosma(CMakePackage): + """ + Distributed Communication-Optimal Matrix-Matrix Multiplication Library + """ + + maintainers = ['teonnik', 'kabicm'] + homepage = 'https://github.com/eth-cscs/COSMA' + url = 'https://github.com/eth-cscs/COSMA/releases/download/v2.0.2/cosma.tar.gz' + git = 'https://github.com/eth-cscs/COSMA.git' + + # note: The default archives produced with github do not have the archives + # of the submodules. + version('master', branch='master', submodules=True) + version('2.0.2', sha256='4f3354828bc718f3eef2f0098c3bdca3499297497a220da32db1acd57920c68d') + # note: this version fails to build at the moment + # version('1.0.0', + # url='https://github.com/eth-cscs/COSMA/releases/download/1.0/cosma.tar.gz', + # sha256='c142104258dcca4c17fa7faffc2990a08d2777235c7980006e93c5dca51061f6') + + variant('cuda', default=False, + description='Build with the CUBLAS back end.') + variant('scalapack', default=False, + description='Build with ScaLAPACK support.') + + depends_on('cmake@3.12:', type='build') + depends_on('mpi@3:') + depends_on('blas', when='~cuda') + depends_on('scalapack', when='+scalapack') + # COSMA is written entirely in C++, it may use cublasXt but a CUDA capable + # compiler is not needed. There is no need for CudaPackage in this recipe. + depends_on('cuda', when='+cuda') + + def setup_build_environment(self, env): + if '+cuda' in self.spec: + env.set('CUDA_PATH', self.spec['cuda'].prefix) + + def cmake_args(self): + spec = self.spec + args = ['-DCOSMA_WITH_TESTS=OFF', + '-DCOSMA_WITH_APPS=OFF', + '-DCOSMA_WITH_PROFILING=OFF', + '-DCOSMA_WITH_BENCHMARKS=OFF'] + + if '^mkl' in spec: + args += ['-DCOSMA_BLAS=MKL'] + elif '^netlib-lapack' in spec: + args += ['-DCOSMA_BLAS=CUSTOM'] + elif '^openblas' in spec: + args += ['-DCOSMA_BLAS=OPENBLAS'] + elif '+cuda' in spec: + args += ['-DCOSMA_BLAS=CUDA'] + else: # TODO '^rocm' in spec: + args += ['-DCOSMA_BLAS=ROCM'] + + if '+scalapack' and '^mkl' in spec: + args += ['-DCOSMA_SCALAPACK=MKL'] + elif '+scalapack' and '^netlib-scalapack' in spec: + args += ['-DCOSMA_SCALAPACK=CUSTOM'] + + return args From e5f8b093a9c1b95ec30ba1a02777c91ad1a1805a Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Thu, 19 Mar 2020 15:11:50 -0700 Subject: [PATCH 121/377] Cray bugfix: TERM missing while reading default target (#15381) Bug: Spack hangs on some Cray machines Reason: The TERM environment variable is necessary to run bash -lc "echo $CRAY_CPU_TARGET", but we run that command within env -i, which wipes the environment. Fix: Manually forward the TERM environment variable to env -i /bin/bash -lc "echo $CRAY_CPU_TARGET" --- lib/spack/spack/platforms/cray.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/lib/spack/spack/platforms/cray.py b/lib/spack/spack/platforms/cray.py index cbeba96461b..8eae51e66a2 100644 --- a/lib/spack/spack/platforms/cray.py +++ b/lib/spack/spack/platforms/cray.py @@ -7,7 +7,7 @@ import re import llnl.util.tty as tty from spack.paths import build_env_path -from spack.util.executable import which +from spack.util.executable import Executable from spack.architecture import Platform, Target, NoPlatformError from spack.operating_systems.cray_frontend import CrayFrontend from spack.operating_systems.cnl import Cnl @@ -117,11 +117,13 @@ def _default_target_from_env(self): ''' # env -i /bin/bash -lc echo $CRAY_CPU_TARGET 2> /dev/null if getattr(self, 'default', None) is None: - env = which('env') - output = env("-i", "/bin/bash", "-lc", "echo $CRAY_CPU_TARGET", - output=str, error=os.devnull) - self.default = output.strip() - tty.debug("Found default module:%s" % self.default) + output = Executable('/bin/bash')('-lc', 'echo $CRAY_CPU_TARGET', + env={'TERM': os.environ['TERM']}, + output=str, error=os.devnull) + output = ''.join(output.split()) # remove all whitespace + if output: + self.default = output + tty.debug("Found default module:%s" % self.default) return self.default def _avail_targets(self): From b522296a5ab84adda4d20b1de1a3f50c3cae70ec Mon Sep 17 00:00:00 2001 From: Nithin Senthil Kumar <52734841+nithintsk@users.noreply.github.com> Date: Thu, 19 Mar 2020 21:59:00 -0400 Subject: [PATCH 122/377] Update MVAPICH2 package for 2.3.3 release (#15578) Co-authored-by: senthilkumar.16 --- var/spack/repos/builtin/packages/mvapich2/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py index 87e9f77848b..f6301a564a8 100644 --- a/var/spack/repos/builtin/packages/mvapich2/package.py +++ b/var/spack/repos/builtin/packages/mvapich2/package.py @@ -10,10 +10,11 @@ class Mvapich2(AutotoolsPackage): """MVAPICH2 is an MPI implementation for Infiniband networks.""" homepage = "http://mvapich.cse.ohio-state.edu/" - url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3.2.tar.gz" + url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3.3.tar.gz" list_url = "http://mvapich.cse.ohio-state.edu/downloads/" # Prefer the latest stable release + version('2.3.3', sha256='41d3261be57e5bc8aabf4e32981543c015c5443ff032a26f18205985e18c2b73') version('2.3.2', sha256='30cc0d7bcaa075d204692f76bca4d65a539e0f661c7460ffa9f835d6249e1ebf') version('2.3.1', sha256='314e12829f75f3ed83cd4779a972572d1787aac6543a3d024ea7c6080e0ee3bf') version('2.3', sha256='01d5fb592454ddd9ecc17e91c8983b6aea0e7559aa38f410b111c8ef385b50dd') From ce7cd7a5ab488abac41007eedb6d4d1550e9b258 Mon Sep 17 00:00:00 2001 From: darmac Date: Fri, 20 Mar 2020 11:35:59 +0800 Subject: [PATCH 123/377] add new package: libiscsi (#15579) --- .../builtin/packages/libiscsi/package.py | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 var/spack/repos/builtin/packages/libiscsi/package.py diff --git a/var/spack/repos/builtin/packages/libiscsi/package.py b/var/spack/repos/builtin/packages/libiscsi/package.py new file mode 100644 index 00000000000..621cc875d64 --- /dev/null +++ b/var/spack/repos/builtin/packages/libiscsi/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Libiscsi(AutotoolsPackage): + """Libiscsi is a client-side library to implement the iSCSI protocol that can + be used to access the resources of an iSCSI target.""" + + homepage = "https://github.com/sahlberg/libiscsi" + url = "https://github.com/sahlberg/libiscsi/archive/1.19.0.tar.gz" + + version('1.19.0', sha256='c7848ac722c8361d5064654bc6e926c2be61ef11dd3875020a63931836d806df') + version('1.18.0', sha256='464d104e12533dc11f0dd7662cbc2f01c132f94aa4f5bd519e3413ef485830e8') + version('1.17.0', sha256='80a7f75bfaffc8bec9920ba7af3f1d14cd862c35c3c5f2c9617b45b975232112') + version('1.16.0', sha256='35c7be63a8c3a7cee7b697901b6d2dd464e098e1881671eb67462983053b3c7b') + version('1.15.0', sha256='489e625e58c1e6da2fa3536f9c4b12290f2d3fb4ce14edc0583b8ba500605c34') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + + def autoreconf(self, spec, prefix): + autoreconf('--install', '--force') From a89c5b36f0bc2b3ab54b6e73b6812f327d016759 Mon Sep 17 00:00:00 2001 From: darmac Date: Fri, 20 Mar 2020 11:57:04 +0800 Subject: [PATCH 124/377] add new package: bcache (#15563) * add new package: bcache * add depends: gettext for libintl --- .../builtin/packages/bcache/func_crc64.patch | 13 +++++++ .../repos/builtin/packages/bcache/package.py | 36 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 var/spack/repos/builtin/packages/bcache/func_crc64.patch create mode 100644 var/spack/repos/builtin/packages/bcache/package.py diff --git a/var/spack/repos/builtin/packages/bcache/func_crc64.patch b/var/spack/repos/builtin/packages/bcache/func_crc64.patch new file mode 100644 index 00000000000..7acc312139c --- /dev/null +++ b/var/spack/repos/builtin/packages/bcache/func_crc64.patch @@ -0,0 +1,13 @@ +diff --git a/bcache.c b/bcache.c +index 8f37445..8b4b986 100644 +--- a/bcache.c ++++ b/bcache.c +@@ -115,7 +115,7 @@ static const uint64_t crc_table[256] = { + 0x9AFCE626CE85B507ULL + }; + +-inline uint64_t crc64(const void *_data, size_t len) ++uint64_t crc64(const void *_data, size_t len) + { + uint64_t crc = 0xFFFFFFFFFFFFFFFFULL; + const unsigned char *data = _data; diff --git a/var/spack/repos/builtin/packages/bcache/package.py b/var/spack/repos/builtin/packages/bcache/package.py new file mode 100644 index 00000000000..63c42de3334 --- /dev/null +++ b/var/spack/repos/builtin/packages/bcache/package.py @@ -0,0 +1,36 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Bcache(MakefilePackage): + """Bcache is a patch for the Linux kernel to use SSDs to cache other block + devices.""" + + homepage = "http://bcache.evilpiepirate.org" + url = "https://github.com/g2p/bcache-tools/archive/v1.0.8.tar.gz" + + version('1.0.8', sha256='d56923936f37287efc57a46315679102ef2c86cd0be5874590320acd48c1201c') + version('1.0.7', sha256='64d76d1085afba8c3d5037beb67bf9d69ee163f357016e267bf328c0b1807abd') + version('1.0.6', sha256='9677c6da3ceac4e1799d560617c4d00ea7e9d26031928f8f94b8ab327496d4e0') + version('1.0.5', sha256='1449294ef545b3dc6f715f7b063bc2c8656984ad73bcd81a0dc048cbba416ea9') + version('1.0.4', sha256='102ffc3a8389180f4b491188c3520f8a4b1a84e5a7ca26d2bd6de1821f4d913d') + + depends_on('libuuid') + depends_on('util-linux') + depends_on('gettext') + + def setup_build_environment(self, env): + env.append_flags('LDFLAGS', '-lintl') + + patch('func_crc64.patch', sha256='558b35cadab4f410ce8f87f0766424a429ca0611aa2fd247326ad10da115737d') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('bcache-register', prefix.bin) + install('bcache-super-show', prefix.bin) + install('make-bcache', prefix.bin) + install('probe-bcache', prefix.bin) From e2cf6f5b1baca2b99e6d95f632e8b7eae9780069 Mon Sep 17 00:00:00 2001 From: Andrew Gaspar Date: Thu, 19 Mar 2020 20:57:41 -0700 Subject: [PATCH 125/377] Improvements to Rust's Installation (#15395) * Add sources and resources for each version of Rust * install bootstrapping compiler into stage * Add libgit2 * Install bootstrapping compiler correctly * implement full rust bootstrap * Remove support for Rust pre-1.14 Also add lots of comments * Support only Rust 1.17 and newer * Remove < 1.23 versions of Rust * Change the layout of rust_releases for maintainability * Remove LLVM variant * Address flake8 issues * Make libgit2 curl variant default False, conflict 0.28 and newer * Remove binutils dependency * Add ARM64 while we're at it * flake8 * use the 'python' routine rather than relying on the correct python to be picked up --- .../repos/builtin/packages/libgit2/package.py | 79 ++- .../repos/builtin/packages/rust/package.py | 476 ++++++++++++++++-- 2 files changed, 511 insertions(+), 44 deletions(-) diff --git a/var/spack/repos/builtin/packages/libgit2/package.py b/var/spack/repos/builtin/packages/libgit2/package.py index 58ea638de0e..222075ffdb5 100644 --- a/var/spack/repos/builtin/packages/libgit2/package.py +++ b/var/spack/repos/builtin/packages/libgit2/package.py @@ -16,8 +16,79 @@ class Libgit2(CMakePackage): homepage = "https://libgit2.github.com/" url = "https://github.com/libgit2/libgit2/archive/v0.26.0.tar.gz" - version('0.28.2', sha256='42b5f1e9b9159d66d86fff0394215c5733b6ef8f9b9d054cdd8c73ad47177fc3') - version('0.26.0', sha256='6a62393e0ceb37d02fe0d5707713f504e7acac9006ef33da1e88960bd78b6eac') + version('0.99.0', sha256='174024310c1563097a6613a0d3f7539d11a9a86517cd67ce533849065de08a11') + version('0.28.4', sha256='30f3877469d09f2e4a21be933b4e2800560d16646028dd800744dc5f7fb0c749') + version('0.28.3', sha256='ee5344730fe11ce7c86646e19c2d257757be293f5a567548d398fb3af8b8e53b') + version('0.28.2', sha256='42b5f1e9b9159d66d86fff0394215c5733b6ef8f9b9d054cdd8c73ad47177fc3') + version('0.28.1', sha256='0ca11048795b0d6338f2e57717370208c2c97ad66c6d5eac0c97a8827d13936b') + version('0.28.0', sha256='9d60d64dc77085e8e530e5c66314057eafe0c06e4a7a61149a70ff3e0688f284') + version('0.27.10', sha256='f6fd26378ff71bd7a4b17b576c82c774a2e9c2d6b74b24718a8fb29551e1c4a5') + version('0.27.9', sha256='adf17310b590e6e7618f070c742b5ee028aeeed2c60099bc4190c386b5060de1') + version('0.27.8', sha256='8313873d49dc01e8b880ec334d7430ae67496a89aaa8c6e7bbd3affb47a00c76') + version('0.27.7', sha256='1a5435a483759b1cd96feb12b11abb5231b0688016db506ce5947178f6ba2531') + version('0.27.6', sha256='d98db2ed11ec82fee94dce4819b466524613852c2c9c3426d351c57729ec49da') + version('0.27.5', sha256='15f2775f4f325951d9139ed906502b6c71fee6787cada9b045f5994072ccbd33') + version('0.27.4', sha256='0b7ca31cb959ff1b22afa0da8621782afe61f99242bf716c403802ffbdb21d51') + version('0.27.3', sha256='50a57bd91f57aa310fb7d5e2a340b3779dc17e67b4e7e66111feac5c2432f1a5') + version('0.27.2', sha256='ffacdbd5588aeb03e98e3866a7e2ceace468723a439bdc9bb01362fe140fa9e5') + version('0.27.1', sha256='837b11927bc5f64e7f9ab0376f57cfe3ca5aa52ffd2007ac41184b21124fb086') + version('0.27.0', sha256='545b0458292c786aba334f1bf1c8f73600ae73dd7205a7bb791a187ee48ab8d2') + version('0.26.8', sha256='0f20d7e239be030db33d7350bab38ada2830b3bffab5539730074e71b0267796') + version('0.26.7', sha256='65584ac1f4de2c3ab8491351c8629eb68bad2d65e67f6411bf0333b8976dc4ef') + version('0.26.6', sha256='7669dd47ebdab86ced8888816c552596ec923b6e126704a3445b2081cb0e5662') + version('0.26.5', sha256='52e28a5166564bc4365a2e4112f5e5c6e334708dbf13596241b2fd34efc1b0a9') + version('0.26.4', sha256='292fa2600bbb4e52641793cfcc1c19ffc0bf97b5fd8378d422a6bfe7afffcb97') + version('0.26.3', sha256='0da4e211dfb63c22e5f43f2a4a5373e86a140afa88a25ca6ba3cc2cae58263d2') + version('0.26.2', sha256='747b47d5b02a2387ff81301c694763785181b895690b6eb91ed1ae4b7904307b') + version('0.26.1', sha256='68cd0f8ee9e0ca84dcf0f0267d0a8297471d3365622d22d3da67c57165bb0722') + version('0.26.0', sha256='6a62393e0ceb37d02fe0d5707713f504e7acac9006ef33da1e88960bd78b6eac') - depends_on('cmake@2.8:', type='build') - depends_on('libssh2') + # Backends + variant( + 'https', default='system', description='HTTPS support', + values=('system', 'openssl', 'none'), multi=False) + variant('ssh', default=True, description='Enable SSH support') + variant('curl', default=False, description='Enable libcurl support (only supported through v0.27)') + + # Build Dependencies + depends_on('cmake@2.8:', type='build', when="@:0.28") + depends_on('cmake@3.5:', type='build', when="@0.99:") + + # Runtime Dependencies + depends_on('libssh2', when='+ssh') + depends_on('openssl', when='https=system platform=linux') + depends_on('openssl', when='https=system platform=cray') + depends_on('openssl', when='https=openssl') + depends_on('curl', when='+curl') + + conflicts('+curl', when='@0.28:') + + def cmake_args(self): + args = [] + if 'https=system' in self.spec: + if 'platform=linux' in self.spec or 'platform=cray' in self.spec: + args.append('-DUSE_HTTPS=OpenSSL') + elif 'platform=darwin' in self.spec: + args.append('-DUSE_HTTPS=SecureTransport') + else: + # Let CMake try to find an HTTPS implementation. Mileage on + # your platform may vary + args.append('-DUSE_HTTPS=ON') + elif 'https=openssl' in self.spec: + args.append('-DUSE_HTTPS=OpenSSL') + else: + args.append('-DUSE_HTTPS=OFF') + + args.append( + '-DUSE_SSH={0}'.format('ON' if '+ssh' in self.spec else 'OFF')) + + # The curl backed is not supported after 0.27.x + if '@:0.27 +curl' in self.spec: + args.append( + '-DCURL={0}'.format('ON' if '+curl' in self.spec else 'OFF')) + + # Control tests + args.append( + '-DBUILD_CLAR={0}'.format('ON' if self.run_tests else 'OFF')) + + return args diff --git a/var/spack/repos/builtin/packages/rust/package.py b/var/spack/repos/builtin/packages/rust/package.py index 2ae30b5c035..59e827f67dc 100644 --- a/var/spack/repos/builtin/packages/rust/package.py +++ b/var/spack/repos/builtin/packages/rust/package.py @@ -4,59 +4,455 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +from six import iteritems class Rust(Package): - """The rust programming language toolchain""" + """The Rust programming language toolchain - homepage = "http://www.rust-lang.org" - git = "https://github.com/rust-lang/rust.git" + This package can bootstrap any version of the Rust compiler since Rust + 1.23. It does this by downloading the platform-appropriate binary + distribution of the desired version of the rust compiler, and then building + that compiler from source. + """ - version('develop', branch='master') - version('1.41.0', tag='1.41.0') - version('1.34.0', tag='1.34.0') - version('1.32.0', tag='1.32.0') - version('1.31.1', tag='1.31.1') - version('1.31.0', tag='1.31.0') # "Rust 2018" edition - version('1.30.1', tag='1.30.1') + homepage = "https://www.rust-lang.org" + url = "https://static.rust-lang.org/dist/rustc-1.42.0-src.tar.gz" + + maintainers = ["AndrewGaspar"] + + phases = ['configure', 'build', 'install'] extendable = True - # Rust - depends_on("llvm") - depends_on("curl") - depends_on("git") - depends_on("cmake") - depends_on("binutils") - depends_on("python@:2.8") + variant( + 'rustfmt', + default=True, + description='Formatting tool for Rust code' + ) - # Cargo - depends_on("openssl") + variant( + 'analysis', + default=True, + description='Outputs code analysis that can be consumed by other tools' + ) - phases = ['configure', 'install'] + variant( + 'clippy', + default=True, + description='Linting tool for Rust' + ) + + variant( + 'rls', + default=False, + description='The Rust Language Server can be used for IDE integration' + ) + + variant( + 'src', + default=True, + description='Install Rust source files' + ) + + depends_on('cmake', type='build') + depends_on('python@:2.8', type='build') + depends_on('openssl') + depends_on('libssh2') + depends_on('libgit2') + + # Version Notes: + # Here's some information on why your favorite Rust version may be missing. + # + # < 1.23: + # Rust seems to eagerly search for ar next to cc. Spack makes wrappers for + # cc and c++, but not for ar, so no ar is found. In future versions, ar + # can be specified in the config. + # + # < 1.17: + # The `x.py` bootstrapping script did not exist prior to Rust 1.17. It + # would be possible to support both, but for simplicitly, we only support + # Rust 1.17 and newer + version('1.42.0', sha256='d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475') + version('1.41.1', sha256='38c93d016e6d3e083aa15e8f65511d3b4983072c0218a529f5ee94dd1de84573') + version('1.41.0', sha256='5546822c09944c4d847968e9b7b3d0e299f143f307c00fa40e84a99fabf8d74b') + version('1.40.0', sha256='dd97005578defc10a482bff3e4e728350d2099c60ffcf1f5e189540c39a549ad') + version('1.39.0', sha256='b4a1f6b6a93931f270691aba4fc85eee032fecda973e6b9c774cd06857609357') + version('1.38.0', sha256='644263ca7c7106f8ee8fcde6bb16910d246b30668a74be20b8c7e0e9f4a52d80') + version('1.37.0', sha256='120e7020d065499cc6b28759ff04153bfdc2ac9b5adeb252331a4eb87cbe38c3') + version('1.36.0', sha256='04c4e4d7213d036d6aaed392841496d272146312c0290f728b7400fccd15bb1b') + version('1.35.0', sha256='5a4d637a716bac18d085f44dd87ef48b32195f71b967d872d80280b38cff712d') + version('1.34.2', sha256='c69a4a85a1c464368597df8878cb9e1121aae93e215616d45ad7d23af3052f56') + version('1.34.1', sha256='b0c785264d17e1dac4598627c248a2d5e07dd39b6666d1881fcfc8e2cf4c40a7') + version('1.34.0', sha256='7ac85acffd79dd3a7c44305d9eaabd1f1e7116e2e6e11e770e4bf5f92c0f1f59') + version('1.33.0', sha256='5a01a8d7e65126f6079042831385e77485fa5c014bf217e9f3e4aff36a485d94') + version('1.32.0', sha256='4c594c7712a0e7e8eae6526c464bf6ea1d82f77b4f61717c3fc28fb27ba2224a') + version('1.31.1', sha256='91d2fc22f08d986adab7a54eb3a6a9b99e490f677d2d092e5b9e4e069c23686a') + version('1.30.1', sha256='36a38902dbd9a3e1240d46ab0f2ca40d2fd07c2ab6508ed7970c6c4c036b5b29') + version('1.30.0', sha256='cd0ba83fcca55b64c0c9f23130fe731dfc1882b73ae21bef96be8f2362c108ee') + version('1.29.2', sha256='5088e796aa2e47478cdf41e7243fc5443fafab0a7c70a11423e57c80c04167c9') + version('1.29.1', sha256='f1b0728b66ce6bce6d72bbe5ea9e3a24ea22a045665da2ed8fcdfad14f61a349') + version('1.29.0', sha256='a4eb34ffd47f76afe2abd813f398512d5a19ef00989d37306217c9c9ec2f61e9') + version('1.28.0', sha256='1d5a81729c6f23a0a23b584dd249e35abe9c6f7569cee967cc42b1758ecd6486') + version('1.27.2', sha256='9a818c50cdb7880abeaa68b3d97792711e6c64c1cdfb6efdc23f75b8ced0e15d') + version('1.27.1', sha256='2133beb01ddc3aa09eebc769dd884533c6cfb08ce684f042497e097068d733d1') + version('1.27.0', sha256='2cb9803f690349c9fd429564d909ddd4676c68dc48b670b8ddf797c2613e2d21') + version('1.26.2', sha256='fb9ecf304488c9b56600ab20cfd1937482057f7e5db7899fddb86e0774548700') + version('1.26.1', sha256='70a7961bd8ec43b2c01e9896e90b0a06804a7fbe0a5c05acc7fd6fed19500df0') + version('1.26.0', sha256='4fb09bc4e233b71dcbe08a37a3f38cabc32219745ec6a628b18a55a1232281dd') + version('1.25.0', sha256='eef63a0aeea5147930a366aee78cbde248bb6e5c6868801bdf34849152965d2d') + version('1.24.1', sha256='3ea53d45e8d2e9a41afb3340cf54b9745f845b552d802d607707cf04450761ef') + version('1.24.0', sha256='bb8276f6044e877e447f29f566e4bbf820fa51fea2f912d59b73233ffd95639f') + version('1.23.0', sha256='7464953871dcfdfa8afcc536916a686dd156a83339d8ec4d5cb4eb2fe146cb91') + + # The Rust bootstrapping process requires a bootstrapping compiler. The + # easiest way to do this is to download the binary distribution of the + # same version of the compiler and build with that. + # + # This dictionary contains a version: hash dictionary for each supported + # Rust target. + rust_releases = { + '1.42.0': { + 'x86_64-unknown-linux-gnu': '7d1e07ad9c8a33d8d039def7c0a131c5917aa3ea0af3d0cc399c6faf7b789052', + 'powerpc64le-unknown-linux-gnu': '805b08fa1e0aad4d706301ca1f13e2d80810d385cece2c15070360b3c4bd6e4a', + 'aarch64-unknown-linux-gnu': 'fdd39f856a062af265012861949ff6654e2b7103be034d046bec84ebe46e8d2d', + 'x86_64-apple-darwin': 'db1055c46e0d54b99da05e88c71fea21b3897e74a4f5ff9390e934f3f050c0a8' + }, + '1.41.1': { + 'x86_64-unknown-linux-gnu': 'a6d5a3b3f574aafc8f787fea37aad9fb8a7946b383ae5348146927192ff0bef0', + 'powerpc64le-unknown-linux-gnu': 'f9b53ca636625b3a2dd87600b6274223c11f866c9b5a34b638ea0013186659d3', + 'aarch64-unknown-linux-gnu': 'd54c0f9165b86216b6f1b499f451141407939c5dc6b36c89a3772895a1370242', + 'x86_64-apple-darwin': '16615288cf74239783de1b435d329f3d56ed13803c7c10cd4b207d7c8ffa8f67' + }, + '1.41.0': { + 'x86_64-unknown-linux-gnu': '343ba8ef7397eab7b3bb2382e5e4cb08835a87bff5c8074382c0b6930a41948b', + 'powerpc64le-unknown-linux-gnu': 'ba231b0d8273d6928f61e2be3456e816a1de8050135e20c0623dc7a6ea03ba68', + 'aarch64-unknown-linux-gnu': '79ddfb5e2563d0ee09a567fbbe121a2aed3c3bc61255b2787f2dd42183a10f27', + 'x86_64-apple-darwin': 'b6504003ab70b11f278e0243a43ba9d6bf75e8ad6819b4058a2b6e3991cc8d7a' + }, + '1.40.0': { + 'x86_64-unknown-linux-gnu': 'fc91f8b4bd18314e83a617f2389189fc7959146b7177b773370d62592d4b07d0', + 'powerpc64le-unknown-linux-gnu': 'b1a23e35c383f99e647df6a9239b1dc9313e293deb70a76ba58e8ebe55ef623b', + 'aarch64-unknown-linux-gnu': '639271f59766d291ebdade6050e7d05d61cb5c822a3ef9a1e2ab185fed68d729', + 'x86_64-apple-darwin': '749ca5e0b94550369cc998416b8854c13157f5d11d35e9b3276064b6766bcb83' + }, + '1.39.0': { + 'x86_64-unknown-linux-gnu': 'b10a73e5ba90034fe51f0f02cb78f297ed3880deb7d3738aa09dc5a4d9704a25', + 'powerpc64le-unknown-linux-gnu': '53b3fd942c52709f7e6fe11ea572d086e315a57a40b84b9b3290ac0ec8c7c84a', + 'aarch64-unknown-linux-gnu': 'e27dc8112fe577012bd88f30e7c92dffd8c796478ce386c49465c03b6db8209f', + 'x86_64-apple-darwin': '3736d49c5e9592844e1a5d5452883aeaf8f1e25d671c1bc8f01e81c1766603b5' + }, + '1.38.0': { + 'x86_64-unknown-linux-gnu': 'adda26b3f0609dbfbdc2019da4a20101879b9db2134fae322a4e863a069ec221', + 'powerpc64le-unknown-linux-gnu': 'f9ed1bb6525abdd4dd6ef10782ad45d2f71496e0c3c88e806b510c81a91c4ff7', + 'aarch64-unknown-linux-gnu': '06afd6d525326cea95c3aa658aaa8542eab26f44235565bb16913ac9d12b7bda', + 'x86_64-apple-darwin': 'bd301b78ddcd5d4553962b115e1dca5436dd3755ed323f86f4485769286a8a5a' + }, + '1.37.0': { + 'x86_64-unknown-linux-gnu': 'cb573229bfd32928177c3835fdeb62d52da64806b844bc1095c6225b0665a1cb', + 'powerpc64le-unknown-linux-gnu': '27c59ec40e9e9f71490dc00bf165156ae3ea77c20ffa4b5e5fd712e67527b477', + 'aarch64-unknown-linux-gnu': '263ef98fa3a6b2911b56f89c06615cdebf6ef676eb9b2493ad1539602f79b6ba', + 'x86_64-apple-darwin': 'b2310c97ffb964f253c4088c8d29865f876a49da2a45305493af5b5c7a3ca73d' + }, + '1.36.0': { + 'x86_64-unknown-linux-gnu': '15e592ec52f14a0586dcebc87a957e472c4544e07359314f6354e2b8bd284c55', + 'powerpc64le-unknown-linux-gnu': '654a7a18d881811c09f630b0c917825b586e94a6142eceaede6b8046718e4054', + 'aarch64-unknown-linux-gnu': 'db78c24d93756f9fe232f081dbc4a46d38f8eec98353a9e78b9b164f9628042d', + 'x86_64-apple-darwin': '91f151ec7e24f5b0645948d439fc25172ec4012f0584dd16c3fb1acb709aa325' + }, + '1.35.0': { + 'x86_64-unknown-linux-gnu': 'cf600e2273644d8629ed57559c70ca8db4023fd0156346facca9ab3ad3e8f86c', + 'powerpc64le-unknown-linux-gnu': 'a933955adec386d75d126e78df5b9941936e156acb3353fc44b85995a81c7bb2', + 'aarch64-unknown-linux-gnu': '31e6da56e67838fd2874211ae896a433badf67c13a7b68481f1d5f7dedcc5952', + 'x86_64-apple-darwin': 'ac14b1c7dc330dcb53d8641d74ebf9b32aa8b03b9d650bcb9258030d8b10dbd6' + }, + '1.34.2': { + 'x86_64-unknown-linux-gnu': '2bf6622d980a52832bae141304e96f317c8a1ccd2dfd69a134a14033e6e43c0f', + 'powerpc64le-unknown-linux-gnu': '4ddd55014bbd954b3499859bfa3146bff471de21c1d73fc6e7cccde290fc1918', + 'aarch64-unknown-linux-gnu': '15fc6b7ec121df9d4e42483dd12c677203680bec8c69b6f4f62e5a35a07341a8', + 'x86_64-apple-darwin': '6fdd4bf7fe26dded0cd57b41ab5f0500a5a99b7bc770523a425e9e34f63d0fd8' + }, + '1.34.1': { + 'x86_64-unknown-linux-gnu': '8e2eead11bd5bf61409e29018d007c6fc874bcda2ff54db3d04d1691e779c14e', + 'powerpc64le-unknown-linux-gnu': '94ac92d08afcfa2d77ae207e91b57c00cb48ff7ba08a27ed3deb2493f33e8fb1', + 'aarch64-unknown-linux-gnu': '0565e50dae58759a3a5287abd61b1a49dfc086c4d6acf2ce604fe1053f704e53', + 'x86_64-apple-darwin': 'f4e46b9994ccfab4a84059298d1dc8fd446b1bbb7449462e0459948f7debea0e' + }, + '1.34.0': { + 'x86_64-unknown-linux-gnu': '170647ed41b497dc937a6b2556700210bc4be187b1735029ef9ccf52e2cb5ab8', + 'powerpc64le-unknown-linux-gnu': '3027e87802e161cce6f3a23d961f6d73b9ed6e829b2cd7af5dfccf6e1207e552', + 'aarch64-unknown-linux-gnu': '370c3a8fb9a69df36d645a95e622fb59ac5b513baecddde706cedaf20defa269', + 'x86_64-apple-darwin': 'e6bea8d865cc7341c17fa3b8f25f7989e6b04f53e9da24878addc524f3a32664' + }, + '1.33.0': { + 'x86_64-unknown-linux-gnu': '6623168b9ee9de79deb0d9274c577d741ea92003768660aca184e04fe774393f', + 'powerpc64le-unknown-linux-gnu': 'db885aa4c2c6896c85257be2ade5c9edea660ca6878970683e8d5796618329b5', + 'aarch64-unknown-linux-gnu': 'a308044e4076b62f637313ea803fa0a8f340b0f1b53136856f2c43afcabe5387', + 'x86_64-apple-darwin': '864e7c074a0b88e38883c87c169513d072300bb52e1d320a067bd34cf14f66bd' + }, + '1.32.0': { + 'x86_64-unknown-linux-gnu': 'e024698320d76b74daf0e6e71be3681a1e7923122e3ebd03673fcac3ecc23810', + 'powerpc64le-unknown-linux-gnu': 'd6d5c9154f4459465d68ebd4fa1e17bad4b6cfe219667dddd9123c3bfb5dd839', + 'aarch64-unknown-linux-gnu': '60def40961728212da4b3a9767d5a2ddb748400e150a5f8a6d5aa0e1b8ba1cee', + 'x86_64-apple-darwin': 'f0dfba507192f9b5c330b5984ba71d57d434475f3d62bd44a39201e36fa76304' + }, + '1.31.1': { + 'x86_64-unknown-linux-gnu': 'a64685535d0c457f49a8712a096a5c21564cd66fd2f7da739487f028192ebe3c', + 'powerpc64le-unknown-linux-gnu': 'a6f61b7a8a06a2b0a785391cc3e6bb8004aa72095eea80db1561039f5bb3e975', + 'aarch64-unknown-linux-gnu': '29a7c6eb536fefd0ca459e48dfaea006aa8bff8a87aa82a9b7d483487033632a', + 'x86_64-apple-darwin': '8398b1b303bdf0e7605d08b87070a514a4f588797c6fb3593718cb9cec233ad6' + }, + '1.30.1': { + 'x86_64-unknown-linux-gnu': 'a01a493ed8946fc1c15f63e74fc53299b26ebf705938b4d04a388a746dfdbf9e', + 'powerpc64le-unknown-linux-gnu': 'a7d4806e6702bdbad5017eeddc62f7ff7eb2438b1b9c39cbc90c2b1207f8e65f', + 'aarch64-unknown-linux-gnu': '6d87d81561285abd6c1987e07b60b2d723936f037c4b46eedcc12e8566fd3874', + 'x86_64-apple-darwin': '3ba1704a7defe3d9a6f0c1f68792c084da83bcba85e936d597bac0c019914b94' + }, + '1.30.0': { + 'x86_64-unknown-linux-gnu': 'f620e3125cc505c842150bd873c0603432b6cee984cdae8b226cf92c8aa1a80f', + 'powerpc64le-unknown-linux-gnu': '0b53e257dc3d9f3d75cd97be569d3bf456d2c0af57ed0bd5e7a437227d8f465a', + 'aarch64-unknown-linux-gnu': '9690c7c50eba5a8461184ee4138b4c284bad31ccc4aa1f2ddeec58b253e6363e', + 'x86_64-apple-darwin': '07008d90932712282bc599f1e9a226e97879c758dc1f935e6e2675e45694cc1b' + }, + '1.29.2': { + 'x86_64-unknown-linux-gnu': 'e9809825c546969a9609ff94b2793c9107d7d9bed67d557ed9969e673137e8d8', + 'powerpc64le-unknown-linux-gnu': '344003b808c20424c4699c9452bd37cdee23857dd4aa125e67d1d6e4bc992091', + 'aarch64-unknown-linux-gnu': 'e11461015ca7106ef8ebf00859842bf4be518ee170226cb8eedaaa666946509f', + 'x86_64-apple-darwin': '63f54e3013406b39fcb5b84bcf5e8ce85860d0b97a1e156700e467bf5fb5d5f2' + }, + '1.29.1': { + 'x86_64-unknown-linux-gnu': 'b36998aea6d58525f25d89f1813b6bfd4cad6ff467e27bd11e761a20dde43745', + 'powerpc64le-unknown-linux-gnu': '26a6d652ade6b6a96e6af18e846701ee28f912233372dfe15432139252f88958', + 'aarch64-unknown-linux-gnu': '2685224f67b2ef951e0e8b48829f786cbfed95e19448ba292ac33af719843dbe', + 'x86_64-apple-darwin': '07b07fbd6fab2390e19550beb8008745a8626cc5e97b72dc659061c1c3b3d008' + }, + '1.29.0': { + 'x86_64-unknown-linux-gnu': '09f99986c17b1b6b1bfbc9dd8785e0e4693007c5feb67915395d115c1a3aea9d', + 'powerpc64le-unknown-linux-gnu': 'd6954f1da53f7b3618fba3284330d99b6142bb25d9febba6dbfedad59ca53329', + 'aarch64-unknown-linux-gnu': '0ed3be0fd9f847afeb4e587fff61f6769ea61b53719d3ea999326284e8975b36', + 'x86_64-apple-darwin': '28a0473637585742f6d80ccd8afd88b6b400e65d623c33cb892412759444da93' + }, + '1.28.0': { + 'x86_64-unknown-linux-gnu': '2a1390340db1d24a9498036884e6b2748e9b4b057fc5219694e298bdaa37b810', + 'powerpc64le-unknown-linux-gnu': '255818156ec1f795ed808a44b4fdb8019187d5ebb7f837ae8f55a1ca40862bb6', + 'aarch64-unknown-linux-gnu': '9b6fbcee73070332c811c0ddff399fa31965bec62ef258656c0c90354f6231c1', + 'x86_64-apple-darwin': '5d7a70ed4701fe9410041c1eea025c95cad97e5b3d8acc46426f9ac4f9f02393' + }, + '1.27.2': { + 'x86_64-unknown-linux-gnu': '5028a18e913ef3eb53e8d8119d2cc0594442725e055a9361012f8e26f754f2bf', + 'powerpc64le-unknown-linux-gnu': '11034d150e811d4903b09fd42f0cb76d467a6365a158101493405fff1054572f', + 'aarch64-unknown-linux-gnu': 'cf84da70269c0e50bb3cc3d248bae1ffcd70ee69dc5a4e3513b54fefc6685fb4', + 'x86_64-apple-darwin': '30c5cc58759caa4efdf2ea7d8438633139c98bee3408beb29ceb26985f3f5f70' + }, + '1.27.1': { + 'x86_64-unknown-linux-gnu': '435778a837af764da2a7a7fb4d386b7b78516c7dfc732d892858e9a8a539989b', + 'powerpc64le-unknown-linux-gnu': 'a08e6b6fed3329fcd1220b2ee4cd7a311d99121cf780fb6e1c6353bfeddfb176', + 'aarch64-unknown-linux-gnu': 'd1146b240e6f628224c3a67e3aae2a57e6c25d544115e5ece9ce91861ec92b3a', + 'x86_64-apple-darwin': '475be237962d6aef1038a2faada26fda1e0eaea5d71d6950229a027a9c2bfe08' + }, + '1.27.0': { + 'x86_64-unknown-linux-gnu': '235ad78e220b10a2d0267aea1e2c0f19ef5eaaff53ad6ff8b12c1d4370dec9a3', + 'powerpc64le-unknown-linux-gnu': '847774a751e848568215739d384e3baf4d6ec37d27fb3add7a8789208c213aff', + 'aarch64-unknown-linux-gnu': 'e74ebc33dc3fc19e501a677a87b619746efdba2901949a0319176352f556673a', + 'x86_64-apple-darwin': 'a1d48190992e01aac1a181bce490c80cb2c1421724b4ff0e2fb7e224a958ce0f' + }, + '1.26.2': { + 'x86_64-unknown-linux-gnu': 'd2b4fb0c544874a73c463993bde122f031c34897bb1eeb653d2ba2b336db83e6', + 'powerpc64le-unknown-linux-gnu': 'ea045869074ae3617eeb51207ce183e6915784b9ed615ecb92ce082ddb86ec1f', + 'aarch64-unknown-linux-gnu': '3dfad0dc9c795f7ee54c2099c9b7edf06b942adbbf02e9ed9e5d4b5e3f1f3759', + 'x86_64-apple-darwin': 'f193705d4c0572a358670dbacbf0ffadcd04b3989728b442f4680fa1e065fa72' + }, + '1.26.1': { + 'x86_64-unknown-linux-gnu': 'b7e964bace1286696d511c287b945f3ece476ba77a231f0c31f1867dfa5080e0', + 'powerpc64le-unknown-linux-gnu': 'ad8b2f6dd8c5cca1251d65b75ed2120aae3c5375d2c8ed690259cf4a652d7d3c', + 'aarch64-unknown-linux-gnu': 'd4a369053c2dfd5f457de6853557dab563944579fa4bb55bc919bacf259bff6d', + 'x86_64-apple-darwin': 'ebf898b9fa7e2aafc53682a41f18af5ca6660ebe82dd78f28cd9799fe4dc189a' + }, + '1.26.0': { + 'x86_64-unknown-linux-gnu': '13691d7782577fc9f110924b26603ade1990de0b691a3ce2dc324b4a72a64a68', + 'powerpc64le-unknown-linux-gnu': '3ba3a4905730ec01007ca1096d9fc3780f4e81f71139a619e1f526244301b7f4', + 'aarch64-unknown-linux-gnu': 'e12dc84bdb569cdb382268a5fe6ae6a8e2e53810cb890ec3a7133c20ba8451ac', + 'x86_64-apple-darwin': '38708803c3096b8f101d1919ee2d7e723b0adf1bc1bb986b060973b57d8c7c28' + }, + '1.25.0': { + 'x86_64-unknown-linux-gnu': '06fb45fb871330a2d1b32a27badfe9085847fe824c189ddc5204acbe27664f5e', + 'powerpc64le-unknown-linux-gnu': '79eeb2a7fafa2e0f65f29a1dc360df69daa725347e4b6a533684f1c07308cc6e', + 'aarch64-unknown-linux-gnu': '19a43451439e515a216d0a885d14203f9a92502ee958abf86bf7000a7d73d73d', + 'x86_64-apple-darwin': 'fcd0302b15e857ba4a80873360cf5453275973c64fa82e33bfbed02d88d0ad17' + }, + '1.24.1': { + 'x86_64-unknown-linux-gnu': '4567e7f6e5e0be96e9a5a7f5149b5452828ab6a386099caca7931544f45d5327', + 'powerpc64le-unknown-linux-gnu': '6f6c4bebbd7d6dc9989bf372c512dea55af8f56a1a0cfe97784667f0ac5430ee', + 'aarch64-unknown-linux-gnu': '64bb25a9689b18ddadf025b90d9bdb150b809ebfb74432dc69cc2e46120adbb2', + 'x86_64-apple-darwin': '9d4aacdb5849977ea619d399903c9378163bd9c76ea11dac5ef6eca27849f501' + }, + '1.24.0': { + 'x86_64-unknown-linux-gnu': '336cf7af6c857cdaa110e1425719fa3a1652351098dc73f156e5bf02ed86443c', + 'powerpc64le-unknown-linux-gnu': '25d9b965a63ad2f345897028094d4c7eafa432237b478754ccbcc299f80629c8', + 'aarch64-unknown-linux-gnu': 'a981de306164b47f3d433c1d53936185260642849c79963af7e07d36b063a557', + 'x86_64-apple-darwin': '1aecba7cab4bc1a9e0e931c04aa00849e930b567d243da7b676ede8f527a2992' + }, + '1.23.0': { + 'x86_64-unknown-linux-gnu': '9a34b23a82d7f3c91637e10ceefb424539dcfa327c2dcd292ff10c047b1fdc7e', + 'powerpc64le-unknown-linux-gnu': '60f1a1cc182c516de08c1f42ada01604a3d94383e9dded6b237ae2233999437b', + 'aarch64-unknown-linux-gnu': '38379fbd976d2286cb73f21466db40a636a583b9f8a80af5eea73617c7912bc7', + 'x86_64-apple-darwin': '9274e977322bb4b153f092255ac9bd85041142c73eaabf900cb2ef3d3abb2eba' + } + } + + # This dictionary maps Rust target architectures to Spack constraints that + # match that target. + rust_archs = { + 'x86_64-unknown-linux-gnu': [ + {'platform': 'linux', 'target': 'x86_64:'}, + {'platform': 'cray', 'target': 'x86_64:'} + ], + 'powerpc64le-unknown-linux-gnu': [ + {'platform': 'linux', 'target': 'ppc64le:'}, + {'platform': 'cray', 'target': 'ppc64le:'} + ], + 'aarch64-unknown-linux-gnu': [ + {'platform': 'linux', 'target': 'aarch64:'}, + {'platform': 'cray', 'target': 'aarch64:'} + ], + 'x86_64-apple-darwin': [ + {'platform': 'darwin', 'target': 'x86_64:'} + ] + } + + # This loop generates resources for each binary distribution, and maps + # them to the version of the compiler they bootstrap. This is in place + # of listing each resource explicitly, which would be potentially even + # more verbose. + # + # NOTE: This loop should technically specify the architecture to be the + # _host_ architecture, not the target architecture, in order to support + # cross compiling. I'm not sure Spack provides a way to specify a + # distinction in the when clause, though. + for rust_version, rust_targets in iteritems(rust_releases): + for rust_target, rust_sha256 in iteritems(rust_targets): + for rust_arch in rust_archs[rust_target]: + resource( + name='rust-{version}-{target}'.format( + version=rust_version, + target=rust_target + ), + url='https://static.rust-lang.org/dist/rust-{version}-{target}.tar.gz'.format( + version=rust_version, + target=rust_target + ), + sha256=rust_sha256, + destination='spack_bootstrap_stage', + when='@{version} platform={platform} target={target}'\ + .format( + version=rust_version, + platform=rust_arch['platform'], + target=rust_arch['target'] + ) + ) + + # This routine returns the target architecture we intend to build for. + def get_rust_target(self): + if 'platform=linux' in self.spec or 'platform=cray' in self.spec: + if 'target=x86_64:' in self.spec: + return 'x86_64-unknown-linux-gnu' + elif 'target=ppc64le:' in self.spec: + return 'powerpc64le-unknown-linux-gnu' + elif 'target=aarch64:' in self.spec: + return 'aarch64-unknown-linux-gnu' + elif 'platform=darwin target=x86_64:' in self.spec: + return 'x86_64-apple-darwin' + + raise InstallError( + "rust is not supported for '{0}'".format( + self.spec.architecture + )) def configure(self, spec, prefix): - configure_args = [ - '--prefix=%s' % prefix, - '--llvm-root=' + spec['llvm'].prefix, - # Workaround for "FileCheck does not exist" error - '--disable-codegen-tests', - # Includes Cargo in the build - # https://github.com/rust-lang/cargo/issues/3772#issuecomment-283109482 - '--enable-extended', - # Prevent build from writing bash completion into system path - '--sysconfdir=%s' % join_path(prefix, 'etc/') - ] + target = self.get_rust_target() + # See the NOTE above the resource loop - should be host architecture, + # not target aarchitecture if we're to support cross-compiling. + bootstrapping_install = Executable( + './spack_bootstrap_stage/rust-{version}-{target}/install.sh' + .format( + version=spec.version, + target=target + ) + ) + # install into the staging area + bootstrapping_install('--prefix={0}'.format( + join_path(self.stage.source_path, 'spack_bootstrap') + )) - configure(*configure_args) + boot_bin = join_path(self.stage.source_path, 'spack_bootstrap/bin') - # Build system defaults to searching in the same path as Spack's - # compiler wrappers which causes the build to fail - filter_file( - '#ar = "ar"', - 'ar = "%s"' % join_path(spec['binutils'].prefix.bin, 'ar'), - 'config.toml') + # Always build rustc and cargo + tools = ['rustc', 'cargo'] + # Only make additional components available in 'rust-bootstrap' + if '+rustfmt' in self.spec: + tools.append('rustfmt') + if '+analysis' in self.spec: + tools.append('analysis') + if '@1.33: +clippy' in self.spec: + tools.append('clippy') + if '+rls' in self.spec: + tools.append('rls') + if '+src' in self.spec: + tools.append('src') + + ar = which('ar', required=True) + + # build.tools was introduced in Rust 1.25 + tools_spec = 'tools={0}'.format(tools) if '@1.25:' in self.spec else '' + # This is a temporary fix due to rust 1.42 breaking self bootstrapping + # See: https://github.com/rust-lang/rust/issues/69953 + # + # In general, this should be safe because bootstrapping typically + # ensures everything but the bootstrapping script is warning free for + # the latest set of warning. + deny_warnings_spec = \ + 'deny-warnings = false' if '@1.42.0' in self.spec else '' + + with open('config.toml', 'w') as out_file: + out_file.write("""\ +[build] +cargo = "{cargo}" +rustc = "{rustc}" +docs = false +vendor = true +extended = true +verbose = 2 +{tools_spec} + +[rust] +channel = "stable" +rpath = true +{deny_warnings_spec} + +[target.{target}] +ar = "{ar}" + +[install] +prefix = "{prefix}" +sysconfdir = "etc" +""".format( + cargo=join_path(boot_bin, 'cargo'), + rustc=join_path(boot_bin, 'rustc'), + prefix=prefix, + target=target, + deny_warnings_spec=deny_warnings_spec, + ar=ar.path, + tools_spec=tools_spec + ) + ) + + def build(self, spec, prefix): + python('./x.py', 'build', extra_env={ + # vendored libgit2 wasn't correctly building (couldn't find the + # vendored libssh2), so let's just have spack build it + 'LIBSSH2_SYS_USE_PKG_CONFIG': '1', + 'LIBGIT2_SYS_USE_PKG_CONFIG': '1' + }) def install(self, spec, prefix): - make() - make("install") + python('./x.py', 'install') From 625bf187d28cda3215c9613e60c3e3b1a3c141d3 Mon Sep 17 00:00:00 2001 From: Kevin Huck Date: Fri, 20 Mar 2020 01:41:36 -0700 Subject: [PATCH 126/377] perfstubs: added new package (#15547) --- .../builtin/packages/perfstubs/package.py | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 var/spack/repos/builtin/packages/perfstubs/package.py diff --git a/var/spack/repos/builtin/packages/perfstubs/package.py b/var/spack/repos/builtin/packages/perfstubs/package.py new file mode 100644 index 00000000000..9162e749fce --- /dev/null +++ b/var/spack/repos/builtin/packages/perfstubs/package.py @@ -0,0 +1,34 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Perfstubs(CMakePackage): + """Profiling API for adding tool instrumentation support to any project. + + This was motivated by the need to quickly add instrumentation to the + [ADIOS2](https://github.com/ornladios/ADIOS2) library without adding a build + dependency, or tying to a specific measurement tool. + + The initial prototype implementation was tied to TAU, but evolved to this more + generic version, which was extracted as a separate repository for testing and + demonstration purposes. + """ + + homepage = "https://github.com/khuck/perfstubs" + git = "https://github.com/khuck/perfstubs.git" + + version('master', branch='master') + variant('static', default=False, description='Build static executable support') + + def cmake_args(self): + spec = self.spec + + args = [ + '-DPERFSTUBS_USE_STATIC:BOOL={0}'.format( + 'ON' if '+static' in spec else 'OFF') + ] + return args From 3f83d4d8f539b401ab27157c8b49c73b8a6fd649 Mon Sep 17 00:00:00 2001 From: Andreas Baumbach Date: Fri, 20 Mar 2020 10:05:30 +0100 Subject: [PATCH 127/377] htop: add missing python build dependency (#15585) --- var/spack/repos/builtin/packages/htop/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/htop/package.py b/var/spack/repos/builtin/packages/htop/package.py index 9de69ae0bfc..e0d99604678 100644 --- a/var/spack/repos/builtin/packages/htop/package.py +++ b/var/spack/repos/builtin/packages/htop/package.py @@ -18,6 +18,7 @@ class Htop(AutotoolsPackage): version('2.0.2', sha256='179be9dccb80cee0c5e1a1f58c8f72ce7b2328ede30fb71dcdf336539be2f487') depends_on('ncurses') + depends_on('python+pythoncmd', type='build') def configure_args(self): return ['--enable-shared'] From fdf363eaadb7edea5c9d9b15e043449742484db9 Mon Sep 17 00:00:00 2001 From: Hadrien G Date: Fri, 20 Mar 2020 10:06:45 +0100 Subject: [PATCH 128/377] acts-core: added v0.18, updated boost dependency (#15584) --- var/spack/repos/builtin/packages/acts-core/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/acts-core/package.py b/var/spack/repos/builtin/packages/acts-core/package.py index 78edad95ab9..421a931604e 100644 --- a/var/spack/repos/builtin/packages/acts-core/package.py +++ b/var/spack/repos/builtin/packages/acts-core/package.py @@ -34,6 +34,7 @@ class ActsCore(CMakePackage): maintainers = ['HadrienG2'] version('develop', branch='master') + version('0.18.0', commit='d58a68cf75b52a5e0f563bc237f09250aa9da80c') version('0.17.0', commit='0789f654ff484b013fd27e5023cf342785ea8d97') version('0.16.0', commit='b3d965fe0b8ae335909d79114ef261c6b996773a') version('0.15.0', commit='267c28f69c561e64369661a6235b03b5a610d6da') @@ -76,7 +77,8 @@ class ActsCore(CMakePackage): depends_on('cmake @3.11:', type='build') depends_on('boost @1.62:1.69.99 +program_options +test', when='@:0.10.3') - depends_on('boost @1.62: +program_options +test', when='@0.10.4:') + depends_on('boost @1.62: +program_options +test', when='@0.10.4:0.18.0') + depends_on('boost @1.69: +program_options +test', when='@0.19.0:') depends_on('eigen @3.2.9:', type='build') depends_on('nlohmann-json @3.2.0:', when='@0.14.0: +json') depends_on('root @6.10: cxxstd=14', when='+tgeo @:0.8.0') From 9a71a7646130017c767a3a85c642fc2b097d824d Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 20 Mar 2020 05:08:54 -0400 Subject: [PATCH 129/377] py-tfdlpack: add new package (#15583) --- .../builtin/packages/py-tfdlpack/package.py | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-tfdlpack/package.py diff --git a/var/spack/repos/builtin/packages/py-tfdlpack/package.py b/var/spack/repos/builtin/packages/py-tfdlpack/package.py new file mode 100644 index 00000000000..678cc2d6db4 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tfdlpack/package.py @@ -0,0 +1,45 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class PyTfdlpack(CMakePackage): + """Tensorflow plugin for DLPack.""" + + homepage = "https://github.com/VoVAllen/tf-dlpack" + git = "https://github.com/VoVAllen/tf-dlpack.git" + + maintainers = ['adamjstewart'] + + version('master', branch='master', submodules=True) + version('0.1.1', tag='v0.1.1', submodules=True) + + variant('cuda', default=True, description='Build with CUDA support') + + depends_on('cmake@3.5:', type='build') + depends_on('cuda', when='+cuda') + + # Python dependencies + extends('python') + depends_on('py-setuptools', type='build') + depends_on('py-tensorflow', type=('build', 'run')) + + def cmake_args(self): + args = ['-DPYTHON_EXECUTABLE=' + self.spec['python'].command.path] + + if '+cuda' in self.spec: + args.append('-DUSE_CUDA=ON') + else: + args.append('-DUSE_CUDA=OFF') + + return args + + def install(self, spec, prefix): + with working_dir('python'): + setup_py('install', '--prefix=' + prefix, + '--single-version-externally-managed', '--root=/') + + def setup_run_environment(self, env): + # Prevent TensorFlow from taking over the whole GPU + env.set('TF_FORCE_GPU_ALLOW_GROWTH', 'true') From b4f1f42e4f92d168fbab102c6fb501baaef519d3 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 20 Mar 2020 05:09:48 -0400 Subject: [PATCH 130/377] py-networkx: add 2.4 (#15582) --- .../builtin/packages/py-networkx/package.py | 29 ++++++++++++++----- 1 file changed, 21 insertions(+), 8 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py index da616eefd4e..04f82dac03a 100644 --- a/var/spack/repos/builtin/packages/py-networkx/package.py +++ b/var/spack/repos/builtin/packages/py-networkx/package.py @@ -9,16 +9,29 @@ class PyNetworkx(PythonPackage): """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.""" - homepage = "http://networkx.github.io/" - url = "https://pypi.io/packages/source/n/networkx/networkx-1.11.tar.gz" - version('2.2', sha256='45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b', - url='https://pypi.io/packages/source/n/networkx/networkx-2.2.zip') - version('2.1', sha256='64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1', - url='https://pypi.io/packages/source/n/networkx/networkx-2.1.zip') + homepage = "http://networkx.github.io/" + url = "https://pypi.io/packages/source/n/networkx/networkx-2.4.tar.gz" + + version('2.4', sha256='f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64') + version('2.3', sha256='8311ddef63cf5c5c5e7c1d0212dd141d9a1fe3f474915281b73597ed5f1d4e3d') + version('2.2', sha256='45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b') + version('2.1', sha256='64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1') + version('2.0', sha256='cd5ff8f75d92c79237f067e2f0876824645d37f017cfffa5b7c9678cae1454aa') version('1.11', sha256='0d0e70e10dfb47601cbb3425a00e03e2a2e97477be6f80638fef91d54dd1e4b8') version('1.10', sha256='ced4095ab83b7451cec1172183eff419ed32e21397ea4e1971d92a5808ed6fb8') - depends_on('py-decorator', type=('build', 'run')) - depends_on('py-decorator@4.1.0:', type=('build', 'run'), when='@2.1:') + depends_on('python@2.7:', type=('build', 'run')) + depends_on('python@3.5:', type=('build', 'run'), when='@2.3:') depends_on('py-setuptools', type='build') + depends_on('py-decorator@3.4.0:', type=('build', 'run')) + depends_on('py-decorator@4.1.0:', type=('build', 'run'), when='@2.0:') + depends_on('py-decorator@4.3.0:', type=('build', 'run'), when='@2.2:') + + def url_for_version(self, version): + ext = 'tar.gz' + if Version('2.0') <= version <= Version('2.3'): + ext = 'zip' + + url = 'https://pypi.io/packages/source/n/networkx/networkx-{0}.{1}' + return url.format(version, ext) From 03a88a2d3f7884c4298e6ef4430042bfcbdeb71b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 20 Mar 2020 05:10:19 -0400 Subject: [PATCH 131/377] py-decorator: added v4.4.2 (#15581) --- var/spack/repos/builtin/packages/py-decorator/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-decorator/package.py b/var/spack/repos/builtin/packages/py-decorator/package.py index 80174932ee1..d174fc8a1f7 100644 --- a/var/spack/repos/builtin/packages/py-decorator/package.py +++ b/var/spack/repos/builtin/packages/py-decorator/package.py @@ -12,8 +12,9 @@ class PyDecorator(PythonPackage): various non-trivial examples.""" homepage = "https://github.com/micheles/decorator" - url = "https://pypi.io/packages/source/d/decorator/decorator-4.4.0.tar.gz" + url = "https://pypi.io/packages/source/d/decorator/decorator-4.4.2.tar.gz" + version('4.4.2', sha256='e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7') version('4.4.0', sha256='86156361c50488b84a3f148056ea716ca587df2f0de1d34750d35c21312725de') version('4.3.2', sha256='33cd704aea07b4c28b3eb2c97d288a06918275dac0ecebdaf1bc8a48d98adb9e') version('4.3.0', sha256='c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c') From 6cccce4932cf19eb8d4faac05f5195d93eb8488c Mon Sep 17 00:00:00 2001 From: darmac Date: Fri, 20 Mar 2020 17:11:12 +0800 Subject: [PATCH 132/377] add new package lksctp-tools (#15564) Co-Authored-By: Massimiliano Culpo --- .../builtin/packages/lksctp-tools/package.py | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/lksctp-tools/package.py diff --git a/var/spack/repos/builtin/packages/lksctp-tools/package.py b/var/spack/repos/builtin/packages/lksctp-tools/package.py new file mode 100644 index 00000000000..ca168aa320d --- /dev/null +++ b/var/spack/repos/builtin/packages/lksctp-tools/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class LksctpTools(AutotoolsPackage): + """A Linux SCTP helper library""" + + homepage = "https://github.com/sctp/lksctp-tools" + url = "https://github.com/sctp/lksctp-tools/archive/v1.0.18.tar.gz" + + version('1.0.18', sha256='3e9ab5b3844a8b65fc8152633aafe85f406e6da463e53921583dfc4a443ff03a') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') From 5f63fc5316f5008858f9d88b14b8eb47295d65e4 Mon Sep 17 00:00:00 2001 From: darmac Date: Fri, 20 Mar 2020 22:18:24 +0800 Subject: [PATCH 133/377] add new package: glusterfs (#15565) * add new package: glusterfs * fix list_depth for url * remove list_depth * add list_url for glusterfs --- .../builtin/packages/glusterfs/package.py | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 var/spack/repos/builtin/packages/glusterfs/package.py diff --git a/var/spack/repos/builtin/packages/glusterfs/package.py b/var/spack/repos/builtin/packages/glusterfs/package.py new file mode 100644 index 00000000000..89024cf9774 --- /dev/null +++ b/var/spack/repos/builtin/packages/glusterfs/package.py @@ -0,0 +1,44 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Glusterfs(AutotoolsPackage): + """Gluster is a software defined distributed storage that can scale to + several petabytes. It provides interfaces for object, block and file + storage.""" + + homepage = "https://www.gluster.org/" + url = "https://download.gluster.org/pub/gluster/glusterfs/7/7.3/glusterfs-7.3.tar.gz" + list_url = "https://download.gluster.org/pub/gluster/glusterfs/" + list_depth = 2 + + version('7.3', sha256='2401cc7c3f5488f6fc5ea09ce2ab30c918612f592571fb3de6124f8482ad4954') + version('7.2', sha256='8e43614967b90d64495fbe2c52230dd72572ce219507fb48bc317b1c228a06e1') + version('7.1', sha256='ffc5bd78b079009382bd01391865646bc9b2e8e72366afc96d62ba891dd9dbce') + version('7.0', sha256='8a872518bf9bd4dc1568f45c716bcde09e3bf7abf5b156ea90405e0fc2e9f07b') + version('6.8', sha256='41e855bdc456759c8c15ef494c636a25cc7b62c55ad132ecd55bec05df64793f') + version('6.7', sha256='e237dd59a2d5b73e156b0b71df49ff64a143b3aaf8f0a65daaf369bb40f5e923') + + depends_on('m4', type='build') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('flex', type='build') + depends_on('bison', type='build') + depends_on('rpcsvc-proto') + depends_on('acl') + depends_on('libuuid') + depends_on('libtirpc') + depends_on('userspace-rcu') + + def url_for_version(self, version): + url = 'https://download.gluster.org/pub/gluster/glusterfs/{0}/{1}/glusterfs-{1}.tar.gz' + return url.format(version.up_to(1), version) + + def autoreconf(self, spec, prefix): + bash = which('bash') + bash('./autogen.sh') From d14a6e6bc7dd44a84557cb853a2c679f5f01ce77 Mon Sep 17 00:00:00 2001 From: Matthieu Dorier Date: Fri, 20 Mar 2020 14:19:06 +0000 Subject: [PATCH 134/377] Added two new versions of spdlog (#15586) --- var/spack/repos/builtin/packages/spdlog/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/spdlog/package.py b/var/spack/repos/builtin/packages/spdlog/package.py index e4aad3bf421..15a0cc1d9da 100644 --- a/var/spack/repos/builtin/packages/spdlog/package.py +++ b/var/spack/repos/builtin/packages/spdlog/package.py @@ -12,6 +12,8 @@ class Spdlog(CMakePackage): homepage = "https://github.com/gabime/spdlog" url = "https://github.com/gabime/spdlog/archive/v0.9.0.tar.gz" + version('1.5.0', sha256='b38e0bbef7faac2b82fed550a0c19b0d4e7f6737d5321d4fd8f216b80f8aee8a') + version('1.4.2', sha256='821c85b120ad15d87ca2bc44185fa9091409777c756029125a02f81354072157') version('1.4.1', sha256='3291958eb54ed942d1bd3aef1b4f8ccf70566cbc04d34296ec61eb96ceb73cff') version('1.2.1', sha256='867a4b7cedf9805e6f76d3ca41889679054f7e5a3b67722fe6d0eae41852a767') version('1.2.0', sha256='0ba31b9e7f8e43a7be328ab0236d57810e5d4fc8a1a7842df665ae22d5cbd128') From 03945c2541be3bba6c38d00aeb59d6b9b998ceda Mon Sep 17 00:00:00 2001 From: "Dr. Christian Tacke" <58549698+ChristianTackeGSI@users.noreply.github.com> Date: Fri, 20 Mar 2020 17:39:04 +0100 Subject: [PATCH 135/377] Show the packaga name for a missing patch sha256 (#15441) When a patches sha256 is missing, also show the packagename, so that analyzing is easier. --- lib/spack/spack/patch.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/patch.py b/lib/spack/spack/patch.py index 3a3c1507e15..3a839c5b0f5 100644 --- a/lib/spack/spack/patch.py +++ b/lib/spack/spack/patch.py @@ -346,7 +346,8 @@ def patch_for_package(self, sha256, pkg): sha_index = self.index.get(sha256) if not sha_index: raise NoSuchPatchError( - "Couldn't find patch with sha256: %s" % sha256) + "Couldn't find patch for package %s with sha256: %s" + % (pkg.fullname, sha256)) patch_dict = sha_index.get(pkg.fullname) if not patch_dict: From cf45d38d243cc3987d8d1a421b58cc91a21a4087 Mon Sep 17 00:00:00 2001 From: "Dr. Christian Tacke" <58549698+ChristianTackeGSI@users.noreply.github.com> Date: Fri, 20 Mar 2020 17:55:48 +0100 Subject: [PATCH 136/377] root: Add version 6.20.{00,02} (#15487) * Add version 6.20.{00,02}, don't yet mark it preferred * It needs zstd * It needs numpy (at least for 6.20.00:6.20.03) * Reorder python dependencies a bit * Add mlp variant, default False Older versions always include mlp, so no conflicts there. * Disable tmva, because it needs mlp * tmva needs mlp, so add conflict --- .../repos/builtin/packages/root/package.py | 21 +++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py index d6275bd882e..9db1a702540 100644 --- a/var/spack/repos/builtin/packages/root/package.py +++ b/var/spack/repos/builtin/packages/root/package.py @@ -26,6 +26,8 @@ class Root(CMakePackage): # Development version (when more recent than production). # Production version + version('6.20.02', sha256='0997586bf097c0afbc6f08edbffcebf5eb6a4237262216114ba3f5c8087dcba6') + version('6.20.00', sha256='68421eb0434b38b66346fa8ea6053a0fdc9a6d254e4a72019f4e3633ae118bf0') version('6.18.04', sha256='315a85fc8363f8eb1bffa0decbf126121258f79bd273513ed64795675485cfa4', preferred=True) @@ -110,6 +112,9 @@ class Root(CMakePackage): # otherwise it crashes with the internal minuit library variant('minuit', default=True, description='Automatically search for support libraries') + variant('mlp', default=False, + description="Enable support for TMultilayerPerceptron " + "classes' federation") variant('mysql', default=False) variant('opengl', default=True, description='Enable OpenGL support') @@ -143,7 +148,7 @@ class Root(CMakePackage): description='TBB multi-threading support') variant('threads', default=True, description='Enable using thread library') - variant('tmva', default=True, + variant('tmva', default=False, description='Build TMVA multi variate analysis library') variant('unuran', default=True, description='Use UNURAN for random number generation') @@ -185,6 +190,7 @@ class Root(CMakePackage): depends_on('xxhash', when='@6.13.02:') # See cmake_args, below. depends_on('xz') depends_on('zlib') + depends_on('zstd', when='@6.20:') # X-Graphics depends_on('libx11', when="+x") @@ -203,8 +209,14 @@ class Root(CMakePackage): # Qt4 depends_on('qt@:4.999', when='+qt4') - # TMVA - depends_on('py-numpy', when='+tmva') + # Python + depends_on('python@2.7:', when='+python', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run'), when='+tmva') + # This numpy dependency was not intended and will hopefully + # be fixed in 6.20.04. + # See: https://sft.its.cern.ch/jira/browse/ROOT-10626 + depends_on('py-numpy', type=('build', 'run'), + when='@6.20.00:6.20.03 +python') # Optional dependencies depends_on('davix @0.7.1:', when='+davix') @@ -219,7 +231,6 @@ class Root(CMakePackage): depends_on('postgresql', when='+postgres') depends_on('pythia6+root', when='+pythia6') depends_on('pythia8', when='+pythia8') - depends_on('python@2.7:', when='+python', type=('build', 'run')) depends_on('r', when='+r', type=('build', 'run')) depends_on('r-rcpp', when='+r', type=('build', 'run')) depends_on('r-rinside', when='+r', type=('build', 'run')) @@ -255,6 +266,7 @@ class Root(CMakePackage): # Incompatible variants conflicts('+opengl', when='~x', msg='OpenGL requires X') conflicts('+tmva', when='~gsl', msg='TVMA requires GSL') + conflicts('+tmva', when='~mlp', msg='TVMA requires MLP') conflicts('cxxstd=11', when='+root7', msg='root7 requires at least C++14') # Feature removed in 6.18: @@ -357,6 +369,7 @@ def cmake_args(self): ['minimal'], ['minuit'], ['minuit2', 'minuit'], + ['mlp'], ['monalisa', False], ['mysql'], ['odbc'], From 3b70c932aac0aaec35f697d5f08e80e5e46abcce Mon Sep 17 00:00:00 2001 From: Kevin Manalo Date: Fri, 20 Mar 2020 13:08:54 -0400 Subject: [PATCH 137/377] papi: add version 6.0.0 (#15590) --- var/spack/repos/builtin/packages/papi/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py index c6dc408eb69..6e0b6cb817a 100644 --- a/var/spack/repos/builtin/packages/papi/package.py +++ b/var/spack/repos/builtin/packages/papi/package.py @@ -23,6 +23,7 @@ class Papi(Package): maintainers = ['G-Ragghianti'] url = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz" + version('6.0.0', sha256='3442709dae3405c2845b304c06a8b15395ecf4f3899a89ceb4d715103cb4055f') version('5.7.0', sha256='d1a3bb848e292c805bc9f29e09c27870e2ff4cda6c2fba3b7da8b4bba6547589') version('5.6.0', sha256='49b7293f9ca2d74d6d80bd06b5c4be303663123267b4ac0884cbcae4c914dc47') version('5.5.1', sha256='49dc2c2323f6164c4a7e81b799ed690ee73158671205e71501f849391dd2c2d4') From e66a7530a1bd4e9ae5b32fb541fed9654fa81258 Mon Sep 17 00:00:00 2001 From: Benjamin Fovet <45510885+bfovet@users.noreply.github.com> Date: Fri, 20 Mar 2020 18:42:01 +0100 Subject: [PATCH 138/377] Add NLopt version 2.6.1 (#15595) --- var/spack/repos/builtin/packages/nlopt/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/nlopt/package.py b/var/spack/repos/builtin/packages/nlopt/package.py index c533bf60e80..509218ea839 100644 --- a/var/spack/repos/builtin/packages/nlopt/package.py +++ b/var/spack/repos/builtin/packages/nlopt/package.py @@ -17,6 +17,7 @@ class Nlopt(CMakePackage): git = "https://github.com/stevengj/nlopt.git" version('master', branch='master') + version('2.6.1', sha256='66d63a505187fb6f98642703bd0ef006fedcae2f9a6d1efa4f362ea919a02650') version('2.5.0', sha256='c6dd7a5701fff8ad5ebb45a3dc8e757e61d52658de3918e38bab233e7fd3b4ae') variant('shared', default=True, description='Enables the build of shared libraries') From 6f3983b1c737dce35bba45a592eb05e44b1730ea Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 20 Mar 2020 13:42:24 -0400 Subject: [PATCH 139/377] py-dgl: add new package (#15594) --- .../repos/builtin/packages/py-dgl/package.py | 94 +++++++++++++++++++ 1 file changed, 94 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-dgl/package.py diff --git a/var/spack/repos/builtin/packages/py-dgl/package.py b/var/spack/repos/builtin/packages/py-dgl/package.py new file mode 100644 index 00000000000..336d69edf24 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-dgl/package.py @@ -0,0 +1,94 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class PyDgl(CMakePackage): + """Deep Graph Library (DGL). + + DGL is an easy-to-use, high performance and scalable Python package for + deep learning on graphs. DGL is framework agnostic, meaning if a deep graph + model is a component of an end-to-end application, the rest of the logics + can be implemented in any major frameworks, such as PyTorch, Apache MXNet + or TensorFlow.""" + + homepage = "https://www.dgl.ai/" + git = "https://github.com/dmlc/dgl.git" + + maintainers = ['adamjstewart'] + + version('master', branch='master', submodules=True) + version('0.4.2', tag='0.4.2', submodules=True) + + variant('cuda', default=True, description='Build with CUDA') + variant('openmp', default=True, description='Build with OpenMP') + variant('backend', default='pytorch', description='Default backend', + values=['pytorch', 'mxnet', 'tensorflow'], multi=False) + + depends_on('cmake@3.5:', type='build') + depends_on('cuda', when='+cuda') + depends_on('llvm-openmp', when='%clang platform=darwin +openmp') + + # Python dependencies + extends('python') + depends_on('python@3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-cython', type='build') + depends_on('py-numpy@1.14.0:', type=('build', 'run')) + depends_on('py-scipy@1.1.0:', type=('build', 'run')) + depends_on('py-networkx@2.1:', type=('build', 'run')) + + # Backends + depends_on('py-torch@0.4.1:', when='backend=pytorch', type='run') + depends_on('mxnet@1.5:', when='backend=mxnet', type='run') + depends_on('py-tensorflow@2.0:', when='backend=tensorflow', type='run') + depends_on('py-tfdlpack', when='backend=tensorflow', type='run') + + build_directory = 'build' + + def cmake_args(self): + args = [] + + if '+cuda' in self.spec: + args.append('-DUSE_CUDA=ON') + else: + args.append('-DUSE_CUDA=OFF') + + if '+openmp' in self.spec: + args.append('-DUSE_OPENMP=ON') + + if self.spec.satisfies('%clang platform=darwin'): + args.extend([ + '-DOpenMP_CXX_FLAGS=' + + self.spec['llvm-openmp'].headers.include_flags, + '-DOpenMP_CXX_LIB_NAMES=' + + self.spec['llvm-openmp'].libs.names[0], + '-DOpenMP_C_FLAGS=' + + self.spec['llvm-openmp'].headers.include_flags, + '-DOpenMP_C_LIB_NAMES=' + + self.spec['llvm-openmp'].libs.names[0], + '-DOpenMP_omp_LIBRARY=' + + self.spec['llvm-openmp'].libs[0], + ]) + else: + args.append('-DUSE_OPENMP=OFF') + + if self.run_tests: + args.append('-DBUILD_CPP_TEST=ON') + else: + args.append('-DBUILD_CPP_TEST=OFF') + + return args + + def install(self, spec, prefix): + with working_dir('python'): + import os + print('Current dir:', os.getcwd()) + setup_py('install', '--prefix=' + prefix, + '--single-version-externally-managed', '--root=/') + + def setup_run_environment(self, env): + # https://docs.dgl.ai/install/backend.html + backend = self.spec.variants['backend'].value + env.set('DGLBACKEND', backend) From 32a3d59bfab37ad0deec1e07d69d02a6ee92b89d Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Wed, 11 Mar 2020 03:24:38 -0700 Subject: [PATCH 140/377] fetch_strategy: remove vestigial code (#15431) --- lib/spack/spack/fetch_strategy.py | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index 5ae01286c4b..eaf9f130c55 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -29,7 +29,6 @@ import re import shutil import sys -import xml.etree.ElementTree import llnl.util.tty as tty import six @@ -760,13 +759,6 @@ def mirror_id(self): result = os.path.sep.join(['git', repo_path, repo_ref]) return result - def get_source_id(self): - if not self.branch: - return - output = self.git('ls-remote', self.url, self.branch, output=str) - if output: - return output.split()[0] - def _repo_info(self): args = '' @@ -944,11 +936,6 @@ def cachable(self): def source_id(self): return self.revision - def get_source_id(self): - output = self.svn('info', '--xml', self.url, output=str) - info = xml.etree.ElementTree.fromstring(output) - return info.find('entry/commit').get('revision') - def mirror_id(self): if self.revision: repo_path = url_util.parse(self.url).path @@ -1064,11 +1051,6 @@ def mirror_id(self): result = os.path.sep.join(['hg', repo_path, self.revision]) return result - def get_source_id(self): - output = self.hg('id', self.url, output=str) - if output: - return output.strip() - @_needs_stage def fetch(self): if self.stage.expanded: From 3753424a87ebb86e9b6c972a8d136c8c2f2f604b Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Mon, 24 Feb 2020 15:34:57 +0100 Subject: [PATCH 141/377] modules: store configure args during build (#11084) This change stores packages' configure arguments during build and makes use of them while refreshing module files. This fixes problems such as in #10716. --- lib/spack/spack/installer.py | 16 ++++++++++++++++ lib/spack/spack/modules/common.py | 13 +++---------- lib/spack/spack/package.py | 15 +++++++++++++++ lib/spack/spack/test/install.py | 8 +++++++- 4 files changed, 41 insertions(+), 11 deletions(-) diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py index f4f39f26409..714dc0f31cc 100755 --- a/lib/spack/spack/installer.py +++ b/lib/spack/spack/installer.py @@ -463,6 +463,10 @@ def log(pkg): # Archive the environment used for the build install(pkg.env_path, pkg.install_env_path) + if os.path.exists(pkg.configure_args_path): + # Archive the args used for the build + install(pkg.configure_args_path, pkg.install_configure_args_path) + # Finally, archive files that are specific to each package with working_dir(pkg.stage.path): errors = six.StringIO() @@ -1013,6 +1017,18 @@ def build_process(): # Save the build environment in a file before building. dump_environment(pkg.env_path) + for attr in ('configure_args', 'cmake_args'): + try: + configure_args = getattr(pkg, attr)() + configure_args = ' '.join(configure_args) + + with open(pkg.configure_args_path, 'w') as args_file: + args_file.write(configure_args) + + break + except Exception: + pass + # cache debug settings debug_enabled = tty.is_debug() diff --git a/lib/spack/spack/modules/common.py b/lib/spack/spack/modules/common.py index d9407a1bf66..d6fb536e8fd 100644 --- a/lib/spack/spack/modules/common.py +++ b/lib/spack/spack/modules/common.py @@ -623,16 +623,9 @@ def configure_options(self): msg = 'unknown, software installed outside of Spack' return msg - # This is quite simple right now, but contains information on how - # to call different build system classes. - for attr in ('configure_args', 'cmake_args'): - try: - configure_args = getattr(pkg, attr)() - return ' '.join(configure_args) - except (AttributeError, IOError, KeyError): - # The method doesn't exist in the current spec, - # or it's not usable - pass + if os.path.exists(pkg.install_configure_args_path): + with open(pkg.install_configure_args_path, 'r') as args_file: + return args_file.read() # Returning a false-like value makes the default templates skip # the configure option section diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index d123f58cdf8..b7efc3989bc 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -68,6 +68,9 @@ # Filename for the Spack build/install environment file. _spack_build_envfile = 'spack-build-env.txt' +# Filename for the Spack configure args file. +_spack_configure_argsfile = 'spack-configure-args.txt' + class InstallPhase(object): """Manages a single phase of the installation. @@ -896,6 +899,18 @@ def install_log_path(self): # Otherwise, return the current install log path name. return os.path.join(install_path, _spack_build_logfile) + @property + def configure_args_path(self): + """Return the configure args file path associated with staging.""" + return os.path.join(self.stage.path, _spack_configure_argsfile) + + @property + def install_configure_args_path(self): + """Return the configure args file path on successful installation.""" + install_path = spack.store.layout.metadata_path(self.spec) + + return os.path.join(install_path, _spack_configure_argsfile) + def _make_fetcher(self): # Construct a composite fetcher that always contains at least # one element (the root package). In case there are resources diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py index f53a760f702..ff7f5a33556 100644 --- a/lib/spack/spack/test/install.py +++ b/lib/spack/spack/test/install.py @@ -15,7 +15,8 @@ import spack.repo import spack.store from spack.spec import Spec -from spack.package import _spack_build_envfile, _spack_build_logfile +from spack.package import (_spack_build_envfile, _spack_build_logfile, + _spack_configure_argsfile) def test_install_and_uninstall(install_mockery, mock_fetch, monkeypatch): @@ -410,6 +411,9 @@ def test_pkg_install_paths(install_mockery): env_path = os.path.join(spec.prefix, '.spack', _spack_build_envfile) assert spec.package.install_env_path == env_path + args_path = os.path.join(spec.prefix, '.spack', _spack_configure_argsfile) + assert spec.package.install_configure_args_path == args_path + # Backward compatibility checks log_dir = os.path.dirname(log_path) mkdirp(log_dir) @@ -448,6 +452,7 @@ def test_pkg_install_log(install_mockery): with working_dir(log_dir): touch(log_path) touch(spec.package.env_path) + touch(spec.package.configure_args_path) install_path = os.path.dirname(spec.package.install_log_path) mkdirp(install_path) @@ -456,6 +461,7 @@ def test_pkg_install_log(install_mockery): assert os.path.exists(spec.package.install_log_path) assert os.path.exists(spec.package.install_env_path) + assert os.path.exists(spec.package.install_configure_args_path) # Cleanup shutil.rmtree(log_dir) From 654914d53e2bb578eb8d82ca02a0547cf7834f5d Mon Sep 17 00:00:00 2001 From: Andrew W Elble Date: Fri, 6 Mar 2020 19:29:01 -0500 Subject: [PATCH 142/377] Fix for being able to 'spack load' packages that have been renamed. (#14348) * Fix for being able to 'spack load' packages that have been renamed. * tests: add test for 'spack load' of a installed, but renamed/deleted package --- lib/spack/spack/modules/common.py | 6 ++++- lib/spack/spack/test/modules/common.py | 31 ++++++++++++++++++++++++++ 2 files changed, 36 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/modules/common.py b/lib/spack/spack/modules/common.py index d6fb536e8fd..c09a2251165 100644 --- a/lib/spack/spack/modules/common.py +++ b/lib/spack/spack/modules/common.py @@ -342,7 +342,11 @@ def get_module(module_type, spec, get_full_path, required=True): The module name or path. May return ``None`` if the module is not available. """ - if spec.package.installed_upstream: + try: + upstream = spec.package.installed_upstream + except spack.repo.UnknownPackageError: + upstream, record = spack.store.db.query_by_spec_hash(spec.dag_hash()) + if upstream: module = (spack.modules.common.upstream_module_index .upstream_module(spec, module_type)) if not module: diff --git a/lib/spack/spack/test/modules/common.py b/lib/spack/spack/test/modules/common.py index cc2eb61d0b9..f2cb60e1db3 100644 --- a/lib/spack/spack/test/modules/common.py +++ b/lib/spack/spack/test/modules/common.py @@ -11,6 +11,7 @@ import spack.spec import spack.modules.tcl from spack.modules.common import UpstreamModuleIndex +from spack.spec import Spec import spack.error @@ -183,3 +184,33 @@ def test_get_module_upstream(): assert m1_path == '/path/to/a' finally: spack.modules.common.upstream_module_index = old_index + + +def test_load_installed_package_not_in_repo(install_mockery, mock_fetch, + monkeypatch): + # Get a basic concrete spec for the trivial install package. + spec = Spec('trivial-install-test-package') + spec.concretize() + assert spec.concrete + + # Get the package + pkg = spec.package + + def find_nothing(*args): + raise spack.repo.UnknownPackageError( + 'Repo package access is disabled for test') + + try: + pkg.do_install() + + spec._package = None + monkeypatch.setattr(spack.repo, 'get', find_nothing) + with pytest.raises(spack.repo.UnknownPackageError): + spec.package + + module_path = spack.modules.common.get_module('tcl', spec, True) + assert module_path + pkg.do_uninstall() + except Exception: + pkg.remove_prefix() + raise From b02981f10ccfa336d6f777d0517468ba0429c42f Mon Sep 17 00:00:00 2001 From: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Date: Mon, 2 Mar 2020 11:16:20 -0800 Subject: [PATCH 143/377] bugfix: ensure proper dependency handling for package-only installs (#15197) The distributed build PR (#13100) -- did not check the install status of dependencies when using the `--only package` option so would refuse to install a package with the claim that it had uninstalled dependencies whether that was the case or not. - [x] add install status checks for the `--only package` case. - [x] add initial set of tests --- lib/spack/spack/installer.py | 77 +++++++++++++++++++++++++---- lib/spack/spack/test/cmd/install.py | 24 +++++++++ lib/spack/spack/test/installer.py | 65 +++++++++++++++++++++--- 3 files changed, 149 insertions(+), 17 deletions(-) diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py index 714dc0f31cc..db82844cc5a 100755 --- a/lib/spack/spack/installer.py +++ b/lib/spack/spack/installer.py @@ -651,6 +651,66 @@ def _add_bootstrap_compilers(self, pkg): if package_id(comp_pkg) not in self.build_tasks: self._push_task(comp_pkg, is_compiler, 0, 0, STATUS_ADDED) + def _check_db(self, spec): + """Determine if the spec is flagged as installed in the database + + Args: + spec (Spec): spec whose database install status is being checked + + Return: + (rec, installed_in_db) tuple where rec is the database record, or + None, if there is no matching spec, and installed_in_db is + ``True`` if the spec is considered installed and ``False`` + otherwise + """ + try: + rec = spack.store.db.get_record(spec) + installed_in_db = rec.installed if rec else False + except KeyError: + # KeyError is raised if there is no matching spec in the database + # (versus no matching specs that are installed). + rec = None + installed_in_db = False + return rec, installed_in_db + + def _check_deps_status(self): + """Check the install status of the explicit spec's dependencies""" + + err = 'Cannot proceed with {0}: {1}' + for dep in self.spec.traverse(order='post', root=False): + dep_pkg = dep.package + dep_id = package_id(dep_pkg) + + # Check for failure since a prefix lock is not required + if spack.store.db.prefix_failed(dep): + action = "'spack install' the dependency" + msg = '{0} is marked as an install failure: {1}' \ + .format(dep_id, action) + raise InstallError(err.format(self.pkg_id, msg)) + + # Attempt to get a write lock to ensure another process does not + # uninstall the dependency while the requested spec is being + # installed + ltype, lock = self._ensure_locked('write', dep_pkg) + if lock is None: + msg = '{0} is write locked by another process'.format(dep_id) + raise InstallError(err.format(self.pkg_id, msg)) + + # Flag external and upstream packages as being installed + if dep_pkg.spec.external or dep_pkg.installed_upstream: + form = 'external' if dep_pkg.spec.external else 'upstream' + tty.debug('Flagging {0} {1} as installed'.format(form, dep_id)) + self.installed.add(dep_id) + continue + + # Check the database to see if the dependency has been installed + # and flag as such if appropriate + rec, installed_in_db = self._check_db(dep) + if installed_in_db: + tty.debug('Flagging {0} as installed per the database' + .format(dep_id)) + self.installed.add(dep_id) + def _prepare_for_install(self, task, keep_prefix, keep_stage, restage=False): """ @@ -680,14 +740,7 @@ def _prepare_for_install(self, task, keep_prefix, keep_stage, return # Determine if the spec is flagged as installed in the database - try: - rec = spack.store.db.get_record(task.pkg.spec) - installed_in_db = rec.installed if rec else False - except KeyError: - # KeyError is raised if there is no matching spec in the database - # (versus no matching specs that are installed). - rec = None - installed_in_db = False + rec, installed_in_db = self._check_db(task.pkg.spec) # Make sure the installation directory is in the desired state # for uninstalled specs. @@ -929,6 +982,11 @@ def _init_queue(self, install_deps, install_package): # Be sure to clear any previous failure spack.store.db.clear_failure(self.pkg.spec, force=True) + # If not installing dependencies, then determine their + # installation status before proceeding + if not install_deps: + self._check_deps_status() + # Now add the package itself, if appropriate self._push_task(self.pkg, False, 0, 0, STATUS_ADDED) @@ -1022,7 +1080,8 @@ def build_process(): configure_args = getattr(pkg, attr)() configure_args = ' '.join(configure_args) - with open(pkg.configure_args_path, 'w') as args_file: + with open(pkg.configure_args_path, 'w') as \ + args_file: args_file.write(configure_args) break diff --git a/lib/spack/spack/test/cmd/install.py b/lib/spack/spack/test/cmd/install.py index 2697a539bf6..1d4a0c68273 100644 --- a/lib/spack/spack/test/cmd/install.py +++ b/lib/spack/spack/test/cmd/install.py @@ -632,6 +632,30 @@ def test_install_only_dependencies(tmpdir, mock_fetch, install_mockery): assert not os.path.exists(root.prefix) +def test_install_only_package(tmpdir, mock_fetch, install_mockery, capfd): + msg = '' + with capfd.disabled(): + try: + install('--only', 'package', 'dependent-install') + except spack.installer.InstallError as e: + msg = str(e) + + assert 'Cannot proceed with dependent-install' in msg + assert '1 uninstalled dependency' in msg + + +def test_install_deps_then_package(tmpdir, mock_fetch, install_mockery): + dep = Spec('dependency-install').concretized() + root = Spec('dependent-install').concretized() + + install('--only', 'dependencies', 'dependent-install') + assert os.path.exists(dep.prefix) + assert not os.path.exists(root.prefix) + + install('--only', 'package', 'dependent-install') + assert os.path.exists(root.prefix) + + @pytest.mark.regression('12002') def test_install_only_dependencies_in_env(tmpdir, mock_fetch, install_mockery, mutable_mock_env_path): diff --git a/lib/spack/spack/test/installer.py b/lib/spack/spack/test/installer.py index 7d2eec8caf0..eadebfd3e45 100644 --- a/lib/spack/spack/test/installer.py +++ b/lib/spack/spack/test/installer.py @@ -27,6 +27,12 @@ def _none(*args, **kwargs): return None +def _not_locked(installer, lock_type, pkg): + """Generic monkeypatch function for _ensure_locked to return no lock""" + tty.msg('{0} locked {1}' .format(lock_type, pkg.spec.name)) + return lock_type, None + + def _true(*args, **kwargs): """Generic monkeypatch function that always returns True.""" return True @@ -285,6 +291,57 @@ def test_dump_packages_deps(install_mockery, tmpdir): inst.dump_packages(spec, '.') +@pytest.mark.tld +def test_check_deps_status_errs(install_mockery, monkeypatch): + """Test to cover _check_deps_status failures.""" + spec, installer = create_installer('a') + + # Make sure the package is identified as failed + orig_fn = spack.database.Database.prefix_failed + monkeypatch.setattr(spack.database.Database, 'prefix_failed', _true) + + with pytest.raises(inst.InstallError, matches='install failure'): + installer._check_deps_status() + + monkeypatch.setattr(spack.database.Database, 'prefix_failed', orig_fn) + + # Ensure do not acquire the lock + monkeypatch.setattr(inst.PackageInstaller, '_ensure_locked', _not_locked) + + with pytest.raises(inst.InstallError, matches='write locked by another'): + installer._check_deps_status() + + +@pytest.mark.tld +def test_check_deps_status_external(install_mockery, monkeypatch): + """Test to cover _check_deps_status for external.""" + spec, installer = create_installer('a') + + deps = spec.dependencies() + assert len(deps) > 0 + dep_id = 'b' + + # Ensure the known dependent is installed if flagged as external + monkeypatch.setattr(spack.spec.Spec, 'external', True) + installer._check_deps_status() + assert dep_id in installer.installed + + +@pytest.mark.tld +def test_check_deps_status_upstream(install_mockery, monkeypatch): + """Test to cover _check_deps_status for upstream.""" + spec, installer = create_installer('a') + + deps = spec.dependencies() + assert len(deps) > 0 + dep_id = 'b' + + # Ensure the known dependent, b, is installed if flagged as upstream + monkeypatch.setattr(spack.package.PackageBase, 'installed_upstream', True) + installer._check_deps_status() + assert dep_id in installer.installed + + def test_add_bootstrap_compilers(install_mockery, monkeypatch): """Test to cover _add_bootstrap_compilers.""" def _pkgs(pkg): @@ -458,10 +515,6 @@ def test_install_lock_failures(install_mockery, monkeypatch, capfd): def _requeued(installer, task): tty.msg('requeued {0}' .format(task.pkg.spec.name)) - def _not_locked(installer, lock_type, pkg): - tty.msg('{0} locked {1}' .format(lock_type, pkg.spec.name)) - return lock_type, None - spec, installer = create_installer('b') # Ensure never acquire a lock @@ -485,10 +538,6 @@ def test_install_lock_installed_requeue(install_mockery, monkeypatch, capfd): def _install(installer, task, **kwargs): tty.msg('{0} installing'.format(task.pkg.spec.name)) - def _not_locked(installer, lock_type, pkg): - tty.msg('{0} locked {1}' .format(lock_type, pkg.spec.name)) - return lock_type, None - def _prep(installer, task, keep_prefix, keep_stage, restage): installer.installed.add('b') tty.msg('{0} is installed' .format(task.pkg.spec.name)) From f3a1a8c6fe13b6f92a6c44e771aff5d1f9683a77 Mon Sep 17 00:00:00 2001 From: "Seth R. Johnson" Date: Wed, 26 Feb 2020 12:03:28 -0500 Subject: [PATCH 144/377] Uniquify suffixes added to module names (#14920) --- lib/spack/spack/modules/common.py | 1 + lib/spack/spack/test/data/modules/tcl/suffix.yaml | 1 + lib/spack/spack/test/modules/tcl.py | 3 ++- 3 files changed, 4 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/modules/common.py b/lib/spack/spack/modules/common.py index c09a2251165..8dee443eb33 100644 --- a/lib/spack/spack/modules/common.py +++ b/lib/spack/spack/modules/common.py @@ -428,6 +428,7 @@ def suffixes(self): for constraint, suffix in self.conf.get('suffixes', {}).items(): if constraint in self.spec: suffixes.append(suffix) + suffixes = sorted(set(suffixes)) if self.hash: suffixes.append(self.hash) return suffixes diff --git a/lib/spack/spack/test/data/modules/tcl/suffix.yaml b/lib/spack/spack/test/data/modules/tcl/suffix.yaml index 015ac63b0f9..57703e17339 100644 --- a/lib/spack/spack/test/data/modules/tcl/suffix.yaml +++ b/lib/spack/spack/test/data/modules/tcl/suffix.yaml @@ -5,3 +5,4 @@ tcl: suffixes: '+debug': foo '~debug': bar + '^mpich': foo diff --git a/lib/spack/spack/test/modules/tcl.py b/lib/spack/spack/test/modules/tcl.py index 70eee244612..40cb7be5ef7 100644 --- a/lib/spack/spack/test/modules/tcl.py +++ b/lib/spack/spack/test/modules/tcl.py @@ -215,9 +215,10 @@ def test_suffixes(self, module_configuration, factory): writer, spec = factory('mpileaks+debug arch=x86-linux') assert 'foo' in writer.layout.use_name + assert 'foo-foo' not in writer.layout.use_name writer, spec = factory('mpileaks~debug arch=x86-linux') - assert 'bar' in writer.layout.use_name + assert 'bar-foo' in writer.layout.use_name def test_setup_environment(self, modulefile_content, module_configuration): """Tests the internal set-up of run-time environment.""" From 5406e1f43ded0f124fe45b1a8568005c6166628b Mon Sep 17 00:00:00 2001 From: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Date: Wed, 26 Feb 2020 18:49:29 -0800 Subject: [PATCH 145/377] bugfix: Add dependents when initializing spec from yaml (#15220) The new build process, introduced in #13100 , relies on a spec's dependents in addition to their dependencies. Loading a spec from a yaml file was not initializing the dependents. - [x] populate dependents when loading from yaml --- lib/spack/spack/spec.py | 4 +-- .../spack/test/concretize_preferences.py | 26 ++++++++++++------- 2 files changed, 18 insertions(+), 12 deletions(-) diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 4b6bd67b6df..1493f0c973a 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -1919,9 +1919,7 @@ def from_dict(data): yaml_deps = node[name]['dependencies'] for dname, dhash, dtypes in Spec.read_yaml_dep_specs(yaml_deps): - # Fill in dependencies by looking them up by name in deps dict - deps[name]._dependencies[dname] = DependencySpec( - deps[name], deps[dname], dtypes) + deps[name]._add_dependency(deps[dname], dtypes) return spec diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py index 0d0d8705066..81b5360869c 100644 --- a/lib/spack/spack/test/concretize_preferences.py +++ b/lib/spack/spack/test/concretize_preferences.py @@ -15,15 +15,15 @@ @pytest.fixture() -def concretize_scope(config, tmpdir): +def concretize_scope(mutable_config, tmpdir): """Adds a scope for concretization preferences""" tmpdir.ensure_dir('concretize') - config.push_scope( + mutable_config.push_scope( ConfigScope('concretize', str(tmpdir.join('concretize')))) yield - config.pop_scope() + mutable_config.pop_scope() spack.repo.path._provider_index = None @@ -84,16 +84,24 @@ def test_preferred_variants(self): 'mpileaks', debug=True, opt=True, shared=False, static=False ) - def test_preferred_compilers(self, mutable_mock_repo): + def test_preferred_compilers(self): """Test preferred compilers are applied correctly """ - update_packages('mpileaks', 'compiler', ['clang@3.3']) - spec = concretize('mpileaks') - assert spec.compiler == spack.spec.CompilerSpec('clang@3.3') + # Need to make sure the test uses an available compiler + compiler_list = spack.compilers.all_compiler_specs() + assert compiler_list - update_packages('mpileaks', 'compiler', ['gcc@4.5.0']) + # Try the first available compiler + compiler = str(compiler_list[0]) + update_packages('mpileaks', 'compiler', [compiler]) spec = concretize('mpileaks') - assert spec.compiler == spack.spec.CompilerSpec('gcc@4.5.0') + assert spec.compiler == spack.spec.CompilerSpec(compiler) + + # Try the last available compiler + compiler = str(compiler_list[-1]) + update_packages('mpileaks', 'compiler', [compiler]) + spec = concretize('mpileaks') + assert spec.compiler == spack.spec.CompilerSpec(compiler) def test_preferred_target(self, mutable_mock_repo): """Test preferred compilers are applied correctly From fa0a5e44aa7616bdef4cc825436bfb207c03bf56 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 5 Mar 2020 11:16:02 +0100 Subject: [PATCH 146/377] Correct pytest.raises matches to match (#15346) --- lib/spack/spack/test/database.py | 2 +- lib/spack/spack/test/installer.py | 14 +++++++------- lib/spack/spack/test/llnl/util/lock.py | 4 ++-- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py index 8f0f4dff6ab..88e6c42693c 100644 --- a/lib/spack/spack/test/database.py +++ b/lib/spack/spack/test/database.py @@ -755,7 +755,7 @@ def test_query_spec_with_non_conditional_virtual_dependency(database): def test_failed_spec_path_error(database): """Ensure spec not concrete check is covered.""" s = spack.spec.Spec('a') - with pytest.raises(ValueError, matches='Concrete spec required'): + with pytest.raises(ValueError, match='Concrete spec required'): spack.store.db._failed_spec_path(s) diff --git a/lib/spack/spack/test/installer.py b/lib/spack/spack/test/installer.py index eadebfd3e45..c261ca7a632 100644 --- a/lib/spack/spack/test/installer.py +++ b/lib/spack/spack/test/installer.py @@ -245,7 +245,7 @@ def test_ensure_locked_have(install_mockery, tmpdir): def test_package_id(install_mockery): """Test to cover package_id functionality.""" pkg = spack.repo.get('trivial-install-test-package') - with pytest.raises(ValueError, matches='spec is not concretized'): + with pytest.raises(ValueError, match='spec is not concretized'): inst.package_id(pkg) spec = spack.spec.Spec('trivial-install-test-package') @@ -280,7 +280,7 @@ def _no_compilers(pkg, arch_spec): # Test up to the dependency check monkeypatch.setattr(spack.compilers, 'compilers_for_spec', _no_compilers) - with pytest.raises(spack.repo.UnknownPackageError, matches='not found'): + with pytest.raises(spack.repo.UnknownPackageError, match='not found'): inst._packages_needed_to_bootstrap_compiler(spec.package) @@ -300,7 +300,7 @@ def test_check_deps_status_errs(install_mockery, monkeypatch): orig_fn = spack.database.Database.prefix_failed monkeypatch.setattr(spack.database.Database, 'prefix_failed', _true) - with pytest.raises(inst.InstallError, matches='install failure'): + with pytest.raises(inst.InstallError, match='install failure'): installer._check_deps_status() monkeypatch.setattr(spack.database.Database, 'prefix_failed', orig_fn) @@ -308,7 +308,7 @@ def test_check_deps_status_errs(install_mockery, monkeypatch): # Ensure do not acquire the lock monkeypatch.setattr(inst.PackageInstaller, '_ensure_locked', _not_locked) - with pytest.raises(inst.InstallError, matches='write locked by another'): + with pytest.raises(inst.InstallError, match='write locked by another'): installer._check_deps_status() @@ -485,7 +485,7 @@ def test_install_uninstalled_deps(install_mockery, monkeypatch, capsys): monkeypatch.setattr(inst.PackageInstaller, '_update_failed', _noop) msg = 'Cannot proceed with dependent-install' - with pytest.raises(spack.installer.InstallError, matches=msg): + with pytest.raises(spack.installer.InstallError, match=msg): installer.install() out = str(capsys.readouterr()) @@ -503,7 +503,7 @@ def test_install_failed(install_mockery, monkeypatch, capsys): monkeypatch.setattr(inst.PackageInstaller, '_install_task', _noop) msg = 'Installation of b failed' - with pytest.raises(spack.installer.InstallError, matches=msg): + with pytest.raises(spack.installer.InstallError, match=msg): installer.install() out = str(capsys.readouterr()) @@ -622,7 +622,7 @@ def _install(installer, task, **kwargs): spec, installer = create_installer('b') - with pytest.raises(dl.InstallDirectoryAlreadyExistsError, matches=err): + with pytest.raises(dl.InstallDirectoryAlreadyExistsError, match=err): installer.install() assert 'b' in installer.installed diff --git a/lib/spack/spack/test/llnl/util/lock.py b/lib/spack/spack/test/llnl/util/lock.py index 7236e1dbf9b..b2b7cf85acc 100644 --- a/lib/spack/spack/test/llnl/util/lock.py +++ b/lib/spack/spack/test/llnl/util/lock.py @@ -1272,7 +1272,7 @@ def test_downgrade_write_fails(tmpdir): lock = lk.Lock('lockfile') lock.acquire_read() msg = 'Cannot downgrade lock from write to read on file: lockfile' - with pytest.raises(lk.LockDowngradeError, matches=msg): + with pytest.raises(lk.LockDowngradeError, match=msg): lock.downgrade_write_to_read() @@ -1292,5 +1292,5 @@ def test_upgrade_read_fails(tmpdir): lock = lk.Lock('lockfile') lock.acquire_write() msg = 'Cannot upgrade lock from read to write on file: lockfile' - with pytest.raises(lk.LockUpgradeError, matches=msg): + with pytest.raises(lk.LockUpgradeError, match=msg): lock.upgrade_read_to_write() From 733f9f8cfa5814cd1df6c34cf7e70f460ce75ff4 Mon Sep 17 00:00:00 2001 From: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Date: Thu, 5 Mar 2020 16:54:29 -0800 Subject: [PATCH 147/377] Recover coverage from subprocesses during unit tests (#15354) * Recover coverage from subprocesses during unit tests --- lib/spack/spack/cmd/test.py | 2 +- lib/spack/spack/test/cmd/test.py | 11 ++++++----- lib/spack/spack/test/llnl/util/log.py | 9 ++++++--- lib/spack/spack/test/pytest.ini => pytest.ini | 2 +- share/spack/qa/run-unit-tests | 8 ++------ 5 files changed, 16 insertions(+), 16 deletions(-) rename lib/spack/spack/test/pytest.ini => pytest.ini (90%) diff --git a/lib/spack/spack/cmd/test.py b/lib/spack/spack/cmd/test.py index f2ca8fc93be..8cbc0fbccf3 100644 --- a/lib/spack/spack/cmd/test.py +++ b/lib/spack/spack/cmd/test.py @@ -154,7 +154,7 @@ def test(parser, args, unknown_args): # The default is to test the core of Spack. If the option `--extension` # has been used, then test that extension. - pytest_root = spack.paths.test_path + pytest_root = spack.paths.spack_root if args.extension: target = args.extension extensions = spack.config.get('config:extensions') diff --git a/lib/spack/spack/test/cmd/test.py b/lib/spack/spack/test/cmd/test.py index 9a64209cfa6..a9ef735afe5 100644 --- a/lib/spack/spack/test/cmd/test.py +++ b/lib/spack/spack/test/cmd/test.py @@ -6,6 +6,7 @@ from spack.main import SpackCommand spack_test = SpackCommand('test') +cmd_test_py = 'lib/spack/spack/test/cmd/test.py' def test_list(): @@ -16,13 +17,13 @@ def test_list(): def test_list_with_pytest_arg(): - output = spack_test('--list', 'cmd/test.py') - assert output.strip() == "cmd/test.py" + output = spack_test('--list', cmd_test_py) + assert output.strip() == cmd_test_py def test_list_with_keywords(): output = spack_test('--list', '-k', 'cmd/test.py') - assert output.strip() == "cmd/test.py" + assert output.strip() == cmd_test_py def test_list_long(capsys): @@ -44,7 +45,7 @@ def test_list_long(capsys): def test_list_long_with_pytest_arg(capsys): with capsys.disabled(): - output = spack_test('--list-long', 'cmd/test.py') + output = spack_test('--list-long', cmd_test_py) assert "test.py::\n" in output assert "test_list" in output assert "test_list_with_pytest_arg" in output @@ -74,7 +75,7 @@ def test_list_names(): def test_list_names_with_pytest_arg(): - output = spack_test('--list-names', 'cmd/test.py') + output = spack_test('--list-names', cmd_test_py) assert "test.py::test_list\n" in output assert "test.py::test_list_with_pytest_arg\n" in output assert "test.py::test_list_with_keywords\n" in output diff --git a/lib/spack/spack/test/llnl/util/log.py b/lib/spack/spack/test/llnl/util/log.py index 1eae1ccf69e..0c879c5a6ed 100644 --- a/lib/spack/spack/test/llnl/util/log.py +++ b/lib/spack/spack/test/llnl/util/log.py @@ -32,7 +32,8 @@ def test_log_python_output_with_fd_stream(capfd, tmpdir): with open('foo.txt') as f: assert f.read() == 'logged\n' - assert capfd.readouterr() == ('', '') + # Coverage is cluttering stderr during tests + assert capfd.readouterr()[0] == '' def test_log_python_output_and_echo_output(capfd, tmpdir): @@ -42,7 +43,8 @@ def test_log_python_output_and_echo_output(capfd, tmpdir): print('echo') print('logged') - assert capfd.readouterr() == ('echo\n', '') + # Coverage is cluttering stderr during tests + assert capfd.readouterr()[0] == 'echo\n' with open('foo.txt') as f: assert f.read() == 'echo\nlogged\n' @@ -75,7 +77,8 @@ def test_log_subproc_and_echo_output(capfd, tmpdir): echo('echo') print('logged') - assert capfd.readouterr() == ('echo\n', '') + # Coverage is cluttering stderr during tests + assert capfd.readouterr()[0] == 'echo\n' with open('foo.txt') as f: assert f.read() == 'logged\n' diff --git a/lib/spack/spack/test/pytest.ini b/pytest.ini similarity index 90% rename from lib/spack/spack/test/pytest.ini rename to pytest.ini index 59839c0005c..baf163ef0b4 100644 --- a/lib/spack/spack/test/pytest.ini +++ b/pytest.ini @@ -1,7 +1,7 @@ # content of pytest.ini [pytest] addopts = --durations=20 -ra -testpaths = . +testpaths = lib/spack/spack/test python_files = *.py markers = db: tests that require creating a DB diff --git a/share/spack/qa/run-unit-tests b/share/spack/qa/run-unit-tests index 52748dacdf6..01f564e5e1f 100755 --- a/share/spack/qa/run-unit-tests +++ b/share/spack/qa/run-unit-tests @@ -37,16 +37,12 @@ bin/spack -h bin/spack help -a # Profile and print top 20 lines for a simple call to spack spec -bin/spack -p --lines 20 spec mpileaks%gcc ^elfutils@0.170 +spack -p --lines 20 spec mpileaks%gcc ^elfutils@0.170 #----------------------------------------------------------- # Run unit tests with code coverage #----------------------------------------------------------- -extra_args="" -if [[ -n "$@" ]]; then - extra_args="-k $@" -fi -$coverage_run bin/spack test -x --verbose "$extra_args" +$coverage_run $(which spack) test -x --verbose #----------------------------------------------------------- # Run tests for setup-env.sh From 59a7963785b0e443d5682d497af373383876da20 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 5 Mar 2020 10:26:50 +0100 Subject: [PATCH 148/377] Bugfix: resolve StopIteration message attribute failure (#15341) Testing the install StopIteration exception resulted in an attribute error: AttributeError: 'StopIteration' object has no attribute 'message' This PR adds a unit test and resolves that error. --- lib/spack/spack/installer.py | 2 +- lib/spack/spack/test/installer.py | 21 +++++++++++++++++++++ 2 files changed, 22 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py index db82844cc5a..bd38d11ea2e 100755 --- a/lib/spack/spack/installer.py +++ b/lib/spack/spack/installer.py @@ -1154,7 +1154,7 @@ def build_process(): except StopIteration as e: # A StopIteration exception means that do_install was asked to # stop early from clients. - tty.msg('{0} {1}'.format(self.pid, e.message)) + tty.msg('{0} {1}'.format(self.pid, str(e))) tty.msg('Package stage directory : {0}' .format(pkg.stage.source_path)) diff --git a/lib/spack/spack/test/installer.py b/lib/spack/spack/test/installer.py index c261ca7a632..8c3a232f19f 100644 --- a/lib/spack/spack/test/installer.py +++ b/lib/spack/spack/test/installer.py @@ -391,6 +391,27 @@ def test_install_task_use_cache(install_mockery, monkeypatch): assert spec.package.name in installer.installed +def test_install_task_stop_iter(install_mockery, monkeypatch, capfd): + """Test _install_task to cover the StopIteration exception.""" + mock_err_msg = 'mock stop iteration' + + def _raise(installer, pkg): + raise StopIteration(mock_err_msg) + + spec, installer = create_installer('a') + task = create_build_task(spec.package) + + monkeypatch.setattr(spack.package.PackageBase, 'unit_test_check', _true) + monkeypatch.setattr(inst.PackageInstaller, '_setup_install_dir', _raise) + + installer._install_task(task) + out = capfd.readouterr()[0] + + assert mock_err_msg in out + assert 'Package stage directory' in out + assert spec.package.stage.source_path in out + + def test_release_lock_write_n_exception(install_mockery, tmpdir, capsys): """Test _release_lock for supposed write lock with exception.""" spec, installer = create_installer('trivial-install-test-package') From 3f4d300c848b24343d7cf05c260e9a6e39b06430 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 20 Mar 2020 14:39:39 -0400 Subject: [PATCH 149/377] sentencepiece: add new package (#15596) --- .../builtin/packages/sentencepiece/package.py | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/sentencepiece/package.py diff --git a/var/spack/repos/builtin/packages/sentencepiece/package.py b/var/spack/repos/builtin/packages/sentencepiece/package.py new file mode 100644 index 00000000000..f3b168db66a --- /dev/null +++ b/var/spack/repos/builtin/packages/sentencepiece/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class Sentencepiece(CMakePackage): + """Unsupervised text tokenizer for Neural Network-based text generation. + + This is the C++ package.""" + + homepage = "https://github.com/google/sentencepiece" + url = "https://github.com/google/sentencepiece/archive/v0.1.85.tar.gz" + + maintainers = ['adamjstewart'] + + version('0.1.85', sha256='dd4956287a1b6af3cbdbbd499b7227a859a4e3f41c9882de5e6bdd929e219ae6') + + depends_on('cmake@3.1:', type='build') + depends_on('gperftools') # optional, 10-40% performance improvement From 9a1ce36e44fb5048952ae98209ddd60e0c137379 Mon Sep 17 00:00:00 2001 From: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Date: Wed, 11 Mar 2020 03:39:23 -0700 Subject: [PATCH 150/377] bugfix: resolve undefined source_pkg_dir failure (#15339) --- lib/spack/spack/installer.py | 11 +++-- lib/spack/spack/test/installer.py | 71 +++++++++++++++++++++++++++++-- 2 files changed, 74 insertions(+), 8 deletions(-) diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py index bd38d11ea2e..4559fd70ba3 100755 --- a/lib/spack/spack/installer.py +++ b/lib/spack/spack/installer.py @@ -407,7 +407,10 @@ def dump_packages(spec, path): source_repo = spack.repo.Repo(source_repo_root) source_pkg_dir = source_repo.dirname_for_package_name( node.name) - except spack.repo.RepoError: + except spack.repo.RepoError as err: + tty.debug('Failed to create source repo for {0}: {1}' + .format(node.name, str(err))) + source_pkg_dir = None tty.warn("Warning: Couldn't copy in provenance for {0}" .format(node.name)) @@ -419,10 +422,10 @@ def dump_packages(spec, path): # Get the location of the package in the dest repo. dest_pkg_dir = repo.dirname_for_package_name(node.name) - if node is not spec: - install_tree(source_pkg_dir, dest_pkg_dir) - else: + if node is spec: spack.repo.path.dump_provenance(node, dest_pkg_dir) + elif source_pkg_dir: + install_tree(source_pkg_dir, dest_pkg_dir) def install_msg(name, pid): diff --git a/lib/spack/spack/test/installer.py b/lib/spack/spack/test/installer.py index 8c3a232f19f..b9730c31657 100644 --- a/lib/spack/spack/test/installer.py +++ b/lib/spack/spack/test/installer.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) import os +import py import pytest import llnl.util.tty as tty @@ -17,6 +18,22 @@ import spack.spec +def _mock_repo(root, namespace): + """Create an empty repository at the specified root + + Args: + root (str): path to the mock repository root + namespace (str): mock repo's namespace + """ + repodir = py.path.local(root) if isinstance(root, str) else root + repodir.ensure(spack.repo.packages_dir_name, dir=True) + yaml = repodir.join('repo.yaml') + yaml.write(""" +repo: + namespace: {0} +""".format(namespace)) + + def _noop(*args, **kwargs): """Generic monkeypatch no-op routine.""" pass @@ -284,11 +301,57 @@ def _no_compilers(pkg, arch_spec): inst._packages_needed_to_bootstrap_compiler(spec.package) -def test_dump_packages_deps(install_mockery, tmpdir): - """Test to add coverage to dump_packages.""" +def test_dump_packages_deps_ok(install_mockery, tmpdir, mock_repo_path): + """Test to add coverage to dump_packages with dependencies happy path.""" + + spec_name = 'simple-inheritance' + spec = spack.spec.Spec(spec_name).concretized() + inst.dump_packages(spec, str(tmpdir)) + + repo = mock_repo_path.repos[0] + dest_pkg = repo.filename_for_package_name(spec_name) + assert os.path.isfile(dest_pkg) + + +def test_dump_packages_deps_errs(install_mockery, tmpdir, monkeypatch, capsys): + """Test to add coverage to dump_packages with dependencies.""" + orig_bpp = spack.store.layout.build_packages_path + orig_dirname = spack.repo.Repo.dirname_for_package_name + repo_err_msg = "Mock dirname_for_package_name" + + def bpp_path(spec): + # Perform the original function + source = orig_bpp(spec) + # Mock the required directory structure for the repository + _mock_repo(os.path.join(source, spec.namespace), spec.namespace) + return source + + def _repoerr(repo, name): + if name == 'cmake': + raise spack.repo.RepoError(repo_err_msg) + else: + return orig_dirname(repo, name) + + # Now mock the creation of the required directory structure to cover + # the try-except block + monkeypatch.setattr(spack.store.layout, 'build_packages_path', bpp_path) + spec = spack.spec.Spec('simple-inheritance').concretized() - with tmpdir.as_cwd(): - inst.dump_packages(spec, '.') + path = str(tmpdir) + + # The call to install_tree will raise the exception since not mocking + # creation of dependency package files within *install* directories. + with pytest.raises(IOError, match=path): + inst.dump_packages(spec, path) + + # Now try the error path, which requires the mock directory structure + # above + monkeypatch.setattr(spack.repo.Repo, 'dirname_for_package_name', _repoerr) + with pytest.raises(spack.repo.RepoError, match=repo_err_msg): + inst.dump_packages(spec, path) + + out = str(capsys.readouterr()[1]) + assert "Couldn't copy in provenance for cmake" in out @pytest.mark.tld From 1c8f792bb5e3fd96d2cfb341d988e42923956f3f Mon Sep 17 00:00:00 2001 From: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Date: Thu, 12 Mar 2020 13:20:20 -0700 Subject: [PATCH 151/377] testing: increase installer coverage (#15237) --- lib/spack/spack/installer.py | 51 +++--- lib/spack/spack/test/install.py | 69 ++++++-- lib/spack/spack/test/installer.py | 269 ++++++++++++++++++++++-------- 3 files changed, 280 insertions(+), 109 deletions(-) diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py index 4559fd70ba3..4e8ec397335 100755 --- a/lib/spack/spack/installer.py +++ b/lib/spack/spack/installer.py @@ -36,6 +36,7 @@ import sys import time +import llnl.util.filesystem as fs import llnl.util.lock as lk import llnl.util.tty as tty import spack.binary_distribution as binary_distribution @@ -43,14 +44,12 @@ import spack.error import spack.hooks import spack.package +import spack.package_prefs as prefs import spack.repo import spack.store -from llnl.util.filesystem import \ - chgrp, install, install_tree, mkdirp, touch, working_dir from llnl.util.tty.color import colorize, cwrite from llnl.util.tty.log import log_output -from spack.package_prefs import get_package_dir_permissions, get_package_group from spack.util.environment import dump_environment from spack.util.executable import which @@ -133,21 +132,21 @@ def _do_fake_install(pkg): chmod = which('chmod') # Install fake command - mkdirp(pkg.prefix.bin) - touch(os.path.join(pkg.prefix.bin, command)) + fs.mkdirp(pkg.prefix.bin) + fs.touch(os.path.join(pkg.prefix.bin, command)) chmod('+x', os.path.join(pkg.prefix.bin, command)) # Install fake header file - mkdirp(pkg.prefix.include) - touch(os.path.join(pkg.prefix.include, header + '.h')) + fs.mkdirp(pkg.prefix.include) + fs.touch(os.path.join(pkg.prefix.include, header + '.h')) # Install fake shared and static libraries - mkdirp(pkg.prefix.lib) + fs.mkdirp(pkg.prefix.lib) for suffix in [dso_suffix, '.a']: - touch(os.path.join(pkg.prefix.lib, library + suffix)) + fs.touch(os.path.join(pkg.prefix.lib, library + suffix)) # Install fake man page - mkdirp(pkg.prefix.man.man1) + fs.mkdirp(pkg.prefix.man.man1) packages_dir = spack.store.layout.build_packages_path(pkg.spec) dump_packages(pkg.spec, packages_dir) @@ -377,14 +376,14 @@ def dump_packages(spec, path): Dump all package information for a spec and its dependencies. This creates a package repository within path for every namespace in the - spec DAG, and fills the repos wtih package files and patch files for every + spec DAG, and fills the repos with package files and patch files for every node in the DAG. Args: spec (Spec): the Spack spec whose package information is to be dumped path (str): the path to the build packages directory """ - mkdirp(path) + fs.mkdirp(path) # Copy in package.py files from any dependencies. # Note that we copy them in as they are in the *install* directory @@ -425,7 +424,7 @@ def dump_packages(spec, path): if node is spec: spack.repo.path.dump_provenance(node, dest_pkg_dir) elif source_pkg_dir: - install_tree(source_pkg_dir, dest_pkg_dir) + fs.install_tree(source_pkg_dir, dest_pkg_dir) def install_msg(name, pid): @@ -461,17 +460,17 @@ def log(pkg): tty.debug(e) # Archive the whole stdout + stderr for the package - install(pkg.log_path, pkg.install_log_path) + fs.install(pkg.log_path, pkg.install_log_path) # Archive the environment used for the build - install(pkg.env_path, pkg.install_env_path) + fs.install(pkg.env_path, pkg.install_env_path) if os.path.exists(pkg.configure_args_path): # Archive the args used for the build - install(pkg.configure_args_path, pkg.install_configure_args_path) + fs.install(pkg.configure_args_path, pkg.install_configure_args_path) # Finally, archive files that are specific to each package - with working_dir(pkg.stage.path): + with fs.working_dir(pkg.stage.path): errors = six.StringIO() target_dir = os.path.join( spack.store.layout.metadata_path(pkg.spec), 'archived-files') @@ -493,8 +492,8 @@ def log(pkg): target = os.path.join(target_dir, f) # We must ensure that the directory exists before # copying a file in - mkdirp(os.path.dirname(target)) - install(f, target) + fs.mkdirp(os.path.dirname(target)) + fs.install(f, target) except Exception as e: tty.debug(e) @@ -505,7 +504,7 @@ def log(pkg): if errors.getvalue(): error_file = os.path.join(target_dir, 'errors.txt') - mkdirp(target_dir) + fs.mkdirp(target_dir) with open(error_file, 'w') as err: err.write(errors.getvalue()) tty.warn('Errors occurred when archiving files.\n\t' @@ -1071,10 +1070,10 @@ def build_process(): pkg.name, 'src') tty.msg('{0} Copying source to {1}' .format(pre, src_target)) - install_tree(pkg.stage.source_path, src_target) + fs.install_tree(pkg.stage.source_path, src_target) # Do the real install in the source directory. - with working_dir(pkg.stage.source_path): + with fs.working_dir(pkg.stage.source_path): # Save the build environment in a file before building. dump_environment(pkg.env_path) @@ -1286,20 +1285,20 @@ def _setup_install_dir(self, pkg): spack.store.layout.create_install_directory(pkg.spec) else: # Set the proper group for the prefix - group = get_package_group(pkg.spec) + group = prefs.get_package_group(pkg.spec) if group: - chgrp(pkg.spec.prefix, group) + fs.chgrp(pkg.spec.prefix, group) # Set the proper permissions. # This has to be done after group because changing groups blows # away the sticky group bit on the directory mode = os.stat(pkg.spec.prefix).st_mode - perms = get_package_dir_permissions(pkg.spec) + perms = prefs.get_package_dir_permissions(pkg.spec) if mode != perms: os.chmod(pkg.spec.prefix, perms) # Ensure the metadata path exists as well - mkdirp(spack.store.layout.metadata_path(pkg.spec), mode=perms) + fs.mkdirp(spack.store.layout.metadata_path(pkg.spec), mode=perms) def _update_failed(self, task, mark=False, exc=None): """ diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py index ff7f5a33556..2f779c6a5f3 100644 --- a/lib/spack/spack/test/install.py +++ b/lib/spack/spack/test/install.py @@ -7,7 +7,7 @@ import pytest import shutil -from llnl.util.filesystem import mkdirp, touch, working_dir +import llnl.util.filesystem as fs from spack.package import InstallError, PackageBase, PackageStillNeededError import spack.error @@ -380,11 +380,11 @@ def test_pkg_build_paths(install_mockery): # Backward compatibility checks log_dir = os.path.dirname(log_path) - mkdirp(log_dir) - with working_dir(log_dir): + fs.mkdirp(log_dir) + with fs.working_dir(log_dir): # Start with the older of the previous log filenames older_log = 'spack-build.out' - touch(older_log) + fs.touch(older_log) assert spec.package.log_path.endswith(older_log) # Now check the newer log filename @@ -416,11 +416,11 @@ def test_pkg_install_paths(install_mockery): # Backward compatibility checks log_dir = os.path.dirname(log_path) - mkdirp(log_dir) - with working_dir(log_dir): + fs.mkdirp(log_dir) + with fs.working_dir(log_dir): # Start with the older of the previous install log filenames older_log = 'build.out' - touch(older_log) + fs.touch(older_log) assert spec.package.install_log_path.endswith(older_log) # Now check the newer install log filename @@ -437,7 +437,8 @@ def test_pkg_install_paths(install_mockery): shutil.rmtree(log_dir) -def test_pkg_install_log(install_mockery): +def test_log_install_without_build_files(install_mockery): + """Test the installer log function when no build files are present.""" # Get a basic concrete spec for the trivial install package. spec = Spec('trivial-install-test-package').concretized() @@ -445,17 +446,40 @@ def test_pkg_install_log(install_mockery): with pytest.raises(IOError, match="No such file or directory"): spack.installer.log(spec.package) - # Set up mock build files and try again + +def test_log_install_with_build_files(install_mockery, monkeypatch): + """Test the installer's log function when have build files.""" + config_log = 'config.log' + + # Retain the original function for use in the monkey patch that is used + # to raise an exception under the desired condition for test coverage. + orig_install_fn = fs.install + + def _install(src, dest): + orig_install_fn(src, dest) + if src.endswith(config_log): + raise Exception('Mock log install error') + + monkeypatch.setattr(fs, 'install', _install) + + spec = Spec('trivial-install-test-package').concretized() + + # Set up mock build files and try again to include archive failure log_path = spec.package.log_path log_dir = os.path.dirname(log_path) - mkdirp(log_dir) - with working_dir(log_dir): - touch(log_path) - touch(spec.package.env_path) - touch(spec.package.configure_args_path) + fs.mkdirp(log_dir) + with fs.working_dir(log_dir): + fs.touch(log_path) + fs.touch(spec.package.env_path) + fs.touch(spec.package.configure_args_path) install_path = os.path.dirname(spec.package.install_log_path) - mkdirp(install_path) + fs.mkdirp(install_path) + + source = spec.package.stage.source_path + config = os.path.join(source, 'config.log') + fs.touchp(config) + spec.package.archive_files = ['missing', '..', config] spack.installer.log(spec.package) @@ -463,6 +487,21 @@ def test_pkg_install_log(install_mockery): assert os.path.exists(spec.package.install_env_path) assert os.path.exists(spec.package.install_configure_args_path) + archive_dir = os.path.join(install_path, 'archived-files') + source_dir = os.path.dirname(source) + rel_config = os.path.relpath(config, source_dir) + + assert os.path.exists(os.path.join(archive_dir, rel_config)) + assert not os.path.exists(os.path.join(archive_dir, 'missing')) + + expected_errs = [ + 'OUTSIDE SOURCE PATH', # for '..' + 'FAILED TO ARCHIVE' # for rel_config + ] + with open(os.path.join(archive_dir, 'errors.txt'), 'r') as fd: + for ln, expected in zip(fd, expected_errs): + assert expected in ln + # Cleanup shutil.rmtree(log_dir) diff --git a/lib/spack/spack/test/installer.py b/lib/spack/spack/test/installer.py index b9730c31657..0be4bc78c02 100644 --- a/lib/spack/spack/test/installer.py +++ b/lib/spack/spack/test/installer.py @@ -7,15 +7,19 @@ import py import pytest +import llnl.util.filesystem as fs import llnl.util.tty as tty +import llnl.util.lock as ulk import spack.binary_distribution import spack.compilers import spack.directory_layout as dl import spack.installer as inst -import spack.util.lock as lk +import spack.package_prefs as prefs import spack.repo import spack.spec +import spack.store +import spack.util.lock as lk def _mock_repo(root, namespace): @@ -152,7 +156,7 @@ def test_process_external_package_module(install_mockery, monkeypatch, capfd): def test_process_binary_cache_tarball_none(install_mockery, monkeypatch, capfd): - """Tests to cover _process_binary_cache_tarball when no tarball.""" + """Tests of _process_binary_cache_tarball when no tarball.""" monkeypatch.setattr(spack.binary_distribution, 'download_tarball', _none) pkg = spack.repo.get('trivial-install-test-package') @@ -162,7 +166,7 @@ def test_process_binary_cache_tarball_none(install_mockery, monkeypatch, def test_process_binary_cache_tarball_tar(install_mockery, monkeypatch, capfd): - """Tests to cover _process_binary_cache_tarball with a tar file.""" + """Tests of _process_binary_cache_tarball with a tar file.""" def _spec(spec): return spec @@ -179,6 +183,25 @@ def _spec(spec): assert 'Installing a from binary cache' in capfd.readouterr()[0] +def test_try_install_from_binary_cache(install_mockery, mock_packages, + monkeypatch, capsys): + """Tests SystemExit path for_try_install_from_binary_cache.""" + def _spec(spec, force): + spec = spack.spec.Spec('mpi').concretized() + return {spec: None} + + spec = spack.spec.Spec('mpich') + spec.concretize() + + monkeypatch.setattr(spack.binary_distribution, 'get_spec', _spec) + + with pytest.raises(SystemExit): + inst._try_install_from_binary_cache(spec.package, False, False) + + captured = capsys.readouterr() + assert 'add a spack mirror to allow download' in str(captured) + + def test_installer_init_errors(install_mockery): """Test to ensure cover installer constructor errors.""" with pytest.raises(ValueError, match='must be a package'): @@ -189,17 +212,18 @@ def test_installer_init_errors(install_mockery): inst.PackageInstaller(pkg) -def test_installer_strings(install_mockery): - """Tests of installer repr and str for coverage purposes.""" +def test_installer_repr(install_mockery): spec, installer = create_installer('trivial-install-test-package') - # Cover __repr__ irep = installer.__repr__() assert irep.startswith(installer.__class__.__name__) assert "installed=" in irep assert "failed=" in irep - # Cover __str__ + +def test_installer_str(install_mockery): + spec, installer = create_installer('trivial-install-test-package') + istr = str(installer) assert "#tasks=0" in istr assert "installed (0)" in istr @@ -207,7 +231,6 @@ def test_installer_strings(install_mockery): def test_installer_last_phase_error(install_mockery, capsys): - """Test to cover last phase error.""" spec = spack.spec.Spec('trivial-install-test-package') spec.concretize() assert spec.concrete @@ -220,7 +243,6 @@ def test_installer_last_phase_error(install_mockery, capsys): def test_installer_ensure_ready_errors(install_mockery): - """Test to cover _ensure_ready errors.""" spec, installer = create_installer('trivial-install-test-package') fmt = r'cannot be installed locally.*{0}' @@ -247,24 +269,102 @@ def test_installer_ensure_ready_errors(install_mockery): installer._ensure_install_ready(spec.package) -def test_ensure_locked_have(install_mockery, tmpdir): - """Test to cover _ensure_locked when already have lock.""" +def test_ensure_locked_err(install_mockery, monkeypatch, tmpdir, capsys): + """Test _ensure_locked when a non-lock exception is raised.""" + mock_err_msg = 'Mock exception error' + + def _raise(lock, timeout): + raise RuntimeError(mock_err_msg) + + spec, installer = create_installer('trivial-install-test-package') + + monkeypatch.setattr(ulk.Lock, 'acquire_read', _raise) + with tmpdir.as_cwd(): + with pytest.raises(RuntimeError): + installer._ensure_locked('read', spec.package) + + out = str(capsys.readouterr()[1]) + assert 'Failed to acquire a read lock' in out + assert mock_err_msg in out + + +def test_ensure_locked_have(install_mockery, tmpdir, capsys): + """Test _ensure_locked when already have lock.""" spec, installer = create_installer('trivial-install-test-package') with tmpdir.as_cwd(): + # Test "downgrade" of a read lock (to a read lock) lock = lk.Lock('./test', default_timeout=1e-9, desc='test') lock_type = 'read' tpl = (lock_type, lock) installer.locks[installer.pkg_id] = tpl assert installer._ensure_locked(lock_type, spec.package) == tpl + # Test "upgrade" of a read lock without read count to a write + lock_type = 'write' + err = 'Cannot upgrade lock' + with pytest.raises(ulk.LockUpgradeError, match=err): + installer._ensure_locked(lock_type, spec.package) -def test_package_id(install_mockery): - """Test to cover package_id functionality.""" + out = str(capsys.readouterr()[1]) + assert 'Failed to upgrade to a write lock' in out + assert 'exception when releasing read lock' in out + + # Test "upgrade" of the read lock *with* read count to a write + lock._reads = 1 + tpl = (lock_type, lock) + assert installer._ensure_locked(lock_type, spec.package) == tpl + + # Test "downgrade" of the write lock to a read lock + lock_type = 'read' + tpl = (lock_type, lock) + assert installer._ensure_locked(lock_type, spec.package) == tpl + + +@pytest.mark.parametrize('lock_type,reads,writes', [ + ('read', 1, 0), + ('write', 0, 1)]) +def test_ensure_locked_new_lock( + install_mockery, tmpdir, lock_type, reads, writes): + pkg_id = 'a' + spec, installer = create_installer(pkg_id) + with tmpdir.as_cwd(): + ltype, lock = installer._ensure_locked(lock_type, spec.package) + assert ltype == lock_type + assert lock is not None + assert lock._reads == reads + assert lock._writes == writes + + +def test_ensure_locked_new_warn(install_mockery, monkeypatch, tmpdir, capsys): + orig_pl = spack.database.Database.prefix_lock + + def _pl(db, spec, timeout): + lock = orig_pl(db, spec, timeout) + lock.default_timeout = 1e-9 if timeout is None else None + return lock + + pkg_id = 'a' + spec, installer = create_installer(pkg_id) + + monkeypatch.setattr(spack.database.Database, 'prefix_lock', _pl) + + lock_type = 'read' + ltype, lock = installer._ensure_locked(lock_type, spec.package) + assert ltype == lock_type + assert lock is not None + + out = str(capsys.readouterr()[1]) + assert 'Expected prefix lock timeout' in out + + +def test_package_id_err(install_mockery): pkg = spack.repo.get('trivial-install-test-package') with pytest.raises(ValueError, match='spec is not concretized'): inst.package_id(pkg) + +def test_package_id_ok(install_mockery): spec = spack.spec.Spec('trivial-install-test-package') spec.concretize() assert spec.concrete @@ -273,36 +373,44 @@ def test_package_id(install_mockery): def test_fake_install(install_mockery): - """Test to cover fake install basics.""" spec = spack.spec.Spec('trivial-install-test-package') spec.concretize() assert spec.concrete + pkg = spec.package inst._do_fake_install(pkg) assert os.path.isdir(pkg.prefix.lib) -def test_packages_needed_to_bootstrap_compiler(install_mockery, monkeypatch): - """Test to cover most of _packages_needed_to_boostrap_compiler.""" - # TODO: More work is needed to go beyond the dependency check - def _no_compilers(pkg, arch_spec): - return [] - - # Test path where no compiler packages returned +def test_packages_needed_to_bootstrap_compiler_none(install_mockery): spec = spack.spec.Spec('trivial-install-test-package') spec.concretize() assert spec.concrete + packages = inst._packages_needed_to_bootstrap_compiler(spec.package) assert not packages - # Test up to the dependency check - monkeypatch.setattr(spack.compilers, 'compilers_for_spec', _no_compilers) - with pytest.raises(spack.repo.UnknownPackageError, match='not found'): - inst._packages_needed_to_bootstrap_compiler(spec.package) + +def test_packages_needed_to_bootstrap_compiler_packages(install_mockery, + monkeypatch): + spec = spack.spec.Spec('trivial-install-test-package') + spec.concretize() + + def _conc_spec(compiler): + return spack.spec.Spec('a').concretized() + + # Ensure we can get past functions that are precluding obtaining + # packages. + monkeypatch.setattr(spack.compilers, 'compilers_for_spec', _none) + monkeypatch.setattr(spack.compilers, 'pkg_spec_for_compiler', _conc_spec) + monkeypatch.setattr(spack.spec.Spec, 'concretize', _noop) + + packages = inst._packages_needed_to_bootstrap_compiler(spec.package) + assert packages def test_dump_packages_deps_ok(install_mockery, tmpdir, mock_repo_path): - """Test to add coverage to dump_packages with dependencies happy path.""" + """Test happy path for dump_packages with dependencies.""" spec_name = 'simple-inheritance' spec = spack.spec.Spec(spec_name).concretized() @@ -314,7 +422,7 @@ def test_dump_packages_deps_ok(install_mockery, tmpdir, mock_repo_path): def test_dump_packages_deps_errs(install_mockery, tmpdir, monkeypatch, capsys): - """Test to add coverage to dump_packages with dependencies.""" + """Test error paths for dump_packages with dependencies.""" orig_bpp = spack.store.layout.build_packages_path orig_dirname = spack.repo.Repo.dirname_for_package_name repo_err_msg = "Mock dirname_for_package_name" @@ -354,59 +462,45 @@ def _repoerr(repo, name): assert "Couldn't copy in provenance for cmake" in out -@pytest.mark.tld -def test_check_deps_status_errs(install_mockery, monkeypatch): - """Test to cover _check_deps_status failures.""" +def test_check_deps_status_install_failure(install_mockery, monkeypatch): spec, installer = create_installer('a') # Make sure the package is identified as failed - orig_fn = spack.database.Database.prefix_failed monkeypatch.setattr(spack.database.Database, 'prefix_failed', _true) with pytest.raises(inst.InstallError, match='install failure'): installer._check_deps_status() - monkeypatch.setattr(spack.database.Database, 'prefix_failed', orig_fn) - # Ensure do not acquire the lock +def test_check_deps_status_write_locked(install_mockery, monkeypatch): + spec, installer = create_installer('a') + + # Ensure the lock is not acquired monkeypatch.setattr(inst.PackageInstaller, '_ensure_locked', _not_locked) with pytest.raises(inst.InstallError, match='write locked by another'): installer._check_deps_status() -@pytest.mark.tld def test_check_deps_status_external(install_mockery, monkeypatch): - """Test to cover _check_deps_status for external.""" spec, installer = create_installer('a') - deps = spec.dependencies() - assert len(deps) > 0 - dep_id = 'b' - - # Ensure the known dependent is installed if flagged as external + # Mock the known dependent, b, as external so assumed to be installed monkeypatch.setattr(spack.spec.Spec, 'external', True) installer._check_deps_status() - assert dep_id in installer.installed + assert 'b' in installer.installed -@pytest.mark.tld def test_check_deps_status_upstream(install_mockery, monkeypatch): - """Test to cover _check_deps_status for upstream.""" spec, installer = create_installer('a') - deps = spec.dependencies() - assert len(deps) > 0 - dep_id = 'b' - - # Ensure the known dependent, b, is installed if flagged as upstream + # Mock the known dependent, b, as installed upstream monkeypatch.setattr(spack.package.PackageBase, 'installed_upstream', True) installer._check_deps_status() - assert dep_id in installer.installed + assert 'b' in installer.installed def test_add_bootstrap_compilers(install_mockery, monkeypatch): - """Test to cover _add_bootstrap_compilers.""" def _pkgs(pkg): spec = spack.spec.Spec('mpi').concretized() return [(spec.package, True)] @@ -445,7 +539,6 @@ def test_installer_init_queue(install_mockery): def test_install_task_use_cache(install_mockery, monkeypatch): - """Test _install_task to cover use_cache path.""" spec, installer = create_installer('trivial-install-test-package') task = create_build_task(spec.package) @@ -454,25 +547,27 @@ def test_install_task_use_cache(install_mockery, monkeypatch): assert spec.package.name in installer.installed -def test_install_task_stop_iter(install_mockery, monkeypatch, capfd): - """Test _install_task to cover the StopIteration exception.""" - mock_err_msg = 'mock stop iteration' +def test_install_task_add_compiler(install_mockery, monkeypatch, capfd): + config_msg = 'mock add_compilers_to_config' - def _raise(installer, pkg): - raise StopIteration(mock_err_msg) + def _add(_compilers): + tty.msg(config_msg) spec, installer = create_installer('a') task = create_build_task(spec.package) + task.compiler = True + # Preclude any meaningful side-effects monkeypatch.setattr(spack.package.PackageBase, 'unit_test_check', _true) - monkeypatch.setattr(inst.PackageInstaller, '_setup_install_dir', _raise) + monkeypatch.setattr(inst.PackageInstaller, '_setup_install_dir', _noop) + monkeypatch.setattr(spack.build_environment, 'fork', _noop) + monkeypatch.setattr(spack.database.Database, 'add', _noop) + monkeypatch.setattr(spack.compilers, 'add_compilers_to_config', _add) installer._install_task(task) - out = capfd.readouterr()[0] - assert mock_err_msg in out - assert 'Package stage directory' in out - assert spec.package.stage.source_path in out + out = capfd.readouterr()[0] + assert config_msg in out def test_release_lock_write_n_exception(install_mockery, tmpdir, capsys): @@ -529,8 +624,36 @@ def _rmtask(installer, pkg_id): assert len(installer.build_tasks) == 1 -def test_cleanup_failed(install_mockery, tmpdir, monkeypatch, capsys): - """Test to increase coverage of _cleanup_failed.""" +def test_setup_install_dir_grp(install_mockery, monkeypatch, capfd): + """Test _setup_install_dir's group change.""" + mock_group = 'mockgroup' + mock_chgrp_msg = 'Changing group for {0} to {1}' + + def _get_group(spec): + return mock_group + + def _chgrp(path, group): + tty.msg(mock_chgrp_msg.format(path, group)) + + monkeypatch.setattr(prefs, 'get_package_group', _get_group) + monkeypatch.setattr(fs, 'chgrp', _chgrp) + + spec, installer = create_installer('trivial-install-test-package') + + fs.touchp(spec.prefix) + metadatadir = spack.store.layout.metadata_path(spec) + # Should fail with a "not a directory" error + with pytest.raises(OSError, match=metadatadir): + installer._setup_install_dir(spec.package) + + out = str(capfd.readouterr()[0]) + + expected_msg = mock_chgrp_msg.format(spec.prefix, mock_group) + assert expected_msg in out + + +def test_cleanup_failed_err(install_mockery, tmpdir, monkeypatch, capsys): + """Test _cleanup_failed exception path.""" msg = 'Fake release_write exception' def _raise_except(lock): @@ -550,13 +673,14 @@ def _raise_except(lock): assert msg in out -def test_update_failed_no_mark(install_mockery): - """Test of _update_failed sans mark and dependent build tasks.""" +def test_update_failed_no_dependent_task(install_mockery): + """Test _update_failed with missing dependent build tasks.""" spec, installer = create_installer('dependent-install') - task = create_build_task(spec.package) - installer._update_failed(task) - assert installer.failed['dependent-install'] is None + for dep in spec.traverse(root=False): + task = create_build_task(dep.package) + installer._update_failed(task, mark=False) + assert installer.failed[task.pkg_id] is None def test_install_uninstalled_deps(install_mockery, monkeypatch, capsys): @@ -710,3 +834,12 @@ def _install(installer, task, **kwargs): installer.install() assert 'b' in installer.installed + + +def test_install_skip_patch(install_mockery, mock_fetch): + """Test the path skip_patch install path.""" + spec, installer = create_installer('b') + + installer.install(fake=False, skip_patch=True) + + assert 'b' in installer.installed From cc8d9eee8ec7fe60235b00d52170f717c703dc0b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 4 Mar 2020 13:16:42 -0600 Subject: [PATCH 152/377] suite-sparse: fix installation for v5.X (#15326) fixes #15184 GraphBLAS depends on m4 according to CMake error message Do not use INSTALL= when compiling the library --- var/spack/repos/builtin/packages/suite-sparse/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py index 10f99dfbb6b..0e6a27f1dd7 100644 --- a/var/spack/repos/builtin/packages/suite-sparse/package.py +++ b/var/spack/repos/builtin/packages/suite-sparse/package.py @@ -33,6 +33,7 @@ class SuiteSparse(Package): depends_on('blas') depends_on('lapack') + depends_on('m4', type='build', when='@5.0.0:') depends_on('cmake', when='@5.2.0:', type='build') depends_on('metis@5.1.0', when='@4.5.1:') @@ -63,7 +64,6 @@ def install(self, spec, prefix): pic_flag = self.compiler.pic_flag if '+pic' in spec else '' make_args = [ - 'INSTALL=%s' % prefix, # By default, the Makefile uses the Intel compilers if # they are found. The AUTOCC flag disables this behavior, # forcing it to use Spack's compiler wrappers. @@ -134,6 +134,7 @@ def install(self, spec, prefix): self.spec.version <= Version('5.6.0')): make('default', *make_args) + make_args.append('INSTALL=%s' % prefix) make('install', *make_args) @property From 901bed48ec2d3e03d45014fdbfc936305897d2e2 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Sat, 7 Mar 2020 13:58:33 +0100 Subject: [PATCH 153/377] ArchSpec: fix semantics of satisfies when not concrete and strict is true (#15319) --- lib/spack/spack/spec.py | 4 ++++ lib/spack/spack/test/architecture.py | 13 +++++++++++++ 2 files changed, 17 insertions(+) diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 1493f0c973a..718b5ef14db 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -369,6 +369,10 @@ def _satisfies_target(self, other_target, strict): if not need_to_check: return True + # self is not concrete, but other_target is there and strict=True + if self.target is None: + return False + for target_range in str(other_target).split(','): t_min, sep, t_max = target_range.partition(':') diff --git a/lib/spack/spack/test/architecture.py b/lib/spack/spack/test/architecture.py index 1f5ff289006..552bc324bf9 100644 --- a/lib/spack/spack/test/architecture.py +++ b/lib/spack/spack/test/architecture.py @@ -214,3 +214,16 @@ def test_optimization_flags_with_custom_versions( ) opt_flags = target.optimization_flags(compiler) assert opt_flags == expected_flags + + +@pytest.mark.regression('15306') +@pytest.mark.parametrize('architecture_tuple,constraint_tuple', [ + (('linux', 'ubuntu18.04', None), ('linux', None, 'x86_64')), + (('linux', 'ubuntu18.04', None), ('linux', None, 'x86_64:')), +]) +def test_satisfy_strict_constraint_when_not_concrete( + architecture_tuple, constraint_tuple +): + architecture = spack.spec.ArchSpec(architecture_tuple) + constraint = spack.spec.ArchSpec(constraint_tuple) + assert not architecture.satisfies(constraint, strict=True) From 62683eb4bf2bcf155c460113be09915f452e9ce6 Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Wed, 4 Mar 2020 19:21:15 -0600 Subject: [PATCH 154/377] Add function replace_prefix_nullterm for use on mach-o rpaths. (#15347) This recovers the old behavior of replace_prefix_bin that was modified to work with elf binaries by prefixing os.sep to new prefix until length is the same as old prefix. --- lib/spack/spack/relocate.py | 39 +++++++++++++++++++++++++++++++++---- 1 file changed, 35 insertions(+), 4 deletions(-) diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py index fb4ff18fae4..56fc993b5f7 100644 --- a/lib/spack/spack/relocate.py +++ b/lib/spack/spack/relocate.py @@ -400,8 +400,8 @@ def replace_prefix_text(path_name, old_dir, new_dir): def replace_prefix_bin(path_name, old_dir, new_dir): """ Attempt to replace old install prefix with new install prefix - in binary files by replacing with null terminated string - that is the same length unless the old path is shorter + in binary files by prefixing new install prefix with os.sep + until the lengths of the prefixes are the same. """ def replace(match): @@ -429,6 +429,38 @@ def replace(match): f.truncate() +def replace_prefix_nullterm(path_name, old_dir, new_dir): + """ + Attempt to replace old install prefix with new install prefix + in binary files by replacing with null terminated string + that is the same length unless the old path is shorter + Used on linux to replace mach-o rpaths + """ + + def replace(match): + occurances = match.group().count(old_dir.encode('utf-8')) + olen = len(old_dir.encode('utf-8')) + nlen = len(new_dir.encode('utf-8')) + padding = (olen - nlen) * occurances + if padding < 0: + return data + return match.group().replace(old_dir.encode('utf-8'), + new_dir.encode('utf-8')) + b'\0' * padding + with open(path_name, 'rb+') as f: + data = f.read() + f.seek(0) + original_data_len = len(data) + pat = re.compile(old_dir.encode('utf-8') + b'([^\0]*?)\0') + if not pat.search(data): + return + ndata = pat.sub(replace, data) + if not len(ndata) == original_data_len: + raise BinaryStringReplacementException( + path_name, original_data_len, len(ndata)) + f.write(ndata) + f.truncate() + + def relocate_macho_binaries(path_names, old_dir, new_dir, allow_root): """ Change old_dir to new_dir in LC_RPATH of mach-o files (on macOS) @@ -466,8 +498,7 @@ def relocate_macho_binaries(path_names, old_dir, new_dir, allow_root): modify_object_macholib(path_name, placeholder, new_dir) modify_object_macholib(path_name, old_dir, new_dir) if len(new_dir) <= len(old_dir): - replace_prefix_bin(path_name, old_dir, - new_dir) + replace_prefix_nullterm(path_name, old_dir, new_dir) else: tty.warn('Cannot do a binary string replacement' ' with padding for %s' From 2f8ff722a9767538d3edddacb2bd8ee6acc9d1a5 Mon Sep 17 00:00:00 2001 From: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com> Date: Fri, 20 Mar 2020 11:44:03 -0700 Subject: [PATCH 155/377] tau: add dependency on hwloc (#15589) --- var/spack/repos/builtin/packages/tau/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/tau/package.py b/var/spack/repos/builtin/packages/tau/package.py index 4ac71b793f4..03298410294 100644 --- a/var/spack/repos/builtin/packages/tau/package.py +++ b/var/spack/repos/builtin/packages/tau/package.py @@ -95,6 +95,7 @@ class Tau(Package): depends_on('gasnet', when='+gasnet') depends_on('adios2', when='+adios2') depends_on('sqlite', when='+sqlite') + depends_on('hwloc') # Elf only required from 2.28.1 on conflicts('+libelf', when='@:2.28.0') From 1e42f0a54589d73fab367de4389aa3318c087af0 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sat, 7 Mar 2020 23:48:18 -0800 Subject: [PATCH 156/377] bugfix: installer.py shouldn't be executable (#15386) This is a minor permission fix on the new installer.py introduced in #13100. --- lib/spack/spack/installer.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 lib/spack/spack/installer.py diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py old mode 100755 new mode 100644 From ec720bf28d04bb5eadafaea5607832428d92d9d5 Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Tue, 10 Mar 2020 10:35:20 -0700 Subject: [PATCH 157/377] bugfix: fix install_missing_compilers option bug from v0.14.0 (#15416) * bugfix: ensure bootstrapped compilers built before packages using the compiler --- lib/spack/spack/installer.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py index 4e8ec397335..a9965c91141 100644 --- a/lib/spack/spack/installer.py +++ b/lib/spack/spack/installer.py @@ -181,6 +181,9 @@ def _packages_needed_to_bootstrap_compiler(pkg): # concrete CompilerSpec has less info than concrete Spec # concretize as Spec to add that information dep.concretize() + # mark compiler as depended-on by the package that uses it + dep._dependents[pkg.name] = spack.spec.DependencySpec( + pkg.spec, dep, ('build',)) packages = [(s.package, False) for s in dep.traverse(order='post', root=False)] packages.append((dep.package, True)) @@ -1610,6 +1613,21 @@ def __init__(self, pkg, compiler, start, attempts, status, installed): self.spec.dependencies() if package_id(d.package) != self.pkg_id) + # Handle bootstrapped compiler + # + # The bootstrapped compiler is not a dependency in the spec, but it is + # a dependency of the build task. Here we add it to self.dependencies + compiler_spec = self.spec.compiler + arch_spec = self.spec.architecture + if not spack.compilers.compilers_for_spec(compiler_spec, + arch_spec=arch_spec): + # The compiler is in the queue, identify it as dependency + dep = spack.compilers.pkg_spec_for_compiler(compiler_spec) + dep.architecture = arch_spec + dep.concretize() + dep_id = package_id(dep.package) + self.dependencies.add(dep_id) + # List of uninstalled dependencies, which is used to establish # the priority of the build task. # From 296d58ef6bf07fa1440c988d6b2e1268d83e671f Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 12 Mar 2020 09:21:19 +0100 Subject: [PATCH 158/377] Creating versions from urls doesn't modify class attributes (#15452) fixes #15449 Before this PR a call to pkg.url_for_version was modifying class attributes determining different results for subsequents calls and an error when the urls was empty. --- lib/spack/spack/fetch_strategy.py | 2 +- lib/spack/spack/package.py | 2 +- lib/spack/spack/test/url_fetch.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py index eaf9f130c55..a01bc143aa3 100644 --- a/lib/spack/spack/fetch_strategy.py +++ b/lib/spack/spack/fetch_strategy.py @@ -1239,7 +1239,7 @@ def _from_merged_attrs(fetcher, pkg, version): # TODO: refactor this logic into its own method or function # TODO: to avoid duplication mirrors = [spack.url.substitute_version(u, version) - for u in getattr(pkg, 'urls', [])] + for u in getattr(pkg, 'urls', [])[1:]] attrs = {fetcher.url_attr: url, 'mirrors': mirrors} else: url = getattr(pkg, fetcher.url_attr) diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index b7efc3989bc..b2d841f145c 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -763,7 +763,7 @@ def url_for_version(self, version): # If no specific URL, use the default, class-level URL url = getattr(self, 'url', None) urls = getattr(self, 'urls', [None]) - default_url = url or urls.pop(0) + default_url = url or urls[0] # if no exact match AND no class-level default, use the nearest URL if not default_url: diff --git a/lib/spack/spack/test/url_fetch.py b/lib/spack/spack/test/url_fetch.py index 71a122455f7..679240049d9 100644 --- a/lib/spack/spack/test/url_fetch.py +++ b/lib/spack/spack/test/url_fetch.py @@ -32,7 +32,7 @@ def pkg_factory(): def factory(url, urls): def fn(v): - main_url = url or urls.pop(0) + main_url = url or urls[0] return spack.url.substitute_version(main_url, v) return Pkg( From 09e13cf7cf0327bb35a9b3d4e7c7ad64ea4a3076 Mon Sep 17 00:00:00 2001 From: Kai Germaschewski Date: Wed, 18 Mar 2020 19:41:18 -0400 Subject: [PATCH 159/377] Upstreams: don't write metadata directory to upstream DB (#15526) When trying to use an upstream Spack repository, as of f2aca86 Spack was attempting to write to the upstream DB based on a new metadata directory added in that commit. Upstream DBs are read-only, so this should not occur. This adds a check to prevent Spack from writing to the upstream DB --- lib/spack/spack/database.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index e04a1f292aa..f3c88a75c3b 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -324,7 +324,7 @@ def __init__(self, root, db_dir=None, upstream_dbs=None, if not os.path.exists(self._db_dir): mkdirp(self._db_dir) - if not os.path.exists(self._failure_dir): + if not os.path.exists(self._failure_dir) and not is_upstream: mkdirp(self._failure_dir) self.is_upstream = is_upstream From 30b4704522316263fff07fc75146f0a7a6dc7952 Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Thu, 19 Mar 2020 15:11:50 -0700 Subject: [PATCH 160/377] Cray bugfix: TERM missing while reading default target (#15381) Bug: Spack hangs on some Cray machines Reason: The TERM environment variable is necessary to run bash -lc "echo $CRAY_CPU_TARGET", but we run that command within env -i, which wipes the environment. Fix: Manually forward the TERM environment variable to env -i /bin/bash -lc "echo $CRAY_CPU_TARGET" --- lib/spack/spack/platforms/cray.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/lib/spack/spack/platforms/cray.py b/lib/spack/spack/platforms/cray.py index cbeba96461b..8eae51e66a2 100644 --- a/lib/spack/spack/platforms/cray.py +++ b/lib/spack/spack/platforms/cray.py @@ -7,7 +7,7 @@ import re import llnl.util.tty as tty from spack.paths import build_env_path -from spack.util.executable import which +from spack.util.executable import Executable from spack.architecture import Platform, Target, NoPlatformError from spack.operating_systems.cray_frontend import CrayFrontend from spack.operating_systems.cnl import Cnl @@ -117,11 +117,13 @@ def _default_target_from_env(self): ''' # env -i /bin/bash -lc echo $CRAY_CPU_TARGET 2> /dev/null if getattr(self, 'default', None) is None: - env = which('env') - output = env("-i", "/bin/bash", "-lc", "echo $CRAY_CPU_TARGET", - output=str, error=os.devnull) - self.default = output.strip() - tty.debug("Found default module:%s" % self.default) + output = Executable('/bin/bash')('-lc', 'echo $CRAY_CPU_TARGET', + env={'TERM': os.environ['TERM']}, + output=str, error=os.devnull) + output = ''.join(output.split()) # remove all whitespace + if output: + self.default = output + tty.debug("Found default module:%s" % self.default) return self.default def _avail_targets(self): From 545fae84075c0cbd54518da7f03e690e708b2861 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Fri, 20 Mar 2020 20:11:42 +0100 Subject: [PATCH 161/377] spack checksum: Use package's fetch_options (#15481) This makes sure that a package's fetch_options are used when fetching new versions to checksum. This allows working around problems with slow servers or those requiring a cookie to be set. --- lib/spack/spack/cmd/checksum.py | 3 ++- lib/spack/spack/stage.py | 12 ++++++++++-- 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/cmd/checksum.py b/lib/spack/spack/cmd/checksum.py index 343915868cd..eaeaf5337f9 100644 --- a/lib/spack/spack/cmd/checksum.py +++ b/lib/spack/spack/cmd/checksum.py @@ -56,7 +56,8 @@ def checksum(parser, args): tty.die("Could not find any versions for {0}".format(pkg.name)) version_lines = spack.stage.get_checksums_for_versions( - url_dict, pkg.name, keep_stage=args.keep_stage) + url_dict, pkg.name, keep_stage=args.keep_stage, + fetch_options=pkg.fetch_options) print() print(version_lines) diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py index dd05131391a..54d370a50d9 100644 --- a/lib/spack/spack/stage.py +++ b/lib/spack/spack/stage.py @@ -752,7 +752,8 @@ def purge(): def get_checksums_for_versions( - url_dict, name, first_stage_function=None, keep_stage=False): + url_dict, name, first_stage_function=None, keep_stage=False, + fetch_options=None): """Fetches and checksums archives from URLs. This function is called by both ``spack checksum`` and ``spack @@ -766,6 +767,8 @@ def get_checksums_for_versions( first_stage_function (callable): function that takes a Stage and a URL; this is run on the stage of the first URL downloaded keep_stage (bool): whether to keep staging area when command completes + fetch_options (dict): Options used for the fetcher (such as timeout + or cookies) Returns: (str): A multi-line string containing versions and corresponding hashes @@ -799,7 +802,12 @@ def get_checksums_for_versions( i = 0 for url, version in zip(urls, versions): try: - with Stage(url, keep=keep_stage) as stage: + if fetch_options: + url_or_fs = fs.URLFetchStrategy( + url, fetch_options=fetch_options) + else: + url_or_fs = url + with Stage(url_or_fs, keep=keep_stage) as stage: # Fetch the archive stage.fetch() if i == 0 and first_stage_function: From 75fafcece9b179f1261bb007deac31bd179e020b Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Fri, 20 Mar 2020 12:22:32 -0700 Subject: [PATCH 162/377] multiprocessing: allow Spack to run uninterrupted in background (#14682) Spack currently cannot run as a background process uninterrupted because some of the logging functions used in the install method (especially to create the dynamic verbosity toggle with the v key) cause the OS to issue a SIGTTOU to Spack when it's backgrounded. This PR puts the necessary gatekeeping in place so that Spack doesn't do anything that will cause a signal to stop the process when operating as a background process. --- etc/spack/defaults/packages.yaml | 1 + lib/spack/llnl/util/tty/log.py | 128 ++++++++++++++++++++----------- 2 files changed, 83 insertions(+), 46 deletions(-) diff --git a/etc/spack/defaults/packages.yaml b/etc/spack/defaults/packages.yaml index fcc39f534ea..46aa5ad9adc 100644 --- a/etc/spack/defaults/packages.yaml +++ b/etc/spack/defaults/packages.yaml @@ -40,6 +40,7 @@ packages: pil: [py-pillow] pkgconfig: [pkgconf, pkg-config] scalapack: [netlib-scalapack] + sycl: [hipsycl] szip: [libszip, libaec] tbb: [intel-tbb] unwind: [libunwind] diff --git a/lib/spack/llnl/util/tty/log.py b/lib/spack/llnl/util/tty/log.py index 10516e59d2e..e6089926425 100644 --- a/lib/spack/llnl/util/tty/log.py +++ b/lib/spack/llnl/util/tty/log.py @@ -13,12 +13,18 @@ import select import sys import traceback +import signal from contextlib import contextmanager from six import string_types from six import StringIO import llnl.util.tty as tty +try: + import termios +except ImportError: + termios = None + # Use this to strip escape sequences _escape = re.compile(r'\x1b[^m]*m|\x1b\[?1034h') @@ -31,12 +37,26 @@ control = re.compile('(\x11\n|\x13\n)') +@contextmanager +def background_safe(): + signal.signal(signal.SIGTTOU, signal.SIG_IGN) + yield + signal.signal(signal.SIGTTOU, signal.SIG_DFL) + + +def _is_background_tty(): + """Return True iff this process is backgrounded and stdout is a tty""" + if sys.stdout.isatty(): + return os.getpgrp() != os.tcgetpgrp(sys.stdout.fileno()) + return False # not writing to tty, not background + + def _strip(line): """Strip color and control characters from a line.""" return _escape.sub('', line) -class keyboard_input(object): +class _keyboard_input(object): """Context manager to disable line editing and echoing. Use this with ``sys.stdin`` for keyboard input, e.g.:: @@ -81,32 +101,30 @@ def __enter__(self): if not self.stream or not self.stream.isatty(): return - try: - # If this fails, self.old_cfg will remain None - import termios - + # If this fails, self.old_cfg will remain None + if termios and not _is_background_tty(): # save old termios settings - fd = self.stream.fileno() - self.old_cfg = termios.tcgetattr(fd) + old_cfg = termios.tcgetattr(self.stream) - # create new settings with canonical input and echo - # disabled, so keypresses are immediate & don't echo. - self.new_cfg = termios.tcgetattr(fd) - self.new_cfg[3] &= ~termios.ICANON - self.new_cfg[3] &= ~termios.ECHO + try: + # create new settings with canonical input and echo + # disabled, so keypresses are immediate & don't echo. + self.new_cfg = termios.tcgetattr(self.stream) + self.new_cfg[3] &= ~termios.ICANON + self.new_cfg[3] &= ~termios.ECHO - # Apply new settings for terminal - termios.tcsetattr(fd, termios.TCSADRAIN, self.new_cfg) + # Apply new settings for terminal + termios.tcsetattr(self.stream, termios.TCSADRAIN, self.new_cfg) + self.old_cfg = old_cfg - except Exception: - pass # some OS's do not support termios, so ignore + except Exception: + pass # some OS's do not support termios, so ignore def __exit__(self, exc_type, exception, traceback): """If termios was avaialble, restore old settings.""" if self.old_cfg: - import termios - termios.tcsetattr( - self.stream.fileno(), termios.TCSADRAIN, self.old_cfg) + with background_safe(): # change it back even if backgrounded now + termios.tcsetattr(self.stream, termios.TCSADRAIN, self.old_cfg) class Unbuffered(object): @@ -426,45 +444,63 @@ def _writer_daemon(self, stdin): istreams = [in_pipe, stdin] if stdin else [in_pipe] log_file = self.log_file + + def handle_write(force_echo): + # Handle output from the with block process. + # If we arrive here it means that in_pipe was + # ready for reading : it should never happen that + # line is false-ish + line = in_pipe.readline() + if not line: + return (True, force_echo) # break while loop + + # find control characters and strip them. + controls = control.findall(line) + line = re.sub(control, '', line) + + # Echo to stdout if requested or forced + if echo or force_echo: + try: + if termios: + conf = termios.tcgetattr(sys.stdout) + tostop = conf[3] & termios.TOSTOP + else: + tostop = True + except Exception: + tostop = True + if not (tostop and _is_background_tty()): + sys.stdout.write(line) + sys.stdout.flush() + + # Stripped output to log file. + log_file.write(_strip(line)) + log_file.flush() + + if xon in controls: + force_echo = True + if xoff in controls: + force_echo = False + return (False, force_echo) + try: - with keyboard_input(stdin): + with _keyboard_input(stdin): while True: # No need to set any timeout for select.select # Wait until a key press or an event on in_pipe. rlist, _, _ = select.select(istreams, [], []) - # Allow user to toggle echo with 'v' key. # Currently ignores other chars. - if stdin in rlist: + # only read stdin if we're in the foreground + if stdin in rlist and not _is_background_tty(): if stdin.read(1) == 'v': echo = not echo - # Handle output from the with block process. if in_pipe in rlist: - # If we arrive here it means that in_pipe was - # ready for reading : it should never happen that - # line is false-ish - line = in_pipe.readline() - if not line: - break # EOF + br, fe = handle_write(force_echo) + force_echo = fe + if br: + break - # find control characters and strip them. - controls = control.findall(line) - line = re.sub(control, '', line) - - # Echo to stdout if requested or forced - if echo or force_echo: - sys.stdout.write(line) - sys.stdout.flush() - - # Stripped output to log file. - log_file.write(_strip(line)) - log_file.flush() - - if xon in controls: - force_echo = True - if xoff in controls: - force_echo = False except BaseException: tty.error("Exception occurred in writer daemon!") traceback.print_exc() From 3826cdf139359de4c346bb72ef0064111b98c3c5 Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Fri, 20 Mar 2020 12:22:32 -0700 Subject: [PATCH 163/377] multiprocessing: allow Spack to run uninterrupted in background (#14682) Spack currently cannot run as a background process uninterrupted because some of the logging functions used in the install method (especially to create the dynamic verbosity toggle with the v key) cause the OS to issue a SIGTTOU to Spack when it's backgrounded. This PR puts the necessary gatekeeping in place so that Spack doesn't do anything that will cause a signal to stop the process when operating as a background process. --- etc/spack/defaults/packages.yaml | 1 + lib/spack/llnl/util/tty/log.py | 128 ++++++++++++++++++++----------- 2 files changed, 83 insertions(+), 46 deletions(-) diff --git a/etc/spack/defaults/packages.yaml b/etc/spack/defaults/packages.yaml index fcc39f534ea..46aa5ad9adc 100644 --- a/etc/spack/defaults/packages.yaml +++ b/etc/spack/defaults/packages.yaml @@ -40,6 +40,7 @@ packages: pil: [py-pillow] pkgconfig: [pkgconf, pkg-config] scalapack: [netlib-scalapack] + sycl: [hipsycl] szip: [libszip, libaec] tbb: [intel-tbb] unwind: [libunwind] diff --git a/lib/spack/llnl/util/tty/log.py b/lib/spack/llnl/util/tty/log.py index 10516e59d2e..e6089926425 100644 --- a/lib/spack/llnl/util/tty/log.py +++ b/lib/spack/llnl/util/tty/log.py @@ -13,12 +13,18 @@ import select import sys import traceback +import signal from contextlib import contextmanager from six import string_types from six import StringIO import llnl.util.tty as tty +try: + import termios +except ImportError: + termios = None + # Use this to strip escape sequences _escape = re.compile(r'\x1b[^m]*m|\x1b\[?1034h') @@ -31,12 +37,26 @@ control = re.compile('(\x11\n|\x13\n)') +@contextmanager +def background_safe(): + signal.signal(signal.SIGTTOU, signal.SIG_IGN) + yield + signal.signal(signal.SIGTTOU, signal.SIG_DFL) + + +def _is_background_tty(): + """Return True iff this process is backgrounded and stdout is a tty""" + if sys.stdout.isatty(): + return os.getpgrp() != os.tcgetpgrp(sys.stdout.fileno()) + return False # not writing to tty, not background + + def _strip(line): """Strip color and control characters from a line.""" return _escape.sub('', line) -class keyboard_input(object): +class _keyboard_input(object): """Context manager to disable line editing and echoing. Use this with ``sys.stdin`` for keyboard input, e.g.:: @@ -81,32 +101,30 @@ def __enter__(self): if not self.stream or not self.stream.isatty(): return - try: - # If this fails, self.old_cfg will remain None - import termios - + # If this fails, self.old_cfg will remain None + if termios and not _is_background_tty(): # save old termios settings - fd = self.stream.fileno() - self.old_cfg = termios.tcgetattr(fd) + old_cfg = termios.tcgetattr(self.stream) - # create new settings with canonical input and echo - # disabled, so keypresses are immediate & don't echo. - self.new_cfg = termios.tcgetattr(fd) - self.new_cfg[3] &= ~termios.ICANON - self.new_cfg[3] &= ~termios.ECHO + try: + # create new settings with canonical input and echo + # disabled, so keypresses are immediate & don't echo. + self.new_cfg = termios.tcgetattr(self.stream) + self.new_cfg[3] &= ~termios.ICANON + self.new_cfg[3] &= ~termios.ECHO - # Apply new settings for terminal - termios.tcsetattr(fd, termios.TCSADRAIN, self.new_cfg) + # Apply new settings for terminal + termios.tcsetattr(self.stream, termios.TCSADRAIN, self.new_cfg) + self.old_cfg = old_cfg - except Exception: - pass # some OS's do not support termios, so ignore + except Exception: + pass # some OS's do not support termios, so ignore def __exit__(self, exc_type, exception, traceback): """If termios was avaialble, restore old settings.""" if self.old_cfg: - import termios - termios.tcsetattr( - self.stream.fileno(), termios.TCSADRAIN, self.old_cfg) + with background_safe(): # change it back even if backgrounded now + termios.tcsetattr(self.stream, termios.TCSADRAIN, self.old_cfg) class Unbuffered(object): @@ -426,45 +444,63 @@ def _writer_daemon(self, stdin): istreams = [in_pipe, stdin] if stdin else [in_pipe] log_file = self.log_file + + def handle_write(force_echo): + # Handle output from the with block process. + # If we arrive here it means that in_pipe was + # ready for reading : it should never happen that + # line is false-ish + line = in_pipe.readline() + if not line: + return (True, force_echo) # break while loop + + # find control characters and strip them. + controls = control.findall(line) + line = re.sub(control, '', line) + + # Echo to stdout if requested or forced + if echo or force_echo: + try: + if termios: + conf = termios.tcgetattr(sys.stdout) + tostop = conf[3] & termios.TOSTOP + else: + tostop = True + except Exception: + tostop = True + if not (tostop and _is_background_tty()): + sys.stdout.write(line) + sys.stdout.flush() + + # Stripped output to log file. + log_file.write(_strip(line)) + log_file.flush() + + if xon in controls: + force_echo = True + if xoff in controls: + force_echo = False + return (False, force_echo) + try: - with keyboard_input(stdin): + with _keyboard_input(stdin): while True: # No need to set any timeout for select.select # Wait until a key press or an event on in_pipe. rlist, _, _ = select.select(istreams, [], []) - # Allow user to toggle echo with 'v' key. # Currently ignores other chars. - if stdin in rlist: + # only read stdin if we're in the foreground + if stdin in rlist and not _is_background_tty(): if stdin.read(1) == 'v': echo = not echo - # Handle output from the with block process. if in_pipe in rlist: - # If we arrive here it means that in_pipe was - # ready for reading : it should never happen that - # line is false-ish - line = in_pipe.readline() - if not line: - break # EOF + br, fe = handle_write(force_echo) + force_echo = fe + if br: + break - # find control characters and strip them. - controls = control.findall(line) - line = re.sub(control, '', line) - - # Echo to stdout if requested or forced - if echo or force_echo: - sys.stdout.write(line) - sys.stdout.flush() - - # Stripped output to log file. - log_file.write(_strip(line)) - log_file.flush() - - if xon in controls: - force_echo = True - if xoff in controls: - force_echo = False except BaseException: tty.error("Exception occurred in writer daemon!") traceback.print_exc() From 9c45c44738049e062916f9df38eb41ff9c1594e3 Mon Sep 17 00:00:00 2001 From: Dan Lipsa Date: Fri, 20 Mar 2020 15:26:41 -0400 Subject: [PATCH 164/377] Add version 5.8 and fix sqlite+column_metadata mismatch. (#15450) --- var/spack/repos/builtin/packages/paraview/package.py | 1 + var/spack/repos/builtin/packages/qt/package.py | 3 +-- var/spack/repos/builtin/packages/sqlite/package.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index 111c8df7a49..48dff877e0a 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -20,6 +20,7 @@ class Paraview(CMakePackage, CudaPackage): maintainers = ['chuckatkins', 'danlipsa'] version('develop', branch='master', submodules=True) + version('5.8.0', sha256='219e4107abf40317ce054408e9c3b22fb935d464238c1c00c0161f1c8697a3f9') version('5.7.0', sha256='e41e597e1be462974a03031380d9e5ba9a7efcdb22e4ca2f3fec50361f310874') version('5.6.2', sha256='1f3710b77c58a46891808dbe23dc59a1259d9c6b7bb123aaaeaa6ddf2be882ea') version('5.6.0', sha256='cb8c4d752ad9805c74b4a08f8ae6e83402c3f11e38b274dba171b99bb6ac2460') diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 1ffb17ceb4d..3f4c767a692 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -128,8 +128,7 @@ class Qt(Package): depends_on("gperf", when='+webkit') depends_on("gtkplus", when='+gtk') depends_on("openssl", when='+ssl') - depends_on("sqlite", when='+sql', type=('build', 'run')) - depends_on("sqlite+column_metadata", when='+sql%intel', type=('build', 'run')) + depends_on("sqlite+column_metadata", when='+sql', type=('build', 'run')) depends_on("libpng@1.2.57", when='@3') depends_on("libsm", when='@3') diff --git a/var/spack/repos/builtin/packages/sqlite/package.py b/var/spack/repos/builtin/packages/sqlite/package.py index f8dd0e49484..4e79463f36b 100644 --- a/var/spack/repos/builtin/packages/sqlite/package.py +++ b/var/spack/repos/builtin/packages/sqlite/package.py @@ -38,7 +38,7 @@ class Sqlite(AutotoolsPackage): '(unsafe for <3.26.0.0 due to Magellan).') variant('rtree', default=False, description='Build with Rtree module') - variant('column_metadata', default=False, description="Build with COLUMN_METADATA") + variant('column_metadata', default=True, description="Build with COLUMN_METADATA") # See https://blade.tencent.com/magellan/index_en.html conflicts('+fts', when='@:3.25.99.99') From ff0abb9838121522321df2a054d18e54b566b44a Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Fri, 20 Mar 2020 11:49:24 -0700 Subject: [PATCH 165/377] version bump: 0.14.1 --- lib/spack/spack/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py index b18acb20942..112a98c01c1 100644 --- a/lib/spack/spack/__init__.py +++ b/lib/spack/spack/__init__.py @@ -5,7 +5,7 @@ #: major, minor, patch version for Spack, in a tuple -spack_version_info = (0, 14, 0) +spack_version_info = (0, 14, 1) #: String containing Spack version joined with .'s spack_version = '.'.join(str(v) for v in spack_version_info) From e2b1737a42c9c0c796671f9dd0c39f623e4c91c0 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Fri, 20 Mar 2020 12:00:13 -0700 Subject: [PATCH 166/377] update CHANGELOG.md for 0.14.1 --- CHANGELOG.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 47657b98257..6fea0528842 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,15 @@ +# v0.14.1 (2019-03-20) + +This is a bugfix release on top of `v0.14.0`. Specific fixes include: + +* several bugfixes for parallel installation (#15339, #15341, #15220, #15197) +* `spack load` now works with packages that have been renamed (#14348) +* bugfix for `suite-sparse` installation (#15326) +* deduplicate identical suffixes added to module names (#14920) +* fix issues with `configure_args` during module refresh (#11084) +* increased test coverage and test fixes (#15237, #15354, #15346) +* remove some unused code (#15431) + # v0.14.0 (2020-02-23) `v0.14.0` is a major feature release, with 3 highlighted features: From 70577e4fd733d146a01c975dc62e2d2f86223ea3 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 20 Mar 2020 15:42:54 -0400 Subject: [PATCH 167/377] py-sentencepiece: add new package (#15601) --- .../packages/py-sentencepiece/package.py | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-sentencepiece/package.py diff --git a/var/spack/repos/builtin/packages/py-sentencepiece/package.py b/var/spack/repos/builtin/packages/py-sentencepiece/package.py new file mode 100644 index 00000000000..9d9552a47b9 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-sentencepiece/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class PySentencepiece(PythonPackage): + """Unsupervised text tokenizer for Neural Network-based text generation. + + These are the Python bindings.""" + + homepage = "https://github.com/google/sentencepiece/blob/master/python/README.md" + url = "https://github.com/google/sentencepiece/archive/v0.1.85.tar.gz" + + maintainers = ['adamjstewart'] + + version('0.1.85', sha256='dd4956287a1b6af3cbdbbd499b7227a859a4e3f41c9882de5e6bdd929e219ae6') + + depends_on('sentencepiece') + depends_on('sentencepiece@0.1.85', when='@0.1.85') + depends_on('pkgconfig', type='build') + depends_on('py-setuptools', type='build') + + build_directory = 'python' From c45644afaabb2415575d6bdf0b85f5e0c1f3380f Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Fri, 20 Mar 2020 14:50:07 -0500 Subject: [PATCH 168/377] Add 33.2.1 version with checksum to lua-luaposix (#15600) --- var/spack/repos/builtin/packages/lua-luaposix/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/lua-luaposix/package.py b/var/spack/repos/builtin/packages/lua-luaposix/package.py index f69c2a36826..f5290eae1c9 100644 --- a/var/spack/repos/builtin/packages/lua-luaposix/package.py +++ b/var/spack/repos/builtin/packages/lua-luaposix/package.py @@ -13,6 +13,7 @@ class LuaLuaposix(Package): url = "https://github.com/luaposix/luaposix/archive/release-v33.4.0.tar.gz" version('33.4.0', sha256='e66262f5b7fe1c32c65f17a5ef5ffb31c4d1877019b4870a5d373e2ab6526a21') + version('33.2.1', sha256='4fb34dfea67f4cf3194cdecc6614c9aea67edc3c4093d34137669ea869c358e1') extends("lua") From d3fafaa868adee6cbeb3ec9ef011ff080cbd70f3 Mon Sep 17 00:00:00 2001 From: Benjamin Fovet <45510885+bfovet@users.noreply.github.com> Date: Fri, 20 Mar 2020 20:51:01 +0100 Subject: [PATCH 169/377] Add Ceres Solver v1.14.0 with new variants (#15597) * Add Ceres Solver version 1.14.0 * Add variants for Ceres Solver --- .../builtin/packages/ceres-solver/package.py | 23 +++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/ceres-solver/package.py b/var/spack/repos/builtin/packages/ceres-solver/package.py index 599c1801213..ab84b4f9b7c 100644 --- a/var/spack/repos/builtin/packages/ceres-solver/package.py +++ b/var/spack/repos/builtin/packages/ceres-solver/package.py @@ -17,19 +17,38 @@ class CeresSolver(CMakePackage): homepage = "http://ceres-solver.org" url = "http://ceres-solver.org/ceres-solver-1.12.0.tar.gz" + version('1.14.0', sha256='4744005fc3b902fed886ea418df70690caa8e2ff6b5a90f3dd88a3d291ef8e8e') version('1.12.0', sha256='745bfed55111e086954126b748eb9efe20e30be5b825c6dec3c525cf20afc895') + variant('suitesparse', default=False, description='Build with SuiteSparse') + variant('shared', default=True, description='Build shared libraries') + variant('examples', default=False, description='Build examples') + depends_on('eigen@3:') depends_on('lapack') depends_on('glog') def cmake_args(self): args = [ - '-DSUITESPARSE=OFF', '-DCXSPARSE=OFF', '-DEIGENSPARSE=ON', '-DLAPACK=ON', - '-DBUILD_SHARED_LIBS=ON', '-DSCHUR_SPECIALIZATIONS=OFF' ] + + if '+suitesparse' in self.spec: + args.append('-DSUITESPARSE=ON') + else: + args.append('-DSUITESPARSE=OFF') + + if '+shared' in self.spec: + args.append('-DBUILD_SHARED_LIBS=ON') + else: + args.append('-DBUILD_SHARED_LIBS=OFF') + + if '+examples' in self.spec: + args.append('-DBUILD_EXAMPLES=ON') + else: + args.append('-DBUILD_EXAMPLES=OFF') + return args From 74ba247839d9845eb897e98de5d8c6c9fc04ad33 Mon Sep 17 00:00:00 2001 From: Benjamin Fovet <45510885+bfovet@users.noreply.github.com> Date: Fri, 20 Mar 2020 20:51:30 +0100 Subject: [PATCH 170/377] Add gmsh v4.5.4 with new options (#15591) * Add gmsh v4.5.4 with new options This adds OpenCASCADE as an alternative to the oce package. A new variant 'privateapi' is added to enable the gmsh private API. * Make oce conflict with opencascade in gmsh --- .../repos/builtin/packages/gmsh/package.py | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index b5d677bd992..522a315f290 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -19,6 +19,7 @@ class Gmsh(CMakePackage): homepage = 'http://gmsh.info' url = 'http://gmsh.info/src/gmsh-4.4.1-source.tgz' + version('4.5.4', sha256='ccf8c74f43cbe3c371abe79862025d41642b3538a0148f018949494e3b3e2ecd') version('4.4.1', sha256='853c6438fc4e4b765206e66a514b09182c56377bb4b73f1d0d26eda7eb8af0dc') version('4.2.2', sha256='e9ee9f5c606bbec5f2adbb8c3d6023c4e2577f487fa4e4ecfcfc94a241cc8dcc') version('4.0.0', sha256='fb0c8afa37425c6f4315ab3b3124e9e102fcf270a35198423a4002796f04155f') @@ -31,16 +32,18 @@ class Gmsh(CMakePackage): variant('shared', default=True, description='Enables the build of shared libraries') variant('mpi', default=True, description='Builds MPI support for parser and solver') - variant('openmp', default=False, description='Enable OpenMP support') + variant('openmp', default=False, description='Enable OpenMP support') variant('fltk', default=False, description='Enables the build of the FLTK GUI') variant('hdf5', default=False, description='Enables HDF5 support') variant('compression', default=True, description='Enables IO compression through zlib') variant('netgen', default=False, description='Build with Netgen') + variant('opencascade', default=False, description='Build with OpenCASCADE') variant('oce', default=False, description='Build with OCE') variant('petsc', default=False, description='Build with PETSc') variant('slepc', default=False, description='Build with SLEPc (only when PETSc is enabled)') variant('tetgen', default=False, description='Build with Tetgen') - variant('metis', default=False, description='Build with Metis') + variant('metis', default=False, description='Build with Metis') + variant('privateapi', default=False, description='Enable the private API') depends_on('blas') depends_on('lapack') @@ -51,6 +54,7 @@ class Gmsh(CMakePackage): depends_on('fltk', when='+fltk') depends_on('hdf5', when='+hdf5') depends_on('netgen', when='+netgen') + depends_on('opencascade', when='+opencascade') depends_on('oce', when='+oce') depends_on('petsc+mpi', when='+petsc+mpi') depends_on('petsc', when='+petsc~mpi') @@ -60,6 +64,7 @@ class Gmsh(CMakePackage): depends_on('metis', when='+metis') conflicts('+slepc', when='~petsc') + conflicts('+oce', when='+opencascade') def cmake_args(self): spec = self.spec @@ -96,6 +101,9 @@ def cmake_args(self): if '+oce' in spec: env['CASROOT'] = self.spec['oce'].prefix options.append('-DENABLE_OCC=ON') + elif '+opencascade' in spec: + env['CASROOT'] = self.spec['opencascade'].prefix + options.append('-DENABLE_OCC=ON') else: options.append('-DENABLE_OCC=OFF') @@ -142,4 +150,9 @@ def cmake_args(self): if '+compression' in spec: options.append('-DENABLE_COMPRESSED_IO:BOOL=ON') + if '+privateapi' in spec: + options.append('-DENABLE_PRIVATE_API=ON') + else: + options.append('-DENABLE_PRIVATE_API=OFF') + return options From 42db143587c674fd1f66483bb7303fccdf349c0f Mon Sep 17 00:00:00 2001 From: Matthias Maiterth Date: Fri, 20 Mar 2020 20:51:51 +0100 Subject: [PATCH 171/377] freeipmi: Initial commit (#15576) * freeipmi: Initial commit Added freeipmi package. Configure and build work fine, install only as root, thus added warning and added reference to issue #4432 . * freeipmi: fixed change requests --- .../builtin/packages/freeipmi/package.py | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 var/spack/repos/builtin/packages/freeipmi/package.py diff --git a/var/spack/repos/builtin/packages/freeipmi/package.py b/var/spack/repos/builtin/packages/freeipmi/package.py new file mode 100644 index 00000000000..bcb3e502cd2 --- /dev/null +++ b/var/spack/repos/builtin/packages/freeipmi/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import llnl.util.tty as tty + + +class Freeipmi(AutotoolsPackage): + """FreeIPMI provides in-band and out-of-band IPMI software based on the IPMI + v1.5/2.0 specification. The IPMI specification defines a set of interfaces + for platform management and is implemented by a number vendors for system + management. The features of IPMI that most users will be interested in are + sensor monitoring, system event monitoring, power control, and + serial-over-LAN (SOL). The FreeIPMI tools and libraries listed below should + provide users with the ability to access and utilize these and many other + features. A number of useful features for large HPC or cluster environments + have also been implemented into FreeIPMI. See the README or FAQ for more + info.""" + + homepage = "https://www.gnu.org/software/freeipmi/" + url = "https://ftp.gnu.org/gnu/freeipmi/freeipmi-1.6.4.tar.gz" + + version('1.6.4', + sha256='65dfbb95a30438ba247f01a58498862a37d2e71c8c950bcfcee459d079241a3c') + + depends_on('libgcrypt') + + parallel = False + + def configure_args(self): + # FIXME: If root checking of root installation is added fix this: + # Discussed in issue #4432 + tty.warn("Requires 'root' for bmc-watchdog.service installation to" + " /lib/systemd/system/ !") + + args = ['--prefix={0}'.format(prefix)] + + return args From 64737e0632e1d9c3a01b55bb19639aba5936037b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 20 Mar 2020 17:01:18 -0400 Subject: [PATCH 172/377] py-torchtext: add new package (#15604) --- .../builtin/packages/py-torchtext/package.py | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-torchtext/package.py diff --git a/var/spack/repos/builtin/packages/py-torchtext/package.py b/var/spack/repos/builtin/packages/py-torchtext/package.py new file mode 100644 index 00000000000..6bcae3d1e9d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-torchtext/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class PyTorchtext(PythonPackage): + """Text utilities and datasets for PyTorch.""" + + homepage = "https://github.com/pytorch/text" + url = "https://pypi.io/packages/source/t/torchtext/torchtext-0.5.0.tar.gz" + + maintainers = ['adamjstewart'] + + version('0.5.0', sha256='7f22e24e9b939fff56b9118c78dc07aafec8dcc67164de15b9b5ed339e4179c6') + + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-tqdm', type=('build', 'run')) + depends_on('py-requests', type=('build', 'run')) + depends_on('py-torch@0.4.0:', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) + depends_on('py-sentencepiece', type=('build', 'run')) From dc5c73968ff9e02a1a72112af24ddfdd38120e01 Mon Sep 17 00:00:00 2001 From: Ryan Mast Date: Fri, 20 Mar 2020 14:01:45 -0700 Subject: [PATCH 173/377] swig: add version 4.0.1 (#15603) From 76c9e6d8719c49977e2f1762dde7b4dd6449d595 Mon Sep 17 00:00:00 2001 From: Ryan Mast Date: Fri, 20 Mar 2020 14:02:01 -0700 Subject: [PATCH 174/377] fix: change typo dependnecies to dependencies (#15602) --- lib/spack/spack/cmd/dependents.py | 2 +- lib/spack/spack/spec.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/cmd/dependents.py b/lib/spack/spack/cmd/dependents.py index e60733f5890..89fd15ffdab 100644 --- a/lib/spack/spack/cmd/dependents.py +++ b/lib/spack/spack/cmd/dependents.py @@ -30,7 +30,7 @@ def setup_parser(subparser): def inverted_dependencies(): """Iterate through all packages and return a dictionary mapping package - names to possible dependnecies. + names to possible dependencies. Virtual packages are included as sources, so that you can query dependents of, e.g., `mpi`, but virtuals are not included as diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py index 718b5ef14db..c6fe2da7627 100644 --- a/lib/spack/spack/spec.py +++ b/lib/spack/spack/spec.py @@ -3120,7 +3120,7 @@ def copy(self, deps=True, **kwargs): A copy of this spec. Examples: - Deep copy with dependnecies:: + Deep copy with dependencies:: spec.copy() spec.copy(deps=True) From e2125c26cea1752ca04aafb0228b7034a33e5f64 Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Fri, 20 Mar 2020 16:54:27 -0500 Subject: [PATCH 175/377] Buildcache: add unit tests for normalized path functions in relocate.py (#15607) --- lib/spack/spack/test/packaging.py | 62 ++++++++++++++++++++++++++++--- 1 file changed, 57 insertions(+), 5 deletions(-) diff --git a/lib/spack/spack/test/packaging.py b/lib/spack/spack/test/packaging.py index 5d5b2ccf8b0..39da7c3ae5e 100644 --- a/lib/spack/spack/test/packaging.py +++ b/lib/spack/spack/test/packaging.py @@ -26,7 +26,9 @@ from spack.relocate import needs_binary_relocation, needs_text_relocation from spack.relocate import relocate_text, relocate_links from spack.relocate import get_relative_elf_rpaths +from spack.relocate import get_normalized_elf_rpaths from spack.relocate import macho_make_paths_relative +from spack.relocate import macho_make_paths_normal from spack.relocate import set_placeholder, macho_find_paths from spack.relocate import file_is_relocatable @@ -471,7 +473,7 @@ def test_replace_paths(tmpdir): def test_macho_make_paths(): - out = macho_make_paths_relative('/Users/Shares/spack/pkgC/lib/libC.dylib', + out = macho_make_paths_relative('/Users/Shared/spack/pkgC/lib/libC.dylib', '/Users/Shared/spack', ('/Users/Shared/spack/pkgA/lib', '/Users/Shared/spack/pkgB/lib', @@ -481,19 +483,43 @@ def test_macho_make_paths(): '/usr/local/lib/libloco.dylib'), '/Users/Shared/spack/pkgC/lib/libC.dylib') assert out == {'/Users/Shared/spack/pkgA/lib': - '@loader_path/../../../../Shared/spack/pkgA/lib', + '@loader_path/../../pkgA/lib', '/Users/Shared/spack/pkgB/lib': - '@loader_path/../../../../Shared/spack/pkgB/lib', + '@loader_path/../../pkgB/lib', '/usr/local/lib': '/usr/local/lib', '/Users/Shared/spack/pkgA/libA.dylib': - '@loader_path/../../../../Shared/spack/pkgA/libA.dylib', + '@loader_path/../../pkgA/libA.dylib', '/Users/Shared/spack/pkgB/libB.dylib': - '@loader_path/../../../../Shared/spack/pkgB/libB.dylib', + '@loader_path/../../pkgB/libB.dylib', '/usr/local/lib/libloco.dylib': '/usr/local/lib/libloco.dylib', '/Users/Shared/spack/pkgC/lib/libC.dylib': '@rpath/libC.dylib'} + out = macho_make_paths_normal('/Users/Shared/spack/pkgC/lib/libC.dylib', + ('@loader_path/../../pkgA/lib', + '@loader_path/../../pkgB/lib', + '/usr/local/lib'), + ('@loader_path/../../pkgA/libA.dylib', + '@loader_path/../../pkgB/libB.dylib', + '/usr/local/lib/libloco.dylib'), + '@rpath/libC.dylib') + + assert out == {'@rpath/libC.dylib': + '/Users/Shared/spack/pkgC/lib/libC.dylib', + '@loader_path/../../pkgA/lib': + '/Users/Shared/spack/pkgA/lib', + '@loader_path/../../pkgB/lib': + '/Users/Shared/spack/pkgB/lib', + '/usr/local/lib': '/usr/local/lib', + '@loader_path/../../pkgA/libA.dylib': + '/Users/Shared/spack/pkgA/libA.dylib', + '@loader_path/../../pkgB/libB.dylib': + '/Users/Shared/spack/pkgB/libB.dylib', + '/usr/local/lib/libloco.dylib': + '/usr/local/lib/libloco.dylib' + } + out = macho_make_paths_relative('/Users/Shared/spack/pkgC/bin/exeC', '/Users/Shared/spack', ('/Users/Shared/spack/pkgA/lib', @@ -515,9 +541,35 @@ def test_macho_make_paths(): '/usr/local/lib/libloco.dylib': '/usr/local/lib/libloco.dylib'} + out = macho_make_paths_normal('/Users/Shared/spack/pkgC/bin/exeC', + ('@loader_path/../../pkgA/lib', + '@loader_path/../../pkgB/lib', + '/usr/local/lib'), + ('@loader_path/../../pkgA/libA.dylib', + '@loader_path/../../pkgB/libB.dylib', + '/usr/local/lib/libloco.dylib'), + None) + + assert out == {'@loader_path/../../pkgA/lib': + '/Users/Shared/spack/pkgA/lib', + '@loader_path/../../pkgB/lib': + '/Users/Shared/spack/pkgB/lib', + '/usr/local/lib': '/usr/local/lib', + '@loader_path/../../pkgA/libA.dylib': + '/Users/Shared/spack/pkgA/libA.dylib', + '@loader_path/../../pkgB/libB.dylib': + '/Users/Shared/spack/pkgB/libB.dylib', + '/usr/local/lib/libloco.dylib': + '/usr/local/lib/libloco.dylib'} + def test_elf_paths(): out = get_relative_elf_rpaths( '/usr/bin/test', '/usr', ('/usr/lib', '/usr/lib64', '/opt/local/lib')) assert out == ['$ORIGIN/../lib', '$ORIGIN/../lib64', '/opt/local/lib'] + + out = get_normalized_elf_rpaths( + '/usr/bin/test', + ['$ORIGIN/../lib', '$ORIGIN/../lib64', '/opt/local/lib']) + assert out == ['/usr/lib', '/usr/lib64', '/opt/local/lib'] From e4d225043f08c9c27900258091bc24a4bb55c272 Mon Sep 17 00:00:00 2001 From: Andrew W Elble Date: Fri, 20 Mar 2020 20:05:51 -0400 Subject: [PATCH 176/377] performance: add a verification file to the database (#14693) Reading the database repeatedly can be quite slow. We need a way to speed up Spack when it reads the DB multiple times, but the DB has not been modified between reads (which is nearly all the time). - [x] Add a file containing a unique uuid that is regenerated at database write time. Use this uuid to suppress re-parsing the database contents if we know a previous uuid and the uuid has not changed. - [x] Fix mutable_database fixture so that it resets the last seen verifier when it resets. - [x] Enable not rereading the database immediately after a write. Make the tests reset the last seen verifier in between tests that use the database fixture. - [x] make presence of uuid module optional --- lib/spack/spack/database.py | 29 ++++++++++++++++++++++++++--- lib/spack/spack/test/conftest.py | 2 ++ lib/spack/spack/test/database.py | 24 ++++++++++++++++++++++++ 3 files changed, 52 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py index 4b889da425b..ca9ed67fb5b 100644 --- a/lib/spack/spack/database.py +++ b/lib/spack/spack/database.py @@ -26,6 +26,12 @@ import socket import sys import time +try: + import uuid + _use_uuid = True +except ImportError: + _use_uuid = False + pass import llnl.util.tty as tty import six @@ -294,6 +300,7 @@ def __init__(self, root, db_dir=None, upstream_dbs=None, # Set up layout of database files within the db dir self._index_path = os.path.join(self._db_dir, 'index.json') + self._verifier_path = os.path.join(self._db_dir, 'index_verifier') self._lock_path = os.path.join(self._db_dir, 'lock') # This is for other classes to use to lock prefix directories. @@ -315,6 +322,7 @@ def __init__(self, root, db_dir=None, upstream_dbs=None, mkdirp(self._failure_dir) self.is_upstream = is_upstream + self.last_seen_verifier = '' # initialize rest of state. self.db_lock_timeout = ( @@ -913,6 +921,11 @@ def _write(self, type, value, traceback): with open(temp_file, 'w') as f: self._write_to_file(f) os.rename(temp_file, self._index_path) + if _use_uuid: + with open(self._verifier_path, 'w') as f: + new_verifier = str(uuid.uuid4()) + f.write(new_verifier) + self.last_seen_verifier = new_verifier except BaseException as e: tty.debug(e) # Clean up temp file if something goes wrong. @@ -928,8 +941,18 @@ def _read(self): write lock. """ if os.path.isfile(self._index_path): - # Read from file if a database exists - self._read_from_file(self._index_path) + current_verifier = '' + if _use_uuid: + try: + with open(self._verifier_path, 'r') as f: + current_verifier = f.read() + except BaseException: + pass + if ((current_verifier != self.last_seen_verifier) or + (current_verifier == '')): + self.last_seen_verifier = current_verifier + # Read from file if a database exists + self._read_from_file(self._index_path) return elif self.is_upstream: raise UpstreamDatabaseLockingError( @@ -1339,7 +1362,7 @@ def _query( # TODO: handling of hashes restriction is not particularly elegant. hash_key = query_spec.dag_hash() if (hash_key in self._data and - (not hashes or hash_key in hashes)): + (not hashes or hash_key in hashes)): return [self._data[hash_key].spec] else: return [] diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py index 04e870d336a..67037421423 100644 --- a/lib/spack/spack/test/conftest.py +++ b/lib/spack/spack/test/conftest.py @@ -525,6 +525,8 @@ def database(mock_store, mock_packages, config): """This activates the mock store, packages, AND config.""" with use_store(mock_store): yield mock_store.db + # Force reading the database again between tests + mock_store.db.last_seen_verifier = '' @pytest.fixture(scope='function') diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py index 88e6c42693c..28311c7501d 100644 --- a/lib/spack/spack/test/database.py +++ b/lib/spack/spack/test/database.py @@ -13,6 +13,12 @@ import os import pytest import json +try: + import uuid + _use_uuid = True +except ImportError: + _use_uuid = False + pass import llnl.util.lock as lk from llnl.util.tty.colify import colify @@ -469,6 +475,21 @@ def test_015_write_and_read(mutable_database): assert new_rec.installed == rec.installed +def test_017_write_and_read_without_uuid(mutable_database, monkeypatch): + monkeypatch.setattr(spack.database, '_use_uuid', False) + # write and read DB + with spack.store.db.write_transaction(): + specs = spack.store.db.query() + recs = [spack.store.db.get_record(s) for s in specs] + + for spec, rec in zip(specs, recs): + new_rec = spack.store.db.get_record(spec) + assert new_rec.ref_count == rec.ref_count + assert new_rec.spec == rec.spec + assert new_rec.path == rec.path + assert new_rec.installed == rec.installed + + def test_020_db_sanity(database): """Make sure query() returns what's actually in the db.""" _check_db_sanity(database) @@ -703,6 +724,9 @@ def test_old_external_entries_prefix(mutable_database): with open(spack.store.db._index_path, 'w') as f: f.write(json.dumps(db_obj)) + if _use_uuid: + with open(spack.store.db._verifier_path, 'w') as f: + f.write(str(uuid.uuid4())) record = spack.store.db.get_record(s) From 4b771bc5214fc731bea6c658b13e78a05736bf40 Mon Sep 17 00:00:00 2001 From: darmac Date: Sat, 21 Mar 2020 23:42:08 +0800 Subject: [PATCH 177/377] add new package: nfs-ganesha (#15580) * add new pacakge: nfs-ganesha * refine package.py * update bison & flex as build depends --- .../builtin/packages/nfs-ganesha/package.py | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 var/spack/repos/builtin/packages/nfs-ganesha/package.py diff --git a/var/spack/repos/builtin/packages/nfs-ganesha/package.py b/var/spack/repos/builtin/packages/nfs-ganesha/package.py new file mode 100644 index 00000000000..1ea286270db --- /dev/null +++ b/var/spack/repos/builtin/packages/nfs-ganesha/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class NfsGanesha(CMakePackage): + """NFS-Ganesha is an NFSv3,v4,v4.1 fileserver that runs in user mode + on most UNIX/Linux systems. It also supports the 9p.2000L protocol.""" + + homepage = "https://github.com/nfs-ganesha/nfs-ganesha/wiki" + url = "https://github.com/nfs-ganesha/nfs-ganesha/archive/V3.2.tar.gz" + + version('3.2', sha256='1e3635f0eb0bc32868ea7d923d061d0f6b1bd03b45da34356c7c53d4c0ebafbd') + version('3.1', sha256='c4cf78929f39b8af44b05e813783b2c39e348b485043c6290c4bca705bb5015f') + version('3.0.3', sha256='fcc0361b9a2752be7eb4e990230765e17de373452ac24514be22c81a5447a460') + version('3.0', sha256='136c5642ff21ec6e8a4e77c037f6218a39b2eeba77798b13556f1abbb0923ccd') + + depends_on('bison', type='build') + depends_on('flex', type='build') + depends_on('userspace-rcu') + depends_on('ntirpc') + + root_cmakelists_dir = 'src' + + def setup_build_environment(self, env): + env.prepend_path('CPATH', self.spec['ntirpc'].prefix.include.ntirpc) From 7bde39d883837a202a9629845eb06a0de228e707 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 21 Mar 2020 12:52:01 -0400 Subject: [PATCH 178/377] Fix bug in py-dgl installation, add unit tests (#15617) --- .../repos/builtin/packages/py-dgl/package.py | 38 ++++++++++++++++++- 1 file changed, 36 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-dgl/package.py b/var/spack/repos/builtin/packages/py-dgl/package.py index 336d69edf24..b1b1c37586f 100644 --- a/var/spack/repos/builtin/packages/py-dgl/package.py +++ b/var/spack/repos/builtin/packages/py-dgl/package.py @@ -47,6 +47,7 @@ class PyDgl(CMakePackage): build_directory = 'build' + # https://docs.dgl.ai/install/index.html#install-from-source def cmake_args(self): args = [] @@ -83,12 +84,45 @@ def cmake_args(self): def install(self, spec, prefix): with working_dir('python'): - import os - print('Current dir:', os.getcwd()) setup_py('install', '--prefix=' + prefix, '--single-version-externally-managed', '--root=/') + # Work around installation bug: https://github.com/dmlc/dgl/issues/1379 + install_tree(prefix.dgl, prefix.lib) + def setup_run_environment(self, env): # https://docs.dgl.ai/install/backend.html backend = self.spec.variants['backend'].value env.set('DGLBACKEND', backend) + + @property + def import_modules(self): + modules = [ + 'dgl', 'dgl.nn', 'dgl.runtime', 'dgl.backend', 'dgl.function', + 'dgl.contrib', 'dgl._ffi', 'dgl.data', 'dgl.runtime.ir', + 'dgl.backend.numpy', 'dgl.contrib.sampling', 'dgl._ffi._cy2', + 'dgl._ffi._cy3', 'dgl._ffi._ctypes', + ] + + if 'backend=pytorch' in self.spec: + modules.extend([ + 'dgl.nn.pytorch', 'dgl.nn.pytorch.conv', 'dgl.backend.pytorch' + ]) + elif 'backend=mxnet' in self.spec: + modules.extend([ + 'dgl.nn.mxnet', 'dgl.nn.mxnet.conv', 'dgl.backend.mxnet' + ]) + elif 'backend=tensorflow' in self.spec: + modules.extend([ + 'dgl.nn.tensorflow', 'dgl.nn.tensorflow.conv', + 'dgl.backend.tensorflow' + ]) + + return modules + + @run_after('install') + @on_package_attributes(run_tests=True) + def import_module_test(self): + with working_dir('spack-test', create=True): + for module in self.import_modules: + python('-c', 'import {0}'.format(module)) From 983f9d341965598dba2ccd285bd92f7fe65e0a73 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 21 Mar 2020 13:42:54 -0400 Subject: [PATCH 179/377] bash: add patches up to 5.0.16 (#15615) --- var/spack/repos/builtin/packages/bash/package.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/var/spack/repos/builtin/packages/bash/package.py b/var/spack/repos/builtin/packages/bash/package.py index 2723b667907..f6c7da81296 100644 --- a/var/spack/repos/builtin/packages/bash/package.py +++ b/var/spack/repos/builtin/packages/bash/package.py @@ -33,6 +33,11 @@ class Bash(AutotoolsPackage, GNUMirrorPackage): ('5.0', '009', 'ed3ca21767303fc3de93934aa524c2e920787c506b601cc40a4897d4b094d903'), ('5.0', '010', 'd6fbc325f0b5dc54ddbe8ee43020bced8bd589ddffea59d128db14b2e52a8a11'), ('5.0', '011', '2c4de332b91eaf797abbbd6c79709690b5cbd48b12e8dfe748096dbd7bf474ea'), + ('5.0', '012', '2943ee19688018296f2a04dbfe30b7138b889700efa8ff1c0524af271e0ee233'), + ('5.0', '013', 'f5d7178d8da30799e01b83a0802018d913d6aa972dd2ddad3b927f3f3eb7099a'), + ('5.0', '014', '5d6eee6514ee6e22a87bba8d22be0a8621a0ae119246f1c5a9a35db1f72af589'), + ('5.0', '015', 'a517df2dda93b26d5cbf00effefea93e3a4ccd6652f152f4109170544ebfa05e'), + ('5.0', '016', 'ffd1d7a54a99fa7f5b1825e4f7e95d8c8876bc2ca151f150e751d429c650b06d'), ] # TODO: patches below are not managed by the GNUMirrorPackage base class From 25893f154ff185e9df54c8a6e11c0fcbc02c2f20 Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Sat, 21 Mar 2020 13:26:37 -0500 Subject: [PATCH 180/377] Buildcache: attempt to build and install buildcaches in test environment (#15577) * Put bindist.py on it's own branch * Working on SL7 with python 3.6 * Flake8 * Put back clearing of compiler cache --- lib/spack/spack/test/bindist.py | 480 ++++++++++++++++++++++++++++++++ 1 file changed, 480 insertions(+) create mode 100644 lib/spack/spack/test/bindist.py diff --git a/lib/spack/spack/test/bindist.py b/lib/spack/spack/test/bindist.py new file mode 100644 index 00000000000..8ca7609942d --- /dev/null +++ b/lib/spack/spack/test/bindist.py @@ -0,0 +1,480 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +""" +This test checks creating and install buildcaches +""" +import os +import py +import pytest +import argparse +import platform +import spack.repo +import spack.store +import spack.binary_distribution as bindist +import spack.cmd.buildcache as buildcache +import spack.cmd.compiler as compiler +import spack.cmd.repo as repocmd +import spack.cmd.install as install +import spack.cmd.uninstall as uninstall +import spack.cmd.mirror as mirror +from spack.spec import Spec +from spack.directory_layout import YamlDirectoryLayout + + +def_install_path_scheme = '${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}' # noqa: E501 +ndef_install_path_scheme = '${PACKAGE}/${VERSION}/${ARCHITECTURE}-${COMPILERNAME}-${COMPILERVER}-${HASH}' # noqa: E501 + +mirror_path_def = None +mirror_path_rel = None + + +@pytest.fixture(scope='function') +def cache_directory(tmpdir): + old_cache_path = spack.caches.fetch_cache + tmpdir.ensure('fetch_cache', dir=True) + fsc = spack.fetch_strategy.FsCache(str(tmpdir.join('fetch_cache'))) + spack.config.caches = fsc + yield spack.config.caches + tmpdir.join('fetch_cache').remove() + spack.config.caches = old_cache_path + + +@pytest.fixture(scope='session') +def session_mirror_def(tmpdir_factory): + dir = tmpdir_factory.mktemp('mirror') + global mirror_path_rel + mirror_path_rel = dir + dir.ensure('build_cache', dir=True) + yield dir + dir.join('build_cache').remove() + + +@pytest.fixture(scope='function') +def mirror_directory_def(session_mirror_def): + yield str(session_mirror_def) + + +@pytest.fixture(scope='session') +def session_mirror_rel(tmpdir_factory): + dir = tmpdir_factory.mktemp('mirror') + global mirror_path_rel + mirror_path_rel = dir + dir.ensure('build_cache', dir=True) + yield dir + dir.join('build_cache').remove() + + +@pytest.fixture(scope='function') +def mirror_directory_rel(session_mirror_rel): + yield(session_mirror_rel) + + +@pytest.fixture(scope='session') +def config_directory(tmpdir_factory): + tmpdir = tmpdir_factory.mktemp('test_configs') + # restore some sane defaults for packages and config + config_path = py.path.local(spack.paths.etc_path) + modules_yaml = config_path.join('spack', 'defaults', 'modules.yaml') + os_modules_yaml = config_path.join('spack', 'defaults', '%s' % + platform.system().lower(), + 'modules.yaml') + packages_yaml = config_path.join('spack', 'defaults', 'packages.yaml') + config_yaml = config_path.join('spack', 'defaults', 'config.yaml') + repos_yaml = config_path.join('spack', 'defaults', 'repos.yaml') + tmpdir.ensure('site', dir=True) + tmpdir.ensure('user', dir=True) + tmpdir.ensure('site/%s' % platform.system().lower(), dir=True) + modules_yaml.copy(tmpdir.join('site', 'modules.yaml')) + os_modules_yaml.copy(tmpdir.join('site/%s' % platform.system().lower(), + 'modules.yaml')) + packages_yaml.copy(tmpdir.join('site', 'packages.yaml')) + config_yaml.copy(tmpdir.join('site', 'config.yaml')) + repos_yaml.copy(tmpdir.join('site', 'repos.yaml')) + yield tmpdir + tmpdir.remove() + + +@pytest.fixture(scope='function') +def default_config(tmpdir_factory, config_directory, monkeypatch): + + mutable_dir = tmpdir_factory.mktemp('mutable_config').join('tmp') + config_directory.copy(mutable_dir) + + cfg = spack.config.Configuration( + *[spack.config.ConfigScope(name, str(mutable_dir)) + for name in ['site/%s' % platform.system().lower(), + 'site', 'user']]) + + monkeypatch.setattr(spack.config, 'config', cfg) + + # This is essential, otherwise the cache will create weird side effects + # that will compromise subsequent tests if compilers.yaml is modified + monkeypatch.setattr(spack.compilers, '_cache_config_file', []) + njobs = spack.config.get('config:build_jobs') + if not njobs: + spack.config.set('config:build_jobs', 4, scope='user') + extensions = spack.config.get('config:template_dirs') + if not extensions: + spack.config.set('config:template_dirs', + [os.path.join(spack.paths.share_path, 'templates')], + scope='user') + + mutable_dir.ensure('build_stage', dir=True) + build_stage = spack.config.get('config:build_stage') + if not build_stage: + spack.config.set('config:build_stage', + [str(mutable_dir.join('build_stage'))], scope='user') + timeout = spack.config.get('config:connect_timeout') + if not timeout: + spack.config.set('config:connect_timeout', 10, scope='user') + print(spack.config.config) + yield spack.config.config + mutable_dir.remove() + + +@pytest.fixture(scope='function') +def install_dir_default_layout(tmpdir): + """Hooks a fake install directory with a default layout""" + real_store = spack.store.store + real_layout = spack.store.layout + spack.store.store = spack.store.Store(str(tmpdir.join('opt'))) + spack.store.layout = YamlDirectoryLayout(str(tmpdir.join('opt')), + path_scheme=def_install_path_scheme) # noqa: E501 + yield spack.store + tmpdir.join('opt').remove() + spack.store.store = real_store + spack.store.layout = real_layout + + +@pytest.fixture(scope='function') +def install_dir_non_default_layout(tmpdir): + """Hooks a fake install directory with a non-default layout""" + real_store = spack.store.store + real_layout = spack.store.layout + spack.store.store = spack.store.Store(str(tmpdir.join('opt'))) + spack.store.layout = YamlDirectoryLayout(str(tmpdir.join('opt')), + path_scheme=ndef_install_path_scheme) # noqa: E501 + yield spack.store + tmpdir.join('opt').remove() + spack.store.store = real_store + spack.store.layout = real_layout + + +@pytest.fixture(scope='session') +def config_setup(): + cparser = argparse.ArgumentParser() + compiler.setup_parser(cparser) + cargs = cparser.parse_args(['add', '--scope', 'site']) + compiler.compiler(cparser, cargs) + cargs = cparser.parse_args(['list', '--scope', 'site']) + compiler.compiler(cparser, cargs) + + rparser = argparse.ArgumentParser() + repocmd.setup_parser(rparser) + rargs = rparser.parse_args(['add', spack.paths.packages_path]) + repocmd.repo(rparser, rargs) + # Set some spec name used globally + zspec = Spec('zlib') + zspec.concretize() + espec = Spec('environment-modules') + espec.concretize() + pspec = Spec('patchelf') + pspec.concretize() + + yield espec, zspec, pspec + + +@pytest.mark.disable_clean_stage_check +@pytest.mark.maybeslow +@pytest.mark.usefixtures('default_config', 'cache_directory', + 'install_dir_default_layout') +def test_default_rpaths_create_install_default_layout(tmpdir, + mirror_directory_def, + config_setup, + mock_stage): + """ + Test the creation and installation of buildcaches with default rpaths + into the default directory layout scheme. + """ + tspec, zspec, pspec = config_setup + # Install patchelf needed for relocate in linux test environment + # Install some packages with dependent packages + iparser = argparse.ArgumentParser() + install.setup_parser(iparser) + if platform.system().lower() != 'darwin': + iargs = iparser.parse_args(['--no-cache', pspec.name]) + install.install(iparser, iargs) + iargs = iparser.parse_args(['--no-cache', tspec.name]) + install.install(iparser, iargs) + + global mirror_path_def + mirror_path_def = mirror_directory_def + mparser = argparse.ArgumentParser() + mirror.setup_parser(mparser) + margs = mparser.parse_args( + ['add', '--scope', 'site', 'test-mirror-def', 'file://%s' % mirror_path_def]) + mirror.mirror(mparser, margs) + margs = mparser.parse_args(['list']) + mirror.mirror(mparser, margs) + + # setup argument parser + parser = argparse.ArgumentParser() + buildcache.setup_parser(parser) + + # Set default buildcache args + create_args = ['create', '-a', '-u', '-d', str(mirror_path_def), + tspec.name] + install_args = ['install', '-a', '-u', tspec.name] + + # Create a buildache of patchelf + if platform.system().lower() != 'darwin': + args = parser.parse_args(['create', '-a', '-u', '-d', + str(mirror_path_def), + pspec.name]) + buildcache.buildcache(parser, args) + + # Create a buildache + args = parser.parse_args(create_args) + buildcache.buildcache(parser, args) + # Test force overwrite create buildcache + create_args.insert(create_args.index('-a'), '-f') + args = parser.parse_args(create_args) + buildcache.buildcache(parser, args) + # list the buildcaches in the mirror + args = parser.parse_args(['list', '-f', '-l', '-v']) + buildcache.buildcache(parser, args) + + # Uninstall the package and deps + uparser = argparse.ArgumentParser() + uninstall.setup_parser(uparser) + uargs = uparser.parse_args(['-y', '--dependents', zspec.name]) + uninstall.uninstall(uparser, uargs) + + # test install + args = parser.parse_args(install_args) + buildcache.buildcache(parser, args) + + # This gives warning that spec is already installed + buildcache.buildcache(parser, args) + + # test overwrite install + install_args.insert(install_args.index('-a'), '-f') + args = parser.parse_args(install_args) + buildcache.buildcache(parser, args) + + args = parser.parse_args(['keys', '-f']) + buildcache.buildcache(parser, args) + + args = parser.parse_args(['list']) + buildcache.buildcache(parser, args) + + args = parser.parse_args(['list', '-f']) + buildcache.buildcache(parser, args) + + args = parser.parse_args(['list', '-l', '-v']) + buildcache.buildcache(parser, args) + bindist._cached_specs = set() + spack.stage.purge() + + +@pytest.mark.disable_clean_stage_check +@pytest.mark.maybeslow +@pytest.mark.nomockstage +@pytest.mark.usefixtures('default_config', 'cache_directory', + 'install_dir_non_default_layout') +def test_default_rpaths_install_nondefault_layout(tmpdir, config_setup, + mock_stage): + """ + Test the creation and installation of buildcaches with default rpaths + into the non-default directory layout scheme. + """ + tspec, zspec, pspec = config_setup + global mirror_path_def + mparser = argparse.ArgumentParser() + mirror.setup_parser(mparser) + margs = mparser.parse_args( + ['add', '--scope', 'site', 'test-mirror-def', 'file://%s' % mirror_path_def]) + mirror.mirror(mparser, margs) + + # setup argument parser + parser = argparse.ArgumentParser() + buildcache.setup_parser(parser) + + # Set default buildcache args + install_args = ['install', '-a', '-u', tspec.name] + + # Install patchelf needed for relocate in linux test environment + if platform.system().lower() != 'darwin': + args = parser.parse_args(['install', '-a', '-u', pspec.name]) + buildcache.buildcache(parser, args) + + # Install some packages with dependent packages + # test install in non-default install path scheme + args = parser.parse_args(install_args) + buildcache.buildcache(parser, args) + # test force install in non-default install path scheme + install_args.insert(install_args.index('-a'), '-f') + args = parser.parse_args(install_args) + buildcache.buildcache(parser, args) + + bindist._cached_specs = set() + spack.stage.purge() + + +@pytest.mark.disable_clean_stage_check +@pytest.mark.maybeslow +@pytest.mark.nomockstage +@pytest.mark.usefixtures('default_config', 'cache_directory', + 'install_dir_default_layout') +def test_relative_rpaths_create_default_layout(tmpdir, mirror_directory_rel, + config_setup, mock_stage): + """ + Test the creation and installation of buildcaches with relative + rpaths into the default directory layout scheme. + """ + tspec, zspec, pspec = config_setup + global mirror_path_rel + global mirror_path_def + mirror_path_rel = mirror_directory_rel + mparser = argparse.ArgumentParser() + mirror.setup_parser(mparser) + margs = mparser.parse_args( + ['add', '--scope', 'site', 'test-mirror-def', 'file://%s' % mirror_path_def]) + mirror.mirror(mparser, margs) + # setup argument parser + parser = argparse.ArgumentParser() + buildcache.setup_parser(parser) + + # install patchelf buildcache on linux + if platform.system().lower() != 'darwin': + args = parser.parse_args(['install', '-a', '-u', pspec.name]) + buildcache.buildcache(parser, args) + + # set default buildcache args + create_args = ['create', '-a', '-u', '-r', '-d', + str(mirror_path_rel), + tspec.name] + install_args = ['install', '-a', '-u', + tspec.name] + + # Create a buildache of patchelf + if platform.system().lower() != 'darwin': + args = parser.parse_args(['create', '-a', '-u', '-d', + str(mirror_path_rel), pspec.name]) + buildcache.buildcache(parser, args) + + # install buildcache created with default rpaths + args = parser.parse_args(install_args) + buildcache.buildcache(parser, args) + + # create build cache with relatived rpaths + args = parser.parse_args(create_args) + buildcache.buildcache(parser, args) + + # Uninstall the package and deps + uparser = argparse.ArgumentParser() + uninstall.setup_parser(uparser) + uargs = uparser.parse_args(['-y', '--dependents', zspec.name]) + uninstall.uninstall(uparser, uargs) + + bindist._cached_specs = set() + spack.stage.purge() + + +@pytest.mark.disable_clean_stage_check +@pytest.mark.maybeslow +@pytest.mark.nomockstage +@pytest.mark.usefixtures('default_config', 'cache_directory', + 'install_dir_default_layout') +def test_relative_rpaths_install_default_layout(tmpdir, config_setup, + mock_stage): + """ + Test the creation and installation of buildcaches with relative + rpaths into the default directory layout scheme. + """ + tspec, zspec, pspec = config_setup + global mirror_path_rel + mparser = argparse.ArgumentParser() + mirror.setup_parser(mparser) + margs = mparser.parse_args( + ['add', '--scope', 'site', 'test-mirror-rel', 'file://%s' % mirror_path_rel]) + mirror.mirror(mparser, margs) + + # setup argument parser + parser = argparse.ArgumentParser() + buildcache.setup_parser(parser) + + # install patchelf buildcache on linux + if platform.system().lower() != 'darwin': + args = parser.parse_args(['install', '-a', '-u', pspec.name]) + buildcache.buildcache(parser, args) + + # set default buildcache args + install_args = ['install', '-a', '-u', + tspec.name] + + # install buildcache created with relativized rpaths + args = parser.parse_args(install_args) + buildcache.buildcache(parser, args) + + # This gives warning that spec is already installed + buildcache.buildcache(parser, args) + + # Uninstall the package and deps + uparser = argparse.ArgumentParser() + uninstall.setup_parser(uparser) + uargs = uparser.parse_args(['-y', '--dependents', zspec.name]) + uninstall.uninstall(uparser, uargs) + + # install build cache + buildcache.buildcache(parser, args) + + # test overwrite install + install_args.insert(install_args.index('-a'), '-f') + args = parser.parse_args(install_args) + buildcache.buildcache(parser, args) + + bindist._cached_specs = set() + spack.stage.purge() + + +@pytest.mark.disable_clean_stage_check +@pytest.mark.maybeslow +@pytest.mark.nomockstage +@pytest.mark.usefixtures('default_config', 'cache_directory', + 'install_dir_non_default_layout') +def test_relative_rpaths_install_nondefault(tmpdir, config_setup, + mock_stage): + """ + Test the installation of buildcaches with relativized rpaths + into the non-default directory layout scheme. + """ + tspec, zspec, pspec = config_setup + global mirror_path_rel + mparser = argparse.ArgumentParser() + mirror.setup_parser(mparser) + margs = mparser.parse_args( + ['add', '--scope', 'site', 'test-mirror-rel', 'file://%s' % mirror_path_rel]) + mirror.mirror(mparser, margs) + + # setup argument parser + parser = argparse.ArgumentParser() + buildcache.setup_parser(parser) + + # Set default buildcache args + install_args = ['install', '-a', '-u', tspec.name] + + # Install patchelf needed for relocate in linux test environment + if platform.system().lower() != 'darwin': + args = parser.parse_args(['install', '-a', '-u', pspec.name]) + buildcache.buildcache(parser, args) + + # test install in non-default install path scheme and relative path + args = parser.parse_args(install_args) + buildcache.buildcache(parser, args) + + bindist._cached_specs = set() + spack.stage.purge() From bb4e9a7b32f5073ca9dc0a0be6d5ddfbdaf91ade Mon Sep 17 00:00:00 2001 From: Ben Morgan Date: Sat, 21 Mar 2020 18:27:35 +0000 Subject: [PATCH 181/377] davix: add cxxstd variant (#15593) * davix: add cxxstd variant Davix is written in C++, so add this variant to allow dependents to specify this so a consistent ABI is used. * davix: fix flake8 errors --- var/spack/repos/builtin/packages/davix/package.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/var/spack/repos/builtin/packages/davix/package.py b/var/spack/repos/builtin/packages/davix/package.py index faed2f16fe0..4062fb4daec 100644 --- a/var/spack/repos/builtin/packages/davix/package.py +++ b/var/spack/repos/builtin/packages/davix/package.py @@ -19,7 +19,18 @@ class Davix(CMakePackage): version('0.6.9', sha256='fbd97eb5fdf82ca48770d06bf8e2805b35f23255478aa381a9d25a49eb98e348') version('0.6.8', sha256='e1820f4cc3fc44858ae97197a3922cce2a1130ff553b080ba19e06eb8383ddf7') + variant('cxxstd', + default='11', + values=('11', '14', '17'), + multi=False, + description='Use the specified C++ standard when building.') + depends_on('pkgconfig', type='build') depends_on('libxml2') depends_on('libuuid') depends_on('openssl') + + def cmake_args(self): + cmake_args = ['-DCMAKE_CXX_STANDARD={0}'.format( + self.spec.variants['cxxstd'].value)] + return cmake_args From a3e3413855f5389b7cab9c7bc6126f150597b0ec Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Sat, 21 Mar 2020 17:36:15 -0500 Subject: [PATCH 182/377] WarpX: Update ES and openPMD (#15611) Update WarpX for recent developments: - add openPMD I/O (default: ON) - remove electro-static solver option (now a runtime option) - enable tiny profiler by default - depend on new CXX std support in make scripts for C++14 - WarpX only supports 2D and 3D in cartesian dims --- .../repos/builtin/packages/warpx/package.py | 25 ++++++++----------- 1 file changed, 10 insertions(+), 15 deletions(-) diff --git a/var/spack/repos/builtin/packages/warpx/package.py b/var/spack/repos/builtin/packages/warpx/package.py index 7755beba9c5..a729f9ac28f 100644 --- a/var/spack/repos/builtin/packages/warpx/package.py +++ b/var/spack/repos/builtin/packages/warpx/package.py @@ -22,21 +22,23 @@ class Warpx(MakefilePackage): version('master', tag='master') - depends_on('mpi') - variant('dims', default='3', - values=('1', '2', '3'), + values=('2', '3'), multi=False, description='Number of spatial dimensions') variant('psatd', default=False, description='Enable PSATD solver') - variant('do_electrostatic', default=False, description='Include electrostatic solver') variant('debug', default=False, description='Enable debugging features') - variant('tprof', default=False, description='Enable tiny profiling features') + variant('tprof', default=True, description='Enable tiny profiling features') variant('openmp', default=True, description='Enable OpenMP features') + variant('openpmd', default=True, description='Enable openPMD I/O') + depends_on('mpi') depends_on('fftw@3:', when='+psatd') + depends_on('pkgconfig', type='build', when='+openpmd') + depends_on('python', type='build') # FIXME upstream + depends_on('openpmd-api@0.11.0:,dev +mpi', when='+openpmd') resource(name='amrex', git='https://github.com/AMReX-Codes/amrex.git', @@ -47,15 +49,7 @@ class Warpx(MakefilePackage): git='https://bitbucket.org/berkeleylab/picsar.git', tag='master') - @property - def build_targets(self): - if self.spec.satisfies('%clang'): - return ['CXXFLAGS={0}'.format(self.compiler.cxx11_flag)] - else: - return [] - def edit(self, spec, prefix): - comp = 'gcc' vendors = {'%gcc': 'gcc', '%intel': 'intel'} for key, value in vendors.items(): @@ -74,16 +68,17 @@ def torf(s): 'DIM = {0}'.format(int(spec.variants['dims'].value))) makefile.filter('USE_PSATD .*', 'USE_PSATD = {0}'.format(torf('+psatd'))) - makefile.filter('DO_ELECTROSTATIC .*', - 'DO_ELECTROSTATIC = %s' % torf('+do_electrostatic')) try: self.compiler.openmp_flag except UnsupportedCompilerFlag: use_omp = 'FALSE' else: use_omp = torf('+openmp') + use_openpmd = torf('+openpmd') makefile.filter('USE_OMP .*', 'USE_OMP = {0}'.format(use_omp)) + makefile.filter('USE_OPENPMD .*', + 'USE_OPENPMD = {0}'.format(use_openpmd)) makefile.filter('DEBUG .*', 'DEBUG = {0}'.format(torf('+debug'))) makefile.filter('TINY_PROFILE .*', From 62787a7a3b504e4382e6a8729d8fd5f4392d5b43 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 22 Mar 2020 15:32:53 -0500 Subject: [PATCH 183/377] NCCL: add 1.2.2 (#15628) --- var/spack/repos/builtin/packages/intel-mkl-dnn/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py b/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py index ab3a7cde461..d5160200f3a 100644 --- a/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py +++ b/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py @@ -11,10 +11,12 @@ class IntelMklDnn(CMakePackage): (Intel(R) MKL-DNN).""" homepage = "https://intel.github.io/mkl-dnn/" - url = "https://github.com/intel/mkl-dnn/archive/v1.1.1.tar.gz" + url = "https://github.com/intel/mkl-dnn/archive/v1.2.2.tar.gz" maintainers = ['adamjstewart'] + version('1.2.2', sha256='a71ec1f27c30b8a176605e8a78444f1f12301a3c313b70ff93290926c140509c') + version('1.2.1', sha256='c69544783c453ab3fbf14c7a5b9a512561267690c9fc3e7fc3470f04756e0ab3') version('1.2', sha256='30979a09753e8e35d942446c3778c9f0eba543acf2fb0282af8b9c89355d0ddf') version('1.1.3', sha256='0e9bcbc86cc215a84a5455a395ce540c68e255eaa586e37222fff622b9b17df7') version('1.1.2', sha256='284b20e0cab67025bb7d21317f805d6217ad77fb3a47ad84b3bacf37bde62da9') @@ -25,6 +27,7 @@ class IntelMklDnn(CMakePackage): version('1.0.2', sha256='3164eb2914e2160ac6ffd345781cf7554ce410830398cc6b2761e8668faf5ca8') version('1.0.1', sha256='91fb84601c18f8a5a87eccd7b63d61f03495f36c5c533bd7f59443e4f8bb2595') version('1.0', sha256='27fd9da9720c452852f1226581e7914efcf74e1ff898468fdcbe1813528831ba') + version('0.21.4', sha256='1e774138203b773b5af2eed9cc6f1973f13a7263a3b80127682246c5a6c5bc45') version('0.21.3', sha256='31e78581e59d7e60d4becaba3834fc6a5bf2dccdae3e16b7f70d89ceab38423f') version('0.21.2', sha256='ed56652dd237deb86ee9bf102c18de5f2625c059e5ab1d7512c8dc01e316b694') version('0.21.1', sha256='766ecfa5ac68be8cf9eacd4c712935c0ed945e5e6fe51640f05ee735cff62a38') From d9c5b7de103321f104fc19019caee6d421cd3c59 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sun, 22 Mar 2020 15:46:54 -0700 Subject: [PATCH 184/377] bugfix: spack test should not output [+] for mock installs (#15609) `spack test` has a spurious '[+] ' in the output: ``` lib/spack/spack/test/install.py .........[+] ...... ``` Output is properly suppressed: ``` lib/spack/spack/test/install.py ............... ``` --- lib/spack/spack/installer.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py index a9965c91141..213a85f0dc7 100644 --- a/lib/spack/spack/installer.py +++ b/lib/spack/spack/installer.py @@ -48,7 +48,7 @@ import spack.repo import spack.store -from llnl.util.tty.color import colorize, cwrite +from llnl.util.tty.color import colorize from llnl.util.tty.log import log_output from spack.util.environment import dump_environment from spack.util.executable import which @@ -253,8 +253,7 @@ def _print_installed_pkg(message): Args: message (str): message to be output """ - cwrite('@*g{[+]} ') - print(message) + print(colorize('@*g{[+]} ') + message) def _process_external_package(pkg, explicit): From 0323f84e790c34d8e33672280ad0817b05abe90c Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sun, 22 Mar 2020 20:47:04 -0700 Subject: [PATCH 185/377] bugfix: TERM may not be in the environment on Cray (#15630) --- lib/spack/spack/platforms/cray.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/lib/spack/spack/platforms/cray.py b/lib/spack/spack/platforms/cray.py index 8eae51e66a2..6e8c79ef0cd 100644 --- a/lib/spack/spack/platforms/cray.py +++ b/lib/spack/spack/platforms/cray.py @@ -117,9 +117,13 @@ def _default_target_from_env(self): ''' # env -i /bin/bash -lc echo $CRAY_CPU_TARGET 2> /dev/null if getattr(self, 'default', None) is None: - output = Executable('/bin/bash')('-lc', 'echo $CRAY_CPU_TARGET', - env={'TERM': os.environ['TERM']}, - output=str, error=os.devnull) + bash = Executable('/bin/bash') + output = bash( + '-lc', 'echo $CRAY_CPU_TARGET', + env={'TERM': os.environ.get('TERM', '')}, + output=str, + error=os.devnull + ) output = ''.join(output.split()) # remove all whitespace if output: self.default = output From d3c1a4c94bbfe95aacbc473dcc24183b04cdb29f Mon Sep 17 00:00:00 2001 From: Piotr Luszczek Date: Mon, 23 Mar 2020 01:10:15 -0400 Subject: [PATCH 186/377] xsdk-examples: add new package at version 0.1.0 (#15621) * xsdk-examples: add new package at version 0.1.0 --- .../builtin/packages/xsdk-examples/package.py | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 var/spack/repos/builtin/packages/xsdk-examples/package.py diff --git a/var/spack/repos/builtin/packages/xsdk-examples/package.py b/var/spack/repos/builtin/packages/xsdk-examples/package.py new file mode 100644 index 00000000000..418651ec72a --- /dev/null +++ b/var/spack/repos/builtin/packages/xsdk-examples/package.py @@ -0,0 +1,39 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class XsdkExamples(CMakePackage): + """xSDK Examples show usage of libraries in the xSDK package.""" + + homepage = 'http://xsdk.info' + url = 'https://github.com/xsdk-project/xsdk-examples/archive/v0.1.0.tar.gz' + + maintainers = ['acfisher', 'balay', 'balos1', 'luszczek'] + + version('0.1.0', sha256='d24cab1db7c0872b6474d69e598df9c8e25d254d09c425fb0a6a8d6469b8018f') + + depends_on('xsdk@0.5.0', when='@0.1.0') + + def cmake_args(self): + spec = self.spec + args = [ + '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc, + '-DMPI_DIR=%s' % spec['mpi'].prefix, + '-DSUNDIALS_DIR=%s' % spec['sundials'].prefix, + '-DPETSC_DIR=%s' % spec['petsc'].prefix, + '-DPETSC_INCLUDE_DIR=%s' % spec['petsc'].prefix.include, + '-DPETSC_LIBRARY_DIR=%s' % spec['petsc'].prefix.lib, + '-DSUPERLUDIST_INCLUDE_DIR=%s' % + spec['superlu-dist'].prefix.include, + '-DSUPERLUDIST_LIBRARY_DIR=%s' % spec['superlu-dist'].prefix.lib, + ] + if 'trilinos' in spec: + args.extend([ + '-DTRILINOS_DIR:PATH=%s' % spec['trilinos'].prefix, + ]) + return args From 54a6c25da637418f568b3419bd1e467ffdd0870b Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Mon, 23 Mar 2020 15:15:36 -0700 Subject: [PATCH 187/377] Bugfix (config): enable "spack test" when in an active environment (#15618) For any Spack test using Spack's YAML configuration, avoid using real Spack configuration that has been cached by other tests and Spack startup logic. Previously this was only done for tests using 'mutable_config' (i.e. those which expected to *change* the configuration of Spack), but in fact all tests that read Spack config should use it. This was an issue when running tests within an environment, because compiler configuration ends up being queried earlier, and the user's real config "leaks" into the cache. Outside an environment, the cache is never set until tests touch it, so we weren't seeing this issue. --- lib/spack/spack/test/conftest.py | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py index 67037421423..a1864639070 100644 --- a/lib/spack/spack/test/conftest.py +++ b/lib/spack/spack/test/conftest.py @@ -301,8 +301,17 @@ def use_configuration(config): """Context manager to swap out the global Spack configuration.""" saved = spack.config.config spack.config.config = config + + # Avoid using real spack configuration that has been cached by other + # tests, and avoid polluting the cache with spack test configuration + # (including modified configuration) + saved_compiler_cache = spack.compilers._cache_config_file + spack.compilers._cache_config_file = [] + yield + spack.config.config = saved + spack.compilers._cache_config_file = saved_compiler_cache @contextlib.contextmanager @@ -427,10 +436,6 @@ def mutable_config(tmpdir_factory, configuration_dir, monkeypatch): *[spack.config.ConfigScope(name, str(mutable_dir)) for name in ['site', 'system', 'user']]) - # This is essential, otherwise the cache will create weird side effects - # that will compromise subsequent tests if compilers.yaml is modified - monkeypatch.setattr(spack.compilers, '_cache_config_file', []) - with use_configuration(cfg): yield cfg From cde4375c96591a3e0297aa514fa0bcdae8be2da3 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Mon, 23 Mar 2020 16:55:07 -0700 Subject: [PATCH 188/377] Vendoring: remove dependency on Setuptools from vendored pytest (#15612) If the Python used by Spack does not include Setuptools, then 'spack test' will fail because Spack's vendored pytest dependency imports and uses Setuptools in some of its functions. It turns out that Spack doesn't use the functionality those methods enable, so this PR removes those functions and thereby allows 'spack test' to run without Setuptools. --- lib/spack/external/__init__.py | 10 +++-- lib/spack/external/_pytest/config.py | 38 ++++++------------- .../_pytest/vendored_packages/pluggy.py | 20 ---------- 3 files changed, 17 insertions(+), 51 deletions(-) diff --git a/lib/spack/external/__init__.py b/lib/spack/external/__init__.py index 27f00efb095..230ec170b26 100644 --- a/lib/spack/external/__init__.py +++ b/lib/spack/external/__init__.py @@ -88,10 +88,11 @@ * Homepage: https://pypi.python.org/pypi/pytest * Usage: Testing framework used by Spack. * Version: 3.2.5 (last version supporting Python 2.6) -* Note: This package has been slightly modified to improve - Python 2.6 compatibility. See the following commit if the - vendored copy ever needs to be updated again: - https://github.com/spack/spack/pull/6801/commits/ff513c39f2c67ff615de5cbc581dd69a8ec96526 +* Note: This package has been slightly modified: + * We improve Python 2.6 compatibility. See: + https://github.com/spack/spack/pull/6801. + * We have patched pytest not to depend on setuptools. See: + https://github.com/spack/spack/pull/15612 ruamel.yaml ------ @@ -125,4 +126,5 @@ * Homepage: https://altgraph.readthedocs.io/en/latest/index.html * Usage: dependency of macholib * Version: 0.16.1 + """ diff --git a/lib/spack/external/_pytest/config.py b/lib/spack/external/_pytest/config.py index 19835d2c39f..513478a972f 100644 --- a/lib/spack/external/_pytest/config.py +++ b/lib/spack/external/_pytest/config.py @@ -1028,34 +1028,13 @@ def _consider_importhook(self, args): except SystemError: mode = 'plain' else: - self._mark_plugins_for_rewrite(hook) + # REMOVED FOR SPACK: This routine imports `pkg_resources` from + # `setuptools`, but we do not need it for Spack. We have removed + # it from Spack to avoid a dependency on setuptools. + # self._mark_plugins_for_rewrite(hook) + pass self._warn_about_missing_assertion(mode) - def _mark_plugins_for_rewrite(self, hook): - """ - Given an importhook, mark for rewrite any top-level - modules or packages in the distribution package for - all pytest plugins. - """ - import pkg_resources - self.pluginmanager.rewrite_hook = hook - - # 'RECORD' available for plugins installed normally (pip install) - # 'SOURCES.txt' available for plugins installed in dev mode (pip install -e) - # for installed plugins 'SOURCES.txt' returns an empty list, and vice-versa - # so it shouldn't be an issue - metadata_files = 'RECORD', 'SOURCES.txt' - - package_files = ( - entry.split(',')[0] - for entrypoint in pkg_resources.iter_entry_points('pytest11') - for metadata in metadata_files - for entry in entrypoint.dist._get_metadata(metadata) - ) - - for name in _iter_rewritable_modules(package_files): - hook.mark_rewrite(name) - def _warn_about_missing_assertion(self, mode): try: assert False @@ -1081,7 +1060,12 @@ def _preparse(self, args, addopts=True): self._checkversion() self._consider_importhook(args) self.pluginmanager.consider_preparse(args) - self.pluginmanager.load_setuptools_entrypoints('pytest11') + + # REMOVED FOR SPACK: This routine imports `pkg_resources` from + # `setuptools`, but we do not need it for Spack. We have removed + # it from Spack to avoid a dependency on setuptools. + # self.pluginmanager.load_setuptools_entrypoints('pytest11') + self.pluginmanager.consider_env() self.known_args_namespace = ns = self._parser.parse_known_args(args, namespace=self.option.copy()) if self.known_args_namespace.confcutdir is None and self.inifile: diff --git a/lib/spack/external/_pytest/vendored_packages/pluggy.py b/lib/spack/external/_pytest/vendored_packages/pluggy.py index aebddad01da..6f26552d73b 100644 --- a/lib/spack/external/_pytest/vendored_packages/pluggy.py +++ b/lib/spack/external/_pytest/vendored_packages/pluggy.py @@ -497,26 +497,6 @@ def check_pending(self): "unknown hook %r in plugin %r" % (name, hookimpl.plugin)) - def load_setuptools_entrypoints(self, entrypoint_name): - """ Load modules from querying the specified setuptools entrypoint name. - Return the number of loaded plugins. """ - from pkg_resources import (iter_entry_points, DistributionNotFound, - VersionConflict) - for ep in iter_entry_points(entrypoint_name): - # is the plugin registered or blocked? - if self.get_plugin(ep.name) or self.is_blocked(ep.name): - continue - try: - plugin = ep.load() - except DistributionNotFound: - continue - except VersionConflict as e: - raise PluginValidationError( - "Plugin %r could not be loaded: %s!" % (ep.name, e)) - self.register(plugin, name=ep.name) - self._plugin_distinfo.append((plugin, ep.dist)) - return len(self._plugin_distinfo) - def list_plugin_distinfo(self): """ return list of distinfo/plugin tuples for all setuptools registered plugins. """ From e1f593b6c6297503f9babf4978d2633f966b838c Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Mon, 23 Mar 2020 19:02:46 -0500 Subject: [PATCH 189/377] lmod: add version 7.8.1 (#15643) --- var/spack/repos/builtin/packages/lmod/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py index 146ef9e3b4e..cf22c80aa27 100644 --- a/var/spack/repos/builtin/packages/lmod/package.py +++ b/var/spack/repos/builtin/packages/lmod/package.py @@ -24,6 +24,7 @@ class Lmod(AutotoolsPackage): version('8.1.5', sha256='3e5846d3d8e593cbcdfa0aed1474569bf5b5cfd19fd288de22051823d449d344') version('8.0.9', sha256='9813c22ae4dd21eb3dc480f6ce307156512092b4bca954bf8aacc15944f23673') version('7.8.15', sha256='00a257f5073d656adc73045997c28f323b7a4f6d901f1c57b7db2b0cd6bee6e6') + version('7.8.1', sha256='74244c22cecd72777e75631f357d2e20ff7f2b9c2ef59e4e38b5a171b7b6eeea') version('7.8', sha256='40388380a36a00c3ce929a9f88c8fffc93deeabf87a7c3f8864a82acad38c3ba') version('7.7.29', sha256='269235d07d8ea387a2578f90bb64cf8ad16b4f28dcce196b293eb48cf1f71fb4') version('7.7.13', sha256='6145f075e5d49e12fcf0e75bb38afb27f205d23ba3496c1ff6c8b2cbaa9908be') From 6a18bfbae813d9c9df52fb0c737c9a4308215cc0 Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Mon, 23 Mar 2020 19:03:25 -0500 Subject: [PATCH 190/377] CMake: add version 3.9.2 (#15644) --- var/spack/repos/builtin/packages/cmake/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index 994ed42392e..444a22e52a5 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -50,6 +50,7 @@ class Cmake(Package): version('3.10.0', sha256='b3345c17609ea0f039960ef470aa099de9942135990930a57c14575aae884987') version('3.9.6', sha256='7410851a783a41b521214ad987bb534a7e4a65e059651a2514e6ebfc8f46b218') version('3.9.4', sha256='b5d86f12ae0072db520fdbdad67405f799eb728b610ed66043c20a92b4906ca1') + version('3.9.2', sha256='954a5801a456ee48e76f01107c9a4961677dd0f3e115275bbd18410dc22ba3c1') version('3.9.0', sha256='167701525183dbb722b9ffe69fb525aa2b81798cf12f5ce1c020c93394dfae0f') version('3.8.2', sha256='da3072794eb4c09f2d782fcee043847b99bb4cf8d4573978d9b2024214d6e92d') version('3.8.1', sha256='ce5d9161396e06501b00e52933783150a87c33080d4bdcef461b5b7fd24ac228') From 7b486fd84dfca220b1415fa2956a8c4bc32dc470 Mon Sep 17 00:00:00 2001 From: Andreas Baumbach Date: Mon, 23 Mar 2020 09:49:54 +0100 Subject: [PATCH 191/377] py-ics: add version 0.7 --- var/spack/repos/builtin/packages/py-ics/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/py-ics/package.py b/var/spack/repos/builtin/packages/py-ics/package.py index 7c91e2c5ff0..c2c4a71346a 100644 --- a/var/spack/repos/builtin/packages/py-ics/package.py +++ b/var/spack/repos/builtin/packages/py-ics/package.py @@ -29,6 +29,7 @@ class PyIcs(PythonPackage): homepage = "https://github.com/C4ptainCrunch/ics.py" url = "https://github.com/C4ptainCrunch/ics.py/archive/v0.6.tar.gz" + version('0.7', sha256='48c637e5eb8dfc817b1f3f6b3f662ba19cfcc25f8f71eb42f5d07e6f2c573994') version('0.6', sha256='4947263136202d0489d4f5e5c7175dfd2db5d3508b8b003ddeaef96347f68830') depends_on('python@3.6:', type=('build', 'run')) From 82830684381b8bbd6c4b95a3cfee03f616e74d51 Mon Sep 17 00:00:00 2001 From: Peter Scheibel Date: Mon, 23 Mar 2020 18:10:44 -0700 Subject: [PATCH 192/377] Bugfix: remove unit tests that install real packages (#15646) Our unit tests run many times. Any unit test which actually installs a package (which involves fetching code on the internet) is a severe bug because it runs an installation many times (i.e. re-downloading the same package for each version of Python that we run unit tests for). This reverts commit 25893f1, which added tests that install real packages. --- lib/spack/spack/test/bindist.py | 480 -------------------------------- 1 file changed, 480 deletions(-) delete mode 100644 lib/spack/spack/test/bindist.py diff --git a/lib/spack/spack/test/bindist.py b/lib/spack/spack/test/bindist.py deleted file mode 100644 index 8ca7609942d..00000000000 --- a/lib/spack/spack/test/bindist.py +++ /dev/null @@ -1,480 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -""" -This test checks creating and install buildcaches -""" -import os -import py -import pytest -import argparse -import platform -import spack.repo -import spack.store -import spack.binary_distribution as bindist -import spack.cmd.buildcache as buildcache -import spack.cmd.compiler as compiler -import spack.cmd.repo as repocmd -import spack.cmd.install as install -import spack.cmd.uninstall as uninstall -import spack.cmd.mirror as mirror -from spack.spec import Spec -from spack.directory_layout import YamlDirectoryLayout - - -def_install_path_scheme = '${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}' # noqa: E501 -ndef_install_path_scheme = '${PACKAGE}/${VERSION}/${ARCHITECTURE}-${COMPILERNAME}-${COMPILERVER}-${HASH}' # noqa: E501 - -mirror_path_def = None -mirror_path_rel = None - - -@pytest.fixture(scope='function') -def cache_directory(tmpdir): - old_cache_path = spack.caches.fetch_cache - tmpdir.ensure('fetch_cache', dir=True) - fsc = spack.fetch_strategy.FsCache(str(tmpdir.join('fetch_cache'))) - spack.config.caches = fsc - yield spack.config.caches - tmpdir.join('fetch_cache').remove() - spack.config.caches = old_cache_path - - -@pytest.fixture(scope='session') -def session_mirror_def(tmpdir_factory): - dir = tmpdir_factory.mktemp('mirror') - global mirror_path_rel - mirror_path_rel = dir - dir.ensure('build_cache', dir=True) - yield dir - dir.join('build_cache').remove() - - -@pytest.fixture(scope='function') -def mirror_directory_def(session_mirror_def): - yield str(session_mirror_def) - - -@pytest.fixture(scope='session') -def session_mirror_rel(tmpdir_factory): - dir = tmpdir_factory.mktemp('mirror') - global mirror_path_rel - mirror_path_rel = dir - dir.ensure('build_cache', dir=True) - yield dir - dir.join('build_cache').remove() - - -@pytest.fixture(scope='function') -def mirror_directory_rel(session_mirror_rel): - yield(session_mirror_rel) - - -@pytest.fixture(scope='session') -def config_directory(tmpdir_factory): - tmpdir = tmpdir_factory.mktemp('test_configs') - # restore some sane defaults for packages and config - config_path = py.path.local(spack.paths.etc_path) - modules_yaml = config_path.join('spack', 'defaults', 'modules.yaml') - os_modules_yaml = config_path.join('spack', 'defaults', '%s' % - platform.system().lower(), - 'modules.yaml') - packages_yaml = config_path.join('spack', 'defaults', 'packages.yaml') - config_yaml = config_path.join('spack', 'defaults', 'config.yaml') - repos_yaml = config_path.join('spack', 'defaults', 'repos.yaml') - tmpdir.ensure('site', dir=True) - tmpdir.ensure('user', dir=True) - tmpdir.ensure('site/%s' % platform.system().lower(), dir=True) - modules_yaml.copy(tmpdir.join('site', 'modules.yaml')) - os_modules_yaml.copy(tmpdir.join('site/%s' % platform.system().lower(), - 'modules.yaml')) - packages_yaml.copy(tmpdir.join('site', 'packages.yaml')) - config_yaml.copy(tmpdir.join('site', 'config.yaml')) - repos_yaml.copy(tmpdir.join('site', 'repos.yaml')) - yield tmpdir - tmpdir.remove() - - -@pytest.fixture(scope='function') -def default_config(tmpdir_factory, config_directory, monkeypatch): - - mutable_dir = tmpdir_factory.mktemp('mutable_config').join('tmp') - config_directory.copy(mutable_dir) - - cfg = spack.config.Configuration( - *[spack.config.ConfigScope(name, str(mutable_dir)) - for name in ['site/%s' % platform.system().lower(), - 'site', 'user']]) - - monkeypatch.setattr(spack.config, 'config', cfg) - - # This is essential, otherwise the cache will create weird side effects - # that will compromise subsequent tests if compilers.yaml is modified - monkeypatch.setattr(spack.compilers, '_cache_config_file', []) - njobs = spack.config.get('config:build_jobs') - if not njobs: - spack.config.set('config:build_jobs', 4, scope='user') - extensions = spack.config.get('config:template_dirs') - if not extensions: - spack.config.set('config:template_dirs', - [os.path.join(spack.paths.share_path, 'templates')], - scope='user') - - mutable_dir.ensure('build_stage', dir=True) - build_stage = spack.config.get('config:build_stage') - if not build_stage: - spack.config.set('config:build_stage', - [str(mutable_dir.join('build_stage'))], scope='user') - timeout = spack.config.get('config:connect_timeout') - if not timeout: - spack.config.set('config:connect_timeout', 10, scope='user') - print(spack.config.config) - yield spack.config.config - mutable_dir.remove() - - -@pytest.fixture(scope='function') -def install_dir_default_layout(tmpdir): - """Hooks a fake install directory with a default layout""" - real_store = spack.store.store - real_layout = spack.store.layout - spack.store.store = spack.store.Store(str(tmpdir.join('opt'))) - spack.store.layout = YamlDirectoryLayout(str(tmpdir.join('opt')), - path_scheme=def_install_path_scheme) # noqa: E501 - yield spack.store - tmpdir.join('opt').remove() - spack.store.store = real_store - spack.store.layout = real_layout - - -@pytest.fixture(scope='function') -def install_dir_non_default_layout(tmpdir): - """Hooks a fake install directory with a non-default layout""" - real_store = spack.store.store - real_layout = spack.store.layout - spack.store.store = spack.store.Store(str(tmpdir.join('opt'))) - spack.store.layout = YamlDirectoryLayout(str(tmpdir.join('opt')), - path_scheme=ndef_install_path_scheme) # noqa: E501 - yield spack.store - tmpdir.join('opt').remove() - spack.store.store = real_store - spack.store.layout = real_layout - - -@pytest.fixture(scope='session') -def config_setup(): - cparser = argparse.ArgumentParser() - compiler.setup_parser(cparser) - cargs = cparser.parse_args(['add', '--scope', 'site']) - compiler.compiler(cparser, cargs) - cargs = cparser.parse_args(['list', '--scope', 'site']) - compiler.compiler(cparser, cargs) - - rparser = argparse.ArgumentParser() - repocmd.setup_parser(rparser) - rargs = rparser.parse_args(['add', spack.paths.packages_path]) - repocmd.repo(rparser, rargs) - # Set some spec name used globally - zspec = Spec('zlib') - zspec.concretize() - espec = Spec('environment-modules') - espec.concretize() - pspec = Spec('patchelf') - pspec.concretize() - - yield espec, zspec, pspec - - -@pytest.mark.disable_clean_stage_check -@pytest.mark.maybeslow -@pytest.mark.usefixtures('default_config', 'cache_directory', - 'install_dir_default_layout') -def test_default_rpaths_create_install_default_layout(tmpdir, - mirror_directory_def, - config_setup, - mock_stage): - """ - Test the creation and installation of buildcaches with default rpaths - into the default directory layout scheme. - """ - tspec, zspec, pspec = config_setup - # Install patchelf needed for relocate in linux test environment - # Install some packages with dependent packages - iparser = argparse.ArgumentParser() - install.setup_parser(iparser) - if platform.system().lower() != 'darwin': - iargs = iparser.parse_args(['--no-cache', pspec.name]) - install.install(iparser, iargs) - iargs = iparser.parse_args(['--no-cache', tspec.name]) - install.install(iparser, iargs) - - global mirror_path_def - mirror_path_def = mirror_directory_def - mparser = argparse.ArgumentParser() - mirror.setup_parser(mparser) - margs = mparser.parse_args( - ['add', '--scope', 'site', 'test-mirror-def', 'file://%s' % mirror_path_def]) - mirror.mirror(mparser, margs) - margs = mparser.parse_args(['list']) - mirror.mirror(mparser, margs) - - # setup argument parser - parser = argparse.ArgumentParser() - buildcache.setup_parser(parser) - - # Set default buildcache args - create_args = ['create', '-a', '-u', '-d', str(mirror_path_def), - tspec.name] - install_args = ['install', '-a', '-u', tspec.name] - - # Create a buildache of patchelf - if platform.system().lower() != 'darwin': - args = parser.parse_args(['create', '-a', '-u', '-d', - str(mirror_path_def), - pspec.name]) - buildcache.buildcache(parser, args) - - # Create a buildache - args = parser.parse_args(create_args) - buildcache.buildcache(parser, args) - # Test force overwrite create buildcache - create_args.insert(create_args.index('-a'), '-f') - args = parser.parse_args(create_args) - buildcache.buildcache(parser, args) - # list the buildcaches in the mirror - args = parser.parse_args(['list', '-f', '-l', '-v']) - buildcache.buildcache(parser, args) - - # Uninstall the package and deps - uparser = argparse.ArgumentParser() - uninstall.setup_parser(uparser) - uargs = uparser.parse_args(['-y', '--dependents', zspec.name]) - uninstall.uninstall(uparser, uargs) - - # test install - args = parser.parse_args(install_args) - buildcache.buildcache(parser, args) - - # This gives warning that spec is already installed - buildcache.buildcache(parser, args) - - # test overwrite install - install_args.insert(install_args.index('-a'), '-f') - args = parser.parse_args(install_args) - buildcache.buildcache(parser, args) - - args = parser.parse_args(['keys', '-f']) - buildcache.buildcache(parser, args) - - args = parser.parse_args(['list']) - buildcache.buildcache(parser, args) - - args = parser.parse_args(['list', '-f']) - buildcache.buildcache(parser, args) - - args = parser.parse_args(['list', '-l', '-v']) - buildcache.buildcache(parser, args) - bindist._cached_specs = set() - spack.stage.purge() - - -@pytest.mark.disable_clean_stage_check -@pytest.mark.maybeslow -@pytest.mark.nomockstage -@pytest.mark.usefixtures('default_config', 'cache_directory', - 'install_dir_non_default_layout') -def test_default_rpaths_install_nondefault_layout(tmpdir, config_setup, - mock_stage): - """ - Test the creation and installation of buildcaches with default rpaths - into the non-default directory layout scheme. - """ - tspec, zspec, pspec = config_setup - global mirror_path_def - mparser = argparse.ArgumentParser() - mirror.setup_parser(mparser) - margs = mparser.parse_args( - ['add', '--scope', 'site', 'test-mirror-def', 'file://%s' % mirror_path_def]) - mirror.mirror(mparser, margs) - - # setup argument parser - parser = argparse.ArgumentParser() - buildcache.setup_parser(parser) - - # Set default buildcache args - install_args = ['install', '-a', '-u', tspec.name] - - # Install patchelf needed for relocate in linux test environment - if platform.system().lower() != 'darwin': - args = parser.parse_args(['install', '-a', '-u', pspec.name]) - buildcache.buildcache(parser, args) - - # Install some packages with dependent packages - # test install in non-default install path scheme - args = parser.parse_args(install_args) - buildcache.buildcache(parser, args) - # test force install in non-default install path scheme - install_args.insert(install_args.index('-a'), '-f') - args = parser.parse_args(install_args) - buildcache.buildcache(parser, args) - - bindist._cached_specs = set() - spack.stage.purge() - - -@pytest.mark.disable_clean_stage_check -@pytest.mark.maybeslow -@pytest.mark.nomockstage -@pytest.mark.usefixtures('default_config', 'cache_directory', - 'install_dir_default_layout') -def test_relative_rpaths_create_default_layout(tmpdir, mirror_directory_rel, - config_setup, mock_stage): - """ - Test the creation and installation of buildcaches with relative - rpaths into the default directory layout scheme. - """ - tspec, zspec, pspec = config_setup - global mirror_path_rel - global mirror_path_def - mirror_path_rel = mirror_directory_rel - mparser = argparse.ArgumentParser() - mirror.setup_parser(mparser) - margs = mparser.parse_args( - ['add', '--scope', 'site', 'test-mirror-def', 'file://%s' % mirror_path_def]) - mirror.mirror(mparser, margs) - # setup argument parser - parser = argparse.ArgumentParser() - buildcache.setup_parser(parser) - - # install patchelf buildcache on linux - if platform.system().lower() != 'darwin': - args = parser.parse_args(['install', '-a', '-u', pspec.name]) - buildcache.buildcache(parser, args) - - # set default buildcache args - create_args = ['create', '-a', '-u', '-r', '-d', - str(mirror_path_rel), - tspec.name] - install_args = ['install', '-a', '-u', - tspec.name] - - # Create a buildache of patchelf - if platform.system().lower() != 'darwin': - args = parser.parse_args(['create', '-a', '-u', '-d', - str(mirror_path_rel), pspec.name]) - buildcache.buildcache(parser, args) - - # install buildcache created with default rpaths - args = parser.parse_args(install_args) - buildcache.buildcache(parser, args) - - # create build cache with relatived rpaths - args = parser.parse_args(create_args) - buildcache.buildcache(parser, args) - - # Uninstall the package and deps - uparser = argparse.ArgumentParser() - uninstall.setup_parser(uparser) - uargs = uparser.parse_args(['-y', '--dependents', zspec.name]) - uninstall.uninstall(uparser, uargs) - - bindist._cached_specs = set() - spack.stage.purge() - - -@pytest.mark.disable_clean_stage_check -@pytest.mark.maybeslow -@pytest.mark.nomockstage -@pytest.mark.usefixtures('default_config', 'cache_directory', - 'install_dir_default_layout') -def test_relative_rpaths_install_default_layout(tmpdir, config_setup, - mock_stage): - """ - Test the creation and installation of buildcaches with relative - rpaths into the default directory layout scheme. - """ - tspec, zspec, pspec = config_setup - global mirror_path_rel - mparser = argparse.ArgumentParser() - mirror.setup_parser(mparser) - margs = mparser.parse_args( - ['add', '--scope', 'site', 'test-mirror-rel', 'file://%s' % mirror_path_rel]) - mirror.mirror(mparser, margs) - - # setup argument parser - parser = argparse.ArgumentParser() - buildcache.setup_parser(parser) - - # install patchelf buildcache on linux - if platform.system().lower() != 'darwin': - args = parser.parse_args(['install', '-a', '-u', pspec.name]) - buildcache.buildcache(parser, args) - - # set default buildcache args - install_args = ['install', '-a', '-u', - tspec.name] - - # install buildcache created with relativized rpaths - args = parser.parse_args(install_args) - buildcache.buildcache(parser, args) - - # This gives warning that spec is already installed - buildcache.buildcache(parser, args) - - # Uninstall the package and deps - uparser = argparse.ArgumentParser() - uninstall.setup_parser(uparser) - uargs = uparser.parse_args(['-y', '--dependents', zspec.name]) - uninstall.uninstall(uparser, uargs) - - # install build cache - buildcache.buildcache(parser, args) - - # test overwrite install - install_args.insert(install_args.index('-a'), '-f') - args = parser.parse_args(install_args) - buildcache.buildcache(parser, args) - - bindist._cached_specs = set() - spack.stage.purge() - - -@pytest.mark.disable_clean_stage_check -@pytest.mark.maybeslow -@pytest.mark.nomockstage -@pytest.mark.usefixtures('default_config', 'cache_directory', - 'install_dir_non_default_layout') -def test_relative_rpaths_install_nondefault(tmpdir, config_setup, - mock_stage): - """ - Test the installation of buildcaches with relativized rpaths - into the non-default directory layout scheme. - """ - tspec, zspec, pspec = config_setup - global mirror_path_rel - mparser = argparse.ArgumentParser() - mirror.setup_parser(mparser) - margs = mparser.parse_args( - ['add', '--scope', 'site', 'test-mirror-rel', 'file://%s' % mirror_path_rel]) - mirror.mirror(mparser, margs) - - # setup argument parser - parser = argparse.ArgumentParser() - buildcache.setup_parser(parser) - - # Set default buildcache args - install_args = ['install', '-a', '-u', tspec.name] - - # Install patchelf needed for relocate in linux test environment - if platform.system().lower() != 'darwin': - args = parser.parse_args(['install', '-a', '-u', pspec.name]) - buildcache.buildcache(parser, args) - - # test install in non-default install path scheme and relative path - args = parser.parse_args(install_args) - buildcache.buildcache(parser, args) - - bindist._cached_specs = set() - spack.stage.purge() From 7e0ec0ec097503c33b842d15d6a5b84c98068c1b Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Sun, 22 Mar 2020 20:12:23 +0100 Subject: [PATCH 193/377] automake: Add 1.16.2 --- var/spack/repos/builtin/packages/automake/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py index aa5d16de5d3..5327c90daf5 100644 --- a/var/spack/repos/builtin/packages/automake/package.py +++ b/var/spack/repos/builtin/packages/automake/package.py @@ -12,6 +12,7 @@ class Automake(AutotoolsPackage, GNUMirrorPackage): homepage = 'http://www.gnu.org/software/automake/' gnu_mirror_path = 'automake/automake-1.15.tar.gz' + version('1.16.2', sha256='b2f361094b410b4acbf4efba7337bdb786335ca09eb2518635a09fb7319ca5c1') version('1.16.1', sha256='608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8') version('1.15.1', sha256='988e32527abe052307d21c8ca000aa238b914df363a617e38f4fb89f5abf6260') version('1.15', sha256='7946e945a96e28152ba5a6beb0625ca715c6e32ac55f2e353ef54def0c8ed924') From 1b4de7813a64f81c65256b98894aba7af86976d7 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Tue, 24 Mar 2020 09:02:54 +0100 Subject: [PATCH 194/377] spack.relocate: add unit test (#15610) * relocate: removed import from statements * relocate: renamed *Exception to *Error This aims at consistency in naming with both the standard library (ValueError, AttributeError, etc.) and other errors in 'spack.error'. Improved existing docstrings * relocate: simplified search function by un-nesting conditionals The search function that searches for patchelf has been refactored to remove deeply nested conditionals. Extended docstring. * relocate: removed a condition specific to unit tests * relocate: added test for _patchelf --- lib/spack/spack/relocate.py | 138 +++++++++++++++++-------------- lib/spack/spack/test/relocate.py | 59 ++++++++++++- 2 files changed, 130 insertions(+), 67 deletions(-) diff --git a/lib/spack/spack/relocate.py b/lib/spack/spack/relocate.py index c7d442a427a..9f8669f3d45 100644 --- a/lib/spack/spack/relocate.py +++ b/lib/spack/spack/relocate.py @@ -2,55 +2,63 @@ # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) - - import os +import platform import re import shutil -import platform -import spack.repo -import spack.cmd + import llnl.util.lang -from spack.util.executable import Executable, ProcessError import llnl.util.tty as tty -from macholib.MachO import MachO -from spack.spec import Spec +import macholib.MachO import macholib.mach_o +import spack.cmd +import spack.repo +import spack.spec +import spack.util.executable as executable -class InstallRootStringException(spack.error.SpackError): - """ - Raised when the relocated binary still has the install root string. - """ - +class InstallRootStringError(spack.error.SpackError): def __init__(self, file_path, root_path): - super(InstallRootStringException, self).__init__( + """Signal that the relocated binary still has the original + Spack's store root string + + Args: + file_path (str): path of the binary + root_path (str): original Spack's store root string + """ + super(InstallRootStringError, self).__init__( "\n %s \ncontains string\n %s \n" "after replacing it in rpaths.\n" "Package should not be relocated.\n Use -a to override." % (file_path, root_path)) -class BinaryStringReplacementException(spack.error.SpackError): - """ - Raised when the size of the file changes after binary path substitution. - """ - +class BinaryStringReplacementError(spack.error.SpackError): def __init__(self, file_path, old_len, new_len): - super(BinaryStringReplacementException, self).__init__( + """The size of the file changed after binary path substitution + + Args: + file_path (str): file with changing size + old_len (str): original length of the file + new_len (str): length of the file after substitution + """ + super(BinaryStringReplacementError, self).__init__( "Doing a binary string replacement in %s failed.\n" "The size of the file changed from %s to %s\n" "when it should have remanined the same." % (file_path, old_len, new_len)) -class BinaryTextReplaceException(spack.error.SpackError): - """ - Raised when the new install path is shorter than the old install path - so binary text replacement cannot occur. - """ - +class BinaryTextReplaceError(spack.error.SpackError): def __init__(self, old_path, new_path): + """Raised when the new install path is longer than the + old one, so binary text replacement cannot occur. + + Args: + old_path (str): original path to be substituted + new_path (str): candidate path for substitution + """ + msg = "New path longer than old path: binary text" msg += " replacement not possible." err_msg = "The new path %s" % new_path @@ -58,33 +66,35 @@ def __init__(self, old_path, new_path): err_msg += "Text replacement in binaries will not work.\n" err_msg += "Create buildcache from an install path " err_msg += "longer than new path." - super(BinaryTextReplaceException, self).__init__(msg, err_msg) + super(BinaryTextReplaceError, self).__init__(msg, err_msg) -def get_patchelf(): +def _patchelf(): + """Return the full path to the patchelf binary, if available, else None. + + Search first the current PATH for patchelf. If not found, try to look + if the default patchelf spec is installed and if not install it. + + Return None on Darwin or if patchelf cannot be found. """ - Returns the full patchelf binary path if available in $PATH. - Builds and installs spack patchelf package on linux platforms - using the first concretized spec if it is not installed and - returns the full patchelf binary path. - """ - # as we may need patchelf, find out where it is + # Check if patchelf is already in the PATH patchelf = spack.util.executable.which('patchelf') if patchelf is not None: return patchelf.path - patchelf_spec = Spec('patchelf').concretized() - patchelf = patchelf_spec.package - if patchelf.installed: - patchelf_executable = os.path.join(patchelf.prefix.bin, "patchelf") - return patchelf_executable - else: - if (str(spack.architecture.platform()) == 'test' or - str(spack.architecture.platform()) == 'darwin'): - return None - else: - patchelf.do_install() - patchelf_executable = os.path.join(patchelf.prefix.bin, "patchelf") - return patchelf_executable + + # Check if patchelf spec is installed + spec = spack.spec.Spec('patchelf').concretized() + exe_path = os.path.join(spec.prefix.bin, "patchelf") + if spec.package.installed and os.path.exists(exe_path): + return exe_path + + # Skip darwin + if str(spack.architecture.platform()) == 'darwin': + return None + + # Install the spec and return its path + spec.package.do_install() + return exe_path if os.path.exists(exe_path) else None def get_existing_elf_rpaths(path_name): @@ -95,17 +105,17 @@ def get_existing_elf_rpaths(path_name): # if we're relocating patchelf itself, use it - if path_name[-13:] == "/bin/patchelf": - patchelf = Executable(path_name) + if path_name.endswith("/bin/patchelf"): + patchelf = executable.Executable(path_name) else: - patchelf = Executable(get_patchelf()) + patchelf = executable.Executable(_patchelf()) rpaths = list() try: output = patchelf('--print-rpath', '%s' % path_name, output=str, error=str) rpaths = output.rstrip('\n').split(':') - except ProcessError as e: + except executable.ProcessError as e: msg = 'patchelf --print-rpath %s produced an error %s' % (path_name, e) tty.warn(msg) return rpaths @@ -266,7 +276,7 @@ def modify_macho_object(cur_path, rpaths, deps, idpath, # avoid error message for libgcc_s if 'libgcc_' in cur_path: return - install_name_tool = Executable('install_name_tool') + install_name_tool = executable.Executable('install_name_tool') if idpath: new_idpath = paths_to_paths.get(idpath, None) @@ -295,7 +305,7 @@ def modify_object_macholib(cur_path, paths_to_paths): dictionary mapping paths in old install layout to new install layout """ - dll = MachO(cur_path) + dll = macholib.MachO.MachO(cur_path) changedict = paths_to_paths @@ -324,7 +334,7 @@ def macholib_get_paths(cur_path): Get rpaths, dependencies and id of mach-o objects using python macholib package """ - dll = MachO(cur_path) + dll = macholib.MachO.MachO(cur_path) ident = None rpaths = list() @@ -359,14 +369,14 @@ def modify_elf_object(path_name, new_rpaths): if path_name[-13:] == "/bin/patchelf": shutil.copy(path_name, bak_path) - patchelf = Executable(bak_path) + patchelf = executable.Executable(bak_path) else: - patchelf = Executable(get_patchelf()) + patchelf = executable.Executable(_patchelf()) try: patchelf('--force-rpath', '--set-rpath', '%s' % new_joined, '%s' % path_name, output=str, error=str) - except ProcessError as e: + except executable.ProcessError as e: msg = 'patchelf --force-rpath --set-rpath %s failed with error %s' % ( path_name, e) tty.warn(msg) @@ -443,7 +453,7 @@ def replace(match): return ndata = pat.sub(replace, data) if not len(ndata) == original_data_len: - raise BinaryStringReplacementException( + raise BinaryStringReplacementError( path_name, original_data_len, len(ndata)) f.write(ndata) f.truncate() @@ -468,7 +478,7 @@ def replace(match): new_dir.encode('utf-8')) + b'\0' * padding if len(new_dir) > len(old_dir): - raise BinaryTextReplaceException(old_dir, new_dir) + raise BinaryTextReplaceError(old_dir, new_dir) with open(path_name, 'rb+') as f: data = f.read() @@ -479,7 +489,7 @@ def replace(match): return ndata = pat.sub(replace, data) if not len(ndata) == original_data_len: - raise BinaryStringReplacementException( + raise BinaryStringReplacementError( path_name, original_data_len, len(ndata)) f.write(ndata) f.truncate() @@ -656,7 +666,7 @@ def check_files_relocatable(cur_path_names, allow_root): for cur_path in cur_path_names: if (not allow_root and not file_is_relocatable(cur_path)): - raise InstallRootStringException( + raise InstallRootStringError( cur_path, spack.store.layout.root) @@ -725,7 +735,7 @@ def relocate_text_bin(path_names, old_layout_root, new_layout_root, replace_prefix_bin(path_name, old_spack_prefix, new_spack_prefix) else: if len(path_names) > 0: - raise BinaryTextReplaceException( + raise BinaryTextReplaceError( old_install_prefix, new_install_prefix) @@ -789,7 +799,7 @@ def file_is_relocatable(file, paths_to_relocate=None): if not os.path.isabs(file): raise ValueError('{0} is not an absolute path'.format(file)) - strings = Executable('strings') + strings = executable.Executable('strings') # Remove the RPATHS from the strings in the executable set_of_strings = set(strings(file, output=str).split()) @@ -851,7 +861,7 @@ def mime_type(file): Returns: Tuple containing the MIME type and subtype """ - file_cmd = Executable('file') + file_cmd = executable.Executable('file') output = file_cmd('-b', '-h', '--mime-type', file, output=str, error=str) tty.debug('[MIME_TYPE] {0} -> {1}'.format(file, output.strip())) # In corner cases the output does not contain a subtype prefixed with a / diff --git a/lib/spack/spack/test/relocate.py b/lib/spack/spack/test/relocate.py index 113bdcf66aa..0a9e9f7f0a3 100644 --- a/lib/spack/spack/test/relocate.py +++ b/lib/spack/spack/test/relocate.py @@ -3,15 +3,18 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import collections import os.path import platform import shutil -import pytest - import llnl.util.filesystem +import pytest +import spack.architecture +import spack.concretize import spack.paths import spack.relocate +import spack.spec import spack.store import spack.tengine import spack.util.executable @@ -45,6 +48,47 @@ def source_file(tmpdir, is_relocatable): return src +@pytest.fixture(params=['which_found', 'installed', 'to_be_installed']) +def expected_patchelf_path(request, mutable_database, monkeypatch): + """Prepare the stage to tests different cases that can occur + when searching for patchelf. + """ + case = request.param + + # Mock the which function + which_fn = { + 'which_found': lambda x: collections.namedtuple( + '_', ['path'] + )('/usr/bin/patchelf') + } + monkeypatch.setattr( + spack.util.executable, 'which', + which_fn.setdefault(case, lambda x: None) + ) + if case == 'which_found': + return '/usr/bin/patchelf' + + # TODO: Mock a case for Darwin architecture + + spec = spack.spec.Spec('patchelf') + spec.concretize() + + patchelf_cls = type(spec.package) + do_install = patchelf_cls.do_install + expected_path = os.path.join(spec.prefix.bin, 'patchelf') + + def do_install_mock(self, **kwargs): + do_install(self, fake=True) + with open(expected_path): + pass + + monkeypatch.setattr(patchelf_cls, 'do_install', do_install_mock) + if case == 'installed': + spec.package.do_install() + + return expected_path + + @pytest.mark.requires_executables( '/usr/bin/gcc', 'patchelf', 'strings', 'file' ) @@ -64,7 +108,7 @@ def test_file_is_relocatable(source_file, is_relocatable): 'patchelf', 'strings', 'file' ) def test_patchelf_is_relocatable(): - patchelf = spack.relocate.get_patchelf() + patchelf = spack.relocate._patchelf() assert llnl.util.filesystem.is_exe(patchelf) assert spack.relocate.file_is_relocatable(patchelf) @@ -87,3 +131,12 @@ def test_file_is_relocatable_errors(tmpdir): with pytest.raises(ValueError) as exc_info: spack.relocate.file_is_relocatable('delete.me') assert 'is not an absolute path' in str(exc_info.value) + + +@pytest.mark.skipif( + platform.system().lower() != 'linux', + reason='implementation for MacOS still missing' +) +def test_search_patchelf(expected_patchelf_path): + current = spack.relocate._patchelf() + assert current == expected_patchelf_path From dfe4e980ea8366e5566dfbdfde7b635f4dce68fd Mon Sep 17 00:00:00 2001 From: "Tomoki, Karatsu" <49965247+t-karatsu@users.noreply.github.com> Date: Tue, 24 Mar 2020 17:56:39 +0900 Subject: [PATCH 195/377] py-onnx: remove_dllexport_decl. (#15648) --- var/spack/repos/builtin/packages/py-onnx/package.py | 3 +++ .../packages/py-onnx/remove_dllexport_decl.patch | 11 +++++++++++ 2 files changed, 14 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-onnx/remove_dllexport_decl.patch diff --git a/var/spack/repos/builtin/packages/py-onnx/package.py b/var/spack/repos/builtin/packages/py-onnx/package.py index fd6d6b0b6db..c6401d8b007 100644 --- a/var/spack/repos/builtin/packages/py-onnx/package.py +++ b/var/spack/repos/builtin/packages/py-onnx/package.py @@ -28,3 +28,6 @@ class PyOnnx(PythonPackage): depends_on('py-six', type=('build', 'run')) depends_on('py-typing@3.6.4:', type=('build', 'run')) depends_on('py-typing-extensions@3.6.4:', type=('build', 'run')) + + # 'python_out' does not recognize dllexport_decl. + patch('remove_dllexport_decl.patch', when='@:1.6.0') diff --git a/var/spack/repos/builtin/packages/py-onnx/remove_dllexport_decl.patch b/var/spack/repos/builtin/packages/py-onnx/remove_dllexport_decl.patch new file mode 100644 index 00000000000..ede1fe66f2a --- /dev/null +++ b/var/spack/repos/builtin/packages/py-onnx/remove_dllexport_decl.patch @@ -0,0 +1,11 @@ +--- spack-src/CMakeLists.txt.org 2020-03-24 14:01:58.856142450 +0900 ++++ spack-src/CMakeLists.txt 2020-03-24 14:01:05.715872685 +0900 +@@ -204,7 +204,7 @@ + ${ONNX_DLLEXPORT_STR}${CMAKE_CURRENT_BINARY_DIR}) + if(BUILD_ONNX_PYTHON) + list(APPEND PROTOC_ARGS --python_out +- ${ONNX_DLLEXPORT_STR}${CMAKE_CURRENT_BINARY_DIR}) ++ ${CMAKE_CURRENT_BINARY_DIR}) + if(ONNX_GEN_PB_TYPE_STUBS) + # Haven't figured out how to generate mypy stubs on Windows yet + if(NOT WIN32) From 3b7c79b225fce47338a703bad28206480c42c225 Mon Sep 17 00:00:00 2001 From: Amjad Kotobi Date: Tue, 24 Mar 2020 10:10:33 +0100 Subject: [PATCH 196/377] r-remotes: added v2.1.1 (#15627) --- var/spack/repos/builtin/packages/r-remotes/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/r-remotes/package.py b/var/spack/repos/builtin/packages/r-remotes/package.py index ca51212143c..1c2c1fba383 100644 --- a/var/spack/repos/builtin/packages/r-remotes/package.py +++ b/var/spack/repos/builtin/packages/r-remotes/package.py @@ -10,12 +10,13 @@ class RRemotes(RPackage): """Download and install R packages stored in 'GitHub', 'BitBucket', or plain 'subversion' or 'git' repositories. This package provides the 'install_*' functions in 'devtools'. Indeed most of the code was copied - over from 'devtools'.""" + over from 'devtools'. """ homepage = "https://github.com/r-lib/remotes#readme" url = "https://cloud.r-project.org/src/contrib/remotes_2.1.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/remotes" + version('2.1.1', sha256='4e590746fce618094089372b185e1ea234b3337b23c44c44118e942d0fb5118b') version('2.1.0', sha256='8944c8f6fc9f0cd0ca04d6cf1221b716eee08facef9f4b4c4d91d0346d6d68a7') depends_on('r@3.0.0:', type=('build', 'run')) From 862e13183d571809d6df6c55eadf1d5b83482830 Mon Sep 17 00:00:00 2001 From: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com> Date: Tue, 24 Mar 2020 14:11:38 -0700 Subject: [PATCH 197/377] workaround for otf2's erroneous python2 configure requirement (#15653) --- var/spack/repos/builtin/packages/otf2/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/otf2/package.py b/var/spack/repos/builtin/packages/otf2/package.py index a44ebc44512..a123f0e8871 100644 --- a/var/spack/repos/builtin/packages/otf2/package.py +++ b/var/spack/repos/builtin/packages/otf2/package.py @@ -32,5 +32,6 @@ def configure_args(self): 'F77={0}'.format(spack_f77), 'FC={0}'.format(spack_fc), 'CFLAGS={0}'.format(self.compiler.pic_flag), - 'CXXFLAGS={0}'.format(self.compiler.pic_flag) + 'CXXFLAGS={0}'.format(self.compiler.pic_flag), + 'PYTHON_FOR_GENERATOR=:' ] From 1a5e4232ed9609d16e7106db4d1d90eb8d69780a Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Tue, 24 Mar 2020 22:26:35 +0100 Subject: [PATCH 198/377] spack.repo: remove "import from" statements (#15505) spack.repo: remove "import from" statements --- lib/spack/spack/cmd/repo.py | 25 ++++++++-------- lib/spack/spack/repo.py | 50 +++++++++++++++----------------- lib/spack/spack/test/cmd/repo.py | 35 ++++++++++++++++++++++ 3 files changed, 71 insertions(+), 39 deletions(-) create mode 100644 lib/spack/spack/test/cmd/repo.py diff --git a/lib/spack/spack/cmd/repo.py b/lib/spack/spack/cmd/repo.py index 83acf796a24..f271790994e 100644 --- a/lib/spack/spack/cmd/repo.py +++ b/lib/spack/spack/cmd/repo.py @@ -8,10 +8,9 @@ import os import llnl.util.tty as tty - -import spack.spec import spack.config -from spack.repo import Repo, create_repo, canonicalize_path, RepoError +import spack.repo +import spack.util.path description = "manage package source repositories" section = "config" @@ -61,7 +60,9 @@ def setup_parser(subparser): def repo_create(args): """Create a new package repository.""" - full_path, namespace = create_repo(args.directory, args.namespace) + full_path, namespace = spack.repo.create_repo( + args.directory, args.namespace + ) tty.msg("Created repo with namespace '%s'." % namespace) tty.msg("To register it with spack, run this command:", 'spack repo add %s' % full_path) @@ -72,7 +73,7 @@ def repo_add(args): path = args.path # real_path is absolute and handles substitution. - canon_path = canonicalize_path(path) + canon_path = spack.util.path.canonicalize_path(path) # check if the path exists if not os.path.exists(canon_path): @@ -83,7 +84,7 @@ def repo_add(args): tty.die("Not a Spack repository: %s" % path) # Make sure it's actually a spack repository by constructing it. - repo = Repo(canon_path) + repo = spack.repo.Repo(canon_path) # If that succeeds, finally add it to the configuration. repos = spack.config.get('repos', scope=args.scope) @@ -104,9 +105,9 @@ def repo_remove(args): namespace_or_path = args.namespace_or_path # If the argument is a path, remove that repository from config. - canon_path = canonicalize_path(namespace_or_path) + canon_path = spack.util.path.canonicalize_path(namespace_or_path) for repo_path in repos: - repo_canon_path = canonicalize_path(repo_path) + repo_canon_path = spack.util.path.canonicalize_path(repo_path) if canon_path == repo_canon_path: repos.remove(repo_path) spack.config.set('repos', repos, args.scope) @@ -116,14 +117,14 @@ def repo_remove(args): # If it is a namespace, remove corresponding repo for path in repos: try: - repo = Repo(path) + repo = spack.repo.Repo(path) if repo.namespace == namespace_or_path: repos.remove(path) spack.config.set('repos', repos, args.scope) tty.msg("Removed repository %s with namespace '%s'." % (repo.root, repo.namespace)) return - except RepoError: + except spack.repo.RepoError: continue tty.die("No repository with path or namespace: %s" @@ -136,8 +137,8 @@ def repo_list(args): repos = [] for r in roots: try: - repos.append(Repo(r)) - except RepoError: + repos.append(spack.repo.Repo(r)) + except spack.repo.RepoError: continue msg = "%d package repositor" % len(repos) diff --git a/lib/spack/spack/repo.py b/lib/spack/spack/repo.py index 8e3dae5d474..4a739189fc2 100644 --- a/lib/spack/spack/repo.py +++ b/lib/spack/spack/repo.py @@ -16,22 +16,20 @@ import stat import sys import traceback - -from six import string_types, add_metaclass +import types try: from collections.abc import Mapping # novm except ImportError: from collections import Mapping -from types import ModuleType +import six import ruamel.yaml as yaml import llnl.util.lang import llnl.util.tty as tty -from llnl.util.filesystem import mkdirp, install - +import llnl.util.filesystem as fs import spack.config import spack.caches import spack.error @@ -39,11 +37,9 @@ import spack.spec import spack.util.spack_json as sjson import spack.util.imp as simp -from spack.provider_index import ProviderIndex -from spack.util.path import canonicalize_path -from spack.util.naming import NamespaceTrie, valid_module_name -from spack.util.naming import mod_to_class, possible_spack_module_names - +import spack.provider_index +import spack.util.path +import spack.util.naming as nm #: Super-namespace for all packages. #: Package modules are imported as spack.pkg... @@ -95,7 +91,7 @@ def converter(self, spec_like, *args, **kwargs): return converter -class SpackNamespace(ModuleType): +class SpackNamespace(types.ModuleType): """ Allow lazy loading of modules.""" def __init__(self, namespace): @@ -151,7 +147,7 @@ def _create_new_cache(self): pkg_dir = os.path.join(self.packages_path, pkg_name) # Warn about invalid names that look like packages. - if not valid_module_name(pkg_name): + if not nm.valid_module_name(pkg_name): if not pkg_name.startswith('.'): tty.warn('Skipping package at {0}. "{1}" is not ' 'a valid Spack module name.'.format( @@ -247,7 +243,7 @@ def update_package(self, pkg_name): self._tag_dict[tag].append(package.name) -@add_metaclass(abc.ABCMeta) +@six.add_metaclass(abc.ABCMeta) class Indexer(object): """Adaptor for indexes that need to be generated when repos are updated.""" @@ -305,10 +301,10 @@ def write(self, stream): class ProviderIndexer(Indexer): """Lifecycle methods for virtual package providers.""" def _create(self): - return ProviderIndex() + return spack.provider_index.ProviderIndex() def read(self, stream): - self.index = ProviderIndex.from_json(stream) + self.index = spack.provider_index.ProviderIndex.from_json(stream) def update(self, pkg_fullname): self.index.remove_provider(pkg_fullname) @@ -447,7 +443,7 @@ class RepoPath(object): def __init__(self, *repos): self.repos = [] - self.by_namespace = NamespaceTrie() + self.by_namespace = nm.NamespaceTrie() self._all_package_names = None self._provider_index = None @@ -456,7 +452,7 @@ def __init__(self, *repos): # Add each repo to this path. for repo in repos: try: - if isinstance(repo, string_types): + if isinstance(repo, six.string_types): repo = Repo(repo) self.put_last(repo) except RepoError as e: @@ -544,7 +540,7 @@ def all_packages(self): def provider_index(self): """Merged ProviderIndex from all Repos in the RepoPath.""" if self._provider_index is None: - self._provider_index = ProviderIndex() + self._provider_index = spack.provider_index.ProviderIndex() for repo in reversed(self.repos): self._provider_index.merge(repo.provider_index) @@ -707,7 +703,7 @@ def __init__(self, root): """ # Root directory, containing _repo.yaml and package dirs # Allow roots to by spack-relative by starting with '$spack' - self.root = canonicalize_path(root) + self.root = spack.util.path.canonicalize_path(root) # check and raise BadRepoError on fail. def check(condition, msg): @@ -803,7 +799,7 @@ def real_name(self, import_name): if import_name in self: return import_name - options = possible_spack_module_names(import_name) + options = nm.possible_spack_module_names(import_name) options.remove(import_name) for name in options: if name in self: @@ -921,18 +917,18 @@ def dump_provenance(self, spec, path): % (self.namespace, spec.fullname)) # Install patch files needed by the package. - mkdirp(path) + fs.mkdirp(path) for patch in itertools.chain.from_iterable( spec.package.patches.values()): if patch.path: if os.path.exists(patch.path): - install(patch.path, path) + fs.install(patch.path, path) else: tty.warn("Patch file did not exist: %s" % patch.path) # Install the package.py file itself. - install(self.filename_for_package_name(spec.name), path) + fs.install(self.filename_for_package_name(spec.name), path) def purge(self): """Clear entire package instance cache.""" @@ -1082,7 +1078,7 @@ def get_pkg_class(self, pkg_name): raise InvalidNamespaceError('Invalid namespace for %s repo: %s' % (self.namespace, namespace)) - class_name = mod_to_class(pkg_name) + class_name = nm.mod_to_class(pkg_name) module = self._get_pkg_module(pkg_name) cls = getattr(module, class_name) @@ -1107,7 +1103,7 @@ def create_repo(root, namespace=None): If the namespace is not provided, use basename of root. Return the canonicalized path and namespace of the created repository. """ - root = canonicalize_path(root) + root = spack.util.path.canonicalize_path(root) if not namespace: namespace = os.path.basename(root) @@ -1141,7 +1137,7 @@ def create_repo(root, namespace=None): config_path = os.path.join(root, repo_config_name) packages_path = os.path.join(root, packages_dir_name) - mkdirp(packages_path) + fs.mkdirp(packages_path) with open(config_path, 'w') as config: config.write("repo:\n") config.write(" namespace: '%s'\n" % namespace) @@ -1163,7 +1159,7 @@ def create_repo(root, namespace=None): def create_or_construct(path, namespace=None): """Create a repository, or just return a Repo if it already exists.""" if not os.path.exists(path): - mkdirp(path) + fs.mkdirp(path) create_repo(path, namespace) return Repo(path) diff --git a/lib/spack/spack/test/cmd/repo.py b/lib/spack/spack/test/cmd/repo.py new file mode 100644 index 00000000000..82fe872710e --- /dev/null +++ b/lib/spack/spack/test/cmd/repo.py @@ -0,0 +1,35 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) +import os.path + +import pytest +import spack.main + +repo = spack.main.SpackCommand('repo') + + +def test_help_option(): + # Test 'spack repo --help' to check basic import works + # and the command exits successfully + with pytest.raises(SystemExit): + repo('--help') + assert repo.returncode in (None, 0) + + +def test_create_add_list_remove(mutable_config, tmpdir): + # Create a new repository and check that the expected + # files are there + repo('create', str(tmpdir), 'mockrepo') + assert os.path.exists(os.path.join(str(tmpdir), 'repo.yaml')) + + # Add the new repository and check it appears in the list output + repo('add', '--scope=site', str(tmpdir)) + output = repo('list', '--scope=site', output=str) + assert 'mockrepo' in output + + # Then remove it and check it's not there + repo('remove', '--scope=site', str(tmpdir)) + output = repo('list', '--scope=site', output=str) + assert 'mockrepo' not in output From cfa8e698351b7aaef044d2d282ba66677180b318 Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Wed, 25 Mar 2020 01:01:00 -0500 Subject: [PATCH 199/377] singularity: add version 3.5.3 (#15669) --- var/spack/repos/builtin/packages/singularity/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/singularity/package.py b/var/spack/repos/builtin/packages/singularity/package.py index e97f18ce833..7e808880cf9 100644 --- a/var/spack/repos/builtin/packages/singularity/package.py +++ b/var/spack/repos/builtin/packages/singularity/package.py @@ -27,6 +27,7 @@ class Singularity(MakefilePackage): maintainers = ['ArangoGutierrez', 'alalazo'] version('master', branch='master') + version('3.5.3', sha256='0c76f1e3808bf4c10e92b17150314b2b816be79f8101be448a6e9d7a96c9e486') version('3.5.2', sha256='f9c21e289377a4c40ed7a78a0c95e1ff416dec202ed49a6c616dd2c37700eab8') version('3.4.1', sha256='638fd7cc5ab2a20e779b8768f73baf21909148339d6c4edf6ff61349c53a70c2') version('3.4.0', sha256='eafb27f1ffbed427922ebe2b5b95d1c9c09bfeb897518867444fe230e3e35e41') From 25e50a994357737dd04ee53afc82b69ab367a55f Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Wed, 25 Mar 2020 01:01:24 -0500 Subject: [PATCH 200/377] pmix: add version 2.2.3 (#15668) --- var/spack/repos/builtin/packages/pmix/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/pmix/package.py b/var/spack/repos/builtin/packages/pmix/package.py index 0ebdce79872..fb4e37e572b 100644 --- a/var/spack/repos/builtin/packages/pmix/package.py +++ b/var/spack/repos/builtin/packages/pmix/package.py @@ -39,6 +39,7 @@ class Pmix(AutotoolsPackage): version('3.0.2', sha256='df68f35a3ed9517eeade80b13855cebad8fde2772b36a3f6be87559b6d430670') version('3.0.1', sha256='b81055d2c0d61ef5a451b63debc39c820bcd530490e2e4dcb4cdbacb618c157c') version('3.0.0', sha256='ee8f68107c24b706237a53333d832445315ae37de6773c5413d7fda415a6e2ee') + version('2.2.3', sha256='6fa5d45eb089e29101190c645e986342a24a03a4ea3a936db0b120aafa45b1f0') version('2.2.2', sha256='cd951dbda623fadc5b32ae149d8cc41f9462eac4d718d089340911b1a7c20714') version('2.1.4', sha256='eb72d292e76e200f02cf162a477eecea2559ef3ac2edf50ee95b3fe3983d033e') version('2.1.3', sha256='281283133498e7e5999ed5c6557542c22408bc9eb51ecbcf7696160616782a41') From d099143999f341cf82c0b5bafefdd08165427179 Mon Sep 17 00:00:00 2001 From: Matthias Diener Date: Tue, 24 Mar 2020 21:53:00 -0500 Subject: [PATCH 201/377] charmpp: add version 6.10.1+cleanups - change URL to http as our server only supports TLSv1.0, which not all HTTPS clients accept anymore - change name of development branch to 'master' --- var/spack/repos/builtin/packages/charmpp/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/charmpp/package.py b/var/spack/repos/builtin/packages/charmpp/package.py index 80213216141..158dd599378 100644 --- a/var/spack/repos/builtin/packages/charmpp/package.py +++ b/var/spack/repos/builtin/packages/charmpp/package.py @@ -18,10 +18,12 @@ class Charmpp(Package): (your laptop) to the largest supercomputers.""" homepage = "http://charmplusplus.org" - url = "https://charm.cs.illinois.edu/distrib/charm-6.8.2.tar.gz" + url = "http://charm.cs.illinois.edu/distrib/charm-6.8.2.tar.gz" git = "https://github.com/UIUC-PPL/charm.git" - version("develop", branch="charm") + version("develop", branch="master") + + version('6.10.1', sha256='ab96198105daabbb8c8bdf370f87b0523521ce502c656cb6cd5b89f69a2c70a8') version('6.10.0', sha256='7c526a78aa0c202b7f0418b345138e7dc40496f0bb7b9e301e0381980450b25c') version("6.9.0", sha256="85ed660e46eeb7a6fc6b32deab08226f647c244241948f6b592ebcd2b6050cbd") version("6.8.2", sha256="08e6001b0e9cd00ebde179f76098767149bf7e454f29028fb9a8bfb55778698e") From 4e6c07529d5af46987b0e6e7ca62bca26e9c9f5c Mon Sep 17 00:00:00 2001 From: Stephanie Brink Date: Tue, 24 Mar 2020 23:05:26 -0700 Subject: [PATCH 202/377] xz: add version 5.2.5 (#15656) --- var/spack/repos/builtin/packages/xz/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/xz/package.py b/var/spack/repos/builtin/packages/xz/package.py index 428993a816f..cbaaaa3ec6f 100644 --- a/var/spack/repos/builtin/packages/xz/package.py +++ b/var/spack/repos/builtin/packages/xz/package.py @@ -13,9 +13,10 @@ class Xz(AutotoolsPackage): to LZMA Utils.""" homepage = "http://tukaani.org/xz/" - url = "http://tukaani.org/xz/xz-5.2.4.tar.bz2" + url = "http://tukaani.org/xz/xz-5.2.5.tar.bz2" list_url = "http://tukaani.org/xz/old.html" + version('5.2.5', sha256='5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df') version('5.2.4', sha256='3313fd2a95f43d88e44264e6b015e7d03053e681860b0d5d3f9baca79c57b7bf') version('5.2.3', sha256='fd9ca16de1052aac899ad3495ad20dfa906c27b4a5070102a2ec35ca3a4740c1') version('5.2.2', sha256='6ff5f57a4b9167155e35e6da8b529de69270efb2b4cf3fbabf41a4ee793840b5') From 16eb86acf2ed3adf157078895ef258cb9f479f01 Mon Sep 17 00:00:00 2001 From: darmac Date: Wed, 25 Mar 2020 15:07:34 +0800 Subject: [PATCH 203/377] libwebp: fix sha256 checksum (#15639) --- var/spack/repos/builtin/packages/libwebp/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/libwebp/package.py b/var/spack/repos/builtin/packages/libwebp/package.py index 9c5f56a8043..fd8dee8e9eb 100644 --- a/var/spack/repos/builtin/packages/libwebp/package.py +++ b/var/spack/repos/builtin/packages/libwebp/package.py @@ -14,7 +14,7 @@ class Libwebp(AutotoolsPackage): homepage = "https://developers.google.com/speed/webp/" url = "https://storage.googleapis.com/downloads.webmproject.org/releases/webp/libwebp-1.0.3.tar.gz" - version('1.0.3', sha256='082d114bcb18a0e2aafc3148d43367c39304f86bf18ba0b2e766447e111a4a91') + version('1.0.3', sha256='e20a07865c8697bba00aebccc6f54912d6bc333bb4d604e6b07491c1a226b34f') variant('libwebpmux', default=False, description='Build libwebpmux') variant('libwebpdemux', default=False, description='Build libwebpdemux') From 7e1e98cf8fface6ed3f018e33be045a18bc03d8f Mon Sep 17 00:00:00 2001 From: Jeffrey Salmond Date: Wed, 25 Mar 2020 09:46:04 +0000 Subject: [PATCH 204/377] julia: added v1.4.0 (#15673) --- var/spack/repos/builtin/packages/julia/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 9dae676d9af..ec86c04886f 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -18,6 +18,7 @@ class Julia(Package): maintainers = ['glennpj'] version('master', branch='master') + version('1.4.0', sha256='880c73a08296ce8d94ad9605149f2a2b2b028e7202a700ef725da899300b8be9') version('1.3.1', sha256='053908ec2706eb76cfdc998c077de123ecb1c60c945b4b5057aa3be19147b723') version('1.2.0', sha256='2419b268fc5c3666dd9aeb554815fe7cf9e0e7265bc9b94a43957c31a68d9184') version('1.1.1', sha256='3c5395dd3419ebb82d57bcc49dc729df3b225b9094e74376f8c649ee35ed79c2') From 24ca07165232addb32ee90f702df4c1fcd365d69 Mon Sep 17 00:00:00 2001 From: Sinan Date: Wed, 25 Mar 2020 02:49:09 -0700 Subject: [PATCH 205/377] pocl: add versions up to v1.4.0 (#15672) Co-authored-by: Sinan81 --- var/spack/repos/builtin/packages/pocl/package.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/var/spack/repos/builtin/packages/pocl/package.py b/var/spack/repos/builtin/packages/pocl/package.py index f9b343271a7..42a862d97b6 100644 --- a/var/spack/repos/builtin/packages/pocl/package.py +++ b/var/spack/repos/builtin/packages/pocl/package.py @@ -20,6 +20,9 @@ class Pocl(CMakePackage): git = "https://github.com/pocl/pocl.git" version("master", branch="master") + version('1.4', sha256='ec237faa83bb1c803fbdf7c6e83d8a2ad68b6f0ed1879c3aa16c0e1dcc478742') + version('1.3', sha256='6527e3f47fab7c21e96bc757c4ae3303901f35e23f64642d6da5cc4c4fcc915a') + version('1.2', sha256='0c43e68f336892f3a64cba19beb99d9212f529bedb77f7879c0331450b982d46') version('1.1', sha256='1e8dd0693a88c84937754df947b202871a40545b1b0a97ebefa370b0281c3c53') version('1.0', sha256='94bd86a2f9847c03e6c3bf8dca12af3734f8b272ffeacbc3fa8fcca58844b1d4') version('0.14', sha256='2127bf925a91fbbe3daf2f1bac0da5c8aceb16e2a9434977a3057eade974106a') @@ -48,6 +51,9 @@ class Pocl(CMakePackage): # (see #1616) # These are the supported LLVM versions depends_on("llvm +clang @6.0:7.0", when="@master") + depends_on("llvm +clang @6.0:9.0", when="@1.4") + depends_on("llvm +clang @5.0:8.0", when="@1.3") + depends_on("llvm +clang @5.0:7.0", when="@1.2") depends_on("llvm +clang @5.0:6.0", when="@1.1") depends_on("llvm +clang @4.0:5.0", when="@1.0") depends_on("llvm +clang @3.7:4.0", when="@0.14") From b8db87e1dc88707da3365dd04fab882d9fed90b2 Mon Sep 17 00:00:00 2001 From: Hadrien G Date: Wed, 25 Mar 2020 10:49:53 +0100 Subject: [PATCH 206/377] ACTS: added v0.19 (#15671) --- var/spack/repos/builtin/packages/acts-core/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/acts-core/package.py b/var/spack/repos/builtin/packages/acts-core/package.py index 421a931604e..d6e328352bc 100644 --- a/var/spack/repos/builtin/packages/acts-core/package.py +++ b/var/spack/repos/builtin/packages/acts-core/package.py @@ -34,6 +34,7 @@ class ActsCore(CMakePackage): maintainers = ['HadrienG2'] version('develop', branch='master') + version('0.19.0', commit='408335636486c421c6222a64372250ef12544df6') version('0.18.0', commit='d58a68cf75b52a5e0f563bc237f09250aa9da80c') version('0.17.0', commit='0789f654ff484b013fd27e5023cf342785ea8d97') version('0.16.0', commit='b3d965fe0b8ae335909d79114ef261c6b996773a') From 24802173876608c4d2c73b5d6fd2eb4ae2927116 Mon Sep 17 00:00:00 2001 From: Ben Morgan Date: Wed, 25 Mar 2020 10:28:06 +0000 Subject: [PATCH 207/377] gitconddb: new package at v0.1.1 (#15651) Git-based conditions database for HEP and other experiments. Use latest release version and current master to support Linux and macOS. Add core known dependencies and conflicts related to C++17 support. cxxstd variant added to help transitive dependencies, and for future support for newer standards in future. --- .../builtin/packages/gitconddb/package.py | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 var/spack/repos/builtin/packages/gitconddb/package.py diff --git a/var/spack/repos/builtin/packages/gitconddb/package.py b/var/spack/repos/builtin/packages/gitconddb/package.py new file mode 100644 index 00000000000..9400ea549ce --- /dev/null +++ b/var/spack/repos/builtin/packages/gitconddb/package.py @@ -0,0 +1,43 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Gitconddb(CMakePackage): + """Conditions Database library using a Git repository as the + storage backend""" + + homepage = "https://gitlab.cern.ch/lhcb/GitCondDB" + url = "https://gitlab.cern.ch/lhcb/GitCondDB/-/archive/0.1.1/GitCondDB-0.1.1.tar.gz" + git = "https://gitlab.cern.ch/lhcb/GitCondDB.git" + + maintainers = ['drbenmorgan'] + + version('master', branch='master') + version('0.1.1', sha256='024a6867722a3a622ed4327ea7d15641dd48e4e8411bdcc21915e406b3c479a2') + + # Add the cxxstd variant for forward compatibility, though we require 17 + _cxxstd_values = ('17',) + variant('cxxstd', + default='17', + values=_cxxstd_values, + multi=False, + description='Use the specified C++ standard when building.') + + depends_on('cmake@3.10:', type='build') + depends_on('pkgconfig', type='build') + depends_on('nlohmann-json@3.2.0:', type='build') + depends_on('googletest@1.8.1:', type='build') + + for s in _cxxstd_values: + depends_on('fmt@5.2.0: cxxstd=' + s, when='cxxstd=' + s) + # Maybe also a boost dependency for macOS older than catalina + + depends_on('libgit2') + + # Known conflicts on C++17 compatibility (aggressive for now) + conflicts('%gcc@:7.9.999', msg="GitCondDB requires GCC 8 or newer for C++17 support") + conflicts('%clang platform=darwin', when="@:0.1.99", msg="No Darwin support for clang in older versions") From f1aec94719d5cd8df9129eeabe91a4b5fda24ff1 Mon Sep 17 00:00:00 2001 From: xfzhao Date: Wed, 25 Mar 2020 05:50:30 -0500 Subject: [PATCH 208/377] mothur: specify version of vsearch (#15661) --- var/spack/repos/builtin/packages/mothur/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/mothur/package.py b/var/spack/repos/builtin/packages/mothur/package.py index 3f2283191a4..4e25a4dd3e1 100644 --- a/var/spack/repos/builtin/packages/mothur/package.py +++ b/var/spack/repos/builtin/packages/mothur/package.py @@ -23,7 +23,7 @@ class Mothur(MakefilePackage): depends_on('boost') depends_on('readline') - depends_on('vsearch', when='+vsearch', type='run') + depends_on('vsearch@2.13.3', when='+vsearch', type='run') def edit(self, spec, prefix): makefile = FileFilter('Makefile') From 3aa225cd5cc14b1e108fc75b128759ad4d6bb1eb Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Wed, 25 Mar 2020 03:57:00 -0700 Subject: [PATCH 209/377] openPMD-api: added v0.11.1 (#15659) Add the latest release with HDF5-1.12 compatibility. --- var/spack/repos/builtin/packages/openpmd-api/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/openpmd-api/package.py b/var/spack/repos/builtin/packages/openpmd-api/package.py index 1459a11271e..644758923ee 100644 --- a/var/spack/repos/builtin/packages/openpmd-api/package.py +++ b/var/spack/repos/builtin/packages/openpmd-api/package.py @@ -15,6 +15,7 @@ class OpenpmdApi(CMakePackage): maintainers = ['ax3l'] version('dev', branch='dev') + version('0.11.1', tag='0.11.1-alpha') version('0.11.0', tag='0.11.0-alpha') version('0.10.3', tag='0.10.3-alpha') version('0.10.2', tag='0.10.2-alpha') From b42a96df980458602c6c5314b3d3fac08f2d7442 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Wed, 25 Mar 2020 17:48:05 +0100 Subject: [PATCH 210/377] provider index: removed import from + refactored a few parts (#15570) Removed provider_index use of 'import from' and refactored a few routines to a further subclassing of _IndexBase for implementing user defined bindings of provider specs. --- lib/spack/spack/provider_index.py | 313 +++++++++++++++++------------- lib/spack/spack/test/spec_dag.py | 2 +- 2 files changed, 182 insertions(+), 133 deletions(-) diff --git a/lib/spack/spack/provider_index.py b/lib/spack/spack/provider_index.py index 9bf4af8911a..326f6aa8f11 100644 --- a/lib/spack/spack/provider_index.py +++ b/lib/spack/spack/provider_index.py @@ -2,54 +2,147 @@ # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +"""Classes and functions to manage providers of virtual dependencies""" +import itertools -""" -The ``virtual`` module contains utility classes for virtual dependencies. -""" - -from itertools import product as iproduct -from six import iteritems -from pprint import pformat - +import six import spack.error import spack.util.spack_json as sjson -class ProviderIndex(object): - """This is a dict of dicts used for finding providers of particular - virtual dependencies. The dict of dicts looks like: - - { vpkg name : - { full vpkg spec : set(packages providing spec) } } - - Callers can use this to first find which packages provide a vpkg, - then find a matching full spec. e.g., in this scenario: - - { 'mpi' : - { mpi@:1.1 : set([mpich]), - mpi@:2.3 : set([mpich2@1.9:]) } } - - Calling providers_for(spec) will find specs that provide a - matching implementation of MPI. +def _cross_provider_maps(lmap, rmap): + """Return a dictionary that combines constraint requests from both input. + Args: + lmap: main provider map + rmap: provider map with additional constraints """ + # TODO: this is pretty darned nasty, and inefficient, but there + # TODO: are not that many vdeps in most specs. + result = {} + for lspec, rspec in itertools.product(lmap, rmap): + try: + constrained = lspec.constrained(rspec) + except spack.error.UnsatisfiableSpecError: + continue + # lp and rp are left and right provider specs. + for lp_spec, rp_spec in itertools.product(lmap[lspec], rmap[rspec]): + if lp_spec.name == rp_spec.name: + try: + const = lp_spec.constrained(rp_spec, deps=False) + result.setdefault(constrained, set()).add(const) + except spack.error.UnsatisfiableSpecError: + continue + return result + + +class _IndexBase(object): + #: This is a dict of dicts used for finding providers of particular + #: virtual dependencies. The dict of dicts looks like: + #: + #: { vpkg name : + #: { full vpkg spec : set(packages providing spec) } } + #: + #: Callers can use this to first find which packages provide a vpkg, + #: then find a matching full spec. e.g., in this scenario: + #: + #: { 'mpi' : + #: { mpi@:1.1 : set([mpich]), + #: mpi@:2.3 : set([mpich2@1.9:]) } } + #: + #: Calling providers_for(spec) will find specs that provide a + #: matching implementation of MPI. Derived class need to construct + #: this attribute according to the semantics above. + providers = None + + def providers_for(self, virtual_spec): + """Return a list of specs of all packages that provide virtual + packages with the supplied spec. + + Args: + virtual_spec: virtual spec to be provided + """ + result = set() + # Allow string names to be passed as input, as well as specs + if isinstance(virtual_spec, six.string_types): + virtual_spec = spack.spec.Spec(virtual_spec) + + # Add all the providers that satisfy the vpkg spec. + if virtual_spec.name in self.providers: + for p_spec, spec_set in self.providers[virtual_spec.name].items(): + if p_spec.satisfies(virtual_spec, deps=False): + result.update(spec_set) + + # Return providers in order. Defensively copy. + return sorted(s.copy() for s in result) + + def __contains__(self, name): + return name in self.providers + + def satisfies(self, other): + """Determine if the providers of virtual specs are compatible. + + Args: + other: another provider index + + Returns: + True if the providers are compatible, False otherwise. + """ + common = set(self.providers) & set(other.providers) + if not common: + return True + + # This ensures that some provider in other COULD satisfy the + # vpkg constraints on self. + result = {} + for name in common: + crossed = _cross_provider_maps( + self.providers[name], other.providers[name] + ) + if crossed: + result[name] = crossed + + return all(c in result for c in common) + + def __eq__(self, other): + return self.providers == other.providers + + def _transform(self, transform_fun, out_mapping_type=dict): + """Transform this provider index dictionary and return it. + + Args: + transform_fun: transform_fun takes a (vpkg, pset) mapping and runs + it on each pair in nested dicts. + out_mapping_type: type to be used internally on the + transformed (vpkg, pset) + + Returns: + Transformed mapping + """ + return _transform(self.providers, transform_fun, out_mapping_type) + + def __str__(self): + return str(self.providers) + + def __repr__(self): + return repr(self.providers) + + +class ProviderIndex(_IndexBase): def __init__(self, specs=None, restrict=False): - """Create a new ProviderIndex. + """Provider index based on a single mapping of providers. - Optional arguments: + Args: + specs (list of specs): if provided, will call update on each + single spec to initialize this provider index. - specs - List (or sequence) of specs. If provided, will call - `update` on this ProviderIndex with each spec in the list. + restrict: "restricts" values to the verbatim input specs; do not + pre-apply package's constraints. - restrict - "restricts" values to the verbatim input specs; do not - pre-apply package's constraints. - - TODO: rename this. It is intended to keep things as broad - as possible without overly restricting results, so it is - not the best name. + TODO: rename this. It is intended to keep things as broad + TODO: as possible without overly restricting results, so it is + TODO: not the best name. """ if specs is None: specs = [] @@ -67,6 +160,11 @@ def __init__(self, specs=None, restrict=False): self.update(spec) def update(self, spec): + """Update the provider index with additional virtual specs. + + Args: + spec: spec potentially providing additional virtual specs + """ if not isinstance(spec, spack.spec.Spec): spec = spack.spec.Spec(spec) @@ -74,10 +172,10 @@ def update(self, spec): # Empty specs do not have a package return - assert(not spec.virtual) + assert not spec.virtual, "cannot update an index using a virtual spec" pkg_provided = spec.package_class.provided - for provided_spec, provider_specs in iteritems(pkg_provided): + for provided_spec, provider_specs in six.iteritems(pkg_provided): for provider_spec in provider_specs: # TODO: fix this comment. # We want satisfaction other than flags @@ -110,94 +208,24 @@ def update(self, spec): constrained.constrain(provider_spec) provider_map[provided_spec].add(constrained) - def providers_for(self, *vpkg_specs): - """Gives specs of all packages that provide virtual packages - with the supplied specs.""" - providers = set() - for vspec in vpkg_specs: - # Allow string names to be passed as input, as well as specs - if type(vspec) == str: - vspec = spack.spec.Spec(vspec) - - # Add all the providers that satisfy the vpkg spec. - if vspec.name in self.providers: - for p_spec, spec_set in self.providers[vspec.name].items(): - if p_spec.satisfies(vspec, deps=False): - providers.update(spec_set) - - # Return providers in order. Defensively copy. - return sorted(s.copy() for s in providers) - - # TODO: this is pretty darned nasty, and inefficient, but there - # are not that many vdeps in most specs. - def _cross_provider_maps(self, lmap, rmap): - result = {} - for lspec, rspec in iproduct(lmap, rmap): - try: - constrained = lspec.constrained(rspec) - except spack.error.UnsatisfiableSpecError: - continue - - # lp and rp are left and right provider specs. - for lp_spec, rp_spec in iproduct(lmap[lspec], rmap[rspec]): - if lp_spec.name == rp_spec.name: - try: - const = lp_spec.constrained(rp_spec, deps=False) - result.setdefault(constrained, set()).add(const) - except spack.error.UnsatisfiableSpecError: - continue - return result - - def __contains__(self, name): - """Whether a particular vpkg name is in the index.""" - return name in self.providers - - def satisfies(self, other): - """Check that providers of virtual specs are compatible.""" - common = set(self.providers) & set(other.providers) - if not common: - return True - - # This ensures that some provider in other COULD satisfy the - # vpkg constraints on self. - result = {} - for name in common: - crossed = self._cross_provider_maps(self.providers[name], - other.providers[name]) - if crossed: - result[name] = crossed - - return all(c in result for c in common) - def to_json(self, stream=None): + """Dump a JSON representation of this object. + + Args: + stream: stream where to dump + """ provider_list = self._transform( lambda vpkg, pset: [ vpkg.to_node_dict(), [p.to_node_dict() for p in pset]], list) sjson.dump({'provider_index': {'providers': provider_list}}, stream) - @staticmethod - def from_json(stream): - data = sjson.load(stream) - - if not isinstance(data, dict): - raise ProviderIndexError("JSON ProviderIndex data was not a dict.") - - if 'provider_index' not in data: - raise ProviderIndexError( - "YAML ProviderIndex does not start with 'provider_index'") - - index = ProviderIndex() - providers = data['provider_index']['providers'] - index.providers = _transform( - providers, - lambda vpkg, plist: ( - spack.spec.Spec.from_node_dict(vpkg), - set(spack.spec.Spec.from_node_dict(p) for p in plist))) - return index - def merge(self, other): - """Merge `other` ProviderIndex into this one.""" + """Merge another provider index into this one. + + Args: + other (ProviderIndex): provider index to be merged + """ other = other.copy() # defensive copy. for pkg in other.providers: @@ -236,40 +264,61 @@ def remove_provider(self, pkg_name): del self.providers[pkg] def copy(self): - """Deep copy of this ProviderIndex.""" + """Return a deep copy of this index.""" clone = ProviderIndex() clone.providers = self._transform( lambda vpkg, pset: (vpkg, set((p.copy() for p in pset)))) return clone - def __eq__(self, other): - return self.providers == other.providers + @staticmethod + def from_json(stream): + """Construct a provider index from its JSON representation. - def _transform(self, transform_fun, out_mapping_type=dict): - return _transform(self.providers, transform_fun, out_mapping_type) + Args: + stream: stream where to read from the JSON data + """ + data = sjson.load(stream) - def __str__(self): - return pformat( - _transform(self.providers, - lambda k, v: (k, list(v)))) + if not isinstance(data, dict): + raise ProviderIndexError("JSON ProviderIndex data was not a dict.") + + if 'provider_index' not in data: + raise ProviderIndexError( + "YAML ProviderIndex does not start with 'provider_index'") + + index = ProviderIndex() + providers = data['provider_index']['providers'] + index.providers = _transform( + providers, + lambda vpkg, plist: ( + spack.spec.Spec.from_node_dict(vpkg), + set(spack.spec.Spec.from_node_dict(p) for p in plist))) + return index def _transform(providers, transform_fun, out_mapping_type=dict): """Syntactic sugar for transforming a providers dict. - transform_fun takes a (vpkg, pset) mapping and runs it on each - pair in nested dicts. + Args: + providers: provider dictionary + transform_fun: transform_fun takes a (vpkg, pset) mapping and runs + it on each pair in nested dicts. + out_mapping_type: type to be used internally on the + transformed (vpkg, pset) + Returns: + Transformed mapping """ def mapiter(mappings): if isinstance(mappings, dict): - return iteritems(mappings) + return six.iteritems(mappings) else: return iter(mappings) return dict( - (name, out_mapping_type([ - transform_fun(vpkg, pset) for vpkg, pset in mapiter(mappings)])) + (name, out_mapping_type( + [transform_fun(vpkg, pset) for vpkg, pset in mapiter(mappings)] + )) for name, mappings in providers.items()) diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py index 419a39968e9..25917f9424a 100644 --- a/lib/spack/spack/test/spec_dag.py +++ b/lib/spack/spack/test/spec_dag.py @@ -189,7 +189,7 @@ def test_conditional_dep_with_user_constraints(): assert ('y@3' in spec) -@pytest.mark.usefixtures('mutable_mock_repo') +@pytest.mark.usefixtures('mutable_mock_repo', 'config') class TestSpecDag(object): def test_conflicting_package_constraints(self, set_dependency): From 9c0b1974606e03e9a780d2a8208aeb041e191d79 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Wed, 25 Mar 2020 14:54:13 -0700 Subject: [PATCH 211/377] WarpX: MPI, Backends, Ascent (#15647) Expose serial/parallel build (MPI), CUDA/OpenMP backends, Clang, and Ascent bindings. Interestingly, `warpx +ascent` currently leads to an infinite loop in the Spack concretizer. --- .../repos/builtin/packages/warpx/package.py | 67 +++++++++++++------ 1 file changed, 46 insertions(+), 21 deletions(-) diff --git a/var/spack/repos/builtin/packages/warpx/package.py b/var/spack/repos/builtin/packages/warpx/package.py index a729f9ac28f..55cdf3cb13b 100644 --- a/var/spack/repos/builtin/packages/warpx/package.py +++ b/var/spack/repos/builtin/packages/warpx/package.py @@ -24,21 +24,32 @@ class Warpx(MakefilePackage): variant('dims', default='3', - values=('2', '3'), + values=('2', '3', 'rz'), multi=False, description='Number of spatial dimensions') - + variant('backend', + default='openmp', + values=('openmp', 'cuda', 'hip'), + multi=True, + description='Programming model for compute kernels') + variant('mpi', default=True, description='Enable MPI support') variant('psatd', default=False, description='Enable PSATD solver') variant('debug', default=False, description='Enable debugging features') variant('tprof', default=True, description='Enable tiny profiling features') - variant('openmp', default=True, description='Enable OpenMP features') variant('openpmd', default=True, description='Enable openPMD I/O') + variant('ascent', default=False, description='Enable Ascent in situ vis') - depends_on('mpi') + depends_on('cuda', when='backend=cuda') + depends_on('mpi', when='+mpi') depends_on('fftw@3:', when='+psatd') + depends_on('fftw +mpi', when='+psatd +mpi') depends_on('pkgconfig', type='build', when='+openpmd') - depends_on('python', type='build') # FIXME upstream - depends_on('openpmd-api@0.11.0:,dev +mpi', when='+openpmd') + depends_on('python', type='build') # AMReX' build system info + depends_on('openpmd-api@0.11.0:,dev', when='+openpmd') + depends_on('openpmd-api +mpi', when='+openpmd +mpi') + depends_on('ascent', when='+ascent') + depends_on('ascent +cuda', when='+ascent backend=cuda') + depends_on('ascent +mpi ^conduit~hdf5', when='+ascent +mpi') resource(name='amrex', git='https://github.com/AMReX-Codes/amrex.git', @@ -49,36 +60,50 @@ class Warpx(MakefilePackage): git='https://bitbucket.org/berkeleylab/picsar.git', tag='master') + conflicts('backend=cuda', when='backend=hip', + msg='WarpX can be compiled with either CUDA or HIP backend') + conflicts('backend=hip', msg='WarpX\' HIP backend is not yet implemented') + def edit(self, spec, prefix): comp = 'gcc' - vendors = {'%gcc': 'gcc', '%intel': 'intel'} + vendors = {'%gcc': 'gcc', '%intel': 'intel', '%clang': 'llvm'} for key, value in vendors.items(): if self.spec.satisfies(key): comp = value - def torf(s): - "Returns the string TRUE or FALSE" - return repr(s in spec).upper() + # Returns the string TRUE or FALSE + torf = lambda s: repr(s in spec).upper() - makefile = FileFilter('GNUmakefile') - makefile.filter('AMREX_HOME .*', 'AMREX_HOME = amrex') - makefile.filter('PICSAR_HOME .*', 'PICSAR_HOME = picsar') - makefile.filter('COMP .*', 'COMP = {0}'.format(comp)) - makefile.filter('DIM .*', - 'DIM = {0}'.format(int(spec.variants['dims'].value))) - makefile.filter('USE_PSATD .*', - 'USE_PSATD = {0}'.format(torf('+psatd'))) try: self.compiler.openmp_flag except UnsupportedCompilerFlag: use_omp = 'FALSE' else: - use_omp = torf('+openmp') - use_openpmd = torf('+openpmd') + use_omp = torf('backend=openmp') + + makefile = FileFilter('GNUmakefile') + makefile.filter('AMREX_HOME .*', 'AMREX_HOME = amrex') + makefile.filter('PICSAR_HOME .*', 'PICSAR_HOME = picsar') + makefile.filter('COMP .*', 'COMP = {0}'.format(comp)) + makefile.filter('USE_MPI .*', + 'USE_MPI = {0}'.format(torf('+mpi'))) + if 'dims=rz' in spec: + makefile.filter('USE_RZ .*', 'USE_RZ = TRUE') + else: + makefile.filter('DIM .*', 'DIM = {0}'.format( + int(spec.variants['dims'].value))) + makefile.filter('USE_PSATD .*', + 'USE_PSATD = {0}'.format(torf('+psatd'))) makefile.filter('USE_OMP .*', 'USE_OMP = {0}'.format(use_omp)) + makefile.filter('USE_GPU .*', + 'USE_GPU = {0}'.format(torf('backend=cuda'))) + makefile.filter('USE_HIP .*', + 'USE_HIP = {0}'.format(torf('backend=hip'))) makefile.filter('USE_OPENPMD .*', - 'USE_OPENPMD = {0}'.format(use_openpmd)) + 'USE_OPENPMD = {0}'.format(torf('+openpmd'))) + makefile.filter('USE_ASCENT_INSITU .*', + 'USE_ASCENT_INSITU = {0}'.format(torf('+ascent'))) makefile.filter('DEBUG .*', 'DEBUG = {0}'.format(torf('+debug'))) makefile.filter('TINY_PROFILE .*', From e042bd9d89670a92e8c0ca44ef5adb6d98659dc7 Mon Sep 17 00:00:00 2001 From: Dan Bonachea Date: Wed, 25 Mar 2020 19:05:13 -0400 Subject: [PATCH 212/377] UPC++ 2020.3.0 update (#15623) ## Summary This PR updates and improves the Spack package for [UPC++](https://upcxx.lbl.gov). I'm an LBL employee and developer on the UPC++ team, as well as the maintainer of this Spack package. ### Key Improvements: * Adding new 2020.3.0 release and support for use of develop/master branches - Our build infrastructure underwent a major change in this release, switching from a hand-rolled Python2 script to a bash-based autoconf work-alike. - The new build system is NOT using autotools (nor does it support some of the more esoteric autoconf options), but the user interface for common builds is similar. * Add explicit support for an MPI optional dependency - New `mpi` variant enables use of the MPI-based spawner (most relevant on loosely coupled clusters), and the (unofficial) mpi-conduit backend - This variant is OFF by default, since UPC++ works fine without MPI on many systems, increasing the likelihood first-time Spack users get a working build without needing to correctly setup MPI * Add support for post-install testing using the test support deployed in the new build infrastructure * Fix or workaround a few bugs observed during testing ### Status The new package has been validated with a variety of specs across over seven different systems, including: NERSC cori, ALCF Theta, OLCF Summit, an in-house Linux cluster, and macOS laptops (Mojave and Catalina). --- .../repos/builtin/packages/upcxx/package.py | 109 ++++++++++++++++-- 1 file changed, 100 insertions(+), 9 deletions(-) diff --git a/var/spack/repos/builtin/packages/upcxx/package.py b/var/spack/repos/builtin/packages/upcxx/package.py index e4806c4c9c5..d5c74bebb97 100644 --- a/var/spack/repos/builtin/packages/upcxx/package.py +++ b/var/spack/repos/builtin/packages/upcxx/package.py @@ -10,7 +10,7 @@ def cross_detect(): if spack.architecture.platform().name == 'cray': if which('srun'): return 'cray-aries-slurm' - if which('alps'): + if which('aprun'): return 'cray-aries-alps' return 'none' @@ -25,9 +25,17 @@ class Upcxx(Package): homepage = "https://upcxx.lbl.gov" maintainers = ['bonachea'] + git = 'https://bonachea@bitbucket.org/berkeleylab/upcxx.git' + version('develop', branch='develop') + version('master', branch='master') + + version('2020.3.0', sha256='01be35bef4c0cfd24e9b3d50c88866521b9cac3ad4cbb5b1fc97aea55078810f') version('2019.9.0', sha256='7d67ccbeeefb59de9f403acc719f52127a30801a2c2b9774a1df03f850f8f1d4') version('2019.3.2', sha256='dcb0b337c05a0feb2ed5386f5da6c60342412b49cab10f282f461e74411018ad') + variant('mpi', default=False, + description='Enables MPI-based spawners and mpi-conduit') + variant('cuda', default=False, description='Builds a CUDA-enabled version of UPC++') @@ -35,10 +43,19 @@ class Upcxx(Package): description="UPC++ cross-compile target (autodetect by default)") conflicts('cross=none', when='platform=cray', - msg='None is unacceptable on Cray.') + msg='cross=none is unacceptable on Cray.' + + 'Please specify an appropriate "cross" value') + depends_on('mpi', when='+mpi') depends_on('cuda', when='+cuda') - depends_on('python@2.7.5:2.999', type=("build", "run")) + # Require Python2 2.7.5+ up to v2019.9.0 + depends_on('python@2.7.5:2.999', + type=("build", "run"), when='@:2019.9.0') + # v2020.3.0 and later also permit Python3 + depends_on('python@2.7.5:', type=("build", "run"), when='@2020.3.0:') + + # All flags should be passed to the build-env in autoconf-like vars + flag_handler = env_flags def url_for_version(self, version): if version > Version('2019.3.2'): @@ -48,8 +65,14 @@ def url_for_version(self, version): return url.format(version) def setup_build_environment(self, env): - if 'platform=cray' in self.spec: - env.set('GASNET_CONFIGURE_ARGS', '--enable-mpi=probe') + # ensure we use the correct python + env.set('UPCXX_PYTHON', self.spec['python'].command.path) + + if '+mpi' in self.spec: + env.set('GASNET_CONFIGURE_ARGS', + '--enable-mpi --enable-mpi-compat') + else: + env.set('GASNET_CONFIGURE_ARGS', '--without-mpicc') if 'cross=none' not in self.spec: env.set('CROSS', self.spec.variants['cross'].value) @@ -59,6 +82,9 @@ def setup_build_environment(self, env): env.set('UPCXX_CUDA_NVCC', self.spec['cuda'].prefix.bin.nvcc) def setup_run_environment(self, env): + # ensure we use the correct python + env.set('UPCXX_PYTHON', self.spec['python'].command.path) + env.set('UPCXX_INSTALL', self.prefix) env.set('UPCXX', self.prefix.bin.upcxx) if 'platform=cray' in self.spec: @@ -76,7 +102,72 @@ def setup_dependent_build_environment(self, env, dependent_spec): env.set('UPCXX_NETWORK', 'aries') def install(self, spec, prefix): - env['CC'] = self.compiler.cc - env['CXX'] = self.compiler.cxx - installsh = Executable("./install") - installsh(prefix) + # UPC++ follows autoconf naming convention for LDLIBS, which is 'LIBS' + if (env.get('LDLIBS')): + env['LIBS'] = env['LDLIBS'] + + if spec.version <= Version('2019.9.0'): + env['CC'] = self.compiler.cc + if '+mpi' in self.spec: + if 'platform=cray' in self.spec: + env['GASNET_CONFIGURE_ARGS'] += \ + " --with-mpicc=" + self.compiler.cc + else: + env['CXX'] = spec['mpi'].mpicxx + else: + env['CXX'] = self.compiler.cxx + installsh = Executable("./install") + installsh(prefix) + else: + if 'platform=cray' in self.spec: + # Spack loads the cray-libsci module incorrectly on ALCF theta, + # breaking the Cray compiler wrappers + # cray-libsci is irrelevant to our build, so disable it + for var in ['PE_PKGCONFIG_PRODUCTS', 'PE_PKGCONFIG_LIBS']: + env[var] = ":".join( + filter(lambda x: "libsci" not in x.lower(), + env[var].split(":"))) + # Undo spack compiler wrappers: + # the C/C++ compilers must work post-install + # hack above no longer works after the fix to UPC++ issue #287 + real_cc = join_path(env['CRAYPE_DIR'], 'bin', 'cc') + real_cxx = join_path(env['CRAYPE_DIR'], 'bin', 'CC') + # workaround a bug in the UPC++ installer: (issue #346) + env['GASNET_CONFIGURE_ARGS'] += \ + " --with-cc=" + real_cc + " --with-cxx=" + real_cxx + if '+mpi' in self.spec: + env['GASNET_CONFIGURE_ARGS'] += " --with-mpicc=" + real_cc + else: + real_cc = self.compiler.cc + real_cxx = self.compiler.cxx + if '+mpi' in self.spec: + real_cxx = spec['mpi'].mpicxx + + env['CC'] = real_cc + env['CXX'] = real_cxx + + installsh = Executable("./configure") + installsh('--prefix=' + prefix) + + make() + + make('install') + + @run_after('install') + @on_package_attributes(run_tests=True) + def test_install(self): + if self.spec.version <= Version('2019.9.0'): + spack.main.send_warning_to_tty( + "run_tests not supported in UPC++ version " + + self.spec.version.string + " -- SKIPPED") + else: + # enable testing of unofficial conduits (mpi) + test_networks = 'NETWORKS=$(CONDUITS)' + # build hello world against installed tree in all configurations + make('test_install', test_networks) + make('tests-clean') # cleanup + # build all tests for all networks in debug mode + make('tests', test_networks) + if 'cross=none' in self.spec: + make('run-tests', 'NETWORKS=smp') # runs tests for smp backend + make('tests-clean') # cleanup From 9f256ed953f611c37e0030f2e5c70155c28b1297 Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Wed, 25 Mar 2020 21:00:15 -0500 Subject: [PATCH 213/377] darshan-util and darshan-runtime: add version 3.1.8 (#15681) --- var/spack/repos/builtin/packages/darshan-runtime/package.py | 1 + var/spack/repos/builtin/packages/darshan-util/package.py | 1 + 2 files changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/darshan-runtime/package.py b/var/spack/repos/builtin/packages/darshan-runtime/package.py index f6487d498ee..3789612f129 100644 --- a/var/spack/repos/builtin/packages/darshan-runtime/package.py +++ b/var/spack/repos/builtin/packages/darshan-runtime/package.py @@ -21,6 +21,7 @@ class DarshanRuntime(Package): maintainers = ['shanedsnyder', 'carns'] version('develop', branch='master') + version('3.1.8', sha256='3ed51c8d5d93b4a8cbb7d53d13052140a9dffe0bc1a3e1ebfc44a36a184b5c82') version('3.1.7', sha256='9ba535df292727ac1e8025bdf2dc42942715205cad8319d925723fd88709e8d6') version('3.1.6', sha256='21cb24e2a971c45e04476e00441b7fbea63d2afa727a5cf8b7a4a9d9004dd856') version('3.1.0', sha256='b847047c76759054577823fbe21075cfabb478cdafad341d480274fb1cef861c') diff --git a/var/spack/repos/builtin/packages/darshan-util/package.py b/var/spack/repos/builtin/packages/darshan-util/package.py index 9fe3012b2c2..8d25fa99650 100644 --- a/var/spack/repos/builtin/packages/darshan-util/package.py +++ b/var/spack/repos/builtin/packages/darshan-util/package.py @@ -19,6 +19,7 @@ class DarshanUtil(Package): maintainers = ['shanedsnyder', 'carns'] version('develop', branch='master') + version('3.1.8', sha256='3ed51c8d5d93b4a8cbb7d53d13052140a9dffe0bc1a3e1ebfc44a36a184b5c82') version('3.1.7', sha256='9ba535df292727ac1e8025bdf2dc42942715205cad8319d925723fd88709e8d6') version('3.1.6', sha256='21cb24e2a971c45e04476e00441b7fbea63d2afa727a5cf8b7a4a9d9004dd856') version('3.1.0', sha256='b847047c76759054577823fbe21075cfabb478cdafad341d480274fb1cef861c') From a2801a8deb62a01f32cc110cd3ace207eb53603b Mon Sep 17 00:00:00 2001 From: iarspider Date: Thu, 26 Mar 2020 03:00:39 +0100 Subject: [PATCH 214/377] OpenJDK: add version 8u222 (#15677) --- var/spack/repos/builtin/packages/openjdk/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/openjdk/package.py b/var/spack/repos/builtin/packages/openjdk/package.py index 9d0b3d54e40..2007ccd78d3 100644 --- a/var/spack/repos/builtin/packages/openjdk/package.py +++ b/var/spack/repos/builtin/packages/openjdk/package.py @@ -16,6 +16,8 @@ class Openjdk(Package): url="https://download.java.net/java/GA/jdk11/9/GPL/openjdk-11.0.2_linux-x64_bin.tar.gz") version("11.0.1", sha256="7a6bb980b9c91c478421f865087ad2d69086a0583aeeb9e69204785e8e97dcfd", url="https://download.java.net/java/GA/jdk11/13/GPL/openjdk-11.0.1_linux-x64_bin.tar.gz") + version("1.8.0_222-b10", sha256="20cff719c6de43f8bb58c7f59e251da7c1fa2207897c9a4768c8c669716dc819", + url="https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u222-b10_openj9-0.15.1/OpenJDK8U-jdk_x64_linux_openj9_8u222b10_openj9-0.15.1.tar.gz") version("1.8.0_202-b08", sha256="533dcd8d9ca15df231a1eb392fa713a66bca85a8e76d9b4ee30975f3823636b7", url="https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u202-b08/OpenJDK8U-jdk_x64_linux_openj9_8u202b08_openj9-0.12.0.tar.gz") version('1.8.0_40-b25', sha256='79e96dce03a14271040023231a7d0ae374b755d48adf68bbdaec30294e4e2b88', From 851fb173c868ac380f7960f74a7baebe63245fdf Mon Sep 17 00:00:00 2001 From: gauthier12 <45069706+gauthier12@users.noreply.github.com> Date: Thu, 26 Mar 2020 03:10:31 +0100 Subject: [PATCH 215/377] med package: add version 4.0.0 (#15652) --- var/spack/repos/builtin/packages/med/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/med/package.py b/var/spack/repos/builtin/packages/med/package.py index 3b416c02742..c4be8dfbea4 100644 --- a/var/spack/repos/builtin/packages/med/package.py +++ b/var/spack/repos/builtin/packages/med/package.py @@ -15,15 +15,17 @@ class Med(CMakePackage): maintainers = ['likask'] + version('4.0.0', sha256='a474e90b5882ce69c5e9f66f6359c53b8b73eb448c5f631fa96e8cd2c14df004') version('3.2.0', sha256='d52e9a1bdd10f31aa154c34a5799b48d4266dc6b4a5ee05a9ceda525f2c6c138') variant('api23', default=True, description='Enable API2.3') depends_on('mpi') - depends_on('hdf5@:1.8.19+mpi') + depends_on('hdf5@:1.8.19+mpi', when='@3.2.0') + depends_on('hdf5@:1.10.2+mpi', when='@4.0.0') # C++11 requires a space between literal and identifier - patch('add_space.patch') + patch('add_space.patch', when='@3.2.0') # FIXME This is minimal installation. From 9f5873324e385ada86ee6bbf2edad82d5aba0f32 Mon Sep 17 00:00:00 2001 From: darmac Date: Thu, 26 Mar 2020 14:50:28 +0800 Subject: [PATCH 216/377] kmod: added package at v27 (#15633) --- .../repos/builtin/packages/kmod/package.py | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 var/spack/repos/builtin/packages/kmod/package.py diff --git a/var/spack/repos/builtin/packages/kmod/package.py b/var/spack/repos/builtin/packages/kmod/package.py new file mode 100644 index 00000000000..0ee203e7a2d --- /dev/null +++ b/var/spack/repos/builtin/packages/kmod/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Kmod(AutotoolsPackage): + """kmod is a set of tools to handle common tasks with Linux kernel modules + like insert, remove, list, check properties, resolve dependencies and + aliases.""" + + homepage = "https://github.com/lucasdemarchi/kmod" + url = "https://github.com/lucasdemarchi/kmod/archive/v27.tar.gz" + + version('27', sha256='969c4573b01f4c9e1d3e3c9d179bd16ec999bbb99dd55b7623f42551328478c3') + version('26', sha256='f28bc40ead548dce4a8e956fccfc36fd80f2b40884d270b812f1bfbd886e858c') + version('25', sha256='16a8bbd3ee321d0847847256ea2fd124f6250257c055c8cf97e78f18bf27559c') + version('24', sha256='f7a5ee07d4901c87711880536604de7e31c182d85a72de7b8d7dd04d4ee0aa59') + version('23', sha256='8f139543d82e8ccc2227dec4c016d6656e9789365a6dce73f90b620a53e62ee6') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') + + def autoreconf(self, spec, prefix): + bash = which("bash") + bash('autogen.sh') From 9e51ba80c724a4a71456f2a42935381421ef0547 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Thu, 26 Mar 2020 16:37:25 +0900 Subject: [PATCH 217/377] ppOpen-Math/VIS: added new package (#15665) --- .../packages/ppopen-math-vis/package.py | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ppopen-math-vis/package.py diff --git a/var/spack/repos/builtin/packages/ppopen-math-vis/package.py b/var/spack/repos/builtin/packages/ppopen-math-vis/package.py new file mode 100644 index 00000000000..ad2ff3a7c8f --- /dev/null +++ b/var/spack/repos/builtin/packages/ppopen-math-vis/package.py @@ -0,0 +1,45 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * +import os + + +class PpopenMathVis(MakefilePackage): + """ + ppOpen-MATH/VIS is a set of libraries for parallel visualization. + + Capabilities of ppOpen-MATH/VIS (ver.0.2.0) are as follows: + + Using background voxels with adaptive mesh refinement (AMR). + Single UCD file. + Flat MPI parallel programming models. + (OpenMP/MPI hybrid will be supported in the future). + Can be called from programs written in both of Fortran 90 and C. + Only FDM-type structured meshes are supported. + """ + + homepage = "http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/" + url = "file://{0}/ppohVIS_0.2.0.tar.gz".format(os.getcwd()) + + version('0.2.0', sha256='f816885cb9fab4802f9df55c1f1e7f8505867dc8862562bce26d193d6a0dc29d') + + depends_on('mpi') + + def edit(self, spec, prefix): + makefile_in = FileFilter('Makefile.in') + makefile_in.filter('mpifccpx', spec['mpi'].mpicc) + makefile_in.filter('mpiFCCpx', spec['mpi'].mpicxx) + makefile_in.filter('mpifrtpx', spec['mpi'].mpifc) + makefile_in.filter('-Kfast', '-O3') + makefile_in.filter(r'~/ppOpen-HPC/.*', prefix) + + def install(self, spec, prefix): + make('install') + mkdir(join_path(prefix, 'examples')) + copy_tree('examples', join_path(prefix, 'examples')) + mkdir(join_path(prefix, 'doc')) + copy_tree('doc', join_path(prefix, 'doc')) From a0c8686105ac8ff35f800600d5365c8cff044f02 Mon Sep 17 00:00:00 2001 From: Andrew Gaspar Date: Thu, 26 Mar 2020 05:46:39 -0600 Subject: [PATCH 218/377] catch2: added versions up to v2.11.3 (#15680) --- var/spack/repos/builtin/packages/catch2/package.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/var/spack/repos/builtin/packages/catch2/package.py b/var/spack/repos/builtin/packages/catch2/package.py index 989c96f7fb6..6961afad299 100644 --- a/var/spack/repos/builtin/packages/catch2/package.py +++ b/var/spack/repos/builtin/packages/catch2/package.py @@ -14,6 +14,14 @@ class Catch2(CMakePackage): url = "https://github.com/catchorg/Catch2/archive/v2.9.1.tar.gz" maintainers = ['ax3l'] + version('2.11.3', sha256='9a6967138062688f04374698fce4ce65908f907d8c0fe5dfe8dc33126bd46543') + version('2.11.2', sha256='a96203fa531092375678ad2d81c43317ee58c684787f24b2a55748f6c6839799') + version('2.11.1', sha256='9af06ca5b10362620c6c9c729821367e1aeb0f76adfc7bc3a468da83db3c50c6') + version('2.11.0', sha256='b9957af46a04327d80833960ae51cf5e67765fd264389bd1e275294907f1a3e0') + version('2.10.2', sha256='79aa46ee6c5a87bc5306bfffc6ecde6a1ad6327715b208ee2e846873f282a494') + version('2.10.1', sha256='dcbbe0a5f4d2a4330bdf5bcb9ef6a02303d679d46596e4ed06ca462f2372d4de') + version('2.10.0', sha256='a3beaa8ba6238c189e1f81238ab38e585836af13204a7099e22eff6c25b98558') + version('2.9.2', sha256='54bea6d80a388a80f895cd0e2343fca72b0d9093a776af40904aefce49c13bda') version('2.9.1', sha256='0b36488aca6265e7be14da2c2d0c748b4ddb9c70a1ea4da75736699c629f14ac') version('2.9.0', sha256='00040cad9b6d6bb817ebd5853ff6dda23f9957153d8c4eedf85def0c9e787c42') version('2.8.0', sha256='b567c37446cd22c8550bfeb7e2fe3f981b8f3ab8b2148499a522e7f61b8a481d') From 7b4354b4c3b6f3aed19bbd6be96e8a42a0c272ef Mon Sep 17 00:00:00 2001 From: Jennifer Herting Date: Thu, 26 Mar 2020 10:01:24 -0400 Subject: [PATCH 219/377] genometools: added v1.6.1 (#15657) --- var/spack/repos/builtin/packages/genometools/package.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/genometools/package.py b/var/spack/repos/builtin/packages/genometools/package.py index 082fc777411..ac7ef818053 100644 --- a/var/spack/repos/builtin/packages/genometools/package.py +++ b/var/spack/repos/builtin/packages/genometools/package.py @@ -11,16 +11,17 @@ class Genometools(MakefilePackage): of genome informatics) combined into a single binary named gt.""" homepage = "http://genometools.org/" - url = "http://genometools.org/pub/genometools-1.5.9.tar.gz" + url = "https://github.com/genometools/genometools/archive/v1.6.1.tar.gz" - version('1.5.9', sha256='36923198a4214422886fd1425ef986bd7e558c73b94194982431cfd3dc7eb387') + version('1.6.1', sha256='528ca143a7f1d42af8614d60ea1e5518012913a23526d82e434f0dad2e2d863f') + version('1.5.9', sha256='bba8e043f097e7c72e823f73cb0efbd20bbd60f1ce797a0e4c0ab632b170c909') depends_on('perl', type=('build', 'run')) depends_on('cairo') depends_on('pango') # build fails with gcc 7" - conflicts('%gcc@7.1.0:') + conflicts('%gcc@7.1.0:', when='@:1.5.9') def install(self, spec, prefix): make('install', 'prefix=%s' % prefix) From ef7837410e32dac1c892a62a5deae10bc0c08da6 Mon Sep 17 00:00:00 2001 From: Roman Briskine Date: Fri, 27 Mar 2020 03:32:19 +0000 Subject: [PATCH 220/377] Fix non-root installations; update homepage (#15701) --- var/spack/repos/builtin/packages/util-linux/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/util-linux/package.py b/var/spack/repos/builtin/packages/util-linux/package.py index b95f8222e2f..d4887601a06 100644 --- a/var/spack/repos/builtin/packages/util-linux/package.py +++ b/var/spack/repos/builtin/packages/util-linux/package.py @@ -9,7 +9,7 @@ class UtilLinux(AutotoolsPackage): """Util-linux is a suite of essential utilities for any Linux system.""" - homepage = "http://freecode.com/projects/util-linux" + homepage = "https://github.com/karelzak/util-linux" url = "https://www.kernel.org/pub/linux/utils/util-linux/v2.29/util-linux-2.29.2.tar.gz" list_url = "https://www.kernel.org/pub/linux/utils/util-linux" list_depth = 1 @@ -36,6 +36,7 @@ def url_for_version(self, version): def configure_args(self): config_args = [ '--disable-use-tty-group', + '--disable-makeinstall-chown', ] config_args.extend(self.enable_or_disable('libuuid')) return config_args From 640df9c20b98eb3e6d0c3d1828a21b5659ae11b8 Mon Sep 17 00:00:00 2001 From: iarspider Date: Fri, 27 Mar 2020 04:36:24 +0100 Subject: [PATCH 221/377] range-v3: add new version (0.10.0) (#15697) --- var/spack/repos/builtin/packages/range-v3/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/range-v3/package.py b/var/spack/repos/builtin/packages/range-v3/package.py index 261922ceb79..9c7a9cd6a32 100644 --- a/var/spack/repos/builtin/packages/range-v3/package.py +++ b/var/spack/repos/builtin/packages/range-v3/package.py @@ -22,6 +22,7 @@ class RangeV3(CMakePackage): maintainers = ['chissg'] version('develop', branch='master') + version('0.10.0', sha256='5a1cd44e7315d0e8dcb1eee4df6802221456a9d1dbeac53da02ac7bd4ea150cd') version('0.5.0', sha256='32e30b3be042246030f31d40394115b751431d9d2b4e0f6d58834b2fd5594280') version('0.4.0', sha256='5dbc878b7dfc500fb04b6b9f99d63993a2731ea34b0a4b8d5f670a5a71a18e39') version('0.3.7', sha256='e6b0fb33bfd07ec32d54bcddd3e8d62e995a3cf0b64b34788ec264da62581207') From bbc76c35517b88cda0af6405c04b3accd40cb67e Mon Sep 17 00:00:00 2001 From: iarspider Date: Fri, 27 Mar 2020 04:37:33 +0100 Subject: [PATCH 222/377] fmt: new version (6.1.2) (#15695) --- var/spack/repos/builtin/packages/fmt/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/fmt/package.py b/var/spack/repos/builtin/packages/fmt/package.py index 8cba74d000a..be39f6cc838 100644 --- a/var/spack/repos/builtin/packages/fmt/package.py +++ b/var/spack/repos/builtin/packages/fmt/package.py @@ -14,6 +14,7 @@ class Fmt(CMakePackage): homepage = "http://fmtlib.net/latest/index.html" url = "https://github.com/fmtlib/fmt/releases/download/5.2.1/fmt-5.2.1.zip" + version('6.1.2', sha256='63650f3c39a96371f5810c4e41d6f9b0bb10305064e6faf201cbafe297ea30e8') version('5.3.0', sha256='4c0741e10183f75d7d6f730b8708a99b329b2f942dad5a9da3385ab92bb4a15c') version('5.2.1', sha256='43894ab8fe561fc9e523a8024efc23018431fa86b95d45b06dbe6ddb29ffb6cd') version('5.2.0', sha256='c016db7f825bce487a7929e1edb747b9902a2935057af6512cad3df3a080a027') From 209c7e3ddd4e0883c4c17515c801b78032059abe Mon Sep 17 00:00:00 2001 From: iarspider Date: Fri, 27 Mar 2020 04:37:56 +0100 Subject: [PATCH 223/377] xrootd: new version (4.11.2) (#15694) --- var/spack/repos/builtin/packages/xrootd/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/xrootd/package.py b/var/spack/repos/builtin/packages/xrootd/package.py index 6f0f9268c13..438e5d385b1 100644 --- a/var/spack/repos/builtin/packages/xrootd/package.py +++ b/var/spack/repos/builtin/packages/xrootd/package.py @@ -13,6 +13,7 @@ class Xrootd(CMakePackage): homepage = "http://xrootd.org" url = "http://xrootd.org/download/v4.6.0/xrootd-4.6.0.tar.gz" + version('4.11.2', sha256='4620824db97fcc37dc3dd26110da8e5c3aab1d8302e4921d4f32e83207060603') version('4.10.0', sha256='f07f85e27d72e9e8ff124173c7b53619aed8fcd36f9d6234c33f8f7fd511995b') version('4.8.5', sha256='42e4d2cc6f8b442135f09bcc12c7be38b1a0c623a005cb5e69ff3d27997bdf73') version('4.8.4', sha256='f148d55b16525567c0f893edf9bb2975f7c09f87f0599463e19e1b456a9d95ba') From e989c05cd0e249be41cd7a4a24f2b126c3ce6f8d Mon Sep 17 00:00:00 2001 From: "Seth R. Johnson" Date: Thu, 26 Mar 2020 23:38:56 -0400 Subject: [PATCH 224/377] Add include-what-you-use (#15691) --- .../packages/iwyu/iwyu-013-cmake.patch | 34 +++++++++++++++++++ .../repos/builtin/packages/iwyu/package.py | 27 +++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 var/spack/repos/builtin/packages/iwyu/iwyu-013-cmake.patch create mode 100644 var/spack/repos/builtin/packages/iwyu/package.py diff --git a/var/spack/repos/builtin/packages/iwyu/iwyu-013-cmake.patch b/var/spack/repos/builtin/packages/iwyu/iwyu-013-cmake.patch new file mode 100644 index 00000000000..78cb1a2d101 --- /dev/null +++ b/var/spack/repos/builtin/packages/iwyu/iwyu-013-cmake.patch @@ -0,0 +1,34 @@ +--- include-what-you-use/CMakeLists.txt 2019-10-24 15:47:52.000000000 -0400 ++++ spack-src/CMakeLists.txt 2020-03-26 07:16:53.284593661 -0400 +@@ -60,21 +60,22 @@ + # Use only major.minor.patch for the resource directory structure; some + # platforms include suffix in LLVM_VERSION. + set(llvm_ver ${LLVM_VERSION_MAJOR}.${LLVM_VERSION_MINOR}.${LLVM_VERSION_PATCH}) +- set(clang_headers_src ${CMAKE_PREFIX_PATH}/lib/clang/${llvm_ver}/include) +- set(clang_headers_dst ${CMAKE_BINARY_DIR}/lib/clang/${llvm_ver}/include) ++ set(clang_headers_src "${LLVM_INSTALL_PREFIX}/lib/clang/${llvm_ver}/include") ++ set(clang_headers_dst "${CMAKE_BINARY_DIR}/lib/clang/${llvm_ver}/include") + +- file(GLOB_RECURSE in_files RELATIVE ${clang_headers_src} ${clang_headers_src}/*) ++ file(GLOB_RECURSE in_files RELATIVE "${clang_headers_src}" ++ "${clang_headers_src}/*") + + set(out_files) + foreach (file ${in_files}) +- set(src ${clang_headers_src}/${file}) +- set(dst ${clang_headers_dst}/${file}) ++ set(src "${clang_headers_src}/${file}") ++ set(dst "${clang_headers_dst}/${file}") + +- add_custom_command(OUTPUT ${dst} +- DEPENDS ${src} +- COMMAND ${CMAKE_COMMAND} -E copy_if_different ${src} ${dst} ++ add_custom_command(OUTPUT "${dst}" ++ DEPENDS "${src}" ++ COMMAND ${CMAKE_COMMAND} -E copy_if_different "${src}" "${dst}" + COMMENT "Copying clang's ${file}...") +- list(APPEND out_files ${dst}) ++ list(APPEND out_files "${dst}") + endforeach() + + add_custom_target(clang-resource-headers ALL DEPENDS ${out_files}) diff --git a/var/spack/repos/builtin/packages/iwyu/package.py b/var/spack/repos/builtin/packages/iwyu/package.py new file mode 100644 index 00000000000..a05ff073b7b --- /dev/null +++ b/var/spack/repos/builtin/packages/iwyu/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Iwyu(CMakePackage): + """include-what-you-use: A tool for use with clang to analyze #includes in + C and C++ source files + """ + + homepage = "https://include-what-you-use.org" + url = "https://include-what-you-use.org/downloads/include-what-you-use-0.13.src.tar.gz" + + maintainers = ['sethrj'] + + version('0.13', sha256='49294270aa64e8c04182369212cd919f3b3e0e47601b1f935f038c761c265bc9') + version('0.12', sha256='a5892fb0abccb820c394e4e245c00ef30fc94e4ae58a048b23f94047c0816025') + version('0.11', sha256='2d2877726c4aed9518cbb37673ffbc2b7da9c239bf8fe29432da35c1c0ec367a') + + patch('iwyu-013-cmake.patch', when='@0.13') + + depends_on('llvm+clang@9.0:9.999', when='@0.13') + depends_on('llvm+clang@8.0:8.999', when='@0.12') + depends_on('llvm+clang@7.0:7.999', when='@0.11') From 82936602172c76da3832f69bc45d5c93e7f16a85 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Fri, 27 Mar 2020 12:40:22 +0900 Subject: [PATCH 225/377] ppOpen-MATH/MP: New package. (#15690) * ppOpen-MATH/MP: New package. * Fix quote. --- .../packages/ppopen-math-mp/package.py | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ppopen-math-mp/package.py diff --git a/var/spack/repos/builtin/packages/ppopen-math-mp/package.py b/var/spack/repos/builtin/packages/ppopen-math-mp/package.py new file mode 100644 index 00000000000..8f622644850 --- /dev/null +++ b/var/spack/repos/builtin/packages/ppopen-math-mp/package.py @@ -0,0 +1,51 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * +import os + + +class PpopenMathMp(MakefilePackage): + """ + ppOpen-Math/MP ia a coupling library that enables weak coupling on various + simulation models, such as an atmospheric model and an ocean model, + a seismic model and a structure model. For getting very wide applicability, + ppOpen-Math/MP is designed so as that it is independent from grid + structure. Instead of grid structure, PpohMATHMP requires a data set + called 'mapping table'. Mapping table is composed of a correspondence + table of grid indexes between a send model and a receive model and + interpolation coefficients. A subroutine for making a mapping table + file is provided by ppOpen-Math/MP API. + + Current version of ppOpen-Math/MP is ver.1.0 which targets scalar + data exchange. An exchange code of vector data which requires rotation + calculation is under development and will be released the next version. + """ + + homepage = "http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/" + url = "file://{0}/ppohMATHMP_1.0.0.tar.gz".format(os.getcwd()) + + version('1.0.0', sha256='eb85a181286e4e7d071bd7c106fa547d38cfd16df87753e9d4e38da1a84a8f22') + + depends_on('mpi') + + build_directory = 'src' + build_targets = ['FC_XXX=spack'] + parallel = False + + def edit(self, spec, prefix): + flags = ['-I.'] + if spec.satisfies('%gcc'): + flags.append('-ffree-line-length-none') + with open('src/Makefile', 'a') as makefile: + makefile.write('FC_spack = {0}\n'.format(spec['mpi'].mpifc)) + makefile.write('FFLAGS_spack = {0}\n'.format(' '.join(flags))) + makefile.write('AR_spack = ar cr\n') + + def install(self, spec, prefix): + for d in ['include', 'lib', 'doc', 'test']: + mkdir(join_path(prefix, d)) + copy_tree(d, join_path(prefix, d)) From 5cb4db8570d42267d209f50778d062e0c72bb4d6 Mon Sep 17 00:00:00 2001 From: noguchi-k <55966120+noguchi-k@users.noreply.github.com> Date: Fri, 27 Mar 2020 12:41:25 +0900 Subject: [PATCH 226/377] gtkorvo-dill: fix argument type of clear_cache (#15689) --- .../gtkorvo-dill/2.1-fix-clear_cache.patch | 148 ++++++++++++++++++ .../gtkorvo-dill/2.4-fix-clear_cache.patch | 148 ++++++++++++++++++ .../builtin/packages/gtkorvo-dill/package.py | 4 + 3 files changed, 300 insertions(+) create mode 100644 var/spack/repos/builtin/packages/gtkorvo-dill/2.1-fix-clear_cache.patch create mode 100644 var/spack/repos/builtin/packages/gtkorvo-dill/2.4-fix-clear_cache.patch diff --git a/var/spack/repos/builtin/packages/gtkorvo-dill/2.1-fix-clear_cache.patch b/var/spack/repos/builtin/packages/gtkorvo-dill/2.1-fix-clear_cache.patch new file mode 100644 index 00000000000..cfab7234149 --- /dev/null +++ b/var/spack/repos/builtin/packages/gtkorvo-dill/2.1-fix-clear_cache.patch @@ -0,0 +1,148 @@ +diff -ur spack-src.org/CMakeLists.txt spack-src/CMakeLists.txt +--- spack-src.org/CMakeLists.txt 2020-03-26 16:38:53.358339744 +0900 ++++ spack-src/CMakeLists.txt 2020-03-26 16:44:04.581014766 +0900 +@@ -184,6 +184,9 @@ + CHECK_INCLUDE_FILES(malloc.h HAVE_MALLOC_H) + CHECK_INCLUDE_FILES(memory.h HAVE_MEMORY_H) + INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR}) ++include(CheckSymbolExists) ++check_symbol_exists(__clear_cache "" CLEAR_CACHE_DEFINED) ++message(STATUS "Clear cache defined is ${CLEAR_CACHE_DEFINED}") + + set (NO_DISASSEMBLER TRUE) + if (ENABLE_DISASSEMBLY) +diff -ur spack-src.org/arm6.c spack-src/arm6.c +--- spack-src.org/arm6.c 2020-03-26 16:38:53.358339744 +0900 ++++ spack-src/arm6.c 2020-03-26 16:45:20.428978615 +0900 +@@ -1524,22 +1524,9 @@ + } + + +-/* Clear the instruction cache from `beg' to `end'. This makes an +- inline system call to SYS_cacheflush. */ +-#define CLEAR_INSN_CACHE(BEG, END) \ +-{ \ +- register unsigned long _beg __asm ("a1") = (unsigned long) (BEG); \ +- register unsigned long _end __asm ("a2") = (unsigned long) (END); \ +- register unsigned long _flg __asm ("a3") = 0; \ +- __asm __volatile ("swi 0x9f0002 @ sys_cacheflush" \ +- : "=r" (_beg) \ +- : "0" (_beg), "r" (_end), "r" (_flg)); \ +-} +-/* +- * Cache flush code grabbed from a Dec 1999 posting on libc-hacker +- * mailing list +- */ +-extern void __clear_cache(char*, char *); ++#ifndef CLEAR_CACHE_DEFINED ++extern void __clear_cache(void *, void *); ++#endif + + static void + arm6_flush(void *base, void *limit) +diff -ur spack-src.org/arm6_rt.c spack-src/arm6_rt.c +--- spack-src.org/arm6_rt.c 2020-03-26 16:38:53.358339744 +0900 ++++ spack-src/arm6_rt.c 2020-03-26 16:48:18.927720543 +0900 +@@ -109,22 +109,9 @@ + } + } + +-/* Clear the instruction cache from `beg' to `end'. This makes an +- inline system call to SYS_cacheflush. */ +-#define CLEAR_INSN_CACHE(BEG, END) \ +-{ \ +- register unsigned long _beg __asm ("a1") = (unsigned long) (BEG); \ +- register unsigned long _end __asm ("a2") = (unsigned long) (END); \ +- register unsigned long _flg __asm ("a3") = 0; \ +- __asm __volatile ("swi 0x9f0002 @ sys_cacheflush" \ +- : "=r" (_beg) \ +- : "0" (_beg), "r" (_end), "r" (_flg)); \ +-} +-/* +- * Cache flush code grabbed from a Dec 1999 posting on libc-hacker +- * mailing list +- */ +-extern void __clear_cache(char*, char *); ++#ifndef CLEAR_CACHE_DEFINED ++extern void __clear_cache(void *, void *); ++#endif + + static void + arm6_flush(void *base, void *limit) +diff -ur spack-src.org/arm8.c spack-src/arm8.c +--- spack-src.org/arm8.c 2020-03-26 16:38:53.358339744 +0900 ++++ spack-src/arm8.c 2020-03-26 16:49:38.386063473 +0900 +@@ -1524,22 +1524,9 @@ + } + + +-/* Clear the instruction cache from `beg' to `end'. This makes an +- inline system call to SYS_cacheflush. */ +-#define CLEAR_INSN_CACHE(BEG, END) \ +-{ \ +- register unsigned long _beg __asm ("a1") = (unsigned long) (BEG); \ +- register unsigned long _end __asm ("a2") = (unsigned long) (END); \ +- register unsigned long _flg __asm ("a3") = 0; \ +- __asm __volatile ("swi 0x9f0002 @ sys_cacheflush" \ +- : "=r" (_beg) \ +- : "0" (_beg), "r" (_end), "r" (_flg)); \ +-} +-/* +- * Cache flush code grabbed from a Dec 1999 posting on libc-hacker +- * mailing list +- */ +-extern void __clear_cache(char*, char *); ++#ifndef CLEAR_CACHE_DEFINED ++extern void __clear_cache(void *, void *); ++#endif + + static void + arm8_flush(void *base, void *limit) +diff -ur spack-src.org/arm8_rt.c spack-src/arm8_rt.c +--- spack-src.org/arm8_rt.c 2020-03-26 16:38:53.358339744 +0900 ++++ spack-src/arm8_rt.c 2020-03-26 16:50:37.902312532 +0900 +@@ -109,22 +109,9 @@ + } + } + +-/* Clear the instruction cache from `beg' to `end'. This makes an +- inline system call to SYS_cacheflush. */ +-#define CLEAR_INSN_CACHE(BEG, END) \ +-{ \ +- register unsigned long _beg __asm ("a1") = (unsigned long) (BEG); \ +- register unsigned long _end __asm ("a2") = (unsigned long) (END); \ +- register unsigned long _flg __asm ("a3") = 0; \ +- __asm __volatile ("swi 0x9f0002 @ sys_cacheflush" \ +- : "=r" (_beg) \ +- : "0" (_beg), "r" (_end), "r" (_flg)); \ +-} +-/* +- * Cache flush code grabbed from a Dec 1999 posting on libc-hacker +- * mailing list +- */ +-extern void __clear_cache(char*, char *); ++#ifndef CLEAR_CACHE_DEFINED ++extern void __clear_cache(void *, void *); ++#endif + + static void + arm8_flush(void *base, void *limit) +diff -ur spack-src.org/config.h.cmake spack-src/config.h.cmake +--- spack-src.org/config.h.cmake 2020-03-26 16:38:53.358339744 +0900 ++++ spack-src/config.h.cmake 2020-03-26 16:52:52.256419382 +0900 +@@ -13,10 +13,13 @@ + #cmakedefine HAVE_DIS_ASM_H + + /* Define to 1 if you have the header file. */ +-#undef HAVE_DLFCN_H ++#cmakedefine HAVE_DLFCN_H + + /* Define to 1 if you have the header file. */ +-#undef HAVE_INTTYPES_H ++#cmakedefine HAVE_INTTYPES_H ++ ++/* Define to 1 if you have __clear_cache is defined */ ++#cmakedefine CLEAR_CACHE_DEFINED + + /* Define to 1 if you have the header file. */ + #cmakedefine HAVE_MALLOC_H diff --git a/var/spack/repos/builtin/packages/gtkorvo-dill/2.4-fix-clear_cache.patch b/var/spack/repos/builtin/packages/gtkorvo-dill/2.4-fix-clear_cache.patch new file mode 100644 index 00000000000..7f47fba9529 --- /dev/null +++ b/var/spack/repos/builtin/packages/gtkorvo-dill/2.4-fix-clear_cache.patch @@ -0,0 +1,148 @@ +diff -ur spack-src.org/CMakeLists.txt spack-src/CMakeLists.txt +--- spack-src.org/CMakeLists.txt 2020-03-26 09:35:43.403836842 +0900 ++++ spack-src/CMakeLists.txt 2020-03-26 09:37:57.397837929 +0900 +@@ -267,6 +267,9 @@ + CHECK_INCLUDE_FILES(stdarg.h STDC_HEADERS) + CHECK_INCLUDE_FILES(malloc.h HAVE_MALLOC_H) + CHECK_INCLUDE_FILES(memory.h HAVE_MEMORY_H) ++include(CheckSymbolExists) ++check_symbol_exists(__clear_cache "" CLEAR_CACHE_DEFINED) ++message(STATUS "Clear cache defined is ${CLEAR_CACHE_DEFINED}") + + set (NO_DISASSEMBLER TRUE) + if (DILL_ENABLE_DISASSEMBLY) +diff -ur spack-src.org/arm6.c spack-src/arm6.c +--- spack-src.org/arm6.c 2020-03-26 09:35:43.403836842 +0900 ++++ spack-src/arm6.c 2020-03-26 09:40:06.021306329 +0900 +@@ -1526,22 +1526,9 @@ + } + + +-/* Clear the instruction cache from `beg' to `end'. This makes an +- inline system call to SYS_cacheflush. */ +-#define CLEAR_INSN_CACHE(BEG, END) \ +-{ \ +- register unsigned long _beg __asm ("a1") = (unsigned long) (BEG); \ +- register unsigned long _end __asm ("a2") = (unsigned long) (END); \ +- register unsigned long _flg __asm ("a3") = 0; \ +- __asm __volatile ("swi 0x9f0002 @ sys_cacheflush" \ +- : "=r" (_beg) \ +- : "0" (_beg), "r" (_end), "r" (_flg)); \ +-} +-/* +- * Cache flush code grabbed from a Dec 1999 posting on libc-hacker +- * mailing list +- */ +-extern void __clear_cache(char*, char *); ++#ifndef CLEAR_CACHE_DEFINED ++extern void __clear_cache(void *, void *); ++#endif + + static void + arm6_flush(void *base, void *limit) +diff -ur spack-src.org/arm6_rt.c spack-src/arm6_rt.c +--- spack-src.org/arm6_rt.c 2020-03-26 09:35:43.403836842 +0900 ++++ spack-src/arm6_rt.c 2020-03-26 09:41:59.823222738 +0900 +@@ -109,22 +109,9 @@ + } + } + +-/* Clear the instruction cache from `beg' to `end'. This makes an +- inline system call to SYS_cacheflush. */ +-#define CLEAR_INSN_CACHE(BEG, END) \ +-{ \ +- register unsigned long _beg __asm ("a1") = (unsigned long) (BEG); \ +- register unsigned long _end __asm ("a2") = (unsigned long) (END); \ +- register unsigned long _flg __asm ("a3") = 0; \ +- __asm __volatile ("swi 0x9f0002 @ sys_cacheflush" \ +- : "=r" (_beg) \ +- : "0" (_beg), "r" (_end), "r" (_flg)); \ +-} +-/* +- * Cache flush code grabbed from a Dec 1999 posting on libc-hacker +- * mailing list +- */ +-extern void __clear_cache(char*, char *); ++#ifndef CLEAR_CACHE_DEFINED ++extern void __clear_cache(void *, void *); ++#endif + + static void + arm6_flush(void *base, void *limit) +diff -ur spack-src.org/arm8.c spack-src/arm8.c +--- spack-src.org/arm8.c 2020-03-26 09:35:43.403836842 +0900 ++++ spack-src/arm8.c 2020-03-26 09:43:04.630008776 +0900 +@@ -1524,22 +1524,9 @@ + } + + +-/* Clear the instruction cache from `beg' to `end'. This makes an +- inline system call to SYS_cacheflush. */ +-#define CLEAR_INSN_CACHE(BEG, END) \ +-{ \ +- register unsigned long _beg __asm ("a1") = (unsigned long) (BEG); \ +- register unsigned long _end __asm ("a2") = (unsigned long) (END); \ +- register unsigned long _flg __asm ("a3") = 0; \ +- __asm __volatile ("swi 0x9f0002 @ sys_cacheflush" \ +- : "=r" (_beg) \ +- : "0" (_beg), "r" (_end), "r" (_flg)); \ +-} +-/* +- * Cache flush code grabbed from a Dec 1999 posting on libc-hacker +- * mailing list +- */ +-extern void __clear_cache(char*, char *); ++#ifndef CLEAR_CACHE_DEFINED ++extern void __clear_cache(void *, void *); ++#endif + + static void + arm8_flush(void *base, void *limit) +diff -ur spack-src.org/arm8_rt.c spack-src/arm8_rt.c +--- spack-src.org/arm8_rt.c 2020-03-26 09:35:43.403836842 +0900 ++++ spack-src/arm8_rt.c 2020-03-26 09:44:19.027799105 +0900 +@@ -109,22 +109,9 @@ + } + } + +-/* Clear the instruction cache from `beg' to `end'. This makes an +- inline system call to SYS_cacheflush. */ +-#define CLEAR_INSN_CACHE(BEG, END) \ +-{ \ +- register unsigned long _beg __asm ("a1") = (unsigned long) (BEG); \ +- register unsigned long _end __asm ("a2") = (unsigned long) (END); \ +- register unsigned long _flg __asm ("a3") = 0; \ +- __asm __volatile ("swi 0x9f0002 @ sys_cacheflush" \ +- : "=r" (_beg) \ +- : "0" (_beg), "r" (_end), "r" (_flg)); \ +-} +-/* +- * Cache flush code grabbed from a Dec 1999 posting on libc-hacker +- * mailing list +- */ +-extern void __clear_cache(char*, char *); ++#ifndef CLEAR_CACHE_DEFINED ++extern void __clear_cache(void *, void *); ++#endif + + static void + arm8_flush(void *base, void *limit) +diff -ur spack-src.org/config.h.cmake spack-src/config.h.cmake +--- spack-src.org/config.h.cmake 2020-03-26 09:35:43.403836842 +0900 ++++ spack-src/config.h.cmake 2020-03-26 09:46:56.124248964 +0900 +@@ -16,10 +16,13 @@ + #cmakedefine HAVE_DIS_ASM_H + + /* Define to 1 if you have the header file. */ +-#undef HAVE_DLFCN_H ++#cmakedefine HAVE_DLFCN_H + + /* Define to 1 if you have the header file. */ +-#undef HAVE_INTTYPES_H ++#cmakedefine HAVE_INTTYPES_H ++ ++/* Define to 1 if you have __clear_cache is defined */ ++#cmakedefine CLEAR_CACHE_DEFINED + + /* Define to 1 if you have the header file. */ + #cmakedefine HAVE_MALLOC_H diff --git a/var/spack/repos/builtin/packages/gtkorvo-dill/package.py b/var/spack/repos/builtin/packages/gtkorvo-dill/package.py index cb5920ae5b5..b708666d4fe 100644 --- a/var/spack/repos/builtin/packages/gtkorvo-dill/package.py +++ b/var/spack/repos/builtin/packages/gtkorvo-dill/package.py @@ -20,6 +20,10 @@ class GtkorvoDill(CMakePackage): version('2.4', sha256='ed7745d13e8c6a556f324dcc0e48a807fc993bdd5bb1daa94c1df116cb7e81fa') version('2.1', sha256='7671e1f3c25ac6a4ec2320cec2c342a2f668efb170e3dba186718ed17d2cf084') + # Ref: https://github.com/GTkorvo/dill/commit/dac6dfcc7fdaceeb4c157f9ecdf5ecc28f20477f + patch('2.4-fix-clear_cache.patch', when='@2.4') + patch('2.1-fix-clear_cache.patch', when='@2.1') + def cmake_args(self): args = [] if self.spec.satisfies('@2.4:'): From 2828815a4942181207ef13fe0f6e080f0ec86616 Mon Sep 17 00:00:00 2001 From: Sinan Date: Thu, 26 Mar 2020 20:41:57 -0700 Subject: [PATCH 227/377] add new versions (#15688) Co-authored-by: Sinan81 --- var/spack/repos/builtin/packages/qca/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/qca/package.py b/var/spack/repos/builtin/packages/qca/package.py index cbf1da89329..9a040bc6674 100644 --- a/var/spack/repos/builtin/packages/qca/package.py +++ b/var/spack/repos/builtin/packages/qca/package.py @@ -20,8 +20,10 @@ class Qca(CMakePackage): homepage = "https://userbase.kde.org/QCA" url = "https://github.com/KDE/qca/archive/v2.1.3.tar.gz" - version('2.2.1', sha256='c67fc0fa8ae6cb3d0ba0fbd8fca8ee8e4c5061b99f1fd685fd7d9800cef17f6b') - version('2.1.3', sha256='a5135ffb0250a40e9c361eb10cd3fe28293f0cf4e5c69d3761481eafd7968067') + version('2.3.0', sha256='39aa18f0985d82949f4dccce04af3eb8d4b6b64e0c71785786738d38d8183b0a') + version('2.2.90', sha256='074ac753b51a6fa15503be9418f7430effe368fd31dc41567942d832e539b17e') + version('2.2.1', sha256='c67fc0fa8ae6cb3d0ba0fbd8fca8ee8e4c5061b99f1fd685fd7d9800cef17f6b') + version('2.1.3', sha256='a5135ffb0250a40e9c361eb10cd3fe28293f0cf4e5c69d3761481eafd7968067') depends_on('qt@4.2:') From 0ebed5a6184ea7090e501487944382904de6846c Mon Sep 17 00:00:00 2001 From: Hector <10837193+he-b@users.noreply.github.com> Date: Thu, 26 Mar 2020 22:45:47 -0500 Subject: [PATCH 228/377] fix gdb installation (#15679) * fix gdb installation * add reference url --- var/spack/repos/builtin/packages/python/package.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index b35584d2c9d..3b675a02b64 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -670,6 +670,11 @@ def libs(self): # to ask Python where its LIBDIR is. libdir = self.get_config_var('LIBDIR') + # In Ubuntu 16.04.6 and python 2.7.12 from the system, lib could be + # in LBPL + # https://mail.python.org/pipermail/python-dev/2013-April/125733.html + libpl = self.get_config_var('LIBPL') + # The system Python installation on macOS and Homebrew installations # install libraries into a Frameworks directory frameworkprefix = self.get_config_var('PYTHONFRAMEWORKPREFIX') @@ -679,6 +684,8 @@ def libs(self): if os.path.exists(os.path.join(libdir, ldlibrary)): return LibraryList(os.path.join(libdir, ldlibrary)) + elif os.path.exists(os.path.join(libpl, ldlibrary)): + return LibraryList(os.path.join(libpl, ldlibrary)) elif os.path.exists(os.path.join(frameworkprefix, ldlibrary)): return LibraryList(os.path.join(frameworkprefix, ldlibrary)) else: From 5f06e50902b3c839ef1d87fefefbf31eadf0e79d Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Fri, 27 Mar 2020 04:50:20 +0100 Subject: [PATCH 229/377] meson: Add 0.53.2 and fix setuptools dependency (#15674) py-setuptools is actually required for running meson. --- var/spack/repos/builtin/packages/meson/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/meson/package.py b/var/spack/repos/builtin/packages/meson/package.py index 2878c712fcb..59edec8167f 100644 --- a/var/spack/repos/builtin/packages/meson/package.py +++ b/var/spack/repos/builtin/packages/meson/package.py @@ -14,6 +14,7 @@ class Meson(PythonPackage): homepage = "http://mesonbuild.com/" url = "https://github.com/mesonbuild/meson/archive/0.49.0.tar.gz" + version('0.53.2', sha256='eab4f5d5dde12d002b7ddd958a9a0658589b63622b6cea2715e0235b95917888') version('0.49.1', sha256='a944e7f25a2bc8e4ba3502ab5835d8a8b8f2530415c9d6fcffb53e0abaea2ced') version('0.49.0', sha256='11bc959e7173e714e4a4e85dd2bd9d0149b0a51c8ba82d5f44cc63735f603c74') version('0.42.0', sha256='6c318a2da3859326a37f8a380e3c50e97aaabff6990067218dffffea674ed76f') @@ -23,7 +24,7 @@ class Meson(PythonPackage): variant('ninjabuild', default=True) depends_on('python@3:', type=('build', 'run')) - depends_on('py-setuptools', type='build') + depends_on('py-setuptools', type=('build', 'run')) depends_on('ninja', when='+ninjabuild', type=('build', 'run')) # By default, Meson strips the rpath on installation. This patch disables From dcc4aabce1d14dfa02b92fff34fba89eacd3ea71 Mon Sep 17 00:00:00 2001 From: Fabian Brandt Date: Fri, 27 Mar 2020 04:55:27 +0100 Subject: [PATCH 230/377] New package libtlx (#15650) * New package libtlx * Replaced dash characters with ascii dash --- .../repos/builtin/packages/libtlx/package.py | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 var/spack/repos/builtin/packages/libtlx/package.py diff --git a/var/spack/repos/builtin/packages/libtlx/package.py b/var/spack/repos/builtin/packages/libtlx/package.py new file mode 100644 index 00000000000..619f90dfb54 --- /dev/null +++ b/var/spack/repos/builtin/packages/libtlx/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Libtlx(CMakePackage): + """ tlx is a collection of C++ helpers and extensions universally needed, + but not found in the STL. + The most important design goals and conventions are: + 1) high modularity with as little dependencies between + modules as possible. + 2) attempt to never break existing interfaces. + 3) compile on all platforms with C++ - smartphones, supercomputers, + windows, etc. + 4) zero external dependencies: no additional libraries are required. + 5) warning and bug-freeness on all compilers. + 6) keep overhead down - small overall size such that is can be included + without bloating applications.""" + + homepage = "https://tlx.github.io/" + url = "https://github.com/tlx/tlx/archive/v0.5.20191212.tar.gz" + + maintainers = ['fabratu'] + + version('0.5.20191212', sha256='5e67d3042a390dbb831b6d46437e3c7fadf738bff362aa7376b210b10ecd532d') From 97c3addad3def86a77054db74316f6ed38003e59 Mon Sep 17 00:00:00 2001 From: iarspider Date: Fri, 27 Mar 2020 08:42:50 +0100 Subject: [PATCH 231/377] cppgsl: added v2.1.0 (#15696) Co-authored-by: Adam J. Stewart --- var/spack/repos/builtin/packages/cppgsl/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/cppgsl/package.py b/var/spack/repos/builtin/packages/cppgsl/package.py index 4f4c68841fd..ce045a7c687 100644 --- a/var/spack/repos/builtin/packages/cppgsl/package.py +++ b/var/spack/repos/builtin/packages/cppgsl/package.py @@ -13,7 +13,8 @@ class Cppgsl(CMakePackage): url = "https://github.com/Microsoft/GSL/archive/v2.0.0.tar.gz" git = "https://github.com/Microsoft/GSL.git" - version('develop', branch='master') + version('master', branch='master') + version('2.1.0', sha256='ef73814657b073e1be86c8f7353718771bf4149b482b6cb54f99e79b23ff899d') version('2.0.0', sha256='6cce6fb16b651e62711a4f58e484931013c33979b795d1b1f7646f640cfa9c8e') version('1.0.0', sha256='9694b04cd78e5b1a769868f19fdd9eea2002de3d4c3a81a1b769209364543c36') From 6a33c269bddda4cdce941930aa834aad05770d62 Mon Sep 17 00:00:00 2001 From: darmac Date: Fri, 27 Mar 2020 15:44:41 +0800 Subject: [PATCH 232/377] sshpass: added new package (#15704) --- .../repos/builtin/packages/sshpass/package.py | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 var/spack/repos/builtin/packages/sshpass/package.py diff --git a/var/spack/repos/builtin/packages/sshpass/package.py b/var/spack/repos/builtin/packages/sshpass/package.py new file mode 100644 index 00000000000..499761a867d --- /dev/null +++ b/var/spack/repos/builtin/packages/sshpass/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Sshpass(AutotoolsPackage): + """Sshpass is a tool for non-interactivly performing password + authentication with SSH's so called "interactive keyboard + password authentication". Most user should use SSH's more + secure public key authentiaction instead.""" + + homepage = "https://sourceforge.net/projects/sshpass/" + url = "https://sourceforge.net/projects/sshpass/files/sshpass/1.06/sshpass-1.06.tar.gz" + + version('1.06', sha256='c6324fcee608b99a58f9870157dfa754837f8c48be3df0f5e2f3accf145dee60') + version('1.05', sha256='c3f78752a68a0c3f62efb3332cceea0c8a1f04f7cf6b46e00ec0c3000bc8483e') + version('1.04', sha256='e8abb9a409f25928722251a5855a74854f6d64af3eb136b804a04fd630d70c80') + version('1.03', sha256='5e8082343f5eae43598bb5723fa11bf49d3c9864dc58c7513fe1a90658e52b2f') + version('1.02', sha256='e580d999eefbd847c5cd0b36315cb6cd187315c4e7d1cb182b9f94c12c7c6a86') + version('1.01', sha256='e2adc378d61b72e63b4381fe123de3c63bd4093c9553d3219e83878f379754f4') + version('1.00', sha256='71d4be85a464a8ce2ae308bc04dcb342918f3989b6a81c74217b5df7f11471f8') + + depends_on('m4', type='build') + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') From e1238bae9053d3c283c1721f85af78f3539f473d Mon Sep 17 00:00:00 2001 From: darmac Date: Fri, 27 Mar 2020 17:21:16 +0800 Subject: [PATCH 233/377] dpdk: added new package at v20.02 (#15635) --- .../repos/builtin/packages/dpdk/package.py | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 var/spack/repos/builtin/packages/dpdk/package.py diff --git a/var/spack/repos/builtin/packages/dpdk/package.py b/var/spack/repos/builtin/packages/dpdk/package.py new file mode 100644 index 00000000000..c25b32c8d7b --- /dev/null +++ b/var/spack/repos/builtin/packages/dpdk/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Dpdk(MakefilePackage): + """DPDK is a set of libraries and drivers for fast packet processing. + It supports many processor architectures and both FreeBSD and Linux.""" + + homepage = "https://github.com/DPDK/dpdk" + url = "https://github.com/DPDK/dpdk/archive/v19.11.tar.gz" + + version('20.02', sha256='29e56ea8e47e30110ecb881fa5a37125a865dd2d45b61f68e93e334caaab16b7') + version('19.11', sha256='ce1befb20a5e5c5399b326a39cfa23314a5229c0ced2553f53b09b1ae630706b') + version('19.08', sha256='1ceff1a6f4f8d5f6f62c1682097249227ac5225ccd9638e0af09f5411c681038') + version('19.05', sha256='5fea95cb726e6adaa506dab330e79563ccd4dacf03f126c826aabdced605d32b') + version('19.02', sha256='04885d32c86fff5aefcfffdb8257fed405233602dbcd22f8298be13c2e285a50') + + depends_on('numactl') + + def build(self, spec, prefix): + make('defconfig') + make() + + def install(self, spec, prefix): + install_tree('.', prefix) From 420b5dd4b96135f219cd15c67c929fe0109e75b1 Mon Sep 17 00:00:00 2001 From: Brian Homerding Date: Fri, 27 Mar 2020 06:07:57 -0500 Subject: [PATCH 234/377] MpiP: adding variant to build shared libraries (#10410) --- var/spack/repos/builtin/packages/mpip/package.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/var/spack/repos/builtin/packages/mpip/package.py b/var/spack/repos/builtin/packages/mpip/package.py index 36fe6e31a7a..ceaaba05b64 100644 --- a/var/spack/repos/builtin/packages/mpip/package.py +++ b/var/spack/repos/builtin/packages/mpip/package.py @@ -16,11 +16,21 @@ class Mpip(AutotoolsPackage): version('master', branch='master') version("3.4.1", sha256="688bf37d73211e6a915f9fc59c358282a266d166c0a10af07a38a01a473296f0") + variant('shared', default=False, description="Build the shared library") + depends_on("elf") depends_on("libdwarf") depends_on('libunwind', when=os.uname()[4] == "x86_64") depends_on("mpi") + @property + def build_targets(self): + targets = [] + if '+shared' in self.spec: + targets.append('shared') + + return targets + def configure_args(self): config_args = ['--without-f77'] config_args.append("--with-cc=%s" % self.spec['mpi'].mpicc) From 7df7b65cecd793ad867288191940714c16aad0b0 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Fri, 27 Mar 2020 22:16:48 +0900 Subject: [PATCH 235/377] ppOpen-AT: New package (#15649) * ppOpen-AT: New package * use install instead of install-after. * use install_tree. * forget remove mkdir. --- .../builtin/packages/ppopen-at/package.py | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ppopen-at/package.py diff --git a/var/spack/repos/builtin/packages/ppopen-at/package.py b/var/spack/repos/builtin/packages/ppopen-at/package.py new file mode 100644 index 00000000000..92a8c302de6 --- /dev/null +++ b/var/spack/repos/builtin/packages/ppopen-at/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * +import os + + +class PpopenAt(MakefilePackage): + """ppOpen-AT is a part of the ppOpenHPC""" + + homepage = "http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/" + url = "file://{0}/ppohAT_1.0.0.tar.gz".format(os.getcwd()) + + version('1.0.0', sha256='2b5664839762c941e0b2dd7c15416e2dcfd5d909558cf7e4347a79ce535f3887') + + def edit(self, spec, prefix): + makefile_in = FileFilter('Makefile.in') + makefile_in.filter('gcc', spack_cxx) + makefile_in.filter('~/ppohAT_1.0.0', prefix) + makefile_in.filter('mkdir', 'mkdir -p') + + def install(self, spec, prefix): + make('install') + install_tree('examples', prefix.examples) + install_tree('doc', prefix.doc) From 108a0c99f15acceb0c1302cbdbc370bb2a0d75fa Mon Sep 17 00:00:00 2001 From: Andrew W Elble Date: Fri, 27 Mar 2020 11:51:04 -0400 Subject: [PATCH 236/377] TensorFlow: Make horovod compilation work (#15692) * TensorFlow: Clean up/simplify the installation, make sure the headers are installed so that horovod can find them successfully. Fix the 2.0.* builds. * Backport of 837c8b6b upstream "Remove contrib cloud bigtable and storage ops/kernels." Allows 2.0.* releases to build with '--config=nogcp' * comment regarding tensorflow issue #31187 Co-authored-by: Andrew W Elble --- ...loud-bigtable-and-storage-ops-kernel.patch | 76 +++++++++++++++++++ .../builtin/packages/py-tensorflow/package.py | 44 ++++++----- 2 files changed, 100 insertions(+), 20 deletions(-) create mode 100644 var/spack/repos/builtin/packages/py-tensorflow/0001-Remove-contrib-cloud-bigtable-and-storage-ops-kernel.patch diff --git a/var/spack/repos/builtin/packages/py-tensorflow/0001-Remove-contrib-cloud-bigtable-and-storage-ops-kernel.patch b/var/spack/repos/builtin/packages/py-tensorflow/0001-Remove-contrib-cloud-bigtable-and-storage-ops-kernel.patch new file mode 100644 index 00000000000..bb742ff1b42 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-tensorflow/0001-Remove-contrib-cloud-bigtable-and-storage-ops-kernel.patch @@ -0,0 +1,76 @@ +--- a/tensorflow/core/BUILD.orig 2020-01-22 18:43:57.000000000 -0500 ++++ b/tensorflow/core/BUILD 2020-03-26 16:33:17.318229701 -0400 +@@ -107,8 +107,6 @@ + load( + "//tensorflow/core/platform:default/build_config.bzl", + "tf_additional_all_protos", +- "tf_additional_cloud_kernel_deps", +- "tf_additional_cloud_op_deps", + "tf_additional_core_deps", + "tf_additional_cupti_wrapper_deps", + "tf_additional_device_tracer_cuda_deps", +@@ -1427,7 +1425,7 @@ + ]) + if_tensorrt([ + "//tensorflow/compiler/tf2tensorrt:trt_engine_resource_ops_op_lib", + "//tensorflow/compiler/tf2tensorrt:trt_op_libs", +- ]) + tf_additional_cloud_op_deps(), ++ ]), + alwayslink = 1, + ) + +@@ -1590,7 +1588,7 @@ + "//tensorflow/core/kernels:summary_kernels", + "//tensorflow/core/kernels:training_ops", + "//tensorflow/core/kernels:word2vec_kernels", +- ] + tf_additional_cloud_kernel_deps() + if_not_windows([ ++ ] + if_not_windows([ + "//tensorflow/core/kernels:fact_op", + "//tensorflow/core/kernels:array_not_windows", + "//tensorflow/core/kernels:math_not_windows", + +diff --git a/tensorflow/core/platform/default/build_config.bzl b/tensorflow/core/platform/default/build_config.bzl +index b822effa14e5..61a19bdf128f 100644 +--- a/tensorflow/core/platform/default/build_config.bzl ++++ b/tensorflow/core/platform/default/build_config.bzl +@@ -682,38 +682,6 @@ def tf_additional_core_deps(): + ], + }) + +-# TODO(jart, jhseu): Delete when GCP is default on. +-def tf_additional_cloud_op_deps(): +- return select({ +- "//tensorflow:android": [], +- "//tensorflow:ios": [], +- "//tensorflow:linux_s390x": [], +- "//tensorflow:windows": [], +- "//tensorflow:api_version_2": [], +- "//tensorflow:windows_and_api_version_2": [], +- "//tensorflow:no_gcp_support": [], +- "//conditions:default": [ +- "//tensorflow/contrib/cloud:bigquery_reader_ops_op_lib", +- "//tensorflow/contrib/cloud:gcs_config_ops_op_lib", +- ], +- }) +- +-# TODO(jhseu): Delete when GCP is default on. +-def tf_additional_cloud_kernel_deps(): +- return select({ +- "//tensorflow:android": [], +- "//tensorflow:ios": [], +- "//tensorflow:linux_s390x": [], +- "//tensorflow:windows": [], +- "//tensorflow:api_version_2": [], +- "//tensorflow:windows_and_api_version_2": [], +- "//tensorflow:no_gcp_support": [], +- "//conditions:default": [ +- "//tensorflow/contrib/cloud/kernels:bigquery_reader_ops", +- "//tensorflow/contrib/cloud/kernels:gcs_config_ops", +- ], +- }) +- + def tf_lib_proto_parsing_deps(): + return [ + ":protos_all_cc", +-- +2.19.1 + diff --git a/var/spack/repos/builtin/packages/py-tensorflow/package.py b/var/spack/repos/builtin/packages/py-tensorflow/package.py index d493c32283f..0444a2e09af 100644 --- a/var/spack/repos/builtin/packages/py-tensorflow/package.py +++ b/var/spack/repos/builtin/packages/py-tensorflow/package.py @@ -3,8 +3,7 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -import glob -import os +from glob import glob import sys @@ -241,6 +240,11 @@ class PyTensorflow(Package, CudaPackage): patch('io_bazel_rules_docker2.patch', when='@1.15:2.0') # Avoide build error: "name 'new_http_archive' is not defined" patch('http_archive.patch', when='@1.12.3') + # Backport of 837c8b6b upstream + # "Remove contrib cloud bigtable and storage ops/kernels." + # Allows 2.0.* releases to build with '--config=nogcp' + patch('0001-Remove-contrib-cloud-bigtable-and-storage-ops-kernel.patch', + when='@2.0.0:2.0.1') phases = ['configure', 'build', 'install'] @@ -581,6 +585,12 @@ def post_configure_fixes(self): spec['nccl'].prefix.include + '"', '.tf_configure.bazelrc') + # see tensorflow issue #31187 on github + if spec.satisfies('@2.0.0:2.0.1'): + filter_file(r'\#define RUY_DONOTUSEDIRECTLY_AVX512 1', + '#define RUY_DONOTUSEDIRECTLY_AVX512 0', + 'tensorflow/lite/experimental/ruy/platform.h') + if spec.satisfies('+cuda'): libs = spec['cuda'].libs.directories libs.extend(spec['cudnn'].libs.directories) @@ -679,30 +689,24 @@ def build(self, spec, prefix): build_pip_package = Executable( 'bazel-bin/tensorflow/tools/pip_package/build_pip_package') - build_pip_package(tmp_path) + buildpath = join_path(self.stage.source_path, 'spack-build') + build_pip_package('--src', buildpath) def install(self, spec, prefix): - with working_dir('spack-build', create=True): - for fn in glob.iglob(join_path( - '../bazel-bin/tensorflow/tools/pip_package', - 'build_pip_package.runfiles/org_tensorflow/*')): - dst = os.path.basename(fn) - if not os.path.exists(dst): - os.symlink(fn, dst) - for fn in glob.iglob('../tensorflow/tools/pip_package/*'): - dst = os.path.basename(fn) - if not os.path.exists(dst): - os.symlink(fn, dst) - - # macOS is case-insensitive, and BUILD file in directory - # containing setup.py causes the following error message: - # error: could not create 'build': File exists - # Delete BUILD file to prevent this. - os.remove('BUILD') + buildpath = join_path(self.stage.source_path, 'spack-build') + with working_dir(buildpath): setup_py('install', '--prefix={0}'.format(prefix), '--single-version-externally-managed', '--root=/') + site_packages_dir = join_path( + prefix.lib, + ('python' + str(self.spec['python'].version.up_to(2))), + 'site-packages') + fn = glob(join_path(site_packages_dir, "tensorflow-*")) + incpath = join_path(fn[0], "tensorflow/include") + setup_py('install_headers', '--install-dir={0}'.format(incpath)) + @run_after('install') @on_package_attributes(run_tests=True) def import_module_test(self): From 6e82761d4e2ac2dd42482c8e81fa68c8b1b138c8 Mon Sep 17 00:00:00 2001 From: Amjad Kotobi Date: Fri, 27 Mar 2020 16:58:50 +0100 Subject: [PATCH 237/377] New package Anaconda2 (#15676) --- .../builtin/packages/anaconda2/package.py | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 var/spack/repos/builtin/packages/anaconda2/package.py diff --git a/var/spack/repos/builtin/packages/anaconda2/package.py b/var/spack/repos/builtin/packages/anaconda2/package.py new file mode 100644 index 00000000000..e22ab88c8ba --- /dev/null +++ b/var/spack/repos/builtin/packages/anaconda2/package.py @@ -0,0 +1,47 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +from os.path import split + + +class Anaconda2(Package): + """Anaconda is a free and open-source distribution of the Python and + R programming languages for scientific computing, that aims to + simplify package management and deployment. Package versions are + managed by the package management system conda. + """ + + homepage = "https://www.anaconda.com" + url = "https://repo.anaconda.com/archive/Anaconda2-2019.10-Linux-x86_64.sh" + + maintainers = ['ajkotobi'] + + version('2019.10', sha256='8b2e7dea2da7d8cc18e822e8ec1804052102f4eefb94c1b3d0e586e126e8cd2f', expand=False) + version('2019.07', sha256='189e16e7adf9ba4b7b7d06ecdc10ce4ad4153e5e3505b9331f3d142243e18e97', expand=False) + version('2019.03', sha256='cedfee5b5a3f62fcdac0a1d2d12396d0f232d2213d24d6dc893df5d8e64b8773', expand=False) + version('2018.12', sha256='1821d4b623ed449e0acb6df3ecbabd3944cffa98f96a5234b7a102a7c0853dc6', expand=False) + version('5.3.1', sha256='f0650ad2f9ca4ae3f3162d7204a32950bc794f37f322eb47b5ad9412454f998c', expand=False) + version('5.3.0', sha256='50eeaab24bfa2472bc6485fe8f0e612ed67e561eda1ff9fbf07b62c96443c1be', expand=False) + version('5.2.0', sha256='cb0d7a08b0e2cec4372033d3269979b4e72e2353ffd1444f57cb38bc9621219f', expand=False) + version('5.1.0', sha256='5f26ee92860d1dffdcd20910ff2cf75572c39d2892d365f4e867a611cca2af5b', expand=False) + version('5.0.1', sha256='23c676510bc87c95184ecaeb327c0b2c88007278e0d698622e2dd8fb14d9faa4', expand=False) + version('5.0.0.1', sha256='18730808d863a5c194ab3f59dd395c1a63cbd769c9bfb1df65efe61ee62fc6d6', expand=False) + version('5.0.0', sha256='58a7117f89c40275114bf7e824a613a963da2b0fe63f2ec3c1175fea785b468e', expand=False) + version('4.4.0', sha256='2d30b91ed4d215b6b4a15162a3389e9057b15445a0c02da71bd7bd272e7b824e', expand=False) + version('4.3.1', sha256='e9b8f2645df6b1527ba56d61343162e0794acc3ee8dde2a6bba353719e2d878d', expand=False) + version('4.3.0', sha256='7c52e6e99aabb24a49880130615a48e685da444c3c14eb48d6a65f3313bf745c', expand=False) + version('4.2.0', sha256='beee286d24fb37dd6555281bba39b3deb5804baec509a9dc5c69185098cf661a', expand=False) + version('4.1.1', sha256='9413b1d3ca9498ba6f53913df9c43d685dd973440ff10b7fe0c45b1cbdcb582e', expand=False) + version('4.1.0', sha256='3b7e504ca0132fb555d1f10e174cae07007f1bc6898cad0f7d416a68aca01f45', expand=False) + version('4.0.0', sha256='ae312143952ca00e061a656c2080e0e4fd3532721282ba8e2978177cad71a5f0', expand=False) + version('2.5.0', sha256='e10abf459cde4a838bd6fc5ca03023c3401b81ad470627acde5a298d56715321', expand=False) + version('2.4.1', sha256='2de682c96edf8cca2852071a84ff860025fbe8c502218e1995acd5ab47e8c9ac', expand=False) + version('2.4.0', sha256='49d19834da06b1b82b6fa85bc647d2e78fa5957d0cbae3ccd6c695a541befa6b', expand=False) + + def install(self, spec, prefix): + dir, anaconda_script = split(self.stage.archive_file) + bash = which('bash') + bash(anaconda_script, '-b', '-f', '-p', self.prefix) From 16f104aafe2bb780f2d03c04aae0ccff333aa821 Mon Sep 17 00:00:00 2001 From: "Dr. Christian Tacke" <58549698+ChristianTackeGSI@users.noreply.github.com> Date: Fri, 27 Mar 2020 16:59:05 +0100 Subject: [PATCH 238/377] intel-tbb: new download url, fix sha256 (#15675) intel moved the repository around. github changes the prefix inside the tar according to the repository name. So all sha256 have changed! I verified that the tar contents for 2019.4 did not change except for the prefix. --- .../builtin/packages/intel-tbb/package.py | 72 ++++++++++--------- 1 file changed, 37 insertions(+), 35 deletions(-) diff --git a/var/spack/repos/builtin/packages/intel-tbb/package.py b/var/spack/repos/builtin/packages/intel-tbb/package.py index 6dbb1971f5c..20d8a2f9e99 100644 --- a/var/spack/repos/builtin/packages/intel-tbb/package.py +++ b/var/spack/repos/builtin/packages/intel-tbb/package.py @@ -17,45 +17,47 @@ class IntelTbb(Package): portable and composable, and that have future-proof scalability. """ homepage = "http://www.threadingbuildingblocks.org/" + url_prefix = 'https://github.com/oneapi-src/oneTBB/' + url = url_prefix + 'archive/v2020.1.tar.gz' # Note: when adding new versions, please check and update the # patches, filters and url_for_version() below as needed. version('2020.1', sha256='7c96a150ed22bc3c6628bc3fef9ed475c00887b26d37bca61518d76a56510971') - version('2020.0', sha256='8eed2377ac62e6ac10af5a8303ce861e4525ffe491a061b48e8fe094fc741ce9') - version('2019.9', sha256='15652f5328cf00c576f065e5cd3eaf3317422fe82afb67a9bcec0dc065bd2abe') - version('2019.8', sha256='7b1fd8caea14be72ae4175896510bf99c809cd7031306a1917565e6de7382fba') - version('2019.7', sha256='4204a93f4c0fd989fb6f79acae74feb02ee39725c93968773d9b6efeb75c7a6a') - version('2019.6', sha256='2ba197b3964fce8a84429dd15b75eba7434cb89afc54f86d5ee6f726fdbe97fd') - version('2019.5', sha256='2ea82d74dec50e18075b4982b8d360f8bd2bf2950f38e2db483aef82e0047444') - version('2019.4', sha256='342a0a2cd583879850658284b86e9351ea019b4f3fcd731f4c18456f0ce9f900') - version('2019.3', sha256='b2244147bc8159cdd8f06a38afeb42f3237d3fc822555499d7ccfbd4b86f8ece') - version('2019.2', sha256='1245aa394a92099e23ce2f60cdd50c90eb3ddcd61d86cae010ef2f1de61f32d9') - version('2019.1', sha256='a4875c6b6853213083e52ecd303546bdf424568ec67cfc7e51d132a7c037c66a') - version('2019', sha256='4d149895826cea785cd3b9a14f4aa743b6ef0df520eca7ee27d438fdc3d73399') - version('2018.6', sha256='d3e5fbca3cc643d03bf332d576ff85e19aa774b483f148f95cd7d09958372109') - version('2018.5', sha256='c4c2896af527392496c5e01ef8579058a71b6eebbd695924cd138841c13f07be') - version('2018.4', sha256='d5604a04787c8a037d4944eeb89792e7c45f6a83c141b20df7ee89c2fb012ed1') - version('2018.3', sha256='23793c8645480148e9559df96b386b780f92194c80120acce79fcdaae0d81f45') - version('2018.2', sha256='78bb9bae474736d213342f01fe1a6d00c6939d5c75b367e2e43e7bf29a6d8eca') - version('2018.1', sha256='c6462217d4ecef2b44fce63cfdf31f9db4f6ff493869899d497a5aef68b05fc5') - version('2018', sha256='94f643f1edfaccb57d64b503c7c96f00dec64e8635c054bbaa33855d72c5822d') - version('2017.8', sha256='1b1357f280e750d42506212adad02f85ac07c9d3e3c0813104f9122ef350497f') - version('2017.7', sha256='78ad6ec9dd492b9dcc4753938b06716f7458506084adc138ced09aa0aa609b6b') - version('2017.6', sha256='40d5409a6fd7e214a21fd1949df422ba113fa78fde42a6aac40a2fba36e9bcdb') - version('2017.5', sha256='3122c87a35fde759567c8579ba36a36037c6df84c3f9c4df6c9e171f866f352f') - version('2017.4', sha256='ed4f0cfc4acec8a0cf253037e8c555dd32ebe1b80b34fb0e3b2bf54087932562') - version('2017.3', sha256='00a8b2798c498507572e24c2db7bf4896f05b760a38ed9ba566ffd348a7c6cef') - version('2017.2', sha256='85e44041d967ce8c70077dbb57941cfa1d351688855aec47eb14c74eb2075f28') - version('2017.1', sha256='a68bb7926fb9bee2a5f17b293c6d6aa33ccb089c3b321569bd4fe281cf65fa77') - version('2017', sha256='c49139279067df1260dae4f0fe7e4d485898ce45e5f7e314c37eb5da8a0c303a') - version('4.4.6', sha256='1d6b7e7db9141238c70984103f04280605dbcaa7fbcd049d332d2e73deed4f6d') - version('4.4.5', sha256='984308f9dd8a36ff274c124b6f7f7d0ff74d4b7ebdf06511af78e098b5b6e70f') - version('4.4.4', sha256='40e94c1adfd13308d207971629316ae9f76639b24f080bae8757c42d35778f10') - version('4.4.3', sha256='9acb1c4e71edc3d5004ab9f0ed2bbd697ecec28a4315bbd2be8c5365e8214b90') - version('4.4.2', sha256='3f6d7a32ac8b58469de7df3a2fcfe318793241ea39ce73aae1e637dbed833375') - version('4.4.1', sha256='d67c5860ba1116b320b0d60a0ce403b088dc19355ab32c28cdaa3e352609713a') - version('4.4', sha256='88e37f08ffcfaa24a2caf6c1a9084000cce689cc4b11edea7e89b20ab74ceceb') + version('2020.0', sha256='57714f2d2cf33935db33cee93af57eb3ecd5a7bef40c1fb7ca4a41d79684b118') + version('2019.9', sha256='3f5ea81b9caa195f1967a599036b473b2e7c347117330cda99b79cfcf5b77c84') + version('2019.8', sha256='6b540118cbc79f9cbc06a35033c18156c21b84ab7b6cf56d773b168ad2b68566') + version('2019.7', sha256='94847fc627ed081c63ea253e31f23645ed3671548106b095ce303d1da5d76275') + version('2019.6', sha256='21cd496ac768560e70d35e5423878aa3bcf0285f7194be77935d8febf0b18f47') + version('2019.5', sha256='abf9236e6ec9a3675fa59ab56c2192c7ab4f7096a82af118e8efa514b2541578') + version('2019.4', sha256='673e540aba6e526b220cbeacc3e4ff7b19a8689a00d7a09a9dc94396d73b24df') + version('2019.3', sha256='4cb6bde796ae056e7c29f31bfdc6cfd0cfe848925219e9c82a20f09158e81542') + version('2019.2', sha256='3bbe21054bd5b593ef99d4dfe451432cbf1f6f9429cd0dd543e879ef7e4e3327') + version('2019.1', sha256='e6fb8dd1a1ae834b4e5f4ae6c4c87a3362f81a3aaeddfa6325168c6cfee59391') + version('2019', sha256='91f00308a4e431bd9632b439d516134d7084f1eb35f52b7c9b111b46bdfcf093') + version('2018.6', sha256='0ebb5fc877871ef15f7395d6e3c86de4ffedb820dc336383a3ab71fc39426aa7') + version('2018.5', sha256='b8dbab5aea2b70cf07844f86fa413e549e099aa3205b6a04059ca92ead93a372') + version('2018.4', sha256='c973b41b6da3db10efa7e14ce64a850e3fbfbcc16374494a005bf994d53a770a') + version('2018.3', sha256='e5f19d747f6adabfc7daf2cc0a1ddcfab0f26bc083d70ea0a63def4a9f3919c5') + version('2018.2', sha256='733c4dba646573b8285b1923dc106f0d771725bea620baa3659c86ab9312a1f4') + version('2018.1', sha256='a9f51e0d081fbdda441d0150e759c7562318d6d7bc5a0c9a9d8064217d4d8d8d') + version('2018', sha256='d427c58a59863c5f9510fffb3d05cd1bcc7abb94cdde1613407559e88b1263ab') + version('2017.8', sha256='227cc1a8329da67f9957285f0020ad4d73d9ce26cbf88614349b8b74bb189ae1') + version('2017.7', sha256='f487243e5931e967479189ef75946f02e3bb666ea73dcc19ac2828edd5550746') + version('2017.6', sha256='b0f40edd010b90ce2519c1cebfa6f33216a1828d4fba19291b5cd23bd7fe809b') + version('2017.5', sha256='b785e7181317350f0bb20f7bffda20bdecde7e82b824d2e5eb6d408a3b9cbeaf') + version('2017.4', sha256='9a70ae3068767bf8c530bf98b9bbc655e36e82a301b347f7de76f99f401df1dd') + version('2017.3', sha256='230ed3ff32bb3e91df1f59e4a3a567bde02639d9970b7e87cee0421b4c0b0f23') + version('2017.2', sha256='dd37c896f95ca2357e828c24c9c4a169c6a6b5c905b3862a6cab09474d164497') + version('2017.1', sha256='9b5b36b6d0ed97a3a1711b9095e78aed79bc998957a4a6b3d8a7af063523f037') + version('2017', sha256='470544b0f374987273cc12e7706353edba8f9547578291d45b5b29358d4e5e81') + version('4.4.6', sha256='65101b3a0eda38320ec3e3603daa79c54e6a60fb59ed2959738eaf4ce6d17f0a') + version('4.4.5', sha256='2e372703fe444442c77760229897f00bb4babff62f7d0861b3f2783883cb257e') + version('4.4.4', sha256='3ed03838c4e368b78305b0561cac48d369919bb4d9d68edd4d8a3becd6f62f5c') + version('4.4.3', sha256='f0ff2e3735c8057b792f29c96f4f7623c1e4c76abfeda88be48645b8338c0f00') + version('4.4.2', sha256='1ab10e70354685cee3ddf614f3e291434cea86c8eb62031e025f4052278152ad') + version('4.4.1', sha256='05737bf6dd220b31aad63d77ca59c742271f81b4cc6643aa6f93d37450ae32b5') + version('4.4', sha256='93c74b6054c69c86fa49d0fce7c50061fc907cb198a7237b8dd058298fd40c0e') provides('tbb') @@ -113,7 +115,7 @@ class IntelTbb(Package): # 4.4.6 --> 4.4.6.tar.gz # def url_for_version(self, version): - url = 'https://github.com/intel/tbb/archive/{0}.tar.gz' + url = self.url_prefix + 'archive/{0}.tar.gz' if version[0] >= 2020: name = 'v{0}'.format(version) elif version[0] >= 2017 and len(version) > 1: From 0f8148b258a2ff0eea08e20876e5f76e842f9e83 Mon Sep 17 00:00:00 2001 From: iarspider Date: Fri, 27 Mar 2020 17:16:40 +0100 Subject: [PATCH 239/377] py-attrs: add version 19.3.0 (#15709) --- var/spack/repos/builtin/packages/py-attrs/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/py-attrs/package.py b/var/spack/repos/builtin/packages/py-attrs/package.py index cf9950c1ce2..64c8aa5426e 100644 --- a/var/spack/repos/builtin/packages/py-attrs/package.py +++ b/var/spack/repos/builtin/packages/py-attrs/package.py @@ -14,6 +14,7 @@ class PyAttrs(PythonPackage): import_modules = ['attr'] + version('19.3.0', sha256='f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72') version('19.2.0', sha256='f913492e1663d3c36f502e5e9ba6cd13cf19d7fab50aa13239e420fef95e1396') version('19.1.0', sha256='f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399') version('18.1.0', sha256='e0d0eb91441a3b53dab4d9b743eafc1ac44476296a2053b6ca3af0b139faf87b') @@ -26,5 +27,6 @@ class PyAttrs(PythonPackage): depends_on('py-hypothesis', type='test') depends_on('py-pympler', type='test') depends_on('py-pytest', type='test') + depends_on('py-pytest@4.3.0:', type='test', when='@19.3.0:') depends_on('py-six', type='test') depends_on('py-zope-interface', type='test') From 953bd04cb375beb745b2993eed815d76ed4e1f9c Mon Sep 17 00:00:00 2001 From: iarspider Date: Fri, 27 Mar 2020 17:21:42 +0100 Subject: [PATCH 240/377] Bison: add version 3.3.2 (#15707) --- var/spack/repos/builtin/packages/bison/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py index a0b04062408..0a51dd583e0 100644 --- a/var/spack/repos/builtin/packages/bison/package.py +++ b/var/spack/repos/builtin/packages/bison/package.py @@ -18,6 +18,7 @@ class Bison(AutotoolsPackage, GNUMirrorPackage): version('3.4.2', sha256='ff3922af377d514eca302a6662d470e857bd1a591e96a2050500df5a9d59facf') version('3.4.1', sha256='7007fc89c216fbfaff5525359b02a7e5b612694df5168c74673f67055f015095') + version('3.3.2', sha256='0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1') version('3.0.5', sha256='cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566') version('3.0.4', sha256='b67fd2daae7a64b5ba862c66c07c1addb9e6b1b05c5f2049392cfd8a2172952e') version('2.7', sha256='19bbe7374fd602f7a6654c131c21a15aebdc06cc89493e8ff250cb7f9ed0a831') From 0ca5ad237a7ec10a148325b2c3601c024345788c Mon Sep 17 00:00:00 2001 From: noguchi-k <55966120+noguchi-k@users.noreply.github.com> Date: Sat, 28 Mar 2020 01:29:30 +0900 Subject: [PATCH 241/377] denovogear: fixed comparison error (#15638) --- .../builtin/packages/denovogear/newmat6.cpp.patch | 11 +++++++++++ .../repos/builtin/packages/denovogear/package.py | 2 ++ 2 files changed, 13 insertions(+) create mode 100644 var/spack/repos/builtin/packages/denovogear/newmat6.cpp.patch diff --git a/var/spack/repos/builtin/packages/denovogear/newmat6.cpp.patch b/var/spack/repos/builtin/packages/denovogear/newmat6.cpp.patch new file mode 100644 index 00000000000..36d2e240cd8 --- /dev/null +++ b/var/spack/repos/builtin/packages/denovogear/newmat6.cpp.patch @@ -0,0 +1,11 @@ +--- spack-src/src/contrib/newmat/newmat6.cpp.org 2020-03-19 14:06:13.679032667 +0900 ++++ spack-src/src/contrib/newmat/newmat6.cpp 2020-03-19 14:07:34.267492838 +0900 +@@ -428,7 +428,7 @@ + { + if (&gm == this) { REPORT tag_val = -1; return; } + REPORT +- if (indx > 0) { delete [] indx; indx = 0; } ++ if (indx != NULL) { delete [] indx; indx = 0; } + ((CroutMatrix&)gm).get_aux(*this); + Eq(gm); + } diff --git a/var/spack/repos/builtin/packages/denovogear/package.py b/var/spack/repos/builtin/packages/denovogear/package.py index 8f475492c15..bc683febeff 100644 --- a/var/spack/repos/builtin/packages/denovogear/package.py +++ b/var/spack/repos/builtin/packages/denovogear/package.py @@ -25,3 +25,5 @@ class Denovogear(CMakePackage): depends_on('zlib', type=('link')) patch('stream-open.patch', when='@:1.1.1') + # fix: ordered comparison between pointer and zero. + patch('newmat6.cpp.patch') From fb5afb4cb4326c745e147c8b6d1d5473297ebc78 Mon Sep 17 00:00:00 2001 From: Hector <10837193+he-b@users.noreply.github.com> Date: Fri, 27 Mar 2020 11:33:33 -0500 Subject: [PATCH 242/377] add source-highlight variant to gdb (#15634) --- var/spack/repos/builtin/packages/gdb/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py index 825291feb09..355f59cbdf4 100644 --- a/var/spack/repos/builtin/packages/gdb/package.py +++ b/var/spack/repos/builtin/packages/gdb/package.py @@ -33,6 +33,7 @@ class Gdb(AutotoolsPackage, GNUMirrorPackage): variant('python', default=True, description='Compile with Python support') variant('xz', default=True, description='Compile with lzma support') + variant('source-highlight', default=False, description='Compile with source-highlight support') # Required dependency depends_on('texinfo', type='build') @@ -40,6 +41,7 @@ class Gdb(AutotoolsPackage, GNUMirrorPackage): # Optional dependencies depends_on('python', when='+python') depends_on('xz', when='+xz') + depends_on('source-highlight', when='+source-highlight') build_directory = 'spack-build' From c3e41444ffe39f158412ac3619bc78a750c2dac2 Mon Sep 17 00:00:00 2001 From: darmac Date: Sat, 28 Mar 2020 00:34:03 +0800 Subject: [PATCH 243/377] Add new package: zfs (#15632) --- .../repos/builtin/packages/zfs/package.py | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 var/spack/repos/builtin/packages/zfs/package.py diff --git a/var/spack/repos/builtin/packages/zfs/package.py b/var/spack/repos/builtin/packages/zfs/package.py new file mode 100644 index 00000000000..819dc2d7553 --- /dev/null +++ b/var/spack/repos/builtin/packages/zfs/package.py @@ -0,0 +1,28 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Zfs(AutotoolsPackage): + """OpenZFS is an advanced file system and volume manager which was + originally developed for Solaris and is now maintained by the OpenZFS + community. This repository contains the code for running OpenZFS on + Linux and FreeBSD.""" + + homepage = "https://zfsonlinux.org/" + url = "https://github.com/openzfs/zfs/releases/download/zfs-0.8.3/zfs-0.8.3.tar.gz" + + version('0.8.3', sha256='545a4897ce30c2d2dd9010a0fdb600a0d3d45805e2387093c473efc03aa9d7fd') + version('0.8.2', sha256='47608e257c8ecebb918014ef1da6172c3a45d990885891af18e80f5cc28beab8') + version('0.8.1', sha256='0af79fde44b7b8ecb94d5166ce2e4fff7409c20ed874c2d759db92909e6c2799') + version('0.8.0', sha256='0fd92e87f4b9df9686f18e2ac707c16b2eeaf00f682d41c20ea519f3a0fe4705') + + depends_on('libuuid') + depends_on('libtirpc') + depends_on('util-linux') + + def setup_build_environment(self, env): + env.prepend_path('CPATH', self.spec['util-linux'].prefix.include) From d7454baa558e28bb3135bfeb03510da323a467a9 Mon Sep 17 00:00:00 2001 From: darmac Date: Sat, 28 Mar 2020 00:35:08 +0800 Subject: [PATCH 244/377] util-linux: add libmount variant (#15631) --- var/spack/repos/builtin/packages/util-linux/package.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/var/spack/repos/builtin/packages/util-linux/package.py b/var/spack/repos/builtin/packages/util-linux/package.py index d4887601a06..ccd6bba9aa3 100644 --- a/var/spack/repos/builtin/packages/util-linux/package.py +++ b/var/spack/repos/builtin/packages/util-linux/package.py @@ -24,15 +24,22 @@ class UtilLinux(AutotoolsPackage): depends_on('python@2.7:') depends_on('pkgconfig') + depends_on('gettext', when='+libmount') # Make it possible to disable util-linux's libuuid so that you may # reliably depend_on(`libuuid`). variant('libuuid', default=True, description='Build libuuid') + variant('libmount', default=False, description='Build libmount.so with gettext') def url_for_version(self, version): url = "https://www.kernel.org/pub/linux/utils/util-linux/v{0}/util-linux-{1}.tar.gz" return url.format(version.up_to(2), version) + def setup_build_environment(self, env): + if '+libmount' in self.spec: + env.append_flags('LDFLAGS', '-L{0} -lintl'.format( + self.spec['gettext'].prefix.lib)) + def configure_args(self): config_args = [ '--disable-use-tty-group', From c5e74fef329cbbc715d9087932bda146c8cdf269 Mon Sep 17 00:00:00 2001 From: "Nichols A. Romero" Date: Fri, 27 Mar 2020 11:38:28 -0500 Subject: [PATCH 245/377] QMCPACK Update March 2020 - Part 2 (#15616) * Add some comments explaining the choice of flag_handler. * Fix QMCPACK install method. * Add support for ppconvert. This requires a custom build method. * Fix QMCPACK setup_run_environment. Nexus should be properly supported now. * Cleaner way to check for intel-mkl in spec. * Remove build method and use build_targets property instead. * Additional fixed for install method. Effectively restoring the original install method. * Add the missing backslash to fix directory names. * Update var/spack/repos/builtin/packages/qmcpack/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/qmcpack/package.py Co-Authored-By: Adam J. Stewart * Update var/spack/repos/builtin/packages/qmcpack/package.py Co-Authored-By: Adam J. Stewart * Omit these conflicts on mkl variants for now, will hopefully be supportted with new concretizer in a couple of months. Co-authored-by: Adam J. Stewart --- .../repos/builtin/packages/qmcpack/package.py | 88 ++++++++----------- .../packages/quantum-espresso/package.py | 9 +- 2 files changed, 44 insertions(+), 53 deletions(-) diff --git a/var/spack/repos/builtin/packages/qmcpack/package.py b/var/spack/repos/builtin/packages/qmcpack/package.py index ba67282c0c2..9484e8a1693 100644 --- a/var/spack/repos/builtin/packages/qmcpack/package.py +++ b/var/spack/repos/builtin/packages/qmcpack/package.py @@ -59,6 +59,8 @@ class Qmcpack(CMakePackage, CudaPackage): variant('afqmc', default=False, description='Install with AFQMC support. NOTE that if used in ' 'combination with CUDA, only AFQMC will have CUDA.') + variant('ppconvert', default=False, + description='Install with pseudopotential converter.') # Notes about CUDA-centric peculiarities: # @@ -92,8 +94,9 @@ class Qmcpack(CMakePackage, CudaPackage): conflicts('^openblas+ilp64', msg='QMCPACK does not support OpenBLAS 64-bit integer variant') - conflicts('^intel-mkl+ilp64', - msg='QMCPACK does not support MKL 64-bit integer variant') + # Omitted for now due to concretizer bug + # conflicts('^intel-mkl+ilp64', + # msg='QMCPACK does not support MKL 64-bit integer variant') # QMCPACK 3.6.0 or later requires support for C++14 compiler_warning = 'QMCPACK 3.6.0 or later requires a ' \ @@ -184,6 +187,8 @@ class Qmcpack(CMakePackage, CudaPackage): patch_checksum = 'c066c79901a612cf8848135e0d544efb114534cca70b90bfccc8ed989d3d9dde' patch(patch_url, sha256=patch_checksum, when='@3.1.0:3.3.0') + # the default flag_handler for Spack causes problems for QMCPACK + # https://spack.readthedocs.io/en/latest/packaging_guide.html#the-build-environment: flag_handler = CMakePackage.build_system_flags @when('@:3.7.0') @@ -194,6 +199,15 @@ def patch(self): '${LIBXML2_HOME}/lib $ENV{LIBXML2_HOME}/lib', 'CMake/FindLibxml2QMC.cmake') + @property + def build_targets(self): + spec = self.spec + targets = ['all'] + if '+ppconvert' in spec: + targets.append('ppconvert') + + return targets + def cmake_args(self): spec = self.spec args = [] @@ -323,21 +337,29 @@ def cmake_args(self): # Next two environment variables were introduced in QMCPACK 3.5.0 # Prior to v3.5.0, these lines should be benign but CMake # may issue a warning. - if 'intel-mkl' in spec: + if '^mkl' in spec: args.append('-DENABLE_MKL=1') args.append('-DMKL_ROOT=%s' % env['MKLROOT']) else: args.append('-DENABLE_MKL=0') + # ppconvert is not build by default because it may exhibit numerical + # issues on some systems + if '+ppconvert' in spec: + args.append('-DBUILD_PPCONVERT=1') + else: + args.append('-DBUILD_PPCONVERT=0') + return args - # QMCPACK 3.6.0 release and later has a functional 'make install', - # the Spack 'def install' is retained for backwards compatiblity. - # Note that the two install methods differ in their directory - # structure. Additionally, we follow the recommendation on the Spack - # website for defining the compilers to be the MPI compiler wrappers. + # QMCPACK needs custom install method for a couple of reasons: + # Firstly, wee follow the recommendation on the Spack website + # for defining the compilers variables to be the MPI compiler wrappers. # https://spack.readthedocs.io/en/latest/packaging_guide.html#compiler-wrappers - @when('@3.6.0:') + # + # Note that 3.6.0 release and later has a functioning 'make install', + # but still does not install nexus, manual, etc. So, there is no compelling + # reason to use QMCPACK's built-in version at this time. def install(self, spec, prefix): if '+mpi' in spec: env['CC'] = spec['mpi'].mpicc @@ -345,57 +367,25 @@ def install(self, spec, prefix): env['F77'] = spec['mpi'].mpif77 env['FC'] = spec['mpi'].mpifc - with working_dir(self.build_directory): - make('install') - - @when('@:3.5.0') - def install(self, spec, prefix): - if '+mpi' in spec: - env['CC'] = spec['mpi'].mpicc - env['CXX'] = spec['mpi'].mpicxx - env['F77'] = spec['mpi'].mpif77 - env['FC'] = spec['mpi'].mpifc - - # QMCPACK 'make install' does nothing, which causes - # Spack to throw an error. - # - # This install method creates the top level directory - # and copies the bin subdirectory into the appropriate - # location. We do not copy include or lib at this time due - # to technical difficulties in qmcpack itself. - + # create top-level directory mkdirp(prefix) - # We assume cwd is self.stage.source_path - - # install manual + # We assume cwd is self.stage.source_path, then + # install manual, labs, and nexus install_tree('manual', prefix.manual) - - # install nexus + install_tree('labs', prefix.labs) install_tree('nexus', prefix.nexus) + # install binaries with working_dir(self.build_directory): - mkdirp(prefix) - - # install binaries install_tree('bin', prefix.bin) - # QMCPACK 3.6.0 install directory structure changed, thus there - # thus are two version of the setup_run_environment method - @when('@:3.5.0') def setup_run_environment(self, env): """Set-up runtime environment for QMCPACK. - Set PYTHONPATH for basic analysis scripts and for Nexus.""" - env.prepend_path('PYTHONPATH', self.prefix.nexus) + Set PATH and PYTHONPATH for basic analysis scripts for Nexus.""" - @when('@3.6.0:') - def setup_run_environment(self, env): - """Set-up runtime environment for QMCPACK. - Set PYTHONPATH for basic analysis scripts and for Nexus. Binaries - are in the 'prefix' directory instead of 'prefix.bin' which is - not set by the default module environment""" - env.prepend_path('PATH', self.prefix) - env.prepend_path('PYTHONPATH', self.prefix) + env.prepend_path('PATH', self.prefix.nexus.bin) + env.prepend_path('PYTHONPATH', self.prefix.nexus.lib) @run_after('build') @on_package_attributes(run_tests=True) diff --git a/var/spack/repos/builtin/packages/quantum-espresso/package.py b/var/spack/repos/builtin/packages/quantum-espresso/package.py index 403a8a3082c..52fb46c7843 100644 --- a/var/spack/repos/builtin/packages/quantum-espresso/package.py +++ b/var/spack/repos/builtin/packages/quantum-espresso/package.py @@ -76,11 +76,12 @@ class QuantumEspresso(Package): patch('dspev_drv_elpa.patch', when='@6.1.0:+patch+elpa ^elpa@2016.05.003') # Conflicts + # Omitted for now due to concretizer bug # MKL with 64-bit integers not supported. - conflicts( - '^mkl+ilp64', - msg='Quantum ESPRESSO does not support MKL 64-bit integer variant' - ) + # conflicts( + # '^mkl+ilp64', + # msg='Quantum ESPRESSO does not support MKL 64-bit integer variant' + # ) # We can't ask for scalapack or elpa if we don't want MPI conflicts( From b397af5d9cfa685d2a41ede488e027561035087c Mon Sep 17 00:00:00 2001 From: Sinan Date: Fri, 27 Mar 2020 09:42:58 -0700 Subject: [PATCH 246/377] Package/qscintilla: python bindings via extend path (#15599) * build python bindings within qscintilla package via extend_path trick * add todo * reflect new setup also in py-pyqt4 package * get rid of qscintilla dependency * also tweak qgis for the new setup * generalize the building of python bindings * generalize building of pythong bindings to all qt versions * add qsci_api variant * add qsci_variant for pyqt4 package as well; add comment * pyqt dependency should build with +qsci_api variant enabled * fix bugs * improve style * reflect recent changes * flake8 * improve style * more flake8 * more flake8 Co-authored-by: Sinan81 --- .../builtin/packages/py-pyqt4/package.py | 64 ++------------- .../builtin/packages/py-pyqt5/package.py | 67 ++-------------- .../repos/builtin/packages/qgis/package.py | 6 +- .../builtin/packages/qscintilla/package.py | 78 ++++++++++++++++++- 4 files changed, 89 insertions(+), 126 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pyqt4/package.py b/var/spack/repos/builtin/packages/py-pyqt4/package.py index d1a90042d95..6c5af83cb26 100644 --- a/var/spack/repos/builtin/packages/py-pyqt4/package.py +++ b/var/spack/repos/builtin/packages/py-pyqt4/package.py @@ -4,7 +4,6 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * -import os class PyPyqt4(SIPPackage): @@ -29,21 +28,13 @@ class PyPyqt4(SIPPackage): version('4.11.3', sha256='853780dcdbe2e6ba785d703d059b096e1fc49369d3e8d41a060be874b8745686', url='http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-4.11.3/PyQt-x11-gpl-4.11.3.tar.gz') - variant('qsci', default=False, description='Build with QScintilla python bindings') + # API files can be installed regardless if QScintilla is installed or not + variant('qsci_api', default=False, description='Install PyQt API file for QScintilla') # Supposedly can also be built with Qt 5 compatibility layer depends_on('qt@:4') - depends_on('qscintilla', when='+qsci') depends_on('py-sip module=PyQt4.sip') - # For building Qscintilla python bindings - resource(name='qscintilla', - url='https://www.riverbankcomputing.com/static/Downloads/QScintilla/2.10.2/QScintilla_gpl-2.10.2.tar.gz', - sha256='14b31d20717eed95ea9bea4cd16e5e1b72cee7ebac647cba878e0f6db6a65ed0', - destination='spack-resource-qscintilla', - when='^qscintilla@2.10.2' - ) - # https://www.riverbankcomputing.com/static/Docs/PyQt4/installation.html def configure_file(self): return 'configure-ng.py' @@ -54,52 +45,7 @@ def configure_args(self): '--sipdir', self.prefix.share.sip.PyQt4, '--stubsdir', join_path(site_packages_dir, 'PyQt4') ] - if '+qsci' in self.spec: - args.extend(['--qsci-api-destdir', self.prefix.share.qsci]) + if '+qsci_api' in self.spec: + args.extend(['--qsci-api', + '--qsci-api-destdir', self.prefix.share.qsci]) return args - - @run_after('install') - def make_qsci(self): - if '+qsci' in self.spec: - rsrc_py_path = os.path.join( - self.stage.source_path, - 'spack-resource-qscintilla/QScintilla_gpl-' + - str(self.spec['qscintilla'].version), 'Python') - with working_dir(rsrc_py_path): - pydir = join_path(site_packages_dir, 'PyQt4') - python = self.spec['python'].command - python('configure.py', - '--sip=' + self.spec['py-sip'].prefix.bin.sip, - '--qsci-incdir=' + - self.spec['qscintilla'].prefix.include, - '--qsci-libdir=' + self.spec['qscintilla'].prefix.lib, - '--qsci-sipdir=' + self.prefix.share.sip.PyQt4, - '--apidir=' + self.prefix.share.qsci, - '--destdir=' + pydir, - '--pyqt-sipdir=' + self.prefix.share.sip.PyQt4, - '--sip-incdir=' + - join_path(self.spec['py-sip'].prefix.include, - 'python' + - str(self.spec['python'].version.up_to(2))), - '--stubsdir=' + pydir) - - # Fix build errors - # "QAbstractScrollArea: No such file or directory" - # "qprinter.h: No such file or directory" - # ".../Qsci.so: undefined symbol: _ZTI10Qsci...." - qscipro = FileFilter('Qsci/Qsci.pro') - link_qscilibs = 'LIBS += -L' + self.prefix.lib +\ - ' -lqscintilla2_qt4' - qscipro.filter('TEMPLATE = lib', - 'TEMPLATE = lib\nQT += widgets' + - '\nQT += printsupport\n' + link_qscilibs) - - make() - - # Fix installation prefixes - makefile = FileFilter('Makefile') - makefile.filter(r'\$\(INSTALL_ROOT\)', '') - makefile = FileFilter('Qsci/Makefile') - makefile.filter(r'\$\(INSTALL_ROOT\)', '') - - make('install') diff --git a/var/spack/repos/builtin/packages/py-pyqt5/package.py b/var/spack/repos/builtin/packages/py-pyqt5/package.py index bc37d4dcab1..e26c66a891c 100644 --- a/var/spack/repos/builtin/packages/py-pyqt5/package.py +++ b/var/spack/repos/builtin/packages/py-pyqt5/package.py @@ -4,7 +4,6 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * -import os class PyPyqt5(SIPPackage): @@ -30,7 +29,8 @@ class PyPyqt5(SIPPackage): version('5.13.0', sha256='0cdbffe5135926527b61cc3692dd301cd0328dd87eeaf1313e610787c46faff9') version('5.12.3', sha256='0db0fa37debab147450f9e052286f7a530404e2aaddc438e97a7dcdf56292110') - variant('qsci', default=False, description='Build with QScintilla python bindings') + # API files can be installed regardless if Qscintilla is installed or not + variant('qsci_api', default=False, description='Install PyQt API file for QScintilla') # Without opengl support, I got the following error: # sip: QOpenGLFramebufferObject is undefined @@ -39,15 +39,6 @@ class PyPyqt5(SIPPackage): depends_on('py-enum34', type=('build', 'run'), when='^python@:3.3') depends_on('py-sip module=PyQt5.sip', type=('build', 'run')) depends_on('py-sip@:4.19.18 module=PyQt5.sip', type=('build', 'run'), when='@:5.13.0') - depends_on('qscintilla', when='+qsci') - - # For building Qscintilla python bindings - resource(name='qscintilla', - url='https://www.riverbankcomputing.com/static/Downloads/QScintilla/2.10.2/QScintilla_gpl-2.10.2.tar.gz', - sha256='14b31d20717eed95ea9bea4cd16e5e1b72cee7ebac647cba878e0f6db6a65ed0', - destination='spack-resource-qscintilla', - when='^qscintilla@2.10.2' - ) # https://www.riverbankcomputing.com/static/Docs/PyQt5/installation.html def configure_args(self): @@ -59,55 +50,7 @@ def configure_args(self): self.spec['python'].package.site_packages_dir, 'PyQt5'), ] - if '+qsci' in self.spec: - args.extend(['--qsci-api-destdir', self.prefix.share.qsci]) + if '+qsci_api' in self.spec: + args.extend(['--qsci-api', + '--qsci-api-destdir', self.prefix.share.qsci]) return args - - @run_after('install') - def make_qsci(self): - if '+qsci' in self.spec: - rsrc_py_path = os.path.join( - self.stage.source_path, - 'spack-resource-qscintilla/QScintilla_gpl-' + - str(self.spec['qscintilla'].version), 'Python') - with working_dir(rsrc_py_path): - pydir = join_path( - self.prefix, - self.spec['python'].package.site_packages_dir, - 'PyQt5') - python = self.spec['python'].command - python('configure.py', '--pyqt=PyQt5', - '--sip=' + self.spec['py-sip'].prefix.bin.sip, - '--qsci-incdir=' + - self.spec['qscintilla'].prefix.include, - '--qsci-libdir=' + self.spec['qscintilla'].prefix.lib, - '--qsci-sipdir=' + self.prefix.share.sip.PyQt5, - '--apidir=' + self.prefix.share.qsci, - '--destdir=' + pydir, - '--pyqt-sipdir=' + self.prefix.share.sip.PyQt5, - '--sip-incdir=' + - join_path(self.spec['py-sip'].prefix.include, - 'python' + - str(self.spec['python'].version.up_to(2))), - '--stubsdir=' + pydir) - - # Fix build errors - # "QAbstractScrollArea: No such file or directory" - # "qprinter.h: No such file or directory" - # ".../Qsci.so: undefined symbol: _ZTI10Qsci...." - qscipro = FileFilter('Qsci/Qsci.pro') - link_qscilibs = 'LIBS += -L' + self.prefix.lib +\ - ' -lqscintilla2_qt5' - qscipro.filter('TEMPLATE = lib', - 'TEMPLATE = lib\nQT += widgets' + - '\nQT += printsupport\n' + link_qscilibs) - - make() - - # Fix installation prefixes - makefile = FileFilter('Makefile') - makefile.filter(r'\$\(INSTALL_ROOT\)', '') - makefile = FileFilter('Qsci/Makefile') - makefile.filter(r'\$\(INSTALL_ROOT\)', '') - - make('install') diff --git a/var/spack/repos/builtin/packages/qgis/package.py b/var/spack/repos/builtin/packages/qgis/package.py index 4a6d6a3583b..89536068da2 100644 --- a/var/spack/repos/builtin/packages/qgis/package.py +++ b/var/spack/repos/builtin/packages/qgis/package.py @@ -74,9 +74,9 @@ class Qgis(CMakePackage): depends_on('qwtpolar') depends_on('expat@1.95:') depends_on('qca@2.2.1') - depends_on('py-pyqt4 +qsci', when='@2') - depends_on('py-pyqt5@5.3: +qsci', when='@3') - depends_on('qscintilla') + depends_on('py-pyqt4', when='@2') + depends_on('py-pyqt5@5.3:', when='@3') + depends_on('qscintilla +python') depends_on('qjson') depends_on('py-requests', type=('build', 'run')) # TODO: is build dependency necessary? depends_on('py-psycopg2', type=('build', 'run')) # TODO: is build dependency necessary? diff --git a/var/spack/repos/builtin/packages/qscintilla/package.py b/var/spack/repos/builtin/packages/qscintilla/package.py index 9bee719c136..ec20257676d 100644 --- a/var/spack/repos/builtin/packages/qscintilla/package.py +++ b/var/spack/repos/builtin/packages/qscintilla/package.py @@ -20,10 +20,14 @@ class Qscintilla(QMakePackage): version('2.10.2', sha256='14b31d20717eed95ea9bea4cd16e5e1b72cee7ebac647cba878e0f6db6a65ed0', preferred=True) variant('designer', default=False, description="Enable pluging for Qt-Designer") - # No 'python' variant, since Python bindings will be - # built by PyQt5+qsci instead + variant('python', default=False, description="Build python bindings") depends_on('qt') + depends_on('py-pyqt5 +qsci_api', type=('build', 'run'), when='+python ^qt@5') + depends_on('py-pyqt4 +qsci_api', type=('build', 'run'), when='+python ^qt@4') + depends_on('python', type=('build', 'run'), when='+python') + + extends('python', when='+python') @run_before('qmake') def chdir(self): @@ -66,3 +70,73 @@ def postinstall(self): makefile.filter(r'\$\(INSTALL_ROOT\)' + self.spec['qt'].prefix, '$(INSTALL_ROOT)') make('install') + + @run_after('install') + def make_qsci(self): + if '+python' in self.spec: + if '^py-pyqt4' in self.spec: + py_pyqtx = 'py-pyqt4' + pyqtx = 'PyQt4' + elif '^py-pyqt5' in self.spec: + py_pyqtx = 'py-pyqt5' + pyqtx = 'PyQt5' + + with working_dir(join_path(self.stage.source_path, 'Python')): + pydir = join_path( + self.prefix, + self.spec['python'].package.site_packages_dir, + pyqtx) + mkdirp(os.path.join(self.prefix.share.sip, pyqtx)) + python = self.spec['python'].command + python('configure.py', '--pyqt=' + pyqtx, + '--sip=' + self.spec['py-sip'].prefix.bin.sip, + '--qsci-incdir=' + self.spec.prefix.include, + '--qsci-libdir=' + self.spec.prefix.lib, + '--qsci-sipdir=' + + os.path.join(self.prefix.share.sip, pyqtx), + '--apidir=' + self.prefix.share.qsci, + '--destdir=' + pydir, + '--pyqt-sipdir=' + os.path.join( + self.spec[py_pyqtx].prefix.share.sip, pyqtx), + '--sip-incdir=' + + join_path(self.spec['py-sip'].prefix.include, + 'python' + + str(self.spec['python'].version.up_to(2))), + '--stubsdir=' + pydir) + + # Fix build errors + # "QAbstractScrollArea: No such file or directory" + # "qprinter.h: No such file or directory" + # ".../Qsci.so: undefined symbol: _ZTI10Qsci...." + qscipro = FileFilter('Qsci/Qsci.pro') + if '^qt@4' in self.spec: + qtx = 'qt4' + elif '^qt@5' in self.spec: + qtx = 'qt5' + + link_qscilibs = 'LIBS += -L' + self.prefix.lib +\ + ' -lqscintilla2_' + qtx + qscipro.filter('TEMPLATE = lib', + 'TEMPLATE = lib\nQT += widgets' + + '\nQT += printsupport\n' + link_qscilibs) + + make() + + # Fix installation prefixes + makefile = FileFilter('Makefile') + makefile.filter(r'\$\(INSTALL_ROOT\)', '') + makefile = FileFilter('Qsci/Makefile') + makefile.filter(r'\$\(INSTALL_ROOT\)', '') + + make('install') + + @run_after('install') + def extend_path_setup(self): + # See github issue #14121 and PR #15297 + module = self.spec['py-sip'].variants['module'].value + if module != 'sip': + module = module.split('.')[0] + with working_dir(site_packages_dir): + with open(os.path.join(module, '__init__.py'), 'w') as f: + f.write('from pkgutil import extend_path\n') + f.write('__path__ = extend_path(__path__, __name__)\n') From b6d2abf8856c1c19d92ce73e81e643e720694493 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 27 Mar 2020 11:43:16 -0500 Subject: [PATCH 247/377] py-grpcio: add new version (#15713) --- var/spack/repos/builtin/packages/py-grpcio/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-grpcio/package.py b/var/spack/repos/builtin/packages/py-grpcio/package.py index bdda7c85e37..18981f20e45 100644 --- a/var/spack/repos/builtin/packages/py-grpcio/package.py +++ b/var/spack/repos/builtin/packages/py-grpcio/package.py @@ -10,8 +10,9 @@ class PyGrpcio(PythonPackage): """HTTP/2-based RPC framework.""" homepage = "https://grpc.io/" - url = "https://pypi.io/packages/source/g/grpcio/grpcio-1.25.0.tar.gz" + url = "https://pypi.io/packages/source/g/grpcio/grpcio-1.27.2.tar.gz" + version('1.27.2', sha256='5ae532b93cf9ce5a2a549b74a2c35e3b690b171ece9358519b3039c7b84c887e') version('1.25.0', sha256='c948c034d8997526011960db54f512756fb0b4be1b81140a15b4ef094c6594a4') depends_on('py-setuptools', type='build') From f40080934e7817e8f7ba370c0e5dce86b3651f25 Mon Sep 17 00:00:00 2001 From: "Daryl W. Grunau" Date: Fri, 27 Mar 2020 11:57:04 -0600 Subject: [PATCH 248/377] New package lesstif (#15703) * new package lesstif * incorporate more of the Homebrew build recipe Co-authored-by: Daryl W. Grunau --- .../repos/builtin/packages/lesstif/package.py | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 var/spack/repos/builtin/packages/lesstif/package.py diff --git a/var/spack/repos/builtin/packages/lesstif/package.py b/var/spack/repos/builtin/packages/lesstif/package.py new file mode 100644 index 00000000000..c36b90e9b70 --- /dev/null +++ b/var/spack/repos/builtin/packages/lesstif/package.py @@ -0,0 +1,51 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Lesstif(AutotoolsPackage): + """LessTif is the Hungry Programmers' version of OSF/Motif.""" + + homepage = "https://sourceforge.net/projects/lesstif" + url = "https://sourceforge.net/projects/lesstif/files/lesstif/0.95.2/lesstif-0.95.2.tar.bz2/download" + + version('0.95.2', sha256='eb4aa38858c29a4a3bcf605cfe7d91ca41f4522d78d770f69721e6e3a4ecf7e3') + + variant('shared', default=True, description='Build shared libraries') + variant('static', default=False, description='Build static libraries') + + depends_on('libice') + depends_on('libsm') + depends_on('libxt') + + def patch(self): + filter_file("ACLOCALDIR=.*", + "ACLOCALDIR='${datarootdir}/aclocal'", + "configure") + + def setup_build_environment(self, env): + # 'sed' fails if LANG=en_US.UTF-8 as is often the case on Macs. + # The configure script finds our superenv sed wrapper, sets + # SED, but then doesn't use that variable. + env.set('LANG', 'C') + + def configure_args(self): + spec = self.spec + + args = [ + '--disable-debug', + '--enable-production', + '--disable-dependency-tracking', + '--enable-shared' if '+shared' in spec else '--disable-shared', + '--enable-static' if '+static' in spec else '--disable-static', + ] + + return args + + # LessTif won't install in parallel 'cause several parts of the + # Makefile will try to make the same directory and `mkdir` will fail. + def install(self, spec, prefix): + make('install', parallel=False) From cd82228c788d74a0be66135a5b3afc2bb800ceb5 Mon Sep 17 00:00:00 2001 From: iarspider Date: Fri, 27 Mar 2020 18:57:29 +0100 Subject: [PATCH 249/377] py-multiprocess: add new version (0.70.9) and dependencies (#15710) * py-multiprocess: add new version (0.70.9) and dependencies * Add new version of py-dill * Update package.py * Update package.py --- var/spack/repos/builtin/packages/py-dill/package.py | 2 ++ var/spack/repos/builtin/packages/py-multiprocess/package.py | 4 +++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-dill/package.py b/var/spack/repos/builtin/packages/py-dill/package.py index 485dfd9d668..0afa8d329ce 100644 --- a/var/spack/repos/builtin/packages/py-dill/package.py +++ b/var/spack/repos/builtin/packages/py-dill/package.py @@ -12,6 +12,7 @@ class PyDill(PythonPackage): homepage = "https://github.com/uqfoundation/dill" url = "https://pypi.io/packages/source/d/dill/dill-0.2.7.tar.gz" + version('0.3.1', sha256='d3ddddf2806a7bc9858b20c02dc174396795545e9d62f243b34481fd26eb3e2c') version('0.2.9', sha256='f6d6046f9f9195206063dd0415dff185ad593d6ee8b0e67f12597c0f4df4986f') version('0.2.7', sha256='ddda0107e68e4eb1772a9f434f62a513c080c7171bd0dd6fb65d992788509812') version('0.2.6', sha256='6c1ccca68be483fa8c66e85a89ffc850206c26373aa77a97b83d8d0994e7f1fd') @@ -23,6 +24,7 @@ class PyDill(PythonPackage): version('0.2', sha256='aba8d4c81c4136310e6ce333bd6f4f3ea2d53bd367e2f69c864428f260c0308c') depends_on('python@2.5:2.8,3.1:', type=('build', 'run')) + depends_on('python@2.6:2.8,3.1:', type=('build', 'run'), when='@0.3.0:') depends_on('py-setuptools@0.6:', type='build') diff --git a/var/spack/repos/builtin/packages/py-multiprocess/package.py b/var/spack/repos/builtin/packages/py-multiprocess/package.py index 97a58a905d9..f382ff050fa 100644 --- a/var/spack/repos/builtin/packages/py-multiprocess/package.py +++ b/var/spack/repos/builtin/packages/py-multiprocess/package.py @@ -12,15 +12,17 @@ class PyMultiprocess(PythonPackage): homepage = "https://github.com/uqfoundation/multiprocess" url = "https://pypi.io/packages/source/m/multiprocess/multiprocess-0.70.5.zip" + version('0.70.9', sha256='9fd5bd990132da77e73dec6e9613408602a4612e1d73caf2e2b813d2b61508e5') version('0.70.7', sha256='3394f1fbd0d87112690a877e49eb7917d851ee8d822294d522dd4deae12febdb') version('0.70.5', sha256='c4c196f3c4561dc1d78139c3e73709906a222d2fc166ef3eef895d8623df7267') version('0.70.4', sha256='a692c6dc8392c25b29391abb58a9fbdc1ac38bca73c6f27d787774201e68e12c') - depends_on('python@2.6:2.8,3.1:') + depends_on('python@2.5:2.8,3.1:', type=('build', 'run')) depends_on('py-setuptools@0.6:', type='build') depends_on('py-dill@0.2.6:', type=('build', 'run')) depends_on('py-dill@0.2.9:', type=('build', 'run'), when='@0.70.7:') + depends_on('py-dill@0.3.1:', type=('build', 'run'), when='@0.70.9:') def url_for_version(self, version): url = self.url.rsplit('/', 1)[0] From 2b915dc517707f801f7bb5117b39280b6569a890 Mon Sep 17 00:00:00 2001 From: JeromeDuboisPro <59056395+JeromeDuboisPro@users.noreply.github.com> Date: Fri, 27 Mar 2020 20:28:51 +0100 Subject: [PATCH 250/377] Adding mesa-glu 9.0.1 (2019) (#15705) Adding mesa-glu 9.0.1 (2019) --- var/spack/repos/builtin/packages/mesa-glu/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/mesa-glu/package.py b/var/spack/repos/builtin/packages/mesa-glu/package.py index 9593c562711..bd3c90b0203 100644 --- a/var/spack/repos/builtin/packages/mesa-glu/package.py +++ b/var/spack/repos/builtin/packages/mesa-glu/package.py @@ -12,6 +12,7 @@ class MesaGlu(AutotoolsPackage): homepage = "https://www.mesa3d.org" url = "https://www.mesa3d.org/archive/glu/glu-9.0.0.tar.gz" + version('9.0.1', sha256='f6f484cfcd51e489afe88031afdea1e173aa652697e4c19ddbcb8260579a10f7') version('9.0.0', sha256='4387476a1933f36fec1531178ea204057bbeb04cc2d8396c9ea32720a1f7e264') depends_on('gl@3:') From d909c6d89d382773152d0c5320babb98d665296a Mon Sep 17 00:00:00 2001 From: Benjamin Fovet <45510885+bfovet@users.noreply.github.com> Date: Fri, 27 Mar 2020 20:29:49 +0100 Subject: [PATCH 251/377] Add new package CMinpack (#15606) * Add new package CMinpack * Add link to CMinpack PR#21 --- .../cminpack/link_with_blas_pr_21.patch | 267 ++++++++++++++++++ .../builtin/packages/cminpack/package.py | 39 +++ 2 files changed, 306 insertions(+) create mode 100644 var/spack/repos/builtin/packages/cminpack/link_with_blas_pr_21.patch create mode 100644 var/spack/repos/builtin/packages/cminpack/package.py diff --git a/var/spack/repos/builtin/packages/cminpack/link_with_blas_pr_21.patch b/var/spack/repos/builtin/packages/cminpack/link_with_blas_pr_21.patch new file mode 100644 index 00000000000..a28d67ea0f9 --- /dev/null +++ b/var/spack/repos/builtin/packages/cminpack/link_with_blas_pr_21.patch @@ -0,0 +1,267 @@ +From 3b386a0ed507a9923f942098a4dcf2df2bcde7d7 Mon Sep 17 00:00:00 2001 +From: Michel Zou +Date: Thu, 6 Dec 2018 23:38:07 +0100 +Subject: [PATCH] cmake to link to cblas + +--- + CMakeLists.txt | 30 ++++--- + cmake/CMakeLists.txt | 2 +- + cmake/FindCBLAS.cmake | 180 ++++++++++++++++++++++++++++++++++++++++++ + 3 files changed, 201 insertions(+), 11 deletions(-) + create mode 100644 cmake/FindCBLAS.cmake + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 6c8d16b..f22039f 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -5,6 +5,8 @@ cmake_minimum_required (VERSION 2.8.9) + project (CMINPACK) + string(TOLOWER ${PROJECT_NAME} PROJECT_NAME_LOWER) + ++set (CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake) ++ + include(${PROJECT_SOURCE_DIR}/cmake/cminpack_utils.cmake) + # Set version and OS-specific settings + set(CMINPACK_VERSION 1.3.6 CACHE STRING "CMinpack version") +@@ -34,7 +36,7 @@ else () + endif(WIN32) + endif () + +-option(USE_BLAS "Compile cminpack using a blas library if possible" ON) ++option(USE_BLAS "Compile cminpack using cblas library if possible" ON) + + #set(CMAKE_INSTALL_PREFIX ${PROJECT_SOURCE_DIR}/../build) + +@@ -61,16 +63,24 @@ if (${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD") + TARGET_LINK_LIBRARIES(cminpack m) + endif() + +-# Link with a BLAS library if requested +-if (USE_BLAS) +- if (NOT BUILD_SHARED_LIBS) +- set(BLA_STATIC True) ++ ++include (CheckLibraryExists) ++include (CheckFunctionExists) ++check_function_exists (sqrt HAVE_SQRT_NO_LIBM) ++if (NOT HAVE_SQRT_NO_LIBM) ++ check_library_exists ("m" sqrt "" HAVE_LIBM) ++ if (HAVE_LIBM) ++ target_link_libraries(cminpack PUBLIC m) + endif() +- find_package(BLAS) +- if (BLAS_FOUND) +- target_link_libraries(cminpack PUBLIC ${BLAS_LIBRARIES}) +- set_target_properties(cminpack PROPERTIES LINK_FLAGS "${BLAS_LINKER_FLAGS}") +- target_compile_definitions(cminpack PUBLIC -DUSE_CBLAS) ++endif () ++ ++# Link with CBLAS library if requested ++if (USE_BLAS) ++ find_package (CBLAS) ++ if (CBLAS_FOUND) ++ target_link_libraries(cminpack PUBLIC ${CBLAS_LIBRARIES}) ++ set_target_properties(cminpack PROPERTIES LINK_FLAGS "${CBLAS_LINKER_FLAGS}") ++ target_compile_definitions(cminpack PUBLIC USE_CBLAS) + endif() + endif() + +diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt +index 058a89b..d8277bc 100644 +--- a/cmake/CMakeLists.txt ++++ b/cmake/CMakeLists.txt +@@ -1,7 +1,7 @@ + set(PKG_DESC "CMinPack") + set(PKG_EXTERNAL_DEPS "") + set(pkg_conf_file ${CMAKE_CURRENT_BINARY_DIR}/cminpack.pc) +-if (USE_BLAS AND BLAS_FOUND) ++if (USE_BLAS AND CBLAS_FOUND) + set(PC_CMINPACK_CFLAGS "-DUSE_CBLAS") + if (NOT "${BLAS_LIBRARIES}" STREQUAL "") + string(REPLACE ";" " -l" PC_CMINPACK_LIBRARIES "${BLAS_LIBRARIES}") +diff --git a/cmake/FindCBLAS.cmake b/cmake/FindCBLAS.cmake +new file mode 100644 +index 0000000..e4fb422 +--- /dev/null ++++ b/cmake/FindCBLAS.cmake +@@ -0,0 +1,180 @@ ++# - Find CBLAS library ++# ++# This module finds an installed fortran library that implements the CBLAS ++# linear-algebra interface (see http://www.netlib.org/blas/), with CBLAS ++# interface. ++# ++# This module sets the following variables: ++# CBLAS_FOUND - set to true if a library implementing the CBLAS interface is found ++# CBLAS_LIBRARIES - list of libraries (using full path name) to link against to use CBLAS ++# CBLAS_INCLUDE_DIR - path to includes ++# CBLAS_INCLUDE_FILE - the file to be included to use CBLAS ++# ++ ++SET(CBLAS_LIBRARIES) ++SET(CBLAS_INCLUDE_DIR) ++SET(CBLAS_INCLUDE_FILE) ++ ++# CBLAS in Intel mkl ++FIND_PACKAGE(MKL) ++IF (MKL_FOUND AND NOT CBLAS_LIBRARIES) ++ SET(CBLAS_LIBRARIES ${MKL_LIBRARIES}) ++ SET(CBLAS_INCLUDE_DIR ${MKL_INCLUDE_DIR}) ++ SET(CBLAS_INCLUDE_FILE "mkl_cblas.h") ++ENDIF (MKL_FOUND AND NOT CBLAS_LIBRARIES) ++ ++# Old CBLAS search ++SET(_verbose TRUE) ++INCLUDE(CheckFunctionExists) ++INCLUDE(CheckIncludeFile) ++ ++MACRO(CHECK_ALL_LIBRARIES LIBRARIES _prefix _name _flags _list _include _search_include) ++ # This macro checks for the existence of the combination of fortran libraries ++ # given by _list. If the combination is found, this macro checks (using the ++ # Check_Fortran_Function_Exists macro) whether can link against that library ++ # combination using the name of a routine given by _name using the linker ++ # flags given by _flags. If the combination of libraries is found and passes ++ # the link test, LIBRARIES is set to the list of complete library paths that ++ # have been found. Otherwise, LIBRARIES is set to FALSE. ++ # N.B. _prefix is the prefix applied to the names of all cached variables that ++ # are generated internally and marked advanced by this macro. ++ SET(__list) ++ FOREACH(_elem ${_list}) ++ IF(__list) ++ SET(__list "${__list} - ${_elem}") ++ ELSE(__list) ++ SET(__list "${_elem}") ++ ENDIF(__list) ++ ENDFOREACH(_elem) ++ IF(_verbose) ++ MESSAGE(STATUS "Checking for [${__list}]") ++ ENDIF(_verbose) ++ SET(_libraries_work TRUE) ++ SET(${LIBRARIES}) ++ SET(_combined_name) ++ SET(_paths) ++ FOREACH(_library ${_list}) ++ SET(_combined_name ${_combined_name}_${_library}) ++ # did we find all the libraries in the _list until now? ++ # (we stop at the first unfound one) ++ IF(_libraries_work) ++ IF(APPLE) ++ FIND_LIBRARY(${_prefix}_${_library}_LIBRARY ++ NAMES ${_library} ++ PATHS /usr/local/lib /usr/lib /usr/local/lib64 /usr/lib64 ENV ++ DYLD_LIBRARY_PATH ++ ) ++ ELSE(APPLE) ++ FIND_LIBRARY(${_prefix}_${_library}_LIBRARY ++ NAMES ${_library} ++ PATHS /usr/local/lib /usr/lib /usr/local/lib64 /usr/lib64 ENV ++ LD_LIBRARY_PATH ++ ) ++ ENDIF(APPLE) ++ MARK_AS_ADVANCED(${_prefix}_${_library}_LIBRARY) ++ IF(${_prefix}_${_library}_LIBRARY) ++ GET_FILENAME_COMPONENT(_path ${${_prefix}_${_library}_LIBRARY} PATH) ++ LIST(APPEND _paths ${_path}/../include ${_path}/../../include) ++ ENDIF(${_prefix}_${_library}_LIBRARY) ++ SET(${LIBRARIES} ${${LIBRARIES}} ${${_prefix}_${_library}_LIBRARY}) ++ SET(_libraries_work ${${_prefix}_${_library}_LIBRARY}) ++ ENDIF(_libraries_work) ++ ENDFOREACH(_library ${_list}) ++ # Test include ++ SET(_bug_search_include ${_search_include}) #CMAKE BUG!!! SHOULD NOT BE THAT ++ IF(_bug_search_include) ++ FIND_PATH(${_prefix}${_combined_name}_INCLUDE ${_include} ${_paths}) ++ MARK_AS_ADVANCED(${_prefix}${_combined_name}_INCLUDE) ++ IF(${_prefix}${_combined_name}_INCLUDE) ++ IF (_verbose) ++ MESSAGE(STATUS "Includes found") ++ ENDIF (_verbose) ++ SET(${_prefix}_INCLUDE_DIR ${${_prefix}${_combined_name}_INCLUDE}) ++ SET(${_prefix}_INCLUDE_FILE ${_include}) ++ ELSE(${_prefix}${_combined_name}_INCLUDE) ++ SET(_libraries_work FALSE) ++ ENDIF(${_prefix}${_combined_name}_INCLUDE) ++ ELSE(_bug_search_include) ++ SET(${_prefix}_INCLUDE_DIR) ++ SET(${_prefix}_INCLUDE_FILE ${_include}) ++ ENDIF(_bug_search_include) ++ # Test this combination of libraries. ++ IF(_libraries_work) ++ SET(CMAKE_REQUIRED_LIBRARIES ${_flags} ${${LIBRARIES}}) ++ CHECK_FUNCTION_EXISTS(${_name} ${_prefix}${_combined_name}_WORKS) ++ SET(CMAKE_REQUIRED_LIBRARIES) ++ MARK_AS_ADVANCED(${_prefix}${_combined_name}_WORKS) ++ SET(_libraries_work ${${_prefix}${_combined_name}_WORKS}) ++ IF(_verbose AND _libraries_work) ++ MESSAGE(STATUS "Libraries found") ++ ENDIF(_verbose AND _libraries_work) ++ ENDIF(_libraries_work) ++ # Fin ++ IF(NOT _libraries_work) ++ SET(${LIBRARIES} NOTFOUND) ++ ENDIF(NOT _libraries_work) ++ENDMACRO(CHECK_ALL_LIBRARIES) ++ ++# Generic CBLAS library ++IF(NOT CBLAS_LIBRARIES) ++ CHECK_ALL_LIBRARIES( ++ CBLAS_LIBRARIES ++ CBLAS ++ cblas_dgemm ++ "" ++ "cblas" ++ "cblas.h" ++ TRUE ) ++ENDIF() ++ ++# CBLAS in ATLAS library? (http://math-atlas.sourceforge.net/) ++IF(NOT CBLAS_LIBRARIES) ++ CHECK_ALL_LIBRARIES( ++ CBLAS_LIBRARIES ++ CBLAS ++ cblas_dgemm ++ "" ++ "cblas;atlas" ++ "cblas.h" ++ TRUE ) ++ENDIF() ++ ++# CBLAS in BLAS library ++IF(NOT CBLAS_LIBRARIES) ++ CHECK_ALL_LIBRARIES( ++ CBLAS_LIBRARIES ++ CBLAS ++ cblas_dgemm ++ "" ++ "blas" ++ "cblas.h" ++ TRUE ) ++ENDIF() ++ ++# Apple CBLAS library? ++IF(NOT CBLAS_LIBRARIES) ++ CHECK_ALL_LIBRARIES( ++ CBLAS_LIBRARIES ++ CBLAS ++ cblas_dgemm ++ "" ++ "Accelerate" ++ "Accelerate/Accelerate.h" ++ FALSE ) ++ENDIF() ++ ++IF( NOT CBLAS_LIBRARIES ) ++ CHECK_ALL_LIBRARIES( ++ CBLAS_LIBRARIES ++ CBLAS ++ cblas_dgemm ++ "" ++ "vecLib" ++ "vecLib/vecLib.h" ++ FALSE ) ++ENDIF() ++ ++include ( FindPackageHandleStandardArgs ) ++find_package_handle_standard_args ( CBLAS DEFAULT_MSG CBLAS_LIBRARIES ++) ++ diff --git a/var/spack/repos/builtin/packages/cminpack/package.py b/var/spack/repos/builtin/packages/cminpack/package.py new file mode 100644 index 00000000000..e269accabf7 --- /dev/null +++ b/var/spack/repos/builtin/packages/cminpack/package.py @@ -0,0 +1,39 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Cminpack(CMakePackage): + """This is a C version of the minpack minimization package. + Minpack includes software for solving nonlinear equations + and nonlinear least squares problems. + """ + + homepage = "http://devernay.free.fr/hacks/cminpack" + url = "https://github.com/devernay/cminpack/archive/v1.3.6.tar.gz" + git = 'https://github.com/devernay/cminpack.git' + + version('master', branch='master') + version('1.3.6', sha256='3c07fd21308c96477a2c900032e21d937739c233ee273b4347a0d4a84a32d09f') + + variant('shared', default=False, description='Build shared libraries') + variant('blas', default=True, description='Compile with BLAS') + + depends_on('blas', when='+blas') + + # Backport a pull request for correctly linking blas. + # See https://github.com/devernay/cminpack/pull/21 + patch('link_with_blas_pr_21.patch', when='@:1.3.6') + + def cmake_args(self): + args = [ + '-DBUILD_SHARED_LIBS=%s' % ( + 'ON' if '+shared' in self.spec else 'OFF'), + '-DUSE_BLAS=%s' % ( + 'ON' if 'blas' in self.spec else 'OFF') + ] + + return args From 829bfb578814d076000d6d0ad8339143322e28ee Mon Sep 17 00:00:00 2001 From: Sinan Date: Fri, 27 Mar 2020 13:28:54 -0700 Subject: [PATCH 252/377] magma now extends CudaPackage class, taking care of the gcc conflicts (#14471) * magma now extends CudaPackage class, taking care of the gcc conflicts * enforce +cuda; thus cuda is dependency via CudaPackage class * add conflict * use cuda_arch to set GPU_TARGET build option * get rid of unnecessary constraint * flake8 * impose cuda version dependency found empirically * add variant description * add conflict Co-authored-by: Sinan81 Co-authored-by: Sinan81 --- .../repos/builtin/packages/magma/package.py | 25 +++++++++++-------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/var/spack/repos/builtin/packages/magma/package.py b/var/spack/repos/builtin/packages/magma/package.py index 27f2f438e97..2e864630188 100644 --- a/var/spack/repos/builtin/packages/magma/package.py +++ b/var/spack/repos/builtin/packages/magma/package.py @@ -7,10 +7,10 @@ from spack import * -class Magma(CMakePackage): - """The MAGMA project aims to develop a dense linear algebra library similar to - LAPACK but for heterogeneous/hybrid architectures, starting with current - "Multicore+GPU" systems. +class Magma(CMakePackage, CudaPackage): + """The MAGMA project aims to develop a dense linear algebra library similar + to LAPACK but for heterogeneous/hybrid architectures, starting with + current "Multicore+GPU" systems. """ homepage = "http://icl.cs.utk.edu/magma/" @@ -28,13 +28,15 @@ class Magma(CMakePackage): description='Enable Fortran bindings support') variant('shared', default=True, description='Enable shared library') + variant('cuda', default=True, description='Build with CUDA') depends_on('blas') depends_on('lapack') - depends_on('cuda') + depends_on('cuda@8:', when='@2.5.1:') # See PR #14471 - conflicts('%gcc@6:', when='^cuda@:8') - conflicts('%gcc@7:', when='^cuda@:9') + conflicts('~cuda', msg='Magma requires cuda') + conflicts('cuda_arch=none', + msg='Please indicate a CUDA arch value or values') patch('ibm-xl.patch', when='@2.2:2.5.0%xl') patch('ibm-xl.patch', when='@2.2:2.5.0%xl_r') @@ -69,11 +71,14 @@ def cmake_args(self): '-DCMAKE_Fortran_COMPILER=%s' % self.compiler.f77 ]) - if spec.satisfies('^cuda@9.0:'): + if spec.satisfies('^cuda'): + cuda_arch = self.spec.variants['cuda_arch'].value if '@:2.2.0' in spec: - options.extend(['-DGPU_TARGET=sm30']) + capabilities = ' '.join('sm{0}'.format(i) for i in cuda_arch) + options.extend(['-DGPU_TARGET=' + capabilities]) else: - options.extend(['-DGPU_TARGET=sm_30']) + capabilities = ' '.join('sm_{0}'.format(i) for i in cuda_arch) + options.extend(['-DGPU_TARGET=' + capabilities]) if '@2.5.0' in spec: options.extend(['-DMAGMA_SPARSE=OFF']) From aed516ad56c855afa65a8aea847fdf64330e797e Mon Sep 17 00:00:00 2001 From: Andrew W Elble Date: Fri, 27 Mar 2020 22:35:13 -0400 Subject: [PATCH 253/377] TensorFlow: let install take care of the headers (#15718) * TensorFlow: let install take care of the headers we don't need to manually install them. * no longer need to import glob --- .../repos/builtin/packages/py-tensorflow/package.py | 9 --------- 1 file changed, 9 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-tensorflow/package.py b/var/spack/repos/builtin/packages/py-tensorflow/package.py index 0444a2e09af..64b97b05b26 100644 --- a/var/spack/repos/builtin/packages/py-tensorflow/package.py +++ b/var/spack/repos/builtin/packages/py-tensorflow/package.py @@ -3,7 +3,6 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -from glob import glob import sys @@ -699,14 +698,6 @@ def install(self, spec, prefix): setup_py('install', '--prefix={0}'.format(prefix), '--single-version-externally-managed', '--root=/') - site_packages_dir = join_path( - prefix.lib, - ('python' + str(self.spec['python'].version.up_to(2))), - 'site-packages') - fn = glob(join_path(site_packages_dir, "tensorflow-*")) - incpath = join_path(fn[0], "tensorflow/include") - setup_py('install_headers', '--install-dir={0}'.format(incpath)) - @run_after('install') @on_package_attributes(run_tests=True) def import_module_test(self): From f6f5604927aeb7cc2fd96d8e441b22bb706d990d Mon Sep 17 00:00:00 2001 From: Sinan Date: Fri, 27 Mar 2020 19:36:33 -0700 Subject: [PATCH 254/377] Package/qgis add versions 3.10.4 3.12.1 (#15720) * add latest versions * order dependencies alphabetically * flake8 Co-authored-by: Sinan81 --- .../repos/builtin/packages/qgis/package.py | 38 ++++++++++--------- 1 file changed, 20 insertions(+), 18 deletions(-) diff --git a/var/spack/repos/builtin/packages/qgis/package.py b/var/spack/repos/builtin/packages/qgis/package.py index 89536068da2..1edf4c29720 100644 --- a/var/spack/repos/builtin/packages/qgis/package.py +++ b/var/spack/repos/builtin/packages/qgis/package.py @@ -17,9 +17,11 @@ class Qgis(CMakePackage): maintainers = ['adamjstewart', 'Sinan81'] + version('3.12.1', sha256='a7dc7af768b8960c08ce72a06c1f4ca4664f4197ce29c7fe238429e48b2881a8') version('3.12.0', sha256='19e9c185dfe88cad7ee6e0dcf5ab7b0bbfe1672307868a53bf771e0c8f9d5e9c') # Prefer latest long term release - version('3.10.3', sha256='0869704df9120dd642996ff1ed50213ac8247650aa0640b62f8c9c581c05d7a7', preferred=True) + version('3.10.4', sha256='a032e2b8144c2fd825bc26766f586cfb1bd8574bc72efd1aa8ce18dfff8b6c9f', preferred=True) + version('3.10.3', sha256='0869704df9120dd642996ff1ed50213ac8247650aa0640b62f8c9c581c05d7a7') version('3.10.2', sha256='381cb01a8ac2f5379a915b124e9c830d727d2c67775ec49609c7153fe765a6f7') version('3.10.1', sha256='466ac9fad91f266cf3b9d148f58e2adebd5b9fcfc03e6730eb72251e6c34c8ab') version('3.10.0', sha256='25eb1c41d9fb922ffa337a720dfdceee43cf2d38409923f087c2010c9742f012') @@ -63,28 +65,28 @@ class Qgis(CMakePackage): # Ref. for dependencies: # http://htmlpreview.github.io/?https://raw.github.com/qgis/QGIS/master/doc/INSTALL.html # https://github.com/qgis/QGIS/blob/master/INSTALL - depends_on('qt+dbus') - depends_on('proj@4.4.0:') - depends_on('geos@3.4.0:') - depends_on('sqlite@3.0.0: +column_metadata') - depends_on('libspatialite@4.2.0:') - depends_on('libspatialindex') - depends_on('gdal@2.1.0: +python', type=('build', 'link', 'run')) - depends_on('qwt@5:') - depends_on('qwtpolar') + depends_on('exiv2') depends_on('expat@1.95:') - depends_on('qca@2.2.1') + depends_on('gdal@2.1.0: +python', type=('build', 'link', 'run')) + depends_on('geos@3.4.0:') + depends_on('libspatialindex') + depends_on('libspatialite@4.2.0:') + depends_on('libzip') + depends_on('proj@4.4.0:') + depends_on('py-psycopg2', type=('build', 'run')) # TODO: is build dependency necessary? depends_on('py-pyqt4', when='@2') depends_on('py-pyqt5@5.3:', when='@3') - depends_on('qscintilla +python') - depends_on('qjson') depends_on('py-requests', type=('build', 'run')) # TODO: is build dependency necessary? - depends_on('py-psycopg2', type=('build', 'run')) # TODO: is build dependency necessary? - depends_on('qtkeychain@0.5:', when='@3:') - depends_on('libzip') - depends_on('exiv2') - depends_on('python@3.0.0:', type=('build', 'run'), when='@3') depends_on('python@2.7:2.8', type=('build', 'run'), when='@2') + depends_on('python@3.0.0:', type=('build', 'run'), when='@3') + depends_on('qca@2.2.1') + depends_on('qjson') + depends_on('qscintilla +python') + depends_on('qt+dbus') + depends_on('qtkeychain@0.5:', when='@3:') + depends_on('qwt@5:') + depends_on('qwtpolar') + depends_on('sqlite@3.0.0: +column_metadata') # Runtime python dependencies, not mentioned in install instructions depends_on('py-pyyaml', type='run') From 6e49f5f0e57c827a49737c0df18d50ba1a7cd866 Mon Sep 17 00:00:00 2001 From: Greg Sjaardema Date: Fri, 27 Mar 2020 20:55:04 -0600 Subject: [PATCH 255/377] netcdf-c: remove maxdims and maxvars variant (#15524) * NETCDF: Remove maxdims maxvars variant I'm not sure of the correct protocol to do this, so decided to make a stab and hopefully it works or I'm told the correct way... The `maxdims` and `maxvars` variants for the NetCDF package were, to the best of my knowledge, only ever used for the Exodus library in the SEACAS package. In versions of NetCDF prior to 4.4.0, Exodus required that the `NC_MAX_DIMS` and `NC_MAX_VARS` be increased over the default values. This requirement was removed in 4.4.0 and later. I do not know of any way to make a variant depend on the version and since the `maxdims` and `maxvars` variants are integer values and not boolean, then every build of NetCDF will have these variants. Typically `maxdims=1024 maxvars=8192` and the build will patch the `netcdf.h` include file for every build even though it is (almost) never needed. The SEACAS package has a NetCDF version requirement of >4.6.2, so it no longer specifies the `maxdims` or `maxvars` variant and I could find no other package in spack that uses this variant either, so removal should not break anything *in* spack. However, there is no guarantee that some other external package doesn't use the variant, so I'm not sure of the correct way to remove the variant. For this PR, I simply removed the variants. If there is a way to specify use of the variant tied to a specific version, I couldn't find it anywhere... * Address review comment Removed `is_integral` and `import numbers` since `is_integral` was only place it was used. * Add blank line for flake8 --- .../builtin/packages/netcdf-c/package.py | 40 ------------------- 1 file changed, 40 deletions(-) diff --git a/var/spack/repos/builtin/packages/netcdf-c/package.py b/var/spack/repos/builtin/packages/netcdf-c/package.py index 01f2acf4253..e7ce1696a8b 100644 --- a/var/spack/repos/builtin/packages/netcdf-c/package.py +++ b/var/spack/repos/builtin/packages/netcdf-c/package.py @@ -5,16 +5,6 @@ from spack import * -import numbers - - -def is_integral(x): - """Any integer value""" - try: - return isinstance(int(x), numbers.Integral) and not isinstance(x, bool) - except ValueError: - return False - class NetcdfC(AutotoolsPackage): """NetCDF (network Common Data Form) is a set of software libraries and @@ -76,22 +66,6 @@ def url_for_version(self, version): # variant('cdmremote', default=False, # description='Enable CDM Remote support') - # These variants control the number of dimensions (i.e. coordinates and - # attributes) and variables (e.g. time, entity ID, number of coordinates) - # that can be used in any particular NetCDF file. - variant( - 'maxdims', - default=1024, - description='Defines the maximum dimensions of NetCDF files.', - values=is_integral - ) - variant( - 'maxvars', - default=8192, - description='Defines the maximum variables of NetCDF files.', - values=is_integral - ) - # The patch for 4.7.0 touches configure.ac. See force_autoreconf below. depends_on('autoconf', type='build', when='@4.7.0') depends_on('automake', type='build', when='@4.7.0') @@ -157,20 +131,6 @@ def force_autoreconf(self): # The patch for 4.7.0 touches configure.ac. return self.spec.satisfies('@4.7.0') - def patch(self): - try: - max_dims = int(self.spec.variants['maxdims'].value) - max_vars = int(self.spec.variants['maxvars'].value) - except (ValueError, TypeError): - raise TypeError('NetCDF variant values max[dims|vars] must be ' - 'integer values.') - - ff = FileFilter(join_path('include', 'netcdf.h')) - ff.filter(r'^(#define\s+NC_MAX_DIMS\s+)\d+(.*)$', - r'\1{0}\2'.format(max_dims)) - ff.filter(r'^(#define\s+NC_MAX_VARS\s+)\d+(.*)$', - r'\1{0}\2'.format(max_vars)) - def configure_args(self): cflags = [] cppflags = [] From 33b19e7bf033df198b3dbcae2b58d6e7e68605a1 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 27 Mar 2020 22:20:15 -0500 Subject: [PATCH 256/377] py-diskcache: add new package (#15721) --- .../builtin/packages/py-diskcache/package.py | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-diskcache/package.py diff --git a/var/spack/repos/builtin/packages/py-diskcache/package.py b/var/spack/repos/builtin/packages/py-diskcache/package.py new file mode 100644 index 00000000000..042183cdf32 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-diskcache/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class PyDiskcache(PythonPackage): + """Disk Cache -- Disk and file backed persistent cache.""" + + homepage = "http://www.grantjenks.com/docs/diskcache/" + url = "https://pypi.io/packages/source/d/diskcache/diskcache-4.1.0.tar.gz" + + version('4.1.0', sha256='bcee5a59f9c264e2809e58d01be6569a3bbb1e36a1e0fb83f7ef9b2075f95ce0') + + depends_on('py-setuptools', type='build') + depends_on('py-tox', type='test') From db67b78fb9133d45645d2fddcff4cbdc14f84917 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 28 Mar 2020 00:30:50 -0500 Subject: [PATCH 257/377] py-petastorm: add new package (#15722) --- .../builtin/packages/py-petastorm/package.py | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-petastorm/package.py diff --git a/var/spack/repos/builtin/packages/py-petastorm/package.py b/var/spack/repos/builtin/packages/py-petastorm/package.py new file mode 100644 index 00000000000..2c6cc5e34ff --- /dev/null +++ b/var/spack/repos/builtin/packages/py-petastorm/package.py @@ -0,0 +1,30 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class PyPetastorm(PythonPackage): + """Petastorm is a library enabling the use of Parquet storage from + Tensorflow, Pytorch, and other Python-based ML training frameworks.""" + + homepage = "https://github.com/uber/petastorm" + url = "https://pypi.io/packages/source/p/petastorm/petastorm-0.8.2.tar.gz" + + maintainers = ['adamjstewart'] + + version('0.8.2', sha256='7782c315e1ee8d15c7741e3eea41e77b9efce661cf58aa0220a801db64f52f91') + + depends_on('py-setuptools', type='build') + depends_on('py-dill@0.2.1:', type=('build', 'run')) + depends_on('py-diskcache@3.0.0:', type=('build', 'run')) + depends_on('py-future@0.10.2:', type=('build', 'run')) + depends_on('py-futures@2.0:', type=('build', 'run'), when='^python@:2') + depends_on('py-numpy@1.13.3:', type=('build', 'run')) + depends_on('py-packaging@15.0:', type=('build', 'run')) + depends_on('py-pandas@0.19.0:', type=('build', 'run')) + depends_on('py-psutil@4.0.0:', type=('build', 'run')) + depends_on('py-pyspark@2.1.0:', type=('build', 'run')) + depends_on('py-pyzmq@14.0.0:', type=('build', 'run')) + depends_on('py-pyarrow@0.12.0:', type=('build', 'run')) + depends_on('py-six@1.5.0:', type=('build', 'run')) From 9f7255da71c3bac2ee55d9b172136c6752fe2f4f Mon Sep 17 00:00:00 2001 From: Veselin Dobrev Date: Sat, 28 Mar 2020 03:30:05 -0700 Subject: [PATCH 258/377] mesa: re-introduce the libs property (#15716) They were originally added in #8904 and later removed (why?) in #10482. --- var/spack/repos/builtin/packages/mesa/package.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/var/spack/repos/builtin/packages/mesa/package.py b/var/spack/repos/builtin/packages/mesa/package.py index d46c75796ed..4132ba0ff49 100644 --- a/var/spack/repos/builtin/packages/mesa/package.py +++ b/var/spack/repos/builtin/packages/mesa/package.py @@ -174,3 +174,11 @@ def configure_args(self): args.append('--with-dri-drivers=' + ','.join(args_dri_drivers)) return args + + @property + def libs(self): + for dir in ['lib64', 'lib']: + libs = find_libraries('libGL', join_path(self.prefix, dir), + shared=True, recursive=False) + if libs: + return libs From 27e4a4750dcdabb55e23b4600ef63204c4ea1006 Mon Sep 17 00:00:00 2001 From: iarspider Date: Sat, 28 Mar 2020 15:10:31 +0100 Subject: [PATCH 259/377] Hack to select iconv implementation - libiconv vs. libc iconv (#15437) (re-do of #15213 due to changes in gnupg recipe) --- etc/spack/defaults/packages.yaml | 1 + .../builtin/packages/apr-util/package.py | 4 ++-- .../repos/builtin/packages/bash/package.py | 4 ++-- .../repos/builtin/packages/dcmtk/package.py | 2 +- .../builtin/packages/diffutils/package.py | 2 +- .../repos/builtin/packages/doxygen/package.py | 4 +++- .../repos/builtin/packages/gcc/package.py | 4 ++-- .../repos/builtin/packages/gdal/package.py | 4 ++-- .../repos/builtin/packages/git/package.py | 4 ++-- .../repos/builtin/packages/glib/package.py | 7 +++++-- .../repos/builtin/packages/gnupg/package.py | 4 ++-- .../repos/builtin/packages/gnuplot/package.py | 2 +- .../repos/builtin/packages/grass/package.py | 5 ++++- .../builtin/packages/gtksourceview/package.py | 2 +- .../repos/builtin/packages/lftp/package.py | 4 ++-- .../repos/builtin/packages/libc/package.py | 19 +++++++++++++++++++ .../repos/builtin/packages/libgd/package.py | 2 +- .../builtin/packages/libiconv/package.py | 1 + .../builtin/packages/libspatialite/package.py | 2 +- .../builtin/packages/libunistring/package.py | 2 +- .../repos/builtin/packages/libxml2/package.py | 4 ++-- .../repos/builtin/packages/libxslt/package.py | 2 +- .../repos/builtin/packages/mono/package.py | 4 ++-- .../repos/builtin/packages/ncl/package.py | 4 ++-- .../repos/builtin/packages/poppler/package.py | 2 +- .../repos/builtin/packages/procps/package.py | 4 ++-- .../repos/builtin/packages/tar/package.py | 4 ++-- .../builtin/packages/unixodbc/package.py | 2 +- .../repos/builtin/packages/wget/package.py | 2 +- .../builtin/packages/xerces-c/package.py | 4 ++-- 30 files changed, 70 insertions(+), 41 deletions(-) create mode 100644 var/spack/repos/builtin/packages/libc/package.py diff --git a/etc/spack/defaults/packages.yaml b/etc/spack/defaults/packages.yaml index 46aa5ad9adc..2c91b75e45d 100644 --- a/etc/spack/defaults/packages.yaml +++ b/etc/spack/defaults/packages.yaml @@ -27,6 +27,7 @@ packages: glx: [mesa+glx, opengl] glu: [mesa-glu, openglu] golang: [gcc] + iconv: [libiconv] ipp: [intel-ipp] java: [openjdk, jdk, ibm-java] jpeg: [libjpeg-turbo, libjpeg] diff --git a/var/spack/repos/builtin/packages/apr-util/package.py b/var/spack/repos/builtin/packages/apr-util/package.py index 2d9354e817a..0bb2fecfa66 100644 --- a/var/spack/repos/builtin/packages/apr-util/package.py +++ b/var/spack/repos/builtin/packages/apr-util/package.py @@ -24,7 +24,7 @@ class AprUtil(AutotoolsPackage): depends_on('apr') depends_on('expat') - depends_on('libiconv') + depends_on('iconv') depends_on('openssl', when='+crypto') depends_on('gdbm', when='+gdbm') @@ -38,7 +38,7 @@ def configure_args(self): args = [ '--with-apr={0}'.format(spec['apr'].prefix), '--with-expat={0}'.format(spec['expat'].prefix), - '--with-iconv={0}'.format(spec['libiconv'].prefix), + '--with-iconv={0}'.format(spec['iconv'].prefix), # TODO: Add support for the following database managers '--without-ndbm', '--without-berkeley-db', diff --git a/var/spack/repos/builtin/packages/bash/package.py b/var/spack/repos/builtin/packages/bash/package.py index f6c7da81296..f6901294242 100644 --- a/var/spack/repos/builtin/packages/bash/package.py +++ b/var/spack/repos/builtin/packages/bash/package.py @@ -19,7 +19,7 @@ class Bash(AutotoolsPackage, GNUMirrorPackage): depends_on('ncurses') depends_on('readline@5.0:') - depends_on('libiconv') + depends_on('iconv') patches = [ ('5.0', '001', 'f2fe9e1f0faddf14ab9bfa88d450a75e5d028fedafad23b88716bd657c737289'), @@ -54,7 +54,7 @@ def configure_args(self): '--with-curses', '--enable-readline', '--with-installed-readline', - '--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix), + '--with-libiconv-prefix={0}'.format(spec['iconv'].prefix), ] def check(self): diff --git a/var/spack/repos/builtin/packages/dcmtk/package.py b/var/spack/repos/builtin/packages/dcmtk/package.py index de7a4c6ef26..2bf3db66d14 100644 --- a/var/spack/repos/builtin/packages/dcmtk/package.py +++ b/var/spack/repos/builtin/packages/dcmtk/package.py @@ -32,7 +32,7 @@ class Dcmtk(CMakePackage): depends_on('libxml2', type=('build', 'link'), when='+xml') variant('iconv', default=True, description="Charset conversion support (iconv)") - depends_on('libiconv', type=('build', 'link')) + depends_on('iconv', type=('build', 'link')) variant('cxx11', default=False, description="Enable c++11 features") variant('stl', default=True, description="Use native STL implementation") diff --git a/var/spack/repos/builtin/packages/diffutils/package.py b/var/spack/repos/builtin/packages/diffutils/package.py index c8f2dca83f3..d41086113a5 100644 --- a/var/spack/repos/builtin/packages/diffutils/package.py +++ b/var/spack/repos/builtin/packages/diffutils/package.py @@ -18,7 +18,7 @@ class Diffutils(AutotoolsPackage, GNUMirrorPackage): build_directory = 'spack-build' - depends_on('libiconv') + depends_on('iconv') def setup_build_environment(self, env): if self.spec.satisfies('%fj'): diff --git a/var/spack/repos/builtin/packages/doxygen/package.py b/var/spack/repos/builtin/packages/doxygen/package.py index aa99ca73ee2..c3c80614d5d 100644 --- a/var/spack/repos/builtin/packages/doxygen/package.py +++ b/var/spack/repos/builtin/packages/doxygen/package.py @@ -29,7 +29,7 @@ class Doxygen(CMakePackage): depends_on("cmake@2.8.12:", type='build') depends_on("python", type='build') # 2 or 3 OK; used in CMake build - depends_on("libiconv") + depends_on("iconv") depends_on("flex", type='build') # code.l just checks subminor version <=2.5.4 or >=2.5.33 # but does not recognize 2.6.x as newer...could be patched if needed @@ -45,6 +45,8 @@ class Doxygen(CMakePackage): patch('shared_ptr.patch', when='@1.8.14') def patch(self): + if self.spec['iconv'].name == 'libc': + return # On Linux systems, iconv is provided by libc. Since CMake finds the # symbol in libc, it does not look for libiconv, which leads to linker # errors. This makes sure that CMake always looks for the external diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index f3891161a2b..b7a08f8538f 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -103,7 +103,7 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage): depends_on('isl@0.15:0.18', when='@6:8.9') depends_on('isl@0.15:0.20', when='@9:') depends_on('zlib', when='@6:') - depends_on('libiconv', when='platform=darwin') + depends_on('iconv', when='platform=darwin') depends_on('gnat', when='languages=ada') depends_on('binutils~libiberty', when='+binutils') depends_on('zip', type='build', when='languages=java') @@ -356,7 +356,7 @@ def configure_args(self): options.extend([ '--with-native-system-header-dir=/usr/include', '--with-sysroot={0}'.format(macos_sdk_path()), - '--with-libiconv-prefix={0}'.format(spec['libiconv'].prefix) + '--with-libiconv-prefix={0}'.format(spec['iconv'].prefix) ]) return options diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py index 21828112335..b6b78f80200 100644 --- a/var/spack/repos/builtin/packages/gdal/package.py +++ b/var/spack/repos/builtin/packages/gdal/package.py @@ -107,7 +107,7 @@ class Gdal(AutotoolsPackage): # Optional dependencies depends_on('libtool', type='build', when='+libtool') depends_on('zlib', when='+libz') - depends_on('libiconv', when='+libiconv') + depends_on('iconv', when='+libiconv') depends_on('xz', when='+liblzma') depends_on('zstd', when='+zstd @2.3:') depends_on('postgresql', when='+pg') @@ -250,7 +250,7 @@ def configure_args(self): if '+libiconv' in spec: args.append('--with-libiconv-prefix={0}'.format( - spec['libiconv'].prefix)) + spec['iconv'].prefix)) else: args.append('--with-libiconv-prefix=no') diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index 1bd236051a7..ba842587e24 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -177,7 +177,7 @@ class Git(AutotoolsPackage): depends_on('curl') depends_on('expat') depends_on('gettext') - depends_on('libiconv') + depends_on('iconv') depends_on('libidn2') depends_on('openssl') depends_on('pcre', when='@:2.13') @@ -221,7 +221,7 @@ def configure_args(self): configure_args = [ '--with-curl={0}'.format(spec['curl'].prefix), '--with-expat={0}'.format(spec['expat'].prefix), - '--with-iconv={0}'.format(spec['libiconv'].prefix), + '--with-iconv={0}'.format(spec['iconv'].prefix), '--with-openssl={0}'.format(spec['openssl'].prefix), '--with-perl={0}'.format(spec['perl'].command.path), '--with-zlib={0}'.format(spec['zlib'].prefix), diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py index e43a9d17284..43195680086 100644 --- a/var/spack/repos/builtin/packages/glib/package.py +++ b/var/spack/repos/builtin/packages/glib/package.py @@ -46,7 +46,7 @@ class Glib(AutotoolsPackage): depends_on('python', type=('build', 'run'), when='@2.53.4:') depends_on('pcre+utf', when='@2.48:') depends_on('util-linux', when='+libmount') - depends_on('libiconv') + depends_on('iconv') # The following patch is needed for gcc-6.1 patch('g_date_strftime.patch', when='@2.42.1') @@ -70,7 +70,10 @@ def configure_args(self): args.append('--with-python={0}'.format( os.path.basename(self.spec['python'].command.path)) ) - args.append('--with-libiconv=gnu') + if 'libc' in self.spec: + args.append('--with-libiconv=maybe') + else: + args.append('--with-libiconv=gnu') args.extend(self.enable_or_disable('tracing')) # SELinux is not available in Spack, so glib should not use it. args.append('--disable-selinux') diff --git a/var/spack/repos/builtin/packages/gnupg/package.py b/var/spack/repos/builtin/packages/gnupg/package.py index 943f14d31f8..d97aa105695 100644 --- a/var/spack/repos/builtin/packages/gnupg/package.py +++ b/var/spack/repos/builtin/packages/gnupg/package.py @@ -25,7 +25,7 @@ class Gnupg(AutotoolsPackage): depends_on('libassuan@2.4:', when='@:2.2.3') depends_on('libassuan@2.5:', when='@2.2.15:') depends_on('pinentry', type='run') - depends_on('libiconv') + depends_on('iconv') depends_on('zlib') def configure_args(self): @@ -42,7 +42,7 @@ def configure_args(self): '--with-libassuan-prefix=' + self.spec['libassuan'].prefix, '--with-ksba-prefix=' + self.spec['libksba'].prefix, '--with-npth-prefix=' + self.spec['npth'].prefix, - '--with-libiconv-prefix=' + self.spec['libiconv'].prefix, + '--with-libiconv-prefix=' + self.spec['iconv'].prefix, '--with-zlib=' + self.spec['zlib'].prefix, '--without-tar', '--without-libiconv-prefix', diff --git a/var/spack/repos/builtin/packages/gnuplot/package.py b/var/spack/repos/builtin/packages/gnuplot/package.py index 17ee973eee9..9fb79e67466 100644 --- a/var/spack/repos/builtin/packages/gnuplot/package.py +++ b/var/spack/repos/builtin/packages/gnuplot/package.py @@ -55,7 +55,7 @@ class Gnuplot(AutotoolsPackage): depends_on('readline') depends_on('pkgconfig', type='build') depends_on('libxpm') - depends_on('libiconv') + depends_on('iconv') # optional dependencies: depends_on('libcerf', when='+libcerf') diff --git a/var/spack/repos/builtin/packages/grass/package.py b/var/spack/repos/builtin/packages/grass/package.py index c80255fb436..cb83a5cc2ab 100644 --- a/var/spack/repos/builtin/packages/grass/package.py +++ b/var/spack/repos/builtin/packages/grass/package.py @@ -58,7 +58,7 @@ class Grass(AutotoolsPackage): # http://htmlpreview.github.io/?https://github.com/OSGeo/grass/blob/master/REQUIREMENTS.html # General requirements depends_on('gmake@3.81:', type='build') - depends_on('libiconv') + depends_on('iconv') depends_on('zlib') depends_on('flex', type='build') depends_on('bison', type='build') @@ -254,5 +254,8 @@ def configure_args(self): # hence invoke the following function afterwards @run_after('configure') def fix_iconv_linking(self): + if self.spec['iconv'].name != 'libiconv': + return + makefile = FileFilter('include/Make/Platform.make') makefile.filter(r'^ICONVLIB\s*=.*', 'ICONVLIB = -liconv') diff --git a/var/spack/repos/builtin/packages/gtksourceview/package.py b/var/spack/repos/builtin/packages/gtksourceview/package.py index 01876610b2b..ed6737133a4 100644 --- a/var/spack/repos/builtin/packages/gtksourceview/package.py +++ b/var/spack/repos/builtin/packages/gtksourceview/package.py @@ -35,7 +35,7 @@ class Gtksourceview(AutotoolsPackage): depends_on('pango') depends_on('gdk-pixbuf') depends_on('atk') - depends_on('libiconv') + depends_on('iconv') def url_for_version(self, version): url = 'https://download.gnome.org/sources/gtksourceview/' diff --git a/var/spack/repos/builtin/packages/lftp/package.py b/var/spack/repos/builtin/packages/lftp/package.py index 508dbdd5869..b67b79bd5b6 100644 --- a/var/spack/repos/builtin/packages/lftp/package.py +++ b/var/spack/repos/builtin/packages/lftp/package.py @@ -18,7 +18,7 @@ class Lftp(AutotoolsPackage): version('4.6.4', sha256='791e783779d3d6b519d0c23155430b9785f2854023eb834c716f5ba78873b15a') depends_on('expat') - depends_on('libiconv') + depends_on('iconv') depends_on('ncurses') depends_on('openssl') depends_on('readline') @@ -27,7 +27,7 @@ class Lftp(AutotoolsPackage): def configure_args(self): return [ '--with-expat={0}'.format(self.spec['expat'].prefix), - '--with-libiconv={0}'.format(self.spec['libiconv'].prefix), + '--with-libiconv={0}'.format(self.spec['iconv'].prefix), '--with-openssl={0}'.format(self.spec['openssl'].prefix), '--with-readline={0}'.format(self.spec['readline'].prefix), '--with-zlib={0}'.format(self.spec['zlib'].prefix), diff --git a/var/spack/repos/builtin/packages/libc/package.py b/var/spack/repos/builtin/packages/libc/package.py new file mode 100644 index 00000000000..a4fa9ac3a64 --- /dev/null +++ b/var/spack/repos/builtin/packages/libc/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Libc(Package): + """Dummy libc package to provide `iconv` virtual package""" + + homepage = "https://en.wikipedia.org/wiki/C_standard_library" + url = "" + has_code = False + phases = [] + + version('1.0') # Dummy + variant('iconv', default=False, description='Set to True if libc provides iconv') + provides('iconv', when='+iconv') diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py index 232b826bbf5..d4907ae3e19 100644 --- a/var/spack/repos/builtin/packages/libgd/package.py +++ b/var/spack/repos/builtin/packages/libgd/package.py @@ -31,7 +31,7 @@ class Libgd(AutotoolsPackage): depends_on('gettext', type='build') depends_on('pkgconfig', type='build') - depends_on('libiconv') + depends_on('iconv') depends_on('libpng') depends_on('jpeg') depends_on('libtiff') diff --git a/var/spack/repos/builtin/packages/libiconv/package.py b/var/spack/repos/builtin/packages/libiconv/package.py index 642ad289fd7..9331dfb399d 100644 --- a/var/spack/repos/builtin/packages/libiconv/package.py +++ b/var/spack/repos/builtin/packages/libiconv/package.py @@ -20,6 +20,7 @@ class Libiconv(AutotoolsPackage, GNUMirrorPackage): # We cannot set up a warning for gets(), since gets() is not part # of C11 any more and thus might not exist. patch('gets.patch', when='@1.14') + provides('iconv') conflicts('@1.14', when='%gcc@5:') diff --git a/var/spack/repos/builtin/packages/libspatialite/package.py b/var/spack/repos/builtin/packages/libspatialite/package.py index e725fdfe0f0..45fe1f6109c 100644 --- a/var/spack/repos/builtin/packages/libspatialite/package.py +++ b/var/spack/repos/builtin/packages/libspatialite/package.py @@ -21,5 +21,5 @@ class Libspatialite(AutotoolsPackage): depends_on('proj@:5') depends_on('geos') depends_on('freexl') - depends_on('libiconv') + depends_on('iconv') depends_on('libxml2') diff --git a/var/spack/repos/builtin/packages/libunistring/package.py b/var/spack/repos/builtin/packages/libunistring/package.py index 94b1c24b984..9812fb32cb1 100644 --- a/var/spack/repos/builtin/packages/libunistring/package.py +++ b/var/spack/repos/builtin/packages/libunistring/package.py @@ -19,7 +19,7 @@ class Libunistring(AutotoolsPackage, GNUMirrorPackage): version('0.9.7', sha256='2e3764512aaf2ce598af5a38818c0ea23dedf1ff5460070d1b6cee5c3336e797') version('0.9.6', sha256='2df42eae46743e3f91201bf5c100041540a7704e8b9abfd57c972b2d544de41b') - depends_on('libiconv') + depends_on('iconv') # glibc 2.28+ removed libio.h and thus _IO_ftrylockfile patch('removed_libio.patch', when='@:0.9.9') diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py index 8c91852ae32..8c024854ea1 100644 --- a/var/spack/repos/builtin/packages/libxml2/package.py +++ b/var/spack/repos/builtin/packages/libxml2/package.py @@ -23,7 +23,7 @@ class Libxml2(AutotoolsPackage): variant('python', default=False, description='Enable Python support') depends_on('pkgconfig@0.9.0:', type='build') - depends_on('libiconv') + depends_on('iconv') depends_on('zlib') depends_on('xz') @@ -49,7 +49,7 @@ def configure_args(self): spec = self.spec args = ['--with-lzma={0}'.format(spec['xz'].prefix), - '--with-iconv={0}'.format(spec['libiconv'].prefix)] + '--with-iconv={0}'.format(spec['iconv'].prefix)] if '+python' in spec: args.extend([ diff --git a/var/spack/repos/builtin/packages/libxslt/package.py b/var/spack/repos/builtin/packages/libxslt/package.py index 7cdb0e41b22..5da6272d833 100644 --- a/var/spack/repos/builtin/packages/libxslt/package.py +++ b/var/spack/repos/builtin/packages/libxslt/package.py @@ -26,7 +26,7 @@ class Libxslt(AutotoolsPackage): variant('python', default=False, description='Build Python bindings') depends_on('pkgconfig@0.9.0:', type='build') - depends_on('libiconv') + depends_on('iconv') depends_on('libxml2') depends_on('libxml2+python', when='+python') depends_on('xz') diff --git a/var/spack/repos/builtin/packages/mono/package.py b/var/spack/repos/builtin/packages/mono/package.py index 73464f0fb94..6a7a96300ac 100644 --- a/var/spack/repos/builtin/packages/mono/package.py +++ b/var/spack/repos/builtin/packages/mono/package.py @@ -25,7 +25,7 @@ class Mono(AutotoolsPackage): # Spack's openssl interacts badly with mono's vendored # "boringssl", don't drag it in w/ cmake depends_on('cmake~openssl', type=('build')) - depends_on('libiconv') + depends_on('iconv') depends_on('perl', type=('build')) version('6.8.0.105', sha256='578799c44c3c86a9eb5daf6dec6c60a24341940fd376371956d4a46cf8612178', @@ -50,6 +50,6 @@ def patch(self): def configure_args(self): args = [] - li = self.spec['libiconv'].prefix + li = self.spec['iconv'].prefix args.append('--with-libiconv-prefix={p}'.format(p=li)) return args diff --git a/var/spack/repos/builtin/packages/ncl/package.py b/var/spack/repos/builtin/packages/ncl/package.py index 0fa063c52cd..e6e09faae1e 100644 --- a/var/spack/repos/builtin/packages/ncl/package.py +++ b/var/spack/repos/builtin/packages/ncl/package.py @@ -48,7 +48,7 @@ class Ncl(Package): # Extra dependencies that may be missing from build system: depends_on('bison', type='build') depends_on('flex+lex') - depends_on('libiconv') + depends_on('iconv') depends_on('tcsh') # Also, the manual says that ncl requires zlib, but that comes as a @@ -57,7 +57,7 @@ class Ncl(Package): # The following dependencies are required, otherwise several components # fail to compile: depends_on('curl') - depends_on('libiconv') + depends_on('iconv') depends_on('libx11') depends_on('libxaw') depends_on('libxmu') diff --git a/var/spack/repos/builtin/packages/poppler/package.py b/var/spack/repos/builtin/packages/poppler/package.py index 8689f817e51..affb9e5359a 100644 --- a/var/spack/repos/builtin/packages/poppler/package.py +++ b/var/spack/repos/builtin/packages/poppler/package.py @@ -49,7 +49,7 @@ class Poppler(CMakePackage): depends_on('qt@4.0:', when='+qt') depends_on('zlib', when='+zlib') depends_on('cairo@1.10.0:', when='+glib') - depends_on('libiconv', when='+iconv') + depends_on('iconv', when='+iconv') depends_on('jpeg', when='+jpeg') depends_on('libpng', when='+png') depends_on('libtiff', when='+tiff') diff --git a/var/spack/repos/builtin/packages/procps/package.py b/var/spack/repos/builtin/packages/procps/package.py index f8b4ed26336..e18d6206cf8 100644 --- a/var/spack/repos/builtin/packages/procps/package.py +++ b/var/spack/repos/builtin/packages/procps/package.py @@ -23,7 +23,7 @@ class Procps(AutotoolsPackage): depends_on('m4', type='build') depends_on('pkgconfig@0.9.0:', type='build') depends_on('dejagnu', type='test') - depends_on('libiconv') + depends_on('iconv') depends_on('gettext') depends_on('ncurses') @@ -35,7 +35,7 @@ def autoreconf(self, spec, prefix): def configure_args(self): return [ - '--with-libiconv-prefix={0}'.format(self.spec['libiconv'].prefix), + '--with-libiconv-prefix={0}'.format(self.spec['iconv'].prefix), '--with-libintl-prefix={0}'.format(self.spec['gettext'].prefix), '--with-ncurses', # Required to avoid libintl linking errors diff --git a/var/spack/repos/builtin/packages/tar/package.py b/var/spack/repos/builtin/packages/tar/package.py index de12fd23447..15c2e4bc0ef 100644 --- a/var/spack/repos/builtin/packages/tar/package.py +++ b/var/spack/repos/builtin/packages/tar/package.py @@ -19,7 +19,7 @@ class Tar(AutotoolsPackage, GNUMirrorPackage): version('1.29', sha256='cae466e6e58c7292355e7080248f244db3a4cf755f33f4fa25ca7f9a7ed09af0') version('1.28', sha256='6a6b65bac00a127a508533c604d5bf1a3d40f82707d56f20cefd38a05e8237de') - depends_on('libiconv') + depends_on('iconv') patch('tar-pgi.patch', when='@1.29') patch('config-pgi.patch', when='@:1.29') @@ -29,5 +29,5 @@ class Tar(AutotoolsPackage, GNUMirrorPackage): def configure_args(self): return [ - '--with-libiconv-prefix={0}'.format(self.spec['libiconv'].prefix), + '--with-libiconv-prefix={0}'.format(self.spec['iconv'].prefix), ] diff --git a/var/spack/repos/builtin/packages/unixodbc/package.py b/var/spack/repos/builtin/packages/unixodbc/package.py index 2802f87aa5e..b93e7eb166d 100644 --- a/var/spack/repos/builtin/packages/unixodbc/package.py +++ b/var/spack/repos/builtin/packages/unixodbc/package.py @@ -16,5 +16,5 @@ class Unixodbc(AutotoolsPackage): version('2.3.4', sha256='2e1509a96bb18d248bf08ead0d74804957304ff7c6f8b2e5965309c632421e39') - depends_on('libiconv') + depends_on('iconv') depends_on('libtool') diff --git a/var/spack/repos/builtin/packages/wget/package.py b/var/spack/repos/builtin/packages/wget/package.py index 122b138d106..c9ef5e9dd81 100644 --- a/var/spack/repos/builtin/packages/wget/package.py +++ b/var/spack/repos/builtin/packages/wget/package.py @@ -43,7 +43,7 @@ class Wget(AutotoolsPackage, GNUMirrorPackage): depends_on('perl@5.12.0:', type='build') depends_on('pkgconfig', type='build') - depends_on('libiconv') + depends_on('iconv') depends_on('valgrind', type='test') diff --git a/var/spack/repos/builtin/packages/xerces-c/package.py b/var/spack/repos/builtin/packages/xerces-c/package.py index 05af3d1a5c9..21caf00e83d 100644 --- a/var/spack/repos/builtin/packages/xerces-c/package.py +++ b/var/spack/repos/builtin/packages/xerces-c/package.py @@ -45,7 +45,7 @@ class XercesC(AutotoolsPackage): multi=False, description='Use the specified transcoder') - depends_on('libiconv', type='link', when='transcoder=gnuiconv') + depends_on('iconv', type='link', when='transcoder=gnuiconv') depends_on('icu4c', type='link', when='transcoder=icu') # Pass flags to configure. This is necessary for CXXFLAGS or else @@ -61,7 +61,7 @@ def flag_handler(self, name, flags): # There is no --with-pkg for gnuiconv. if name == 'ldflags' and 'transcoder=gnuiconv' in spec: - flags.append(spec['libiconv'].libs.ld_flags) + flags.append(spec['iconv'].libs.ld_flags) return (None, None, flags) From 0b1c0bdd6e34172d7beb75387e561815de518074 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Sat, 28 Mar 2020 08:11:37 -0600 Subject: [PATCH 260/377] xsbench: fix build of v19 (#15715) * xsbench: fix build of v19 * Flake8 --- var/spack/repos/builtin/packages/xsbench/package.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/xsbench/package.py b/var/spack/repos/builtin/packages/xsbench/package.py index 3648edc298a..b6040714d42 100644 --- a/var/spack/repos/builtin/packages/xsbench/package.py +++ b/var/spack/repos/builtin/packages/xsbench/package.py @@ -28,7 +28,12 @@ class Xsbench(MakefilePackage): depends_on('mpi', when='+mpi') - build_directory = 'src' + @property + def build_directory(self): + if self.spec.satisfies('@:18'): + return 'src' + else: + return 'openmp-threading' @property def build_targets(self): @@ -50,4 +55,5 @@ def build_targets(self): def install(self, spec, prefix): mkdir(prefix.bin) - install('src/XSBench', prefix.bin) + with working_dir(self.build_directory): + install('XSBench', prefix.bin) From 33f424ff1de48f76b9b93390209df9d4271bb30a Mon Sep 17 00:00:00 2001 From: iarspider Date: Sat, 28 Mar 2020 15:15:28 +0100 Subject: [PATCH 261/377] Update URL for new py2neo versions (#15324) * Update URL for new py2neo versions * Use pypi for py-py2neo * Add version 4.3.0 * Update py2neo dependencies * Apply suggestions from code review Co-Authored-By: Adam J. Stewart Co-authored-by: Adam J. Stewart --- .../builtin/packages/py-neobolt/package.py | 18 +++++++++++++++ .../builtin/packages/py-neotime/package.py | 20 +++++++++++++++++ .../builtin/packages/py-py2neo/package.py | 22 ++++++++++++++----- 3 files changed, 54 insertions(+), 6 deletions(-) create mode 100644 var/spack/repos/builtin/packages/py-neobolt/package.py create mode 100644 var/spack/repos/builtin/packages/py-neotime/package.py diff --git a/var/spack/repos/builtin/packages/py-neobolt/package.py b/var/spack/repos/builtin/packages/py-neobolt/package.py new file mode 100644 index 00000000000..7e19e529fd9 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-neobolt/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyNeobolt(PythonPackage): + """Neo4j Bolt connector for Python""" + + homepage = "https://github.com/neo4j-drivers/neobolt" + url = "https://pypi.io/packages/source/n/neobolt/neobolt-1.7.16.tar.gz" + + version('1.7.16', sha256='ca4e87679fe3ed39aec23638658e02dbdc6bbc3289a04e826f332e05ab32275d') + + depends_on('py-setuptools', type='build') + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-neotime/package.py b/var/spack/repos/builtin/packages/py-neotime/package.py new file mode 100644 index 00000000000..31769361c14 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-neotime/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyNeotime(PythonPackage): + """Nanosecond resolution temporal types""" + + homepage = "https://neotime.readthedocs.io/" + url = "https://pypi.io/packages/source/n/neotime/neotime-1.7.4.tar.gz" + + version('1.7.4', sha256='4e0477ba0f24e004de2fa79a3236de2bd941f20de0b5db8d976c52a86d7363eb') + + depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-pytz', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-py2neo/package.py b/var/spack/repos/builtin/packages/py-py2neo/package.py index ef4ed46cd59..69e98d7b0b6 100644 --- a/var/spack/repos/builtin/packages/py-py2neo/package.py +++ b/var/spack/repos/builtin/packages/py-py2neo/package.py @@ -11,12 +11,22 @@ class PyPy2neo(PythonPackage): within Python applications and from the command line.""" homepage = "http://py2neo.org/" - url = "https://github.com/nigelsmall/py2neo/archive/py2neo-2.0.8.tar.gz" + url = "https://pypi.io/packages/source/p/py2neo/py2neo-2.0.8.tar.gz" - version('2.0.8', sha256='57b4a1c4aa800e03904b2adfd7c8ec467b072bae2d24baf150fd580916255f2e') - version('2.0.7', sha256='aa7c86fec70823111d2f932cb20a978889f1c47c2f58461309f644ecb9a22204') - version('2.0.6', sha256='bcf00ebc82a80c7e2da00288e8f90f81682abfc991e19d92d21726c2deac823f') - version('2.0.5', sha256='024b42261b06e5e2c92a1f24e62398847f090862005add0b5c69a79a7e1e87b5') - version('2.0.4', sha256='19074b7b892f2e989f39eae21fc59b26a05e1a820adad8aa58bc470b70d9056d') + version('4.3.0', sha256='a218ccb4b636e3850faa6b74ebad80f00600217172a57f745cf223d38a219222') + version('2.0.8', sha256='06167f5a91a0d9b9b73431baacd876f2d507650a681fdce1fcf3b383a9b991c1') + version('2.0.7', sha256='9b154053eb93c7f5fb3ebd48b6a5b99df450d3f2e9c6682153c6f8d59369378c') + version('2.0.6', sha256='6bb828d6d3e48b4d095b3f7d79dbb690a47633f0a9812eb62f141b042bab3186') + version('2.0.5', sha256='2c04d4223d2d356c4800c586f30c048757334f9391553c852c29aebf2368d101') + version('2.0.4', sha256='727726b87268ca1e929191b960a5473409e5bd81559ee83a304951104bb6b866') depends_on("py-setuptools", type='build') + depends_on("py-certifi", type=('build', 'run'), when='@4.3.0:') + depends_on("py-click@7.0", type=('build', 'run'), when='@4.3.0:') + depends_on("py-colorama", type=('build', 'run'), when='@4.3.0:') + depends_on("py-neobolt@1.7.12:1.7.999", type=('build', 'run'), when='@4.3.0:') + depends_on("py-neotime@1.7.4:1.7.999", type=('build', 'run'), when='@4.3.0:') + depends_on("py-prompt-toolkit@2.0.7:2.0.999", type=('build', 'run'), when='@4.3.0:') + depends_on("py-pygments@2.3.1:2.3.999", type=('build', 'run'), when='@4.3.0:') + depends_on("py-pytz", type=('build', 'run'), when='@4.3.0:') + depends_on("py-urllib3@1.23:1.24", type=('build', 'run'), when='@4.3.0:') From 8beeeeb74c7e19f0c6146d91e80819701f4d2309 Mon Sep 17 00:00:00 2001 From: "Daryl W. Grunau" Date: Sat, 28 Mar 2020 11:12:49 -0600 Subject: [PATCH 262/377] new package ddd (#15717) * new package ddd * mitigate build/installs on case-insensitive filesystems * add missing variants * flake8 fixes * flake8: E124 closing bracket does not match visual indentation Co-authored-by: Daryl W. Grunau --- .../repos/builtin/packages/ddd/package.py | 75 +++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ddd/package.py diff --git a/var/spack/repos/builtin/packages/ddd/package.py b/var/spack/repos/builtin/packages/ddd/package.py new file mode 100644 index 00000000000..d0edde042d8 --- /dev/null +++ b/var/spack/repos/builtin/packages/ddd/package.py @@ -0,0 +1,75 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os + + +class Ddd(AutotoolsPackage, GNUMirrorPackage): + """A graphical front-end for command-line debuggers such as GDB, DBX, + WDB, Ladebug, JDB, XDB, the Perl debugger, the bash debugger bashdb, + the GNU Make debugger remake, or the Python debugger pydb.""" + + homepage = "https://www.gnu.org/software/ddd" + gnu_mirror_path = "ddd/ddd-3.3.12.tar.gz" + + version('3.3.12', sha256='3ad6cd67d7f4b1d6b2d38537261564a0d26aaed077bf25c51efc1474d0e8b65c') + + variant('shared', default=True, description='Build shared libraries') + variant('static', default=False, description='Build static libraries') + + depends_on('gdb@4.16:') + depends_on('lesstif@0.89:') + + # Needed for OSX 10.9 DP6 build failure: + # https://savannah.gnu.org/patch/?8178 + patch('https://savannah.gnu.org/patch/download.php?file_id=29114', + sha256='aaacae79ce27446ead3483123abef0f8222ebc13fd61627bfadad96016248af6', + working_dir='ddd') + + # https://savannah.gnu.org/bugs/?41997 + patch('https://savannah.gnu.org/patch/download.php?file_id=31132', + sha256='f3683f23c4b4ff89ba701660031d4b5ef27594076f6ef68814903ff3141f6714') + + # Patch to fix compilation with Xcode 9 + # https://savannah.gnu.org/bugs/?52175 + patch('https://raw.githubusercontent.com/macports/macports-ports/a71fa9f4/devel/ddd/files/patch-unknown-type-name-a_class.diff', + sha256='c187a024825144f186f0cf9cd175f3e972bb84590e62079793d0182cb15ca183', + working_dir='ddd') + + def configure_args(self): + spec = self.spec + + args = [ + '--disable-debug', + '--disable-dependency-tracking', + '--enable-builtin-app-defaults', + '--enable-builtin-manual', + '--enable-shared' if '+shared' in spec else '--disable-shared', + '--enable-static' if '+static' in spec else '--disable-static', + ] + + return args + + # From MacPorts: make will build the executable "ddd" and the X + # resource file "Ddd" in the same directory. As HFS+ is case- + # insensitive by default this will loosely FAIL. Mitigate this by + # building/installing 'dddexe' on Darwin and fixing up post install. + def build(self, spec, prefix): + make('EXEEXT={0}'. + format('exe' if spec.satisfies('platform=darwin') else '')) + + # DDD won't install in parallel + def install(self, spec, prefix): + make('install', + 'EXEEXT={0}'. + format('exe' if spec.satisfies('platform=darwin') else ''), + parallel=False) + + @run_after('install') + def _rename_exe_on_darwin(self): + if self.spec.satisfies('platform=darwin'): + with working_dir(self.prefix.bin): + os.rename('dddexe', 'ddd') From 6969526e0f746a07ad7d9fcd073928ff1cc3a473 Mon Sep 17 00:00:00 2001 From: iarspider Date: Sat, 28 Mar 2020 18:13:47 +0100 Subject: [PATCH 263/377] py-statsmodels: update to 0.102 and fix dependencies (#15708) * py-statsmodels: update to 0.102 and fix dependencies * Update var/spack/repos/builtin/packages/py-statsmodels/package.py Co-Authored-By: Adam J. Stewart Co-authored-by: Adam J. Stewart --- .../packages/py-statsmodels/package.py | 25 ++++++++++--------- 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-statsmodels/package.py b/var/spack/repos/builtin/packages/py-statsmodels/package.py index eebc2066406..26c006bccff 100644 --- a/var/spack/repos/builtin/packages/py-statsmodels/package.py +++ b/var/spack/repos/builtin/packages/py-statsmodels/package.py @@ -13,31 +13,32 @@ class PyStatsmodels(PythonPackage): homepage = "http://www.statsmodels.org" url = "https://pypi.io/packages/source/s/statsmodels/statsmodels-0.8.0.tar.gz" + version('0.10.2', sha256='9cd2194c6642a8754e85f9a6e6912cdf996bebf6ff715d3cc67f65dadfd37cc9') version('0.10.1', sha256='320659a80f916c2edf9dfbe83512d9004bb562b72eedb7d9374562038697fa10') version('0.8.0', sha256='26431ab706fbae896db7870a0892743bfbb9f5c83231644692166a31d2d86048') variant('plotting', default=False, description='With matplotlib') - depends_on('python@:3.6', when='@:0.8.0', type=('build', 'run')) + depends_on('python@:3.6', when='@:0.8.0', type=('build', 'run')) + depends_on('python@2.7:2.8,3.4:', when='@0.10.1:', type=('build', 'run')) # according to http://www.statsmodels.org/dev/install.html earlier versions # might work. depends_on('py-setuptools@0.6c5:', type='build') - depends_on('py-numpy@1.7.0:', type=('build', 'run'), when='@0.8.0') - depends_on('py-pandas@0.12:', type=('build', 'run'), when='@0.8.0') - depends_on('py-patsy@0.2.1:', type=('build', 'run'), when='@0.8.0') - depends_on('py-scipy@0.11:', type=('build', 'run'), when='@0.8.0') - depends_on('py-matplotlib@1.3:', type=('build', 'run'), when='@0.8.0 +plotting') - # patsy@0.5.1 works around a Python change # https://github.com/statsmodels/statsmodels/issues/5343 and # https://github.com/pydata/patsy/pull/131 - depends_on('py-numpy', type=('build', 'run'), when='@0.10.1') - depends_on('py-pandas', type=('build', 'run'), when='@0.10.1') - depends_on('py-patsy', type=('build', 'run'), when='@0.10.1') - depends_on('py-scipy@0.5.1:', type=('build', 'run'), when='@0.10.1') - depends_on('py-matplotlib', type=('build', 'run'), when='@0.10.1 +plotting') + + depends_on('py-numpy@1.7.0:', type=('build', 'run'), when='@0.8.0:') + depends_on('py-numpy@1.11.0:', type=('build', 'run'), when='@0.10.1:') + depends_on('py-pandas@0.12:', type=('build', 'run'), when='@0.8.0:') + depends_on('py-pandas@0.19:', type=('build', 'run'), when='@0.10.1:') + depends_on('py-patsy@0.2.1:', type=('build', 'run'), when='@0.8.0:') + depends_on('py-patsy@0.4.0:', type=('build', 'run'), when='@0.10.1:') + depends_on('py-scipy@0.11:', type=('build', 'run'), when='@0.8.0:') + depends_on('py-scipy@0.18:', type=('build', 'run'), when='@0.10.1:') + depends_on('py-matplotlib@1.3:', type=('build', 'run'), when='@0.8.0 +plotting') depends_on('py-pytest', type='test') From c1d111af74355dc911229e05982b60ae77b4d057 Mon Sep 17 00:00:00 2001 From: Amjad Kotobi Date: Sat, 28 Mar 2020 18:14:05 +0100 Subject: [PATCH 264/377] Add package swiftclient (#15700) * Add package swiftclient * Fix on url * Package name changed to py-python-swiftclient and changes on dependencies --- .../packages/py-python-swiftclient/package.py | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-python-swiftclient/package.py diff --git a/var/spack/repos/builtin/packages/py-python-swiftclient/package.py b/var/spack/repos/builtin/packages/py-python-swiftclient/package.py new file mode 100644 index 00000000000..bd8f766624b --- /dev/null +++ b/var/spack/repos/builtin/packages/py-python-swiftclient/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPythonSwiftclient(PythonPackage): + """This is a python client for the Swift API.""" + + homepage = "https://docs.openstack.org/python-swiftclient" + url = "https://pypi.io/packages/source/p/python-swiftclient/python-swiftclient-3.9.0.tar.gz" + + maintainers = ['ajkotobi'] + + import_modules = ['sys', 'setuptools', 'requests'] + + version('3.9.0', sha256='4f2097492e4c76e948882fc859bfa033ade09bed72f8e6b328e34a3467d9a377') + version('3.8.1', sha256='3a013303643f77a99befa05582dfb93671e1fba1aed9f4a517418129700aedb8') + version('3.8.0', sha256='107a9d5356663365a9f7c0b3a2b55da97a0a9ba7f10da2319b3972481510f33d') + version('3.7.1', sha256='06bda5a6f81ea132e5cb52d0eb0616a0ab0958b4ec0d1cb7f850f04bf178852f') + + depends_on('py-setuptools', type=('build', 'run')) + depends_on('python@2.7:', type=('build', 'run')) + depends_on('py-futures@3:', type=('build', 'run'), when='^python@:2') + depends_on('py-requests@1.1.0:', type=('build', 'run')) + depends_on('py-six@1.9:', type=('build', 'run')) + depends_on('py-pbr', type='build') From f3c2ebbfb82cb9d88c32bb0bd301c529d1a0ee0b Mon Sep 17 00:00:00 2001 From: Kai Germaschewski Date: Sat, 28 Mar 2020 14:06:17 -0400 Subject: [PATCH 265/377] fix gcc@8.4.0 build (#15729) the gcc package.py includes patches for a sanitizer related bug that look like they've been fixed in gcc 8.4.0, which caused `spack install` to fail. This PR excludes patching gcc >= 8.4.0 and < 9.0.0. --- var/spack/repos/builtin/packages/gcc/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index b7a08f8538f..cf16f1bc8f7 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -237,8 +237,8 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage): # Backport libsanitizer patch for glibc >= 2.31 and 8.1.0 <= gcc <= 9.2.0 # https://bugs.gentoo.org/708346 - patch('glibc-2.31-libsanitizer-1.patch', when='@8.1.0:9.2.0') - patch('glibc-2.31-libsanitizer-2.patch', when='@8.1.0:9.2.0') + patch('glibc-2.31-libsanitizer-1.patch', when='@8.1.0:8.3.99,9.0.0:9.2.0') + patch('glibc-2.31-libsanitizer-2.patch', when='@8.1.0:8.3.99,9.0.0:9.2.0') # Older versions do not compile with newer versions of glibc # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81712 patch('ucontext_t.patch', when='@4.9,5.1:5.4,6.1:6.4,7.1') From a3e1b2bd58d02d43c2dce65b8e0cfc89791486f1 Mon Sep 17 00:00:00 2001 From: Tom Scogland Date: Sat, 28 Mar 2020 13:20:06 -0700 Subject: [PATCH 266/377] llvm: libomptarget support (#14060) This allows the llvm build to support: * clang cuda * libomptarget for: * current host * cuda * bitcode compilation of libomptarget device runtime for inlining by bootstrapping libomptarget * split dwarf information support as an option for debug builds, if you need a debug build, for the love of all that's good in the universe use this flag * adds necessary dependencies for shared library builds and libomp and libomp target to build correctly * new version of z3 to make it sufficient to build recent llvm The actual change is much smaller than the diff, this is because it's been formatted with black. I realize this kinda sucks right now, but I'm hoping it will make future updates here less painful. --- .../repos/builtin/packages/llvm/package.py | 456 +++++++++++------- .../repos/builtin/packages/z3/package.py | 1 + 2 files changed, 287 insertions(+), 170 deletions(-) diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 1644a8e7501..588c1cae1dd 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -15,14 +15,17 @@ class Llvm(CMakePackage): is not an acronym; it is the full name of the project. """ - homepage = 'http://llvm.org/' - url = "https://github.com/llvm/llvm-project/archive/llvmorg-7.1.0.tar.gz" - list_url = 'http://releases.llvm.org/download.html' - git = 'https://github.com/llvm/llvm-project' + homepage = "http://llvm.org/" + url = "https://github.com/llvm/llvm-project/archive/llvmorg-7.1.0.tar.gz" + list_url = "http://releases.llvm.org/download.html" + git = "https://github.com/llvm/llvm-project" + maintainers = ['trws'] - family = 'compiler' # Used by lmod + family = "compiler" # Used by lmod + # fmt: off version('master', branch='master') + version('10.0.0', sha256='b81c96d2f8f40dc61b14a167513d87c0d813aae0251e06e11ae8a4384ca15451') version('9.0.1', sha256='be7b034641a5fda51ffca7f5d840b1a768737779f75f7c4fd18fe2d37820289a') version('9.0.0', sha256='7807fac25330e24e9955ca46cd855dd34bbc9cc4fdba8322366206654d1036f2') version('8.0.0', sha256='d81238b4a69e93e29f74ce56f8107cbfcf0c7d7b40510b7879e98cc031e25167') @@ -43,123 +46,176 @@ class Llvm(CMakePackage): version('3.7.0', sha256='dc00bc230be2006fb87b84f6fe4800ca28bc98e6692811a98195da53c9cb28c6') version('3.6.2', sha256='f75d703a388ba01d607f9cf96180863a5e4a106827ade17b221d43e6db20778a') version('3.5.1', sha256='5d739684170d5b2b304e4fb521532d5c8281492f71e1a8568187bfa38eb5909d') + # fmt: on # NOTE: The debug version of LLVM is an order of magnitude larger than # the release version, and may take up 20-30 GB of space. If you want # to save space, build with `build_type=Release`. - variant('clang', default=True, - description="Build the LLVM C/C++/Objective-C compiler frontend") + variant( + "clang", + default=True, + description="Build the LLVM C/C++/Objective-C compiler frontend", + ) - # TODO: The current version of this package unconditionally disables CUDA. - # Better would be to add a "cuda" variant that: - # - Adds dependency on the "cuda" package when enabled - # - Sets the necessary CMake flags when enabled - # - Disables CUDA (as this current version does) only when the - # variant is also disabled. + variant( + "cuda", + default=False, + description="Build LLVM with CUDA, required for nvptx offload", + ) + variant( + "nvptx_offload_ccs", + default="35,60,70,75", + multi=True, + description="NVIDIA compute cabailities to make inlining capable", + ) - # variant('cuda', default=False, - # description="Build the LLVM with CUDA features enabled") + variant( + "omp_debug", + default=False, + description="Include debugging code in OpenMP runtime libraries", + ) + variant("lldb", default=True, description="Build the LLVM debugger") + variant("lld", default=True, description="Build the LLVM linker") + variant( + "internal_unwind", + default=True, + description="Build the libcxxabi libunwind", + ) + variant( + "polly", + default=True, + description="Build the LLVM polyhedral optimization plugin, " + "only builds for 3.7.0+", + ) + variant( + "libcxx", + default=True, + description="Build the LLVM C++ standard library", + ) + variant( + "compiler-rt", + default=True, + description="Build LLVM compiler runtime, including sanitizers", + ) + variant( + "gold", + default=(sys.platform != "darwin"), + description="Add support for LTO with the gold linker plugin", + ) + variant( + "split_dwarf", + default=False, + description="Build with split dwarf information", + ) + variant( + "shared_libs", + default=False, + description="Build all components as shared libraries, faster, " + "less memory to build, less stable", + ) + variant( + "all_targets", + default=False, + description="Build all supported targets, default targets " + ",NVPTX,AMDGPU,CppBackend", + ) + variant( + "build_type", + default="Release", + description="CMake build type", + values=("Debug", "Release", "RelWithDebInfo", "MinSizeRel"), + ) + variant( + "omp_tsan", + default=False, + description="Build with OpenMP capable thread sanitizer", + ) + variant("python", default=False, description="Install python bindings") + variant( + "flang", + default=False, + description="Build flang branch version instead", + ) - variant('lldb', default=True, description="Build the LLVM debugger") - variant('lld', default=True, description="Build the LLVM linker") - variant('internal_unwind', default=True, - description="Build the libcxxabi libunwind") - variant('polly', default=True, - description="Build the LLVM polyhedral optimization plugin, " - "only builds for 3.7.0+") - variant('libcxx', default=True, - description="Build the LLVM C++ standard library") - variant('compiler-rt', default=True, - description="Build LLVM compiler runtime, including sanitizers") - variant('gold', default=(sys.platform != 'darwin'), - description="Add support for LTO with the gold linker plugin") - variant('shared_libs', default=False, - description="Build all components as shared libraries, faster, " - "less memory to build, less stable") - variant('link_dylib', default=False, - description="Build and link the libLLVM shared library rather " - "than static") - variant('all_targets', default=False, - description="Build all supported targets, default targets " - ",NVPTX,AMDGPU,CppBackend") - variant('build_type', default='Release', - description='CMake build type', - values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel')) - variant('omp_tsan', default=False, - description="Build with OpenMP capable thread sanitizer") - variant('python', default=False, description="Install python bindings") - - extends('python', when='+python') + extends("python", when="+python") # Build dependency - depends_on('cmake@3.4.3:', type='build') - depends_on('python@2.7:2.8', when='@:4.999 ~python', type='build') - depends_on('python', when='@5: ~python', type='build') + depends_on("cmake@3.4.3:", type="build") + depends_on("python@2.7:2.8", when="@:4.999 ~python", type="build") + depends_on("python@2.7:2.8", when="@5: ~python +flang", type="build") + depends_on("python", when="@5: ~python", type="build") # Universal dependency - depends_on('python@2.7:2.8', when='@:4.999+python') - depends_on('python', when='@5:+python') + depends_on("python@2.7:2.8", when="@:4.999+python") + depends_on("python@2.7:2.8", when="@5:+python+flang") + depends_on("python", when="@5:+python") + depends_on("z3", when="@9:") + + # CUDA dependency + depends_on("cuda", when="+cuda") # openmp dependencies - depends_on('perl-data-dumper', type=('build')) + depends_on("perl-data-dumper", type=("build")) + depends_on("hwloc") + depends_on("libelf") # libomptarget + depends_on("libffi") # libomptarget # ncurses dependency - depends_on('ncurses+termlib') + depends_on("ncurses+termlib") # lldb dependencies - depends_on('swig', when='+lldb') - depends_on('libedit', when='+lldb') - depends_on('py-six', when='@5.0.0: +lldb +python') + depends_on("swig", when="+lldb") + depends_on("libedit", when="+lldb") + depends_on("py-six", when="@5.0.0: +lldb +python") - # gold support - depends_on('binutils+gold', when='+gold') + # gold support, required for some features + depends_on("binutils+gold", when="+gold") # polly plugin - depends_on('gmp', when='@:3.6.999 +polly') - depends_on('isl', when='@:3.6.999 +polly') + depends_on("gmp", when="@:3.6.999 +polly") + depends_on("isl", when="@:3.6.999 +polly") - conflicts('+clang_extra', when='~clang') - conflicts('+lldb', when='~clang') - conflicts('+libcxx', when='~clang') - conflicts('+internal_unwind', when='~clang') - conflicts('+compiler-rt', when='~clang') + conflicts("+clang_extra", when="~clang") + conflicts("+lldb", when="~clang") + conflicts("+libcxx", when="~clang") + conflicts("+internal_unwind", when="~clang") + conflicts("+compiler-rt", when="~clang") # LLVM 4 and 5 does not build with GCC 8 - conflicts('%gcc@8:', when='@:5') - conflicts('%gcc@:5.0.999', when='@8:') + conflicts("%gcc@8:", when="@:5") + conflicts("%gcc@:5.0.999", when="@8:") # OMP TSAN exists in > 5.x - conflicts('+omp_tsan', when='@:5.99') + conflicts("+omp_tsan", when="@:5.99") # Github issue #4986 - patch('llvm_gcc7.patch', when='@4.0.0:4.0.1+lldb %gcc@7.0:') + patch("llvm_gcc7.patch", when="@4.0.0:4.0.1+lldb %gcc@7.0:") # Backport from llvm master + additional fix # see https://bugs.llvm.org/show_bug.cgi?id=39696 # for a bug report about this problem in llvm master. - patch('constexpr_longdouble.patch', when='@6:8+libcxx') - patch('constexpr_longdouble_9.0.patch', when='@9+libcxx') + patch("constexpr_longdouble.patch", when="@6:8+libcxx") + patch("constexpr_longdouble_9.0.patch", when="@9+libcxx") # Backport from llvm master; see # https://bugs.llvm.org/show_bug.cgi?id=38233 # for a bug report about this problem in llvm master. - patch('llvm_py37.patch', when='@4:6 ^python@3.7:') + patch("llvm_py37.patch", when="@4:6 ^python@3.7:") # https://bugs.llvm.org/show_bug.cgi?id=39696 - patch('thread-p9.patch', when='@develop+libcxx') + patch("thread-p9.patch", when="@develop+libcxx") - @run_before('cmake') + @run_before("cmake") def check_darwin_lldb_codesign_requirement(self): - if not self.spec.satisfies('+lldb platform=darwin'): + if not self.spec.satisfies("+lldb platform=darwin"): return - codesign = which('codesign') - mkdir('tmp') - llvm_check_file = join_path('tmp', 'llvm_check') - copy('/usr/bin/false', llvm_check_file) + codesign = which("codesign") + mkdir("tmp") + llvm_check_file = join_path("tmp", "llvm_check") + copy("/usr/bin/false", llvm_check_file) try: - codesign('-f', '-s', 'lldb_codesign', '--dryrun', - llvm_check_file) + codesign("-f", "-s", "lldb_codesign", "--dryrun", llvm_check_file) except ProcessError: # Newer LLVM versions have a simple script that sets up @@ -170,140 +226,200 @@ def check_darwin_lldb_codesign_requirement(self): except Exception: raise RuntimeError( 'The "lldb_codesign" identity must be available to build ' - 'LLVM with LLDB. See https://lldb.llvm.org/resources/' - 'build.html#code-signing-on-macos for details on how to ' - 'create this identity.' + "LLVM with LLDB. See https://lldb.llvm.org/resources/" + "build.html#code-signing-on-macos for details on how to " + "create this identity." ) def setup_build_environment(self, env): - env.append_flags('CXXFLAGS', self.compiler.cxx11_flag) + env.append_flags("CXXFLAGS", self.compiler.cxx11_flag) def setup_run_environment(self, env): - if '+clang' in self.spec: - env.set('CC', join_path(self.spec.prefix.bin, 'clang')) - env.set('CXX', join_path(self.spec.prefix.bin, 'clang++')) + if "+clang" in self.spec: + env.set("CC", join_path(self.spec.prefix.bin, "clang")) + env.set("CXX", join_path(self.spec.prefix.bin, "clang++")) - root_cmakelists_dir = 'llvm' + root_cmakelists_dir = "llvm" def cmake_args(self): spec = self.spec cmake_args = [ - '-DLLVM_REQUIRES_RTTI:BOOL=ON', - '-DLLVM_ENABLE_RTTI:BOOL=ON', - '-DLLVM_ENABLE_EH:BOOL=ON', - '-DCLANG_DEFAULT_OPENMP_RUNTIME:STRING=libomp', - '-DPYTHON_EXECUTABLE:PATH={0}'.format(spec['python'].command.path), + "-DLLVM_REQUIRES_RTTI:BOOL=ON", + "-DLLVM_ENABLE_RTTI:BOOL=ON", + "-DLLVM_ENABLE_EH:BOOL=ON", + "-DCLANG_DEFAULT_OPENMP_RUNTIME:STRING=libomp", + "-DPYTHON_EXECUTABLE:PATH={0}".format(spec["python"].command.path), + "-DLIBOMP_USE_HWLOC=On", ] projects = [] - # TODO: Instead of unconditionally disabling CUDA, add a "cuda" variant - # (see TODO above), and set the paths if enabled. - cmake_args.extend([ - '-DCUDA_TOOLKIT_ROOT_DIR:PATH=IGNORE', - '-DCUDA_SDK_ROOT_DIR:PATH=IGNORE', - '-DCUDA_NVCC_EXECUTABLE:FILEPATH=IGNORE', - '-DLIBOMPTARGET_DEP_CUDA_DRIVER_LIBRARIES:STRING=IGNORE']) + if "+cuda" in spec: + cmake_args.extend( + [ + "-DCUDA_TOOLKIT_ROOT_DIR:PATH=" + spec["cuda"].prefix, + "-DLIBOMPTARGET_NVPTX_COMPUTE_CAPABILITIES={0}".format( + ",".join(spec.variants["nvptx_offload_ccs"].value) + ), + "-DCLANG_OPENMP_NVPTX_DEFAULT_ARCH=sm_{0}".format( + spec.variants["nvptx_offload_ccs"].value[-1] + ), + ] + ) + else: + # still build libomptarget but disable cuda + cmake_args.extend( + [ + "-DCUDA_TOOLKIT_ROOT_DIR:PATH=IGNORE", + "-DCUDA_SDK_ROOT_DIR:PATH=IGNORE", + "-DCUDA_NVCC_EXECUTABLE:FILEPATH=IGNORE", + "-DLIBOMPTARGET_DEP_CUDA_DRIVER_LIBRARIES:STRING=IGNORE", + ] + ) - if '+python' in spec and '+lldb' in spec and spec.satisfies('@5.0.0:'): - cmake_args.append('-DLLDB_USE_SYSTEM_SIX:Bool=TRUE') + if "+omp_debug" in spec: + cmake_args.append("-DLIBOMPTARGET_ENABLE_DEBUG:Bool=ON") - if '~python' in spec and '+lldb' in spec: - cmake_args.append('-DLLDB_DISABLE_PYTHON:Bool=TRUE') + if "+python" in spec and "+lldb" in spec and spec.satisfies("@5.0.0:"): + cmake_args.append("-DLLDB_USE_SYSTEM_SIX:Bool=TRUE") - if '+gold' in spec: - cmake_args.append('-DLLVM_BINUTILS_INCDIR=' + - spec['binutils'].prefix.include) + if "~python" in spec and "+lldb" in spec: + cmake_args.append("-DLLDB_DISABLE_PYTHON:Bool=TRUE") - if '+clang' in spec: - projects.append('clang') - projects.append('clang-tools-extra') - projects.append('openmp') - if '+lldb' in spec: - projects.append('lldb') - if '+lld' in spec: - projects.append('lld') - if '+compiler-rt' in spec: - projects.append('compiler-rt') - if '+libcxx' in spec: - projects.append('libcxx') - projects.append('libcxxabi') - if spec.satisfies('@3.9.0:'): - cmake_args.append('-DCLANG_DEFAULT_CXX_STDLIB=libc++') - if '+internal_unwind' in spec: - projects.append('libunwind') - if '+polly' in spec: - projects.append('polly') - cmake_args.append('-DLINK_POLLY_INTO_TOOLS:Bool=ON') + if "+gold" in spec: + cmake_args.append( + "-DLLVM_BINUTILS_INCDIR=" + spec["binutils"].prefix.include + ) - if '+shared_libs' in spec: - cmake_args.append('-DBUILD_SHARED_LIBS:Bool=ON') + if "+clang" in spec: + projects.append("clang") + projects.append("clang-tools-extra") + projects.append("openmp") + if "+lldb" in spec: + projects.append("lldb") + if "+lld" in spec: + projects.append("lld") + if "+compiler-rt" in spec: + projects.append("compiler-rt") + if "+libcxx" in spec: + projects.append("libcxx") + projects.append("libcxxabi") + if spec.satisfies("@3.9.0:"): + cmake_args.append("-DCLANG_DEFAULT_CXX_STDLIB=libc++") + if "+internal_unwind" in spec: + projects.append("libunwind") + if "+polly" in spec: + projects.append("polly") + cmake_args.append("-DLINK_POLLY_INTO_TOOLS:Bool=ON") - if '+link_dylib' in spec: - cmake_args.append('-DLLVM_LINK_LLVM_DYLIB:Bool=ON') + if "+shared_libs" in spec: + cmake_args.append("-DBUILD_SHARED_LIBS:Bool=ON") + if "+omp_debug" in spec: + cmake_args.append("-DLIBOMPTARGET_ENABLE_DEBUG:Bool=ON") - if '+all_targets' not in spec: # all is default on cmake + if "+split_dwarf" in spec: + cmake_args.append("-DLLVM_USE_SPLIT_DWARF:Bool=ON") - targets = ['NVPTX', 'AMDGPU'] - if (spec.version < Version('3.9.0')): + if "+all_targets" not in spec: # all is default on cmake + + targets = ["NVPTX", "AMDGPU"] + if spec.version < Version("3.9.0"): # Starting in 3.9.0 CppBackend is no longer a target (see # LLVM_ALL_TARGETS in llvm's top-level CMakeLists.txt for # the complete list of targets) - targets.append('CppBackend') + targets.append("CppBackend") - if spec.target.family == 'x86' or spec.target.family == 'x86_64': - targets.append('X86') - elif spec.target.family == 'arm': - targets.append('ARM') - elif spec.target.family == 'aarch64': - targets.append('AArch64') - elif (spec.target.family == 'sparc' or - spec.target.family == 'sparc64'): - targets.append('Sparc') - elif (spec.target.family == 'ppc64' or - spec.target.family == 'ppc64le' or - spec.target.family == 'ppc' or - spec.target.family == 'ppcle'): - targets.append('PowerPC') + if spec.target.family == "x86" or spec.target.family == "x86_64": + targets.append("X86") + elif spec.target.family == "arm": + targets.append("ARM") + elif spec.target.family == "aarch64": + targets.append("AArch64") + elif ( + spec.target.family == "sparc" + or spec.target.family == "sparc64" + ): + targets.append("Sparc") + elif ( + spec.target.family == "ppc64" + or spec.target.family == "ppc64le" + or spec.target.family == "ppc" + or spec.target.family == "ppcle" + ): + targets.append("PowerPC") cmake_args.append( - '-DLLVM_TARGETS_TO_BUILD:STRING=' + ';'.join(targets)) + "-DLLVM_TARGETS_TO_BUILD:STRING=" + ";".join(targets) + ) - if '+omp_tsan' in spec: - cmake_args.append('-DLIBOMP_TSAN_SUPPORT=ON') + if "+omp_tsan" in spec: + cmake_args.append("-DLIBOMP_TSAN_SUPPORT=ON") - if self.compiler.name == 'gcc': + if self.compiler.name == "gcc": gcc_prefix = ancestor(self.compiler.cc, 2) - cmake_args.append('-DGCC_INSTALL_PREFIX=' + gcc_prefix) + cmake_args.append("-DGCC_INSTALL_PREFIX=" + gcc_prefix) - if spec.satisfies('@4.0.0:'): - if spec.satisfies('platform=cray') or \ - spec.satisfies('platform=linux'): - cmake_args.append('-DCMAKE_BUILD_WITH_INSTALL_RPATH=1') + if spec.satisfies("@4.0.0:"): + if spec.satisfies("platform=cray") or spec.satisfies( + "platform=linux" + ): + cmake_args.append("-DCMAKE_BUILD_WITH_INSTALL_RPATH=1") # Semicolon seperated list of projects to enable cmake_args.append( - '-DLLVM_ENABLE_PROJECTS:STRING={0}'.format(';'.join(projects))) + "-DLLVM_ENABLE_PROJECTS:STRING={0}".format(";".join(projects)) + ) return cmake_args - @run_before('build') + @run_before("build") def pre_install(self): with working_dir(self.build_directory): # When building shared libraries these need to be installed first - make('install-LLVMTableGen') - if self.spec.version >= Version('4.0.0'): + make("install-LLVMTableGen") + if self.spec.version >= Version("4.0.0"): # LLVMDemangle target was added in 4.0.0 - make('install-LLVMDemangle') - make('install-LLVMSupport') + make("install-LLVMDemangle") + make("install-LLVMSupport") - @run_after('install') + @run_after("install") def post_install(self): - if '+python' in self.spec: - install_tree('llvm/bindings/python', site_packages_dir) + spec = self.spec - if '+clang' in self.spec: - install_tree('clang/bindings/python', site_packages_dir) + # unnecessary if we get bootstrap builds in here + if "+cuda" in self.spec: + ompdir = "build-bootstrapped-omp" + # rebuild libomptarget to get bytecode runtime library files + with working_dir(ompdir, create=True): + cmake_args = [ + self.stage.source_path + "/openmp", + "-DCMAKE_C_COMPILER:PATH={0}".format( + spec.prefix.bin + "/clang" + ), + "-DCMAKE_CXX_COMPILER:PATH={0}".format( + spec.prefix.bin + "/clang++" + ), + "-DCMAKE_INSTALL_PREFIX:PATH={0}".format(spec.prefix), + ] + cmake_args.extend(self.cmake_args()) + cmake_args.append('-DLIBOMPTARGET_NVPTX_ENABLE_BCLIB=true') + + # work around bad libelf detection in libomptarget + cmake_args.append( + "-DCMAKE_CXX_FLAGS:String=-I{0} -I{1}".format( + spec["libelf"].prefix.include, + spec["hwloc"].prefix.include, + ) + ) + + cmake(*cmake_args) + make() + make("install") + if "+python" in self.spec: + install_tree("llvm/bindings/python", site_packages_dir) + + if "+clang" in self.spec: + install_tree("clang/bindings/python", site_packages_dir) with working_dir(self.build_directory): - install_tree('bin', join_path(self.prefix, 'libexec', 'llvm')) + install_tree("bin", join_path(self.prefix, "libexec", "llvm")) diff --git a/var/spack/repos/builtin/packages/z3/package.py b/var/spack/repos/builtin/packages/z3/package.py index bd02c0c0dbd..71eafb0a3b8 100644 --- a/var/spack/repos/builtin/packages/z3/package.py +++ b/var/spack/repos/builtin/packages/z3/package.py @@ -14,6 +14,7 @@ class Z3(MakefilePackage): homepage = "https://github.com/Z3Prover/z3/wiki" url = "https://github.com/Z3Prover/z3/archive/z3-4.5.0.tar.gz" + version('4.8.7', sha256='8c1c49a1eccf5d8b952dadadba3552b0eac67482b8a29eaad62aa7343a0732c3') version('4.5.0', sha256='aeae1d239c5e06ac183be7dd853775b84698db1265cb2258e5918a28372d4a0c') version('4.4.1', sha256='50967cca12c5c6e1612d0ccf8b6ebf5f99840a783d6cf5216336a2b59c37c0ce') version('4.4.0', sha256='65b72f9eb0af50949e504b47080fb3fc95f11c435633041d9a534473f3142cba') From ddccad14c90e8485ee2e87368fc51765a765cf50 Mon Sep 17 00:00:00 2001 From: Daniele Cesarini Date: Sat, 28 Mar 2020 21:49:21 +0100 Subject: [PATCH 267/377] XIOS: add new versions (#15728) * XIOS: add new versions Patch has been removed because it was not applied to any previously existing versions and it actually breaks the new versions added by this PR. * Sort versions from newest to oldest --- .../packages/xios/bld_extern_1.x.patch | 27 ------------------- .../repos/builtin/packages/xios/package.py | 7 +++-- 2 files changed, 5 insertions(+), 29 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch diff --git a/var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch b/var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch deleted file mode 100644 index fe52da11923..00000000000 --- a/var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch +++ /dev/null @@ -1,27 +0,0 @@ ---- a/bld.cfg 2017-12-23 15:21:01.458603785 +1100 -+++ b/bld.cfg 2017-12-23 15:36:36.667684136 +1100 -@@ -24,9 +24,6 @@ - - search_src true - src::zzz . --src::date $PWD/extern/boost/src/date_time --src::blitz $PWD/extern/blitz/src --src::netcdf $PWD/extern/netcdf4 - src::remap $PWD/extern/remap/src - bld::lib xios - bld::target libxios.a -@@ -46,11 +43,11 @@ - bld::tool::fc %FCOMPILER - bld::tool::fpp %FPP - bld::tool::cpp %CPP --bld::tool::cppflags %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include --bld::tool::fppflags %BASE_INC -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -+bld::tool::cppflags %CBASE_INC -I${PWD}/extern/rapidxml/include -+bld::tool::fppflags %BASE_INC -I${PWD}/extern/rapidxml/include - bld::tool::ld %LINKER - bld::tool::ldflags %LD_FLAGS --bld::tool::cflags %CFLAGS %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include -+bld::tool::cflags %CFLAGS %CBASE_INC -I${PWD}/extern/rapidxml/include - bld::tool::fflags %FFLAGS %FBASE_INC - bld::tool::cppkeys %CPP_KEY - bld::tool::fppkeys %CPP_KEY diff --git a/var/spack/repos/builtin/packages/xios/package.py b/var/spack/repos/builtin/packages/xios/package.py index 55769026cf1..54eca9fead0 100644 --- a/var/spack/repos/builtin/packages/xios/package.py +++ b/var/spack/repos/builtin/packages/xios/package.py @@ -13,9 +13,13 @@ class Xios(Package): homepage = "https://forge.ipsl.jussieu.fr/ioserver/wiki" + version('develop', svn='http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk') + version('2.5', revision=1860, + svn='http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.5') + version('2.0', revision=1627, + svn='http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-2.0') version('1.0', revision=910, svn='http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0') - version('develop', svn='http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk') variant('mode', values=('debug', 'dev', 'prod'), default='dev', description='Build for debugging, development or production') @@ -24,7 +28,6 @@ class Xios(Package): # Use spack versions of blitz and netcdf-c for compatibility # with recent compilers and optimised platform libraries: patch('bld_extern_1.0.patch', when='@:1.0') - patch('bld_extern_1.x.patch', when='@1.1:') # Workaround bug #17782 in llvm, where reading a double # followed by a character is broken (e.g. duration '1d'): From beaa4fbe3ce1a9fef95187e8caf7f13dba32c4f7 Mon Sep 17 00:00:00 2001 From: Andrew W Elble Date: Sat, 28 Mar 2020 17:44:23 -0400 Subject: [PATCH 268/377] New package: gdrcopy (#15732) * New package: gdrcopy provides the userspace libraries for gdrcopy. * Update var/spack/repos/builtin/packages/gdrcopy/package.py Co-Authored-By: Adam J. Stewart Co-authored-by: Adam J. Stewart --- .../repos/builtin/packages/gdrcopy/package.py | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 var/spack/repos/builtin/packages/gdrcopy/package.py diff --git a/var/spack/repos/builtin/packages/gdrcopy/package.py b/var/spack/repos/builtin/packages/gdrcopy/package.py new file mode 100644 index 00000000000..e85c8fb0c00 --- /dev/null +++ b/var/spack/repos/builtin/packages/gdrcopy/package.py @@ -0,0 +1,27 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Gdrcopy(MakefilePackage): + """A fast GPU memory copy library based on NVIDIA GPUDirect + RDMA technology.""" + + homepage = "https://github.com/NVIDIA/gdrcopy" + url = "https://github.com/NVIDIA/gdrcopy/archive/v2.0-beta.3.tar.gz" + git = "https://github.com/NVIDIA/gdrcopy" + + version('master', branch='master') + version('2.0', sha256='98320e6e980a7134ebc4eedd6cf23647104f2b3c557f2eaf0d31a02609f5f2b0') + version('1.3', sha256='f11cdfe389b685f6636b80b4a3312dc014a385ad7220179c1318c60e2e28af3a') + + def build(self, spec, prefix): + make('lib') + + def install(self, spec, prefix): + mkdir(prefix.include) + mkdir(prefix.lib64) + make('lib_install', 'PREFIX={0}'.format(self.prefix)) From cbcac722547cae2a25ea4c8503c71adda271c557 Mon Sep 17 00:00:00 2001 From: Patrick Gartung Date: Sat, 28 Mar 2020 16:49:34 -0500 Subject: [PATCH 269/377] Buildcache keys command speed up (#15727) * Limit the spidering to depth=0 for keys * depth=0 is default argument --- lib/spack/spack/binary_distribution.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/binary_distribution.py b/lib/spack/spack/binary_distribution.py index 7902e5fc584..0fb6feae028 100644 --- a/lib/spack/spack/binary_distribution.py +++ b/lib/spack/spack/binary_distribution.py @@ -903,7 +903,7 @@ def get_keys(install=False, trust=False, force=False): url_util.format(fetch_url_build_cache)) # For s3 mirror need to request index.html directly p, links = web_util.spider( - url_util.join(fetch_url_build_cache, 'index.html'), depth=1) + url_util.join(fetch_url_build_cache, 'index.html')) for link in links: if re.search(r'\.key', link) or re.search(r'\.pub', link): From c3d0973c3e34f35453f2d5bdb7b6179cb3ec09fe Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 29 Mar 2020 10:55:57 -0500 Subject: [PATCH 270/377] motif: add pkgconfig dependency (#15736) --- var/spack/repos/builtin/packages/motif/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/motif/package.py b/var/spack/repos/builtin/packages/motif/package.py index 7a6bc0de8f2..c64d35fc430 100644 --- a/var/spack/repos/builtin/packages/motif/package.py +++ b/var/spack/repos/builtin/packages/motif/package.py @@ -33,6 +33,7 @@ class Motif(AutotoolsPackage): depends_on("autoconf", type="build") depends_on("m4", type="build") depends_on("libtool", type="build") + depends_on("pkgconfig", type="build") patch('add_xbitmaps_dependency.patch') From 4b3b0232847157f3ab1939bb46ba41961053a2b3 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sun, 29 Mar 2020 17:56:15 +0200 Subject: [PATCH 271/377] deal.II: Update dependencies and fix target for vectorisation (#15731) * Update ADOL-C homepage url * Update SymEngine to v0.6 * deal.II: Add code to add target vectorisation flags --- var/spack/repos/builtin/packages/adol-c/package.py | 2 +- var/spack/repos/builtin/packages/dealii/package.py | 9 +++++++++ var/spack/repos/builtin/packages/symengine/package.py | 3 ++- 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py index 741b57773b5..def99d8a4ef 100644 --- a/var/spack/repos/builtin/packages/adol-c/package.py +++ b/var/spack/repos/builtin/packages/adol-c/package.py @@ -11,7 +11,7 @@ class AdolC(AutotoolsPackage): derivatives of vector functions in C and C++ programs by operator overloading.""" - homepage = "https://projects.coin-or.org/ADOL-C" + homepage = "https://github.com/coin-or/ADOL-C" url = "https://github.com/coin-or/ADOL-C/archive/releases/2.7.2.tar.gz" git = "https://github.com/coin-or/ADOL-C.git" version('master', branch='master') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 1b9e02c0440..d3a58cb835f 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -5,6 +5,8 @@ from spack import * +import os + class Dealii(CMakePackage, CudaPackage): """C++ software library providing well-documented tools to build finite @@ -459,6 +461,13 @@ def cmake_args(self): ' '.join(cxx_flags)) ]) + # Add flags for machine vectorization, used when tutorials + # and user code is built. + # See https://github.com/dealii/dealii/issues/9164 + options.extend([ + '-DDEAL_II_CXX_FLAGS=%s' % os.environ['SPACK_TARGET_ARGS'] + ]) + return options def setup_run_environment(self, env): diff --git a/var/spack/repos/builtin/packages/symengine/package.py b/var/spack/repos/builtin/packages/symengine/package.py index ceb1b9a5ed4..a9c866edb77 100644 --- a/var/spack/repos/builtin/packages/symengine/package.py +++ b/var/spack/repos/builtin/packages/symengine/package.py @@ -14,7 +14,8 @@ class Symengine(CMakePackage): url = "https://github.com/symengine/symengine/archive/v0.2.0.tar.gz" git = "https://github.com/symengine/symengine.git" - version('develop', branch='master') + version('master', branch='master') + version('0.6.0', sha256='4d2caa86c03eaaa8ed004084d02f87b5c51b6229f8ba70d161227e22d6302f0a') version('0.5.0', sha256='5d02002f00d16a0928d1056e6ecb8f34fd59f3bfd8ed0009a55700334dbae29b') version('0.4.0', sha256='dd755901a9e2a49e53ba3bbe3f565f94265af05299e57a7b592186dd35916a1b') version('0.3.0', sha256='591463cb9e741d59f6dfd39a7943e3865d3afe9eac47d1a9cbf5ca74b9c49476') From df4e89770a0462275628b0a1239f5976ea598d9d Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 29 Mar 2020 16:34:18 -0500 Subject: [PATCH 272/377] py-traits: add new package (#15741) --- .../repos/builtin/packages/py-traits/package.py | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-traits/package.py diff --git a/var/spack/repos/builtin/packages/py-traits/package.py b/var/spack/repos/builtin/packages/py-traits/package.py new file mode 100644 index 00000000000..868e1de0a2f --- /dev/null +++ b/var/spack/repos/builtin/packages/py-traits/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class PyTraits(PythonPackage): + """Explicitly typed attributes for Python.""" + + homepage = "https://docs.enthought.com/traits" + url = "https://pypi.io/packages/source/t/traits/traits-6.0.0.tar.gz" + + version('6.0.0', sha256='dbcd70166feca434130a1193284d5819ca72ffbc8dbce8deeecc0cebb41a3bfb') + + depends_on('python@3.5:', type=('build', 'run')) + depends_on('py-setuptools', type='build') From 4287d2290c581b907b08efabc1e6bccea4019ac6 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 29 Mar 2020 17:22:24 -0500 Subject: [PATCH 273/377] py-pyface: add new package (#15743) --- .../builtin/packages/py-pyface/package.py | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-pyface/package.py diff --git a/var/spack/repos/builtin/packages/py-pyface/package.py b/var/spack/repos/builtin/packages/py-pyface/package.py new file mode 100644 index 00000000000..197e3d9ab24 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pyface/package.py @@ -0,0 +1,33 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class PyPyface(PythonPackage): + """The pyface project contains a toolkit-independent GUI abstraction layer, + which is used to support the "visualization" features of the Traits + package. Thus, you can write code in terms of the Traits API (views, items, + editors, etc.), and let pyface and your selected toolkit and back-end take + care of the details of displaying them.""" + + homepage = "https://docs.enthought.com/pyface" + url = "https://pypi.io/packages/source/p/pyface/pyface-6.1.2.tar.gz" + + version('6.1.2', sha256='7c2ac3d5cbec85e8504b3b0b63e9307be12c6d710b46bae372ce6562d41f4fbc') + + variant('backend', default='pyqt5', description='Default backend', + values=('wx', 'pyqt', 'pyqt5', 'pyside'), multi=False) + + depends_on('py-setuptools', type='build') + depends_on('py-traits', type=('build', 'run')) + + # Backends + depends_on('py-wxpython@2.8.10:', when='backend=wx', type=('build', 'run')) + depends_on('py-numpy', when='backend=wx', type=('build', 'run')) + depends_on('py-pyqt4@4.10:', when='backend=pyqt', type=('build', 'run')) + depends_on('py-pygments', when='backend=pyqt', type=('build', 'run')) + depends_on('py-pyqt5@5:', when='backend=pyqt5', type=('build', 'run')) + depends_on('py-pygments', when='backend=pyqt5', type=('build', 'run')) + depends_on('py-pyside@1.2:', when='backend=pyside', type=('build', 'run')) + depends_on('py-pygments', when='backend=pyside', type=('build', 'run')) From f1aab835fe5d77b4ce31c7e6b38ee22f2fb386c5 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 29 Mar 2020 17:23:21 -0500 Subject: [PATCH 274/377] CitcomS: add maintainer, master version, python dep (#15742) --- var/spack/repos/builtin/packages/citcoms/package.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/var/spack/repos/builtin/packages/citcoms/package.py b/var/spack/repos/builtin/packages/citcoms/package.py index f05c3d7cd60..35fe86b2b4d 100644 --- a/var/spack/repos/builtin/packages/citcoms/package.py +++ b/var/spack/repos/builtin/packages/citcoms/package.py @@ -12,7 +12,11 @@ class Citcoms(AutotoolsPackage): homepage = "https://geodynamics.org/cig/software/citcoms/" url = "https://github.com/geodynamics/citcoms/releases/download/v3.3.1/CitcomS-3.3.1.tar.gz" + git = "https://github.com/geodynamics/citcoms.git" + maintainers = ['adamjstewart'] + + version('master', branch='master', submodules=True) version('3.3.1', sha256='e3520e0a933e4699d31e86fe309b8c154ea6ecb0f42a1cf6f25e8d13d825a4b3') version('3.2.0', sha256='773a14d91ecbb4a4d1e04317635fab79819d83c57b47f19380ff30b9b19cb07a') @@ -23,6 +27,11 @@ class Citcoms(AutotoolsPackage): # Required dependencies depends_on('mpi') depends_on('zlib') + depends_on('python@:2', type='run') # needed for post-processing scripts + depends_on('automake', when='@master', type='build') + depends_on('autoconf', when='@master', type='build') + depends_on('libtool', when='@master', type='build') + depends_on('m4', when='@master', type='build') # Optional dependencies depends_on('hc', when='+ggrd') From 17cd359ddff4cd27217f7bf4671a54af7fbc536d Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 29 Mar 2020 19:38:02 -0500 Subject: [PATCH 275/377] py-traitsui: add new package (#15744) --- .../builtin/packages/py-traitsui/package.py | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-traitsui/package.py diff --git a/var/spack/repos/builtin/packages/py-traitsui/package.py b/var/spack/repos/builtin/packages/py-traitsui/package.py new file mode 100644 index 00000000000..f77e92cc4fd --- /dev/null +++ b/var/spack/repos/builtin/packages/py-traitsui/package.py @@ -0,0 +1,36 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class PyTraitsui(PythonPackage): + """The TraitsUI project contains a toolkit-independent GUI abstraction + layer, which is used to support the "visualization" features of the Traits + package. Thus, you can write model in terms of the Traits API and specify a + GUI in terms of the primitives supplied by TraitsUI (views, items, editors, + etc.), and let TraitsUI and your selected toolkit and back-end take care of + the details of displaying them.""" + + homepage = "https://docs.enthought.com/traitsui" + url = "https://pypi.io/packages/source/t/traitsui/traitsui-6.1.3.tar.gz" + + version('6.1.3', sha256='48381763b181efc58eaf288431d1d92d028d0d97dfdd33eba7809aae8aef814f') + + variant('backend', default='pyqt5', description='Default backend', + values=('wx', 'pyqt', 'pyqt5', 'pyside'), multi=False) + + depends_on('py-setuptools', type='build') + depends_on('py-traits', type=('build', 'run')) + depends_on('py-pyface@6.0.0:', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) + + # Backends + depends_on('py-wxpython@2.8.10:', when='backend=wx', type=('build', 'run')) + depends_on('py-numpy', when='backend=wx', type=('build', 'run')) + depends_on('py-pyqt4@4.10:', when='backend=pyqt', type=('build', 'run')) + depends_on('py-pygments', when='backend=pyqt', type=('build', 'run')) + depends_on('py-pyqt5@5:', when='backend=pyqt5', type=('build', 'run')) + depends_on('py-pygments', when='backend=pyqt5', type=('build', 'run')) + depends_on('py-pyside@1.2:', when='backend=pyside', type=('build', 'run')) + depends_on('py-pygments', when='backend=pyside', type=('build', 'run')) From 61c1322430b66ef887af1bd7125e321eb993776c Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Sun, 29 Mar 2020 19:46:16 -0500 Subject: [PATCH 276/377] new package: intel-mpi-benchmarks (#15745) * Add initial attempt at intel-mpi-benchmarks package * Add more checksummed versions * Changes to how makefile is handled * First working install version. Needs tuning to support building specific benchmarks * Add variant for building specific benchmarks rather than all of them * Minor syntax change --- .../packages/intel-mpi-benchmarks/package.py | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 var/spack/repos/builtin/packages/intel-mpi-benchmarks/package.py diff --git a/var/spack/repos/builtin/packages/intel-mpi-benchmarks/package.py b/var/spack/repos/builtin/packages/intel-mpi-benchmarks/package.py new file mode 100644 index 00000000000..a619d0d8cbf --- /dev/null +++ b/var/spack/repos/builtin/packages/intel-mpi-benchmarks/package.py @@ -0,0 +1,81 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class IntelMpiBenchmarks(MakefilePackage): + """Intel(R) MPI Benchmarks provides a set of elementary benchmarks + that conform to MPI-1, MPI-2, and MPI-3 standard. + You can run all of the supported benchmarks, or a subset specified + in the command line using one executable file. + Use command-line parameters to specify various settings, such as + time measurement, message lengths, and selection of communicators. """ + + homepage = "https://software.intel.com/en-us/articles/intel-mpi-benchmarks" + url = "https://github.com/intel/mpi-benchmarks/archive/IMB-v2019.5.tar.gz" + + maintainers = ['carsonwoods'] + + version('2019.5', sha256='61f8e872a3c3076af53007a68e4da3a8d66be2ba7a051dc21e626a4e2d26e651') + version('2019.4', sha256='aeb336be10275c1a2f579b491b6631122876b461ac7148b1d0764f13b7552690') + version('2019.3', sha256='4f256d11bfed9ca6166548486d61a062e67be61f13dd9f30690232720e185f31') + version('2019.2', sha256='0bc2224a913073aaa5958f6ae08341e5fcd39cedc6722a09bfd4a3d7591a340b') + + depends_on('mpi') + + variant( + 'benchmark', default='all', + values=('mpi1', 'ext', 'io', 'nbc', + 'p2p', 'rma', 'mt', 'all'), + multi=False, + description='Specify which benchmark to build') + + def build(self, spec, prefix): + env['CC'] = spec['mpi'].mpicc + env['CXX'] = spec['mpi'].mpicxx + + if 'benchmark=mpi1' in spec: + make('IMB-MPI1') + elif 'benchmark=ext' in spec: + make('IMB-EXT') + elif 'benchmark=io' in spec: + make('IMB-IO') + elif 'benchmark=nbc' in spec: + make('IMB-NBC') + elif 'benchmark=p2p' in spec: + make('IMB-P2P') + elif 'benchmark=rma' in spec: + make('IMB-RMA') + elif 'benchmark=mt' in spec: + make('IMB-MT') + else: + make("all") + + def install(self, spec, prefix): + mkdir(prefix.bin) + + if 'benchmark=mpi1' in spec: + install('IMB-MPI1', prefix.bin) + elif 'benchmark=ext' in spec: + install('IMB-EXT', prefix.bin) + elif 'benchmark=io' in spec: + install('IMB-IO', prefix.bin) + elif 'benchmark=nbc' in spec: + install('IMB-NBC', prefix.bin) + elif 'benchmark=p2p' in spec: + install('IMB-P2P', prefix.bin) + elif 'benchmark=rma' in spec: + install('IMB-RMA', prefix.bin) + elif 'benchmark=mt' in spec: + install('IMB-MT', prefix.bin) + else: + install('IMB-EXT', prefix.bin) + install('IMB-IO', prefix.bin) + install('IMB-MPI1', prefix.bin) + install('IMB-MT', prefix.bin) + install('IMB-NBC', prefix.bin) + install('IMB-P2P', prefix.bin) + install('IMB-RMA', prefix.bin) From 0372582bf01a49b977f0c522fe900b73b6ba6658 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 29 Mar 2020 20:08:52 -0500 Subject: [PATCH 277/377] py-apptools: add new package (#15747) --- .../builtin/packages/py-apptools/package.py | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-apptools/package.py diff --git a/var/spack/repos/builtin/packages/py-apptools/package.py b/var/spack/repos/builtin/packages/py-apptools/package.py new file mode 100644 index 00000000000..4ac8da1c791 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-apptools/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class PyApptools(PythonPackage): + """The apptools project includes a set of packages that Enthought has found + useful in creating a number of applications. They implement functionality + that is commonly needed by many applications.""" + + homepage = "https://docs.enthought.com/apptools" + url = "https://pypi.io/packages/source/a/apptools/apptools-4.5.0.tar.gz" + + version('4.5.0', sha256='260ae0e2a86cb2df2fede631ab6ac8ece694a58a1def78cd015c890c57140582') + + depends_on('py-setuptools', type='build') + depends_on('py-configobj', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) + depends_on('py-traitsui', type=('build', 'run')) From 7bed5e7c1ac2b1e4a50f5889a2eeea17320f332b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 29 Mar 2020 20:41:24 -0500 Subject: [PATCH 278/377] py-envisage: add new package (#15748) --- .../builtin/packages/py-envisage/package.py | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-envisage/package.py diff --git a/var/spack/repos/builtin/packages/py-envisage/package.py b/var/spack/repos/builtin/packages/py-envisage/package.py new file mode 100644 index 00000000000..06783c8fcb2 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-envisage/package.py @@ -0,0 +1,25 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class PyEnvisage(PythonPackage): + """Envisage is a Python-based framework for building extensible + applications, that is, applications whose functionality can be extended by + adding "plug-ins". Envisage provides a standard mechanism for features to + be added to an application, whether by the original developer or by someone + else. In fact, when you build an application using Envisage, the entire + application consists primarily of plug-ins. In this respect, it is similar + to the Eclipse and Netbeans frameworks for Java applications.""" + + homepage = "https://docs.enthought.com/envisage" + url = "https://pypi.io/packages/source/e/envisage/envisage-4.9.2.tar.gz" + + version('4.9.2', sha256='ed9580ac6ea17b333f1cce5b94656aed584798d56d8bd364f996a06fe1ac32eb') + + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) + depends_on('py-apptools', type=('build', 'run')) + depends_on('py-setuptools', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) + depends_on('py-traits', type=('build', 'run')) From 757d768a07ce5829cd63dd3c3c9313503f0b5d00 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 29 Mar 2020 21:11:13 -0500 Subject: [PATCH 279/377] py-mayavi: add new package (#15751) --- .../builtin/packages/py-mayavi/package.py | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-mayavi/package.py diff --git a/var/spack/repos/builtin/packages/py-mayavi/package.py b/var/spack/repos/builtin/packages/py-mayavi/package.py new file mode 100644 index 00000000000..1fe477bbc70 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-mayavi/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class PyMayavi(PythonPackage): + """Mayavi: 3D visualization of scientific data in Python.""" + + homepage = "https://docs.enthought.com/mayavi/mayavi/index.html" + url = "https://pypi.io/packages/source/m/mayavi/mayavi-4.7.1.tar.bz2" + + version('4.7.1', sha256='be51fb6f886f304f7c593c907e6a2e88d7919f8f446cdccfcd184fa35b3db724') + + depends_on('py-setuptools', type='build') + depends_on('py-apptools', type=('build', 'run')) + depends_on('py-envisage', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-pyface@6.1.1:', type=('build', 'run')) + depends_on('py-pygments', type=('build', 'run')) + depends_on('py-traits@4.6.0:', type=('build', 'run')) + depends_on('py-traitsui@6.0.0:', type=('build', 'run')) + depends_on('vtk+python', type=('build', 'run')) From 3310eaab99e1ceee270a70cac6fe88831d65040a Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sun, 29 Mar 2020 19:38:15 -0700 Subject: [PATCH 280/377] spack-python should exec `spack python` (#15738) The current implementation of `spack-python` will leave an extra shell around while it runs. That shell should really replace itself with spack. - [x] add exec to spack-python script --- bin/spack-python | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/spack-python b/bin/spack-python index b81c8b7dbb9..22141b46d69 100755 --- a/bin/spack-python +++ b/bin/spack-python @@ -22,4 +22,4 @@ # # This is compatible across platforms. # -/usr/bin/env spack python "$@" +exec /usr/bin/env spack python "$@" From 3cbc26cfa6a3d23148e2ce62d6c80accf7fa3ca6 Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Sun, 29 Mar 2020 23:05:11 -0500 Subject: [PATCH 281/377] Add additional configuration options for binutils (#15753) --- var/spack/repos/builtin/packages/binutils/package.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index 4a647e7e888..60cd9563fa1 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -35,6 +35,9 @@ class Binutils(AutotoolsPackage, GNUMirrorPackage): variant('libiberty', default=False, description='Also install libiberty.') variant('nls', default=True, description='Enable Native Language Support') variant('headers', default=False, description='Install extra headers (e.g. ELF)') + variant('lto', default=False, description='Enable lto.') + variant('ld', default=False, description='Enable ld.') + variant('interwork', default=False, description='Enable interwork.') patch('cr16.patch', when='@:2.29.1') patch('update_symbol-2.26.patch', when='@2.26') @@ -68,6 +71,15 @@ def configure_args(self): '--with-sysroot=/', ] + if '+lto' in spec: + configure_args.append('--enable-lto') + + if '+ld' in spec: + configure_args.append('--enable-ld') + + if '+interwork' in spec: + configure_args.append('--enable-interwork') + if '+gold' in spec: configure_args.append('--enable-gold') From 05b7ec48c5d38b70e4bcd010979869302032cb81 Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Sun, 29 Mar 2020 23:05:24 -0500 Subject: [PATCH 282/377] Add additional config options to gdb (#15754) --- var/spack/repos/builtin/packages/gdb/package.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py index 355f59cbdf4..e6aef7d6719 100644 --- a/var/spack/repos/builtin/packages/gdb/package.py +++ b/var/spack/repos/builtin/packages/gdb/package.py @@ -34,6 +34,10 @@ class Gdb(AutotoolsPackage, GNUMirrorPackage): variant('python', default=True, description='Compile with Python support') variant('xz', default=True, description='Compile with lzma support') variant('source-highlight', default=False, description='Compile with source-highlight support') + variant('lto', default=False, description='Enable lto') + variant('quad', default=False, description='Enable quad') + variant('gold', default=False, description='Enable gold linker') + variant('ld', default=False, description='Enable ld') # Required dependency depends_on('texinfo', type='build') @@ -51,4 +55,17 @@ def configure_args(self): args.append('--with-python') args.append('LDFLAGS={0}'.format( self.spec['python'].libs.ld_flags)) + + if '+lto' in self.spec: + args.append('--enable-lto') + + if '+quad' in self.spec: + args.append('--with-quad') + + if '+gold' in self.spec: + args.append('--enable-gold') + + if '+ld' in self.spec: + args.append('--enable-ld') + return args From e9d573d1101002b127d5c789d86d3c1e92d81309 Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Mon, 30 Mar 2020 08:14:07 -0500 Subject: [PATCH 283/377] package: add additional configuration options to lmod (#15682) * Add further configuration options * Convert auto-swap to auto_swap. Might eventually switch to key-value pair instead. --- .../repos/builtin/packages/lmod/package.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py index cf22c80aa27..2f12d47587d 100644 --- a/var/spack/repos/builtin/packages/lmod/package.py +++ b/var/spack/repos/builtin/packages/lmod/package.py @@ -46,6 +46,9 @@ class Lmod(AutotoolsPackage): depends_on('lua-luafilesystem', type=('build', 'run')) depends_on('tcl', type=('build', 'link', 'run')) + variant('auto_swap', default=False, description='Enable auto swapping conflicting modules') + variant('redirect', default=True, description='Enables redirect instead of pager') + patch('fix_tclsh_paths.patch', when='@:6.4.3') patch('0001-fix-problem-with-MODULESHOME-and-issue-271.patch', when='@7.3.28:7.4.10') @@ -65,3 +68,18 @@ def patch(self): if self.spec.version <= Version('6.4.3'): for tclscript in glob('src/*.tcl'): filter_file(r'^#!.*tclsh', '#!@path_to_tclsh@', tclscript) + + def configure_args(self): + args = [] + + if '+auto_swap' in self.spec: + args.append('--with-autoSwap=yes') + else: + args.append('--with-autoSwap=no') + + if '+redirect' in self.spec: + args.append('--with-redirect=yes') + else: + args.append('--with-redirect=no') + + return args From 605b7b5d23968d80dc1b045babc4866db8792f58 Mon Sep 17 00:00:00 2001 From: Fabian Brandt Date: Mon, 30 Mar 2020 15:17:21 +0200 Subject: [PATCH 284/377] New package: libnetworkit (#15714) * New package libnetworkit * Fixed artificial dependency restriction --- ...-Name-agnostic-import-of-tlx-library.patch | 17 +++++++ .../builtin/packages/libnetworkit/package.py | 44 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 var/spack/repos/builtin/packages/libnetworkit/0001-Name-agnostic-import-of-tlx-library.patch create mode 100644 var/spack/repos/builtin/packages/libnetworkit/package.py diff --git a/var/spack/repos/builtin/packages/libnetworkit/0001-Name-agnostic-import-of-tlx-library.patch b/var/spack/repos/builtin/packages/libnetworkit/0001-Name-agnostic-import-of-tlx-library.patch new file mode 100644 index 00000000000..900a298d9b4 --- /dev/null +++ b/var/spack/repos/builtin/packages/libnetworkit/0001-Name-agnostic-import-of-tlx-library.patch @@ -0,0 +1,17 @@ +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -203,10 +203,11 @@ if(NOT NETWORKIT_EXT_TLX) + "Please run `git submodule update --init` to fetch the submodule.") + endif() + else() ++ file(GLOB tlx_path ${NETWORKIT_EXT_TLX}/lib/**.a) + add_library(tlx STATIC IMPORTED) + set_target_properties(tlx PROPERTIES +- IMPORTED_LOCATION "${NETWORKIT_EXT_TLX}/lib/libtlx.a" +- INTERFACE_INCLUDE_DIRECTORIES "${NETWORKIT_EXT_TLX}/include/") ++ IMPORTED_LOCATION "${tlx_path}" ++ INTERFACE_INCLUDE_DIRECTORIES "${NETWORKIT_EXT_TLX}/include/") + endif() + + ################################################################################ + diff --git a/var/spack/repos/builtin/packages/libnetworkit/package.py b/var/spack/repos/builtin/packages/libnetworkit/package.py new file mode 100644 index 00000000000..5d7f58eb906 --- /dev/null +++ b/var/spack/repos/builtin/packages/libnetworkit/package.py @@ -0,0 +1,44 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Libnetworkit(CMakePackage): + """NetworKit is a growing open-source toolkit for large-scale network + analysis. Its aim is to provide tools for the analysis of large networks + in the size range from thousands to billions of edges. For this purpose, + it implements efficient graph algorithms, many of them parallel to + utilize multicore architectures. These are meant to compute standard + measures of network analysis, such as degree sequences, clustering + coefficients, and centrality measures. In this respect, NetworKit is + comparable to packages such as NetworkX, albeit with a focus on + parallelism and scalability.""" + + homepage = "https://networkit.github.io/" + url = "https://github.com/networkit/networkit/archive/6.1.tar.gz" + + maintainers = ['fabratu'] + + version('6.1', sha256='22c953ea1054c356663b31c77114c2f0c8fec17e0e707aeec23026241beab9b2') + + variant('static', default=False, description='Enables the build of shared libraries') + variant('doc', default=False, description='Enables the build with sphinx documentation') + + depends_on('libtlx') + depends_on('py-sphinx', when='+doc', type='build') + + patch('0001-Name-agnostic-import-of-tlx-library.patch', when='@6.1') + + def cmake_args(self): + spec = self.spec + + tlx_libs = spec['libtlx'].prefix + + args = ['-DNETWORKIT_EXT_TLX=%s' % tlx_libs, + '-DNETWORKIT_STATIC=%s' % + ('ON' if '+static' in spec else 'OFF')] + + return args From abdada03a88b28bfdfe0698a99a977eea4c54bd8 Mon Sep 17 00:00:00 2001 From: Hadrien G Date: Mon, 30 Mar 2020 17:48:36 +0200 Subject: [PATCH 285/377] Add ACTS v0.20 and take move to GitHub into account (#15757) --- var/spack/repos/builtin/packages/acts-core/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/acts-core/package.py b/var/spack/repos/builtin/packages/acts-core/package.py index d6e328352bc..d0c9498d404 100644 --- a/var/spack/repos/builtin/packages/acts-core/package.py +++ b/var/spack/repos/builtin/packages/acts-core/package.py @@ -30,10 +30,11 @@ class ActsCore(CMakePackage): """ homepage = "http://acts.web.cern.ch/ACTS/" - git = "https://gitlab.cern.ch/acts/acts-core.git" + git = "https://github.com/acts-project/acts.git" maintainers = ['HadrienG2'] version('develop', branch='master') + version('0.20.0', commit='1d37a849a9c318e8ca4fa541ef8433c1f004637b') version('0.19.0', commit='408335636486c421c6222a64372250ef12544df6') version('0.18.0', commit='d58a68cf75b52a5e0f563bc237f09250aa9da80c') version('0.17.0', commit='0789f654ff484b013fd27e5023cf342785ea8d97') From 8d1e88658dfc8b0d830a15cbff27d4e3cbcee9dc Mon Sep 17 00:00:00 2001 From: Robert Pavel Date: Mon, 30 Mar 2020 10:56:23 -0600 Subject: [PATCH 286/377] Aded Option to Disable Shared Lua library Generation (#15758) * Aded Option to Disable Shared Lua library Added option to disable generation of shared object library for lua to avoid build issues on static only platforms * Fixed Flake8 Issue with Lua Spackage Fixed indentation issue with lua spackage --- var/spack/repos/builtin/packages/lua/package.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py index ea6265e28a0..c8fe652c39d 100644 --- a/var/spack/repos/builtin/packages/lua/package.py +++ b/var/spack/repos/builtin/packages/lua/package.py @@ -27,6 +27,9 @@ class Lua(Package): version('5.1.4', sha256='b038e225eaf2a5b57c9bcc35cd13aa8c6c8288ef493d52970c9545074098af3a') version('5.1.3', sha256='6b5df2edaa5e02bf1a2d85e1442b2e329493b30b0c0780f77199d24f087d296d') + variant('shared', default=True, + description='Builds a shared version of the library') + extendable = True depends_on('ncurses') @@ -58,10 +61,11 @@ def install(self, spec, prefix): make('INSTALL_TOP=%s' % prefix, 'install') - static_to_shared_library(join_path(prefix.lib, 'liblua.a'), - arguments=['-lm', '-ldl'], - version=self.version, - compat_version=self.version.up_to(2)) + if '+shared' in spec: + static_to_shared_library(join_path(prefix.lib, 'liblua.a'), + arguments=['-lm', '-ldl'], + version=self.version, + compat_version=self.version.up_to(2)) # compatibility with ax_lua.m4 from autoconf-archive # https://www.gnu.org/software/autoconf-archive/ax_lua.html From 0c7fff60651ce3c129551e1c1657ccc80ee816f8 Mon Sep 17 00:00:00 2001 From: Amjad Kotobi Date: Mon, 30 Mar 2020 18:56:40 +0200 Subject: [PATCH 287/377] Update git version to 2.26.0 (#15756) * Update git version to 2.26.0 * Fix1 --- var/spack/repos/builtin/packages/git/package.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index ba842587e24..7b92fb65454 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -24,6 +24,11 @@ class Git(AutotoolsPackage): # You can find the source here: https://mirrors.edge.kernel.org/pub/software/scm/git/sha256sums.asc releases = [ + { + 'version': '2.26.0', + 'sha256': 'aa168c2318e7187cd295a645f7370cc6d71a324aafc932f80f00c780b6a26bed', + 'sha256_manpages': 'c1ffaf0b4cd1e80a0eb0d4039e208c9d411ef94d5da44e38363804e1a7961218' + }, { 'version': '2.25.0', 'sha256': 'a98c9b96d91544b130f13bf846ff080dda2867e77fe08700b793ab14ba5346f6', From 6747ecde166fee0b1d82eb826f3421cc2cf7468b Mon Sep 17 00:00:00 2001 From: Andrew W Elble Date: Mon, 30 Mar 2020 15:58:57 -0400 Subject: [PATCH 288/377] py-onnx: depends on cmake >= 3.1 (#15762) * py-onnx: depends on cmake >= 3.1 * Update var/spack/repos/builtin/packages/py-onnx/package.py Co-Authored-By: Adam J. Stewart Co-authored-by: Adam J. Stewart --- var/spack/repos/builtin/packages/py-onnx/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/py-onnx/package.py b/var/spack/repos/builtin/packages/py-onnx/package.py index c6401d8b007..b92e910db27 100644 --- a/var/spack/repos/builtin/packages/py-onnx/package.py +++ b/var/spack/repos/builtin/packages/py-onnx/package.py @@ -28,6 +28,7 @@ class PyOnnx(PythonPackage): depends_on('py-six', type=('build', 'run')) depends_on('py-typing@3.6.4:', type=('build', 'run')) depends_on('py-typing-extensions@3.6.4:', type=('build', 'run')) + depends_on('cmake@3.1:', type='build') # 'python_out' does not recognize dllexport_decl. patch('remove_dllexport_decl.patch', when='@:1.6.0') From ccc7c9b86de790dd268b530e1cfa7336b596fd04 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 30 Mar 2020 16:09:17 -0500 Subject: [PATCH 289/377] py-horovod: fix compilation of ~cuda (#15719) * py-horovod: fix compilation of ~cuda * Rewrite py-horovod with only 3 variants * Add upstream patch to workaround compilation issue --- .../builtin/packages/py-horovod/fma.patch | 52 +++++++ .../builtin/packages/py-horovod/package.py | 136 ++++++++++-------- 2 files changed, 125 insertions(+), 63 deletions(-) create mode 100644 var/spack/repos/builtin/packages/py-horovod/fma.patch diff --git a/var/spack/repos/builtin/packages/py-horovod/fma.patch b/var/spack/repos/builtin/packages/py-horovod/fma.patch new file mode 100644 index 00000000000..13ccb8c9c5d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-horovod/fma.patch @@ -0,0 +1,52 @@ +From 717e72f91f02d1dc3c859719ef1d804b10f88017 Mon Sep 17 00:00:00 2001 +From: Nicolas V Castet +Date: Mon, 30 Mar 2020 12:47:50 -0500 +Subject: [PATCH] Add extra preprocessor guard for FMA optimization + +Fixes #1832 + +Signed-off-by: Nicolas V Castet +--- + horovod/common/ops/adasum/adasum.h | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/horovod/common/ops/adasum/adasum.h b/horovod/common/ops/adasum/adasum.h +index 0330f5850..876f7f12b 100644 +--- a/horovod/common/ops/adasum/adasum.h ++++ b/horovod/common/ops/adasum/adasum.h +@@ -19,7 +19,7 @@ + #include + #include + +-#if __AVX__ && __F16C__ ++#if __AVX__ && __F16C__ && __FMA__ + #include + #include + #endif +@@ -104,7 +104,7 @@ template class Adasum { + int count, double& dotProduct, + double& anormsq, double& bnormsq, + int layerid) { +-#if __AVX__ && __F16C__ ++#if __AVX__ && __F16C__ && __FMA__ + if (horovod_datatype == DataType::HOROVOD_FLOAT16) { + ComputeDotAndNormSqrdsfp16((uint16_t*)a, (uint16_t*)b, count, dotProduct, + anormsq, bnormsq, layerid); +@@ -125,7 +125,7 @@ template class Adasum { + double acoeff, void* __restrict__ a, + double bcoeff, void* __restrict__ b, + int layerid) { +-#if __AVX__ && __F16C__ ++#if __AVX__ && __F16C__ && __FMA__ + if (horovod_datatype == DataType::HOROVOD_FLOAT16) { + ScaledAddfp16(count, acoeff, (uint16_t*)a, bcoeff, (uint16_t*)b, layerid); + } else +@@ -425,7 +425,7 @@ template class Adasum { + } + + +-#if __AVX__ && __F16C__ ++#if __AVX__ && __F16C__ && __FMA__ + inline void ComputeDotAndNormSqrdsfp16(const uint16_t* __restrict__ a, + const uint16_t* __restrict__ b, + int len, double& dotProduct, diff --git a/var/spack/repos/builtin/packages/py-horovod/package.py b/var/spack/repos/builtin/packages/py-horovod/package.py index 598e01c6f91..c740486853d 100644 --- a/var/spack/repos/builtin/packages/py-horovod/package.py +++ b/var/spack/repos/builtin/packages/py-horovod/package.py @@ -25,96 +25,106 @@ class PyHorovod(PythonPackage): version('0.16.3', tag='v0.16.3', submodules=True) version('0.16.2', tag='v0.16.2', submodules=True) - # Deep learning frameworks - variant('pytorch', default=True, description='Enables PyTorch') - variant('tensorflow', default=False, description='Enables TensorFlow') - variant('mxnet', default=False, description='Enables Apache MXNet') - - # Distributed support - variant('gloo', default=False, description='Enables features related to distributed support') - variant('mpi', default=True, description='Enables MPI build') - - # GPU support - variant('cuda', default=True, description='Enables CUDA build') - variant('gpu_allreduce', default='mpi', - description='Backend to use for GPU_ALLREDUCE', - values=('mpi', 'nccl'), multi=False) # DDL support is deprecated - variant('gpu_allgather', default='mpi', - description='Backend to use for GPU_ALLGATHER', - values=('mpi',), multi=False) - variant('gpu_broadcast', default='mpi', - description='Backend to use for GPU_BROADCAST', - values=('mpi', 'nccl'), multi=False) + # https://github.com/horovod/horovod/blob/master/docs/install.rst + variant('frameworks', default='pytorch', + description='Deep learning frameworks to build support for', + values=('tensorflow', 'pytorch', 'mxnet', 'keras', 'spark'), + multi=True) + variant('controllers', default='mpi', + description='Controllers to coordinate work between processes', + values=('mpi', 'gloo'), multi=True) + variant('tensor_ops', default='nccl', + description='Framework to use for GPU/CPU operations', + values=('nccl', 'mpi', 'gloo', 'ccl'), multi=False) # Required dependencies - depends_on('py-setuptools', type='build') + depends_on('py-setuptools', type='build') depends_on('py-cloudpickle', type=('build', 'run')) - depends_on('py-psutil', type=('build', 'run')) - depends_on('py-pyyaml', type=('build', 'run')) - depends_on('py-six', type=('build', 'run')) + depends_on('py-psutil', type=('build', 'run')) + depends_on('py-pyyaml', type=('build', 'run')) + depends_on('py-six', type=('build', 'run')) - # Deep learning frameworks - depends_on('py-torch@0.4.0:', type=('build', 'run'), when='+pytorch') - depends_on('py-torch+cuda', type=('build', 'run'), when='+pytorch+cuda') - depends_on('py-cffi@1.4.0:', type=('build', 'run'), when='+pytorch') - depends_on('py-tensorflow@1.1.0:', type=('build', 'link', 'run'), when='+tensorflow') - depends_on('mxnet@1.4.0:+python', type=('build', 'link', 'run'), when='+mxnet') - depends_on('mxnet+cuda', type=('build', 'link', 'run'), when='+mxnet+cuda') + # Framework dependencies + depends_on('py-tensorflow@1.1.0:', type=('build', 'link', 'run'), when='frameworks=tensorflow') + depends_on('py-torch@0.4.0:', type=('build', 'run'), when='frameworks=pytorch') + depends_on('py-torchvision', type=('build', 'run'), when='frameworks=pytorch') + depends_on('py-cffi@1.4.0:', type=('build', 'run'), when='frameworks=pytorch') + depends_on('mxnet@1.4.1:+python', type=('build', 'link', 'run'), when='frameworks=mxnet') + depends_on('py-keras@2.0.8,2.1.2:', type=('build', 'run'), when='frameworks=keras') + depends_on('py-h5py@2.9:', type=('build', 'run'), when='frameworks=spark') + depends_on('py-numpy', type=('build', 'run'), when='frameworks=spark') + depends_on('py-petastorm@0.8.2', type=('build', 'run'), when='frameworks=spark') + depends_on('py-pyarrow@0.15.0:', type=('build', 'run'), when='frameworks=spark') + depends_on('py-pyspark@2.3.2:', type=('build', 'run'), when='frameworks=spark') - # Distributed support + # Controller dependencies + depends_on('mpi', when='controllers=mpi') # There does not appear to be a way to use an external Gloo installation - depends_on('cmake', type='build', when='+gloo') - depends_on('mpi', when='+mpi') - depends_on('mpi', when='gpu_allreduce=mpi') - depends_on('mpi', when='gpu_allgather=mpi') - depends_on('mpi', when='gpu_broadcast=mpi') + depends_on('cmake', type='build', when='controllers=gloo') - # GPU support - depends_on('cuda', when='+cuda') - depends_on('nccl@2.0:', when='gpu_allreduce=nccl') - depends_on('nccl@2.0:', when='gpu_broadcast=nccl') + # Tensor Operations dependencies + depends_on('nccl', when='tensor_ops=nccl') + depends_on('mpi', when='tensor_ops=mpi') + # There does not appear to be a way to use an external Gloo installation + depends_on('cmake', type='build', when='tensor_ops=gloo') # Test dependencies depends_on('py-mock', type='test') depends_on('py-pytest', type='test') depends_on('py-pytest-forked', type='test') - conflicts('+gloo', when='platform=darwin', msg='Gloo cannot be compiled on MacOS') - conflicts('~gloo~mpi', msg='One of Gloo or MPI are required for Horovod to run') - conflicts('~pytorch~tensorflow~mxnet', msg='At least one deep learning backend is required') + conflicts('controllers=gloo', when='platform=darwin', msg='Gloo cannot be compiled on MacOS') + + # https://github.com/horovod/horovod/pull/1835 + patch('fma.patch', when='@0.19.0:0.19.1') def setup_build_environment(self, env): - # Deep learning frameworks - if '~pytorch' in self.spec: - env.set('HOROVOD_WITHOUT_PYTORCH', 1) - if '~tensorflow' in self.spec: + # Frameworks + if 'frameworks=tensorflow' in self.spec: + env.set('HOROVOD_WITH_TENSORFLOW', 1) + else: env.set('HOROVOD_WITHOUT_TENSORFLOW', 1) - if '~mxnet' in self.spec: + if 'frameworks=pytorch' in self.spec: + env.set('HOROVOD_WITH_PYTORCH', 1) + else: + env.set('HOROVOD_WITHOUT_PYTORCH', 1) + if 'frameworks=mxnet' in self.spec: + env.set('HOROVOD_WITH_MXNET', 1) + else: env.set('HOROVOD_WITHOUT_MXNET', 1) - # Distributed support - if '~gloo' in self.spec: - env.set('HOROVOD_WITHOUT_GLOO', 1) - if '+mpi' in self.spec: + # Controllers + if 'controllers=mpi' in self.spec: env.set('HOROVOD_WITH_MPI', 1) else: env.set('HOROVOD_WITHOUT_MPI', 1) + if 'controllers=gloo' in self.spec: + env.set('HOROVOD_WITH_GLOO', 1) + else: + env.set('HOROVOD_WITHOUT_GLOO', 1) + + # Tensor Operations + if 'tensor_ops=nccl' in self.spec: + env.set('HOROVOD_GPU', 'CUDA') - # GPU support - if '+cuda' in self.spec: env.set('HOROVOD_CUDA_HOME', self.spec['cuda'].prefix) env.set('HOROVOD_CUDA_INCLUDE', self.spec['cuda'].headers.directories[0]) env.set('HOROVOD_CUDA_LIB', self.spec['cuda'].libs.directories[0]) - if '^nccl' in self.spec: + env.set('HOROVOD_NCCL_HOME', self.spec['nccl'].prefix) env.set('HOROVOD_NCCL_INCLUDE', self.spec['nccl'].headers.directories[0]) env.set('HOROVOD_NCCL_LIB', self.spec['nccl'].libs.directories[0]) - env.set('HOROVOD_GPU_ALLREDUCE', - self.spec.variants['gpu_allreduce'].value.upper()) - env.set('HOROVOD_GPU_ALLGATHER', - self.spec.variants['gpu_allgather'].value.upper()) - env.set('HOROVOD_GPU_BROADCAST', - self.spec.variants['gpu_broadcast'].value.upper()) - env.set('HOROVOD_ALLOW_MIXED_GPU_IMPL', 1) + + env.set('HOROVOD_GPU_ALLREDUCE', 'NCCL') + env.set('HOROVOD_GPU_BROADCAST', 'NCCL') + else: + env.set('HOROVOD_CPU_OPERATIONS', + self.spec.variants['tensor_ops'].value.upper()) + + @run_after('install') + @on_package_attributes(run_tests=True) + def install_test(self): + horovodrun = Executable(self.prefix.bin.horovodrun) + horovodrun('--check-build') From 3f50b9e08dcd16c71946183376cf58414ea9b958 Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Mon, 30 Mar 2020 14:24:05 -0700 Subject: [PATCH 290/377] CUDA 10.1+ supports ICC 19.0 (#15764) Fix the CUDA-ICC conflict check. Simplify the XL 17 check. --- lib/spack/spack/build_systems/cuda.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/spack/spack/build_systems/cuda.py b/lib/spack/spack/build_systems/cuda.py index 50a7002dbb3..cbee7100496 100644 --- a/lib/spack/spack/build_systems/cuda.py +++ b/lib/spack/spack/build_systems/cuda.py @@ -140,12 +140,12 @@ def cuda_flags(arch_list): conflicts('%intel@16.0:', when='+cuda ^cuda@:8.0.43') conflicts('%intel@17.0:', when='+cuda ^cuda@:8.0.60') conflicts('%intel@18.0:', when='+cuda ^cuda@:9.9') - conflicts('%intel@19.0:', when='+cuda ^cuda@:10.2.89') + conflicts('%intel@19.0:', when='+cuda ^cuda@:10.0') # XL is mostly relevant for ppc64le Linux conflicts('%xl@:12,14:', when='+cuda ^cuda@:9.1') conflicts('%xl@:12,14:15,17:', when='+cuda ^cuda@9.2') - conflicts('%xl@17:', when='+cuda ^cuda@10.0.130:10.2.89') + conflicts('%xl@17:', when='+cuda ^cuda@:10.2.89') # Mac OS X # platform = ' platform=darwin' From 3c18d2a0e8564443b0bbd87e6f394ef821e69661 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 30 Mar 2020 17:44:58 -0500 Subject: [PATCH 291/377] py-torch: make sure unit tests are registered (#15765) --- var/spack/repos/builtin/packages/py-torch/package.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py index c0be1176e42..e1dbdccb6df 100644 --- a/var/spack/repos/builtin/packages/py-torch/package.py +++ b/var/spack/repos/builtin/packages/py-torch/package.py @@ -287,9 +287,11 @@ def enable_or_disable(variant, keyword='USE', var=None, newer=False): enable_or_disable('zstd', newer=True) enable_or_disable('tbb', newer=True) - def test(self): - pass - def install_test(self): with working_dir('test'): python('run_test.py') + + # Tests need to be re-added since `phases` was overridden + run_after('install')( + PythonPackage._run_default_install_time_test_callbacks) + run_after('install')(PythonPackage.sanity_check_prefix) From a96b7427971591e24011fd73ddf498331bbc6ab6 Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Mon, 30 Mar 2020 19:50:29 -0500 Subject: [PATCH 292/377] Balay/petsc 3.13.0 (#15767) * petsc: add 3.13.0 (using petsc-lite) and 3.12.5 * petsc@3.13.0: update hdf5 and superlu-dist dependencies * flake8 fix * fixes for comments Co-authored-by: Jed Brown --- .../repos/builtin/packages/petsc/package.py | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py index 577f53a1636..6c5ab4a5641 100644 --- a/var/spack/repos/builtin/packages/petsc/package.py +++ b/var/spack/repos/builtin/packages/petsc/package.py @@ -16,14 +16,15 @@ class Petsc(Package): """ homepage = "http://www.mcs.anl.gov/petsc/index.html" - url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz" - git = "https://gitlab.com/petsc/petsc.git" - + url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.13.0.tar.gz" + git = "https://gitlab.com/petsc/petsc.git" maintainers = ['balay', 'barrysmith', 'jedbrown'] version('develop', branch='master') version('xsdk-0.2.0', tag='xsdk-0.2.0') + version('3.13.0', sha256='f0ea543a54145c5d1387e25b121c3fd1b1ca834032c5a33f6f1d929e95bdf0e5') + version('3.12.5', sha256='d676eb67e79314d6cca6422d7c477d2b192c830b89d5edc6b46934f7453bcfc0') version('3.12.4', sha256='56a941130da93bbacb3cfa74dcacea1e3cd8e36a0341f9ced09977b1457084c3') version('3.12.3', sha256='91f77d7b0f54056f085b9e27938922db3d9bb1734a2e2a6d26f43d3e6c0cf631') version('3.12.2', sha256='d874b2e198c4cb73551c2eca1d2c5d27da710be4d00517adb8f9eb3d6d0375e8') @@ -146,7 +147,8 @@ class Petsc(Package): depends_on('metis@5:~int64', when='@3.8:+metis~int64') depends_on('metis@5:+int64', when='@3.8:+metis+int64') - depends_on('hdf5@:1.10.99+mpi+hl+fortran', when='+hdf5+mpi') + depends_on('hdf5@:1.10.99+mpi+hl+fortran', when='@:3.12.99+hdf5+mpi') + depends_on('hdf5+mpi+hl+fortran', when='@3.13:+hdf5+mpi') depends_on('zlib', when='+hdf5') depends_on('parmetis', when='+metis+mpi') depends_on('valgrind', when='+valgrind') @@ -172,6 +174,8 @@ class Petsc(Package): depends_on('superlu-dist@5.4:5.4.99+int64', when='@3.10:3.10.2+superlu-dist+mpi+int64') depends_on('superlu-dist@6.1:6.1.99~int64', when='@3.10.3:3.12.99+superlu-dist+mpi~int64') depends_on('superlu-dist@6.1:6.1.99+int64', when='@3.10.3:3.12.99+superlu-dist+mpi+int64') + depends_on('superlu-dist@6.1:6.3.99~int64', when='@3.13.0:3.13.99+superlu-dist+mpi~int64') + depends_on('superlu-dist@6.1:6.3.99+int64', when='@3.13.0:3.13.99+superlu-dist+mpi+int64') depends_on('superlu-dist@xsdk-0.2.0~int64', when='@xsdk-0.2.0+superlu-dist+mpi~int64') depends_on('superlu-dist@xsdk-0.2.0+int64', when='@xsdk-0.2.0+superlu-dist+mpi+int64') depends_on('superlu-dist@develop~int64', when='@develop+superlu-dist+mpi~int64') @@ -185,6 +189,13 @@ class Petsc(Package): depends_on('suite-sparse', when='+suite-sparse') depends_on('libx11', when='+X') + def url_for_version(self, version): + if version >= Version('3.13.0'): + # petsc-lite tarballs are smaller by skipping docs + return "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-{0}.tar.gz".format(version) + else: + return "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-{0}.tar.gz".format(version) + def mpi_dependent_options(self): if '~mpi' in self.spec: compiler_opts = [ From 8bc6b290e53f26807fee42a23f7a7ba9861d9cdd Mon Sep 17 00:00:00 2001 From: Ryan Mast Date: Mon, 30 Mar 2020 17:50:53 -0700 Subject: [PATCH 293/377] helics: add new package (#15763) * helics: add new package * Remove FIXME boilerplate * Use open @master: verison range for git dependency and remove mpi fix branch version * Add blank line after spack import --- .../repos/builtin/packages/helics/package.py | 105 ++++++++++++++++++ 1 file changed, 105 insertions(+) create mode 100644 var/spack/repos/builtin/packages/helics/package.py diff --git a/var/spack/repos/builtin/packages/helics/package.py b/var/spack/repos/builtin/packages/helics/package.py new file mode 100644 index 00000000000..7aa4a06c466 --- /dev/null +++ b/var/spack/repos/builtin/packages/helics/package.py @@ -0,0 +1,105 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Helics(CMakePackage): + """HELICS is a general-purpose, modular, highly-scalable co-simulation + framework that runs cross-platform (Linux, Windows, and Mac OS X) and + supports both event driven and time series simulation.""" + + homepage = "https://github.com/GMLC-TDC/HELICS" + url = "https://github.com/GMLC-TDC/HELICS/releases/download/v2.4.1/Helics-v2.4.1-source.tar.gz" + git = "https://github.com/GMLC-TDC/HELICS.git" + + maintainers = ['nightlark'] + + version('develop', branch='develop', submodules=True) + version('master', branch='master', submodules=True) + version('2.4.2', sha256='957856f06ed6d622f05dfe53df7768bba8fe2336d841252f5fac8345070fa5cb') + version('2.4.1', sha256='ac077e9efe466881ea366721cb31fb37ea0e72a881a717323ba4f3cdda338be4') + + variant('build_type', default='Release', + description='CMake build type', + values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel')) + variant('apps', default=True, description="Install the HELICS apps") + variant('c_shared', default=True, description="Install the C shared library") + variant('cxx_shared', default=True, description="Install the CXX shared library") + variant('zmq', default=True, description="Enable ZeroMQ core types") + variant('tcp', default=True, description="Enable TCP core types") + variant('udp', default=True, description="Enable UDP core type") + variant('ipc', default=True, description="Enable IPC core type") + variant('inproc', default=True, description="Enable in-process core type") + variant('mpi', default=False, description="Enable MPI core type") + variant('boost', default=True, description="Compile with Boost libraries") + variant('asio', default=True, description="Compile with ASIO libraries") + variant('swig', default=False, description="Build language bindings with SWIG") + variant('webserver', default=True, description="Enable the integrated webserver in the HELICS broker server") + + # Build dependency + depends_on('git', type='build', when='@master:') + depends_on('cmake@3.4:', type='build') + depends_on('boost@1.70: ~atomic ~chrono ~date_time ~exception ~filesystem ~graph ~iostreams ~locale ~log ~math ~program_options ~random ~regex ~serialization ~signals ~system ~test ~thread ~timer ~wave', type='build', when='+boost') + depends_on('swig@3.0:', type='build', when='+swig') + + depends_on('libzmq@4.3:', when='+zmq') + depends_on('mpi@2', when='+mpi') + + # OpenMPI doesn't work with HELICS <=2.4.1 + conflicts('^openmpi', when='@:2.4.1 +mpi') + + # Boost is required for ipc and webserver options + conflicts('+ipc', when='~boost') + conflicts('+webserver', when='~boost') + + # ASIO (vendored in HELICS repo) is required for tcp and udp options + conflicts('+tcp', when='~asio') + conflicts('+udp', when='~asio') + + def cmake_args(self): + spec = self.spec + args = [ + '-DHELICS_BUILD_EXAMPLES=OFF', + '-DHELICS_BUILD_TESTS=OFF', + ] + + # HELICS core type CMake options + args.append('-DENABLE_ZMQ_CORE={0}'.format( + 'ON' if '+zmq' in spec else 'OFF')) + args.append('-DENABLE_TCP_CORE={0}'.format( + 'ON' if '+tcp' in spec else 'OFF')) + args.append('-DENABLE_UDP_CORE={0}'.format( + 'ON' if '+udp' in spec else 'OFF')) + args.append('-DENABLE_IPC_CORE={0}'.format( + 'ON' if '+ipc' in spec else 'OFF')) + args.append('-DENABLE_INPROC_CORE={0}'.format( + 'ON' if '+inproc' in spec else 'OFF')) + args.append('-DENABLE_MPI_CORE={0}'.format( + 'ON' if '+mpi' in spec else 'OFF')) + + # HELICS shared library options + args.append('-DHELICS_DISABLE_C_SHARED_LIB={0}'.format( + 'OFF' if '+c_shared' in spec else 'ON')) + args.append('-DHELICS_BUILD_CXX_SHARED_LIB={0}'.format( + 'ON' if '+cxx_shared' in spec else 'OFF')) + + # HELICS executable app options + args.append('-DHELICS_BUILD_APP_EXECUTABLES={0}'.format( + 'ON' if '+apps' in spec else 'OFF')) + args.append('-DHELICS_DISABLE_WEBSERVER={0}'.format( + 'OFF' if '+webserver' in spec else 'ON')) + + # Extra HELICS library dependencies + args.append('-DHELICS_DISABLE_BOOST={0}'.format( + 'OFF' if '+boost' in spec else 'ON')) + args.append('-DHELICS_DISABLE_ASIO={0}'.format( + 'OFF' if '+asio' in spec else 'ON')) + + # SWIG + args.append('-DHELICS_ENABLE_SWIG={0}'.format( + 'ON' if '+swig' in spec else 'OFF')) + + return args From 864960937dfdc7e65faba99fd12ece6578b0b490 Mon Sep 17 00:00:00 2001 From: Satish Balay Date: Mon, 30 Mar 2020 19:52:31 -0500 Subject: [PATCH 294/377] superlu-dist: add new version 6.3.0 (#15766) --- var/spack/repos/builtin/packages/superlu-dist/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py index 989158356d8..799b413f7d3 100644 --- a/var/spack/repos/builtin/packages/superlu-dist/package.py +++ b/var/spack/repos/builtin/packages/superlu-dist/package.py @@ -18,6 +18,7 @@ class SuperluDist(CMakePackage): version('develop', branch='master') version('xsdk-0.2.0', tag='xsdk-0.2.0') + version('6.3.0', sha256='daf3264706caccae2b8fd5a572e40275f1e128fa235cb7c21ee2f8051c11af95') version('6.1.1', sha256='35d25cff592c724439870444ed45e1d1d15ca2c65f02ccd4b83a6d3c9d220bd1') version('6.1.0', sha256='92c6d1424dd830ee2d1e7396a418a5f6645160aea8472e558c4e4bfe006593c4') version('6.0.0', sha256='ff6cdfa0263d595708bbb6d11fb780915d8cfddab438db651e246ea292f37ee4') From 628516c7611126f2a1b1f72d57e4cfd95535cf30 Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Tue, 31 Mar 2020 13:02:14 +0900 Subject: [PATCH 295/377] ppOpen-APPL/FVM: new package. (#15772) * ppOpen-APPL/FVM: new package. * copy_tree -> install_tree. --- .../packages/ppopen-appl-fvm/package.py | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ppopen-appl-fvm/package.py diff --git a/var/spack/repos/builtin/packages/ppopen-appl-fvm/package.py b/var/spack/repos/builtin/packages/ppopen-appl-fvm/package.py new file mode 100644 index 00000000000..2dd6872cc29 --- /dev/null +++ b/var/spack/repos/builtin/packages/ppopen-appl-fvm/package.py @@ -0,0 +1,63 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * +import os + + +class PpopenApplFvm(MakefilePackage): + """ + ppOpen-APPL/FVM ia a coupling library that enables weak + coupling on various simulation models, such as an + atmospheric model and an ocean model, a seismic model + and a structure model. For getting very wide + applicability, ppohMATHMP is designed so as that it is + independent from grid structure. Instead of grid + structure, ppOpen-APPL/FVM requires a data set + called 'mapping table'. Mapping table is composed of + a correspondence table of grid indexes between a send + model and a receive model and interpolation coefficients. + A subroutine for making a mapping table file is provided + by ppohMATHMP API. + + Current version of ppohMATHMP is ver.1.0 which targets + scalar data exchange. An exchange code of vector data + which requires rotation calculation is under + """ + + homepage = "http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/" + url = "file://{0}/ppohFVM_0.3.0.tar.gz".format(os.getcwd()) + + version('0.3.0', sha256='4e05dd71f4eeda62c9683b7c3069a2537f3c2c7e86ba50a00d4963f41d9cbe29') + + depends_on('mpi') + depends_on('metis@:4') + + def edit(self, spec, prefix): + fflags = ['-O3'] + if spec.satisfies('%gcc'): + fflags.append('-ffree-line-length-none') + makefile_in = FileFilter('Makefile.in') + makefile_in.filter( + r'^PREFIX *=.*$', + 'PREFIX = {0}'.format(prefix) + ) + makefile_in.filter( + r'^METISDIR *=.*$', + 'METISDIR = {0}'.format(spec['metis'].prefix.lib) + ) + makefile_in.filter('mpifrtpx', spec['mpi'].mpifc) + makefile_in.filter('frtpx', spack_fc) + makefile_in.filter('-Kfast', ' '.join(fflags)) + makefile_in.filter( + ',openmp', + ' {0}'.format(self.compiler.openmp_flag) + ) + + def install(self, spec, prefix): + make('install') + install_tree('examples', prefix.examples) + install_tree('doc', prefix.doc) From 77e13849026b9b177c27fcaefd134dd32e4329e4 Mon Sep 17 00:00:00 2001 From: Ben Morgan Date: Tue, 31 Mar 2020 09:54:31 +0100 Subject: [PATCH 296/377] geant4: new version 10.6 plus simplifications (#15447) * geant4: new version 10.6 plus simplifications Add new 10.6.0 release, migrating download of source to use Geant4's public release repo on CERN GitLab. Change versioning scheme to use clearer and standard semantic scheme. Update geant4-data and g4XXX data packages with new versions. Migrate geant4-data as a BundlePackage of the g4XXX packages, installing links to each under a single directory under share for geant4-data. Ensure each g4XXX package exports the environment variable pointing to its location expected by Geant4. Remove "data" variant from Geant4 package and always use geant4-data. Simplify cxxstd variant transport to dependencies. * g4: Use self to resolve correct prefix * geant4, data: Fix flake8 errors * g4photonevaporation: flake8 fix * geant4: vecgeom version depends_on Geant4 major.minor versions have specific dependencies on vecgeom versions. Add missing vecgeom version for geant4 10.5, and match version requirements for vecgeom in geant4 depends_on. * geant4: c++17 patch specific for 10.4.3 * geant4: simplify geant4-data setup * geant4: Use new define_from_variant function * geant4: fix flake8 errors --- .../repos/builtin/packages/g4abla/package.py | 13 +- .../repos/builtin/packages/g4emlow/package.py | 17 +- .../builtin/packages/g4ensdfstate/package.py | 7 +- .../repos/builtin/packages/g4incl/package.py | 34 ++++ .../repos/builtin/packages/g4ndl/package.py | 6 + .../builtin/packages/g4neutronxs/package.py | 7 + .../builtin/packages/g4particlexs/package.py | 35 ++++ .../packages/g4photonevaporation/package.py | 11 +- .../repos/builtin/packages/g4pii/package.py | 6 + .../packages/g4radioactivedecay/package.py | 14 +- .../builtin/packages/g4realsurface/package.py | 10 +- .../builtin/packages/g4saiddata/package.py | 7 + .../repos/builtin/packages/g4tendl/package.py | 8 +- .../builtin/packages/geant4-data/package.py | 151 ++++++++------- ...geant4-10.4.3-cxx17-removed-features.patch | 18 ++ .../repos/builtin/packages/geant4/package.py | 176 ++++++++---------- .../repos/builtin/packages/vecgeom/package.py | 1 + 17 files changed, 328 insertions(+), 193 deletions(-) create mode 100644 var/spack/repos/builtin/packages/g4incl/package.py create mode 100644 var/spack/repos/builtin/packages/g4particlexs/package.py create mode 100644 var/spack/repos/builtin/packages/geant4/geant4-10.4.3-cxx17-removed-features.patch diff --git a/var/spack/repos/builtin/packages/g4abla/package.py b/var/spack/repos/builtin/packages/g4abla/package.py index b14f88d4d91..bed114d825b 100644 --- a/var/spack/repos/builtin/packages/g4abla/package.py +++ b/var/spack/repos/builtin/packages/g4abla/package.py @@ -11,12 +11,12 @@ class G4abla(Package): """Geant4 data for nuclear shell effects in INCL/ABLA hadronic mode""" homepage = "http://geant4.web.cern.ch" url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4ABLA.3.0.tar.gz" + maintainers = ['drbenmorgan'] - version( - '3.0', sha256='99fd4dcc9b4949778f14ed8364088e45fa4ff3148b3ea36f9f3103241d277014') - version( - '3.1', sha256='7698b052b58bf1b9886beacdbd6af607adc1e099fc730ab6b21cf7f090c027ed') + # Only versions relevant to Geant4 releases built by spack are added + version('3.1', sha256='7698b052b58bf1b9886beacdbd6af607adc1e099fc730ab6b21cf7f090c027ed') + version('3.0', sha256='99fd4dcc9b4949778f14ed8364088e45fa4ff3148b3ea36f9f3103241d277014') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) @@ -24,6 +24,11 @@ def install(self, spec, prefix): .format(self.version)) install_tree(self.stage.source_path, install_path) + def setup_dependent_run_environment(self, env, dependent_spec): + install_path = join_path(self.prefix.share, 'data', 'G4ABLA{0}' + .format(self.version)) + env.set('G4ABLADATA', install_path) + def url_for_version(self, version): """Handle version string.""" return ("http://geant4-data.web.cern.ch/geant4-data/datasets/G4ABLA.%s.tar.gz" % version) diff --git a/var/spack/repos/builtin/packages/g4emlow/package.py b/var/spack/repos/builtin/packages/g4emlow/package.py index df6af19e262..713b9da6311 100644 --- a/var/spack/repos/builtin/packages/g4emlow/package.py +++ b/var/spack/repos/builtin/packages/g4emlow/package.py @@ -11,12 +11,14 @@ class G4emlow(Package): """Geant4 data files for low energy electromagnetic processes.""" homepage = "http://geant4.web.cern.ch" url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4EMLOW.6.50.tar.gz" + maintainers = ['drbenmorgan'] - version( - '6.50', sha256='c97be73fece5fb4f73c43e11c146b43f651c6991edd0edf8619c9452f8ab1236') - version( - '7.3', sha256='583aa7f34f67b09db7d566f904c54b21e95a9ac05b60e2bfb794efb569dba14e') + # Only versions relevant to Geant4 releases built by spack are added + version('7.9', sha256='4abf9aa6cda91e4612676ce4d2d8a73b91184533aa66f9aad19a53a8c4dc3aff') + version('7.7', sha256='16dec6adda6477a97424d749688d73e9bd7d0b84d0137a67cf341f1960984663') + version('7.3', sha256='583aa7f34f67b09db7d566f904c54b21e95a9ac05b60e2bfb794efb569dba14e') + version('6.50', sha256='c97be73fece5fb4f73c43e11c146b43f651c6991edd0edf8619c9452f8ab1236') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) @@ -24,6 +26,11 @@ def install(self, spec, prefix): .format(self.version)) install_tree(self.stage.source_path, install_path) + def setup_dependent_run_environment(self, env, dependent_spec): + install_path = join_path(self.prefix.share, 'data', 'G4EMLOW{0}' + .format(self.version)) + env.set('G4LEDATA', install_path) + def url_for_version(self, version): """Handle version string.""" - return ("http://geant4.web.cern.ch/support/source/G4EMLOW.%s.tar.gz" % version) + return ("http://geant4-data.web.cern.ch/geant4-data/datasets/G4EMLOW.%s.tar.gz" % version) diff --git a/var/spack/repos/builtin/packages/g4ensdfstate/package.py b/var/spack/repos/builtin/packages/g4ensdfstate/package.py index 06b50b37545..36bc897f4b1 100644 --- a/var/spack/repos/builtin/packages/g4ensdfstate/package.py +++ b/var/spack/repos/builtin/packages/g4ensdfstate/package.py @@ -14,8 +14,9 @@ class G4ensdfstate(Package): maintainers = ['drbenmorgan'] - version('2.1', sha256='933e7f99b1c70f24694d12d517dfca36d82f4e95b084c15d86756ace2a2790d9') + # Only versions relevant to Geant4 releases built by spack are added version('2.2', sha256='dd7e27ef62070734a4a709601f5b3bada6641b111eb7069344e4f99a01d6e0a6') + version('2.1', sha256='933e7f99b1c70f24694d12d517dfca36d82f4e95b084c15d86756ace2a2790d9') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) @@ -24,7 +25,9 @@ def install(self, spec, prefix): install_tree(self.stage.source_path, install_path) def setup_dependent_run_environment(self, env, dependent_spec): - env.set('G4ENSDFSTATEDATA', self.prefix.share.data) + install_path = join_path(self.prefix.share, 'data', 'G4ENSDFSTATE{0}' + .format(self.version)) + env.set('G4ENSDFSTATEDATA', install_path) def url_for_version(self, version): """Handle version string.""" diff --git a/var/spack/repos/builtin/packages/g4incl/package.py b/var/spack/repos/builtin/packages/g4incl/package.py new file mode 100644 index 00000000000..e21010f411a --- /dev/null +++ b/var/spack/repos/builtin/packages/g4incl/package.py @@ -0,0 +1,34 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class G4incl(Package): + """Geant4 data for evaluated particle cross-sections on natural + composition of elements""" + homepage = "http://geant4.web.cern.ch" + url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4INCL.1.0.tar.gz" + + maintainers = ['drbenmorgan'] + + # Only versions relevant to Geant4 releases built by spack are added + version('1.0', sha256='716161821ae9f3d0565fbf3c2cf34f4e02e3e519eb419a82236eef22c2c4367d') + + def install(self, spec, prefix): + mkdirp(join_path(prefix.share, 'data')) + install_path = join_path(prefix.share, 'data', "G4INCL{0}" + .format(self.version)) + install_tree(self.stage.source_path, install_path) + + def setup_dependent_run_environment(self, env, dependent_spec): + install_path = join_path(self.prefix.share, 'data', 'G4INCL{0}' + .format(self.version)) + env.set('G4INCLDATA', install_path) + + def url_for_version(self, version): + """Handle version string.""" + return ("http://geant4-data.web.cern.ch/geant4-data/datasets/G4INCL.%s.tar.gz" % version) \ No newline at end of file diff --git a/var/spack/repos/builtin/packages/g4ndl/package.py b/var/spack/repos/builtin/packages/g4ndl/package.py index 7ab6c9f26dc..3eaad0f101f 100644 --- a/var/spack/repos/builtin/packages/g4ndl/package.py +++ b/var/spack/repos/builtin/packages/g4ndl/package.py @@ -14,6 +14,7 @@ class G4ndl(Package): maintainers = ['drbenmorgan'] + version('4.6', sha256='9d287cf2ae0fb887a2adce801ee74fb9be21b0d166dab49bcbee9408a5145408') version('4.5', sha256='cba928a520a788f2bc8229c7ef57f83d0934bb0c6a18c31ef05ef4865edcdf8e') def install(self, spec, prefix): @@ -22,6 +23,11 @@ def install(self, spec, prefix): .format(self.version)) install_tree(self.stage.source_path, install_path) + def setup_dependent_run_environment(self, env, dependent_spec): + install_path = join_path(self.prefix.share, 'data', 'G4NDL{0}' + .format(self.version)) + env.set('G4NEUTRONHPDATA', install_path) + def url_for_version(self, version): """Handle version string.""" return ("http://geant4-data.web.cern.ch/geant4-data/datasets/G4NDL.%s.tar.gz" % version) diff --git a/var/spack/repos/builtin/packages/g4neutronxs/package.py b/var/spack/repos/builtin/packages/g4neutronxs/package.py index df3de0696cf..41acc423a6f 100644 --- a/var/spack/repos/builtin/packages/g4neutronxs/package.py +++ b/var/spack/repos/builtin/packages/g4neutronxs/package.py @@ -15,6 +15,8 @@ class G4neutronxs(Package): maintainers = ['drbenmorgan'] + # Only versions relevant to Geant4 releases built by spack are added + # Dataset not used after Geant4 10.4.x version('1.4', sha256='57b38868d7eb060ddd65b26283402d4f161db76ed2169437c266105cca73a8fd') def install(self, spec, prefix): @@ -23,6 +25,11 @@ def install(self, spec, prefix): .format(self.version)) install_tree(self.stage.source_path, install_path) + def setup_dependent_run_environment(self, env, dependent_spec): + install_path = join_path(self.prefix.share, 'data', 'G4NEUTRONXS{0}' + .format(self.version)) + env.set('G4NEUTRONXSDATA', install_path) + def url_for_version(self, version): """Handle version string.""" return "http://geant4-data.web.cern.ch/geant4-data/datasets/G4NEUTRONXS.%s.tar.gz" % version diff --git a/var/spack/repos/builtin/packages/g4particlexs/package.py b/var/spack/repos/builtin/packages/g4particlexs/package.py new file mode 100644 index 00000000000..e573025b64e --- /dev/null +++ b/var/spack/repos/builtin/packages/g4particlexs/package.py @@ -0,0 +1,35 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +from spack import * + + +class G4particlexs(Package): + """Geant4 data for evaluated particle cross-sections on + natural composition of elements""" + homepage = "http://geant4.web.cern.ch" + url = "http://geant4-data.web.cern.ch/geant4-data/datasets/G4PARTICLEXS.2.1.tar.gz" + + maintainers = ['drbenmorgan'] + + # Only versions relevant to Geant4 releases built by spack are added + version('2.1', sha256='094d103372bbf8780d63a11632397e72d1191dc5027f9adabaf6a43025520b41') + version('1.1', sha256='100a11c9ed961152acfadcc9b583a9f649dda4e48ab314fcd4f333412ade9d62') + + def install(self, spec, prefix): + mkdirp(join_path(prefix.share, 'data')) + install_path = join_path(prefix.share, 'data', "G4PARTICLEXS{0}" + .format(self.version)) + install_tree(self.stage.source_path, install_path) + + def setup_dependent_run_environment(self, env, dependent_spec): + install_path = join_path(self.prefix.share, 'data', 'G4PARTICLEXS{0}' + .format(self.version)) + env.set('G4PARTICLEXSDATA', install_path) + + def url_for_version(self, version): + """Handle version string.""" + return ("http://geant4-data.web.cern.ch/geant4-data/datasets/G4PARTICLEXS.%s.tar.gz" % version) \ No newline at end of file diff --git a/var/spack/repos/builtin/packages/g4photonevaporation/package.py b/var/spack/repos/builtin/packages/g4photonevaporation/package.py index 4e5c62b9992..93d7f82de42 100644 --- a/var/spack/repos/builtin/packages/g4photonevaporation/package.py +++ b/var/spack/repos/builtin/packages/g4photonevaporation/package.py @@ -14,8 +14,11 @@ class G4photonevaporation(Package): maintainers = ['drbenmorgan'] - version('4.3.2', sha256='d4641a6fe1c645ab2a7ecee09c34e5ea584fb10d63d2838248bfc487d34207c7') + # Only versions relevant to Geant4 releases built by spack are added + version('5.5', sha256='5995dda126c18bd7f68861efde87b4af438c329ecbe849572031ceed8f5e76d7') + version('5.3', sha256='d47ababc8cbe548065ef644e9bd88266869e75e2f9e577ebc36bc55bf7a92ec8') version('5.2', sha256='83607f8d36827b2a7fca19c9c336caffbebf61a359d0ef7cee44a8bcf3fc2d1f') + version('4.3.2', sha256='d4641a6fe1c645ab2a7ecee09c34e5ea584fb10d63d2838248bfc487d34207c7') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) @@ -24,6 +27,12 @@ def install(self, spec, prefix): .format(self.version)) install_tree(self.stage.source_path, install_path) + def setup_dependent_run_environment(self, env, dependent_spec): + install_path = join_path(self.prefix.share, 'data', + 'PhotonEvaporation{0}' + .format(self.version)) + env.set('G4LEVELGAMMADATA', install_path) + def url_for_version(self, version): """Handle version string.""" return ("http://geant4-data.web.cern.ch/geant4-data/datasets/G4PhotonEvaporation.%s.tar.gz" % version) diff --git a/var/spack/repos/builtin/packages/g4pii/package.py b/var/spack/repos/builtin/packages/g4pii/package.py index 2e238a64180..ea91b5b9c92 100644 --- a/var/spack/repos/builtin/packages/g4pii/package.py +++ b/var/spack/repos/builtin/packages/g4pii/package.py @@ -14,6 +14,7 @@ class G4pii(Package): maintainers = ['drbenmorgan'] + # Only versions relevant to Geant4 releases built by spack are added version('1.3', sha256='6225ad902675f4381c98c6ba25fc5a06ce87549aa979634d3d03491d6616e926') def install(self, spec, prefix): @@ -22,6 +23,11 @@ def install(self, spec, prefix): .format(self.version)) install_tree(self.stage.source_path, install_path) + def setup_dependent_run_environment(self, env, dependent_spec): + install_path = join_path(self.prefix.share, 'data', 'G4PII{0}' + .format(self.version)) + env.set('G4PIIDATA', install_path) + def url_for_version(self, version): """Handle version string.""" return ("http://geant4-data.web.cern.ch/geant4-data/datasets/G4PII.1.3.tar.gz" % version) diff --git a/var/spack/repos/builtin/packages/g4radioactivedecay/package.py b/var/spack/repos/builtin/packages/g4radioactivedecay/package.py index c281ff63cdc..6f34e89cea4 100644 --- a/var/spack/repos/builtin/packages/g4radioactivedecay/package.py +++ b/var/spack/repos/builtin/packages/g4radioactivedecay/package.py @@ -14,15 +14,25 @@ class G4radioactivedecay(Package): maintainers = ['drbenmorgan'] - version('5.1.1', sha256='f7a9a0cc998f0d946359f2cb18d30dff1eabb7f3c578891111fc3641833870ae') + # Only versions relevant to Geant4 releases built by spack are added + version('5.4', sha256='240779da7d13f5bf0db250f472298c3804513e8aca6cae301db97f5ccdcc4a61') + version('5.3', sha256='5c8992ac57ae56e66b064d3f5cdfe7c2fee76567520ad34a625bfb187119f8c1') version('5.2', sha256='99c038d89d70281316be15c3c98a66c5d0ca01ef575127b6a094063003e2af5d') + version('5.1.1', sha256='f7a9a0cc998f0d946359f2cb18d30dff1eabb7f3c578891111fc3641833870ae') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) - install_path = join_path(prefix.share, 'data', 'RadioactiveDecay{0}' + install_path = join_path(prefix.share, 'data', + 'RadioactiveDecay{0}' .format(self.version)) install_tree(self.stage.source_path, install_path) + def setup_dependent_run_environment(self, env, dependent_spec): + install_path = join_path(self.prefix.share, 'data', + 'RadioactiveDecay{0}' + .format(self.version)) + env.set('G4RADIOACTIVEDATA', install_path) + def url_for_version(self, version): """Handle version string.""" return ("http://geant4-data.web.cern.ch/geant4-data/datasets/G4RadioactiveDecay.%s.tar.gz" % version) diff --git a/var/spack/repos/builtin/packages/g4realsurface/package.py b/var/spack/repos/builtin/packages/g4realsurface/package.py index b741b61ef88..dee32da8b93 100644 --- a/var/spack/repos/builtin/packages/g4realsurface/package.py +++ b/var/spack/repos/builtin/packages/g4realsurface/package.py @@ -14,9 +14,10 @@ class G4realsurface(Package): maintainers = ['drbenmorgan'] - version('1.0', sha256='3e2d2506600d2780ed903f1f2681962e208039329347c58ba1916740679020b1') - version('2.1', sha256='2a287adbda1c0292571edeae2082a65b7f7bd6cf2bf088432d1d6f889426dcf3') + # Only versions relevant to Geant4 releases built by spack are added version('2.1.1', sha256='90481ff97a7c3fa792b7a2a21c9ed80a40e6be386e581a39950c844b2dd06f50') + version('2.1', sha256='2a287adbda1c0292571edeae2082a65b7f7bd6cf2bf088432d1d6f889426dcf3') + version('1.0', sha256='3e2d2506600d2780ed903f1f2681962e208039329347c58ba1916740679020b1') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) @@ -24,6 +25,11 @@ def install(self, spec, prefix): .format(self.version)) install_tree(self.stage.source_path, install_path) + def setup_dependent_run_environment(self, env, dependent_spec): + install_path = join_path(self.prefix.share, 'data', 'RealSurface{0}' + .format(self.version)) + env.set('G4REALSURFACEDATA', install_path) + def url_for_version(self, version): """Handle version string.""" return "http://geant4-data.web.cern.ch/geant4-data/datasets/{0}RealSurface.{1}.tar.gz".format( diff --git a/var/spack/repos/builtin/packages/g4saiddata/package.py b/var/spack/repos/builtin/packages/g4saiddata/package.py index 7b03177f735..0091d09744d 100644 --- a/var/spack/repos/builtin/packages/g4saiddata/package.py +++ b/var/spack/repos/builtin/packages/g4saiddata/package.py @@ -14,6 +14,8 @@ class G4saiddata(Package): maintainers = ['drbenmorgan'] + # Only versions relevant to Geant4 releases built by spack are added + version('2.0', sha256='1d26a8e79baa71e44d5759b9f55a67e8b7ede31751316a9e9037d80090c72e91') version('1.1', sha256='a38cd9a83db62311922850fe609ecd250d36adf264a88e88c82ba82b7da0ed7f') def install(self, spec, prefix): @@ -22,6 +24,11 @@ def install(self, spec, prefix): .format(self.version)) install_tree(self.stage.source_path, install_path) + def setup_dependent_run_environment(self, env, dependent_spec): + install_path = join_path(self.prefix.share, 'data', 'G4SAIDDATA{0}' + .format(self.version)) + env.set('G4SAIDXSDATA', install_path) + def url_for_version(self, version): """Handle version string.""" return "http://geant4-data.web.cern.ch/geant4-data/datasets/G4SAIDDATA.%s.tar.gz" % version diff --git a/var/spack/repos/builtin/packages/g4tendl/package.py b/var/spack/repos/builtin/packages/g4tendl/package.py index 2a3ecbc0749..aac083f539b 100644 --- a/var/spack/repos/builtin/packages/g4tendl/package.py +++ b/var/spack/repos/builtin/packages/g4tendl/package.py @@ -14,8 +14,9 @@ class G4tendl(Package): maintainers = ['drbenmorgan'] - version('1.3', sha256='52ad77515033a5d6f995c699809b464725a0e62099b5e55bf07c8bdd02cd3bce') + # Only versions relevant to Geant4 releases built by spack are added version('1.3.2', sha256='3b2987c6e3bee74197e3bd39e25e1cc756bb866c26d21a70f647959fc7afb849') + version('1.3', sha256='52ad77515033a5d6f995c699809b464725a0e62099b5e55bf07c8bdd02cd3bce') def install(self, spec, prefix): mkdirp(join_path(prefix.share, 'data')) @@ -23,6 +24,11 @@ def install(self, spec, prefix): .format(self.version)) install_tree(self.stage.source_path, install_path) + def setup_dependent_run_environment(self, env, dependent_spec): + install_path = join_path(self.prefix.share, 'data', 'G4TENDL{0}' + .format(self.version)) + env.set('G4PARTICLEHPDATA', install_path) + def url_for_version(self, version): """Handle version string.""" return ("http://geant4-data.web.cern.ch/geant4-data/datasets/G4TENDL.%s.tar.gz" % version) diff --git a/var/spack/repos/builtin/packages/geant4-data/package.py b/var/spack/repos/builtin/packages/geant4-data/package.py index f5c4e72fac0..4157fb76c6e 100644 --- a/var/spack/repos/builtin/packages/geant4-data/package.py +++ b/var/spack/repos/builtin/packages/geant4-data/package.py @@ -8,90 +8,89 @@ import glob -class Geant4Data(Package): - """An umbrella package to hold Geant4 data packages""" +class Geant4Data(BundlePackage): + """A bundle package to hold Geant4 data packages""" homepage = "http://geant4.cern.ch" - url = "http://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.3.html" maintainers = ['drbenmorgan'] - version('10.03.p03', sha256='3e0d4d4e6854c8667d930fd5beaec09b7e6ec41f4847935e5d6a2720d0094b30', expand=False) - version('10.04', sha256='f67fb899b99348a1a7e471a05f249f972e7e303c78238fc5f693b99968642255', expand=False) + version('10.6.0') + version('10.5.1') + version('10.4.3') + version('10.4.0') + version('10.3.3') - # geant4@10.03.p03 - depends_on("g4abla@3.0", when='@10.03.p03 ') - depends_on("g4emlow@6.50", when='@10.03.p03 ') - depends_on("g4ndl@4.5", when='@10.03.p03 ') - depends_on("g4neutronxs@1.4", when='@10.03.p03 ') - depends_on("g4saiddata@1.1", when='@10.03.p03 ') - depends_on("g4ensdfstate@2.1", when='@10.03.p03 ') - depends_on("g4photonevaporation@4.3.2", when='@10.03.p03 ') - depends_on("g4pii@1.3", when='@10.03.p03 ') - depends_on("g4radioactivedecay@5.1.1", when='@10.03.p03 ') - depends_on("g4realsurface@1.0", when='@10.03.p03 ') - depends_on("g4tendl@1.3", when='@10.03.p03 ') - # geant4@10.04 - depends_on("g4abla@3.1", when='@10.04 ') - depends_on("g4emlow@7.3", when='@10.04 ') - depends_on("g4ndl@4.5", when='@10.04 ') - depends_on("g4neutronxs@1.4", when='@10.04 ') - depends_on("g4saiddata@1.1", when='@10.04 ') - depends_on("g4ensdfstate@2.2", when='@10.04 ') - depends_on("g4photonevaporation@5.2", when='@10.04 ') - depends_on("g4pii@1.3", when='@10.04 ') - depends_on("g4radioactivedecay@5.2", when='@10.04 ') - depends_on("g4realsurface@2.1", when='@10.04 ') - depends_on("g4tendl@1.3.2", when='@10.04 ') + # Add install phase so we can create the data "view" + phases = ['install'] + + # For clarity, declare deps on a Major-Minor version basis as + # they generally don't change on the patch level + # Can move to declaring on a dataset basis if needed + # geant4@10.6.X + depends_on("g4ndl@4.6", when='@10.6.0') + depends_on("g4emlow@7.9", when='@10.6.0') + depends_on("g4photonevaporation@5.5", when='@10.6.0') + depends_on("g4radioactivedecay@5.4", when='@10.6.0') + depends_on("g4particlexs@2.1", when='@10.6.0') + depends_on("g4pii@1.3", when='@10.6.0') + depends_on("g4realsurface@2.1.1", when='@10.6.0') + depends_on("g4saiddata@2.0", when='@10.6.0') + depends_on("g4abla@3.1", when='@10.6.0') + depends_on("g4incl@1.0", when='@10.6.0') + depends_on("g4ensdfstate@2.2", when='@10.6.0') + + # geant4@10.5.X + depends_on("g4ndl@4.5", when='@10.5.0:10.5.9999') + depends_on("g4emlow@7.7", when='@10.5.0:10.5.9999') + depends_on("g4photonevaporation@5.3", when='@10.5.0:10.5.9999') + depends_on("g4radioactivedecay@5.3", when='@10.5.0:10.5.9999') + depends_on("g4particlexs@1.1", when='@10.5.0:10.5.9999') + depends_on("g4pii@1.3", when='@10.5.0:10.5.9999') + depends_on("g4realsurface@2.1.1", when='@10.5.0:10.5.9999') + depends_on("g4saiddata@2.0", when='@10.5.0:10.5.9999') + depends_on("g4abla@3.1", when='@10.5.0:10.5.9999') + depends_on("g4incl@1.0", when='@10.5.0:10.5.9999') + depends_on("g4ensdfstate@2.2", when='@10.5.0:10.5.9999') + + # geant4@10.4.X + depends_on("g4ndl@4.5", when='@10.4.0:10.4.9999') + depends_on("g4emlow@7.3", when='@10.4.0:10.4.9999') + depends_on("g4photonevaporation@5.2", when='@10.4.0:10.4.9999') + depends_on("g4radioactivedecay@5.2", when='@10.4.0:10.4.9999') + depends_on("g4neutronxs@1.4", when='@10.4.0:10.4.9999') + depends_on("g4pii@1.3", when='@10.4.0:10.4.9999') + + depends_on("g4realsurface@2.1.1", when='@10.4.2:10.4.9999') + depends_on("g4realsurface@2.1", when='@10.4.0:10.4.1') + + depends_on("g4saiddata@1.1", when='@10.4.0:10.4.9999') + depends_on("g4abla@3.1", when='@10.4.0:10.4.9999') + depends_on("g4ensdfstate@2.2", when='@10.4.0:10.4.9999') + + # geant4@10.3.X + depends_on("g4ndl@4.5", when='@10.3.0:10.3.9999') + depends_on("g4emlow@6.50", when='@10.3.0:10.3.9999') + + depends_on("g4photonevaporation@4.3.2", when='@10.3.1:10.3.9999') + depends_on("g4photonevaporation@4.3", when='@10.3.0') + + depends_on("g4radioactivedecay@5.1.1", when='@10.3.1:10.3.9999') + depends_on("g4radioactivedecay@5.1", when='@10.3.0') + + depends_on("g4neutronxs@1.4", when='@10.3.0:10.3.9999') + depends_on("g4pii@1.3", when='@10.3.0:10.3.9999') + depends_on("g4realsurface@1.0", when='@10.3.0:10.3.9999') + depends_on("g4saiddata@1.1", when='@10.3.0:10.3.9999') + depends_on("g4abla@3.0", when='@10.3.0:10.3.9999') + depends_on("g4ensdfstate@2.1", when='@10.3.0:10.3.9999') def install(self, spec, prefix): spec = self.spec - version = self.version - major = version[0] - minor = version[1] - if len(version) > 2: - patch = version[-1] - else: - patch = 0 - data = 'Geant4-%s.%s.%s/data' % (major, minor, patch) + data = '{0}-{1}'.format(self.name, self.version.dotted) datadir = join_path(spec.prefix.share, data) - with working_dir(datadir, create=True): - for d in glob.glob('%s/share/data/*' % - spec['g4abla'].prefix): - os.symlink(d, os.path.basename(d)) - for d in glob.glob('%s/share/data/*' % - spec['g4emlow'].prefix): - os.symlink(d, os.path.basename(d)) - for d in glob.glob('%s/share/data/*' % - spec['g4ndl'].prefix): - os.symlink(d, os.path.basename(d)) - for d in glob.glob('%s/share/data/*' % - spec['g4saiddata'].prefix): - os.symlink(d, os.path.basename(d)) - for d in glob.glob('%s/share/data/*' % - spec['g4neutronxs'].prefix): - os.symlink(d, os.path.basename(d)) - for d in glob.glob('%s/share/data/*' % - spec['g4ensdfstate'].prefix): - os.symlink(d, os.path.basename(d)) - for d in glob.glob('%s/share/data/*' % - spec['g4photonevaporation'].prefix): - os.symlink(d, os.path.basename(d)) - for d in glob.glob('%s/share/data/*' % - spec['g4pii'].prefix): - os.symlink(d, os.path.basename(d)) - for d in glob.glob('%s/share/data/*' % - spec['g4radioactivedecay'].prefix): - os.symlink(d, os.path.basename(d)) - for d in glob.glob('%s/share/data/*' % - spec['g4realsurface'].prefix): - os.symlink(d, os.path.basename(d)) - for d in glob.glob('%s/share/data/*' % - spec['g4tendl'].prefix): - os.symlink(d, os.path.basename(d)) - def url_for_version(self, version): - """Handle version string.""" - url = 'http://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/' - url = url + 'ReleaseNotes4.{0}.{1}.html'.format(version[0], version[1]) - return url + with working_dir(datadir, create=True): + for s in spec.dependencies(): + for d in glob.glob('{0}/data/*'.format(s.prefix.share)): + os.symlink(d, os.path.basename(d)) diff --git a/var/spack/repos/builtin/packages/geant4/geant4-10.4.3-cxx17-removed-features.patch b/var/spack/repos/builtin/packages/geant4/geant4-10.4.3-cxx17-removed-features.patch new file mode 100644 index 00000000000..a4938876794 --- /dev/null +++ b/var/spack/repos/builtin/packages/geant4/geant4-10.4.3-cxx17-removed-features.patch @@ -0,0 +1,18 @@ +diff --git a/cmake/Modules/G4BuildSettings.cmake b/cmake/Modules/G4BuildSettings.cmake +index f68cb0a44..6bf4b6948 100644 +--- a/cmake/Modules/G4BuildSettings.cmake ++++ b/cmake/Modules/G4BuildSettings.cmake +@@ -205,6 +205,13 @@ endif() + # Add Definition to flags for temporary back compatibility + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DG4USE_STD11") + ++# Spack patch to support use of C++ features deprecated/removed in C++17 ++# Only checked on AppleClang for now ++if(GEANT4_BUILD_CXXSTD GREATER 14) ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_LIBCPP_ENABLE_CXX17_REMOVED_FEATURES=1") ++endif() ++#---- ++ + # Hold any appropriate compile flag(s) in variable for later export to + # config files. Needed to support clients using late CMake 2.8 where compile features + # are not available. diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py index f3bcb121f60..4bf35792aac 100644 --- a/var/spack/repos/builtin/packages/geant4/package.py +++ b/var/spack/repos/builtin/packages/geant4/package.py @@ -4,8 +4,6 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * -import os -import glob class Geant4(CMakePackage): @@ -15,84 +13,113 @@ class Geant4(CMakePackage): science.""" homepage = "http://geant4.cern.ch/" - url = "http://geant4.cern.ch/support/source/geant4.10.01.p03.tar.gz" + url = "https://gitlab.cern.ch/geant4/geant4/-/archive/v10.6.0/geant4-v10.6.0.tar.gz" maintainers = ['drbenmorgan'] - version('10.05.p01', sha256='f4a292220500fad17e0167ce3153e96e3410ecbe96284e572dc707f63523bdff') - version('10.04', sha256='f6d883132f110eb036c69da2b21df51f13c585dc7b99d4211ddd32f4ccee1670') - version('10.03.p03', sha256='a164f49c038859ab675eec474d08c9d02be8c4be9c0c2d3aa8e69adf89e1e138') + version('10.6.0', sha256='eebe6a170546064ff81ab3b00f513ccd1d4122a026514982368d503ac55a4ee4') + version('10.5.1', sha256='2397eb859dc4de095ff66059d8bda9f060fdc42e10469dd7890946293eeb0e39') + version('10.4.3', sha256='67f3bb6405a2c77e573936c2b933f5a4a33915aa379626a2eb3012009b91e1da') + version('10.4.0', sha256='e919b9b0a88476e00c0b18ab65d40e6a714b55ee4778f66bac32a5396c22aa74') + version('10.3.3', sha256='bcd36a453da44de9368d1d61b0144031a58e4b43a6d2d875e19085f2700a89d8') - variant('qt', default=False, description='Enable Qt support') + _cxxstd_values = ('11', '14', '17') + variant('cxxstd', + default=_cxxstd_values[0], + values=_cxxstd_values, + multi=False, + description='Use the specified C++ standard when building.') + + variant('threads', default=True, description='Build with multithreading') variant('vecgeom', default=False, description='Enable vecgeom support') variant('opengl', default=False, description='Optional OpenGL support') variant('x11', default=False, description='Optional X11 support') variant('motif', default=False, description='Optional motif support') - variant('threads', default=True, description='Build with multithreading') - variant('data', default=True, description='Install geant4 data') - - variant('cxxstd', - default='11', - values=('11', '14', '17'), - multi=False, - description='Use the specified C++ standard when building.') + variant('qt', default=False, description='Enable Qt support') depends_on('cmake@3.5:', type='build') + depends_on('cmake@3.8:', type='build', when='@10.6.0:') - # C++11 support - depends_on("xerces-c cxxstd=11", when="cxxstd=11") - depends_on("clhep@2.3.3.0: cxxstd=11", when="@10.03.p03: cxxstd=11") - depends_on("vecgeom cxxstd=11", when="+vecgeom cxxstd=11") - - # C++14 support - depends_on("xerces-c cxxstd=14", when="cxxstd=14") - depends_on("clhep@2.3.3.0: cxxstd=14", when="@10.03.p03: cxxstd=14") - depends_on("vecgeom cxxstd=14", when="+vecgeom cxxstd=14") - - # C++17 support - depends_on("xerces-c cxxstd=17", when="cxxstd=17") - depends_on("clhep@2.3.3.0: cxxstd=17", when="@10.03.p03: cxxstd=17") - patch('cxx17.patch', when='@:10.03.p99 cxxstd=17') - patch('cxx17_geant4_10_0.patch', level=1, when='@10.04.00: cxxstd=17') - depends_on("vecgeom cxxstd=17", when="+vecgeom cxxstd=17") + depends_on('geant4-data@10.6.0', when='@10.6.0') + depends_on('geant4-data@10.5.1', when='@10.5.1') + depends_on('geant4-data@10.4.3', when='@10.4.3') + depends_on('geant4-data@10.4.0', when='@10.4.0') + depends_on('geant4-data@10.3.3', when='@10.3.3') depends_on("expat") depends_on("zlib") + + for std in _cxxstd_values: + # CLHEP version requirements to be reviewed + depends_on('clhep@2.3.3.0: cxxstd=' + std, + when='@10.3.3: cxxstd=' + std) + + # Spack only supports Xerces-c 3 and above, so no version req + depends_on('xerces-c cxxstd=' + std, when='cxxstd=' + std) + + # Vecgeom specific versions for each Geant4 version + depends_on('vecgeom@1.1.5 cxxstd=' + std, + when='@10.6.0:10.6.99 +vecgeom cxxstd=' + std) + depends_on('vecgeom@1.1.0 cxxstd=' + std, + when='@10.5.0:10.5.99 +vecgeom cxxstd=' + std) + depends_on('vecgeom@0.5.2 cxxstd=' + std, + when='@10.4.0:10.4.99 +vecgeom cxxstd=' + std) + depends_on('vecgeom@0.3rc cxxstd=' + std, + when='@10.3.0:10.3.99 +vecgeom cxxstd=' + std) + + # Visualization driver ependencies depends_on("gl", when='+opengl') depends_on("glx", when='+opengl+x11') depends_on("libx11", when='+x11') depends_on("libxmu", when='+x11') depends_on("motif", when='+motif') - depends_on("qt@4.8:", when="+qt") - - # if G4 data not installed with geant4 - # depend on G4 data packages - # this allows external data installations - # to avoid duplication - - depends_on('geant4-data@10.03.p03', when='@10.03.p03 ~data') - depends_on('geant4-data@10.04', when='@10.04 ~data') - depends_on('geant4-data@10.05.p01', when='@10.05.p01 ~data') + depends_on("qt@5:", when="+qt") # As released, 10.03.03 has issues with respect to using external # CLHEP. - patch('CLHEP-10.03.03.patch', level=1, when='@10.03.p03') + patch('CLHEP-10.03.03.patch', level=1, when='@10.3.3') + # These patches can be applied independent of the cxxstd value? + patch('cxx17.patch', when='@:10.3.99 cxxstd=17') + patch('cxx17_geant4_10_0.patch', level=1, when='@10.4.0 cxxstd=17') + patch('geant4-10.4.3-cxx17-removed-features.patch', + level=1, when='@10.4.3 cxxstd=17') def cmake_args(self): spec = self.spec + # Core options options = [ - '-DGEANT4_USE_GDML=ON', + '-DGEANT4_BUILD_CXXSTD=c++{0}'.format( + self.spec.variants['cxxstd'].value), '-DGEANT4_USE_SYSTEM_CLHEP=ON', - '-DGEANT4_USE_SYSTEM_CLHEP_GRANULAR=ON', - '-DGEANT4_USE_G3TOG4=ON', - '-DGEANT4_INSTALL_DATA=ON', - '-DGEANT4_BUILD_TLS_MODEL=global-dynamic', '-DGEANT4_USE_SYSTEM_EXPAT=ON', '-DGEANT4_USE_SYSTEM_ZLIB=ON', - '-DXERCESC_ROOT_DIR:STRING=%s' % - spec['xerces-c'].prefix, ] + '-DGEANT4_USE_G3TOG4=ON', + '-DGEANT4_USE_GDML=ON', + '-DXERCESC_ROOT_DIR={0}'.format(spec['xerces-c'].prefix) + ] + # Multithreading + options.append(self.define_from_variant('GEANT4_BUILD_MULTITHREADED', + 'threads')) + if '+threads' in spec: + # This should be a variant + options.append('-DGEANT4_BUILD_TLS_MODEL=global-dynamic') + + # install the data with geant4 + datadir = spec['geant4-data'].prefix.share + dataver = '{0}-{1}'.format(spec['geant4-data'].name, + spec['geant4-data'].version.dotted) + datapath = join_path(datadir, dataver) + options.append('-DGEANT4_INSTALL_DATADIR={0}'.format(datapath)) + + # Vecgeom + if '+vecgeom' in spec: + options.append('-DGEANT4_USE_USOLIDS=ON') + options.append('-DUSolids_DIR=%s' % spec[ + 'vecgeom'].prefix.lib.CMake.USolids) + + # Visualization options if 'platform=darwin' not in spec: if "+x11" in spec and "+opengl" in spec: options.append('-DGEANT4_USE_OPENGL_X11=ON') @@ -101,61 +128,10 @@ def cmake_args(self): if "+x11" in spec: options.append('-DGEANT4_USE_RAYTRACER_X11=ON') - options.append('-DGEANT4_BUILD_CXXSTD=c++{0}'.format( - self.spec.variants['cxxstd'].value)) - if '+qt' in spec: options.append('-DGEANT4_USE_QT=ON') options.append( '-DQT_QMAKE_EXECUTABLE=%s' % spec['qt'].prefix.bin.qmake) - if '+vecgeom' in spec: - options.append('-DGEANT4_USE_USOLIDS=ON') - options.append('-DUSolids_DIR=%s' % spec[ - 'vecgeom'].prefix.lib.CMake.USolids) - - on_or_off = lambda opt: 'ON' if '+' + opt in spec else 'OFF' - options.append('-DGEANT4_BUILD_MULTITHREADED=' + on_or_off('threads')) - - # install the data with geant4 - options.append('-DGEANT4_INSTALL_DATA=' + on_or_off('data')) - return options - - def url_for_version(self, version): - """Handle Geant4's unusual version string.""" - return ("http://geant4.cern.ch/support/source/geant4.%s.tar.gz" % version) - - @run_before('cmake') - def make_data_links(self): - if '+data' in self.spec: - return - spec = self.spec - version = self.version - major = version[0] - minor = version[1] - if len(version) > 2: - patch = version[-1] - else: - patch = 0 - datadir = 'Geant4-%s.%s.%s/data' % (major, minor, patch) - with working_dir(join_path(spec.prefix.share, datadir), - create=True): - dirs = glob.glob('%s/%s/*' % - (spec['geant4-data'].prefix.share, datadir)) - for d in dirs: - target = os.readlink(d) - os.symlink(target, os.path.basename(target)) - - def setup_dependent_build_environment(self, env, dependent_spec): - version = self.version - major = version[0] - minor = version[1] - if len(version) > 2: - patch = version[-1] - else: - patch = 0 - datadir = 'Geant4-%s.%s.%s' % (major, minor, patch) - env.append_path('CMAKE_MODULE_PATH', join_path( - self.prefix.lib64, datadir, 'Modules')) diff --git a/var/spack/repos/builtin/packages/vecgeom/package.py b/var/spack/repos/builtin/packages/vecgeom/package.py index 2e28586ef63..20352f77123 100644 --- a/var/spack/repos/builtin/packages/vecgeom/package.py +++ b/var/spack/repos/builtin/packages/vecgeom/package.py @@ -21,6 +21,7 @@ class Vecgeom(CMakePackage, CudaPackage): version('1.1.6', sha256='c4806a6b67d01b40074b8cc6865d78574a6a1c573be51696f2ecdf98b9cb954a') version('1.1.5', sha256='da674f3bbc75c30f56c1a2d251fa8930c899f27fa64b03a36569924030d87b95') version('1.1.3', sha256='ada09e8b6b2fa6c058290302b2cb5a6c2e644192aab1623c31d18c6a2f4c01c8') + version('1.1.0', sha256='e9d1ef83ff591fe4f9ef744a4d3155a3dc7e90ddb6735b24f3afe4c2dc3f7064') version('1.0.1', sha256='1eae7ac9014c608e8d8db5568058b8c0fea1a1dc7a8f54157a3a1c997b6fd9eb') version('0.5.2', tag='v00.05.02', commit='a7e0828c915ff936a79e672d1dd84b087a323b51') From 7357b7023eb9c062ceb8febd0cce9db2f7f27ab3 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Tue, 31 Mar 2020 16:49:25 +0200 Subject: [PATCH 297/377] Update link for codecov's browser extensions (#15779) --- lib/spack/docs/contribution_guide.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/spack/docs/contribution_guide.rst b/lib/spack/docs/contribution_guide.rst index 0b79141ee37..9935ec0c83a 100644 --- a/lib/spack/docs/contribution_guide.rst +++ b/lib/spack/docs/contribution_guide.rst @@ -385,8 +385,8 @@ coverage. This helps us tell what percentage of lines of code in Spack are covered by unit tests. Although code covered by unit tests can still contain bugs, it is much less error prone than code that is not covered by unit tests. -Codecov provides `browser extensions `_ -for Google Chrome, Firefox, and Opera. These extensions integrate with GitHub +Codecov provides `browser extensions `_ +for Google Chrome and Firefox. These extensions integrate with GitHub and allow you to see coverage line-by-line when viewing the Spack repository. If you are new to Spack, a great way to get started is to write unit tests to increase coverage! From 663c3d21b55165be2019ddeb2262d490012c13b3 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 31 Mar 2020 12:08:26 -0500 Subject: [PATCH 298/377] JasPer: add 2.0.16 (#15781) --- var/spack/repos/builtin/packages/jasper/package.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/var/spack/repos/builtin/packages/jasper/package.py b/var/spack/repos/builtin/packages/jasper/package.py index f8351bbbc63..9599aec8f4f 100644 --- a/var/spack/repos/builtin/packages/jasper/package.py +++ b/var/spack/repos/builtin/packages/jasper/package.py @@ -10,13 +10,11 @@ class Jasper(Package): """Library for manipulating JPEG-2000 images""" homepage = "https://www.ece.uvic.ca/~frodo/jasper/" - url = "https://www.ece.uvic.ca/~frodo/jasper/software/jasper-2.0.14.tar.gz" - list_url = homepage + url = "https://github.com/mdadams/jasper/archive/version-2.0.16.tar.gz" - version('2.0.14', sha256='2a1f61e55afe8b4ce8115e1508c5d7cb314d56dfcc2dd323f90c072f88ccf57b', - url="https://www.ece.uvic.ca/~frodo/jasper/software/jasper-2.0.14.tar.gz") - version('1.900.1', sha256='6b905a9c2aca2e275544212666eefc4eb44d95d0a57e4305457b407fe63f9494', - url="https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip") + version('2.0.16', sha256='f1d8b90f231184d99968f361884e2054a1714fdbbd9944ba1ae4ebdcc9bbfdb1') + version('2.0.14', sha256='85266eea728f8b14365db9eaf1edc7be4c348704e562bb05095b9a077cf1a97b') + version('1.900.1', sha256='c2b03f28166f9dc8ae434918839ae9aa9962b880fcfd24eebddd0a2daeb9192c') variant('jpeg', default=True, description='Enable the use of the JPEG library') variant('opengl', default=False, description='Enable the use of the OpenGL and GLUT libraries') From 25a65638ff19119dcb04db784170eaa44d545a8e Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 31 Mar 2020 13:02:20 -0500 Subject: [PATCH 299/377] autoconf-archive: add new package (#15782) --- .../builtin/packages/autoconf-archive/package.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 var/spack/repos/builtin/packages/autoconf-archive/package.py diff --git a/var/spack/repos/builtin/packages/autoconf-archive/package.py b/var/spack/repos/builtin/packages/autoconf-archive/package.py new file mode 100644 index 00000000000..91e89d46e9b --- /dev/null +++ b/var/spack/repos/builtin/packages/autoconf-archive/package.py @@ -0,0 +1,14 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class AutoconfArchive(AutotoolsPackage, GNUMirrorPackage): + """The GNU Autoconf Archive is a collection of more than 500 macros for + GNU Autoconf.""" + + homepage = "https://www.gnu.org/software/autoconf-archive/" + gnu_mirror_path = "autoconf-archive/autoconf-archive-2019.01.06.tar.xz" + + version('2019.01.06', sha256='17195c833098da79de5778ee90948f4c5d90ed1a0cf8391b4ab348e2ec511e3f') From 87481609845310c3cb2a7bc324beeffe1c38f4b3 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 31 Mar 2020 15:44:17 -0500 Subject: [PATCH 300/377] GMT: add 6.0.0 (#15785) --- .../repos/builtin/packages/gmt/package.py | 88 ++++++++++++++++--- 1 file changed, 75 insertions(+), 13 deletions(-) diff --git a/var/spack/repos/builtin/packages/gmt/package.py b/var/spack/repos/builtin/packages/gmt/package.py index b9bb7b71d98..003c0d24be1 100644 --- a/var/spack/repos/builtin/packages/gmt/package.py +++ b/var/spack/repos/builtin/packages/gmt/package.py @@ -14,34 +14,49 @@ class Gmt(Package): contour maps to artificially illuminated surfaces and 3D perspective views. """ - homepage = "http://gmt.soest.hawaii.edu/" - url = "https://github.com/GenericMappingTools/gmt/archive/5.4.4.tar.gz" + homepage = "https://www.generic-mapping-tools.org/" + url = "https://github.com/GenericMappingTools/gmt/archive/6.0.0.tar.gz" + git = "https://github.com/GenericMappingTools/gmt.git" + maintainers = ['adamjstewart'] + + version('master', branch='master') + version('6.0.0', sha256='7a733e670f01d99f8fc0da51a4337320d764c06a68746621f83ccf2e3453bcb7') version('5.4.4', sha256='b593dfb101e6507c467619f3d2190a9f78b09d49fe2c27799750b8c4c0cd2da0') version('4.5.9', sha256='9b13be96ccf4bbd38c14359c05dfa7eeeb4b5f06d6f4be9c33d6c3ea276afc86', url='ftp://ftp.soest.hawaii.edu/gmt/legacy/gmt-4.5.9.tar.bz2') - variant('pcre', default=False, description='Enable the PCRE interface') - variant('gdal', default=False, description='Enable the GDAL interface') - variant('fftw', default=True, description='Fast FFTs') - variant('lapack', default=True, description='Fast matrix inversion') - variant('blas', default=True, description='Fast matrix multiplications') + variant('ghostscript', default=False, description='Ability to convert PostScript plots to PDF and rasters') + variant('gdal', default=False, description='Ability to read and write numerous grid and image formats') + variant('pcre', default=False, description='Regular expression support') + variant('fftw', default=False, description='Fast FFTs') + variant('glib', default=False, description='GTHREAD support') + variant('lapack', default=False, description='Fast matrix inversion') + variant('blas', default=False, description='Fast matrix multiplications') + variant('graphicsmagick', default=False, description='Convert images to animated GIFs') + variant('ffmpeg', default=False, description='Convert images to videos') + variant('docs', default=False, description='Build manpage and HTML documentation') - # http://gmt.soest.hawaii.edu/projects/gmt/wiki/BuildingGMT + # https://github.com/GenericMappingTools/gmt/blob/master/BUILDING.md + # https://github.com/GenericMappingTools/gmt/blob/master/MAINTENANCE.md # Required dependencies - depends_on('ghostscript') - depends_on('subversion') - depends_on('cmake@2.8.5:', type='build', when='@5:') + depends_on('cmake@2.8.7:', type='build', when='@5:') depends_on('netcdf-c@4:') depends_on('curl', when='@5.4:') # Optional dependencies - depends_on('pcre', when='+pcre') + depends_on('ghostscript', when='+ghostscript') depends_on('gdal', when='+gdal') + depends_on('pcre', when='+pcre') depends_on('fftw', when='+fftw') + depends_on('glib', when='+glib') depends_on('lapack', when='+lapack') depends_on('blas', when='+blas') + depends_on('graphicsmagick', when='+graphicsmagick') + depends_on('ffmpeg', when='+ffmpeg') + depends_on('py-sphinx@1.4:', when='+docs', type='build') + depends_on('graphicsmagick', type='test') patch('type.patch', when='@4.5.9') @@ -49,9 +64,56 @@ class Gmt(Package): @when('@5:') def install(self, spec, prefix): with working_dir('spack-build', create=True): - cmake('..', *std_cmake_args) + args = std_cmake_args + + args.extend([ + '-DNETCDF_CONFIG={0}'.format( + spec['netcdf-c'].prefix.bin.join('nc-config')), + '-DNETCDF_INCLUDE_DIR={0}'.format( + spec['netcdf-c'].headers.directories[0]), + '-DNETCDF_LIBRARY={0}'.format( + spec['netcdf-c'].libs[0]) + ]) + + # If these options aren't explicitly disabled, + # CMake will search OS for dependencies + if '+ghostscript' in spec: + args.append('-DGS={0}'.format( + spec['ghostscript'].prefix.bin.gs)) + else: + args.append('-DGS=') + + if '+gdal' in spec: + args.extend([ + '-DGDAL_TRANSLATE={0}'.format( + spec['gdal'].prefix.bin.gdal_translate), + '-DOGR2OGR={0}'.format( + spec['gdal'].prefix.bin.ogr2ogr), + ]) + else: + args.extend(['-DGDAL_TRANSLATE=', '-DOGR2OGR=']) + + if 'graphicsmagick' in spec: + args.extend([ + '-DGM={0}'.format( + spec['graphicsmagick'].prefix.bin.gm), + '-DGRAPHICSMAGICK={0}'.format( + spec['graphicsmagick'].prefix.bin.gm), + ]) + else: + args.extend(['-DGM=', '-DGRAPHICSMAGICK=']) + + if '+ffmpeg' in spec: + args.append('-DFFMPEG={0}'.format( + spec['ffmpeg'].prefix.bin.ffmpeg)) + else: + args.append('-DFFMPEG=') + + cmake('..', *args) make() + if self.run_tests: + make('check') make('install') @when('@:4') From 336191c25145823be104011fda23651e6e6aa723 Mon Sep 17 00:00:00 2001 From: Greg Becker Date: Tue, 31 Mar 2020 16:09:08 -0700 Subject: [PATCH 301/377] packages.yaml: allow virtuals to specify buildable: false (#14934) Currently, to force Spack to use an external MPI, you have to specify `buildable: False` for every MPI provider in Spack in your packages.yaml file. This is both tedious and fragile, as new MPI providers can be added and break your workflow when you do a git pull. This PR allows you to specify an entire virtual dependency as non-buildable, and specify particular implementations to be built: ``` packages: all: providers: mpi: [mpich] mpi: buildable: false paths: mpich@3.2 %gcc@7.3.0: /usr/packages/mpich-3.2-gcc-7.3.0 ``` will force all Spack builds to use the specified `mpich` install. --- lib/spack/docs/build_settings.rst | 33 ++++++++ lib/spack/spack/package.py | 8 ++ lib/spack/spack/package_prefs.py | 78 ++++++------------ .../spack/test/concretize_preferences.py | 59 ++++++------- lib/spack/spack/test/conftest.py | 7 ++ lib/spack/spack/test/mirror.py | 82 +++++++++---------- lib/spack/spack/test/module_parsing.py | 30 ++----- lib/spack/spack/test/spec_dag.py | 2 - lib/spack/spack/util/module_cmd.py | 9 +- 9 files changed, 155 insertions(+), 153 deletions(-) diff --git a/lib/spack/docs/build_settings.rst b/lib/spack/docs/build_settings.rst index b141f2b717c..cfd850af28a 100644 --- a/lib/spack/docs/build_settings.rst +++ b/lib/spack/docs/build_settings.rst @@ -124,6 +124,39 @@ The ``buildable`` does not need to be paired with external packages. It could also be used alone to forbid packages that may be buggy or otherwise undesirable. +Virtual packages in Spack can also be specified as not buildable, and +external implementations can be provided. In the example above, +OpenMPI is configured as not buildable, but Spack will often prefer +other MPI implementations over the externally available OpenMPI. Spack +can be configured with every MPI provider not buildable individually, +but more conveniently: + +.. code-block:: yaml + + packages: + mpi: + buildable: False + openmpi: + paths: + openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64: /opt/openmpi-1.4.3 + openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64+debug: /opt/openmpi-1.4.3-debug + openmpi@1.6.5%intel@10.1 arch=linux-debian7-x86_64: /opt/openmpi-1.6.5-intel + +Implementations can also be listed immediately under the virtual they provide: + +.. code-block:: yaml + + packages: + mpi: + buildable: False + openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64: /opt/openmpi-1.4.3 + openmpi@1.4.3%gcc@4.4.7 arch=linux-debian7-x86_64+debug: /opt/openmpi-1.4.3-debug + openmpi@1.6.5%intel@10.1 arch=linux-debian7-x86_64: /opt/openmpi-1.6.5-intel + mpich@3.3 %clang@9.0.0 arch=linux-debian7-x86_64: /opt/mpich-3.3-intel + +Spack can then use any of the listed external implementations of MPI +to satisfy a dependency, and will choose depending on the compiler and +architecture. .. _concretization-preferences: diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py index 9156d7d0dd3..b8ded0364b3 100644 --- a/lib/spack/spack/package.py +++ b/lib/spack/spack/package.py @@ -1035,6 +1035,14 @@ def provides(self, vpkg_name): for s, constraints in self.provided.items() if s.name == vpkg_name ) + @property + def virtuals_provided(self): + """ + virtual packages provided by this package with its spec + """ + return [vspec for vspec, constraints in self.provided.items() + if any(self.spec.satisfies(c) for c in constraints)] + @property def installed(self): """Installation status of a package. diff --git a/lib/spack/spack/package_prefs.py b/lib/spack/spack/package_prefs.py index 2801a6d1230..0158c7063a6 100644 --- a/lib/spack/spack/package_prefs.py +++ b/lib/spack/spack/package_prefs.py @@ -6,7 +6,6 @@ import stat from six import string_types -from six import iteritems import spack.repo import spack.error @@ -23,27 +22,6 @@ def _spec_type(component): return _lesser_spec_types.get(component, spack.spec.Spec) -def get_packages_config(): - """Wrapper around get_packages_config() to validate semantics.""" - config = spack.config.get('packages') - - # Get a list of virtuals from packages.yaml. Note that because we - # check spack.repo, this collects virtuals that are actually provided - # by sometihng, not just packages/names that don't exist. - # So, this won't include, e.g., 'all'. - virtuals = [(pkg_name, pkg_name._start_mark) for pkg_name in config - if spack.repo.path.is_virtual(pkg_name)] - - # die if there are virtuals in `packages.py` - if virtuals: - errors = ["%s: %s" % (line_info, name) for name, line_info in virtuals] - raise VirtualInPackagesYAMLError( - "packages.yaml entries cannot be virtual packages:", - '\n'.join(errors)) - - return config - - class PackagePrefs(object): """Defines the sort order for a set of specs. @@ -116,7 +94,7 @@ def order_for_package(cls, pkgname, component, vpkg=None, all=True): pkglist.append('all') for pkg in pkglist: - pkg_entry = get_packages_config().get(pkg) + pkg_entry = spack.config.get('packages').get(pkg) if not pkg_entry: continue @@ -160,7 +138,8 @@ def has_preferred_targets(cls, pkg_name): def preferred_variants(cls, pkg_name): """Return a VariantMap of preferred variants/values for a spec.""" for pkg in (pkg_name, 'all'): - variants = get_packages_config().get(pkg, {}).get('variants', '') + variants = spack.config.get('packages').get(pkg, {}).get( + 'variants', '') if variants: break @@ -181,33 +160,29 @@ def spec_externals(spec): # break circular import. from spack.util.module_cmd import get_path_from_module # NOQA: ignore=F401 - allpkgs = get_packages_config() - name = spec.name + allpkgs = spack.config.get('packages') + names = set([spec.name]) + names |= set(vspec.name for vspec in spec.package.virtuals_provided) external_specs = [] - pkg_paths = allpkgs.get(name, {}).get('paths', None) - pkg_modules = allpkgs.get(name, {}).get('modules', None) - if (not pkg_paths) and (not pkg_modules): - return [] - - for external_spec, path in iteritems(pkg_paths): - if not path: - # skip entries without paths (avoid creating extra Specs) + for name in names: + pkg_config = allpkgs.get(name, {}) + pkg_paths = pkg_config.get('paths', {}) + pkg_modules = pkg_config.get('modules', {}) + if (not pkg_paths) and (not pkg_modules): continue - external_spec = spack.spec.Spec(external_spec, - external_path=canonicalize_path(path)) - if external_spec.satisfies(spec): - external_specs.append(external_spec) + for external_spec, path in pkg_paths.items(): + external_spec = spack.spec.Spec( + external_spec, external_path=canonicalize_path(path)) + if external_spec.satisfies(spec): + external_specs.append(external_spec) - for external_spec, module in iteritems(pkg_modules): - if not module: - continue - - external_spec = spack.spec.Spec( - external_spec, external_module=module) - if external_spec.satisfies(spec): - external_specs.append(external_spec) + for external_spec, module in pkg_modules.items(): + external_spec = spack.spec.Spec( + external_spec, external_module=module) + if external_spec.satisfies(spec): + external_specs.append(external_spec) # defensively copy returned specs return [s.copy() for s in external_specs] @@ -215,12 +190,11 @@ def spec_externals(spec): def is_spec_buildable(spec): """Return true if the spec pkgspec is configured as buildable""" - allpkgs = get_packages_config() - if spec.name not in allpkgs: - return True - if 'buildable' not in allpkgs[spec.name]: - return True - return allpkgs[spec.name]['buildable'] + allpkgs = spack.config.get('packages') + do_not_build = [name for name, entry in allpkgs.items() + if not entry.get('buildable', True)] + return not (spec.name in do_not_build or + any(spec.package.provides(name) for name in do_not_build)) def get_package_dir_permissions(spec): diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py index 81b5360869c..922d5a11d87 100644 --- a/lib/spack/spack/test/concretize_preferences.py +++ b/lib/spack/spack/test/concretize_preferences.py @@ -185,34 +185,6 @@ def test_develop(self): spec.concretize() assert spec.version == Version('0.2.15.develop') - def test_no_virtuals_in_packages_yaml(self): - """Verify that virtuals are not allowed in packages.yaml.""" - - # set up a packages.yaml file with a vdep as a key. We use - # syaml.load_config here to make sure source lines in the config are - # attached to parsed strings, as the error message uses them. - conf = syaml.load_config("""\ -mpi: - paths: - mpi-with-lapack@2.1: /path/to/lapack -""") - spack.config.set('packages', conf, scope='concretize') - - # now when we get the packages.yaml config, there should be an error - with pytest.raises(spack.package_prefs.VirtualInPackagesYAMLError): - spack.package_prefs.get_packages_config() - - def test_all_is_not_a_virtual(self): - """Verify that `all` is allowed in packages.yaml.""" - conf = syaml.load_config("""\ -all: - variants: [+mpi] -""") - spack.config.set('packages', conf, scope='concretize') - - # should be no error for 'all': - spack.package_prefs.get_packages_config() - def test_external_mpi(self): # make sure this doesn't give us an external first. spec = Spec('mpi') @@ -236,6 +208,37 @@ def test_external_mpi(self): spec.concretize() assert spec['mpich'].external_path == '/dummy/path' + def test_external_module(self, monkeypatch): + """Test that packages can find externals specified by module + + The specific code for parsing the module is tested elsewhere. + This just tests that the preference is accounted for""" + # make sure this doesn't give us an external first. + def mock_module(cmd, module): + return 'prepend-path PATH /dummy/path' + monkeypatch.setattr(spack.util.module_cmd, 'module', mock_module) + + spec = Spec('mpi') + spec.concretize() + assert not spec['mpi'].external + + # load config + conf = syaml.load_config("""\ +all: + providers: + mpi: [mpich] +mpi: + buildable: false + modules: + mpich@3.0.4: dummy +""") + spack.config.set('packages', conf, scope='concretize') + + # ensure that once config is in place, external is used + spec = Spec('mpi') + spec.concretize() + assert spec['mpich'].external_path == '/dummy/path' + def test_config_permissions_from_all(self, configure_permissions): # Although these aren't strictly about concretization, they are # configured in the same file and therefore convenient to test here. diff --git a/lib/spack/spack/test/conftest.py b/lib/spack/spack/test/conftest.py index a1864639070..8912c0219b7 100644 --- a/lib/spack/spack/test/conftest.py +++ b/lib/spack/spack/test/conftest.py @@ -1040,6 +1040,13 @@ def __init__(self, name, dependencies, dependency_types, conditions=None, self.conflicts = {} self.patches = {} + def provides(self, vname): + return vname in self.provided + + @property + def virtuals_provided(self): + return [v.name for v, c in self.provided] + class MockPackageMultiRepo(object): def __init__(self, packages): diff --git a/lib/spack/spack/test/mirror.py b/lib/spack/spack/test/mirror.py index 570c329b717..05cf46dc200 100644 --- a/lib/spack/spack/test/mirror.py +++ b/lib/spack/spack/test/mirror.py @@ -52,52 +52,52 @@ def check_mirror(): mirror_root = os.path.join(stage.path, 'test-mirror') # register mirror with spack config mirrors = {'spack-mirror-test': 'file://' + mirror_root} - spack.config.set('mirrors', mirrors) - with spack.config.override('config:checksum', False): - specs = [Spec(x).concretized() for x in repos] - spack.mirror.create(mirror_root, specs) - - # Stage directory exists - assert os.path.isdir(mirror_root) - - for spec in specs: - fetcher = spec.package.fetcher[0] - per_package_ref = os.path.join( - spec.name, '-'.join([spec.name, str(spec.version)])) - mirror_paths = spack.mirror.mirror_archive_paths( - fetcher, - per_package_ref) - expected_path = os.path.join( - mirror_root, mirror_paths.storage_path) - assert os.path.exists(expected_path) - - # Now try to fetch each package. - for name, mock_repo in repos.items(): - spec = Spec(name).concretized() - pkg = spec.package - + with spack.config.override('mirrors', mirrors): with spack.config.override('config:checksum', False): - with pkg.stage: - pkg.do_stage(mirror_only=True) + specs = [Spec(x).concretized() for x in repos] + spack.mirror.create(mirror_root, specs) - # Compare the original repo with the expanded archive - original_path = mock_repo.path - if 'svn' in name: - # have to check out the svn repo to compare. - original_path = os.path.join( - mock_repo.path, 'checked_out') + # Stage directory exists + assert os.path.isdir(mirror_root) - svn = which('svn', required=True) - svn('checkout', mock_repo.url, original_path) + for spec in specs: + fetcher = spec.package.fetcher[0] + per_package_ref = os.path.join( + spec.name, '-'.join([spec.name, str(spec.version)])) + mirror_paths = spack.mirror.mirror_archive_paths( + fetcher, + per_package_ref) + expected_path = os.path.join( + mirror_root, mirror_paths.storage_path) + assert os.path.exists(expected_path) - dcmp = filecmp.dircmp( - original_path, pkg.stage.source_path) + # Now try to fetch each package. + for name, mock_repo in repos.items(): + spec = Spec(name).concretized() + pkg = spec.package - # make sure there are no new files in the expanded - # tarball - assert not dcmp.right_only - # and that all original files are present. - assert all(l in exclude for l in dcmp.left_only) + with spack.config.override('config:checksum', False): + with pkg.stage: + pkg.do_stage(mirror_only=True) + + # Compare the original repo with the expanded archive + original_path = mock_repo.path + if 'svn' in name: + # have to check out the svn repo to compare. + original_path = os.path.join( + mock_repo.path, 'checked_out') + + svn = which('svn', required=True) + svn('checkout', mock_repo.url, original_path) + + dcmp = filecmp.dircmp( + original_path, pkg.stage.source_path) + + # make sure there are no new files in the expanded + # tarball + assert not dcmp.right_only + # and that all original files are present. + assert all(l in exclude for l in dcmp.left_only) def test_url_mirror(mock_archive): diff --git a/lib/spack/spack/test/module_parsing.py b/lib/spack/spack/test/module_parsing.py index bbe18b1ad05..0bf485913f5 100644 --- a/lib/spack/spack/test/module_parsing.py +++ b/lib/spack/spack/test/module_parsing.py @@ -20,28 +20,11 @@ 'setenv LDFLAGS -L/path/to/lib', 'prepend-path PATH /path/to/bin'] - -@pytest.fixture -def module_function_test_mode(): - old_mode = spack.util.module_cmd._test_mode - spack.util.module_cmd._test_mode = True - - yield - - spack.util.module_cmd._test_mode = old_mode +_test_template = "'. %s 2>&1' % args[1]" -@pytest.fixture -def save_module_func(): - old_func = spack.util.module_cmd.module - - yield - - spack.util.module_cmd.module = old_func - - -def test_module_function_change_env(tmpdir, working_env, - module_function_test_mode): +def test_module_function_change_env(tmpdir, working_env, monkeypatch): + monkeypatch.setattr(spack.util.module_cmd, '_cmd_template', _test_template) src_file = str(tmpdir.join('src_me')) with open(src_file, 'w') as f: f.write('export TEST_MODULE_ENV_VAR=TEST_SUCCESS\n') @@ -53,7 +36,8 @@ def test_module_function_change_env(tmpdir, working_env, assert os.environ['NOT_AFFECTED'] == "NOT_AFFECTED" -def test_module_function_no_change(tmpdir, module_function_test_mode): +def test_module_function_no_change(tmpdir, monkeypatch): + monkeypatch.setattr(spack.util.module_cmd, '_cmd_template', _test_template) src_file = str(tmpdir.join('src_me')) with open(src_file, 'w') as f: f.write('echo TEST_MODULE_FUNCTION_PRINT') @@ -65,11 +49,11 @@ def test_module_function_no_change(tmpdir, module_function_test_mode): assert os.environ == old_env -def test_get_path_from_module_faked(save_module_func): +def test_get_path_from_module_faked(monkeypatch): for line in test_module_lines: def fake_module(*args): return line - spack.util.module_cmd.module = fake_module + monkeypatch.setattr(spack.util.module_cmd, 'module', fake_module) path = get_path_from_module('mod') assert path == '/path/to' diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py index 25917f9424a..e031f02c255 100644 --- a/lib/spack/spack/test/spec_dag.py +++ b/lib/spack/spack/test/spec_dag.py @@ -387,7 +387,6 @@ def test_unsatisfiable_architecture(self, set_dependency): with pytest.raises(spack.spec.UnsatisfiableArchitectureSpecError): spec.normalize() - @pytest.mark.usefixtures('config') def test_invalid_dep(self): spec = Spec('libelf ^mpich') with pytest.raises(spack.spec.InvalidDependencyError): @@ -602,7 +601,6 @@ def test_copy_normalized(self): copy_ids = set(id(s) for s in copy.traverse()) assert not orig_ids.intersection(copy_ids) - @pytest.mark.usefixtures('config') def test_copy_concretized(self): orig = Spec('mpileaks') orig.concretize() diff --git a/lib/spack/spack/util/module_cmd.py b/lib/spack/spack/util/module_cmd.py index 0edf7e6102a..74790156ae0 100644 --- a/lib/spack/spack/util/module_cmd.py +++ b/lib/spack/spack/util/module_cmd.py @@ -19,16 +19,11 @@ # If we need another option that changes the environment, add it here. module_change_commands = ['load', 'swap', 'unload', 'purge', 'use', 'unuse'] py_cmd = "'import os;import json;print(json.dumps(dict(os.environ)))'" - -# This is just to enable testing. I hate it but we can't find a better way -_test_mode = False +_cmd_template = "'module ' + ' '.join(args) + ' 2>&1'" def module(*args): - module_cmd = 'module ' + ' '.join(args) + ' 2>&1' - if _test_mode: - tty.warn('module function operating in test mode') - module_cmd = ". %s 2>&1" % args[1] + module_cmd = eval(_cmd_template) # So we can monkeypatch for testing if args[0] in module_change_commands: # Do the module manipulation, then output the environment in JSON # and read the JSON back in the parent process to update os.environ From 315faf8b775e1db1baa7030b5f645fa926ecb2ad Mon Sep 17 00:00:00 2001 From: Phil Tooley <32297355+ptooley@users.noreply.github.com> Date: Wed, 1 Apr 2020 00:14:43 +0100 Subject: [PATCH 302/377] Extrae: update package shasum and binutils version (#15516) Co-authored-by: telemin --- var/spack/repos/builtin/packages/extrae/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/extrae/package.py b/var/spack/repos/builtin/packages/extrae/package.py index 4ea5928b023..bab7b365d8e 100644 --- a/var/spack/repos/builtin/packages/extrae/package.py +++ b/var/spack/repos/builtin/packages/extrae/package.py @@ -35,7 +35,7 @@ class Extrae(AutotoolsPackage): OpenMP, CUDA, OpenCL, pthread, OmpSs""" homepage = "https://tools.bsc.es/extrae" url = "https://ftp.tools.bsc.es/extrae/extrae-3.4.1-src.tar.bz2" - version('3.7.1', sha256='95810b057f95e91bfc89813eb8bd320dfe40614fc8e98c63d95c5101c56dd213') + version('3.7.1', sha256='c83ddd18a380c9414d64ee5de263efc6f7bac5fe362d5b8374170c7f18360378') version('3.4.1', sha256='77bfec16d6b5eee061fbaa879949dcef4cad28395d6a546b1ae1b9246f142725') depends_on("autoconf", type='build') @@ -51,7 +51,7 @@ class Extrae(AutotoolsPackage): depends_on("elf", type="link") depends_on("libxml2") depends_on("numactl") - depends_on("binutils+libiberty") + depends_on("binutils+libiberty@:2.33") depends_on("gettext") # gettext dependency added to find -lintl # https://www.gnu.org/software/gettext/FAQ.html#integrating_undefined From a4b3edd68a91543f62146919670e7627bd9e21c0 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 31 Mar 2020 18:57:14 -0500 Subject: [PATCH 303/377] Allow Spack Environments with '-h' in the name (#15429) If a user invoked "spack env activate example-henv", Spack would mistakenly interpret the "-h" from "example-henv" as the "-h" option. This commit allows users to create and activate environments with "-h" in the name. This issue existed for bash shell support as well as csh support, and this commit addresses both, along with some other unrelated csh support issues. --- share/spack/csh/spack.csh | 46 ++++++++++++++++++++++++------------ share/spack/setup-env.sh | 49 +++++++++++++++++++++++++-------------- 2 files changed, 63 insertions(+), 32 deletions(-) diff --git a/share/spack/csh/spack.csh b/share/spack/csh/spack.csh index b4d963ae101..7a510502812 100644 --- a/share/spack/csh/spack.csh +++ b/share/spack/csh/spack.csh @@ -66,7 +66,7 @@ case cd: [ $#_sp_args -gt 0 ] && set _sp_arg = ($_sp_args[1]) shift _sp_args - if ( "$_sp_arg" == "-h" ) then + if ( "$_sp_arg" == "-h" || "$_sp_args" == "--help" ) then \spack cd -h else cd `\spack location $_sp_arg $_sp_args` @@ -78,7 +78,7 @@ case env: set _sp_arg="" [ $#_sp_args -gt 0 ] && set _sp_arg = ($_sp_args[1]) - if ( "$_sp_arg" == "-h" ) then + if ( "$_sp_arg" == "-h" || "$_sp_arg" == "--help" ) then \spack env -h else switch ($_sp_arg) @@ -86,12 +86,18 @@ case env: set _sp_env_arg="" [ $#_sp_args -gt 1 ] && set _sp_env_arg = ($_sp_args[2]) - if ( "$_sp_env_arg" == "" || "$_sp_args" =~ "*--sh*" || "$_sp_args" =~ "*--csh*" || "$_sp_args" =~ "*-h*" ) then - # no args or args contain -h/--help, --sh, or --csh: just execute + # Space needed here to differentiate between `-h` + # argument and environments with "-h" in the name. + if ( "$_sp_env_arg" == "" || \ + "$_sp_args" =~ "* --sh*" || \ + "$_sp_args" =~ "* --csh*" || \ + "$_sp_args" =~ "* -h*" || \ + "$_sp_args" =~ "* --help*" ) then + # No args or args contain --sh, --csh, or -h/--help: just execute. \spack $_sp_flags env $_sp_args else shift _sp_args # consume 'activate' or 'deactivate' - # actual call to activate: source the output + # Actual call to activate: source the output. eval `\spack $_sp_flags env activate --csh $_sp_args` endif breaksw @@ -99,30 +105,40 @@ case env: set _sp_env_arg="" [ $#_sp_args -gt 1 ] && set _sp_env_arg = ($_sp_args[2]) - if ( "$_sp_env_arg" != "" ) then - # with args: execute the command + # Space needed here to differentiate between `--sh` + # argument and environments with "--sh" in the name. + if ( "$_sp_args" =~ "* --sh*" || \ + "$_sp_args" =~ "* --csh*" ) then + # Args contain --sh or --csh: just execute. \spack $_sp_flags env $_sp_args + else if ( "$_sp_env_arg" != "" ) then + # Any other arguments are an error or -h/--help: just run help. + \spack $_sp_flags env deactivate -h else - # no args: source the output + # No args: source the output of the command. eval `\spack $_sp_flags env deactivate --csh` endif breaksw default: - echo default \spack $_sp_flags env $_sp_args breaksw endsw endif + breaksw + case load: case unload: - # Space in `-h` portion is important for differentiating -h option - # from variants that begin with "h" or packages with "-h" in name - if ( "$_sp_spec" =~ "*--sh*" || "$_sp_spec" =~ "*--csh*" || \ - " $_sp_spec" =~ "* -h*" || "$_sp_spec" =~ "*--help*") then - # IF a shell is given, print shell output + # Get --sh, --csh, -h, or --help arguments. + # Space needed here to differentiate between `-h` + # argument and specs with "-h" in the name. + if ( " $_sp_spec" =~ "* --sh*" || \ + " $_sp_spec" =~ "* --csh*" || \ + " $_sp_spec" =~ "* -h*" || \ + " $_sp_spec" =~ "* --help*") then + # Args contain --sh, --csh, or -h/--help: just execute. \spack $_sp_flags $_sp_subcommand $_sp_spec else - # otherwise eval with csh + # Otherwise, eval with csh. eval `\spack $_sp_flags $_sp_subcommand --csh $_sp_spec || \ echo "exit 1"` endif diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh index c3d9ef260cd..5968c4c0160 100755 --- a/share/spack/setup-env.sh +++ b/share/spack/setup-env.sh @@ -115,31 +115,44 @@ spack() { else case $_sp_arg in activate) - _a="$@" + # Get --sh, --csh, or -h/--help arguments. + # Space needed here becauses regexes start with a space + # and `-h` may be the only argument. + _a=" $@" + # Space needed here to differentiate between `-h` + # argument and environments with "-h" in the name. + # Also see: https://www.gnu.org/software/bash/manual/html_node/Shell-Parameter-Expansion.html#Shell-Parameter-Expansion if [ -z ${1+x} ] || \ - [ "${_a#*--sh}" != "$_a" ] || \ - [ "${_a#*--csh}" != "$_a" ] || \ - [ "${_a#*-h}" != "$_a" ]; + [ "${_a#* --sh}" != "$_a" ] || \ + [ "${_a#* --csh}" != "$_a" ] || \ + [ "${_a#* -h}" != "$_a" ] || \ + [ "${_a#* --help}" != "$_a" ]; then - # no args or args contain -h/--help, --sh, or --csh: just execute + # No args or args contain --sh, --csh, or -h/--help: just execute. command spack env activate "$@" else - # actual call to activate: source the output + # Actual call to activate: source the output. eval $(command spack $_sp_flags env activate --sh "$@") fi ;; deactivate) - _a="$@" - if [ "${_a#*--sh}" != "$_a" ] || \ - [ "${_a#*--csh}" != "$_a" ]; + # Get --sh, --csh, or -h/--help arguments. + # Space needed here becauses regexes start with a space + # and `-h` may be the only argument. + _a=" $@" + # Space needed here to differentiate between `--sh` + # argument and environments with "--sh" in the name. + # Also see: https://www.gnu.org/software/bash/manual/html_node/Shell-Parameter-Expansion.html#Shell-Parameter-Expansion + if [ "${_a#* --sh}" != "$_a" ] || \ + [ "${_a#* --csh}" != "$_a" ]; then - # just execute the command if --sh or --csh are provided + # Args contain --sh or --csh: just execute. command spack env deactivate "$@" elif [ -n "$*" ]; then - # any other arguments are an error or help, so just run help + # Any other arguments are an error or -h/--help: just run help. command spack env deactivate -h else - # no args: source the output of the command + # No args: source the output of the command. eval $(command spack $_sp_flags env deactivate --sh) fi ;; @@ -151,17 +164,19 @@ spack() { return ;; "load"|"unload") - # get --sh, --csh, --help, or -h arguments - # space is important for -h case to differentiate between `-h` - # argument and specs with "-h" in package name or variant settings + # Get --sh, --csh, -h, or --help arguments. + # Space needed here becauses regexes start with a space + # and `-h` may be the only argument. _a=" $@" + # Space needed here to differentiate between `-h` + # argument and specs with "-h" in the name. + # Also see: https://www.gnu.org/software/bash/manual/html_node/Shell-Parameter-Expansion.html#Shell-Parameter-Expansion if [ "${_a#* --sh}" != "$_a" ] || \ [ "${_a#* --csh}" != "$_a" ] || \ [ "${_a#* -h}" != "$_a" ] || \ [ "${_a#* --help}" != "$_a" ]; then - # just execute the command if --sh or --csh are provided - # or if the -h or --help arguments are provided + # Args contain --sh, --csh, or -h/--help: just execute. command spack $_sp_flags $_sp_subcommand "$@" else eval $(command spack $_sp_flags $_sp_subcommand --sh "$@" || \ From 97cfef320c3b601fbaea870aeba1f93b5dd69c20 Mon Sep 17 00:00:00 2001 From: "Dr. Christian Tacke" <58549698+ChristianTackeGSI@users.noreply.github.com> Date: Wed, 1 Apr 2020 15:07:41 +0200 Subject: [PATCH 304/377] slurm: new version, system configuration path (#15466) * Add version 18-08-9-1 * Add variant to allow setting the sysconfdir: See below About sysconfdir: slurm has a server and a client. To use the correct communication channel, the client needs to be able to read the correct config. This config is in PREFIX/etc. Let's assume one has the server part installed as a system package. This generally is a good idea, so that the server gets started during boot. This means, that the config is in /etc/slurm. If one now wants to use the client part (library!) via spack, one has a problem: spack's slurm looks in SPACK-PACKAGE-PREFIX/etc for the config. There needs to be a way to let the spack installed package use the system's config. So add a variant to override the path during build: sysconfdir=/etc/slurm. This is much like what happened in #15307 for munge. --- var/spack/repos/builtin/packages/slurm/package.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/var/spack/repos/builtin/packages/slurm/package.py b/var/spack/repos/builtin/packages/slurm/package.py index bfa6621f077..daae7743a03 100644 --- a/var/spack/repos/builtin/packages/slurm/package.py +++ b/var/spack/repos/builtin/packages/slurm/package.py @@ -24,6 +24,7 @@ class Slurm(AutotoolsPackage): homepage = 'https://slurm.schedmd.com' url = 'https://github.com/SchedMD/slurm/archive/slurm-17-02-6-1.tar.gz' + version('18-08-9-1', sha256='32eb0b612ca18ade1e35c3c9d3b4d71aba2b857446841606a9e54d0a417c3b03') version('18-08-0-1', sha256='62129d0f2949bc8a68ef86fe6f12e0715cbbf42f05b8da6ef7c3e7e7240b50d9') version('17-11-9-2', sha256='6e34328ed68262e776f524f59cca79ac75bcd18030951d45ea545a7ba4c45906') version('17-02-6-1', sha256='97b3a3639106bd6d44988ed018e2657f3d640a3d5c105413d05b4721bc8ee25e') @@ -35,6 +36,8 @@ class Slurm(AutotoolsPackage): variant('hdf5', default=False, description='Enable hdf5 support') variant('readline', default=True, description='Enable readline support') variant('pmix', default=False, description='Enable PMIx support') + variant('sysconfdir', default='PREFIX/etc', values=any, + description='Set system configuration path (possibly /etc/slurm)') # TODO: add variant for BG/Q and Cray support @@ -94,6 +97,10 @@ def configure_args(self): else: args.append('--without-pmix') + sysconfdir = spec.variants['sysconfdir'].value + if sysconfdir != 'PREFIX/etc': + args.append('--sysconfdir={0}'.format(sysconfdir)) + return args def install(self, spec, prefix): From 49aa28790c5df2c8d2640eabc2f2058ef140194b Mon Sep 17 00:00:00 2001 From: Sinan Date: Wed, 1 Apr 2020 06:09:39 -0700 Subject: [PATCH 305/377] new package: py-spatialite (#12597) * new package: py-spatialite * make flake8 happy Co-authored-by: Sinan81 --- .../builtin/packages/py-spatialite/package.py | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-spatialite/package.py diff --git a/var/spack/repos/builtin/packages/py-spatialite/package.py b/var/spack/repos/builtin/packages/py-spatialite/package.py new file mode 100644 index 00000000000..e78cff81ad3 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-spatialite/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PySpatialite(PythonPackage): + """Wrapper for standard Python module "sqlite3" which adds SpatiaLite + support. + """ + + homepage = "https://github.com/malexer/spatialite" + url = "https://pypi.io/packages/source/s/spatialite/spatialite-0.0.3.tar.gz" + + version('0.0.3', sha256='a0761f239a52f326b14ce41ba61b6614dfcc808b978a0bec4a37c1de9ad9071e') + + depends_on('py-setuptools', type='build') + depends_on('libspatialite') From c430ad91c39d625d6da7e7410a1fff3b0c6d9d9f Mon Sep 17 00:00:00 2001 From: Axel Huebl Date: Wed, 1 Apr 2020 08:58:09 -0700 Subject: [PATCH 306/377] pybind11 2.5.0: Include Change (#13905) Add pybind11, version 2.5.0. This release adds improved include helpers. --- .../repos/builtin/packages/py-pybind11/package.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pybind11/package.py b/var/spack/repos/builtin/packages/py-pybind11/package.py index cda6cada32f..3fe7402a0f5 100644 --- a/var/spack/repos/builtin/packages/py-pybind11/package.py +++ b/var/spack/repos/builtin/packages/py-pybind11/package.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import os class PyPybind11(CMakePackage): @@ -23,6 +24,7 @@ class PyPybind11(CMakePackage): maintainers = ['ax3l'] version('master', branch='master') + version('2.5.0', sha256='97504db65640570f32d3fdf701c25a340c8643037c3b69aec469c10c93dc8504') version('2.4.3', sha256='1eed57bc6863190e35637290f97a20c81cfe4d9090ac0a24f3bbf08f265eb71d') version('2.3.0', sha256='0f34838f2c8024a6765168227ba587b3687729ebf03dc912f88ff75c7aa9cfe8') version('2.2.4', sha256='b69e83658513215b8d1443544d0549b7d231b9f201f6fc787a2b2218b408181e') @@ -56,6 +58,8 @@ def cmake_args(self): def setup_build_environment(self, env): env.set('PYBIND11_USE_CMAKE', 1) + # https://github.com/pybind/pybind11/pull/1995 + @when('@:2.4.99') def patch(self): """ see https://github.com/spack/spack/issues/13559 """ filter_file('import sys', @@ -74,9 +78,11 @@ def test(self): with working_dir('spack-test', create=True): # test include helper points to right location python = self.spec['python'].command - inc = python( + py_inc = python( '-c', 'import pybind11 as py; ' + self.spec['python'].package.print_string('py.get_include()'), - output=str) - assert inc.strip() == str(self.prefix.include) + output=str).strip() + for inc in [py_inc, self.prefix.include]: + inc_file = join_path(inc, 'pybind11', 'pybind11.h') + assert os.path.isfile(inc_file) From c3e8825f8ec9aecc7e25380e34e8851b065c21e1 Mon Sep 17 00:00:00 2001 From: Greg Sjaardema Date: Wed, 1 Apr 2020 11:02:26 -0600 Subject: [PATCH 307/377] Spelling fixes (#15805) * Spelling fixes * spelling fixes * spelling fixes * spelling fixes * spelling fix * spelling fix * spelling fix * spelling fixes * spelling fix --- .flake8_packages | 2 +- CHANGELOG.md | 6 +++--- lib/spack/docs/basic_usage.rst | 2 +- lib/spack/docs/build_systems/intelpackage.rst | 6 +++--- lib/spack/docs/containers.rst | 6 +++--- lib/spack/docs/getting_started.rst | 2 +- lib/spack/docs/packaging_guide.rst | 2 +- lib/spack/docs/pipelines.rst | 2 +- lib/spack/docs/workflows.rst | 6 +++--- 9 files changed, 17 insertions(+), 17 deletions(-) diff --git a/.flake8_packages b/.flake8_packages index d17a34951d1..fc2dbf98afd 100644 --- a/.flake8_packages +++ b/.flake8_packages @@ -9,7 +9,7 @@ # # Note that we also add *per-line* exemptions for certain patterns in the # `spack flake8` command. This is where F403 for `from spack import *` -# is added (beause we *only* allow that wildcard). +# is added (because we *only* allow that wildcard). # # See .flake8 for regular exceptions. # diff --git a/CHANGELOG.md b/CHANGELOG.md index 6fea0528842..092959aff98 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,7 +25,7 @@ This is a bugfix release on top of `v0.14.0`. Specific fixes include: 2. **Build pipelines.** You can also build in parallel through Gitlab CI. Simply create a Spack environment and push it to Gitlab to build - on Gitlab runners. Pipeline support is now integreated into a single + on Gitlab runners. Pipeline support is now integrated into a single `spack ci` command, so setting it up is easier than ever. See the [Pipelines section](https://spack.readthedocs.io/en/v0.14.0/pipelines.html) in the docs. @@ -125,8 +125,8 @@ RHEL8. * mirror bugfixes: symlinks, duplicate patches, and exception handling (#13789) * don't try to fetch `BundlePackages` (#13908) * avoid re-fetching patches already added to a mirror (#13908) -* avoid re-fetching alread added patches (#13908) -* avoid re-fetching alread added patches (#13908) +* avoid re-fetching already added patches (#13908) +* avoid re-fetching already added patches (#13908) * allow repeated invocations of `spack mirror create` on the same dir (#13908) * bugfix for RHEL8 when `python` is unavailable (#14252) * improve concretization performance in environments (#14190) diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst index d63dec8827e..2f047c07853 100644 --- a/lib/spack/docs/basic_usage.rst +++ b/lib/spack/docs/basic_usage.rst @@ -925,7 +925,7 @@ contains any spaces. Any of ``cppflags=-O3``, ``cppflags="-O3"``, ``cppflags='-O3'``, and ``cppflags="-O3 -fPIC"`` are acceptable, but ``cppflags=-O3 -fPIC`` is not. Additionally, if the value of the compiler flags is not the last thing on the line, it must be followed -by a space. The commmand ``spack install libelf cppflags="-O3"%intel`` +by a space. The command ``spack install libelf cppflags="-O3"%intel`` will be interpreted as an attempt to set ``cppflags="-O3%intel"``. The six compiler flags are injected in the order of implicit make commands diff --git a/lib/spack/docs/build_systems/intelpackage.rst b/lib/spack/docs/build_systems/intelpackage.rst index c14fc34f519..153b41bdc75 100644 --- a/lib/spack/docs/build_systems/intelpackage.rst +++ b/lib/spack/docs/build_systems/intelpackage.rst @@ -553,7 +553,7 @@ follow `the next section `_ instead. f77: stub fc: stub - Replace ``18.0.3`` with the version that you determined in the preceeding + Replace ``18.0.3`` with the version that you determined in the preceding step. The contents under ``paths:`` do not matter yet. You are right to ask: "Why on earth is that necessary?" [fn8]_. @@ -696,7 +696,7 @@ follow `the next section `_ instead. - /home/$user/spack-stage Do not duplicate the ``config:`` line if it already is present. - Adapt the location, which here is the same as in the preceeding example. + Adapt the location, which here is the same as in the preceding example. 3. Retry installing the large package. @@ -965,7 +965,7 @@ a *virtual* ``mkl`` package is declared in Spack. Likewise, in a :ref:`MakefilePackage ` - or similiar package that does not use AutoTools you may need to provide include + or similar package that does not use AutoTools you may need to provide include and link options for use on command lines or in environment variables. For example, to generate an option string of the form ``-I``, use: diff --git a/lib/spack/docs/containers.rst b/lib/spack/docs/containers.rst index 18500ff7648..2ca25b7207b 100644 --- a/lib/spack/docs/containers.rst +++ b/lib/spack/docs/containers.rst @@ -44,7 +44,7 @@ Environments: && echo " install_tree: /opt/software" \ && echo " view: /opt/view") > /opt/spack-environment/spack.yaml - # Install the software, remove unecessary deps + # Install the software, remove unnecessary deps RUN cd /opt/spack-environment && spack install && spack gc -y # Strip all the binaries @@ -266,7 +266,7 @@ following ``Dockerfile``: && echo " install_tree: /opt/software" \ && echo " view: /opt/view") > /opt/spack-environment/spack.yaml - # Install the software, remove unecessary deps + # Install the software, remove unnecessary deps RUN cd /opt/spack-environment && spack install && spack gc -y # Strip all the binaries @@ -304,4 +304,4 @@ following ``Dockerfile``: .. note:: Spack can also produce Singularity definition files to build the image. The minimum version of Singularity required to build a SIF (Singularity Image Format) - from them is ``3.5.3``. \ No newline at end of file + from them is ``3.5.3``. diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst index 3a9b2d42b2e..8de9d276623 100644 --- a/lib/spack/docs/getting_started.rst +++ b/lib/spack/docs/getting_started.rst @@ -851,7 +851,7 @@ from websites and from git. .. warning:: - This workaround should be used ONLY as a last resort! Wihout SSL + This workaround should be used ONLY as a last resort! Without SSL certificate verification, spack and git will download from sites you wouldn't normally trust. The code you download and run may then be compromised! While this is not a major issue for archives that will diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst index 3c588c240b8..88b78148389 100644 --- a/lib/spack/docs/packaging_guide.rst +++ b/lib/spack/docs/packaging_guide.rst @@ -3607,7 +3607,7 @@ the command line. For most compilers, ``$rpath_flag`` is ``-Wl,-rpath,``. However, NAG passes its flags to GCC instead of passing them directly to the linker. Therefore, its ``$rpath_flag`` is doubly wrapped: ``-Wl,-Wl,,-rpath,``. - ``$rpath_flag`` can be overriden on a compiler specific basis in + ``$rpath_flag`` can be overridden on a compiler specific basis in ``lib/spack/spack/compilers/$compiler.py``. The compiler wrappers also pass the compiler flags specified by the user from diff --git a/lib/spack/docs/pipelines.rst b/lib/spack/docs/pipelines.rst index f70b39a16d8..a8f81988528 100644 --- a/lib/spack/docs/pipelines.rst +++ b/lib/spack/docs/pipelines.rst @@ -132,7 +132,7 @@ A pipeline-enabled spack environment ------------------------------------ Here's an example of a spack environment file that has been enhanced with -sections desribing a build pipeline: +sections describing a build pipeline: .. code-block:: yaml diff --git a/lib/spack/docs/workflows.rst b/lib/spack/docs/workflows.rst index b329a0205c8..89d17e98b28 100644 --- a/lib/spack/docs/workflows.rst +++ b/lib/spack/docs/workflows.rst @@ -444,7 +444,7 @@ environment. A single-prefix filesystem view is a single directory tree that is the union of the directory hierarchies of a number of installed packages; -it is similar to the directory hiearchy that might exist under +it is similar to the directory hierarchy that might exist under ``/usr/local``. The files of the view's installed packages are brought into the view by symbolic or hard links, referencing the original Spack installation. @@ -1237,7 +1237,7 @@ you can also manually set them in your ``.bashrc``. 2. Other package managers like Homebrew will try to install things to the same directory. If you plan on using Homebrew in conjunction with Spack, don't symlink things to ``/usr/local``. - 3. If you are on a shared workstation, or don't have sudo priveleges, you + 3. If you are on a shared workstation, or don't have sudo privileges, you can't do this. If you still want to do this anyway, there are several ways around SIP. @@ -1467,7 +1467,7 @@ In order to build and run the image, execute: SPACK_ROOT=/usr/local \ FORCE_UNSAFE_CONFIGURE=1 - # install minimal spack depedencies + # install minimal spack dependencies RUN apt-get update \ && apt-get install -y --no-install-recommends \ autoconf \ From 58cb2e509232cbc4ea42d95b6899f37d95639968 Mon Sep 17 00:00:00 2001 From: Andrew Gaspar Date: Wed, 1 Apr 2020 11:02:55 -0600 Subject: [PATCH 308/377] Add libgit2 1.0.0 and 0.28.5 (#15801) --- var/spack/repos/builtin/packages/libgit2/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/libgit2/package.py b/var/spack/repos/builtin/packages/libgit2/package.py index 222075ffdb5..dcd5259a27c 100644 --- a/var/spack/repos/builtin/packages/libgit2/package.py +++ b/var/spack/repos/builtin/packages/libgit2/package.py @@ -16,7 +16,11 @@ class Libgit2(CMakePackage): homepage = "https://libgit2.github.com/" url = "https://github.com/libgit2/libgit2/archive/v0.26.0.tar.gz" + maintainers = ["AndrewGaspar"] + + version('1.0.0', sha256='6a1fa16a7f6335ce8b2630fbdbb5e57c4027929ebc56fcd1ac55edb141b409b4') version('0.99.0', sha256='174024310c1563097a6613a0d3f7539d11a9a86517cd67ce533849065de08a11') + version('0.28.5', sha256='2b7b68aee6f123bc84cc502a9c12738435b8054e7d628962e091cd2a25be4f42') version('0.28.4', sha256='30f3877469d09f2e4a21be933b4e2800560d16646028dd800744dc5f7fb0c749') version('0.28.3', sha256='ee5344730fe11ce7c86646e19c2d257757be293f5a567548d398fb3af8b8e53b') version('0.28.2', sha256='42b5f1e9b9159d66d86fff0394215c5733b6ef8f9b9d054cdd8c73ad47177fc3') From 67fbf257f09763b8217b0b51ac9ad5ebc8acd4c9 Mon Sep 17 00:00:00 2001 From: Sinan Date: Wed, 1 Apr 2020 10:05:53 -0700 Subject: [PATCH 309/377] Package/sfcgal fix typo (#15796) * fix typo in dependency definition * remove arbitrary dependency constraint Co-authored-by: Sinan81 --- var/spack/repos/builtin/packages/sfcgal/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/sfcgal/package.py b/var/spack/repos/builtin/packages/sfcgal/package.py index 021ba1bb97b..c1e80174e0c 100644 --- a/var/spack/repos/builtin/packages/sfcgal/package.py +++ b/var/spack/repos/builtin/packages/sfcgal/package.py @@ -20,8 +20,8 @@ class Sfcgal(CMakePackage): version('1.3.7', sha256='30ea1af26cb2f572c628aae08dd1953d80a69d15e1cac225390904d91fce031b') # Ref: http://oslandia.github.io/SFCGAL/installation.html - depends_on('cgal@4.3 +core') - depends_on('boost@1.54.0:1.69.0') + depends_on('cgal@4.3: +core') + depends_on('boost@1.54.0:') depends_on('mpfr@2.2.1:') depends_on('gmp@4.2:') From 917c0a0efd4258b76fe62f66233a9cca3186c5d4 Mon Sep 17 00:00:00 2001 From: "Nichols A. Romero" Date: Wed, 1 Apr 2020 12:28:36 -0500 Subject: [PATCH 310/377] Minor LLVM libomptarget fixes (#15788) * Add myself as a maintainer * This was a regression that occured in previous PR. Flang has been excised from LLVM for now until f18 is merged upstream. * Libraries only needed when a GPU backend is present. --- var/spack/repos/builtin/packages/llvm/package.py | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index 588c1cae1dd..a5aedb625d8 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -19,7 +19,7 @@ class Llvm(CMakePackage): url = "https://github.com/llvm/llvm-project/archive/llvmorg-7.1.0.tar.gz" list_url = "http://releases.llvm.org/download.html" git = "https://github.com/llvm/llvm-project" - maintainers = ['trws'] + maintainers = ['trws', 'naromero77'] family = "compiler" # Used by lmod @@ -132,23 +132,16 @@ class Llvm(CMakePackage): description="Build with OpenMP capable thread sanitizer", ) variant("python", default=False, description="Install python bindings") - variant( - "flang", - default=False, - description="Build flang branch version instead", - ) extends("python", when="+python") # Build dependency depends_on("cmake@3.4.3:", type="build") depends_on("python@2.7:2.8", when="@:4.999 ~python", type="build") - depends_on("python@2.7:2.8", when="@5: ~python +flang", type="build") depends_on("python", when="@5: ~python", type="build") # Universal dependency depends_on("python@2.7:2.8", when="@:4.999+python") - depends_on("python@2.7:2.8", when="@5:+python+flang") depends_on("python", when="@5:+python") depends_on("z3", when="@9:") @@ -158,8 +151,8 @@ class Llvm(CMakePackage): # openmp dependencies depends_on("perl-data-dumper", type=("build")) depends_on("hwloc") - depends_on("libelf") # libomptarget - depends_on("libffi") # libomptarget + depends_on("libelf", when="+cuda") # libomptarget + depends_on("libffi", when="+cuda") # libomptarget # ncurses dependency depends_on("ncurses+termlib") From 6ad717cc9df8799a56d6a126180cbc380f4e57c1 Mon Sep 17 00:00:00 2001 From: Robert Pavel Date: Wed, 1 Apr 2020 11:31:01 -0600 Subject: [PATCH 311/377] Fixed Remaining Shared Objects in Static Lua (#15787) Fixed removal of remaining references and symlinks to so files when building lua with static libraries --- .../repos/builtin/packages/lua/package.py | 55 ++++++++++--------- 1 file changed, 30 insertions(+), 25 deletions(-) diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py index c8fe652c39d..420e3b041a4 100644 --- a/var/spack/repos/builtin/packages/lua/package.py +++ b/var/spack/repos/builtin/packages/lua/package.py @@ -69,24 +69,25 @@ def install(self, spec, prefix): # compatibility with ax_lua.m4 from autoconf-archive # https://www.gnu.org/software/autoconf-archive/ax_lua.html - with working_dir(prefix.lib): - # e.g., liblua.so.5.1.5 - src_path = 'liblua.{0}.{1}'.format(dso_suffix, - str(self.version.up_to(3))) + if '+shared' in spec: + with working_dir(prefix.lib): + # e.g., liblua.so.5.1.5 + src_path = 'liblua.{0}.{1}'.format(dso_suffix, + str(self.version.up_to(3))) - # For lua version 5.1.X, the symlinks should be: - # liblua5.1.so - # liblua51.so - # liblua-5.1.so - # liblua-51.so - version_formats = [str(self.version.up_to(2)), - Version(str(self.version.up_to(2))).joined] - for version_str in version_formats: - for joiner in ['', '-']: - dest_path = 'liblua{0}{1}.{2}'.format(joiner, - version_str, - dso_suffix) - os.symlink(src_path, dest_path) + # For lua version 5.1.X, the symlinks should be: + # liblua5.1.so + # liblua51.so + # liblua-5.1.so + # liblua-51.so + version_formats = [str(self.version.up_to(2)), + Version(str(self.version.up_to(2))).joined] + for version_str in version_formats: + for joiner in ['', '-']: + dest_path = 'liblua{0}{1}.{2}'.format(joiner, + version_str, + dso_suffix) + os.symlink(src_path, dest_path) with working_dir(os.path.join('luarocks', 'luarocks')): configure('--prefix=' + prefix, '--with-lua=' + prefix) @@ -96,7 +97,8 @@ def install(self, spec, prefix): def append_paths(self, paths, cpaths, path): paths.append(os.path.join(path, '?.lua')) paths.append(os.path.join(path, '?', 'init.lua')) - cpaths.append(os.path.join(path, '?.so')) + if '+shared' in self.spec: + cpaths.append(os.path.join(path, '?.so')) def _setup_dependent_env_helper(self, env, dependent_spec): lua_paths = [] @@ -126,7 +128,8 @@ def setup_dependent_build_environment(self, env, dependent_spec): env, dependent_spec) env.set('LUA_PATH', ';'.join(lua_patterns), separator=';') - env.set('LUA_CPATH', ';'.join(lua_cpatterns), separator=';') + if '+shared' in self.spec: + env.set('LUA_CPATH', ';'.join(lua_cpatterns), separator=';') def setup_dependent_run_environment(self, env, dependent_spec): # For run time environment set only the path for dependent_spec and @@ -136,8 +139,9 @@ def setup_dependent_run_environment(self, env, dependent_spec): if dependent_spec.package.extends(self.spec): env.prepend_path('LUA_PATH', ';'.join(lua_patterns), separator=';') - env.prepend_path('LUA_CPATH', ';'.join(lua_cpatterns), - separator=';') + if '+shared' in spec: + env.prepend_path('LUA_CPATH', ';'.join(lua_cpatterns), + separator=';') def setup_run_environment(self, env): env.prepend_path( @@ -156,10 +160,11 @@ def setup_run_environment(self, env): 'LUA_PATH', os.path.join(self.spec.prefix, self.lua_lib_dir, '?', 'init.lua'), separator=';') - env.prepend_path( - 'LUA_CPATH', - os.path.join(self.spec.prefix, self.lua_lib_dir, '?.so'), - separator=';') + if '+shared' in self.spec: + env.prepend_path( + 'LUA_CPATH', + os.path.join(self.spec.prefix, self.lua_lib_dir, '?.so'), + separator=';') @property def lua_lib_dir(self): From 64b14b64c00bc6885acc1ff4d9b76898f66a8a86 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 1 Apr 2020 13:30:03 -0500 Subject: [PATCH 312/377] OpenDX: add new package (#15737) --- .../repos/builtin/packages/opendx/package.py | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/opendx/package.py diff --git a/var/spack/repos/builtin/packages/opendx/package.py b/var/spack/repos/builtin/packages/opendx/package.py new file mode 100644 index 00000000000..2cf5a9e5e36 --- /dev/null +++ b/var/spack/repos/builtin/packages/opendx/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + + +class Opendx(AutotoolsPackage): + """Open Visualization Data Explorer.""" + + homepage = "https://github.com/Mwoolsey/OpenDX" + git = "https://github.com/Mwoolsey/OpenDX.git" + + version('master', branch='master') + + depends_on('motif') # lesstif also works, but exhibits odd behaviors + depends_on('gl') + + @run_before('autoreconf') + def distclean(self): + make('distclean') From 47f135534ca3a8cf5f370fb0656c5d238741cdb7 Mon Sep 17 00:00:00 2001 From: Robert Pavel Date: Wed, 1 Apr 2020 12:32:15 -0600 Subject: [PATCH 313/377] Added v3 of Laghos (#15806) * Added v3 of Laghos Added v3 of Laghos as per https://github.com/CEED/Laghos/blob/v3.0/README.md * Update var/spack/repos/builtin/packages/laghos/package.py Changed develop->master as per PR Co-Authored-By: Adam J. Stewart * Made Metis Dependency Explicit Added explicit metis dependency * Folded @develop Laghos Deps in to @3.0: Theoretically there will be a difference between develop and 3.0: in the future but currently there is not Co-authored-by: Adam J. Stewart --- .../repos/builtin/packages/laghos/package.py | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/laghos/package.py b/var/spack/repos/builtin/packages/laghos/package.py index 7edb886a83c..438da2f5cf2 100644 --- a/var/spack/repos/builtin/packages/laghos/package.py +++ b/var/spack/repos/builtin/packages/laghos/package.py @@ -18,15 +18,15 @@ class Laghos(MakefilePackage): url = "https://github.com/CEED/Laghos/archive/v1.0.tar.gz" git = "https://github.com/CEED/Laghos.git" - version('develop', branch='master') + version('master', branch='master') + version('3.0', sha256='4db56286e15b42ecdc8d540c4888a7dec698b019df9c7ccb8319b7ea1f92d8b4') version('2.0', sha256='dd3632d5558889beec2cd3c49eb60f633f99e6d886ac868731610dd006c44c14') version('1.1', sha256='53b9bfe2af263c63eb4544ca1731dd26f40b73a0d2775a9883db51821bf23b7f') version('1.0', sha256='af50a126355a41c758fcda335a43fdb0a3cd97e608ba51c485afda3dd84a5b34') variant('metis', default=True, description='Enable/disable METIS support') - depends_on('mfem@develop+mpi+metis', when='@develop+metis') - depends_on('mfem@develop+mpi~metis', when='@develop~metis') + depends_on('metis@4.0.3:', when='+metis') # Recommended mfem version for laghos v2.0 is: ^mfem@3.4.1-laghos-v2.0 depends_on('mfem@3.4.0:+mpi+metis', when='@2.0+metis') @@ -36,6 +36,11 @@ class Laghos(MakefilePackage): depends_on('mfem@3.3.1-laghos-v1.0:+mpi+metis', when='@1.0,1.1+metis') depends_on('mfem@3.3.1-laghos-v1.0:+mpi~metis', when='@1.0,1.1~metis') + # 3.0 requirements + depends_on('hypre@2.11.2', when='@3.0:') + depends_on('mfem@develop+mpi+metis', when='@3.0:+metis') + depends_on('mfem@develop+mpi~metis', when='@3.0:~metis') + @property def build_targets(self): targets = [] @@ -46,6 +51,11 @@ def build_targets(self): targets.append('TEST_MK=%s' % spec['mfem'].package.test_mk) targets.append('CXX=%s' % spec['mpi'].mpicxx) + if self.version >= ver('3.0'): + targets.append('HYPRE_DIR=%s' % spec['hypre'].prefix) + if '+metis' in self.spec: + targets.append('METIS_DIR=%s' % spec['metis'].prefix) + return targets # See lib/spack/spack/build_systems/makefile.py From 8552efe54f55c4db14ec5923ff7b0d3025edfb15 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Wed, 1 Apr 2020 14:41:23 -0400 Subject: [PATCH 314/377] amrex: New version 20.04 (#15808) --- var/spack/repos/builtin/packages/amrex/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/amrex/package.py b/var/spack/repos/builtin/packages/amrex/package.py index aaf28a9d602..5bd19e582ba 100644 --- a/var/spack/repos/builtin/packages/amrex/package.py +++ b/var/spack/repos/builtin/packages/amrex/package.py @@ -18,6 +18,7 @@ class Amrex(CMakePackage): maintainers = ['mic84', 'asalmgren'] version('develop', branch='development') + version('20.04', sha256='ce951105336d6fcc07abe3eadf9f71161f0ccbe3e45f4547be4d0ae99e15f3c6') version('20.03', sha256='a535dcc016f0d38b55d0ab8e9067c1c53e3686961f6a1fb471cb18a0ebc909e6') version('20.02', sha256='33529a23694283d12eb37d4682aa86c9cc1240bd50124efcf4464747a7554147') version('20.01', sha256='f7026d267ca5de79ec7e740264d54230f419776d40feae705e939be0b1d8e0d3') From 37c0039eb946ce7149dae106d6ae37207d8fa335 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Wed, 1 Apr 2020 13:57:19 -0600 Subject: [PATCH 315/377] openssl: add v1.1.1f (#15802) --- var/spack/repos/builtin/packages/openssl/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 3f8e4647c41..fe650f71337 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -25,6 +25,7 @@ class Openssl(Package): # Uses Fake Autotools, should subclass Package # The latest stable version is the 1.1.1 series. This is also our Long Term # Support (LTS) version, supported until 11th September 2023. + version('1.1.1f', sha256='186c6bfe6ecfba7a5b48c47f8a1673d0f3b0e5ba2e25602dd23b629975da3f35') version('1.1.1e', sha256='694f61ac11cb51c9bf73f54e771ff6022b0327a43bbdfa1b2f19de1662a6dcbe') version('1.1.1d', sha256='1e3a91bc1f9dfce01af26026f856e064eab4c8ee0a8f457b5ae30b40b8b711f2') version('1.1.1c', sha256='f6fb3079ad15076154eda9413fed42877d668e7069d9b87396d0804fdb3f4c90') From e260eb4775d3c90b11bdc897438612cea1908257 Mon Sep 17 00:00:00 2001 From: Jonathon Anderson Date: Wed, 1 Apr 2020 15:51:59 -0600 Subject: [PATCH 316/377] Version bump for slurm package (#15790) --- var/spack/repos/builtin/packages/slurm/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/slurm/package.py b/var/spack/repos/builtin/packages/slurm/package.py index daae7743a03..c0d4cc01a91 100644 --- a/var/spack/repos/builtin/packages/slurm/package.py +++ b/var/spack/repos/builtin/packages/slurm/package.py @@ -22,8 +22,10 @@ class Slurm(AutotoolsPackage): """ homepage = 'https://slurm.schedmd.com' - url = 'https://github.com/SchedMD/slurm/archive/slurm-17-02-6-1.tar.gz' + url = 'https://github.com/SchedMD/slurm/archive/slurm-19-05-6-1.tar.gz' + version('19-05-6-1', sha256='1b83bce4260af06d644253b1f2ec2979b80b4418c631e9c9f48c2729ae2c95ba') + version('19-05-5-1', sha256='e53e67bd0bb4c37a9c481998764a746467a96bc41d6527569080514f36452c07') version('18-08-9-1', sha256='32eb0b612ca18ade1e35c3c9d3b4d71aba2b857446841606a9e54d0a417c3b03') version('18-08-0-1', sha256='62129d0f2949bc8a68ef86fe6f12e0715cbbf42f05b8da6ef7c3e7e7240b50d9') version('17-11-9-2', sha256='6e34328ed68262e776f524f59cca79ac75bcd18030951d45ea545a7ba4c45906') From 5a814ad0c5859605f66b9d4c1f6a99a656c388b7 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Wed, 1 Apr 2020 18:36:04 -0700 Subject: [PATCH 317/377] hdf5: prefer version 1.10 for now (#15810) HDF5 1.12 broke backward compatibility, so we're preferring version 1.10 for now. Packages that need the new API should specify: depends_on("hdf5@1.12:") to be explicit. We can eventually change the preference, but at the moment most libraries have not udpated to use the new HDF5. --- var/spack/repos/builtin/packages/hdf5/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index e560c23f44c..9d5505b5f78 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -25,7 +25,10 @@ class Hdf5(AutotoolsPackage): version('1.12.0', sha256='a62dcb276658cb78e6795dd29bf926ed7a9bc4edf6e77025cd2c689a8f97c17a') - version('1.10.6', sha256='5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa') + # HDF5 1.12 broke API compatibility, so we currently prefer the latest + # 1.10 release. packages that want later versions of HDF5 should specify, + # e.g., depends_on("hdf5@1.12:") to get 1.12 or higher. + version('1.10.6', sha256='5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa', preferred=True) version('1.10.5', sha256='6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8') version('1.10.4', sha256='8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2') version('1.10.3', sha256='b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39') From 814996eebcd15c036afb5bc43a29e7bf3780ca8e Mon Sep 17 00:00:00 2001 From: takanori-ihara <62980219+takanori-ihara@users.noreply.github.com> Date: Thu, 2 Apr 2020 10:38:09 +0900 Subject: [PATCH 318/377] New package:dhpmm-f (#15798) * New package:dhpmm-f * Remove unnecessary line --- .../repos/builtin/packages/dhpmm-f/package.py | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 var/spack/repos/builtin/packages/dhpmm-f/package.py diff --git a/var/spack/repos/builtin/packages/dhpmm-f/package.py b/var/spack/repos/builtin/packages/dhpmm-f/package.py new file mode 100644 index 00000000000..5e2bfa31548 --- /dev/null +++ b/var/spack/repos/builtin/packages/dhpmm-f/package.py @@ -0,0 +1,51 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class DhpmmF(MakefilePackage): + """DHPMM_P:High-precision Matrix Multiplication with Faithful Rounding""" + + homepage = "http://www.math.twcu.ac.jp/ogita/post-k/" + url = "http://www.math.twcu.ac.jp/ogita/post-k/software/DHPMM_F/DHPMM_F_alpha.tar.gz" + + version('alpha', sha256='35321ecbc749f2682775ffcd27833afc8c8eb4fa7753ce769727c9d1fe097848') + + depends_on('blas', type='link') + depends_on('lapack', type='link') + + def patch(self): + math_libs = self.spec['lapack'].libs + self.spec['blas'].libs + makefile = FileFilter('Makefile') + if self.spec.satisfies('%gcc'): + makefile.filter(r'^MKL\s+=\s1', 'MKL=0') + makefile.filter(r'^CC\s+=\sgcc', + 'CC={0}'.format(spack_cc)) + makefile.filter(r'^CXX\s+=\sg\+\+', + 'CXX={0}'.format(spack_cxx)) + makefile.filter(r'^BLASLIBS\s+=\s-llapack\s-lblas', + 'BLASLIBS={0}'.format(math_libs.ld_flags)) + elif self.spec.satisfies('%fj'): + makefile.filter(r'^#ENV\s+=\sFX100', 'ENV=FX100') + makefile.filter(r'^ENV\s+=\sGCC', '#ENV=GCC') + makefile.filter(r'^MKL\s+=\s1', 'MKL=0') + makefile.filter(r'^CC\s+=\sfccpx', + 'CC={0}'.format(spack_cc)) + makefile.filter(r'^CXX\s+=\sFCCpx', + 'CXX={0}'.format(spack_cxx)) + makefile.filter(r'^BLASLIBS\s+=\s-llapack\s-lblas', + 'BLASLIBS={0}'.format(math_libs.ld_flags)) + elif self.spec.satisfies('%intel'): + makefile.filter(r'^ENV\s+=\sGCC', '#ENV=GCC') + makefile.filter(r'^ENV\s+=\sICC', 'ENV=ICC') + makefile.filter(r'^CC\s+=\sicc', + 'CC={0}'.format(spack_cc)) + makefile.filter(r'^CXX\s+=\sicc', + 'CXX={0}'.format(spack_cxx)) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('test/source4_SpMV', prefix.bin) From 9b1820c2de6f92b322038f059baadb2f9f4060c2 Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Wed, 1 Apr 2020 21:39:04 -0400 Subject: [PATCH 319/377] package: add static library build option for yaml-cpp (#15814) * Add static build option * Fix flake8 errors and standardize spacing of build commands Co-authored-by: Carson Woods --- var/spack/repos/builtin/packages/yaml-cpp/package.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/var/spack/repos/builtin/packages/yaml-cpp/package.py b/var/spack/repos/builtin/packages/yaml-cpp/package.py index 321792bd2ef..3679b571d83 100644 --- a/var/spack/repos/builtin/packages/yaml-cpp/package.py +++ b/var/spack/repos/builtin/packages/yaml-cpp/package.py @@ -23,6 +23,8 @@ class YamlCpp(CMakePackage): variant('shared', default=True, description='Enable build of shared libraries') + variant('static', default=False, + description='Build with static libraries') variant('pic', default=True, description='Build with position independent code') variant('tests', default=False, @@ -65,6 +67,8 @@ def cmake_args(self): options.extend([ '-DBUILD_SHARED_LIBS:BOOL=%s' % ( 'ON' if '+shared' in spec else 'OFF'), + '-DBUILD_STATIC_LIBS=%s' % ( + 'ON' if '+static' in spec else 'OFF'), '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=%s' % ( 'ON' if '+pic' in spec else 'OFF'), '-DYAML_CPP_BUILD_TESTS:BOOL=%s' % ( From bb0c79b50436297861781a11b24441ca348df136 Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Wed, 1 Apr 2020 21:39:57 -0400 Subject: [PATCH 320/377] package: add variants to cgns (#15816) * Add additional configuration options for cgns * Fix syntax errors * Further syntax fixes * Convert tabs to spaces Co-authored-by: Carson Woods --- .../repos/builtin/packages/cgns/package.py | 32 +++++++++++++++---- 1 file changed, 25 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/cgns/package.py b/var/spack/repos/builtin/packages/cgns/package.py index a4f6aa05826..5e05c805af9 100644 --- a/var/spack/repos/builtin/packages/cgns/package.py +++ b/var/spack/repos/builtin/packages/cgns/package.py @@ -26,12 +26,18 @@ class Cgns(CMakePackage): version('3.3.1', sha256='81093693b2e21a99c5640b82b267a495625b663d7b8125d5f1e9e7aaa1f8d469') version('3.3.0', sha256='8422c67994f8dc6a2f201523a14f6c7d7e16313bdd404c460c16079dbeafc662') - variant('hdf5', default=True, description='Enable HDF5 interface') - variant('fortran', default=False, description='Enable Fortran interface') - variant('scoping', default=True, description='Enable scoping') - variant('mpi', default=True, description='Enable parallel cgns') - variant('int64', default=False, description='Build with 64-bit integers') - variant('shared', default=True, description='Enable shared library') + variant('hdf5', default=True, description='Enable HDF5 interface') + variant('fortran', default=False, description='Enable Fortran interface') + variant('base_scope', default=False, description='Enable base scope') + variant('scoping', default=True, description='Enable scoping') + variant('mpi', default=True, description='Enable parallel cgns') + variant('int64', default=False, description='Build with 64-bit integers') + variant('shared', default=True, description='Enable shared library') + variant('static', default=False, description='Build static libraries') + variant('testing', default=False, description='Build CGNS testing') + variant('legacy', default=False, description='Enable legacy options') + variant('parallel', default=False, description='Enable parallel features') + variant('mem_debug', default=False, description='Enable memory debugging option') depends_on('hdf5~mpi', when='+hdf5~mpi') depends_on('hdf5+mpi', when='+hdf5+mpi') @@ -49,9 +55,21 @@ def cmake_args(self): '-DCGNS_ENABLE_PARALLEL:BOOL=%s' % ( 'ON' if '+mpi' in spec else 'OFF'), '-DCGNS_ENABLE_TESTS:BOOL=OFF', + '-DCGNS_BUILD_TESTING:BOOL=%s' % ( + 'ON' if '+testing' in spec else 'OFF'), '-DCGNS_BUILD_CGNSTOOLS:BOOL=OFF', '-DCGNS_BUILD_SHARED:BOOL=%s' % ( - 'ON' if '+shared' in spec else 'OFF') + 'ON' if '+shared' in spec else 'OFF'), + '-DCGNS_BUILD_STATIC:BOOL=%s' % ( + 'ON' if '+static' in spec else 'OFF'), + '-DCGNS_ENABLE_BASE_SCOPE:BOOL=%s' % ( + 'ON' if '+base_scope' in spec else 'OFF'), + '-DCGNS_ENABLE_LEGACY:BOOL=%s' % ( + 'ON' if '+legacy' in spec else 'OFF'), + '-DCGNS_ENABLE_PARALLEL:BOOL=%s' % ( + 'ON' if '+parallel' in spec else 'OFF'), + '-DCGNS_ENABLE_MEM_DEBUG:BOOL=%s' % ( + 'ON' if '+mem_debug' in spec else 'OFF') ]) if '+mpi' in spec: From c3c057f2b3a15aad87adc8389c83c6faf1929ecb Mon Sep 17 00:00:00 2001 From: Michael Bentley Date: Wed, 1 Apr 2020 21:05:58 -0600 Subject: [PATCH 321/377] package: update flit and py-pyelftools versions (#15817) * Update flit package to v2.1.0 and add dependencies * flit: comment out bash dependency The host system should have bash available and compiling bash through spack failed for me. I'm not sure if binutils and coreutils should be listed as dependencies as well. * Add new version of py-pyelftools * py-pyelftools: add py-setuptools as a build dependency * Address review comments --- .../repos/builtin/packages/flit/package.py | 20 ++++++++++--------- .../builtin/packages/py-pyelftools/package.py | 5 ++++- 2 files changed, 15 insertions(+), 10 deletions(-) diff --git a/var/spack/repos/builtin/packages/flit/package.py b/var/spack/repos/builtin/packages/flit/package.py index 66f4c43452c..fbe1d2f3423 100644 --- a/var/spack/repos/builtin/packages/flit/package.py +++ b/var/spack/repos/builtin/packages/flit/package.py @@ -14,16 +14,18 @@ class Flit(MakefilePackage): homepage = "https://pruners.github.io/flit" url = "https://github.com/PRUNERS/FLiT" - url = "https://github.com/PRUNERS/FLiT/archive/v2.0-alpha.1.tar.gz" + url = "https://github.com/PRUNERS/FLiT/archive/v2.1.0.tar.gz" - version('2.0-alpha.1', sha256='8de2bd400acf0f513d69f3dbf588e8984dfb18b8ccaaf684391811a0582f694b') + version('2.1.0', sha256='b31ffa02fda1ab0f5555acdc6edc353d93d53ae8ef85e099f83bcf1c83e70885') + + maintainers = ['mikebentley15'] # Add dependencies - depends_on('python@3:', type='run') - depends_on('py-numpy', type='run') - depends_on('py-matplotlib tk=False', type='run') - depends_on('py-toml', type='run') + depends_on('python@3:', type='run') + depends_on('py-toml', type='run') + depends_on('py-pyelftools', type='run') + depends_on('gmake', type=('run', 'build')) + depends_on('sqlite@3:', type='run') - @property - def install_targets(self): - return ['install', 'PREFIX=%s' % self.prefix] + def edit(self, spec, prefix): + env['PREFIX'] = prefix diff --git a/var/spack/repos/builtin/packages/py-pyelftools/package.py b/var/spack/repos/builtin/packages/py-pyelftools/package.py index a69d0a2e7e9..0607560e0b3 100644 --- a/var/spack/repos/builtin/packages/py-pyelftools/package.py +++ b/var/spack/repos/builtin/packages/py-pyelftools/package.py @@ -10,6 +10,9 @@ class PyPyelftools(PythonPackage): """A pure-Python library for parsing and analyzing ELF files and DWARF debugging information""" homepage = "https://pypi.python.org/pypi/pyelftools" - url = "https://pypi.io/packages/source/p/pyelftools/pyelftools-0.23.tar.gz" + url = "https://pypi.io/packages/source/p/pyelftools/pyelftools-0.26.tar.gz" + version('0.26', sha256='86ac6cee19f6c945e8dedf78c6ee74f1112bd14da5a658d8c9d4103aed5756a2') version('0.23', sha256='fc57aadd096e8f9b9b03f1a9578f673ee645e1513a5ff0192ef439e77eab21de') + + depends_on('py-setuptools', when='@0.25:', type='build') From 60f29a9f80ea11a4a0a11c7265e336191f847b9d Mon Sep 17 00:00:00 2001 From: Jonathon Anderson Date: Thu, 2 Apr 2020 02:54:05 -0600 Subject: [PATCH 322/377] qt: added v5.14.2 (#15824) --- var/spack/repos/builtin/packages/qt/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 3f4c767a692..408ebc9f591 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -24,6 +24,7 @@ class Qt(Package): phases = ['configure', 'build', 'install'] + version('5.14.2', sha256='c6fcd53c744df89e7d3223c02838a33309bd1c291fcb6f9341505fe99f7f19fa') version('5.14.1', sha256='6f17f488f512b39c2feb57d83a5e0a13dcef32999bea2e2a8f832f54a29badb8') version('5.14.0', sha256='be9a77cd4e1f9d70b58621d0753be19ea498e6b0da0398753e5038426f76a8ba') version('5.13.1', sha256='adf00266dc38352a166a9739f1a24a1e36f1be9c04bf72e16e142a256436974e') From 7d44a0090dc04ddaa81cb2653f2211e8928996e9 Mon Sep 17 00:00:00 2001 From: Jonathon Anderson Date: Thu, 2 Apr 2020 02:55:20 -0600 Subject: [PATCH 323/377] cryptsetup: added v2.2.2, v2.2.3 and v2.3.1 (#15823) Also confined the included patch to the earlier versions, as indicated. --- var/spack/repos/builtin/packages/cryptsetup/package.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/cryptsetup/package.py b/var/spack/repos/builtin/packages/cryptsetup/package.py index ccde594c84f..99c14de004b 100644 --- a/var/spack/repos/builtin/packages/cryptsetup/package.py +++ b/var/spack/repos/builtin/packages/cryptsetup/package.py @@ -16,6 +16,9 @@ class Cryptsetup(AutotoolsPackage): # If you're adding newer versions, check whether the patch below # still needs to be applied. + version('2.3.1', sha256='92aba4d559a2cf7043faed92e0f22c5addea36bd63f8c039ba5a8f3a159fe7d2') + version('2.2.3', sha256='2af0ec9551ab9c870074cae9d3f68d82cab004f4095fa89db0e4413713424a46') + version('2.2.2', sha256='2af0ec9551ab9c870074cae9d3f68d82cab004f4095fa89db0e4413713424a46') version('2.2.1', sha256='94e79a31ed38bdb0acd9af7ccca1605a2ac62ca850ed640202876b1ee11c1c61') depends_on('libuuid', type=('build', 'link')) @@ -36,7 +39,7 @@ class Cryptsetup(AutotoolsPackage): # the LDFLAGS. See https://gitlab.com/cryptsetup/cryptsetup/issues/479 # This *should* be unnecessary starting with release 2.2.2, see # https://gitlab.com/cryptsetup/cryptsetup/issues/479#note_227617031 - patch('autotools-libintl.patch') + patch('autotools-libintl.patch', when='@:2.2.1') def url_for_version(self, version): url = "https://www.kernel.org/pub/linux/utils/cryptsetup/v{0}/cryptsetup-{1}.tar.xz" From 8078089914b9df029bc98f87d0dd29de0018a403 Mon Sep 17 00:00:00 2001 From: "Kelly (KT) Thompson" Date: Thu, 2 Apr 2020 03:06:21 -0600 Subject: [PATCH 324/377] cmake: added v3.17.0 (#15822) --- var/spack/repos/builtin/packages/cmake/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index 444a22e52a5..ce436d2ea9f 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -13,6 +13,7 @@ class Cmake(Package): url = 'https://github.com/Kitware/CMake/releases/download/v3.15.5/cmake-3.15.5.tar.gz' maintainers = ['chuckatkins'] + version('3.17.0', sha256='b74c05b55115eacc4fa2b77a814981dbda05cdc95a53e279fe16b7b272f00847') version('3.16.5', sha256='5f760b50b8ecc9c0c37135fae5fbf00a2fef617059aa9d61c1bb91653e5a8bfc') version('3.16.2', sha256='8c09786ec60ca2be354c29829072c38113de9184f29928eb9da8446a5f2ce6a9') version('3.16.1', sha256='a275b3168fa8626eca4465da7bb159ff07c8c6cb0fb7179be59e12cbdfa725fd') From d921974db1510831757efcbe12dc26eebab791eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=81=A5=E7=BE=8E=E7=8C=9E=E7=8C=81?= Date: Thu, 2 Apr 2020 17:13:17 +0800 Subject: [PATCH 325/377] py-ephem: added new package at v3.7.71 (#15438) --- .../repos/builtin/packages/py-ephem/package.py | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-ephem/package.py diff --git a/var/spack/repos/builtin/packages/py-ephem/package.py b/var/spack/repos/builtin/packages/py-ephem/package.py new file mode 100644 index 00000000000..b3f62ae3cf7 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-ephem/package.py @@ -0,0 +1,16 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyEphem(PythonPackage): + """PyEphem provides an ephem Python package for + performing high-precision astronomy computations.""" + + homepage = "https://rhodesmill.org/pyephem/" + url = "https://github.com/brandon-rhodes/pyephem/archive/v3.7.7.1.tar.gz" + + version('3.7.7.1', sha256='d9d05d85c0d38a79169acaef25964ac9df2d808f0d833354545b9ef681ff584d') From d2b6ef98f129e1a7b8dba7b267c9c49bdcb1683f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=81=A5=E7=BE=8E=E7=8C=9E=E7=8C=81?= Date: Thu, 2 Apr 2020 18:07:22 +0800 Subject: [PATCH 326/377] py-pyfits: added new package at v3.5 (#15825) --- .../builtin/packages/py-pyfits/package.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-pyfits/package.py diff --git a/var/spack/repos/builtin/packages/py-pyfits/package.py b/var/spack/repos/builtin/packages/py-pyfits/package.py new file mode 100644 index 00000000000..f013175d339 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pyfits/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPyfits(PythonPackage): + """The PyFITS module is a Python library providing access to + FITS(Flexible Image Transport System) files.""" + + homepage = "https://github.com/spacetelescope/pyfits" + url = "https://github.com/spacetelescope/PyFITS/archive/3.5.tar.gz" + + version('3.5', sha256='fd32596ee09170a70ddc87d0dfc5503d860ef6b68abcff486d7aa6993dff6162') + + depends_on('py-setuptools', type='build') + depends_on('py-numpy', type=('build', 'run')) From 1f6f395337988ad8b35d9603a5f54abf38b91e3c Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Thu, 2 Apr 2020 19:08:09 +0900 Subject: [PATCH 327/377] ppOpen-APPL/BEM: added new package at v0.5.0 (#15819) --- .../packages/ppopen-appl-bem/package.py | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ppopen-appl-bem/package.py diff --git a/var/spack/repos/builtin/packages/ppopen-appl-bem/package.py b/var/spack/repos/builtin/packages/ppopen-appl-bem/package.py new file mode 100644 index 00000000000..7260e1befcd --- /dev/null +++ b/var/spack/repos/builtin/packages/ppopen-appl-bem/package.py @@ -0,0 +1,79 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os + + +class PpopenApplBem(MakefilePackage): + """ppOpen-APPL/BEM is software used to support a boundary element analysis + executed on a parallel computer. + + The current version includes a software framework for a parallel BEM + analysis and an H-matrix library. + If you want to use the framework based on dense matrix computations, + please move to the directory 'src/framework' and + 'src/framework_with_template'. + If you want to use the H-matrix library, please + move to the directly 'src/HACApK_with_BEM-BB-framework_1.0.0'. + """ + + homepage = "http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/" + url = "file://{0}/ppohBEM_0.5.0.tar.gz".format(os.getcwd()) + + version('0.5.0', sha256='bf5e32902c97674c99353ee35de9c89206659e82b9c3d1f6edc9beffbb7c9d5f') + + depends_on('mpi') + + parallel = False + hacapk_src_dir = join_path( + 'HACApK_1.0.0', + 'src', + 'HACApK_with_BEM-BB-framework_1.0.0' + ) + src_directories = [ + join_path('bem-bb-framework_dense', 'src', 'framework_with_templates'), + join_path('bem-bb-framework_dense', 'src', 'framework'), + hacapk_src_dir + ] + + def edit(self, spec, prefix): + flags = [self.compiler.openmp_flag] + fflags = flags[:] + if spec.satisfies('%gcc'): + fflags.append('-ffree-line-length-none') + filter_file( + 'bem-bb-SCM.out', + 'HACApK-bem-bb-sSCM.out', + join_path(self.hacapk_src_dir, 'Makefile') + ) + for d in self.src_directories: + with working_dir(d): + with open('Makefile', 'a') as m: + m.write('ifeq ($(SYSTEM),spack)\n') + m.write(' CC = {0}\n'.format(spec['mpi'].mpicc)) + m.write(' F90 = {0}\n'.format(spec['mpi'].mpifc)) + m.write(' CCFLAGS = {0}\n'.format(' '.join(flags))) + m.write(' F90FLAGS = {0}\n'.format(' '.join(fflags))) + m.write(' FFLAGS = {0}\n'.format(' '.join(fflags))) + m.write(' LDFLAGS = {0}\n'.format(' '.join(flags))) + m.write('endif\n') + + def build(self, spec, prefix): + for d in self.src_directories: + with working_dir(d): + make('SYSTEM=spack') + + def install(self, spec, prefix): + mkdir(prefix.bin) + mkdir(prefix.src) + for d in self.src_directories: + for f in find(d, '*.out'): + copy(f, prefix.bin) + install_src = join_path(prefix.src, os.path.basename(d)) + mkdir(install_src) + install_tree(d, install_src) + with working_dir(install_src): + make('clean') From 144557e945ca71a4d7e790d471137874bf6bfb05 Mon Sep 17 00:00:00 2001 From: iarspider Date: Thu, 2 Apr 2020 15:52:37 +0200 Subject: [PATCH 328/377] c-blosc: Add variants to disable building tests and benchmarks (#15789) * Add variants to disable building tests and benchmarks * Flake8 * Update package.py * Update package.py * Update package.py --- var/spack/repos/builtin/packages/c-blosc/package.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/var/spack/repos/builtin/packages/c-blosc/package.py b/var/spack/repos/builtin/packages/c-blosc/package.py index 8e11cb0956a..71280590566 100644 --- a/var/spack/repos/builtin/packages/c-blosc/package.py +++ b/var/spack/repos/builtin/packages/c-blosc/package.py @@ -50,6 +50,13 @@ def cmake_args(self): args.append('-DPREFER_EXTERNAL_ZSTD=ON') args.append('-DPREFER_EXTERNAL_LZ4=ON') + if self.run_tests: + args.append('-DBUILD_TESTS=ON') + args.append('-DBUILD_BENCHMARKS=ON') + else: + args.append('-DBUILD_TESTS=OFF') + args.append('-DBUILD_BENCHMARKS=OFF') + return args @run_after('install') From 8b52f9f37d904a8c401da0096d9e5a1f1d600a13 Mon Sep 17 00:00:00 2001 From: Matthieu Dorier Date: Thu, 2 Apr 2020 23:15:45 +0100 Subject: [PATCH 329/377] unqlite: Patching unqlite to be able to build a shared library (#15830) * Patching unqlite to be able to build a shared library * Correcting a whitespace for flake8 to pass * added comment about PR on unqlite * extra commit to force github to merge --- ...IC-key-word-to-enable-building-a-sha.patch | 26 +++++++++++++++++++ .../repos/builtin/packages/unqlite/package.py | 8 ++++++ 2 files changed, 34 insertions(+) create mode 100644 var/spack/repos/builtin/packages/unqlite/0001-Removed-the-STATIC-key-word-to-enable-building-a-sha.patch diff --git a/var/spack/repos/builtin/packages/unqlite/0001-Removed-the-STATIC-key-word-to-enable-building-a-sha.patch b/var/spack/repos/builtin/packages/unqlite/0001-Removed-the-STATIC-key-word-to-enable-building-a-sha.patch new file mode 100644 index 00000000000..70602845e27 --- /dev/null +++ b/var/spack/repos/builtin/packages/unqlite/0001-Removed-the-STATIC-key-word-to-enable-building-a-sha.patch @@ -0,0 +1,26 @@ +From 7c14b18c4967c04344ceba2da90467cd27ee5678 Mon Sep 17 00:00:00 2001 +From: Matthieu Dorier +Date: Thu, 2 Apr 2020 12:43:19 +0100 +Subject: [PATCH] Removed the STATIC key word to enable building a shared + library + +--- + CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index f2bb3cd..efb63a7 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -18,7 +18,7 @@ SET(SOURCES_UNQLITE + ) + + SET(UNQLITE_STATIC_LIB unqlite) +-ADD_LIBRARY(${UNQLITE_STATIC_LIB} STATIC ${HEADERS_UNQLITE} ${SOURCES_UNQLITE}) ++ADD_LIBRARY(${UNQLITE_STATIC_LIB} ${HEADERS_UNQLITE} ${SOURCES_UNQLITE}) + + INSTALL(TARGETS ${UNQLITE_STATIC_LIB} COMPONENT devel ARCHIVE DESTINATION lib) + INSTALL(FILES ${HEADERS_UNQLITE} COMPONENT devel DESTINATION include) +-- +2.20.1 + diff --git a/var/spack/repos/builtin/packages/unqlite/package.py b/var/spack/repos/builtin/packages/unqlite/package.py index 84c3b5575e4..e23f97c02b0 100644 --- a/var/spack/repos/builtin/packages/unqlite/package.py +++ b/var/spack/repos/builtin/packages/unqlite/package.py @@ -16,3 +16,11 @@ class Unqlite(CMakePackage): version('master', branch='master') version('1.1.9', sha256='33d5b5e7b2ca223942e77d31112d2e20512bc507808414451c8a98a7be5e15c0') + + # This patch corresponds to https://github.com/symisc/unqlite/pull/99 + # It should restricted to @1.1.9 once the PR lands. + patch('0001-Removed-the-STATIC-key-word-to-enable-building-a-sha.patch') + + def cmake_args(self): + args = ["-DBUILD_SHARED_LIBS:BOOL=ON"] + return args From 06ebb94f375b70ceae59fb2f4689c3c4e25e87aa Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Thu, 2 Apr 2020 14:59:48 +0200 Subject: [PATCH 330/377] go: Add 1.14.1 and 1.13.9 --- var/spack/repos/builtin/packages/go/package.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py index 09d5796c09d..50ade3e2c30 100644 --- a/var/spack/repos/builtin/packages/go/package.py +++ b/var/spack/repos/builtin/packages/go/package.py @@ -35,16 +35,18 @@ class Go(Package): extendable = True - version('1.14', sha256='6d643e46ad565058c7a39dac01144172ef9bd476521f42148be59249e4b74389') + version('1.14.1', sha256='2ad2572115b0d1b4cb4c138e6b3a31cee6294cb48af75ee86bec3dca04507676') + version('1.14', sha256='6d643e46ad565058c7a39dac01144172ef9bd476521f42148be59249e4b74389') + version('1.13.9', sha256='34bb19d806e0bc4ad8f508ae24bade5e9fedfa53d09be63b488a9314d2d4f31d') version('1.13.8', sha256='b13bf04633d4d8cf53226ebeaace8d4d2fd07ae6fa676d0844a688339debec34') version('1.13.7', sha256='e4ad42cc5f5c19521fbbbde3680995f2546110b5c6aa2b48c3754ff7af9b41f4') version('1.13.6', sha256='aae5be954bdc40bcf8006eb77e8d8a5dde412722bc8effcdaf9772620d06420c') version('1.13.5', sha256='27d356e2a0b30d9983b60a788cf225da5f914066b37a6b4f69d457ba55a626ff') - version('1.13.4', sha256='95dbeab442ee2746b9acf0934c8e2fc26414a0565c008631b04addb8c02e7624') + version('1.13.4', sha256='95dbeab442ee2746b9acf0934c8e2fc26414a0565c008631b04addb8c02e7624') version('1.13.3', sha256='4f7123044375d5c404280737fbd2d0b17064b66182a65919ffe20ffe8620e3df') version('1.13.2', sha256='1ea68e01472e4276526902b8817abd65cf84ed921977266f0c11968d5e915f44') version('1.13.1', sha256='81f154e69544b9fa92b1475ff5f11e64270260d46e7e36c34aafc8bc96209358') - version('1.13', sha256='3fc0b8b6101d42efd7da1da3029c0a13f22079c0c37ef9730209d8ec665bf122') + version('1.13', sha256='3fc0b8b6101d42efd7da1da3029c0a13f22079c0c37ef9730209d8ec665bf122') version('1.12.17', sha256='de878218c43aa3c3bad54c1c52d95e3b0e5d336e1285c647383e775541a28b25') version('1.12.15', sha256='8aba74417e527524ad5724e6e6c21016795d1017692db76d1b0851c6bdec84c3') version('1.12.14', sha256='39dbf05f7e2ffcb19b08f07d53dcc96feadeb1987fef9e279e7ff0c598213064') From 4d2de863ef8f0e0cb4a11b54942375fc069d6de8 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 2 Apr 2020 14:45:29 -0500 Subject: [PATCH 331/377] intel-mkl-dnn: add 1.3 --- var/spack/repos/builtin/packages/intel-mkl-dnn/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py b/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py index d5160200f3a..c57b3c70a77 100644 --- a/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py +++ b/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py @@ -11,10 +11,11 @@ class IntelMklDnn(CMakePackage): (Intel(R) MKL-DNN).""" homepage = "https://intel.github.io/mkl-dnn/" - url = "https://github.com/intel/mkl-dnn/archive/v1.2.2.tar.gz" + url = "https://github.com/intel/mkl-dnn/archive/v1.3.tar.gz" maintainers = ['adamjstewart'] + version('1.3', sha256='7396c20bd0c2dcf71cec84422bd6f9b91778938c10a7578424a7681fb822b077') version('1.2.2', sha256='a71ec1f27c30b8a176605e8a78444f1f12301a3c313b70ff93290926c140509c') version('1.2.1', sha256='c69544783c453ab3fbf14c7a5b9a512561267690c9fc3e7fc3470f04756e0ab3') version('1.2', sha256='30979a09753e8e35d942446c3778c9f0eba543acf2fb0282af8b9c89355d0ddf') From 0083c87c262d6baeed2c3d28df73fc6b536348db Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Thu, 2 Apr 2020 20:37:35 -0400 Subject: [PATCH 332/377] mpip: add demangling and setjmp variants (#15837) * Add demangling to mpip * Add setjmp support to mpip * Flake8 fixes --- var/spack/repos/builtin/packages/mpip/package.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/var/spack/repos/builtin/packages/mpip/package.py b/var/spack/repos/builtin/packages/mpip/package.py index ceaaba05b64..65c2453c25c 100644 --- a/var/spack/repos/builtin/packages/mpip/package.py +++ b/var/spack/repos/builtin/packages/mpip/package.py @@ -17,6 +17,10 @@ class Mpip(AutotoolsPackage): version("3.4.1", sha256="688bf37d73211e6a915f9fc59c358282a266d166c0a10af07a38a01a473296f0") variant('shared', default=False, description="Build the shared library") + variant('demangling', default=False, description="Build with demangling support") + variant('setjmp', + default=False, + description="Replace glic backtrace() with setjmp for stack trace") depends_on("elf") depends_on("libdwarf") @@ -36,4 +40,14 @@ def configure_args(self): config_args.append("--with-cc=%s" % self.spec['mpi'].mpicc) config_args.append("--with-cxx=%s" % self.spec['mpi'].mpicxx) + if '+demangling' in self.spec: + config_args.append('--enable-demangling') + else: + config_args.append('--disable-demangling') + + if '+setjmp' in self.spec: + config_args.append('--enable-setjmp') + else: + config_args.append('--disable-setjmp') + return config_args From 37e9e450c94a7f5ff94e4267f7b8d10acaf79824 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 3 Apr 2020 02:39:44 +0200 Subject: [PATCH 333/377] Updates versions of Intel packages (#15839) * update version: intel packages daal, ipp, mkl-dnn, mkl, mpi, parallel-studio, pin, tbb and makes url parameter consistent and always use single quote. * Fixes a typo with one of the sha256 checksum.. * Adds version entries for new versions of Intel packages. Co-authored-by: Robert Mijakovic --- var/spack/repos/builtin/packages/intel-daal/package.py | 2 ++ var/spack/repos/builtin/packages/intel-ipp/package.py | 2 ++ var/spack/repos/builtin/packages/intel-mkl/package.py | 2 ++ var/spack/repos/builtin/packages/intel-mpi/package.py | 2 ++ .../repos/builtin/packages/intel-parallel-studio/package.py | 3 +++ var/spack/repos/builtin/packages/intel-pin/package.py | 1 + var/spack/repos/builtin/packages/intel-tbb/package.py | 1 + var/spack/repos/builtin/packages/intel/package.py | 1 + 8 files changed, 14 insertions(+) diff --git a/var/spack/repos/builtin/packages/intel-daal/package.py b/var/spack/repos/builtin/packages/intel-daal/package.py index 9d5ab0f2eff..8ac099e65d9 100644 --- a/var/spack/repos/builtin/packages/intel-daal/package.py +++ b/var/spack/repos/builtin/packages/intel-daal/package.py @@ -11,6 +11,8 @@ class IntelDaal(IntelPackage): homepage = "https://software.intel.com/en-us/daal" + version('2020.1.217', sha256='3f84dea0ce1038ac1b9c25b3e2c02e9fac440fa36cc8adfce69edfc06fe0edda', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16536/l_daal_2020.1.217.tgz') version('2020.0.166', sha256='695166c9ab32ac5d3006d6d35162db3c98734210507144e315ed7c3b7dbca9c1', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16234/l_daal_2020.0.166.tgz') version('2019.5.281', sha256='e92aaedbe35c9daf1c9483260cb2363da8a85fa1aa5566eb38cf4b1f410bc368', diff --git a/var/spack/repos/builtin/packages/intel-ipp/package.py b/var/spack/repos/builtin/packages/intel-ipp/package.py index 1727e488be9..04df142bf5f 100644 --- a/var/spack/repos/builtin/packages/intel-ipp/package.py +++ b/var/spack/repos/builtin/packages/intel-ipp/package.py @@ -11,6 +11,8 @@ class IntelIpp(IntelPackage): homepage = "https://software.intel.com/en-us/intel-ipp" + version('2020.1.217', sha256='0bf8ac7e635e7e602cf201063a1a7dea3779b093104563fdb15e6b7ecf2f00a7', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16534/l_ipp_2020.1.217.tgz') version('2020.0.166', sha256='6844007892ba524e828f245355cee44e8149f4c233abbbea16f7bb55a7d6ecff', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16233/l_ipp_2020.0.166.tgz') version('2019.5.281', sha256='61d1e1da1a4a50f1cf02a3ed44e87eed05e94d58b64ef1e67a3bdec363bee713', diff --git a/var/spack/repos/builtin/packages/intel-mkl/package.py b/var/spack/repos/builtin/packages/intel-mkl/package.py index 423223589af..4247f9bb8ed 100644 --- a/var/spack/repos/builtin/packages/intel-mkl/package.py +++ b/var/spack/repos/builtin/packages/intel-mkl/package.py @@ -13,6 +13,8 @@ class IntelMkl(IntelPackage): homepage = "https://software.intel.com/en-us/intel-mkl" + version('2020.1.217', sha256='082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/l_mkl_2020.1.217.tgz') version('2020.0.166', sha256='f6d92deb3ff10b11ba3df26b2c62bb4f0f7ae43e21905a91d553e58f0f5a8ae0', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16232/l_mkl_2020.0.166.tgz') version('2019.5.281', sha256='9995ea4469b05360d509c9705e9309dc983c0a10edc2ae3a5384bc837326737e', diff --git a/var/spack/repos/builtin/packages/intel-mpi/package.py b/var/spack/repos/builtin/packages/intel-mpi/package.py index 27885ed1f21..15cb84150ef 100644 --- a/var/spack/repos/builtin/packages/intel-mpi/package.py +++ b/var/spack/repos/builtin/packages/intel-mpi/package.py @@ -11,6 +11,8 @@ class IntelMpi(IntelPackage): homepage = "https://software.intel.com/en-us/intel-mpi-library" + version('2019.7.217', sha256='90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07', + url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/l_mpi_2019.7.217.tgz') version('2019.6.166', sha256='119be69f1117c93a9e5e9b8b4643918e55d2a55a78ad9567f77d16cdaf18cd6e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16120/l_mpi_2019.6.166.tgz') version('2019.5.281', sha256='9c59da051f1325b221e5bc4d8b689152e85d019f143069fa39e17989306811f4', diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py index f1b453c257c..410cd4045e4 100644 --- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py +++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py @@ -20,6 +20,7 @@ class IntelParallelStudio(IntelPackage): # in the 'intel' package. # Cluster Edition (top tier; all components included) + version('cluster.2020.1', sha256='fd11d8de72b2bd60474f8bce7b463e4cbb2255969b9eaf24f689575aa2a2abab', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16526/parallel_studio_xe_2020_update1_cluster_edition.tgz') version('cluster.2020.0', sha256='573b1d20707d68ce85b70934cfad15b5ad9cc14124a261c17ddd7717ba842c64', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16225/parallel_studio_xe_2020_cluster_edition.tgz') # version('cluster.2019.5', sha256='c03421de616bd4e640ed25ce4103ec9c5c85768a940a5cb5bd1e97b45be33904', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15809/parallel_studio_xe_2019_update5_cluster_edition.tgz') @@ -58,6 +59,7 @@ class IntelParallelStudio(IntelPackage): # NB: Pre-2018 download packages for Professional are the same as for # Cluster; differences manifest only in the tokens present in the license # file delivered as part of the purchase. + version('professional.2020.1', sha256='5b547be92ecf50cb338b3038a565f5609135b27aa98a8b7964879eb2331eb29a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16527/parallel_studio_xe_2020_update1_professional_edition.tgz') version('professional.2020.0', sha256='e88cad18d28da50ed9cb87b12adccf13efd91bf94731dc33290481306c6f15ac', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16226/parallel_studio_xe_2020_professional_edition.tgz') # version('professional.2019.5', sha256='0ec638330214539361f8632e20759f385a5a78013dcc980ee93743d86d354452', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15810/parallel_studio_xe_2019_update5_professional_edition.tgz') @@ -92,6 +94,7 @@ class IntelParallelStudio(IntelPackage): version('professional.2015.1', sha256='84fdf48d1de20e1d580ba5d419a5bc1c55d217a4f5dc1807190ecffe0229a62b', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4992/parallel_studio_xe_2015_update1.tgz') # Composer Edition (basic tier; excluded: MPI/..., Advisor/Inspector/Vtune) + version('composer.2020.1', sha256='26c7e7da87b8a83adfd408b2a354d872be97736abed837364c1bf10f4469b01e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16530/parallel_studio_xe_2020_update1_composer_edition.tgz') version('composer.2020.0', sha256='9168045466139b8e280f50f0606b9930ffc720bbc60bc76f5576829ac15757ae', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/parallel_studio_xe_2020_composer_edition.tgz') # version('composer.2019.5', sha256='e8c8e4b9b46826a02c49325c370c79f896858611bf33ddb7fb204614838ad56c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15813/parallel_studio_xe_2019_update5_composer_edition.tgz') diff --git a/var/spack/repos/builtin/packages/intel-pin/package.py b/var/spack/repos/builtin/packages/intel-pin/package.py index ae0473734c3..e886ba0784c 100644 --- a/var/spack/repos/builtin/packages/intel-pin/package.py +++ b/var/spack/repos/builtin/packages/intel-pin/package.py @@ -15,6 +15,7 @@ class IntelPin(Package): homepage = "http://www.pintool.org" maintainers = ['matthiasdiener'] + version('3.13', sha256='04a36e91f3f85119c3496f364a8806c82bb675f7536a8ab45344c9890b5e2714', url='https://software.intel.com/sites/landingpage/pintool/downloads/pin-3.13-98189-g60a6ef199-gcc-linux.tar.gz') version('3.11', sha256='aa5abca475a6e106a75e6ed4ba518fb75a57549a59f00681e6bd6e3f221bd23a', url='https://software.intel.com/sites/landingpage/pintool/downloads/pin-3.11-97998-g7ecce2dac-gcc-linux.tar.gz') version('3.10', sha256='7c8f14c3a0654bab662b58aba460403138fa44517bd40052501e8e0075b2702a', url='https://software.intel.com/sites/landingpage/pintool/downloads/pin-3.10-97971-gc5e41af74-gcc-linux.tar.gz') version('3.7', sha256='4730328795be61f1addb0e505a3792a4b4ca80b1b9405acf217beec6b5b90fb8', url='https://software.intel.com/sites/landingpage/pintool/downloads/pin-3.7-97619-g0d0c92f4f-gcc-linux.tar.gz') diff --git a/var/spack/repos/builtin/packages/intel-tbb/package.py b/var/spack/repos/builtin/packages/intel-tbb/package.py index 20d8a2f9e99..94eec8a06e6 100644 --- a/var/spack/repos/builtin/packages/intel-tbb/package.py +++ b/var/spack/repos/builtin/packages/intel-tbb/package.py @@ -23,6 +23,7 @@ class IntelTbb(Package): # Note: when adding new versions, please check and update the # patches, filters and url_for_version() below as needed. + version('2020.2', sha256='4804320e1e6cbe3a5421997b52199e3c1a3829b2ecb6489641da4b8e32faf500') version('2020.1', sha256='7c96a150ed22bc3c6628bc3fef9ed475c00887b26d37bca61518d76a56510971') version('2020.0', sha256='57714f2d2cf33935db33cee93af57eb3ecd5a7bef40c1fb7ca4a41d79684b118') version('2019.9', sha256='3f5ea81b9caa195f1967a599036b473b2e7c347117330cda99b79cfcf5b77c84') diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py index 5f3c19d5788..3bb9ea5c0e2 100644 --- a/var/spack/repos/builtin/packages/intel/package.py +++ b/var/spack/repos/builtin/packages/intel/package.py @@ -13,6 +13,7 @@ class Intel(IntelPackage): # Same as in ../intel-parallel-studio/package.py, Composer Edition, # but the version numbering in Spack differs. + version('19.1.1', sha256='26c7e7da87b8a83adfd408b2a354d872be97736abed837364c1bf10f4469b01e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16530/parallel_studio_xe_2020_update1_composer_edition.tgz') version('19.1.0', sha256='9168045466139b8e280f50f0606b9930ffc720bbc60bc76f5576829ac15757ae', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16229/parallel_studio_xe_2020_composer_edition.tgz') version('19.0.5', sha256='e8c8e4b9b46826a02c49325c370c79f896858611bf33ddb7fb204614838ad56c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15813/parallel_studio_xe_2019_update5_composer_edition.tgz') version('19.0.4', sha256='1915993445323e1e78d6de73702a88fa3df2036109cde03d74ee38fef9f1abf2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15537/parallel_studio_xe_2019_update4_composer_edition.tgz') From 73ac853c3d7d5346210aadb5dc48cd1613cd759a Mon Sep 17 00:00:00 2001 From: Shintaro Iwasaki Date: Thu, 2 Apr 2020 20:11:06 -0500 Subject: [PATCH 334/377] argobots: new version 1.0 (#15786) --- var/spack/repos/builtin/packages/argobots/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/argobots/package.py b/var/spack/repos/builtin/packages/argobots/package.py index 11c8febea6a..8f967d020b1 100644 --- a/var/spack/repos/builtin/packages/argobots/package.py +++ b/var/spack/repos/builtin/packages/argobots/package.py @@ -21,6 +21,7 @@ class Argobots(AutotoolsPackage): maintainers = ['shintaro-iwasaki'] version("master", branch="master") + version("1.0", sha256="36a0815f7bf99900a9c9c1eef61ef9b3b76aa2cfc4594a304f6c8c3296da8def") version("1.0rc2", sha256="7496b8bd39930a548b01aa3b1fe8f8b582c272600ef6a05ddc4398cf21dc12a2") version("1.0rc1", sha256="2dc4487556dce602655a6535f501136f0edc3575708029c80b1af6dccd069ce7") version("1.0b1", sha256="480b85b0e8db288400088a57c2dc5639f556843b06b0492841920c38348a2a3e") From 1d14f74d197e9851ac56fb6edce17b4610bad0d1 Mon Sep 17 00:00:00 2001 From: Jennifer Herting Date: Thu, 2 Apr 2020 21:11:48 -0400 Subject: [PATCH 335/377] New Package: py-astropy-helpers (#15658) * [py-astropy-helpers] created template * [py-astropy-helpers] - removed boilerplate - added homepage - added depends_on('py-astropy') * [py-astropy-helpers] Setuptools versioning * [py-astropy-helpers] cleaned up unused build_args method * [py-astropy-helpers] py-astropy is a runtime dependency * [py-astropy-helpers] requires python@3.6: * [py-astropy-helpers] cleaned up unnecessary older versions * [py-astropy-helpers] turns out py-astropy isn't actually a dependency --- .../packages/py-astropy-helpers/package.py | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-astropy-helpers/package.py diff --git a/var/spack/repos/builtin/packages/py-astropy-helpers/package.py b/var/spack/repos/builtin/packages/py-astropy-helpers/package.py new file mode 100644 index 00000000000..636fcb8b305 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-astropy-helpers/package.py @@ -0,0 +1,21 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyAstropyHelpers(PythonPackage): + """The astropy-helpers package includes many build, + installation, and documentation-related tools used by the + Astropy project, but packaged separately for use by other + projects that wish to leverage this work.""" + + homepage = "https://github.com/astropy/astropy-helpers" + url = "https://github.com/astropy/astropy-helpers/archive/v4.0.1.tar.gz" + + version('4.0.1', sha256='88602971c3b63d6aaa6074d013f995d1e234acb3d517d70d7fcebd30cdaf5c89') + + depends_on('python@3.6:', type=('build', 'run')) + depends_on('py-setuptools@30.3:', type='build') From 1662c3581bb8e07a4a59841b31354877b24ed7c9 Mon Sep 17 00:00:00 2001 From: Carson Woods Date: Thu, 2 Apr 2020 22:09:33 -0400 Subject: [PATCH 336/377] pmix: add option for toggling pmi backwards compatibility (#15838) * Add option for toggling pmi backwards compatibility * Remove trailing whitespace --- var/spack/repos/builtin/packages/pmix/package.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/var/spack/repos/builtin/packages/pmix/package.py b/var/spack/repos/builtin/packages/pmix/package.py index fb4e37e572b..2cb5126b535 100644 --- a/var/spack/repos/builtin/packages/pmix/package.py +++ b/var/spack/repos/builtin/packages/pmix/package.py @@ -50,6 +50,10 @@ class Pmix(AutotoolsPackage): depends_on('libevent@2.0.20:2.0.22,2.1.8') depends_on('hwloc@1.11.0:1.11.99,2.0.1:', when='@3.0.0:') + variant('pmi_backwards_compatibility', + default=True, + description="Toggle pmi backwards compatibility") + def configure_args(self): spec = self.spec @@ -58,6 +62,11 @@ def configure_args(self): '--enable-static' ] + if '+pmi_backwards_compatibility' in self.spec: + config_args.append('--enable-pmi-backward-compatibility') + else: + config_args.append('--disable-pmi-backward-compatibility') + # libevent support config_args.append( '--with-libevent={0}'.format(spec['libevent'].prefix)) From 75a2f8046a5782dc227f2679d6860558db4b1bfb Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 3 Apr 2020 01:12:03 -0500 Subject: [PATCH 337/377] Add commands to facilitate Spack/Python/OS reporting (#15834) * Add --version arg to spack python command * Add `spack debug report` command --- .github/ISSUE_TEMPLATE/bug_report.md | 48 ++++++++-------------------- lib/spack/spack/cmd/debug.py | 18 ++++++++++- lib/spack/spack/cmd/python.py | 9 ++++++ lib/spack/spack/test/cmd/debug.py | 14 +++++++- lib/spack/spack/test/cmd/python.py | 7 ++++ share/spack/spack-completion.bash | 8 +++-- 6 files changed, 65 insertions(+), 39 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index b38a6774164..9a568285ea1 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -1,21 +1,11 @@ --- -name: "\U0001F41E Bug report" -about: Report a bug in the core of Spack (command not working as expected, etc.) +name: "\U0001F41E Bug report" +about: Report a bug in the core of Spack (command not working as expected, etc.) labels: "bug,triage" --- - - - -### Spack version - -```console -$ spack --version - -``` + ### Steps to reproduce the issue @@ -27,38 +17,26 @@ $ spack ### Error Message - ```console -$ spack -d --stacktrace -$ spack -d --stacktrace -... +$ spack --debug --stacktrace ``` -that activate the full debug output. ---> ### Information on your system - ---> + -### General information +### Additional information -- [ ] I have run `spack --version` and reported the version of Spack + +- [ ] I have run `spack debug report` and reported the version of Spack/Python/Platform - [ ] I have searched the issues of this repo and believe this is not a duplicate - [ ] I have run the failing commands in debug mode and reported the output - \ No newline at end of file +Other than that, thanks for taking the time to contribute to Spack! --> diff --git a/lib/spack/spack/cmd/debug.py b/lib/spack/spack/cmd/debug.py index 4fc39251aff..074e95209af 100644 --- a/lib/spack/spack/cmd/debug.py +++ b/lib/spack/spack/cmd/debug.py @@ -3,7 +3,10 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +from __future__ import print_function + import os +import platform import re from datetime import datetime from glob import glob @@ -11,7 +14,9 @@ import llnl.util.tty as tty from llnl.util.filesystem import working_dir +import spack.architecture as architecture import spack.paths +from spack.main import get_version from spack.util.executable import which description = "debugging commands for troubleshooting Spack" @@ -23,6 +28,7 @@ def setup_parser(subparser): sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='debug_command') sp.add_parser('create-db-tarball', help="create a tarball of Spack's installation metadata") + sp.add_parser('report', help='print information useful for bug reports') def _debug_tarball_suffix(): @@ -78,6 +84,16 @@ def create_db_tarball(args): tty.msg('Created %s' % tarball_name) +def report(args): + print('* **Spack:**', get_version()) + print('* **Python:**', platform.python_version()) + print('* **Platform:**', architecture.Arch( + architecture.platform(), 'frontend', 'frontend')) + + def debug(parser, args): - action = {'create-db-tarball': create_db_tarball} + action = { + 'create-db-tarball': create_db_tarball, + 'report': report, + } action[args.debug_command](args) diff --git a/lib/spack/spack/cmd/python.py b/lib/spack/spack/cmd/python.py index 2f2290aad8a..a91f3663fbe 100644 --- a/lib/spack/spack/cmd/python.py +++ b/lib/spack/spack/cmd/python.py @@ -3,6 +3,8 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +from __future__ import print_function + import os import sys import code @@ -20,6 +22,9 @@ def setup_parser(subparser): + subparser.add_argument( + '-V', '--version', action='store_true', + help='print the Python version number and exit') subparser.add_argument( '-c', dest='python_command', help='command to execute') subparser.add_argument( @@ -31,6 +36,10 @@ def setup_parser(subparser): def python(parser, args, unknown_args): + if args.version: + print('Python', platform.python_version()) + return + if args.module: sys.argv = ['spack-python'] + unknown_args + args.python_args runpy.run_module(args.module, run_name="__main__", alter_sys=True) diff --git a/lib/spack/spack/test/cmd/debug.py b/lib/spack/spack/test/cmd/debug.py index 4a06276abf0..2898ad670eb 100644 --- a/lib/spack/spack/test/cmd/debug.py +++ b/lib/spack/spack/test/cmd/debug.py @@ -3,12 +3,15 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import platform + import pytest import os import os.path -from spack.main import SpackCommand +import spack.architecture as architecture +from spack.main import SpackCommand, get_version from spack.util.executable import which debug = SpackCommand('debug') @@ -41,3 +44,12 @@ def test_create_db_tarball(tmpdir, database): spec_suffix = '%s/.spack/spec.yaml' % spec.dag_hash() assert spec_suffix in contents + + +def test_report(): + out = debug('report') + arch = architecture.Arch(architecture.platform(), 'frontend', 'frontend') + + assert get_version() in out + assert platform.python_version() in out + assert str(arch) in out diff --git a/lib/spack/spack/test/cmd/python.py b/lib/spack/spack/test/cmd/python.py index 5bc05e0127e..b1c9d3db00e 100644 --- a/lib/spack/spack/test/cmd/python.py +++ b/lib/spack/spack/test/cmd/python.py @@ -3,6 +3,8 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import platform + import pytest import spack @@ -16,6 +18,11 @@ def test_python(): assert out.strip() == spack.spack_version +def test_python_version(): + out = python('-V') + assert platform.python_version() in out + + def test_python_with_module(): # pytest rewrites a lot of modules, which interferes with runpy, so # it's hard to test this. Trying to import a module like sys, that diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash index 38788438f7d..6df546e89f0 100755 --- a/share/spack/spack-completion.bash +++ b/share/spack/spack-completion.bash @@ -655,7 +655,7 @@ _spack_debug() { then SPACK_COMPREPLY="-h --help" else - SPACK_COMPREPLY="create-db-tarball" + SPACK_COMPREPLY="create-db-tarball report" fi } @@ -663,6 +663,10 @@ _spack_debug_create_db_tarball() { SPACK_COMPREPLY="-h --help" } +_spack_debug_report() { + SPACK_COMPREPLY="-h --help" +} + _spack_dependencies() { if $list_options then @@ -1272,7 +1276,7 @@ _spack_pydoc() { _spack_python() { if $list_options then - SPACK_COMPREPLY="-h --help -c -m" + SPACK_COMPREPLY="-h --help -V --version -c -m" else SPACK_COMPREPLY="" fi From e227a684b93b9eabf78deaa51847a6f14fa322fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=81=A5=E7=BE=8E=E7=8C=9E=E7=8C=81?= Date: Fri, 3 Apr 2020 16:29:25 +0800 Subject: [PATCH 338/377] py-d2to1: added v0.2.12 (#15844) --- .../builtin/packages/py-d2to1/package.py | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-d2to1/package.py diff --git a/var/spack/repos/builtin/packages/py-d2to1/package.py b/var/spack/repos/builtin/packages/py-d2to1/package.py new file mode 100644 index 00000000000..040d0b8d4b5 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-d2to1/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyD2to1(PythonPackage): + """d2to1 (the 'd' is for 'distutils') allows + using distutils2-like setup.cfg files for a package's + metadata with a distribute/setuptools setup.py script.""" + + homepage = "https://github.com/embray/d2to1" + url = "https://github.com/embray/d2to1/archive/0.2.12.tar.gz" + + version('0.2.12.post1', sha256='80e026ccc604850d8171fd8599b3130d234c0d443e1dc4e2039be0b204cea9b4') + version('0.2.12', sha256='04ab9f3ac255d367ecda1eb59379e5031816740c3a3eda95d0dba9f6bb3b7ca4') + + depends_on('py-setuptools', type='build') From 87444aef7e939e9c10a66fb9eb288d02074c856a Mon Sep 17 00:00:00 2001 From: Toyohisa Kameyama Date: Fri, 3 Apr 2020 18:11:46 +0900 Subject: [PATCH 339/377] ppOpen-APPL/BEM-AT: added new package at v0.1.0 (#15841) --- .../ppopen-appl-bem-at/duplicate_defs.patch | 13 +++++ .../packages/ppopen-appl-bem-at/package.py | 58 +++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100755 var/spack/repos/builtin/packages/ppopen-appl-bem-at/duplicate_defs.patch create mode 100644 var/spack/repos/builtin/packages/ppopen-appl-bem-at/package.py diff --git a/var/spack/repos/builtin/packages/ppopen-appl-bem-at/duplicate_defs.patch b/var/spack/repos/builtin/packages/ppopen-appl-bem-at/duplicate_defs.patch new file mode 100755 index 00000000000..d21d9364e58 --- /dev/null +++ b/var/spack/repos/builtin/packages/ppopen-appl-bem-at/duplicate_defs.patch @@ -0,0 +1,13 @@ +diff --git a/framework_with_templates/OAT_bem-bb-fw-dense-0.1.0.f90 b/framework_with_templates/OAT_bem-bb-fw-dense-0.1.0.f90 +index edabbed..16c6a52 100644 +--- a/framework_with_templates/OAT_bem-bb-fw-dense-0.1.0.f90 ++++ b/framework_with_templates/OAT_bem-bb-fw-dense-0.1.0.f90 +@@ -1201,8 +1201,6 @@ contains + integer i, j + + include "OAT.h" +- integer iusw1_ppohBEMresidual_direct +- integer iusw1_ppohBEMmatvec_direct + + character*100 ctmp + diff --git a/var/spack/repos/builtin/packages/ppopen-appl-bem-at/package.py b/var/spack/repos/builtin/packages/ppopen-appl-bem-at/package.py new file mode 100644 index 00000000000..cba923eeeac --- /dev/null +++ b/var/spack/repos/builtin/packages/ppopen-appl-bem-at/package.py @@ -0,0 +1,58 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * +import os + + +class PpopenApplBemAt(MakefilePackage): + """ + ppOpen-APPL/BEM-AT is ppOpen-APPL/Bem with auto tuning. + If you want to use ppOpen-APPL/BERM-AT, please copy files in + src/framework_with_template from ppOpen-APPL/BEM install directory. + """ + + homepage = "http://ppopenhpc.cc.u-tokyo.ac.jp/ppopenhpc/" + url = "file://{0}/ppohBEM_AT_0.1.0.tar.gz".format(os.getcwd()) + + version('0.1.0', sha256='215034fea7d9f64e6361d8e605e04c7f5d302c87ce048dcd6d146b14d22c17f9') + # In OAT_bem-bb-fw-dense-0.1.0.f90 the 2 variables are defined. + # But ame variables are already defined in include file DAT.h. + # This patch is deleted the variables definitions + # in OAT_bem-bb-fw-dense-0.1.0.f90. + patch('duplicate_defs.patch', when="@0.1.0") + + depends_on('mpi') + depends_on('ppopen-appl-bem', type='run') + + parallel = False + build_directory = 'framework_with_templates' + build_targets = ['SYSTEM=spack'] + + def edit(self, spec, prefix): + flags = ['-O3', self.compiler.openmp_flag] + fflags = flags[:] + if spec.satisfies('%gcc'): + fflags.append('-ffree-line-length-none') + with open(join_path(self.build_directory, 'Makefile'), 'a') as m: + m.write('ifeq ($(SYSTEM),spack)\n') + m.write(' CC = {0}\n'.format(spec['mpi'].mpicc)) + m.write(' F90 = {0}\n'.format(spec['mpi'].mpifc)) + m.write(' CCFLAGS = {0}\n'.format(' '.join(flags))) + m.write(' F90FLAGS = {0}\n'.format(' '.join(fflags))) + m.write(' FFLAGS = {0}\n'.format(' '.join(fflags))) + m.write(' LDFLAGS = {0}\n'.format(' '.join(flags))) + m.write('endif\n') + + def install(self, spec, prefix): + install_src_dir = join_path(prefix.src, self.build_directory) + mkdir(prefix.bin) + mkdirp(install_src_dir) + for f in find(self.build_directory, '*.out'): + copy(f, prefix.bin) + install_src = join_path(prefix.src, self.build_directory) + install_tree(self.build_directory, install_src_dir) + with working_dir(install_src): + make('clean') From c0d2f70d02856508d4edd61d710de05d2a5ef178 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=81=A5=E7=BE=8E=E7=8C=9E=E7=8C=81?= Date: Fri, 3 Apr 2020 17:12:59 +0800 Subject: [PATCH 340/377] py-stsci-distutils: new package at v0.3.8 (#15845) --- .../packages/py-stsci-distutils/package.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-stsci-distutils/package.py diff --git a/var/spack/repos/builtin/packages/py-stsci-distutils/package.py b/var/spack/repos/builtin/packages/py-stsci-distutils/package.py new file mode 100644 index 00000000000..f14a6ebd468 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-stsci-distutils/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyStsciDistutils(PythonPackage): + """This package contains utilities used to + package some of STScI's Python projects.""" + + homepage = "https://github.com/spacetelescope/stsci.distutils" + url = "https://github.com/spacetelescope/stsci.distutils/archive/0.3.8.tar.gz" + + version('0.3.8', sha256='a52f3ec3b392a9cecd98d143b678c27346cbfa8f34c34698821d7e167907edce') + + depends_on('py-setuptools', type='build') + depends_on('py-d2to1', type='build') From 1461332e9712c48bc5b0ade5ea4c2c1d0f99db11 Mon Sep 17 00:00:00 2001 From: Jennifer Herting Date: Fri, 3 Apr 2020 12:07:25 -0400 Subject: [PATCH 341/377] New package: libnotify (#15769) * [libnotify] created template * [libnotify] added homepage and description * [libnotify] added dependencies * [libnotify] patch location to docbook * [libnotify] more dependency work * [libnotify] reorder dependencies * [libnotify] added variant docbook * [libnotify] more accurate dependency version * [libnotify] xsltproc still needed * [libnotify] created test variant * [libnotify] added gtkdoc varient * [libnotify] cleaned up leftover fixme * [libnotify] flake8 * [libnotify] test variant became self.run_tests * [libnotify] pkgconfig is build dependency * [libnotify] commented out broken variants * [libnotify] flake8 --- .../packages/libnotify/docbook-location.patch | 11 ++++ .../builtin/packages/libnotify/package.py | 57 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 var/spack/repos/builtin/packages/libnotify/docbook-location.patch create mode 100644 var/spack/repos/builtin/packages/libnotify/package.py diff --git a/var/spack/repos/builtin/packages/libnotify/docbook-location.patch b/var/spack/repos/builtin/packages/libnotify/docbook-location.patch new file mode 100644 index 00000000000..5fcaf2ddb77 --- /dev/null +++ b/var/spack/repos/builtin/packages/libnotify/docbook-location.patch @@ -0,0 +1,11 @@ +--- a/meson.build 2020-03-30 14:00:26.851258170 -0400 ++++ b/meson.build 2020-03-30 14:03:43.134195999 -0400 +@@ -54,7 +54,7 @@ + + if get_option('man') + xsltproc = find_program('xsltproc', required: true) +- stylesheet = 'http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl' ++ stylesheet = 'http://cdn.docbook.org/release/xsl/current/manpages/docbook.xsl' + xsltproc_command = [ + xsltproc, + '--nonet', diff --git a/var/spack/repos/builtin/packages/libnotify/package.py b/var/spack/repos/builtin/packages/libnotify/package.py new file mode 100644 index 00000000000..6407fd6406b --- /dev/null +++ b/var/spack/repos/builtin/packages/libnotify/package.py @@ -0,0 +1,57 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Libnotify(MesonPackage): + """libnotify is a library for sending desktop notifications""" + + homepage = "https://github.com/GNOME/libnotify" + url = "https://github.com/GNOME/libnotify/archive/0.7.9.tar.gz" + + version('0.7.9', sha256='9bd4f5fa911d27567e7cc2d2d09d69356c16703c4e8d22c0b49a5c45651f3af0') + + # Libnotify is having trouble with finding the DTD and XSLT for docbook, + # which is required for both of these varients. + # variant('docbook', default=False, + # description='Build docbook docs. Currently broken') + # variant('gtkdoc', default=False, + # description='Build with gtkdoc. Currently broken') + + depends_on('pkgconfig', type='build') + depends_on('glib@2.26.0:') + depends_on('gtkplus@2.90:') + depends_on('gobject-introspection') + depends_on('libxslt', type='build') + depends_on('docbook-xsl', type='build') + # depends_on('gtk-doc', when='+gtkdoc', type='build') + # depends_on('xmlto', when='+docbook', type='build') + + patch('docbook-location.patch') + + def meson_args(self): + # spec = self.spec + args = [] + + # if '+docbook' in spec: + # args.append('-Ddocbook_docs=enabled') + # else: + # args.append('-Ddocbook_docs=disabled') + args.append('-Ddocbook_docs=disabled') + + # if self.run_tests: + # args.append('-Dtests=true') + # else: + # args.append('-Dtests=false') + args.append('-Dtests=false') + + # if '+gtkdoc' in spec: + # args.append('-Dgtk_doc=true') + # else: + # args.append('-Dgtk_doc=false') + args.append('-Dgtk_doc=false') + + return args From be57c0f6e716425d624eaaa9c56c0ea603eef8f8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Simonis?= Date: Fri, 3 Apr 2020 18:33:47 +0200 Subject: [PATCH 342/377] precice: Add version 2.0.2 (#15846) --- var/spack/repos/builtin/packages/precice/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/precice/package.py b/var/spack/repos/builtin/packages/precice/package.py index 40661e43291..986bfa7f146 100644 --- a/var/spack/repos/builtin/packages/precice/package.py +++ b/var/spack/repos/builtin/packages/precice/package.py @@ -19,6 +19,7 @@ class Precice(CMakePackage): maintainers = ['fsimonis', 'MakisH'] version('develop', branch='develop') + version('2.0.2', sha256='72864480f32696e7b6da94fd404ef5cd6586e2e1640613e46b75f1afac8569ed') version('2.0.1', sha256='e4fe2d2063042761ab325f8c802f88ae088c90862af288ad1a642967d074bd50') version('2.0.0', sha256='c8979d366f06e35626a8da08a1c589df77ec13972eb524a1ba99a011e245701f') version('1.6.1', sha256='7d0c54faa2c69e52304f36608d93c408629868f16f3201f663a0f9b2008f0763') From 5e5b68c063d16e5574a66ffa216299d2d30f71d4 Mon Sep 17 00:00:00 2001 From: G-Ragghianti <33492707+G-Ragghianti@users.noreply.github.com> Date: Fri, 3 Apr 2020 12:39:29 -0400 Subject: [PATCH 343/377] Papi package: updating with new bugfix version and variant (#15849) * Added new variant "sde" to papi * Updated papi with new version and new variant "sde" --- var/spack/repos/builtin/packages/papi/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py index 6e0b6cb817a..f82f319fa0c 100644 --- a/var/spack/repos/builtin/packages/papi/package.py +++ b/var/spack/repos/builtin/packages/papi/package.py @@ -23,6 +23,7 @@ class Papi(Package): maintainers = ['G-Ragghianti'] url = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz" + version('6.0.0.1', sha256='3cd7ed50c65b0d21d66e46d0ba34cd171178af4bbf9d94e693915c1aca1e287f') version('6.0.0', sha256='3442709dae3405c2845b304c06a8b15395ecf4f3899a89ceb4d715103cb4055f') version('5.7.0', sha256='d1a3bb848e292c805bc9f29e09c27870e2ff4cda6c2fba3b7da8b4bba6547589') version('5.6.0', sha256='49b7293f9ca2d74d6d80bd06b5c4be303663123267b4ac0884cbcae4c914dc47') @@ -37,6 +38,7 @@ class Papi(Package): variant('powercap', default=False, description='Enable powercap interface support') variant('rapl', default=False, description='Enable RAPL support') variant('lmsensors', default=False, description='Enable lm_sensors support') + variant('sde', default=False, description='Enable software defined events') depends_on('lm-sensors', when='+lmsensors') From 0a9d4f6720a0695ee08095a5b051b8dd814a52f1 Mon Sep 17 00:00:00 2001 From: Jennifer Herting Date: Fri, 3 Apr 2020 14:58:02 -0400 Subject: [PATCH 344/377] New package: py-portalocker (#15854) * [py-portalocker] Create template * [py-portalocker] added homepage and description * [py-portalocker] specified dependencies * [py-portalocker] cleaned up fixmes * [py-portalocker] removed unnecessary python dependency listing --- .../builtin/packages/py-portalocker/package.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-portalocker/package.py diff --git a/var/spack/repos/builtin/packages/py-portalocker/package.py b/var/spack/repos/builtin/packages/py-portalocker/package.py new file mode 100644 index 00000000000..f4aa5145509 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-portalocker/package.py @@ -0,0 +1,18 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPortalocker(PythonPackage): + """Portalocker is a library to provide an easy API to file + locking.""" + + homepage = "https://github.com/WoLpH/portalocker" + url = "https://github.com/WoLpH/portalocker/archive/v1.6.0.tar.gz" + + version('1.6.0', sha256='084ff315ccb9fb38a7c06155d409da5df29647da7c6d2bc2b24637f9f79001ff') + + depends_on('py-setuptools@38.3.0:', type='build') From 0b99cc2261c075dd2abaf829ffc5b3bcce954bb9 Mon Sep 17 00:00:00 2001 From: Peter Scheibel Date: Fri, 3 Apr 2020 13:26:33 -0700 Subject: [PATCH 345/377] Environments/views: only override spec prefix for non-external packages (#15475) * only override spec prefix for non-external packages * add test that environment shell modifications respect explicitly-specified prefixes for external packages * add clarifying comment --- lib/spack/spack/test/cmd/env.py | 48 +++++++++++++++++++++++++++++ lib/spack/spack/user_environment.py | 2 +- 2 files changed, 49 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/test/cmd/env.py b/lib/spack/spack/test/cmd/env.py index 841e6e20c8a..4f3abb4438d 100644 --- a/lib/spack/spack/test/cmd/env.py +++ b/lib/spack/spack/test/cmd/env.py @@ -370,6 +370,54 @@ def test_init_from_yaml(tmpdir): assert not e2.specs_by_hash +@pytest.mark.usefixtures('config') +def test_env_view_external_prefix(tmpdir_factory, mutable_database, + mock_packages): + fake_prefix = tmpdir_factory.mktemp('a-prefix') + fake_bin = fake_prefix.join('bin') + fake_bin.ensure(dir=True) + + initial_yaml = StringIO("""\ +env: + specs: + - a + view: true +""") + + external_config = StringIO("""\ +packages: + a: + paths: + a: {a_prefix} + buildable: false +""".format(a_prefix=str(fake_prefix))) + external_config_dict = spack.util.spack_yaml.load_config(external_config) + + test_scope = spack.config.InternalConfigScope( + 'env-external-test', data=external_config_dict) + with spack.config.override(test_scope): + + e = ev.create('test', initial_yaml) + e.concretize() + # Note: normally installing specs in a test environment requires doing + # a fake install, but not for external specs since no actions are + # taken to install them. The installation commands also include + # post-installation functions like DB-registration, so are important + # to do (otherwise the package is not considered installed). + e.install_all() + e.write() + + env_modifications = e.add_default_view_to_shell('sh') + individual_modifications = env_modifications.split('\n') + + def path_includes_fake_prefix(cmd): + return 'export PATH' in cmd and str(fake_bin) in cmd + + assert any( + path_includes_fake_prefix(cmd) for cmd in individual_modifications + ) + + def test_init_with_file_and_remove(tmpdir): """Ensure a user can remove from any position in the spack.yaml file.""" path = tmpdir.join('spack.yaml') diff --git a/lib/spack/spack/user_environment.py b/lib/spack/spack/user_environment.py index 4c9fdc3d67f..5f2c1c6f502 100644 --- a/lib/spack/spack/user_environment.py +++ b/lib/spack/spack/user_environment.py @@ -65,7 +65,7 @@ def environment_modifications_for_spec(spec, view=None): This list is specific to the location of the spec or its projection in the view.""" spec = spec.copy() - if view: + if view and not spec.external: spec.prefix = prefix.Prefix(view.view().get_projection_for_spec(spec)) # generic environment modifications determined by inspecting the spec From bae4f91bfe4e93cb8f2364c6580a54dfda0e3832 Mon Sep 17 00:00:00 2001 From: G-Ragghianti <33492707+G-Ragghianti@users.noreply.github.com> Date: Fri, 3 Apr 2020 16:33:20 -0400 Subject: [PATCH 346/377] Add option "--first" for "spack load" (#15622) * Implemented --first option for "spack load" * added test for "spack load --first" Co-authored-by: gragghia --- lib/spack/docs/workflows.rst | 6 ++++-- lib/spack/spack/cmd/__init__.py | 10 +++++++--- lib/spack/spack/cmd/load.py | 10 +++++++++- lib/spack/spack/test/cmd/load.py | 15 ++++++++++++++- share/spack/spack-completion.bash | 2 +- 5 files changed, 35 insertions(+), 8 deletions(-) diff --git a/lib/spack/docs/workflows.rst b/lib/spack/docs/workflows.rst index 89d17e98b28..9ce664b6cad 100644 --- a/lib/spack/docs/workflows.rst +++ b/lib/spack/docs/workflows.rst @@ -284,8 +284,10 @@ have some drawbacks: The ``spack load`` and ``spack module tcl loads`` commands, on the other hand, are not very smart: if the user-supplied spec matches more than one installed package, then ``spack module tcl loads`` will - fail. This may change in the future. For now, the workaround is to - be more specific on any ``spack load`` commands that fail. + fail. This default behavior may change in the future. For now, + the workaround is to either be more specific on any failing ``spack load`` + commands or to use ``spack load --first`` to allow spack to load the + first matching spec. """""""""""""""""""""" diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py index 2a75a87b549..83e12004a19 100644 --- a/lib/spack/spack/cmd/__init__.py +++ b/lib/spack/spack/cmd/__init__.py @@ -177,7 +177,7 @@ def elide_list(line_list, max_num=10): return line_list -def disambiguate_spec(spec, env, local=False, installed=True): +def disambiguate_spec(spec, env, local=False, installed=True, first=False): """Given a spec, figure out which installed package it refers to. Arguments: @@ -190,10 +190,11 @@ def disambiguate_spec(spec, env, local=False, installed=True): database query. See ``spack.database.Database._query`` for details. """ hashes = env.all_hashes() if env else None - return disambiguate_spec_from_hashes(spec, hashes, local, installed) + return disambiguate_spec_from_hashes(spec, hashes, local, installed, first) -def disambiguate_spec_from_hashes(spec, hashes, local=False, installed=True): +def disambiguate_spec_from_hashes(spec, hashes, local=False, + installed=True, first=False): """Given a spec and a list of hashes, get concrete spec the spec refers to. Arguments: @@ -213,6 +214,9 @@ def disambiguate_spec_from_hashes(spec, hashes, local=False, installed=True): if not matching_specs: tty.die("Spec '%s' matches no installed packages." % spec) + elif first: + return matching_specs[0] + elif len(matching_specs) > 1: format_string = '{name}{@version}{%compiler}{arch=architecture}' args = ["%s matches multiple packages." % spec, diff --git a/lib/spack/spack/cmd/load.py b/lib/spack/spack/cmd/load.py index 9a00ad1c589..3ef485941fe 100644 --- a/lib/spack/spack/cmd/load.py +++ b/lib/spack/spack/cmd/load.py @@ -33,6 +33,14 @@ def setup_parser(subparser): '--csh', action='store_const', dest='shell', const='csh', help="print csh commands to load the package") + subparser.add_argument( + '--first', + action='store_true', + default=False, + dest='load_first', + help="load the first match if multiple packages match the spec" + ) + subparser.add_argument( '--only', default='package,dependencies', @@ -47,7 +55,7 @@ def setup_parser(subparser): def load(parser, args): env = ev.get_env(args, 'load') - specs = [spack.cmd.disambiguate_spec(spec, env) + specs = [spack.cmd.disambiguate_spec(spec, env, first=args.load_first) for spec in spack.cmd.parse_specs(args.specs)] if not args.shell: diff --git a/lib/spack/spack/test/cmd/load.py b/lib/spack/spack/test/cmd/load.py index a10b99d45b4..e6664a9d39b 100644 --- a/lib/spack/spack/test/cmd/load.py +++ b/lib/spack/spack/test/cmd/load.py @@ -3,7 +3,8 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) import os -from spack.main import SpackCommand +import pytest +from spack.main import SpackCommand, SpackCommandError import spack.spec import spack.user_environment as uenv @@ -83,6 +84,18 @@ def test_load_includes_run_env(install_mockery, mock_fetch, mock_archive, assert 'setenv FOOBAR mpileaks' in csh_out +def test_load_first(install_mockery, mock_fetch, mock_archive, mock_packages): + """Test with and without the --first option""" + install('libelf@0.8.12') + install('libelf@0.8.13') + # Now there are two versions of libelf + with pytest.raises(SpackCommandError): + # This should cause an error due to multiple versions + load('--sh', 'libelf') + # Using --first should avoid the error condition + load('--sh', '--first', 'libelf') + + def test_load_fails_no_shell(install_mockery, mock_fetch, mock_archive, mock_packages): """Test that spack load prints an error message without a shell.""" diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash index 6df546e89f0..a4d59220fa3 100755 --- a/share/spack/spack-completion.bash +++ b/share/spack/spack-completion.bash @@ -984,7 +984,7 @@ _spack_list() { _spack_load() { if $list_options then - SPACK_COMPREPLY="-h --help -r --dependencies --sh --csh --only" + SPACK_COMPREPLY="-h --help -r --dependencies --sh --csh --first --only" else _installed_packages fi From 4173c2786832b2eec57c4098668586d0e8985db4 Mon Sep 17 00:00:00 2001 From: Matthieu Dorier Date: Fri, 3 Apr 2020 21:48:29 +0100 Subject: [PATCH 347/377] unqlite: restricted patch to version 1.1.9 (#15857) * restricted unqlite patch to version 1.1.9 * putting back the URL of the PR corresponding to the patch --- var/spack/repos/builtin/packages/unqlite/package.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/unqlite/package.py b/var/spack/repos/builtin/packages/unqlite/package.py index e23f97c02b0..ff746cc75a7 100644 --- a/var/spack/repos/builtin/packages/unqlite/package.py +++ b/var/spack/repos/builtin/packages/unqlite/package.py @@ -18,8 +18,7 @@ class Unqlite(CMakePackage): version('1.1.9', sha256='33d5b5e7b2ca223942e77d31112d2e20512bc507808414451c8a98a7be5e15c0') # This patch corresponds to https://github.com/symisc/unqlite/pull/99 - # It should restricted to @1.1.9 once the PR lands. - patch('0001-Removed-the-STATIC-key-word-to-enable-building-a-sha.patch') + patch('0001-Removed-the-STATIC-key-word-to-enable-building-a-sha.patch', when='@1.1.9') def cmake_args(self): args = ["-DBUILD_SHARED_LIBS:BOOL=ON"] From bf8fea1d53a34214b9ecec1298af011b7d58f74f Mon Sep 17 00:00:00 2001 From: G-Ragghianti <33492707+G-Ragghianti@users.noreply.github.com> Date: Fri, 3 Apr 2020 16:48:44 -0400 Subject: [PATCH 348/377] Added support for new config process for papi@6:+lmsensors (#15858) * Added support for new configuration process of lmsensors component for papi@6: * Removed extraneous blank lines --- .../repos/builtin/packages/papi/package.py | 23 +++++++++++++------ 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py index f82f319fa0c..7ec1217640a 100644 --- a/var/spack/repos/builtin/packages/papi/package.py +++ b/var/spack/repos/builtin/packages/papi/package.py @@ -46,15 +46,24 @@ class Papi(Package): # https://bitbucket.org/icl/papi/issues/46/cannot-compile-on-arch-linux patch('https://bitbucket.org/icl/papi/commits/53de184a162b8a7edff48fed01a15980664e15b1/raw', sha256='64c57b3ad4026255238cc495df6abfacc41de391a0af497c27d0ac819444a1f8', when='@5.4.0:5.6.99%gcc@8:') + def setup_build_environment(self, env): + if '+lmsensors' in self.spec and self.version >= Version('6'): + env.set('PAPI_LMSENSORS_ROOT', self.spec['lm-sensors'].prefix) + + def setup_run_environment(self, env): + if '+lmsensors' in self.spec and self.version >= Version('6'): + env.set('PAPI_LMSENSORS_ROOT', self.spec['lm-sensors'].prefix) + def install(self, spec, prefix): if '+lmsensors' in spec: - with working_dir("src/components/lmsensors"): - configure_args = [ - "--with-sensors_incdir=%s/sensors" % - spec['lm-sensors'].headers.directories[0], - "--with-sensors_libdir=%s" % - spec['lm-sensors'].libs.directories[0]] - configure(*configure_args) + if self.version < Version('6'): + with working_dir("src/components/lmsensors"): + configure_args = [ + "--with-sensors_incdir=%s/sensors" % + spec['lm-sensors'].headers.directories[0], + "--with-sensors_libdir=%s" % + spec['lm-sensors'].libs.directories[0]] + configure(*configure_args) with working_dir("src"): configure_args = ["--prefix=%s" % prefix] From 0891c5d85405e2f0b08a8a4d300115e900d043f4 Mon Sep 17 00:00:00 2001 From: Jennifer Herting Date: Fri, 3 Apr 2020 16:49:21 -0400 Subject: [PATCH 349/377] New package: py-gluoncv (#15856) * [py-gluoncv] created template * [py-gluoncv] added description and homepage * [py-gluoncv] added dependencies * [py-gluoncv] unicode in readme is causing build to fail * [py-gluoncv] cleaned up fixmes * [py-gluoncv] removed unnecessary python dependency listing * [py-gluoncv] added cython --- .../py-gluoncv/no-unicode-readme.patch | 11 ++++++ .../builtin/packages/py-gluoncv/package.py | 36 +++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-gluoncv/no-unicode-readme.patch create mode 100644 var/spack/repos/builtin/packages/py-gluoncv/package.py diff --git a/var/spack/repos/builtin/packages/py-gluoncv/no-unicode-readme.patch b/var/spack/repos/builtin/packages/py-gluoncv/no-unicode-readme.patch new file mode 100644 index 00000000000..43d0a6c5e87 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-gluoncv/no-unicode-readme.patch @@ -0,0 +1,11 @@ +--- a/README.md 2020-04-03 11:56:41.820271316 -0400 ++++ b/README.md 2020-04-03 11:56:55.901335611 -0400 +@@ -72,7 +72,7 @@ + + There are multiple versions of MXNet pre-built package available. Please refer to [mxnet packages](https://gluon-crash-course.mxnet.io/mxnet_packages.html) if you need more details about MXNet versions. + +-# Docs 📖 ++# Docs + GluonCV documentation is available at [our website](https://gluon-cv.mxnet.io/index.html). + + # Examples diff --git a/var/spack/repos/builtin/packages/py-gluoncv/package.py b/var/spack/repos/builtin/packages/py-gluoncv/package.py new file mode 100644 index 00000000000..05966766543 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-gluoncv/package.py @@ -0,0 +1,36 @@ +# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyGluoncv(PythonPackage): + """GluonCV provides implementations of state-of-the-art + (SOTA) deep learning algorithms in computer vision. It aims + to help engineers, researchers, and students quickly + prototype products, validate new ideas and learn computer + vision.""" + + homepage = "https://gluon-cv.mxnet.io/" + url = "https://github.com/dmlc/gluon-cv/archive/v0.6.0.tar.gz" + + version('0.6.0', sha256='5ac89d73f34d02b2e60595a5cc35f46d0a69376567fae3a9518005dd89161305') + + depends_on('py-setuptools', type='build') + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-tqdm', type=('build', 'run')) + depends_on('py-requests', type=('build', 'run')) + depends_on('py-matplotlib', type=('build', 'run')) + depends_on('py-portalocker', type=('build', 'run')) + depends_on('py-pillow', type=('build', 'run')) + depends_on('py-scipy', type=('build', 'run')) + depends_on('py-cython', type='build') + + patch('no-unicode-readme.patch') + + def build_args(self, spec, prefix): + args = [] + args.append('--with-cython') + return args From a7f418e0b2806eeaf832e55c6faa4707ca54b00f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=81=A5=E7=BE=8E=E7=8C=9E=E7=8C=81?= Date: Sun, 5 Apr 2020 00:10:48 +0800 Subject: [PATCH 350/377] Check if CPU family is x86_64. (#15862) * Check if CPU family is x86_64. * Remove the leading space. --- var/spack/repos/builtin/packages/fl/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/fl/package.py b/var/spack/repos/builtin/packages/fl/package.py index f314ca6cdca..98809a21f10 100644 --- a/var/spack/repos/builtin/packages/fl/package.py +++ b/var/spack/repos/builtin/packages/fl/package.py @@ -17,7 +17,7 @@ class Fl(Package): def install(self, spec, prefix): if (self.spec.satisfies('platform=linux') and - self.spec.satisfies('target=x86_64')): + self.spec.target.family == 'x86_64'): with working_dir('fl_{0}'.format(spec.version)): install_tree('.', prefix) else: From 4bb1392d7da081d071701e0f77674fd068e3216f Mon Sep 17 00:00:00 2001 From: Simon Pintarelli <1237199+simonpintarelli@users.noreply.github.com> Date: Sat, 4 Apr 2020 18:11:17 +0200 Subject: [PATCH 351/377] SIRIUS add version 6.5.1 and 6.5.2 (#15860) --- var/spack/repos/builtin/packages/sirius/package.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/var/spack/repos/builtin/packages/sirius/package.py b/var/spack/repos/builtin/packages/sirius/package.py index f45aa077819..ff81b120d4d 100644 --- a/var/spack/repos/builtin/packages/sirius/package.py +++ b/var/spack/repos/builtin/packages/sirius/package.py @@ -19,6 +19,8 @@ class Sirius(CMakePackage, CudaPackage): version('develop', branch='develop') version('master', branch='master') + version('6.5.2', sha256='c18adc45b069ebae03f94eeeeed031ee99b3d8171fa6ee73c7c6fb1e42397fe7') + version('6.5.1', sha256='599dd0fa25a4e83db2a359257a125e855d4259188cf5b0065b8e7e66378eacf3') version('6.5.0', sha256='5544f3abbb71dcd6aa08d18aceaf53c38373de4cbd0c3af44fbb39c20cfeb7cc') version('6.4.4', sha256='1c5de9565781847658c3cc11edcb404e6e6d1c5a9dfc81e977de7a9a7a162c8a') version('6.4.3', sha256='4d1effeadb84b3e1efd7d9ac88018ef567aa2e0aa72e1112f0abf2e493e2a189') From 4ee9fd46bc41759e1c8e70b70d538a458edf8413 Mon Sep 17 00:00:00 2001 From: "Nichols A. Romero" Date: Sat, 4 Apr 2020 11:12:21 -0500 Subject: [PATCH 352/377] LLVM support for mlir (#15859) --- var/spack/repos/builtin/packages/llvm/package.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py index a5aedb625d8..810203a9f00 100644 --- a/var/spack/repos/builtin/packages/llvm/package.py +++ b/var/spack/repos/builtin/packages/llvm/package.py @@ -77,6 +77,7 @@ class Llvm(CMakePackage): ) variant("lldb", default=True, description="Build the LLVM debugger") variant("lld", default=True, description="Build the LLVM linker") + variant("mlir", default=False, description="Build with MLIR support") variant( "internal_unwind", default=True, @@ -182,6 +183,9 @@ class Llvm(CMakePackage): # OMP TSAN exists in > 5.x conflicts("+omp_tsan", when="@:5.99") + # MLIR exists in > 10.x + conflicts("+mlir", when="@:9") + # Github issue #4986 patch("llvm_gcc7.patch", when="@4.0.0:4.0.1+lldb %gcc@7.0:") # Backport from llvm master + additional fix @@ -299,6 +303,8 @@ def cmake_args(self): projects.append("libcxxabi") if spec.satisfies("@3.9.0:"): cmake_args.append("-DCLANG_DEFAULT_CXX_STDLIB=libc++") + if "+mlir" in spec: + projects.append("mlir") if "+internal_unwind" in spec: projects.append("libunwind") if "+polly" in spec: From 9b9b46c0a98ec311db79592d716b27c79d501437 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 4 Apr 2020 11:35:23 -0500 Subject: [PATCH 353/377] Package rename: intel-mkl-dnn -> dnnl (#15852) --- .../{intel-mkl-dnn => dnnl}/package.py | 47 +++++++++++++++---- .../builtin/packages/py-torch/package.py | 2 +- 2 files changed, 39 insertions(+), 10 deletions(-) rename var/spack/repos/builtin/packages/{intel-mkl-dnn => dnnl}/package.py (71%) diff --git a/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py b/var/spack/repos/builtin/packages/dnnl/package.py similarity index 71% rename from var/spack/repos/builtin/packages/intel-mkl-dnn/package.py rename to var/spack/repos/builtin/packages/dnnl/package.py index c57b3c70a77..9b339a5a015 100644 --- a/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py +++ b/var/spack/repos/builtin/packages/dnnl/package.py @@ -3,14 +3,15 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) -from spack import * +import sys -class IntelMklDnn(CMakePackage): - """Intel(R) Math Kernel Library for Deep Neural Networks - (Intel(R) MKL-DNN).""" +class Dnnl(CMakePackage): + """Deep Neural Network Library (DNNL). - homepage = "https://intel.github.io/mkl-dnn/" + Formerly known as Intel MKL-DNN.""" + + homepage = "https://01.org/dnnl" url = "https://github.com/intel/mkl-dnn/archive/v1.3.tar.gz" maintainers = ['adamjstewart'] @@ -46,15 +47,38 @@ class IntelMklDnn(CMakePackage): version('0.10', sha256='59828764ae43f1151f77b8997012c52e0e757bc50af1196b86fce8934178c570') version('0.9', sha256='8606a80851c45b0076f7d4047fbf774ce13d6b6d857cb2edf95c7e1fd4bca1c7') + default_cpu_runtime = 'omp' + if sys.platform == 'darwin': + default_cpu_runtime = 'tbb' + + variant('cpu_runtime', default=default_cpu_runtime, + description='CPU threading runtime to use', + values=('omp', 'tbb', 'seq'), multi=False) + variant('gpu_runtime', default='none', + description='Runtime to use for GPU engines', + values=('ocl', 'none'), multi=False) + + # https://github.com/intel/mkl-dnn#requirements-for-building-from-source depends_on('cmake@2.8.11:', type='build') - depends_on('intel-mkl') - depends_on('llvm-openmp', when='%clang platform=darwin') + depends_on('tbb@2017:', when='cpu_runtime=tbb') + depends_on('llvm-openmp', when='%clang platform=darwin cpu_runtime=omp') + depends_on('opencl@1.2:', when='gpu_runtime=ocl') def cmake_args(self): - args = [] + args = [ + '-DDNNL_CPU_RUNTIME={0}'.format( + self.spec.variants['cpu_runtime'].value.upper()), + '-DDNNL_GPU_RUNTIME={0}'.format( + self.spec.variants['gpu_runtime'].value.upper()), + ] + + if self.run_tests: + args.append('-DDNNL_BUILD_TESTS=ON') + else: + args.append('-DDNNL_BUILD_TESTS=OFF') # https://github.com/intel/mkl-dnn/issues/591 - if self.spec.satisfies('%clang platform=darwin'): + if self.spec.satisfies('%clang platform=darwin cpu_runtime=omp'): args.extend([ '-DOpenMP_CXX_FLAGS={0}'.format(self.compiler.openmp_flag), '-DOpenMP_C_FLAGS={0}'.format(self.compiler.openmp_flag), @@ -67,5 +91,10 @@ def cmake_args(self): self.spec['llvm-openmp'].libs.ld_flags ), ]) + elif self.spec.satisfies('cpu_runtime=tbb'): + args.append('-DTBBROOT=' + self.spec['tbb'].prefix) + + if self.spec.satisfies('gpu_runtime=ocl'): + args.append('-DOPENCLROOT=' + self.spec['opencl'].prefix) return args diff --git a/var/spack/repos/builtin/packages/py-torch/package.py b/var/spack/repos/builtin/packages/py-torch/package.py index e1dbdccb6df..a60486a64ca 100644 --- a/var/spack/repos/builtin/packages/py-torch/package.py +++ b/var/spack/repos/builtin/packages/py-torch/package.py @@ -154,7 +154,7 @@ class PyTorch(PythonPackage, CudaPackage): # TODO: See if there is a way to use an external mkldnn installation. # Currently, only older versions of py-torch use an external mkldnn # library. - depends_on('intel-mkl-dnn', when='@0.4:0.4.1+mkldnn') + depends_on('dnnl', when='@0.4:0.4.1+mkldnn') # TODO: add dependency: https://github.com/Maratyszcza/NNPACK # depends_on('nnpack', when='+nnpack') depends_on('qnnpack', when='+qnnpack') From 7f8102d6d0149a13a5bf61e6ec4ad310c0debd52 Mon Sep 17 00:00:00 2001 From: darmac Date: Sun, 5 Apr 2020 00:35:46 +0800 Subject: [PATCH 354/377] openjdk: support aarch64 platform (#15840) --- .../repos/builtin/packages/openjdk/package.py | 47 ++++++++++++++----- 1 file changed, 34 insertions(+), 13 deletions(-) diff --git a/var/spack/repos/builtin/packages/openjdk/package.py b/var/spack/repos/builtin/packages/openjdk/package.py index 2007ccd78d3..437c1701ddb 100644 --- a/var/spack/repos/builtin/packages/openjdk/package.py +++ b/var/spack/repos/builtin/packages/openjdk/package.py @@ -5,6 +5,32 @@ from spack import * import os +import platform + + +# If you need to add a new version, please be aware that: +# - versions in the following dict are automatically added to the package +# - version tuple must be in the form (checksum, url) +# - checksum must be sha256 +# - package key must be in the form '{os}-{arch}' where 'os' is in the +# format returned by platform.system() and 'arch' by platform.machine() + +_versions = { + '11.0.0-2020-01-01': { + 'Linux-aarch64': ('05c7d9c90edacd853850fbb0f52f8aa482809d0452c599cb9fe0b28b3b4bf329', 'https://github.com/AdoptOpenJDK/openjdk11-binaries/releases/download/jdk11u-2020-01-01-06-13/OpenJDK11U-jdk_aarch64_linux_hotspot_2020-01-01-06-13.tar.gz')}, + '11.0.2': { + 'Linux-x86_64': ('99be79935354f5c0df1ad293620ea36d13f48ec3ea870c838f20c504c9668b57', 'https://download.java.net/java/GA/jdk11/9/GPL/openjdk-11.0.2_linux-x64_bin.tar.gz')}, + '11.0.1': { + 'Linux-x86_64': ('7a6bb980b9c91c478421f865087ad2d69086a0583aeeb9e69204785e8e97dcfd', 'https://download.java.net/java/GA/jdk11/13/GPL/openjdk-11.0.1_linux-x64_bin.tar.gz')}, + '1.8.0_191-b12': { + 'Linux-aarch64': ('8eee0aede947b804f9a5f49c8a38b52aace8a30a9ebd9383b7d06042fb5a237c', 'https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u191-b12/OpenJDK8U-jdk_aarch64_linux_hotspot_8u191b12.tar.gz')}, + '1.8.0_222-b10': { + 'Linux-x86_64': ('20cff719c6de43f8bb58c7f59e251da7c1fa2207897c9a4768c8c669716dc819', 'https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u222-b10_openj9-0.15.1/OpenJDK8U-jdk_x64_linux_openj9_8u222b10_openj9-0.15.1.tar.gz')}, + '1.8.0_202-b08': { + 'Linux-x86_64': ('533dcd8d9ca15df231a1eb392fa713a66bca85a8e76d9b4ee30975f3823636b7', 'https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u202-b08/OpenJDK8U-jdk_x64_linux_openj9_8u202b08_openj9-0.12.0.tar.gz')}, + '1.8.0_40-b25': { + 'Linux-x86_64': ('79e96dce03a14271040023231a7d0ae374b755d48adf68bbdaec30294e4e2b88', 'https://download.java.net/openjdk/jdk8u40/ri/jdk_ri-8u40-b25-linux-x64-10_feb_2015.tar.gz')}, +} class Openjdk(Package): @@ -12,22 +38,17 @@ class Openjdk(Package): homepage = "https://jdk.java.net" - version("11.0.2", sha256="99be79935354f5c0df1ad293620ea36d13f48ec3ea870c838f20c504c9668b57", - url="https://download.java.net/java/GA/jdk11/9/GPL/openjdk-11.0.2_linux-x64_bin.tar.gz") - version("11.0.1", sha256="7a6bb980b9c91c478421f865087ad2d69086a0583aeeb9e69204785e8e97dcfd", - url="https://download.java.net/java/GA/jdk11/13/GPL/openjdk-11.0.1_linux-x64_bin.tar.gz") - version("1.8.0_222-b10", sha256="20cff719c6de43f8bb58c7f59e251da7c1fa2207897c9a4768c8c669716dc819", - url="https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u222-b10_openj9-0.15.1/OpenJDK8U-jdk_x64_linux_openj9_8u222b10_openj9-0.15.1.tar.gz") - version("1.8.0_202-b08", sha256="533dcd8d9ca15df231a1eb392fa713a66bca85a8e76d9b4ee30975f3823636b7", - url="https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u202-b08/OpenJDK8U-jdk_x64_linux_openj9_8u202b08_openj9-0.12.0.tar.gz") - version('1.8.0_40-b25', sha256='79e96dce03a14271040023231a7d0ae374b755d48adf68bbdaec30294e4e2b88', - url='https://download.java.net/openjdk/jdk8u40/ri/jdk_ri-8u40-b25-linux-x64-10_feb_2015.tar.gz') + for ver, packages in _versions.items(): + key = "{0}-{1}".format(platform.system(), platform.machine()) + pkg = packages.get(key) + if pkg: + version(ver, sha256=pkg[0], url=pkg[1], expand=False) - provides('java@11', when='@11.0:11.99') provides('java@8', when='@1.8.0:1.8.999') + provides('java@11', when='@11.0:11.99') - conflicts('target=ppc64:', msg='openjdk is only available for x86_64') - conflicts('target=ppc64le:', msg='openjdk is only available for x86_64') + conflicts('target=ppc64:', msg='openjdk is only available for x86_64 and aarch64') + conflicts('target=ppc64le:', msg='openjdk is only available for x86_64 and aarch64') # FIXME: # 1. `extends('java')` doesn't work, you need to use `extends('openjdk')` From b4271d1a262f7e4bdb4e4619480910aa7fa3a8bf Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Sat, 4 Apr 2020 12:00:04 -0600 Subject: [PATCH 355/377] py-espressopp: pin py-numpy to py2 version (#15865) --- var/spack/repos/builtin/packages/py-espressopp/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-espressopp/package.py b/var/spack/repos/builtin/packages/py-espressopp/package.py index a4524da78eb..779873bc98c 100644 --- a/var/spack/repos/builtin/packages/py-espressopp/package.py +++ b/var/spack/repos/builtin/packages/py-espressopp/package.py @@ -35,7 +35,7 @@ class PyEspressopp(CMakePackage): depends_on("fftw") depends_on("py-sphinx", when="+ug", type='build') depends_on("py-sphinx", when="+pdf", type='build') - depends_on('py-numpy', type=('build', 'run')) + depends_on('py-numpy@:1.16.6', type=('build', 'run')) depends_on('py-matplotlib', when="+ug", type='build') depends_on('py-matplotlib', when="+pdf", type='build') depends_on("texlive", when="+pdf", type='build') From c99a88128ad6baf803fdb87dc51924219a211015 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Trahay?= Date: Sun, 5 Apr 2020 16:39:57 +0200 Subject: [PATCH 356/377] Version bump: eztrace-1.1-10 (#15866) * version bump: eztrace-1.1-10 * 'trahay' is the maintainer for package 'eztrace' --- var/spack/repos/builtin/packages/eztrace/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/eztrace/package.py b/var/spack/repos/builtin/packages/eztrace/package.py index 9468ce82147..ddf9808f7b7 100644 --- a/var/spack/repos/builtin/packages/eztrace/package.py +++ b/var/spack/repos/builtin/packages/eztrace/package.py @@ -11,9 +11,10 @@ class Eztrace(AutotoolsPackage): of HPC applications.""" homepage = "http://eztrace.gforge.inria.fr" - url = "https://gforge.inria.fr/frs/download.php/file/37703/eztrace-1.1-8.tar.gz" + url = "https://gitlab.com/eztrace/eztrace/-/archive/eztrace-1.1-10/eztrace-eztrace-1.1-10.tar.gz" + maintainers = ['trahay'] - version('1.1-8', sha256='d80d78a25f1eb0e6e60a3e535e3972cd178c6a8663a3d6109105dfa6a880b8ec') + version('1.1-10', sha256='97aba8f3b3b71e8e2f7ef47e00c262234e27b9cb4a870c85c525317a83a3f0d4') depends_on('mpi') From 34627fcbe55c19357dc99a5106045106160681ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=81=A5=E7=BE=8E=E7=8C=9E=E7=8C=81?= Date: Mon, 6 Apr 2020 00:21:54 +0800 Subject: [PATCH 357/377] py-pywcs: a new package. (#15826) * py-pywcs: a new package. * Fix a flake8 issue. * Add missing dependencies. * run -> build. * Add version specifications. --- .../builtin/packages/py-pywcs/package.py | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-pywcs/package.py diff --git a/var/spack/repos/builtin/packages/py-pywcs/package.py b/var/spack/repos/builtin/packages/py-pywcs/package.py new file mode 100644 index 00000000000..dea2adb2d92 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-pywcs/package.py @@ -0,0 +1,24 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class PyPywcs(PythonPackage): + """pywcs is a set of routines for + handling the FITS World Coordinate System (WCS) standard.""" + + homepage = "https://github.com/spacetelescope/pywcs" + url = "https://github.com/spacetelescope/pywcs/archive/1.12.1.tar.gz" + + version('1.12.1', sha256='efd4e0ea190e3a2521ebcde583452e126acdeac85cc8a9c78c8a96f10805b5e1') + + depends_on('python@2.6:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-d2to1@0.2.3:', type='build') + depends_on('py-stsci-distutils@0.3.2:', type='build') + depends_on('py-numpy@1.5.1:', type=('build', 'run')) + depends_on('py-pyfits@1.4:', type=('build', 'run')) + depends_on('py-astropy@0.3.1:', type=('build', 'run')) From 51fbe518b8d7400d4df806ad9c60edcb83510e4b Mon Sep 17 00:00:00 2001 From: Stephen McDowell Date: Sun, 5 Apr 2020 15:08:13 -0400 Subject: [PATCH 358/377] verify `other.exe` attr exists before use in __eq__ (#15882) --- lib/spack/spack/util/executable.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/spack/util/executable.py b/lib/spack/spack/util/executable.py index ce30e18f420..1f5fdfb7614 100644 --- a/lib/spack/spack/util/executable.py +++ b/lib/spack/spack/util/executable.py @@ -209,7 +209,7 @@ def streamify(arg, mode): istream.close() def __eq__(self, other): - return self.exe == other.exe + return hasattr(other, 'exe') and self.exe == other.exe def __neq__(self, other): return not (self == other) From 05532f9e271e18be697918fb37e348c0e4134752 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 5 Apr 2020 15:42:44 -0500 Subject: [PATCH 359/377] py-ecdsa: add new version, fix download url (#15871) --- var/spack/repos/builtin/packages/py-ecdsa/package.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-ecdsa/package.py b/var/spack/repos/builtin/packages/py-ecdsa/package.py index 18d6d7eddbf..2401b9bd276 100644 --- a/var/spack/repos/builtin/packages/py-ecdsa/package.py +++ b/var/spack/repos/builtin/packages/py-ecdsa/package.py @@ -10,11 +10,12 @@ class PyEcdsa(PythonPackage): """ECDSA cryptographic signature library (pure python)""" homepage = "https://github.com/warner/python-ecdsa" - url = "https://files.pythonhosted.org/packages/source/e/ecdsa/ecdsa-0.13.2.tar.gz" + url = "https://pypi.io/packages/source/e/ecdsa/ecdsa-0.15.tar.gz" + version('0.15', sha256='8f12ac317f8a1318efa75757ef0a651abe12e51fc1af8838fb91079445227277') version('0.13.2', sha256='5c034ffa23413ac923541ceb3ac14ec15a0d2530690413bff58c12b80e56d884') - depends_on('py-setuptools', type='build') - depends_on('py-six', type=('build', 'run')) depends_on('python@2.6:2.8,3.3:', type=('build', 'run')) + depends_on('py-setuptools', type='build') + depends_on('py-six@1.9.0:', type=('build', 'run')) depends_on('openssl', type='test') From 68b4beb725ffee6859918edc2e79bdccecdf478a Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 5 Apr 2020 15:42:57 -0500 Subject: [PATCH 360/377] py-sphinx: add 3.0.0 (#15881) --- var/spack/repos/builtin/packages/py-sphinx/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-sphinx/package.py b/var/spack/repos/builtin/packages/py-sphinx/package.py index 550b503e6c8..5aed1f39eb7 100644 --- a/var/spack/repos/builtin/packages/py-sphinx/package.py +++ b/var/spack/repos/builtin/packages/py-sphinx/package.py @@ -10,7 +10,7 @@ class PySphinx(PythonPackage): """Sphinx Documentation Generator.""" homepage = "http://sphinx-doc.org" - url = "https://pypi.io/packages/source/S/Sphinx/Sphinx-2.2.0.tar.gz" + url = "https://pypi.io/packages/source/S/Sphinx/Sphinx-3.0.0.tar.gz" import_modules = [ 'sphinx', 'sphinx.testing', 'sphinx.ext', 'sphinx.pycode', @@ -22,6 +22,7 @@ class PySphinx(PythonPackage): 'sphinx.environment.collectors', 'sphinx.environment.adapters' ] + version('3.0.0', sha256='6a099e6faffdc3ceba99ca8c2d09982d43022245e409249375edf111caf79ed3') version('2.2.0', sha256='0d586b0f8c2fc3cc6559c5e8fd6124628110514fda0e5d7c82e682d749d2e845') version('1.8.4', sha256='c1c00fc4f6e8b101a0d037065043460dffc2d507257f2f11acaed71fd2b0c83c') version('1.8.2', sha256='120732cbddb1b2364471c3d9f8bfd4b0c5b550862f99a65736c77f970b142aea') From a3b9dbcbfbfabdb0c06ef1d1ab44a980109fa9d0 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 5 Apr 2020 15:43:09 -0500 Subject: [PATCH 361/377] package urls: pypi.org -> pypi.io (#15880) --- .../repos/builtin/packages/py-backports-weakref/package.py | 2 +- var/spack/repos/builtin/packages/py-colorlog/package.py | 2 +- var/spack/repos/builtin/packages/py-colorpy/package.py | 2 +- var/spack/repos/builtin/packages/py-exodus-bundler/package.py | 2 +- var/spack/repos/builtin/packages/py-hdfs/package.py | 2 +- var/spack/repos/builtin/packages/py-jprops/package.py | 2 +- var/spack/repos/builtin/packages/py-progress/package.py | 2 +- var/spack/repos/builtin/packages/py-pyarrow/package.py | 2 +- var/spack/repos/builtin/packages/py-pyspark/package.py | 2 +- .../repos/builtin/packages/py-requests-futures/package.py | 2 +- var/spack/repos/builtin/packages/py-testinfra/package.py | 2 +- var/spack/repos/builtin/packages/py-usgs/package.py | 4 +++- var/spack/repos/builtin/packages/py-uwsgi/package.py | 2 +- 13 files changed, 15 insertions(+), 13 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-backports-weakref/package.py b/var/spack/repos/builtin/packages/py-backports-weakref/package.py index b3e5ad65bca..ef88d792566 100644 --- a/var/spack/repos/builtin/packages/py-backports-weakref/package.py +++ b/var/spack/repos/builtin/packages/py-backports-weakref/package.py @@ -10,7 +10,7 @@ class PyBackportsWeakref(PythonPackage): """Backports of new features in Python's weakref module""" homepage = "https://github.com/PiDelport/backports.weakref" - url = "https://pypi.org/packages/source/b/backports.weakref/backports.weakref-1.0.post1.tar.gz" + url = "https://pypi.io/packages/source/b/backports.weakref/backports.weakref-1.0.post1.tar.gz" version('1.0.post1', sha256='bc4170a29915f8b22c9e7c4939701859650f2eb84184aee80da329ac0b9825c2', preferred=True) version('1.0rc1', sha256='8813bf712a66b3d8b85dc289e1104ed220f1878cf981e2fe756dfaabe9a82892') diff --git a/var/spack/repos/builtin/packages/py-colorlog/package.py b/var/spack/repos/builtin/packages/py-colorlog/package.py index 7eb42c2976a..05268384f29 100644 --- a/var/spack/repos/builtin/packages/py-colorlog/package.py +++ b/var/spack/repos/builtin/packages/py-colorlog/package.py @@ -10,7 +10,7 @@ class PyColorlog(PythonPackage): """A colored formatter for the python logging module""" homepage = "https://github.com/borntyping/python-colorlog" - url = "https://pypi.org/packages/source/c/colorlog/colorlog-4.0.2.tar.gz" + url = "https://pypi.io/packages/source/c/colorlog/colorlog-4.0.2.tar.gz" version('4.0.2', sha256='3cf31b25cbc8f86ec01fef582ef3b840950dea414084ed19ab922c8b493f9b42') version('3.1.4', sha256='418db638c9577f37f0fae4914074f395847a728158a011be2a193ac491b9779d') diff --git a/var/spack/repos/builtin/packages/py-colorpy/package.py b/var/spack/repos/builtin/packages/py-colorpy/package.py index da11077eaf3..909ad673efc 100644 --- a/var/spack/repos/builtin/packages/py-colorpy/package.py +++ b/var/spack/repos/builtin/packages/py-colorpy/package.py @@ -15,7 +15,7 @@ class PyColorpy(PythonPackage): """ homepage = "http://markkness.net/colorpy/ColorPy.html" - url = "https://pypi.org/packages/source/c/colorpy/colorpy-0.1.1.tar.gz" + url = "https://pypi.io/packages/source/c/colorpy/colorpy-0.1.1.tar.gz" version('0.1.1', sha256='e400a7e879adc83c6098dde13cdd093723f3936778c245b1caf88f5f1411170d') diff --git a/var/spack/repos/builtin/packages/py-exodus-bundler/package.py b/var/spack/repos/builtin/packages/py-exodus-bundler/package.py index b14570f54b5..c13f30eb469 100644 --- a/var/spack/repos/builtin/packages/py-exodus-bundler/package.py +++ b/var/spack/repos/builtin/packages/py-exodus-bundler/package.py @@ -11,7 +11,7 @@ class PyExodusBundler(PythonPackage): ELF binaries from one system to another.""" homepage = "https://github.com/intoli/exodus" - url = "https://pypi.org/packages/source/e/exodus-bundler/exodus-bundler-2.0.2.tar.gz" + url = "https://pypi.io/packages/source/e/exodus-bundler/exodus-bundler-2.0.2.tar.gz" version('2.0.2', sha256='4e896a2034b94cf7b4fb33d86a68e29a7d3b08e57541e444db34dddc6ac1ef68') diff --git a/var/spack/repos/builtin/packages/py-hdfs/package.py b/var/spack/repos/builtin/packages/py-hdfs/package.py index 599a00fad8f..c84c3faca92 100644 --- a/var/spack/repos/builtin/packages/py-hdfs/package.py +++ b/var/spack/repos/builtin/packages/py-hdfs/package.py @@ -9,7 +9,7 @@ class PyHdfs(PythonPackage): """API and command line interface for HDFS""" homepage = "https://hdfscli.readthedocs.io/en/latest/" - url = "https://pypi.org/packages/source/h/hdfs/hdfs-2.1.0.tar.gz" + url = "https://pypi.io/packages/source/h/hdfs/hdfs-2.1.0.tar.gz" version('2.1.0', sha256='a40fe99ccb03b5c3247b33a4110eb21b57405dd7c3f1b775e362e66c19b44bc6') diff --git a/var/spack/repos/builtin/packages/py-jprops/package.py b/var/spack/repos/builtin/packages/py-jprops/package.py index 16fed619ddd..2e6749077f3 100644 --- a/var/spack/repos/builtin/packages/py-jprops/package.py +++ b/var/spack/repos/builtin/packages/py-jprops/package.py @@ -10,7 +10,7 @@ class PyJprops(PythonPackage): """Java properties file parser for Python""" homepage = "https://github.com/mgood/jprops/" - url = "https://pypi.org/packages/source/j/jprops/jprops-2.0.2.tar.gz" + url = "https://pypi.io/packages/source/j/jprops/jprops-2.0.2.tar.gz" version('2.0.2', sha256='d297231833b6cd0a3f982a48fe148a7f9817f2895661743d166b267e4d3d5b2c') diff --git a/var/spack/repos/builtin/packages/py-progress/package.py b/var/spack/repos/builtin/packages/py-progress/package.py index 3ae16e5e59e..cff57e9f779 100644 --- a/var/spack/repos/builtin/packages/py-progress/package.py +++ b/var/spack/repos/builtin/packages/py-progress/package.py @@ -10,7 +10,7 @@ class PyProgress(PythonPackage): """Easy progress reporting for Python""" homepage = "https://github.com/verigak/progress/" - url = "https://pypi.org/packages/source/p/progress/progress-1.4.tar.gz" + url = "https://pypi.io/packages/source/p/progress/progress-1.4.tar.gz" version('1.4', sha256='5e2f9da88ed8236a76fffbee3ceefd259589cf42dfbc2cec2877102189fae58a') diff --git a/var/spack/repos/builtin/packages/py-pyarrow/package.py b/var/spack/repos/builtin/packages/py-pyarrow/package.py index ed104821453..4daa0e00614 100644 --- a/var/spack/repos/builtin/packages/py-pyarrow/package.py +++ b/var/spack/repos/builtin/packages/py-pyarrow/package.py @@ -13,7 +13,7 @@ class PyPyarrow(PythonPackage): """ homepage = "http://arrow.apache.org" - url = 'https://pypi.org/packages/source/p/pyarrow/pyarrow-0.15.1.tar.gz' + url = 'https://pypi.io/packages/source/p/pyarrow/pyarrow-0.15.1.tar.gz' version('0.15.1', sha256='7ad074690ba38313067bf3bbda1258966d38e2037c035d08b9ffe3cce07747a5') version('0.12.1', sha256='10db6e486c918c3af999d0114a22d92770687e3a6607ea3f14e6748854824c2a') diff --git a/var/spack/repos/builtin/packages/py-pyspark/package.py b/var/spack/repos/builtin/packages/py-pyspark/package.py index 15285d3c304..7a7cf1d286a 100644 --- a/var/spack/repos/builtin/packages/py-pyspark/package.py +++ b/var/spack/repos/builtin/packages/py-pyspark/package.py @@ -10,7 +10,7 @@ class PyPyspark(PythonPackage): """Python bindings for Apache Spark""" homepage = "http://spark.apache.org" - url = "https://pypi.org/packages/source/p/pyspark/pyspark-2.3.0.tar.gz" + url = "https://pypi.io/packages/source/p/pyspark/pyspark-2.3.0.tar.gz" version('2.3.0', sha256='0b3536910e154c36a94239f0ba0a201f476aadc72006409e5787198ffd01986e') diff --git a/var/spack/repos/builtin/packages/py-requests-futures/package.py b/var/spack/repos/builtin/packages/py-requests-futures/package.py index 4c79bcf871a..a11d577e1cc 100644 --- a/var/spack/repos/builtin/packages/py-requests-futures/package.py +++ b/var/spack/repos/builtin/packages/py-requests-futures/package.py @@ -10,7 +10,7 @@ class PyRequestsFutures(PythonPackage): """Asynchronous Python HTTP Requests for Humans using Futures""" homepage = "https://github.com/ross/requests-futures" - url = "https://pypi.org/packages/source/r/requests-futures/requests-futures-1.0.0.tar.gz" + url = "https://pypi.io/packages/source/r/requests-futures/requests-futures-1.0.0.tar.gz" version('1.0.0', sha256='35547502bf1958044716a03a2f47092a89efe8f9789ab0c4c528d9c9c30bc148') diff --git a/var/spack/repos/builtin/packages/py-testinfra/package.py b/var/spack/repos/builtin/packages/py-testinfra/package.py index bae58db30df..40e7cd440cf 100644 --- a/var/spack/repos/builtin/packages/py-testinfra/package.py +++ b/var/spack/repos/builtin/packages/py-testinfra/package.py @@ -12,7 +12,7 @@ class PyTestinfra(PythonPackage): Chef and so on.""" homepage = "https://testinfra.readthedocs.io" - url = "https://pypi.python.org/packages/source/t/testinfra/testinfra-1.11.1.tar.gz" + url = "https://pypi.io/packages/source/t/testinfra/testinfra-1.11.1.tar.gz" version('1.18.0', sha256='4a0a70355b007729d78446c86bffd80bcea4ffe9adc9571f9c9779476c49153d') version('1.13.0', sha256='b5afa23d71ee49ad81aed104e4a0f1c02819ef791291cd308fe27aa7f3d3b01f') diff --git a/var/spack/repos/builtin/packages/py-usgs/package.py b/var/spack/repos/builtin/packages/py-usgs/package.py index 14d20b62cd4..69f2b970563 100644 --- a/var/spack/repos/builtin/packages/py-usgs/package.py +++ b/var/spack/repos/builtin/packages/py-usgs/package.py @@ -10,7 +10,9 @@ class PyUsgs(PythonPackage): """Client library for interfacing with USGS datasets""" homepage = "https://github.com/kapadia/usgs" - url = "https://pypi.org/packages/source/u/usgs/usgs-0.2.7.tar.gz" + url = "https://pypi.io/packages/source/u/usgs/usgs-0.2.7.tar.gz" + + maintainers = ['adamjstewart'] version('0.2.7', sha256='484e569ea1baf9574e11ccf15219957364690dcf06ee3d09afef030df944e79b') diff --git a/var/spack/repos/builtin/packages/py-uwsgi/package.py b/var/spack/repos/builtin/packages/py-uwsgi/package.py index aed1882b045..fdc990d48d1 100644 --- a/var/spack/repos/builtin/packages/py-uwsgi/package.py +++ b/var/spack/repos/builtin/packages/py-uwsgi/package.py @@ -11,7 +11,7 @@ class PyUwsgi(PythonPackage): """Web Application framework for low overhead web services""" homepage = "https://github.com/unbit/uwsgi/" - url = "https://pypi.org/packages/source/u/uwsgi/uwsgi-2.0.18.tar.gz" + url = "https://pypi.io/packages/source/u/uwsgi/uwsgi-2.0.18.tar.gz" version('2.0.18', sha256='4972ac538800fb2d421027f49b4a1869b66048839507ccf0aa2fda792d99f583') From cf68193ebeaf3009c17bb7f8a9978635effedce7 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 5 Apr 2020 15:43:20 -0500 Subject: [PATCH 362/377] py-tblib: add new version, fix url and deps (#15879) --- var/spack/repos/builtin/packages/py-tblib/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-tblib/package.py b/var/spack/repos/builtin/packages/py-tblib/package.py index 5234fde4e04..f32e292c125 100644 --- a/var/spack/repos/builtin/packages/py-tblib/package.py +++ b/var/spack/repos/builtin/packages/py-tblib/package.py @@ -11,8 +11,10 @@ class PyTblib(PythonPackage): """Traceback fiddling library. Allows you to pickle tracebacks.""" homepage = "https://github.com/ionelmc/python-tblib" - url = "https://files.pythonhosted.org/packages/source/t/tblib/tblib-1.4.0.tar.gz" + url = "https://pypi.io/packages/source/t/tblib/tblib-1.6.0.tar.gz" + version('1.6.0', sha256='229bee3754cb5d98b4837dd5c4405e80cfab57cb9f93220410ad367f8b352344') version('1.4.0', sha256='bd1ad564564a158ff62c290687f3db446038f9ac11a0bf6892712e3601af3bcd') + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') From d87f44e987c72313d74b3b885dab01aa3faf7e87 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 5 Apr 2020 15:44:10 -0500 Subject: [PATCH 363/377] py-scoop: fix url and deps (#15877) --- var/spack/repos/builtin/packages/py-scoop/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-scoop/package.py b/var/spack/repos/builtin/packages/py-scoop/package.py index 2fc309bbd63..e1e25abd019 100644 --- a/var/spack/repos/builtin/packages/py-scoop/package.py +++ b/var/spack/repos/builtin/packages/py-scoop/package.py @@ -13,10 +13,11 @@ class PyScoop(PythonPackage): environments, from heterogeneous grids to supercomputers.""" homepage = "https://github.com/soravux/scoop" - url = "https://files.pythonhosted.org/packages/source/s/scoop/scoop-0.7.1.1.tar.gz" + url = "https://pypi.io/packages/source/s/scoop/scoop-0.7.1.1.tar.gz" version('0.7.1.1', sha256='d8b6444c7bac901171e3327a97e241dde63f060354e162a65551fd8083ca62b4') depends_on('py-setuptools', type='build') depends_on('py-greenlet@0.3.4:', type=('build', 'run')) depends_on('py-pyzmq@13.1.0:', type=('build', 'run')) + depends_on('py-argparse@1.1:', type=('build', 'run')) From f5fde735b68531dcf1f86e51b7641a0048705d2e Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 5 Apr 2020 15:44:23 -0500 Subject: [PATCH 364/377] py-python-utils: add new version, fix url and deps (#15876) --- var/spack/repos/builtin/packages/py-python-utils/package.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/py-python-utils/package.py b/var/spack/repos/builtin/packages/py-python-utils/package.py index bc6057a0780..6c8e3aa732d 100644 --- a/var/spack/repos/builtin/packages/py-python-utils/package.py +++ b/var/spack/repos/builtin/packages/py-python-utils/package.py @@ -12,8 +12,12 @@ class PyPythonUtils(PythonPackage): which make common patterns shorter and easier.""" homepage = "https://github.com/WoLpH/python-utils" - url = "https://files.pythonhosted.org/packages/source/p/python-utils/python-utils-2.3.0.tar.gz" + url = "https://pypi.io/packages/source/p/python-utils/python-utils-2.4.0.tar.gz" + version('2.4.0', sha256='f21fc09ff58ea5ebd1fd2e8ef7f63e39d456336900f26bdc9334a03a3f7d8089') version('2.3.0', sha256='34aaf26b39b0b86628008f2ae0ac001b30e7986a8d303b61e1357dfcdad4f6d3') depends_on('py-setuptools', type='build') + depends_on('py-six', type=('build', 'run')) + depends_on('py-pytest', type='test') + depends_on('py-pytest-runner', type='test') From 4dc034a8e59e2bcabc0da583350973891a48d67b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 5 Apr 2020 15:44:36 -0500 Subject: [PATCH 365/377] py-progressbar2: add new version, fix url (#15875) --- var/spack/repos/builtin/packages/py-progressbar2/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-progressbar2/package.py b/var/spack/repos/builtin/packages/py-progressbar2/package.py index 31f2688a570..196d3035916 100644 --- a/var/spack/repos/builtin/packages/py-progressbar2/package.py +++ b/var/spack/repos/builtin/packages/py-progressbar2/package.py @@ -11,10 +11,11 @@ class PyProgressbar2(PythonPackage): """A progress bar for Python 2 and Python 3""" homepage = "https://github.com/WoLpH/python-progressbar" - url = "https://files.pythonhosted.org/packages/source/p/progressbar2/progressbar2-3.39.3.tar.gz" + url = "https://pypi.io/packages/source/p/progressbar2/progressbar2-3.50.1.tar.gz" + version('3.50.1', sha256='2c21c14482016162852c8265da03886c2b4dea6f84e5a817ad9b39f6bd82a772') version('3.39.3', sha256='8e5b5419e04193bb7c3fea71579937bbbcd64c26472b929718c2fe7ec420fe39') depends_on('py-setuptools', type='build') depends_on('py-six', type=('build', 'run')) - depends_on('py-python-utils', type=('build', 'run')) + depends_on('py-python-utils@2.3.0:', type=('build', 'run')) From e359bb91e90ed98a6b951fc42c89b8347b5cdf19 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 5 Apr 2020 15:44:50 -0500 Subject: [PATCH 366/377] py-pep8-naming: add new version, fix url and deps (#15874) --- .../repos/builtin/packages/py-pep8-naming/package.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-pep8-naming/package.py b/var/spack/repos/builtin/packages/py-pep8-naming/package.py index ed123b773d1..fe3e929996c 100644 --- a/var/spack/repos/builtin/packages/py-pep8-naming/package.py +++ b/var/spack/repos/builtin/packages/py-pep8-naming/package.py @@ -9,10 +9,11 @@ class PyPep8Naming(PythonPackage): """Check PEP-8 naming conventions, plugin for flake8.""" - homepage = "https://pypi.org/project/pep8-naming/" - url = "https://files.pythonhosted.org/packages/3e/4a/125425d6b1e017f48dfc9c961f4bb9510168db7a090618906c750184ed03/pep8-naming-0.7.0.tar.gz" + homepage = "https://github.com/PyCQA/pep8-naming" + url = "https://pypi.io/packages/source/p/pep8-naming/pep8-naming-0.10.0.tar.gz" - extends('python', ignore='bin/(flake8|pyflakes|pycodestyle)') - version('0.7.0', sha256='624258e0dd06ef32a9daf3c36cc925ff7314da7233209c5b01f7e5cdd3c34826') + version('0.10.0', sha256='f3b4a5f9dd72b991bf7d8e2a341d2e1aa3a884a769b5aaac4f56825c1763bf3a') + version('0.7.0', sha256='624258e0dd06ef32a9daf3c36cc925ff7314da7233209c5b01f7e5cdd3c34826') - depends_on('py-flake8-polyfill', type='run') + depends_on('py-setuptools', type='build') + depends_on('py-flake8-polyfill@1.0.2:1.999', type=('build', 'run')) From 638e6d0f9e5d37b1a8cdee529b060092f59ec745 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 5 Apr 2020 15:45:04 -0500 Subject: [PATCH 367/377] py-humanfriendly: add new version, fix url and deps (#15873) --- .../repos/builtin/packages/py-humanfriendly/package.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-humanfriendly/package.py b/var/spack/repos/builtin/packages/py-humanfriendly/package.py index a1b63e82332..c023e2e41bf 100644 --- a/var/spack/repos/builtin/packages/py-humanfriendly/package.py +++ b/var/spack/repos/builtin/packages/py-humanfriendly/package.py @@ -8,9 +8,12 @@ class PyHumanfriendly(PythonPackage): """Human friendly output for text interfaces using Python""" - homepage = "https://pypi.org/project/humanfriendly/" - url = "https://files.pythonhosted.org/packages/26/71/e7daf57e819a70228568ff5395fdbc4de81b63067b93167e07825fcf0bcf/humanfriendly-4.18.tar.gz" + homepage = "https://humanfriendly.readthedocs.io/" + url = "https://pypi.io/packages/source/h/humanfriendly/humanfriendly-8.1.tar.gz" + version('8.1', sha256='25c2108a45cfd1e8fbe9cdb30b825d34ef5d5675c8e11e4775c9aedbfb0bdee2') version('4.18', sha256='33ee8ceb63f1db61cce8b5c800c531e1a61023ac5488ccde2ba574a85be00a85') + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') + depends_on('py-monotonic', when='^python@:2', type=('build', 'run')) From 2a074ce445a474df02fef4656908aed5e66a1fb1 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 5 Apr 2020 15:45:17 -0500 Subject: [PATCH 368/377] py-gensim: fix url and deps, add maintainer (#15870) --- .../builtin/packages/py-gensim/package.py | 25 +++++++++---------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-gensim/package.py b/var/spack/repos/builtin/packages/py-gensim/package.py index 06eaacfe945..a08cbbe98d1 100644 --- a/var/spack/repos/builtin/packages/py-gensim/package.py +++ b/var/spack/repos/builtin/packages/py-gensim/package.py @@ -8,21 +8,20 @@ class PyGensim(PythonPackage): """Gensim is a Python library for topic modelling, document indexing and - similarity retrieval with large corpora. Target audience is the natural - language processing (NLP) and information retrieval (IR) community.""" + similarity retrieval with large corpora. Target audience is the natural + language processing (NLP) and information retrieval (IR) community.""" - homepage = "https://pypi.org/project/gensim/" - url = "https://files.pythonhosted.org/packages/3a/bc/1415be59292a23ff123298b4b46ec4be80b3bfe72c8d188b58ab2653dee4/gensim-3.8.0.tar.gz" + homepage = "https://radimrehurek.com/gensim" + url = "https://pypi.io/packages/source/g/gensim/gensim-3.8.1.tar.gz" - version('3.8.1', sha256='33277fc0a8d7b0c7ce70fcc74bb82ad39f944c009b334856c6e86bf552b1dfdc', - url='https://files.pythonhosted.org/packages/73/f2/e9af000df6419bf1a63ffed3e6033a1b1d8fcf2f971fcdac15296619aff8/gensim-3.8.1.tar.gz') + maintainers = ['adamjstewart'] + + version('3.8.1', sha256='33277fc0a8d7b0c7ce70fcc74bb82ad39f944c009b334856c6e86bf552b1dfdc') version('3.8.0', sha256='ec5de7ff2bfa8692fa96a846bb5aae52f267fc322fbbe303c1f042d258af5766') - depends_on('python@3.5:', type=('build', 'run')) - + depends_on('python@2.7:2.8,3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') - - depends_on('py-numpy', type=('build', 'run')) - depends_on('py-scipy', type=('build', 'run')) - depends_on('py-smart-open', type=('build', 'run')) - depends_on('py-six', type=('build', 'run')) + depends_on('py-numpy@1.11.3:', type=('build', 'run')) + depends_on('py-scipy@0.18.1:', type=('build', 'run')) + depends_on('py-six@1.5.0:', type=('build', 'run')) + depends_on('py-smart-open@1.8.1:', type=('build', 'run')) From a08d5fed0a333e26ede4a7047957fed7d25f31f4 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 5 Apr 2020 15:45:29 -0500 Subject: [PATCH 369/377] py-flake8-polyfill: fix url and deps (#15872) --- .../repos/builtin/packages/py-flake8-polyfill/package.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py b/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py index 8de1f375051..cc61a2e936b 100644 --- a/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py +++ b/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py @@ -11,10 +11,10 @@ class PyFlake8Polyfill(PythonPackage): for Flake8 plugins that intend to support Flake8 2.x and 3.x simultaneously. """ - homepage = "https://pypi.org/project/flake8-polyfill/" - url = "https://files.pythonhosted.org/packages/e6/67/1c26634a770db5c442e361311bee73cb3a177adb2eb3f7af8953cfd9f553/flake8-polyfill-1.0.2.tar.gz" + homepage = "https://gitlab.com/pycqa/flake8-polyfill" + url = "https://pypi.io/packages/source/f/flake8-polyfill/flake8-polyfill-1.0.2.tar.gz" version('1.0.2', sha256='e44b087597f6da52ec6393a709e7108b2905317d0c0b744cdca6208e670d8eda') - extends('python', ignore='bin/(flake8|pyflakes|pycodestyle)') - depends_on('py-flake8', type='run') + depends_on('py-setuptools', type='build') + depends_on('py-flake8', type=('build', 'run')) From 1249d73630c0a7f49014022c3183e66a9d9ead9f Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 5 Apr 2020 17:31:09 -0500 Subject: [PATCH 370/377] py-spatialist: add maintainer and new version, fix url and deps (#15878) --- .../builtin/packages/py-spatialist/package.py | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-spatialist/package.py b/var/spack/repos/builtin/packages/py-spatialist/package.py index e1beee57e5f..ff7386fd00f 100644 --- a/var/spack/repos/builtin/packages/py-spatialist/package.py +++ b/var/spack/repos/builtin/packages/py-spatialist/package.py @@ -12,16 +12,24 @@ class PySpatialist(PythonPackage): processing using GDAL and OGR.""" homepage = "https://github.com/johntruckenbrodt/spatialist" - url = "https://files.pythonhosted.org/packages/source/s/spatialist/spatialist-0.2.8.tar.gz" + url = "https://pypi.io/packages/source/s/spatialist/spatialist-0.4.tar.gz" + maintainers = ['adamjstewart'] + + version('0.4', sha256='153b118022c06ad2d1d51fb6cd9ecbfc8020bc1995b643ec7fa689a8c5dde7e9') version('0.2.8', sha256='97de7f9c0fbf28497ef28970bdf8093a152e691a783e7edad22998cb235154c6') + depends_on('python@2.7.9:', type=('build', 'run')) depends_on('py-setuptools', type='build') + depends_on('py-setuptools-scm', type='build') depends_on('py-progressbar2', type=('build', 'run')) - depends_on('py-pathos@0.2.0:', type=('build', 'run')) - depends_on('py-numpy', type=('build', 'run')) - depends_on('py-matplotlib', type=('build', 'run')) - depends_on('py-jupyter-core', type=('build', 'run')) + depends_on('py-jupyter', type=('build', 'run')) depends_on('py-ipython', type=('build', 'run')) depends_on('py-ipywidgets', type=('build', 'run')) + depends_on('py-matplotlib', type=('build', 'run')) + depends_on('py-prompt-toolkit@2.0.10:2.0.999', type=('build', 'run')) + depends_on('py-pathos@0.2:', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) + depends_on('py-scoop', type=('build', 'run')) depends_on('py-tblib', type=('build', 'run')) + depends_on('py-pyyaml', type=('build', 'run')) From 268c2a19da2085083ad3a61d0ce0a27ecd1e2343 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Sun, 5 Apr 2020 17:42:27 -0600 Subject: [PATCH 371/377] boost: boost-python in 1.72.0 broken with cxxstd=98 (#15885) * boost: boost-python in 1.72.0 broken with cxxstd=98 * py-espressopp: depend on boost with cxxstd=11 --- var/spack/repos/builtin/packages/boost/package.py | 3 +++ var/spack/repos/builtin/packages/py-espressopp/package.py | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index 41be592a528..c0998e23d0a 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -178,6 +178,9 @@ def libs(self): conflicts('+taggedlayout', when='+versionedlayout') conflicts('+numpy', when='~python') + # boost-python in 1.72.0 broken with cxxstd=98 + conflicts('cxxstd=98', when='+mpi+python @1.72.0:') + # Container's Extended Allocators were not added until 1.56.0 conflicts('+container', when='@:1.55.99') diff --git a/var/spack/repos/builtin/packages/py-espressopp/package.py b/var/spack/repos/builtin/packages/py-espressopp/package.py index 779873bc98c..f243fcb4d28 100644 --- a/var/spack/repos/builtin/packages/py-espressopp/package.py +++ b/var/spack/repos/builtin/packages/py-espressopp/package.py @@ -27,7 +27,7 @@ class PyEspressopp(CMakePackage): depends_on("cmake@2.8:", type='build') depends_on("mpi") - depends_on("boost+serialization+filesystem+system+python+mpi", when='@1.9.4:') + depends_on("boost+serialization+filesystem+system+python+mpi cxxstd=11", when='@1.9.4:') extends("python") depends_on("python@2:2.8") depends_on("py-mpi4py@2.0.0:", when='@1.9.4', type=('build', 'run')) From 359d7adf7ee07aa1adc09f2ad4aace1a0cd6316a Mon Sep 17 00:00:00 2001 From: Jonathon Anderson Date: Mon, 6 Apr 2020 02:00:42 -0600 Subject: [PATCH 372/377] Source devnull in environment_after_sourcing_files (closes #15775) (#15791) spack.util.environment_after_sourcing_files compares the local environment against a shell environment after having sourced a file; but this ends up including the default shell profile and rc, which might differ from the local environment. To change this, compare against the default shell environment, expressed here as 'source /dev/null'. --- lib/spack/spack/util/environment.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py index 248a6d3c8c0..862f04f8eb6 100644 --- a/lib/spack/spack/util/environment.py +++ b/lib/spack/spack/util/environment.py @@ -602,7 +602,8 @@ def from_sourcing_file(filename, *arguments, **kwargs): # Compute the environments before and after sourcing before = sanitize( - dict(os.environ), blacklist=blacklist, whitelist=whitelist + environment_after_sourcing_files(os.devnull, **kwargs), + blacklist=blacklist, whitelist=whitelist ) file_and_args = (filename,) + arguments after = sanitize( From 06f3381dfd4355939350a6f20004fcebe3a25d24 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Mon, 6 Apr 2020 10:02:03 +0200 Subject: [PATCH 373/377] Blacklist Lmod variable modifications when sourcing files (#15778) fixes #15775 Add all the variables listed here: https://lmod.readthedocs.io/en/latest/090_configuring_lmod.html to the list of those blacklisted when constructing environment modifications by sourcing files. --- lib/spack/spack/test/data/sourceme_lmod.sh | 10 ++++++++++ lib/spack/spack/test/environment_modifications.py | 11 +++++++++++ lib/spack/spack/util/environment.py | 4 +++- 3 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 lib/spack/spack/test/data/sourceme_lmod.sh diff --git a/lib/spack/spack/test/data/sourceme_lmod.sh b/lib/spack/spack/test/data/sourceme_lmod.sh new file mode 100644 index 00000000000..b71e338ec98 --- /dev/null +++ b/lib/spack/spack/test/data/sourceme_lmod.sh @@ -0,0 +1,10 @@ +#!/usr/bin/env bash +# +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +export LMOD_VARIABLE=foo +export LMOD_ANOTHER_VARIABLE=bar +export NEW_VAR=new diff --git a/lib/spack/spack/test/environment_modifications.py b/lib/spack/spack/test/environment_modifications.py index 9983594a843..d1f5a4b791a 100644 --- a/lib/spack/spack/test/environment_modifications.py +++ b/lib/spack/spack/test/environment_modifications.py @@ -437,3 +437,14 @@ def test_from_environment_diff(before, after, search_list): for item in search_list: assert item in mod + + +@pytest.mark.regression('15775') +def test_blacklist_lmod_variables(): + # Construct the list of environment modifications + file = os.path.join(datadir, 'sourceme_lmod.sh') + env = EnvironmentModifications.from_sourcing_file(file) + + # Check that variables related to lmod are not in there + modifications = env.group_by_name() + assert not any(x.startswith('LMOD_') for x in modifications) diff --git a/lib/spack/spack/util/environment.py b/lib/spack/spack/util/environment.py index 862f04f8eb6..8069f514319 100644 --- a/lib/spack/spack/util/environment.py +++ b/lib/spack/spack/util/environment.py @@ -597,7 +597,9 @@ def from_sourcing_file(filename, *arguments, **kwargs): 'SHLVL', '_', 'PWD', 'OLDPWD', 'PS1', 'PS2', 'ENV', # Environment modules v4 'LOADEDMODULES', '_LMFILES_', 'BASH_FUNC_module()', 'MODULEPATH', - 'MODULES_(.*)', r'(\w*)_mod(quar|share)' + 'MODULES_(.*)', r'(\w*)_mod(quar|share)', + # Lmod configuration + r'LMOD_(.*)', 'MODULERCFILE' ]) # Compute the environments before and after sourcing From 55d15fc07e28de32d458ab556775e82c7f8d8d11 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Trahay?= Date: Mon, 6 Apr 2020 15:01:58 +0200 Subject: [PATCH 374/377] new packages: libbacktrace, libpfm, numap, numamma (#15868) * new packages: libbacktrace, libpfm, numap, numamma * numap: use the existing libpfm4 package * formatting --- .../builtin/packages/libbacktrace/package.py | 23 +++++++++++++++ .../repos/builtin/packages/numamma/package.py | 29 +++++++++++++++++++ .../repos/builtin/packages/numap/package.py | 20 +++++++++++++ 3 files changed, 72 insertions(+) create mode 100644 var/spack/repos/builtin/packages/libbacktrace/package.py create mode 100644 var/spack/repos/builtin/packages/numamma/package.py create mode 100644 var/spack/repos/builtin/packages/numap/package.py diff --git a/var/spack/repos/builtin/packages/libbacktrace/package.py b/var/spack/repos/builtin/packages/libbacktrace/package.py new file mode 100644 index 00000000000..64e58321148 --- /dev/null +++ b/var/spack/repos/builtin/packages/libbacktrace/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Libbacktrace(AutotoolsPackage): + """A C library that may be linked into a C/C++ program to produce + symbolic backtraces.""" + + homepage = "https://github.com/ianlancetaylor/libbacktrace" + git = "https://github.com/ianlancetaylor/libbacktrace.git" + maintainers = ['trahay'] + + version('master', branch='master') + version('2020-02-19', commit='ca0de0517f3be44fedf5a2c01cfaf6437d4cae68') + + depends_on('autoconf', type='build') + depends_on('automake', type='build') + depends_on('libtool', type='build') + depends_on('m4', type='build') diff --git a/var/spack/repos/builtin/packages/numamma/package.py b/var/spack/repos/builtin/packages/numamma/package.py new file mode 100644 index 00000000000..cc714954498 --- /dev/null +++ b/var/spack/repos/builtin/packages/numamma/package.py @@ -0,0 +1,29 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Numamma(CMakePackage): + """NumaMMa is a lightweight memory profiler that reports the + memory access patterns of applications.""" + + homepage = "https://numamma.github.io/numamma/" + url = "https://github.com/numamma/numamma/archive/numamma-1.1.1.tar.gz" + maintainers = ['trahay'] + + version('1.1.1', sha256='f79ca22a95df33a1af529ddd653d043f7f0d32a6d196e559aee8bef8fc74771f') + + depends_on('numap') + depends_on('libbacktrace') + depends_on('numactl') + depends_on('libelf') + + def cmake_args(self): + spec = self.spec + cmake_args = [ + "-DBACKTRACE_DIR:PATH={0}".format(spec["libbacktrace"].prefix) + ] + return cmake_args diff --git a/var/spack/repos/builtin/packages/numap/package.py b/var/spack/repos/builtin/packages/numap/package.py new file mode 100644 index 00000000000..2df4cfd9950 --- /dev/null +++ b/var/spack/repos/builtin/packages/numap/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Numap(CMakePackage): + """Numap is a Linux library dedicated to memory profiling based on + hardware performance monitoring unit (PMU).""" + + homepage = "https://github.com/numap-library/numap" + git = "https://github.com/numap-library/numap.git" + maintainers = ['trahay'] + + version('master', branch='master') + version('2019-09-06', commit='ffcdb88c64b59b7a3220eb1077d2b237029ca96a') + + depends_on('libpfm4') From b1bea70df1f62e4c0447a406b77266b804eec5df Mon Sep 17 00:00:00 2001 From: "Dr. Christian Tacke" <58549698+ChristianTackeGSI@users.noreply.github.com> Date: Mon, 6 Apr 2020 18:15:57 +0200 Subject: [PATCH 375/377] nanomsg: add new Package (#15894) --- .../repos/builtin/packages/nanomsg/package.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 var/spack/repos/builtin/packages/nanomsg/package.py diff --git a/var/spack/repos/builtin/packages/nanomsg/package.py b/var/spack/repos/builtin/packages/nanomsg/package.py new file mode 100644 index 00000000000..c3c5bb05e6e --- /dev/null +++ b/var/spack/repos/builtin/packages/nanomsg/package.py @@ -0,0 +1,17 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class Nanomsg(CMakePackage): + """The nanomsg library is a simple high-performance + implementation of several 'scalability protocols'""" + + homepage = "https://nanomsg.org/" + url = "https://github.com/nanomsg/nanomsg/archive/1.0.0.tar.gz" + + version('1.1.5', sha256='218b31ae1534ab897cb5c419973603de9ca1a5f54df2e724ab4a188eb416df5a') + version('1.0.0', sha256='24afdeb71b2e362e8a003a7ecc906e1b84fd9f56ce15ec567481d1bb33132cc7') From 18a9a265fde2feb08f9be8e58ed138eeb29e8bfd Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 6 Apr 2020 11:16:20 -0500 Subject: [PATCH 376/377] py-smart-open: fix url/checksum, add deps (#15892) --- var/spack/repos/builtin/packages/py-smart-open/package.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/py-smart-open/package.py b/var/spack/repos/builtin/packages/py-smart-open/package.py index 5def4a84f38..fd2ed92ef2b 100644 --- a/var/spack/repos/builtin/packages/py-smart-open/package.py +++ b/var/spack/repos/builtin/packages/py-smart-open/package.py @@ -13,9 +13,13 @@ class PySmartOpen(PythonPackage): different formats.""" homepage = "https://github.com/piskvorky/smart_open" - url = "https://github.com/RaRe-Technologies/smart_open/archive/1.8.4.tar.gz" + url = "https://pypi.io/packages/source/s/smart_open/smart_open-1.10.0.tar.gz" - version('1.8.4', sha256='788e07f035defcbb62e3c1e313329a70b0976f4f65406ee767db73ad5d2d04f9') + version('1.10.0', sha256='bea5624c0c2e49987c227bdf3596573157eccd96fd1d53198856c8d53948fa2c') + version('1.8.4', sha256='788e07f035defcbb62e3c1e313329a70b0976f4f65406ee767db73ad5d2d04f9') depends_on('py-setuptools', type='build') + depends_on('py-requests', type=('build', 'run')) depends_on('py-boto3', type=('build', 'run')) + depends_on('py-google-cloud-storage', type=('build', 'run')) + depends_on('py-bz2file', when='^python@:2', type=('build', 'run')) From fab1f68399c016fa93ec049121e3b4075d560ebd Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 6 Apr 2020 11:54:22 -0500 Subject: [PATCH 377/377] Docs: fix Spack Environments command (#15891) --- lib/spack/docs/environments.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/spack/docs/environments.rst b/lib/spack/docs/environments.rst index 5ec1ec9032a..5d091dee30c 100644 --- a/lib/spack/docs/environments.rst +++ b/lib/spack/docs/environments.rst @@ -285,7 +285,7 @@ be called using the ``spack -E`` flag to specify the environment. .. code-block:: console - $ spack activate myenv + $ spack env activate myenv $ spack add mpileaks or