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update tutorial version of hdf5 (#25368)

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Chris White 2021-09-17 17:34:56 -07:00 committed by GitHub
parent b847bb72f0
commit 79ac572f21
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GPG Key ID: 4AEE18F83AFDEB23
5 changed files with 411 additions and 111 deletions
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11
var/spack/repos/tutorial/packages/hdf5/h5public-skip-mpicxx.patch Normal file
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@ -0,0 +1,11 @@
--- a/src/H5public.h 2019-08-28 18:51:39.393781356 -0400
+++ b/src/H5public.h 2019-08-28 20:59:50.315181711 -0400
@@ -57,6 +57,8 @@
# include <stddef.h>
#endif
#ifdef H5_HAVE_PARALLEL
+# define MPICH_SKIP_MPICXX 1
+# define OMPI_SKIP_MPICXX 1
# include <mpi.h>
#ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already */
# include <mpio.h>

12
var/spack/repos/tutorial/packages/hdf5/hdf5_1.8_gcc10.patch Normal file
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@ -0,0 +1,12 @@
diff -Naur hdf5.orig/fortran/test/tH5T_F03.f90 hdf5/fortran/test/tH5T_F03.f90
--- hdf5.orig/fortran/test/tH5T_F03.f90 2021-01-19 13:23:11.298000000 +0100
+++ hdf5/fortran/test/tH5T_F03.f90 2021-01-19 13:19:17.637000000 +0100
@@ -1541,7 +1541,7 @@
INTEGER :: A, B, C, D
INTEGER :: Aw, Bw, Cw, Dw
INTEGER :: i, j
- INTEGER, PARAMETER :: hex = Z'00000003'
+ INTEGER, PARAMETER :: hex = INT(Z'00000003')
TYPE(C_PTR) :: f_ptr
INTEGER :: error ! Error flag
!

452
var/spack/repos/tutorial/packages/hdf5/package.py
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@ -3,62 +3,109 @@
# #
# SPDX-License-Identifier: (Apache-2.0 OR MIT) # SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
import shutil import shutil
import sys import sys
from spack import * import llnl.util.tty as tty
class Hdf5(AutotoolsPackage): class Hdf5(CMakePackage):
"""HDF5 is a data model, library, and file format for storing and managing """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 data. It supports an unlimited variety of datatypes, and is designed for
flexible and efficient I/O and for high volume and complex data. flexible and efficient I/O and for high volume and complex data.
""" """
homepage = "https://support.hdfgroup.org/HDF5/" homepage = "https://portal.hdfgroup.org"
url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz" url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.7/src/hdf5-1.10.7.tar.gz"
list_url = "https://support.hdfgroup.org/ftp/HDF5/releases" list_url = "https://support.hdfgroup.org/ftp/HDF5/releases"
list_depth = 3 list_depth = 3
git = "https://github.com/HDFGroup/hdf5.git"
maintainers = ['lrknox', 'brtnfld', 'byrnHDF', 'ChristopherHogan', 'epourmal',
'gheber', 'hyoklee', 'lkurz', 'soumagne']
version('1.10.4', '8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2') test_requires_compiler = True
version('1.10.3', 'b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39')
version('1.10.2', '8d4eae84e533efa57496638fd0dca8c3') # The 'develop' version is renamed so that we could uninstall (or patch) it
version('1.10.1', '43a2f9466702fb1db31df98ae6677f15') # without affecting other develop version.
version('1.10.0-patch1', '9180ff0ef8dc2ef3f61bd37a7404f295') version('develop-1.13', branch='develop')
version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199') version('develop-1.12', branch='hdf5_1_12')
version('1.8.19', '7f568e2464d4ab0a74d16b23956d900b') version('develop-1.10', branch='hdf5_1_10')
version('1.8.18', 'dd2148b740713ca0295442ec683d7b1c') version('develop-1.8', branch='hdf5_1_8')
version('1.8.17', '7d572f8f3b798a628b8245af0391a0ca')
version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618') version('1.12.1', sha256='79c66ff67e666665369396e9c90b32e238e501f345afd2234186bfb8331081ca')
version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24') version('1.12.0', sha256='a62dcb276658cb78e6795dd29bf926ed7a9bc4edf6e77025cd2c689a8f97c17a')
version('1.8.14', 'a482686e733514a51cde12d6fe5c5d95') # HDF5 1.12 broke API compatibility, so we currently prefer the latest
version('1.8.13', 'c03426e9e77d7766944654280b467289') # 1.10 release. packages that want later versions of HDF5 should specify,
version('1.8.12', 'd804802feb99b87fc668a90e6fa34411') # e.g., depends_on("hdf5@1.12:") to get 1.12 or higher.
version('1.8.10', '710aa9fb61a51d61a7e2c09bf0052157') version('1.10.7', sha256='7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15', preferred=True)
version('1.10.6', sha256='5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa')
version('1.10.5', sha256='6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8')
version('1.10.4', sha256='8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2')
version('1.10.3', sha256='b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39')
version('1.10.2', sha256='bfec1be8c366965a99812cf02ddc97e4b708c1754fccba5414d4adccdc073866')
version('1.10.1', sha256='048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172')
version('1.10.0-patch1', sha256='6e78cfe32a10e6e0629393cdfddf6cfa536571efdaf85f08e35326e1b4e9eff0')
version('1.10.0', sha256='81f6201aba5c30dced5dcd62f5d5477a2790fd5850e02ac514ca8bf3e2bb375a')
version('1.8.22', sha256='8406d96d9355ef8961d2739fb8fd5474ad4cdf52f3cfac657733defd9709bfaa')
version('1.8.21', sha256='87d8c82eba5cf766d97cd06c054f4639c1049c4adeaa3a79f77f8bd374f80f37')
version('1.8.19', sha256='a4335849f19fae88c264fd0df046bc321a78c536b2548fc508627a790564dc38')
version('1.8.18', sha256='cdb195ad8d9e6782acf24b2488061289f615628c2ccda8457b0a0c3fb7a8a063')
version('1.8.17', sha256='d9cda297ee76ade9881c4208987939250d397bae6252d0ccb66fa7d24d67e263')
version('1.8.16', sha256='ed17178abd9928a7237f30370189ba767b9e39e0db45917c2ac4665eb9cb4771')
version('1.8.15', sha256='4e963216b7d32469596bc1321a8c3f6e0c278dcbbdb7be6414c63c081b34c275')
version('1.8.14', sha256='1dbefeeef7f591897c632b2b090db96bb8d35ad035beaa36bc39cb2bc67e0639')
version('1.8.13', sha256='82f6b38eec103b4fccfbf14892786e0c27a8135d3252d8601cf5bf20066d38c1')
version('1.8.12', sha256='b5cccea850096962b5fd9e96f22c4f47d2379224bb41130d9bc038bb6c37dfcb')
version('1.8.10', sha256='4813b79c5fb8701a625b9924b8203bc7154a77f9b826ad4e034144b4056a160a')
variant('debug', default=False,
description='Builds a debug version of the library')
variant('shared', default=True, variant('shared', default=True,
description='Builds a shared version of the library') description='Builds a shared version of the library')
variant('hl', default=False, description='Enable the high-level library') variant('hl', default=False, description='Enable the high-level library')
variant('cxx', default=False, description='Enable C++ support') variant('cxx', default=False, description='Enable C++ support')
variant('fortran', default=False, description='Enable Fortran support') variant('fortran', default=False, description='Enable Fortran support')
variant('java', default=False, description='Enable Java support')
variant('threadsafe', default=False, variant('threadsafe', default=False,
description='Enable thread-safe capabilities') description='Enable thread-safe capabilities')
variant('tools', default=True, description='Enable building tools')
variant('mpi', default=True, description='Enable MPI support') variant('mpi', default=True, description='Enable MPI support')
variant('szip', default=False, description='Enable szip support') variant('szip', default=False, description='Enable szip support')
variant('pic', default=True, # Build HDF5 with API compatibility.
description='Produce position-independent code (for shared libs)') variant('api', default='default',
description='Choose api compatibility for earlier version',
values=('default', 'v114', 'v112', 'v110', 'v18', 'v16'),
multi=False)
depends_on('cmake@3.12:', type='build')
depends_on('mpi', when='+mpi') depends_on('mpi', when='+mpi')
depends_on('java', type=('build', 'run'), when='+java')
# numactl does not currently build on darwin # numactl does not currently build on darwin
if sys.platform != 'darwin': if sys.platform != 'darwin':
depends_on('numactl', when='+mpi+fortran') depends_on('numactl', when='+mpi+fortran')
depends_on('szip', when='+szip') depends_on('szip', when='+szip')
depends_on('zlib@1.1.2:') depends_on('zlib@1.1.2:')
# The compiler wrappers (h5cc, h5fc, etc.) run 'pkg-config'.
depends_on('pkgconfig', type='run')
conflicts('api=v114', when='@1.6:1.12.99',
msg='v114 is not compatible with this release')
conflicts('api=v112', when='@1.6:1.10.99',
msg='v112 is not compatible with this release')
conflicts('api=v110', when='@1.6:1.8.99',
msg='v110 is not compatible with this release')
conflicts('api=v18', when='@1.6:1.6.99',
msg='v18 is not compatible with this release')
# The Java wrappers and associated libhdf5_java library
# were first available in 1.10
conflicts('+java', when='@:1.9')
# The Java wrappers cannot be built without shared libs.
conflicts('+java', when='~shared')
# There are several officially unsupported combinations of the features: # There are several officially unsupported combinations of the features:
# 1. Thread safety is not guaranteed via high-level C-API but in some cases # 1. Thread safety is not guaranteed via high-level C-API but in some cases
# it works. # it works.
@ -96,14 +143,74 @@ class Hdf5(AutotoolsPackage):
# There are build errors with GCC 8, see # 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 # 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:') 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') # Disable MPI C++ interface when C++ is disabled, otherwise downstream
# libraries fail to link; see https://github.com/spack/spack/issues/12586
patch('h5public-skip-mpicxx.patch', when='@1.8.10:1.8.21,1.10.0:1.10.5+mpi~cxx',
sha256='b61e2f058964ad85be6ee5ecea10080bf79e73f83ff88d1fa4b602d00209da9c')
# Fixes BOZ literal constant error when compiled with GCC 10.
# The issue is described here: https://github.com/spack/spack/issues/18625
patch('hdf5_1.8_gcc10.patch', when='@:1.8.21',
sha256='0e20187cda3980a4fdff410da92358b63de7ebef2df1d7a425371af78e50f666')
# The argument 'buf_size' of the C function 'h5fget_file_image_c' is
# declared as intent(in) though it is modified by the invocation. As a
# result, aggressive compilers such as Fujitsu's may do a wrong
# optimization to cause an error.
def patch(self):
filter_file(
'INTEGER(SIZE_T), INTENT(IN) :: buf_size',
'INTEGER(SIZE_T), INTENT(OUT) :: buf_size',
'fortran/src/H5Fff.F90',
string=True, ignore_absent=True)
filter_file(
'INTEGER(SIZE_T), INTENT(IN) :: buf_size',
'INTEGER(SIZE_T), INTENT(OUT) :: buf_size',
'fortran/src/H5Fff_F03.f90',
string=True, ignore_absent=True)
# The parallel compiler wrappers (i.e. h5pcc, h5pfc, etc.) reference MPI
# compiler wrappers and do not need to be changed.
filter_compiler_wrappers('h5cc', 'h5hlcc',
'h5fc', 'h5hlfc',
'h5c++', 'h5hlc++',
relative_root='bin')
def url_for_version(self, version): def url_for_version(self, version):
url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-{0}/hdf5-{1}/src/hdf5-{1}.tar.gz" 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) return url.format(version.up_to(2), version)
def flag_handler(self, name, flags):
cmake_flags = []
if name == "cflags":
if self.spec.satisfies('%gcc') \
or self.spec.satisfies('%clang'):
# Quiet warnings/errors about implicit declaration of functions
# in C99:
cmake_flags.append("-Wno-implicit-function-declaration")
# Note that this flag will cause an error if building %nvhpc.
if self.spec.satisfies('@:1.8.12~shared'):
# More recent versions set CMAKE_POSITION_INDEPENDENT_CODE to
# True and build with PIC flags.
cmake_flags.append(self.compiler.cc_pic_flag)
elif name == 'cxxflags':
if self.spec.satisfies('@:1.8.12+cxx~shared'):
cmake_flags.append(self.compiler.cxx_pic_flag)
elif name == "fflags":
if self.spec.satisfies('@:1.8.12+fortran~shared'):
cmake_flags.append(self.compiler.fc_pic_flag)
elif name == "ldlibs":
if '+fortran %fj' in self.spec:
cmake_flags.extend(['-lfj90i', '-lfj90f',
'-lfjsrcinfo', '-lelf'])
return flags, None, (cmake_flags or None)
@property @property
def libs(self): def libs(self):
"""HDF5 can be queried for the following parameters: """HDF5 can be queried for the following parameters:
@ -111,18 +218,46 @@ def libs(self):
- "hl": high-level interface - "hl": high-level interface
- "cxx": C++ APIs - "cxx": C++ APIs
- "fortran": Fortran APIs - "fortran": Fortran APIs
- "java": Java APIs
:return: list of matching libraries :return: list of matching libraries
""" """
query_parameters = self.spec.last_query.extra_parameters
shared = '+shared' in self.spec
# This map contains a translation from query_parameters # This map contains a translation from query_parameters
# to the libraries needed # to the libraries needed
query2libraries = { # noqa: F841 query2libraries = {
tuple(): ['libhdf5'], tuple(): ['libhdf5'],
('cxx', 'fortran', 'hl'): [ ('cxx', 'fortran', 'hl', 'java'): [
'libhdf5hl_fortran', # When installed with Autotools, the basename of the real
# library file implementing the High-level Fortran interface is
# 'libhdf5hl_fortran'. Starting versions 1.8.22, 1.10.5 and
# 1.12.0, the Autotools installation also produces a symbolic
# link 'libhdf5_hl_fortran.<so/a>' to
# 'libhdf5hl_fortran.<so/a>'. Note that in the case of the
# dynamic library, the latter is a symlink to the real sonamed
# file 'libhdf5_fortran.so.<abi-version>'. This means that all
# dynamically linked executables/libraries of the dependent
# packages need 'libhdf5_fortran.so.<abi-version>' with the same
# DT_SONAME entry. However, the CMake installation (at least
# starting version 1.8.10) does not produce it. Instead, the
# basename of the library file is 'libhdf5_hl_fortran'. Which
# means that switching to CMake requires rebuilding of all
# dependant packages that use the High-level Fortran interface.
# Therefore, we do not try to preserve backward compatibility
# with Autotools installations by creating symlinks. The only
# packages that could benefit from it would be those that
# hardcode the library name in their building systems. Such
# packages should simply be patched.
'libhdf5_hl_fortran',
'libhdf5_hl_f90cstub',
'libhdf5_hl_cpp', 'libhdf5_hl_cpp',
'libhdf5_hl', 'libhdf5_hl',
'libhdf5_fortran', 'libhdf5_fortran',
'libhdf5_f90cstub',
'libhdf5_java',
'libhdf5', 'libhdf5',
], ],
('cxx', 'hl'): [ ('cxx', 'hl'): [
@ -131,9 +266,11 @@ def libs(self):
'libhdf5', 'libhdf5',
], ],
('fortran', 'hl'): [ ('fortran', 'hl'): [
'libhdf5hl_fortran', 'libhdf5_hl_fortran',
'libhdf5_hl_f90cstub',
'libhdf5_hl', 'libhdf5_hl',
'libhdf5_fortran', 'libhdf5_fortran',
'libhdf5_f90cstub',
'libhdf5', 'libhdf5',
], ],
('hl',): [ ('hl',): [
@ -142,6 +279,7 @@ def libs(self):
], ],
('cxx', 'fortran'): [ ('cxx', 'fortran'): [
'libhdf5_fortran', 'libhdf5_fortran',
'libhdf5_f90cstub',
'libhdf5_cpp', 'libhdf5_cpp',
'libhdf5', 'libhdf5',
], ],
@ -151,112 +289,155 @@ def libs(self):
], ],
('fortran',): [ ('fortran',): [
'libhdf5_fortran', 'libhdf5_fortran',
'libhdf5_f90cstub',
'libhdf5',
],
('java',): [
'libhdf5_java',
'libhdf5', 'libhdf5',
] ]
} }
# TUTORIAL: you need to fix the implementation below, and # Turn the query into the appropriate key
# return the correct list of libraries according to the key = tuple(sorted(query_parameters))
# query parameters your dependency has used. libraries = query2libraries[key]
#
# 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') return find_libraries(
libraries, root=self.prefix, shared=shared, recursive=True
)
@when('@:1.8.21,1.10.0:1.10.5+szip')
def setup_build_environment(self, env):
env.set('SZIP_INSTALL', self.spec['szip'].prefix)
@run_before('cmake')
def fortran_check(self): def fortran_check(self):
if '+fortran' in self.spec and not self.compiler.fc: if '+fortran' in self.spec and not self.compiler.fc:
msg = 'cannot build a Fortran variant without a Fortran compiler' msg = 'cannot build a Fortran variant without a Fortran compiler'
raise RuntimeError(msg) raise RuntimeError(msg)
def configure_args(self): def cmake_args(self):
spec = self.spec
if spec.satisfies('@:1.8.15+shared'):
tty.warn('hdf5@:1.8.15+shared does not produce static libraries')
args = [
# Always enable this option. This does not actually enable any # Always enable this option. This does not actually enable any
# features: it only *allows* the user to specify certain # features: it only *allows* the user to specify certain
# combinations of other arguments. Enabling it just skips a # combinations of other arguments.
# sanity check in configure, so this doesn't merit a variant. self.define('ALLOW_UNSUPPORTED', True),
extra_args = ['--enable-unsupported'] # Speed-up the building by skipping the examples:
extra_args += self.enable_or_disable('threadsafe') self.define('HDF5_BUILD_EXAMPLES', False),
extra_args += self.enable_or_disable('cxx') self.define(
extra_args += self.enable_or_disable('hl') 'BUILD_TESTING',
extra_args += self.enable_or_disable('fortran') self.run_tests or
# Version 1.8.22 fails to build the tools when shared libraries
# are enabled but the tests are disabled.
spec.satisfies('@1.8.22+shared+tools')),
self.define('HDF5_ENABLE_Z_LIB_SUPPORT', True),
self.define_from_variant('HDF5_ENABLE_SZIP_SUPPORT', 'szip'),
self.define_from_variant('HDF5_ENABLE_SZIP_ENCODING', 'szip'),
self.define_from_variant('BUILD_SHARED_LIBS', 'shared'),
self.define('ONLY_SHARED_LIBS', False),
self.define_from_variant('HDF5_ENABLE_PARALLEL', 'mpi'),
self.define_from_variant('HDF5_ENABLE_THREADSAFE', 'threadsafe'),
self.define_from_variant('HDF5_BUILD_HL_LIB', 'hl'),
self.define_from_variant('HDF5_BUILD_CPP_LIB', 'cxx'),
self.define_from_variant('HDF5_BUILD_FORTRAN', 'fortran'),
self.define_from_variant('HDF5_BUILD_JAVA', 'java'),
self.define_from_variant('HDF5_BUILD_TOOLS', 'tools')
]
if '+szip' in self.spec: api = spec.variants['api'].value
extra_args.append('--with-szlib=%s' % self.spec['szip'].prefix) if api != 'default':
else: args.append(self.define('DEFAULT_API_VERSION', api))
extra_args.append('--without-szlib')
if self.spec.satisfies('@1.10:'): if '+mpi' in spec:
if '+debug' in self.spec: args.append(self.define('CMAKE_C_COMPILER', spec['mpi'].mpicc))
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: if '+cxx' in self.spec:
extra_args.append('CXX=%s' % self.spec['mpi'].mpicxx) args.append(self.define('CMAKE_CXX_COMPILER',
spec['mpi'].mpicxx))
if '+fortran' in self.spec: if '+fortran' in self.spec:
extra_args.append('FC=%s' % self.spec['mpi'].mpifc) args.append(self.define('CMAKE_Fortran_COMPILER',
spec['mpi'].mpifc))
extra_args.append('--with-zlib=%s' % self.spec['zlib'].prefix) return args
return extra_args @run_after('install')
def ensure_parallel_compiler_wrappers(self):
# When installed with Autotools and starting at least version 1.8.10,
# the package produces C compiler wrapper called either 'h5cc' (when MPI
# support is disabled) or 'h5pcc' (when MPI support is enabled). The
# CMake installation produces the wrapper called 'h5cc' (regardless of
# whether MPI support is enabled) only starting versions 1.8.21, 1.10.2
# and 1.12.0. The current develop versions also produce 'h5pcc' when MPI
# support is enabled and the file is identical to 'h5cc'. Here, we make
# sure that 'h5pcc' is available when MPI support is enabled (only for
# versions that generate 'h5cc').
if self.spec.satisfies('@1.8.21:1.8.22,1.10.2:1.10.7,1.12.0+mpi'):
with working_dir(self.prefix.bin):
# No try/except here, fix the condition above instead:
symlink('h5cc', 'h5pcc')
@run_after('configure') # The same as for 'h5pcc'. However, the CMake installation produces the
def patch_postdeps(self): # Fortran compiler wrapper called 'h5fc' only starting versions 1.8.22,
if '@:1.8.14' in self.spec: # 1.10.6 and 1.12.0. The current develop versions do not produce 'h5pfc'
# On Ubuntu14, HDF5 1.8.12 (and maybe other versions) # at all. Here, we make sure that 'h5pfc' is available when Fortran and
# mysteriously end up with "-l -l" in the postdeps in the # MPI support are enabled (only for versions that generate 'h5fc').
# libtool script. Patch this by removing the spurious -l's. if self.spec.satisfies('@1.8.22:1.8.999,'
'1.10.6:1.10.999,'
'1.12.0:1.12.999,'
'develop:'
'+fortran+mpi'):
with working_dir(self.prefix.bin):
# No try/except here, fix the condition above instead:
symlink('h5fc', 'h5pfc')
@run_after('install')
def fix_package_config(self):
# We need to fix the pkg-config files, which are also used by the
# compiler wrappers. The files are created starting versions 1.8.21,
# 1.10.2 and 1.12.0. However, they are broken (except for the version
# 1.8.22): the files are named <name>-<version>.pc but reference <name>
# packages. This was fixed in the develop versions at some point: the
# files started referencing <name>-<version> packages but got broken
# again: the files got names <name>.pc but references had not been
# updated accordingly. Another issue, which we address here, is that
# some Linux distributions install pkg-config files named hdf5.pc and we
# want to override them. Therefore, the following solution makes sure
# that each <name>-<version>.pc file is symlinked by <name>.pc and all
# references to <name>-<version> packages in the original files are
# replaced with references to <name> packages.
pc_files = find(self.prefix.lib.pkgconfig, 'hdf5*.pc', recursive=False)
if not pc_files:
# This also tells us that the pkgconfig directory does not exist.
return
# Replace versioned references in all pkg-config files:
filter_file( filter_file(
r'postdeps="([^"]*)"', r'(Requires(?:\.private)?:.*)(hdf5[^\s,]*)(?:-[^\s,]*)(.*)',
lambda m: 'postdeps="%s"' % ' '.join( r'\1\2\3', *pc_files, backup=False)
arg for arg in m.group(1).split(' ') if arg != '-l'),
'libtool') # Create non-versioned symlinks to the versioned pkg-config files:
with working_dir(self.prefix.lib.pkgconfig):
for f in pc_files:
src_filename = os.path.basename(f)
version_sep_idx = src_filename.find('-')
if version_sep_idx > -1:
tgt_filename = src_filename[:version_sep_idx] + '.pc'
if not os.path.exists(tgt_filename):
symlink(src_filename, tgt_filename)
@run_after('install') @run_after('install')
@on_package_attributes(run_tests=True) @on_package_attributes(run_tests=True)
def check_install(self): def check_install(self):
self._check_install()
def _check_install(self):
# Build and run a small program to test the installed HDF5 library # Build and run a small program to test the installed HDF5 library
spec = self.spec spec = self.spec
print("Checking HDF5 installation...") print("Checking HDF5 installation...")
@ -305,3 +486,54 @@ def check_install(self):
print('-' * 80) print('-' * 80)
raise RuntimeError("HDF5 install check failed") raise RuntimeError("HDF5 install check failed")
shutil.rmtree(checkdir) shutil.rmtree(checkdir)
def _test_check_versions(self):
"""Perform version checks on selected installed package binaries."""
spec_vers_str = 'Version {0}'.format(self.spec.version)
exes = [
'h5copy', 'h5diff', 'h5dump', 'h5format_convert', 'h5ls',
'h5mkgrp', 'h5repack', 'h5stat', 'h5unjam',
]
use_short_opt = ['h52gif', 'h5repart', 'h5unjam']
for exe in exes:
reason = 'test: ensuring version of {0} is {1}' \
.format(exe, spec_vers_str)
option = '-V' if exe in use_short_opt else '--version'
self.run_test(exe, option, spec_vers_str, installed=True,
purpose=reason, skip_missing=True)
def _test_example(self):
"""This test performs copy, dump, and diff on an example hdf5 file."""
test_data_dir = self.test_suite.current_test_data_dir
filename = 'spack.h5'
h5_file = test_data_dir.join(filename)
reason = 'test: ensuring h5dump produces expected output'
expected = get_escaped_text_output(test_data_dir.join('dump.out'))
self.run_test('h5dump', filename, expected, installed=True,
purpose=reason, skip_missing=True,
work_dir=test_data_dir)
reason = 'test: ensuring h5copy runs'
options = ['-i', h5_file, '-s', 'Spack', '-o', 'test.h5', '-d',
'Spack']
self.run_test('h5copy', options, [], installed=True,
purpose=reason, skip_missing=True, work_dir='.')
reason = ('test: ensuring h5diff shows no differences between orig and'
' copy')
self.run_test('h5diff', [h5_file, 'test.h5'], [], installed=True,
purpose=reason, skip_missing=True, work_dir='.')
def test(self):
"""Perform smoke tests on the installed package."""
# Simple version check tests on known binaries
self._test_check_versions()
# Run sequence of commands on an hdf5 file
self._test_example()
# Run existing install check
self._check_install()

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@ -0,0 +1,45 @@
HDF5 "spack.h5" {
GROUP "/" {
GROUP "Spack" {
GROUP "Software" {
ATTRIBUTE "Distribution" {
DATATYPE H5T_STRING {
STRSIZE H5T_VARIABLE;
STRPAD H5T_STR_NULLTERM;
CSET H5T_CSET_UTF8;
CTYPE H5T_C_S1;
}
DATASPACE SCALAR
DATA {
(0): "Open Source"
}
}
DATASET "data" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 7, 11 ) / ( 7, 11 ) }
DATA {
(0,0): 0.371141, 0.508482, 0.585975, 0.0944911, 0.684849,
(0,5): 0.580396, 0.720271, 0.693561, 0.340432, 0.217145,
(0,10): 0.636083,
(1,0): 0.686996, 0.773501, 0.656767, 0.617543, 0.226132,
(1,5): 0.768632, 0.0548711, 0.54572, 0.355544, 0.591548,
(1,10): 0.233007,
(2,0): 0.230032, 0.192087, 0.293845, 0.0369338, 0.038727,
(2,5): 0.0977931, 0.966522, 0.0821391, 0.857921, 0.495703,
(2,10): 0.746006,
(3,0): 0.598494, 0.990266, 0.993009, 0.187481, 0.746391,
(3,5): 0.140095, 0.122661, 0.929242, 0.542415, 0.802758,
(3,10): 0.757941,
(4,0): 0.372124, 0.411982, 0.270479, 0.950033, 0.329948,
(4,5): 0.936704, 0.105097, 0.742285, 0.556565, 0.18988, 0.72797,
(5,0): 0.801669, 0.271807, 0.910649, 0.186251, 0.868865,
(5,5): 0.191484, 0.788371, 0.920173, 0.582249, 0.682022,
(5,10): 0.146883,
(6,0): 0.826824, 0.0886705, 0.402606, 0.0532444, 0.72509,
(6,5): 0.964683, 0.330362, 0.833284, 0.630456, 0.411489, 0.247806
}
}
}
}
}
}

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