diff options
| -rw-r--r-- | var/spack/repos/tutorial/packages/hdf5/h5public-skip-mpicxx.patch | 11 | ||||
| -rw-r--r-- | var/spack/repos/tutorial/packages/hdf5/hdf5_1.8_gcc10.patch | 12 | ||||
| -rw-r--r-- | var/spack/repos/tutorial/packages/hdf5/package.py | 466 | ||||
| -rw-r--r-- | var/spack/repos/tutorial/packages/hdf5/test/dump.out | 45 | ||||
| -rw-r--r-- | var/spack/repos/tutorial/packages/hdf5/test/spack.h5 | bin | 0 -> 8928 bytes |
5 files changed, 417 insertions, 117 deletions
diff --git a/var/spack/repos/tutorial/packages/hdf5/h5public-skip-mpicxx.patch b/var/spack/repos/tutorial/packages/hdf5/h5public-skip-mpicxx.patch new file mode 100644 index 0000000000..d609345527 --- /dev/null +++ b/var/spack/repos/tutorial/packages/hdf5/h5public-skip-mpicxx.patch @@ -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> diff --git a/var/spack/repos/tutorial/packages/hdf5/hdf5_1.8_gcc10.patch b/var/spack/repos/tutorial/packages/hdf5/hdf5_1.8_gcc10.patch new file mode 100644 index 0000000000..0de8c33c09 --- /dev/null +++ b/var/spack/repos/tutorial/packages/hdf5/hdf5_1.8_gcc10.patch @@ -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 + ! diff --git a/var/spack/repos/tutorial/packages/hdf5/package.py b/var/spack/repos/tutorial/packages/hdf5/package.py index 333b0a566f..e188bb94b1 100644 --- a/var/spack/repos/tutorial/packages/hdf5/package.py +++ b/var/spack/repos/tutorial/packages/hdf5/package.py @@ -3,62 +3,109 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +import os import shutil 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 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" + 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://github.com/HDFGroup/hdf5.git" + maintainers = ['lrknox', 'brtnfld', 'byrnHDF', 'ChristopherHogan', 'epourmal', + 'gheber', 'hyoklee', 'lkurz', 'soumagne'] + + 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('1.12.1', 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('1.10.7', 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') - version('1.10.4', '8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2') - version('1.10.3', 'b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39') - version('1.10.2', '8d4eae84e533efa57496638fd0dca8c3') - 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') - version('1.8.10', '710aa9fb61a51d61a7e2c09bf0052157') - - 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('tools', default=True, description='Enable building tools') 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 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='@1.6:1.12.99', + 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: # 1. Thread safety is not guaranteed via high-level C-API but in some cases # it works. @@ -96,14 +143,74 @@ class Hdf5(AutotoolsPackage): # 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:') - - filter_compiler_wrappers('h5cc', 'h5c++', 'h5fc', relative_root='bin') + 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) + + # 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): + 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 def libs(self): """HDF5 can be queried for the following parameters: @@ -111,18 +218,46 @@ class Hdf5(AutotoolsPackage): - "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 = { # noqa: F841 + query2libraries = { tuple(): ['libhdf5'], - ('cxx', 'fortran', 'hl'): [ - 'libhdf5hl_fortran', + ('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'): [ @@ -131,9 +266,11 @@ class Hdf5(AutotoolsPackage): 'libhdf5', ], ('fortran', 'hl'): [ - 'libhdf5hl_fortran', + 'libhdf5_hl_fortran', + 'libhdf5_hl_f90cstub', 'libhdf5_hl', 'libhdf5_fortran', + 'libhdf5_f90cstub', 'libhdf5', ], ('hl',): [ @@ -142,6 +279,7 @@ class Hdf5(AutotoolsPackage): ], ('cxx', 'fortran'): [ 'libhdf5_fortran', + 'libhdf5_f90cstub', 'libhdf5_cpp', 'libhdf5', ], @@ -151,112 +289,155 @@ class Hdf5(AutotoolsPackage): ], ('fortran',): [ 'libhdf5_fortran', + 'libhdf5_f90cstub', + 'libhdf5', + ], + ('java',): [ + 'libhdf5_java', 'libhdf5', ] } - # TUTORIAL: you need to fix the implementation below, and - # return the correct list of libraries according to the - # query parameters your dependency has used. - # - # 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') + # 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 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') + def cmake_args(self): + spec = self.spec - # '--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 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: - extra_args.append('CXX=%s' % self.spec['mpi'].mpicxx) + args.append(self.define('CMAKE_CXX_COMPILER', + spec['mpi'].mpicxx)) 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') + + # 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('@1.8.22:1.8.999,' + '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('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') + 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...") @@ -305,3 +486,54 @@ HDF5 version {version} {version} 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() diff --git a/var/spack/repos/tutorial/packages/hdf5/test/dump.out b/var/spack/repos/tutorial/packages/hdf5/test/dump.out new file mode 100644 index 0000000000..58decefc12 --- /dev/null +++ b/var/spack/repos/tutorial/packages/hdf5/test/dump.out @@ -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 + } + } + } + } +} +} diff --git a/var/spack/repos/tutorial/packages/hdf5/test/spack.h5 b/var/spack/repos/tutorial/packages/hdf5/test/spack.h5 Binary files differnew file mode 100644 index 0000000000..c2f3a6f39d --- /dev/null +++ b/var/spack/repos/tutorial/packages/hdf5/test/spack.h5 |