Merge remote-tracking branch 'upstream/develop' into develop

.travis.yml

@@ -12,6 +12,7 @@ branches:
 # Build matrix
 #=============================================================================
 matrix:
+  fast_finish: true
   include:
     - python: '2.6'
       os: linux

lib/spack/external/distro.py

@@ -993,13 +993,18 @@ def _get_distro_release_info(self):
                     continue
                 match = _DISTRO_RELEASE_BASENAME_PATTERN.match(basename)
                 if match:
-                    filepath = os.path.join(_UNIXCONFDIR, basename)
-                    distro_info = self._parse_distro_release_file(filepath)
-                    if 'name' in distro_info:
-                        # The name is always present if the pattern matches
-                        self.distro_release_file = filepath
-                        distro_info['id'] = match.group(1)
-                        return distro_info
+                    try:
+                        filepath = os.path.join(_UNIXCONFDIR, basename)
+                        distro_info = self._parse_distro_release_file(filepath)
+                        if 'name' in distro_info:
+                            # The name is always present if the pattern matches
+                            self.distro_release_file = filepath
+                            distro_info['id'] = match.group(1)
+                            return distro_info
+                    except IOError:
+                        # We found a file we do not have permission to read
+                        # Continue checking candidate files for distro file.
+                        continue
             return {}
 
     def _parse_distro_release_file(self, filepath):

lib/spack/spack/fetch_strategy.py

@@ -719,7 +719,7 @@ def fetch(self):
 
         tty.msg("Trying to check out svn repository: %s" % self.url)
 
-        args = ['checkout', '--force']
+        args = ['checkout', '--force', '--quiet']
         if self.revision:
             args += ['-r', self.revision]
         args.append(self.url)

lib/spack/spack/modules.py

@@ -389,7 +389,6 @@ def write(self, overwrite=False):
             for mod in modules:
                 set_module_variables_for_package(package, mod)
             set_module_variables_for_package(package, package.module)
-            package.setup_environment(spack_env, env)
             package.setup_dependent_package(self.pkg.module, self.spec)
             package.setup_dependent_environment(spack_env, env, self.spec)
 

lib/spack/spack/package.py

@@ -1452,7 +1452,7 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         This is useful if there are some common steps to installing
         all extensions for a certain package.
         """
-        self.setup_environment(spack_env, run_env)
+        pass
 
     def setup_dependent_package(self, module, dependent_spec):
         """Set up Python module-scope variables for dependent packages.

lib/spack/spack/test/modules.py

@@ -357,6 +357,21 @@ def test_suffixes(self, tcl_factory):
         generator = tcl_factory(spec)
         assert 'bar' in generator.use_name
 
+    def test_setup_environment(self, tcl_factory):
+        spec = spack.spec.Spec('mpileaks')
+        spec.concretize()
+        content = get_modulefile_content(tcl_factory, spec)
+        assert len([x for x in content if 'setenv FOOBAR' in x]) == 1
+        assert len(
+            [x for x in content if 'setenv FOOBAR "mpileaks"' in x]
+        ) == 1
+
+        content = get_modulefile_content(tcl_factory, spec['callpath'])
+        assert len([x for x in content if 'setenv FOOBAR' in x]) == 1
+        assert len(
+            [x for x in content if 'setenv FOOBAR "callpath"' in x]
+        ) == 1
+
 
 @pytest.mark.usefixtures('config', 'builtin_mock', 'stringio_open')
 class TestLmod(object):

var/spack/repos/builtin.mock/packages/callpath/package.py

@@ -40,3 +40,6 @@ def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
         make("install")
+
+    def setup_environment(self, senv, renv):
+        renv.set('FOOBAR', self.name)

var/spack/repos/builtin.mock/packages/mpileaks/package.py

@@ -44,3 +44,6 @@ class Mpileaks(Package):
 
     def install(self, spec, prefix):
         pass
+
+    def setup_environment(self, senv, renv):
+        renv.set('FOOBAR', self.name)

var/spack/repos/builtin/packages/adlbx/package.py

@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Adlbx(AutotoolsPackage):
+    """ADLB/X: Master-worker library + work stealing and data dependencies"""
+
+    homepage = "http://swift-lang.org/Swift-T"
+    url      = "http://swift-lang.github.io/swift-t-downloads/adlbx-0.8.0.tar.gz"
+    version('0.8.0', '34ade59ce3be5bc296955231d47a27dd')
+
+    depends_on('exmcutils')
+    depends_on('mpi')
+
+    def configure_args(self):
+        args = ["--with-c-utils=" + self.spec['exmcutils'].prefix]
+        return args

var/spack/repos/builtin/packages/bison/package.py

@@ -35,6 +35,8 @@ class Bison(AutotoolsPackage):
 
     version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8')
 
-    depends_on("m4", type='build')
+    depends_on('m4', type='build')
+
+    patch('pgi.patch', when='@3.0.4')
 
     build_directory = 'spack-build'

var/spack/repos/builtin/packages/bison/pgi.patch

@@ -0,0 +1,10 @@
+--- a/lib/config.in.h
++++ b/lib/config.in.h
+@@ -2182,6 +2182,7 @@
+       ? defined __GNUC_STDC_INLINE__ && __GNUC_STDC_INLINE__ \
+       : (199901L <= __STDC_VERSION__ \
+          && !defined __HP_cc \
++         && !defined __PGI \
+          && !(defined __SUNPRO_C && __STDC__))) \
+      && !defined _GL_EXTERN_INLINE_STDHEADER_BUG)
+ # define _GL_INLINE inline

var/spack/repos/builtin/packages/es/package.py

@@ -37,3 +37,5 @@ class Es(AutotoolsPackage):
     url      = "https://github.com/wryun/es-shell/releases/download/v0.9.1/es-0.9.1.tar.gz"
 
     version('0.9.1', 'bf4db55b47bcc99892468b2e0aec0c9e')
+
+    depends_on('readline')

var/spack/repos/builtin/packages/exmcutils/package.py

@@ -0,0 +1,37 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Exmcutils(AutotoolsPackage):
+    """ExM C-Utils: Generic C utility library for ADLB/X and Swift/T"""
+
+    homepage = "http://swift-lang.org/Swift-T"
+    url      = "http://swift-lang.github.io/swift-t-downloads/exmcutils-0.5.3.tar.gz"
+
+    version('0.5.3', '0e3ed6cc2991c684cd8f08db45c99a39')
+
+    # This package has no dependencies.

var/spack/repos/builtin/packages/glib/package.py

@@ -34,6 +34,7 @@ class Glib(AutotoolsPackage):
     homepage = "https://developer.gnome.org/glib/"
     url      = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz"
 
+    version('2.49.7', '397ead3fcf325cb921d54e2c9e7dfd7a')
     version('2.49.4', 'e2c87c03017b0cd02c4c73274b92b148')
     version('2.48.1', '67bd3b75c9f6d5587b457dc01cdcd5bb')
     version('2.42.1', '89c4119e50e767d3532158605ee9121a')

var/spack/repos/builtin/packages/intel-mkl/package.py

@@ -43,6 +43,8 @@ class IntelMkl(IntelInstaller):
 
     homepage = "https://software.intel.com/en-us/intel-mkl"
 
+    version('2017.0.098', '3cdcb739ab5ab1e047eb130b9ffdd8d0',
+            url="file://%s/l_mkl_2017.0.098.tgz" % os.getcwd())
     version('11.3.2.181', '536dbd82896d6facc16de8f961d17d65',
             url="file://%s/l_mkl_11.3.2.181.tgz" % os.getcwd())
     version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34',

var/spack/repos/builtin/packages/ipp/package.py

@@ -37,6 +37,8 @@ class Ipp(IntelInstaller):
 
     homepage = "https://software.intel.com/en-us/intel-ipp"
 
+    version('2017.0.098', 'e7be757ebe351d9f9beed7efdc7b7118',
+            url="file://%s/l_ipp_2017.0.098.tgz" % os.getcwd())
     version('9.0.3.210', '0e1520dd3de7f811a6ef6ebc7aa429a3',
             url="file://%s/l_ipp_9.0.3.210.tgz" % os.getcwd())
 

var/spack/repos/builtin/packages/jmol/package.py

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+from distutils.dir_util import copy_tree
+
+
+class Jmol(Package):
+    """Jmol: an open-source Java viewer for chemical structures in 3D
+    with features for chemicals, crystals, materials and biomolecules."""
+
+    homepage = "http://jmol.sourceforge.net/"
+    url      = "https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.8/Jmol%2014.8.0/Jmol-14.8.0-binary.tar.gz"
+
+    version('14.8.0', '3c9f4004b9e617ea3ea0b78ab32397ea')
+
+    depends_on('jdk', type='run')
+
+    def install(self, spec, prefix):
+        copy_tree('jmol-{0}'.format(self.version), prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix)
+        run_env.set('JMOL_HOME', self.prefix)

var/spack/repos/builtin/packages/mpc/package.py

@@ -35,11 +35,18 @@ class Mpc(AutotoolsPackage):
     version('1.0.3', 'd6a1d5f8ddea3abd2cc3e98f58352d26')
     version('1.0.2', '68fadff3358fb3e7976c7a398a0af4c3')
 
-    depends_on('gmp')   # mpir is a drop-in replacement for this
-    depends_on('mpfr')  # Could also be built against mpir
+    depends_on('gmp@4.3.2:')   # mpir is a drop-in replacement for this
+    depends_on('mpfr@2.4.2:')  # Could also be built against mpir
 
     def url_for_version(self, version):
         if version < Version("1.0.1"):
             return "http://www.multiprecision.org/mpc/download/mpc-%s.tar.gz" % version
         else:
             return "https://ftp.gnu.org/gnu/mpc/mpc-%s.tar.gz" % version
+
+    def configure_args(self):
+        spec = self.spec
+        return [
+            '--with-mpfr={0}'.format(spec['mpfr'].prefix),
+            '--with-gmp={0}'.format(spec['gmp'].prefix)
+        ]

var/spack/repos/builtin/packages/numdiff/package.py

@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import sys
 
 
 class Numdiff(AutotoolsPackage):
@@ -34,6 +33,35 @@ class Numdiff(AutotoolsPackage):
     homepage  = 'https://www.nongnu.org/numdiff'
     url       = 'http://nongnu.askapache.com/numdiff/numdiff-5.8.1.tar.gz'
 
-    version('5.8.1',    'a295eb391f6cb1578209fc6b4f9d994e')
+    version('5.8.1', 'a295eb391f6cb1578209fc6b4f9d994e')
 
-    depends_on('gettext', when=sys.platform == 'darwin')
+    variant('nls', default=False,
+            description="Enable Natural Language Support")
+    variant('gmp', default=False,
+            description="Use GNU Multiple Precision Arithmetic Library")
+
+    depends_on('gettext', when='+nls')
+    depends_on('gmp', when='+gmp')
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+        if '+nls' in spec:
+            args.append('--enable-nls')
+        else:
+            args.append('--disable-nls')
+
+        if '+gmp' in spec:
+            # compile with -O0 as per upstream known issue with optimization
+            # and GMP; https://launchpad.net/ubuntu/+source/numdiff/+changelog
+            # http://www.nongnu.org/numdiff/#issues
+            # keep this variant off by default as one still encounter
+            # GNU MP: Cannot allocate memory (size=2305843009206983184)
+            args.extend([
+                '--enable-gmp',
+                'CFLAGS=-O0'
+            ])
+        else:
+            args.append('--disable-gmp')
+
+        return args

var/spack/repos/builtin/packages/pgi/package.py

@@ -40,9 +40,10 @@ class Pgi(Package):
 
     homepage = "http://www.pgroup.com/"
 
-    version('16.5', 'a40e8852071b5d600cb42f31631b3de1')
-    version('16.3', '618cb7ddbc57d4e4ed1f21a0ab25f427')
-    version('15.7', '84a689217b17cdaf78c39270c70bea5d')
+    version('16.10', '9bb6bfb7b1052f9e6a45829ba7a24e47')
+    version('16.5',  'a40e8852071b5d600cb42f31631b3de1')
+    version('16.3',  '618cb7ddbc57d4e4ed1f21a0ab25f427')
+    version('15.7',  '84a689217b17cdaf78c39270c70bea5d')
 
     variant('network', default=True,
             description="Perform a network install")

var/spack/repos/builtin/packages/turbine/package.py

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+from spack import *
+
+
+class Turbine(AutotoolsPackage):
+
+    homepage = "http://swift-lang.org/Swift-T"
+    url      = "http://swift-lang.github.io/swift-t-downloads/turbine-1.0.0.tar.gz"
+
+    version('1.0.0', '7ed56d65d6db0bfe15a439d818b4259e')
+
+    depends_on('adlbx')
+    depends_on('tcl')
+    depends_on('zsh')
+
+    def configure_args(self):
+        args = ["--with-c-utils=" + self.spec['exmcutils'].prefix,
+                "--with-adlb="    + self.spec['adlbx'].prefix,
+                "--with-tcl="     + self.spec['tcl'].prefix,
+                "--with-mpi="     + self.spec['mpi'].prefix]
+        return args

var/spack/repos/builtin/packages/valgrind/package.py

@@ -22,11 +22,11 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-
 from spack import *
+import sys
 
 
-class Valgrind(Package):
+class Valgrind(AutotoolsPackage):
     """An instrumentation framework for building dynamic analysis.
 
     There are Valgrind tools that can automatically detect many memory
@@ -44,17 +44,31 @@ class Valgrind(Package):
     version('3.11.0', '4ea62074da73ae82e0162d6550d3f129')
     version('3.10.1', '60ddae962bc79e7c95cfc4667245707f')
     version('3.10.0', '7c311a72a20388aceced1aa5573ce970')
+    version('develop', svn='svn://svn.valgrind.org/valgrind/trunk')
 
-    variant('mpi', default=True, description='Activates MPI support for valgrind')
+    variant('mpi', default=True,
+            description='Activates MPI support for valgrind')
     variant('boost', default=True,
             description='Activates boost support for valgrind')
 
     depends_on('mpi', when='+mpi')
     depends_on('boost', when='+boost')
 
-    def install(self, spec, prefix):
-        options = ['--prefix=%s' % prefix,
-                   '--enable-ubsan']
-        configure(*options)
-        make()
-        make("install")
+    depends_on("autoconf", type='build', when='@develop')
+    depends_on("automake", type='build', when='@develop')
+    depends_on("libtool", type='build', when='@develop')
+
+    def configure_args(self):
+        spec = self.spec
+        options = []
+        if not (spec.satisfies('%clang') and sys.platform == 'darwin'):
+            # Otherwise with (Apple's) clang there is a linker error:
+            # clang: error: unknown argument: '-static-libubsan'
+            options.append('--enable-ubsan')
+
+        if sys.platform == 'darwin':
+            options.extend([
+                '--build=amd64-darwin',
+                '--enable-only64bit'
+            ])
+        return options