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New repo for advanced packaging tutorial (#9711)

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* modified tutorial packages

* update hint in hdf5 tutorial file (typo for suggested argument)

* add repo.yaml to tutorial repository

* update tutorial docs to refer user to tutorial package repository

* flake edits

* recommend site scope vs. defaults

* you don't specify the repo's name when adding a repo, just the path
This commit is contained in:
Peter Scheibel
2018-11-06 19:57:32 -08:00
committed by Greg Becker
parent 058cf81312
commit 7d97e8b067
14 changed files with 959 additions and 36 deletions
Download Patch File Download Diff File Expand all files Collapse all files

62
var/spack/repos/tutorial/packages/armadillo/package.py Normal file
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# Copyright 2013-2018 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 Armadillo(CMakePackage):
"""Armadillo is a high quality linear algebra library (matrix maths)
for the C++ language, aiming towards a good balance between speed and
ease of use.
"""
homepage = "http://arma.sourceforge.net/"
url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz"
version('8.100.1', 'd9762d6f097e0451d0cfadfbda295e7c')
version('7.950.1', 'c06eb38b12cae49cab0ce05f96147147')
version('7.900.1', '5ef71763bd429a3d481499878351f3be')
version('7.500.0', '7d316fdf3c3c7ea92b64704180ae315d')
version('7.200.2', 'b21585372d67a8876117fd515d8cf0a2')
version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e')
variant('hdf5', default=False, description='Include HDF5 support')
depends_on('cmake@2.8.12:', type='build')
depends_on('arpack-ng') # old arpack causes undefined symbols
depends_on('blas')
depends_on('lapack')
depends_on('superlu@5.2:')
depends_on('hdf5', when='+hdf5')
patch('undef_linux.patch', when='platform=linux')
def cmake_args(self):
spec = self.spec
# TUTORIAL: fix the lines below by adding the appropriate query to
# the right dependency. To ask a dependency, e.g. `blas`, for the
# list of libraries it provides it suffices to access its `libs`
# attribute:
#
# blas_libs = spec['blas'].libs
#
# The CMake variables below require a semicolon separated list:
#
# blas_libs.joined(';')
return [
# ARPACK support
'-DARPACK_LIBRARY={0}'.format('FIXME: arpack-ng'),
# BLAS support
'-DBLAS_LIBRARY={0}'.format('FIXME: blas'),
# LAPACK support
'-DLAPACK_LIBRARY={0}'.format('FIXME: lapack'),
# SuperLU support
'-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include),
'-DSuperLU_LIBRARY={0}'.format('FIXME: superlu'),
# HDF5 support
'-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF')
]

4
var/spack/repos/tutorial/packages/armadillo/undef_linux.patch Normal file
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--- a/include/armadillo_bits/compiler_setup.hpp
+++ b/include/armadillo_bits/compiler_setup.hpp
@@ -0,0 +1 @@
+#undef linux

78
var/spack/repos/tutorial/packages/elpa/package.py Normal file
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# Copyright 2013-2018 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 Elpa(AutotoolsPackage):
"""Eigenvalue solvers for Petaflop-Applications (ELPA)"""
homepage = 'http://elpa.mpcdf.mpg.de/'
url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
version('2018.05.001.rc1', 'ccd77bd8036988ee624f43c04992bcdd')
version('2017.11.001', '4a437be40cc966efb07aaab84c20cd6e', preferred=True)
version('2017.05.003', '7c8e5e58cafab212badaf4216695700f')
version('2017.05.002', 'd0abc1ac1f493f93bf5e30ec8ab155dc')
version('2016.11.001.pre', '5656fd066cf0dcd071dbcaf20a639b37')
version('2016.05.004', 'c0dd3a53055536fc3a2a221e78d8b376')
version('2016.05.003', '88a9f3f3bfb63e16509dd1be089dcf2c')
version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6')
variant('openmp', default=False, description='Activates OpenMP support')
variant('optflags', default=True, description='Build with optimization flags')
depends_on('mpi')
depends_on('blas')
depends_on('lapack')
depends_on('scalapack')
def url_for_version(self, version):
t = 'http://elpa.mpcdf.mpg.de/html/Releases/{0}/elpa-{0}.tar.gz'
if version < Version('2016.05.003'):
t = 'http://elpa.mpcdf.mpg.de/elpa-{0}.tar.gz'
return t.format(str(version))
@property
def libs(self):
libname = 'libelpa_openmp' if '+openmp' in self.spec else 'libelpa'
return find_libraries(
libname, root=self.prefix, shared=True, recursive=True
)
build_directory = 'spack-build'
def setup_environment(self, spack_env, run_env):
# TUTORIAL: set the following environment variables:
#
# CC=spec['mpi'].mpicc
# FC=spec['mpi'].mpifc
# CXX=spec['mpi'].mpicxx
# SCALAPACK_LDFLAGS=spec['scalapack'].libs.joined()
#
# and append the following flags:
#
# LDFLAGS -> spec['lapack'].libs.search_flags
# LIBS -> spec['lapack'].libs.link_flags
pass
def configure_args(self):
# TODO: set optimum flags for platform+compiler combo, see
# https://github.com/hfp/xconfigure/tree/master/elpa
# also see:
# https://src.fedoraproject.org/cgit/rpms/elpa.git/
# https://packages.qa.debian.org/e/elpa.html
options = []
# without -march=native there is configure error for 2017.05.02
# Could not compile test program, try with --disable-sse, or
# adjust the C compiler or CFLAGS
if '+optflags' in self.spec:
options.extend([
'FCFLAGS=-O2 -march=native -ffree-line-length-none',
'CFLAGS=-O2 -march=native'
])
if '+openmp' in self.spec:
options.append('--enable-openmp')
return options

16
var/spack/repos/tutorial/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch Normal file
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diff --git a/fortran/src/H5f90global.F90 b/fortran/src/H5f90global.F90
index dd2b171..629418a 100644
--- a/fortran/src/H5f90global.F90
+++ b/fortran/src/H5f90global.F90
@@ -142,10 +142,7 @@ MODULE H5GLOBAL
INTEGER(HID_T), DIMENSION(PREDEF_TYPES_LEN) :: predef_types
EQUIVALENCE (predef_types(1), H5T_NATIVE_INTEGER_KIND(1))
- EQUIVALENCE (predef_types(2), H5T_NATIVE_INTEGER_KIND(2))
- EQUIVALENCE (predef_types(3), H5T_NATIVE_INTEGER_KIND(3))
- EQUIVALENCE (predef_types(4), H5T_NATIVE_INTEGER_KIND(4))
- EQUIVALENCE (predef_types(5), H5T_NATIVE_INTEGER_KIND(5))
+ ! EQUIVALENCE predef_types(2:5) are unnecessary and violate the standard
EQUIVALENCE (predef_types(6), H5T_NATIVE_INTEGER)
EQUIVALENCE (predef_types(7), H5T_NATIVE_REAL)
EQUIVALENCE (predef_types(8), H5T_NATIVE_DOUBLE)

307
var/spack/repos/tutorial/packages/hdf5/package.py Normal file
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# Copyright 2013-2018 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 shutil
import sys
from spack import *
class Hdf5(AutotoolsPackage):
"""HDF5 is a data model, library, and file format for storing and managing
data. It supports an unlimited variety of datatypes, and is designed for
flexible and efficient I/O and for high volume and complex data.
"""
homepage = "https://support.hdfgroup.org/HDF5/"
url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz"
list_url = "https://support.hdfgroup.org/ftp/HDF5/releases"
list_depth = 3
version('1.10.4', '8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2')
version('1.10.3', 'b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39')
version('1.10.2', '8d4eae84e533efa57496638fd0dca8c3')
version('1.10.1', '43a2f9466702fb1db31df98ae6677f15')
version('1.10.0-patch1', '9180ff0ef8dc2ef3f61bd37a7404f295')
version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199')
version('1.8.19', '7f568e2464d4ab0a74d16b23956d900b')
version('1.8.18', 'dd2148b740713ca0295442ec683d7b1c')
version('1.8.17', '7d572f8f3b798a628b8245af0391a0ca')
version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618')
version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
version('1.8.14', 'a482686e733514a51cde12d6fe5c5d95')
version('1.8.13', 'c03426e9e77d7766944654280b467289')
version('1.8.12', 'd804802feb99b87fc668a90e6fa34411')
version('1.8.10', '710aa9fb61a51d61a7e2c09bf0052157')
variant('debug', default=False,
description='Builds a debug version of the library')
variant('shared', default=True,
description='Builds a shared version of the library')
variant('hl', default=False, description='Enable the high-level library')
variant('cxx', default=False, description='Enable C++ support')
variant('fortran', default=False, description='Enable Fortran support')
variant('threadsafe', default=False,
description='Enable thread-safe capabilities')
variant('mpi', default=True, description='Enable MPI support')
variant('szip', default=False, description='Enable szip support')
variant('pic', default=True,
description='Produce position-independent code (for shared libs)')
depends_on('mpi', when='+mpi')
# numactl does not currently build on darwin
if sys.platform != 'darwin':
depends_on('numactl', when='+mpi+fortran')
depends_on('szip', when='+szip')
depends_on('zlib@1.1.2:')
# There are several officially unsupported combinations of the features:
# 1. Thread safety is not guaranteed via high-level C-API but in some cases
# it works.
# conflicts('+threadsafe+hl')
# 2. Thread safety is not guaranteed via Fortran (CXX) API, but it's
# possible for a dependency tree to contain a package that uses Fortran
# (CXX) API in a single thread and another one that uses low-level C-API
# in multiple threads. To allow for such scenarios, we don't specify the
# following conflicts.
# conflicts('+threadsafe+cxx')
# conflicts('+threadsafe+fortran')
# 3. Parallel features are not supported via CXX API, but for the reasons
# described in #2 we allow for such combination.
# conflicts('+mpi+cxx')
# There are known build failures with intel@18.0.1. This issue is
# discussed and patch is provided at
# https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951.
patch('h5f90global-mult-obj-same-equivalence-same-common-block.patch',
when='@1.10.1%intel@18')
# Turn line comments into block comments to conform with pre-C99 language
# standards. Versions of hdf5 after 1.8.10 don't require this patch,
# either because they conform to pre-C99 or neglect to ask for pre-C99
# language standards from their compiler. The hdf5 build system adds
# the -ansi cflag (run 'man gcc' for info on -ansi) for some versions
# of some compilers (see hdf5-1.8.10/config/gnu-flags). The hdf5 build
# system does not provide an option to disable -ansi, but since the
# pre-C99 code is restricted to just five lines of line comments in
# three src files, this patch accomplishes the simple task of patching the
# three src files and leaves the hdf5 build system alone.
patch('pre-c99-comments.patch', when='@1.8.10')
# There are build errors with GCC 8, see
# https://forum.hdfgroup.org/t/1-10-2-h5detect-compile-error-gcc-8-1-0-on-centos-7-2-solved/4441
patch('https://salsa.debian.org/debian-gis-team/hdf5/raw/bf94804af5f80f662cad80a5527535b3c6537df6/debian/patches/gcc-8.patch', sha256='57cee5ff1992b4098eda079815c36fc2da9b10e00a9056df054f2384c4fc7523', when='@1.10.2%gcc@8:')
filter_compiler_wrappers('h5cc', 'h5c++', 'h5fc', relative_root='bin')
def url_for_version(self, version):
url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-{0}/hdf5-{1}/src/hdf5-{1}.tar.gz"
return url.format(version.up_to(2), version)
@property
def libs(self):
"""HDF5 can be queried for the following parameters:
- "hl": high-level interface
- "cxx": C++ APIs
- "fortran": Fortran APIs
:return: list of matching libraries
"""
# This map contains a translation from query_parameters
# to the libraries needed
query2libraries = { # noqa: F841
tuple(): ['libhdf5'],
('cxx', 'fortran', 'hl'): [
'libhdf5hl_fortran',
'libhdf5_hl_cpp',
'libhdf5_hl',
'libhdf5_fortran',
'libhdf5',
],
('cxx', 'hl'): [
'libhdf5_hl_cpp',
'libhdf5_hl',
'libhdf5',
],
('fortran', 'hl'): [
'libhdf5hl_fortran',
'libhdf5_hl',
'libhdf5_fortran',
'libhdf5',
],
('hl',): [
'libhdf5_hl',
'libhdf5',
],
('cxx', 'fortran'): [
'libhdf5_fortran',
'libhdf5_cpp',
'libhdf5',
],
('cxx',): [
'libhdf5_cpp',
'libhdf5',
],
('fortran',): [
'libhdf5_fortran',
'libhdf5',
]
}
# TUTORIAL: you need to fix the implementation below, and
# return the correct list of libraries according to the
# query parameters your dependency has used.
#
# You can retrieve the query parameters by doing
#
# query_parameters = self.spec.last_query.extra_parameters
#
# and use the map above to query the list of libraries you need
# to search.
#
# Finally uncomment the lines below to return a LibraryList
#
# shared = '+shared' in self.spec
# return find_libraries(
# libraries, root=self.prefix, shared=shared, recursive=True
# )
return []
@run_before('configure')
def fortran_check(self):
if '+fortran' in self.spec and not self.compiler.fc:
msg = 'cannot build a Fortran variant without a Fortran compiler'
raise RuntimeError(msg)
def configure_args(self):
# Always enable this option. This does not actually enable any
# features: it only *allows* the user to specify certain
# combinations of other arguments. Enabling it just skips a
# sanity check in configure, so this doesn't merit a variant.
extra_args = ['--enable-unsupported']
extra_args += self.enable_or_disable('threadsafe')
extra_args += self.enable_or_disable('cxx')
extra_args += self.enable_or_disable('hl')
extra_args += self.enable_or_disable('fortran')
if '+szip' in self.spec:
extra_args.append('--with-szlib=%s' % self.spec['szip'].prefix)
else:
extra_args.append('--without-szlib')
if self.spec.satisfies('@1.10:'):
if '+debug' in self.spec:
extra_args.append('--enable-build-mode=debug')
else:
extra_args.append('--enable-build-mode=production')
else:
if '+debug' in self.spec:
extra_args.append('--enable-debug=all')
else:
extra_args.append('--enable-production')
# '--enable-fortran2003' no longer exists as of version 1.10.0
if '+fortran' in self.spec:
extra_args.append('--enable-fortran2003')
else:
extra_args.append('--disable-fortran2003')
if '+shared' in self.spec:
extra_args.append('--enable-shared')
else:
extra_args.append('--disable-shared')
extra_args.append('--enable-static-exec')
if '+pic' in self.spec:
extra_args += ['%s=%s' % (f, self.compiler.pic_flag)
for f in ['CFLAGS', 'CXXFLAGS', 'FCFLAGS']]
if '+mpi' in self.spec:
# The HDF5 configure script warns if cxx and mpi are enabled
# together. There doesn't seem to be a real reason for this, except
# that parts of the MPI interface are not accessible via the C++
# interface. Since they are still accessible via the C interface,
# this is not actually a problem.
extra_args += ['--enable-parallel',
'CC=%s' % self.spec['mpi'].mpicc]
if '+cxx' in self.spec:
extra_args.append('CXX=%s' % self.spec['mpi'].mpicxx)
if '+fortran' in self.spec:
extra_args.append('FC=%s' % self.spec['mpi'].mpifc)
extra_args.append('--with-zlib=%s' % self.spec['zlib'].prefix)
return extra_args
@run_after('configure')
def patch_postdeps(self):
if '@:1.8.14' in self.spec:
# On Ubuntu14, HDF5 1.8.12 (and maybe other versions)
# mysteriously end up with "-l -l" in the postdeps in the
# libtool script. Patch this by removing the spurious -l's.
filter_file(
r'postdeps="([^"]*)"',
lambda m: 'postdeps="%s"' % ' '.join(
arg for arg in m.group(1).split(' ') if arg != '-l'),
'libtool')
@run_after('install')
@on_package_attributes(run_tests=True)
def check_install(self):
# Build and run a small program to test the installed HDF5 library
spec = self.spec
print("Checking HDF5 installation...")
checkdir = "spack-check"
with working_dir(checkdir, create=True):
source = r"""
#include <hdf5.h>
#include <assert.h>
#include <stdio.h>
int main(int argc, char **argv) {
unsigned majnum, minnum, relnum;
herr_t herr = H5get_libversion(&majnum, &minnum, &relnum);
assert(!herr);
printf("HDF5 version %d.%d.%d %u.%u.%u\n", H5_VERS_MAJOR, H5_VERS_MINOR,
H5_VERS_RELEASE, majnum, minnum, relnum);
return 0;
}
"""
expected = """\
HDF5 version {version} {version}
""".format(version=str(spec.version.up_to(3)))
with open("check.c", 'w') as f:
f.write(source)
if '+mpi' in spec:
cc = Executable(spec['mpi'].mpicc)
else:
cc = Executable(self.compiler.cc)
cc(*(['-c', "check.c"] + spec['hdf5'].headers.cpp_flags.split()))
cc(*(['-o', "check",
"check.o"] + spec['hdf5'].libs.ld_flags.split()))
try:
check = Executable('./check')
output = check(output=str)
except ProcessError:
output = ""
success = output == expected
if not success:
print("Produced output does not match expected output.")
print("Expected output:")
print('-' * 80)
print(expected)
print('-' * 80)
print("Produced output:")
print('-' * 80)
print(output)
print('-' * 80)
raise RuntimeError("HDF5 install check failed")
shutil.rmtree(checkdir)

43
var/spack/repos/tutorial/packages/hdf5/pre-c99-comments.patch Normal file
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diff --git a/test/th5s.c b/test/th5s.c
index 462bc36..8e18fad 100644
--- a/test/th5s.c
+++ b/test/th5s.c
@@ -730,8 +730,8 @@ test_h5s_zero_dim(void)
ret = H5Pset_chunk(plist_id, SPACE1_RANK, chunk_dims);
CHECK(ret, FAIL, "H5Pset_chunk");
- // ret = H5Pset_alloc_time(plist_id, alloc_time);
- // CHECK(ret, FAIL, "H5Pset_alloc_time");
+ /* ret = H5Pset_alloc_time(plist_id, alloc_time); */
+ /* CHECK(ret, FAIL, "H5Pset_alloc_time"); */
dset1 = H5Dcreate2(fid1, BASICDATASET1, H5T_NATIVE_INT, sid_chunk, H5P_DEFAULT, plist_id, H5P_DEFAULT);
CHECK(dset1, FAIL, "H5Dcreate2");
diff --git a/tools/h5dump/h5dump_ddl.c b/tools/h5dump/h5dump_ddl.c
index ee6de5e..3ed6045 100644
--- a/tools/h5dump/h5dump_ddl.c
+++ b/tools/h5dump/h5dump_ddl.c
@@ -1341,8 +1341,8 @@ handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe
string_dataformat.do_escape = display_escape;
outputformat = &string_dataformat;
- //attr_name = attr + j + 1;
- // need to replace escape characters
+ /* attr_name = attr + j + 1; */
+ /* need to replace escape characters */
attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/");
diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
index 9ce3524..3b4e5e7 100644
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -632,7 +632,7 @@ h5tools_str_indent(h5tools_str_t *str, const h5tool_format_t *info,
h5tools_str_append(str, "%s", OPT(info->line_indent, ""));
}
-// ctx->need_prefix = 0;
+/* ctx->need_prefix = 0; */
}
/*-------------------------------------------------------------------------

13
var/spack/repos/tutorial/packages/mpich/mpich32_clang.patch Normal file
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diff --git a/src/include/mpiimpl.h b/src/include/mpiimpl.h
index e705e5d..3bfcbee 100644
--- a/src/include/mpiimpl.h
+++ b/src/include/mpiimpl.h
@@ -1528,7 +1528,7 @@ typedef struct MPID_Request {
#ifdef MPID_DEV_REQUEST_DECL
MPID_DEV_REQUEST_DECL
#endif
-} MPID_Request ATTRIBUTE((__aligned__(32)));
+} ATTRIBUTE((__aligned__(32))) MPID_Request;
extern MPIU_Object_alloc_t MPID_Request_mem;
/* Preallocated request objects */

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var/spack/repos/tutorial/packages/mpich/package.py Normal file
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# Copyright 2013-2018 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 Mpich(AutotoolsPackage):
"""MPICH is a high performance and widely portable implementation of
the Message Passing Interface (MPI) standard."""
homepage = "http://www.mpich.org"
url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"
git = "https://github.com/pmodels/mpich.git"
list_url = "http://www.mpich.org/static/downloads/"
list_depth = 1
version('develop', submodules=True)
version('3.2.1', 'e175452f4d61646a52c73031683fc375')
version('3.2', 'f414cfa77099cd1fa1a5ae4e22db508a')
version('3.1.4', '2ab544607986486562e076b83937bba2')
version('3.1.3', '93cb17f91ac758cbf9174ecb03563778')
version('3.1.2', '7fbf4b81dcb74b07ae85939d1ceee7f1')
version('3.1.1', '40dc408b1e03cc36d80209baaa2d32b7')
version('3.1', '5643dd176499bfb7d25079aaff25f2ec')
version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
variant('hydra', default=True, description='Build the hydra process manager')
variant('pmi', default=True, description='Build with PMI support')
variant('romio', default=True, description='Enable ROMIO MPI I/O implementation')
variant('verbs', default=False, description='Build support for OpenFabrics verbs.')
variant(
'device',
default='ch3',
description='''Abstract Device Interface (ADI)
implementation. The ch4 device is currently in experimental state''',
values=('ch3', 'ch4'),
multi=False
)
variant(
'netmod',
default='tcp',
description='''Network module. Only single netmod builds are
supported. For ch3 device configurations, this presumes the
ch3:nemesis communication channel. ch3:sock is not supported by this
spack package at this time.''',
values=('tcp', 'mxm', 'ofi', 'ucx'),
multi=False
)
provides('mpi')
provides('mpi@:3.0', when='@3:')
provides('mpi@:1.3', when='@1:')
filter_compiler_wrappers(
'mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpifort', relative_root='bin'
)
# fix MPI_Barrier segmentation fault
# see https://lists.mpich.org/pipermail/discuss/2016-May/004764.html
# and https://lists.mpich.org/pipermail/discuss/2016-June/004768.html
patch('mpich32_clang.patch', when='@3.2:3.2.0%clang')
depends_on('findutils', type='build')
depends_on('libfabric', when='netmod=ofi')
conflicts('device=ch4', when='@:3.2')
conflicts('netmod=ofi', when='@:3.1.4')
conflicts('netmod=ucx', when='device=ch3')
conflicts('netmod=mxm', when='device=ch4')
conflicts('netmod=mxm', when='@:3.1.3')
conflicts('netmod=tcp', when='device=ch4')
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
# TUTORIAL: set the following variables for dependents:
#
# MPICC=join_path(self.prefix.bin, 'mpicc')
# MPICXX=join_path(self.prefix.bin, 'mpic++')
# MPIF77=join_path(self.prefix.bin, 'mpif77')
# MPIF90=join_path(self.prefix.bin, 'mpif90')
# MPICH_CC=spack_cc
# MPICH_CXX=spack_cxx
# MPICH_F77=spack_f77
# MPICH_F90=spack_fc
# MPICH_FC=spack_fc
pass
def setup_dependent_package(self, module, dependent_spec):
if 'platform=cray' in self.spec:
self.spec.mpicc = spack_cc
self.spec.mpicxx = spack_cxx
self.spec.mpifc = spack_fc
self.spec.mpif77 = spack_f77
else:
self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++')
self.spec.mpifc = join_path(self.prefix.bin, 'mpif90')
self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
self.spec.mpicxx_shared_libs = [
join_path(self.prefix.lib, 'libmpicxx.{0}'.format(dso_suffix)),
join_path(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix))
]
def autoreconf(self, spec, prefix):
"""Not needed usually, configure should be already there"""
# If configure exists nothing needs to be done
if os.path.exists(self.configure_abs_path):
return
# Else bootstrap with autotools
bash = which('bash')
bash('./autogen.sh')
@run_before('autoreconf')
def die_without_fortran(self):
# Until we can pass variants such as +fortran through virtual
# dependencies depends_on('mpi'), require Fortran compiler to
# avoid delayed build errors in dependents.
if (self.compiler.f77 is None) or (self.compiler.fc is None):
raise InstallError(
'Mpich requires both C and Fortran compilers!'
)
def configure_args(self):
spec = self.spec
config_args = [
'--enable-shared',
'--with-pm={0}'.format('hydra' if '+hydra' in spec else 'no'),
'--with-pmi={0}'.format('yes' if '+pmi' in spec else 'no'),
'--{0}-romio'.format('enable' if '+romio' in spec else 'disable'),
'--{0}-ibverbs'.format('with' if '+verbs' in spec else 'without')
]
# setup device configuration
device_config = ''
if 'device=ch4' in spec:
device_config = '--with-device=ch4:'
elif 'device=ch3' in spec:
device_config = '--with-device=ch3:nemesis:'
if 'netmod=ucx' in spec:
device_config += 'ucx'
elif 'netmod=ofi' in spec:
device_config += 'ofi'
elif 'netmod=mxm' in spec:
device_config += 'mxm'
elif 'netmod=tcp' in spec:
device_config += 'tcp'
config_args.append(device_config)
return config_args

42
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@@ -0,0 +1,42 @@
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -62,7 +62,7 @@
set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fp-model strict")
endif()
if("${CMAKE_Fortran_COMPILER}" MATCHES "xlf")
- set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qnosave -qstrict=none")
+ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qnosave -qstrict")
endif()
# Delete libmtsk in linking sequence for Sun/Oracle Fortran Compiler.
# This library is not present in the Sun package SolarisStudio12.3-linux-x86-bin
--- a/CMAKE/CheckLAPACKCompilerFlags.cmake
+++ b/CMAKE/CheckLAPACKCompilerFlags.cmake
@@ -43,12 +43,6 @@
if( "${CMAKE_Fortran_FLAGS}" MATCHES "-qflttrap=[a-zA-Z:]:enable" )
set( FPE_EXIT TRUE )
endif()
-
- if( NOT ("${CMAKE_Fortran_FLAGS}" MATCHES "-qfixed") )
- message( STATUS "Enabling fixed format F90/F95 with -qfixed" )
- set( CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qfixed"
- CACHE STRING "Flags for Fortran compiler." FORCE )
- endif()
# HP Fortran
elseif( CMAKE_Fortran_COMPILER_ID STREQUAL "HP" )
--- a/CBLAS/CMakeLists.txt
+++ b/CBLAS/CMakeLists.txt
@@ -12,8 +12,8 @@
SYMBOL_NAMESPACE "F77_")
if(NOT FortranCInterface_GLOBAL_FOUND OR NOT FortranCInterface_MODULE_FOUND)
message(WARNING "Reverting to pre-defined include/lapacke_mangling.h")
- configure_file(include/lapacke_mangling_with_flags.h.in
- ${LAPACK_BINARY_DIR}/include/lapacke_mangling.h)
+ configure_file(include/cblas_mangling_with_flags.h.in
+ ${LAPACK_BINARY_DIR}/include/cblas_mangling.h)
endif()
include_directories(include ${LAPACK_BINARY_DIR}/include)

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@@ -0,0 +1,186 @@
# Copyright 2013-2018 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 NetlibLapack(CMakePackage):
"""LAPACK version 3.X is a comprehensive FORTRAN library that does
linear algebra operations including matrix inversions, least squared
solutions to linear sets of equations, eigenvector analysis, singular
value decomposition, etc. It is a very comprehensive and reputable
package that has found extensive use in the scientific community.
"""
homepage = "http://www.netlib.org/lapack/"
url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
version('3.8.0', '96591affdbf58c450d45c1daa540dbd2',
url='http://www.netlib.org/lapack/lapack-3.8.0.tar.gz')
version('3.7.1', 'dcdeeed73de152c4643ccc5b1aeb453c')
version('3.7.0', '697bb8d67c7d336a0f339cc9dd0fa72f')
version('3.6.1', '421b2cb72e15f237e144428f9c460ee0')
version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101')
version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478')
version('3.4.1', '44c3869c38c8335c2b9c2a8bb276eb55')
version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
variant('shared', default=True, description="Build shared library version")
variant('external-blas', default=False,
description='Build lapack with an external blas')
variant('lapacke', default=True,
description='Activates the build of the LAPACKE C interface')
variant('xblas', default=False,
description='Builds extended precision routines using XBLAS')
patch('ibm-xl.patch', when='@3.7: %xl')
patch('ibm-xl.patch', when='@3.7: %xl_r')
# https://github.com/Reference-LAPACK/lapack/issues/228
# TODO: update 'when' once the version of lapack
# containing the fix is released and added to Spack.
patch('undefined_declarations.patch', when='@3.8.0:')
# https://github.com/Reference-LAPACK/lapack/pull/268
# TODO: update 'when' once the version of lapack
# containing the fix is released and added to Spack.
patch('testing.patch', when='@3.7.0:')
# virtual dependency
provides('blas', when='~external-blas')
provides('lapack')
depends_on('blas', when='+external-blas')
depends_on('netlib-xblas+fortran+plain_blas', when='+xblas')
depends_on('python@2.7:', type='test')
# We need to run every phase twice in order to get static and shared
# versions of the libraries. When ~shared, we run the default
# implementations of the CMakePackage's phases and get only one building
# directory 'spack-build-static' with -DBUILD_SHARED_LIBS:BOOL=OFF (see
# implementations of self.build_directory and self.cmake_args() below).
# When +shared, we run the overridden methods for the phases, each
# running the default implementation twice with different values for
# self._building_shared. As a result, we get two building directories:
# 'spack-build-static' with -DBUILD_SHARED_LIBS:BOOL=OFF and
# 'spack-build-shared' with -DBUILD_SHARED_LIBS:BOOL=ON.
_building_shared = False
def patch(self):
# Fix cblas CMakeLists.txt -- has wrong case for subdirectory name.
if self.spec.satisfies('@3.6.0:'):
filter_file(
'${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/',
'${CMAKE_CURRENT_SOURCE_DIR}/cmake/',
'CBLAS/CMakeLists.txt', string=True)
@property
def blas_libs(self):
shared = True if '+shared' in self.spec else False
query_parameters = self.spec.last_query.extra_parameters
query2libraries = {
tuple(): ['libblas'],
('c', 'fortran'): [
'libcblas',
'libblas',
],
('c',): [
'libcblas',
],
('fortran',): [
'libblas',
]
}
key = tuple(sorted(query_parameters))
libraries = query2libraries[key]
return find_libraries(
libraries, root=self.prefix, shared=shared, recursive=True
)
# TUTORIAL: add a proper `lapack_lib` property, along the lines
# of the `blas_lib` property above. The library that provides
# the lapack API is called `liblapack`.
@property
def headers(self):
include_dir = self.spec.prefix.include
cblas_h = join_path(include_dir, 'cblas.h')
lapacke_h = join_path(include_dir, 'lapacke.h')
return HeaderList([cblas_h, lapacke_h])
@property
def build_directory(self):
return join_path(self.stage.source_path,
'spack-build-shared' if self._building_shared
else 'spack-build-static')
def cmake_args(self):
args = ['-DBUILD_SHARED_LIBS:BOOL=' +
('ON' if self._building_shared else 'OFF')]
if self.spec.satisfies('+lapacke'):
args.extend(['-DLAPACKE:BOOL=ON', '-DLAPACKE_WITH_TMG:BOOL=ON'])
else:
args.extend(['-DLAPACKE:BOOL=OFF', '-DLAPACKE_WITH_TMG:BOOL=OFF'])
if self.spec.satisfies('@3.6.0:'):
args.append('-DCBLAS=ON') # always build CBLAS
if self.spec.satisfies('%intel'):
# Intel compiler finds serious syntax issues when trying to
# build CBLAS and LapackE
args.extend(['-DCBLAS=OFF', '-DLAPACKE:BOOL=OFF'])
if self.spec.satisfies('%xl') or self.spec.satisfies('%xl_r'):
# use F77 compiler if IBM XL
args.extend(['-DCMAKE_Fortran_COMPILER=' + self.compiler.f77,
'-DCMAKE_Fortran_FLAGS=' +
(' '.join(self.spec.compiler_flags['fflags'])) +
" -O3 -qnohot"])
# deprecated routines are commonly needed by, for example, suitesparse
# Note that OpenBLAS spack is built with deprecated routines
args.append('-DBUILD_DEPRECATED:BOOL=ON')
if self.spec.satisfies('+external-blas'):
args.extend(['-DUSE_OPTIMIZED_BLAS:BOOL=ON',
'-DBLAS_LIBRARIES:PATH=' +
self.spec['blas'].libs.joined(';')])
if self.spec.satisfies('+xblas'):
args.extend(['-DXBLAS_INCLUDE_DIR=' +
self.spec['netlib-xblas'].prefix.include,
'-DXBLAS_LIBRARY=' +
self.spec['netlib-xblas'].libs.joined(';')])
args.append('-DBUILD_TESTING:BOOL=' +
('ON' if self.run_tests else 'OFF'))
return args
# Build, install, and check both static and shared versions of the
# libraries when +shared
@when('+shared')
def cmake(self, spec, prefix):
for self._building_shared in (False, True):
super(NetlibLapack, self).cmake(spec, prefix)
@when('+shared')
def build(self, spec, prefix):
for self._building_shared in (False, True):
super(NetlibLapack, self).build(spec, prefix)
@when('+shared')
def install(self, spec, prefix):
for self._building_shared in (False, True):
super(NetlibLapack, self).install(spec, prefix)
@when('+shared')
def check(self):
for self._building_shared in (False, True):
super(NetlibLapack, self).check()

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@@ -0,0 +1,13 @@
diff --git a/TESTING/LIN/alahd.f b/TESTING/LIN/alahd.f
index 8f4cd58d..6a4946e0 100644
--- a/TESTING/LIN/alahd.f
+++ b/TESTING/LIN/alahd.f
@@ -1036,7 +1036,7 @@
9929 FORMAT( ' Test ratios (1-3: ', A1, 'TZRZF):' )
9920 FORMAT( 3X, ' 7-10: same as 3-6', 3X, ' 11-14: same as 3-6' )
9921 FORMAT( ' Test ratios:', / ' (1-2: ', A1, 'GELS, 3-6: ', A1,
- $ 'GELSY, 7-10: ', A1, 'GELSS, 11-14: ', A1, 'GELSD, 15-16: '
+ $ 'GELSY, 7-10: ', A1, 'GELSS, 11-14: ', A1, 'GELSD, 15-16: ',
$ A1, 'GETSLS)')
9928 FORMAT( 7X, 'where ALPHA = ( 1 + SQRT( 17 ) ) / 8' )
9927 FORMAT( 3X, I2, ': ABS( Largest element in L )', / 12X,

26
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@@ -0,0 +1,26 @@
diff --git a/SRC/dsytrf_aa_2stage.f b/SRC/dsytrf_aa_2stage.f
index 2991305..f5f06cc 100644
--- a/SRC/dsytrf_aa_2stage.f
+++ b/SRC/dsytrf_aa_2stage.f
@@ -191,7 +191,7 @@
EXTERNAL LSAME, ILAENV
* ..
* .. External Subroutines ..
- EXTERNAL XERBLA, DCOPY, DLACGV, DLACPY,
+ EXTERNAL XERBLA, DCOPY, DLACPY,
$ DLASET, DGBTRF, DGEMM, DGETRF,
$ DSYGST, DSWAP, DTRSM
* ..
diff --git a/SRC/ssytrf_aa_2stage.f b/SRC/ssytrf_aa_2stage.f
index be6809d..a929749 100644
--- a/SRC/ssytrf_aa_2stage.f
+++ b/SRC/ssytrf_aa_2stage.f
@@ -191,7 +191,7 @@
EXTERNAL LSAME, ILAENV
* ..
* .. External Subroutines ..
- EXTERNAL XERBLA, SCOPY, SLACGV, SLACPY,
+ EXTERNAL XERBLA, SCOPY, SLACPY,
$ SLASET, SGBTRF, SGEMM, SGETRF,
$ SSYGST, SSWAP, STRSM
* ..

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var/spack/repos/tutorial/repo.yaml Normal file
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@@ -0,0 +1,2 @@
repo:
namespace: tutorial