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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 shutil
import sys
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://portal.hdfgroup.org"
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_depth = 3
git = "https://bitbucket.hdfgroup.org/scm/hdffv/hdf5.git"
maintainers = ['lrknox']
test_requires_compiler = True
# We rely on the *.la files to be removed and, therefore, do not try to make
# sure that they are correct. The following is a precaution against someone
# blindly changing the value to True, either here or in the baseclass.
install_libtool_archives = False
version('develop', branch='develop')
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('1.10.7', 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('1.8.21', 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,
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('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)')
# Build HDF5 with API compaitibility.
variant('api', default='none', description='choose api compatibility', values=('none', 'v114', 'v112', 'v110', 'v18', 'v16'), multi=False)
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')
depends_on('autoconf', type='build', when='@develop')
depends_on('automake', type='build', when='@develop')
depends_on('libtool', type='build', when='@develop')
depends_on('m4', type='build', when='@develop')
depends_on('mpi', when='+mpi')
depends_on('java', 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:')
# 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='@:1.8.21,1.10.0:1.10.5+mpi~cxx',
sha256='b61e2f058964ad85be6ee5ecea10080bf79e73f83ff88d1fa4b602d00209da9c')
# 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)
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)
@when('@develop')
def autoreconf(self, spec, prefix):
autogen = Executable('./autogen.sh')
autogen()
@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
"""
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'): [
'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',
]
}
# 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
)
@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 with_or_without_szip(self, activated):
return '--{0}-szlib'.format('with' if activated else 'without')
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',
'--enable-symbols=yes',
'--with-zlib']
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')
extra_args += self.enable_or_disable('java')
extra_args += self.with_or_without('szip')
api = self.spec.variants['api'].value
if api != 'none':
extra_args.append('--with-default-api-version=' + api)
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.extend([
'CFLAGS=' + self.compiler.cc_pic_flag,
'CXXFLAGS=' + self.compiler.cxx_pic_flag,
'FCFLAGS=' + self.compiler.fc_pic_flag,
])
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)
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('configure')
def patch_libtool(self):
"""AOCC support for HDF5"""
if '%aocc' in self.spec:
filter_file(
r'\$wl-soname \$wl\$soname',
r'-fuse-ld=ld -Wl,-soname,\$soname',
'libtool', string=True)
@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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