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##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
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://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('1.10.1', '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')
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')
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
"""
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, recurse=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 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)
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