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|
# Copyright 2013-2021 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
import shutil
import sys
import llnl.util.tty as tty
class Hdf5(CMakePackage):
"""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://portal.hdfgroup.org"
url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.8/src/hdf5-1.10.8.tar.gz"
list_url = "https://support.hdfgroup.org/ftp/HDF5/releases"
list_depth = 3
git = "https://github.com/HDFGroup/hdf5.git"
maintainers = ['lrknox', 'brtnfld', 'byrnHDF', 'ChristopherHogan', 'epourmal',
'gheber', 'hyoklee', 'lkurz', 'soumagne']
tags = ['e4s']
test_requires_compiler = True
# The 'develop' version is renamed so that we could uninstall (or patch) it
# without affecting other develop version.
version('develop-1.13', branch='develop')
version('develop-1.12', branch='hdf5_1_12')
version('develop-1.10', branch='hdf5_1_10')
version('develop-1.8', branch='hdf5_1_8')
version('1.13.0', sha256='3049faf900f0c52e09ea4cddfb83af057615f2fc1cc80eb5202dd57b09820115')
version('1.12.1', sha256='79c66ff67e666665369396e9c90b32e238e501f345afd2234186bfb8331081ca')
version('1.12.0', sha256='a62dcb276658cb78e6795dd29bf926ed7a9bc4edf6e77025cd2c689a8f97c17a')
# 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('1.10.8', sha256='d341b80d380dd763753a0ebe22915e11e87aac4e44a084a850646ff934d19c80', preferred=True)
version('1.10.7', sha256='7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15')
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('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('java', default=False, description='Enable Java support')
variant('threadsafe', default=False,
description='Enable thread-safe capabilities')
variant('tools', default=True, description='Enable building tools')
variant('mpi', default=True, description='Enable MPI support')
variant('szip', default=False, description='Enable szip support')
# Build HDF5 with API compatibility.
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('java', type=('build', 'run'), when='+java')
# 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:')
# The compiler wrappers (h5cc, h5fc, etc.) run 'pkg-config'.
depends_on('pkgconfig', type='run')
conflicts('api=v114', when='@1.6:1.12',
msg='v114 is not compatible with this release')
conflicts('api=v112', when='@1.6:1.10',
msg='v112 is not compatible with this release')
conflicts('api=v110', when='@1.6:1.8',
msg='v110 is not compatible with this release')
conflicts('api=v18', when='@1.6.0:1.6',
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:
# 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:')
# 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)
if self.run_tests:
# hdf5 has ~2200 CPU-intensive tests, some of them have races:
# Often, these loop endless(at least on one Xeon and one EPYC).
# testphdf5 fails indeterministic. This fixes finishing the tests
filter_file('REMOVE_ITEM H5P_TESTS',
'REMOVE_ITEM H5P_TESTS t_bigio t_shapesame testphdf5',
'testpar/CMakeTests.cmake')
# 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):
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)
def flag_handler(self, name, flags):
spec = self.spec
cmake_flags = []
if name == "cflags":
if spec.compiler.name in ['gcc', 'clang', 'apple-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 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 spec.satisfies('@:1.8.12+cxx~shared'):
cmake_flags.append(self.compiler.cxx_pic_flag)
elif name == "fflags":
if spec.satisfies('%cce+fortran'):
# Cray compiler generates module files with uppercase names by
# default, which is not handled by the CMake scripts. The
# following flag forces the compiler to produce module files
# with lowercase names.
cmake_flags.append('-ef')
if spec.satisfies('@:1.8.12+fortran~shared'):
cmake_flags.append(self.compiler.fc_pic_flag)
elif name == "ldlibs":
if '+fortran %fj' in spec:
cmake_flags.extend(['-lfj90i', '-lfj90f',
'-lfjsrcinfo', '-lelf'])
return flags, None, (cmake_flags or None)
@property
def libs(self):
"""HDF5 can be queried for the following parameters:
- "hl": high-level interface
- "cxx": C++ APIs
- "fortran": Fortran APIs
- "java": Java APIs
: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
# to the libraries needed
query2libraries = {
tuple(): ['libhdf5'],
('cxx', 'fortran', 'hl', 'java'): [
# 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',
'libhdf5_fortran',
'libhdf5_f90cstub',
'libhdf5_java',
'libhdf5',
],
('cxx', 'hl'): [
'libhdf5_hl_cpp',
'libhdf5_hl',
'libhdf5',
],
('fortran', 'hl'): [
'libhdf5_hl_fortran',
'libhdf5_hl_f90cstub',
'libhdf5_hl',
'libhdf5_fortran',
'libhdf5_f90cstub',
'libhdf5',
],
('hl',): [
'libhdf5_hl',
'libhdf5',
],
('cxx', 'fortran'): [
'libhdf5_fortran',
'libhdf5_f90cstub',
'libhdf5_cpp',
'libhdf5',
],
('cxx',): [
'libhdf5_cpp',
'libhdf5',
],
('fortran',): [
'libhdf5_fortran',
'libhdf5_f90cstub',
'libhdf5',
],
('java',): [
'libhdf5_java',
'libhdf5',
]
}
# Turn the query into the appropriate key
key = tuple(sorted(query_parameters))
libraries = query2libraries[key]
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):
if '+fortran' in self.spec and not self.compiler.fc:
msg = 'cannot build a Fortran variant without a Fortran compiler'
raise RuntimeError(msg)
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
# features: it only *allows* the user to specify certain
# combinations of other arguments.
self.define('ALLOW_UNSUPPORTED', True),
# Speed-up the building by skipping the examples:
self.define('HDF5_BUILD_EXAMPLES', False),
self.define(
'BUILD_TESTING',
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')
]
api = spec.variants['api'].value
if api != 'default':
args.append(self.define('DEFAULT_API_VERSION', api))
if '+mpi' in spec:
args.append(self.define('CMAKE_C_COMPILER', spec['mpi'].mpicc))
if '+cxx' in self.spec:
args.append(self.define('CMAKE_CXX_COMPILER',
spec['mpi'].mpicxx))
if '+fortran' in self.spec:
args.append(self.define('CMAKE_Fortran_COMPILER',
spec['mpi'].mpifc))
# work-around for https://github.com/HDFGroup/hdf5/issues/1320
if spec.satisfies('@1.10.8,1.13.0'):
args.append(self.define('HDF5_INSTALL_CMAKE_DIR',
'share/cmake/hdf5'))
return 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')
# The same as for 'h5pcc'. However, the CMake installation produces the
# Fortran compiler wrapper called 'h5fc' only starting versions 1.8.22,
# 1.10.6 and 1.12.0. The current develop versions do not produce 'h5pfc'
# at all. Here, we make sure that 'h5pfc' is available when Fortran and
# MPI support are enabled (only for versions that generate 'h5fc').
if self.spec.satisfies('@1.8.22:1.8,'
'1.10.6:1.10,'
'1.12.0:1.12,'
'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(
r'(Requires(?:\.private)?:.*)(hdf5[^\s,]*)(?:-[^\s,]*)(.*)',
r'\1\2\3', *pc_files, backup=False)
# 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')
@on_package_attributes(run_tests=True)
def check_install(self):
self._check_install()
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)
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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