path: root/var/spack/repos/builtin/packages/hdf5/package.py

# 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

    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 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 += ['--enable-symbols=yes']
        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')

        api = self.spec.variants['api'].value
        if api != 'none':
            extra_args.append('--with-default-api-version=' + api)

        if '+szip' in self.spec:
            szip_spec = self.spec['szip']
            # The configure script of HDF5 accepts a comma-separated tuple of
            # two paths: the first one points to the directory with include
            # files, the second one points to the directory with library files.
            # If the second path is not specified, the configure script assumes
            # that it equals to prefix/lib. However, the correct directory
            # might be prefix/lib64. It is not a problem when the building is
            # done with Spack's compiler wrapper but it makes the Libtool
            # files (*.la) invalid, which makes it problematic to use the
            # installed library outside of Spack environment.
            extra_args.append('--with-szlib=%s,%s' %
                              (szip_spec.headers.directories[0],
                               szip_spec.libs.directories[0]))
        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.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)

        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):
        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()