Date: Wednesday, May 23, 2018 @ 14:56:08 Author: archange Revision: 328322
archrelease: copy trunk to community-staging-x86_64 Added: hdf5-openmpi/repos/community-staging-x86_64/ hdf5-openmpi/repos/community-staging-x86_64/PKGBUILD (from rev 328321, hdf5-openmpi/trunk/PKGBUILD) hdf5-openmpi/repos/community-staging-x86_64/mpi.patch (from rev 328321, hdf5-openmpi/trunk/mpi.patch) -----------+ PKGBUILD | 87 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ mpi.patch | 18 ++++++++++++ 2 files changed, 105 insertions(+) Copied: hdf5-openmpi/repos/community-staging-x86_64/PKGBUILD (from rev 328321, hdf5-openmpi/trunk/PKGBUILD) =================================================================== --- community-staging-x86_64/PKGBUILD (rev 0) +++ community-staging-x86_64/PKGBUILD 2018-05-23 14:56:08 UTC (rev 328322) @@ -0,0 +1,87 @@ +# $Id$ +# Maintainer: Ronald van Haren <ronald.archlinux.org> +# Maintainer: Bruno Pagani <archa...@archlinux.org> +# Contributor: Stefan Husmann <stefan-husm...@t-online.de> +# Contributor: damir <da...@archlinux.org> +# Contributor: Tom K <t...@runbox.com> +# Contributor: Jed Brown <j...@59a2.org> +# Contributor: Simone Pezzuto <junki....@gmail.com> + +_pkgname=hdf5 +_mpi=openmpi +pkgname=${_pkgname}-${_mpi} +pkgver=1.10.2 +pkgrel=2 +pkgdesc="General purpose library and file format for storing scientific data (${_mpi} version)" +arch=('x86_64') +url="https://www.hdfgroup.org/HDF5/" +license=('custom') +depends=('zlib' 'libaec' 'bash' 'openmpi') +makedepends=('time' 'gcc-fortran') +provides=('hdf5' 'hdf5-cpp-fortran' "hdf5-fortran-${_mpi}") +conflicts=('hdf5') +replaces=("hdf5-fortran-${_mpi}") +source=("https://support.hdfgroup.org/ftp/HDF5/releases/${_pkgname}-${pkgver:0:4}/${_pkgname}-${pkgver/_/-}/src/${_pkgname}-${pkgver/_/-}.tar.bz2" + 'mpi.patch') +md5sums=('41fb9347801b546fba323523a1c1af51' + 'dfa8dd50b8a7ebb3ad7249c627156cf9') +sha256sums=('1cad5b7bfdf128dfc53cd16fba48f6e7ae4e93c75c371d9ec8dfc4df0c1fcb71' + '603006358175b7a8b35fa44c484cddf45c0381cf50db4fb7c50ea5969d361eca') + +prepare() { + cd ${_pkgname}-${pkgver/_/-} + # Fix building with GCC 8.1 + sed 's/\(.*\)(void) HDF_NO_UBSAN/HDF_NO_UBSAN \1(void)/' -i src/H5detect.c + + # FS#33343 + patch -p1 -i ../mpi.patch +} + +build() { + cd ${_pkgname}-${pkgver/_/-} + ./configure \ + CXX="mpicxx" \ + CC="mpicc" \ + FC="mpif90" \ + F9X="mpif90" \ + RUNPARALLEL="mpirun" \ + OMPI_MCA_disable_memory_allocator=1 \ + --prefix=/usr \ + --docdir=/usr/share/doc/hdf5/ \ + --disable-static \ + --disable-sharedlib-rpath \ + --enable-build-mode=production \ + --enable-hl \ + --enable-cxx \ + --enable-fortran \ + --enable-parallel \ + --enable-unsupported \ + --with-pic \ + --with-zlib \ + --with-szlib + make +} + +check() { + cd ${_pkgname}-${pkgver/_/-} + # Without this, checks are failing with messages like “error while loading shared libraries: libhdf5.so.101: cannot open shared object file: No such file or directory” + export LD_LIBRARY_PATH="${srcdir}"/${pkgname}-${pkgver/_/-}/src/.libs/ + export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"${srcdir}"/${pkgname}-${pkgver/_/-}/c++/src/.libs/ + export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"${srcdir}"/${pkgname}-${pkgver/_/-}/fortran/src/.libs/ + export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"${srcdir}"/${pkgname}-${pkgver/_/-}/hl/src/.libs/ + export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"${srcdir}"/${pkgname}-${pkgver/_/-}/hl/c++/src/.libs/ + export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"${srcdir}"/${pkgname}-${pkgver/_/-}/hl/fortran/src/.libs/ + # This is a parallel build, they are always OpenMPI bugs + make check || warning "Tests failed" +} + +package() { + cd ${_pkgname}-${pkgver/_/-} + + make DESTDIR="${pkgdir}" install + + install -dm755 "${pkgdir}"/usr/share/doc/${_pkgname} + mv "${pkgdir}"/usr/share/{hdf5_examples,doc/${_pkgname}/examples} + + install -Dm644 COPYING "${pkgdir}"/usr/share/licenses/${_pkgname}/LICENSE +} Copied: hdf5-openmpi/repos/community-staging-x86_64/mpi.patch (from rev 328321, hdf5-openmpi/trunk/mpi.patch) =================================================================== --- community-staging-x86_64/mpi.patch (rev 0) +++ community-staging-x86_64/mpi.patch 2018-05-23 14:56:08 UTC (rev 328322) @@ -0,0 +1,18 @@ +Prevent accidental inclusion of mpi c++ headers +when hdf5.h is included third party library + +https://bugs.gentoo.org/show_bug.cgi?id=420777 +https://bugs.archlinux.org/task/33343 + +--- a/src/H5public.h ++++ b/src/H5public.h +@@ -58,6 +58,8 @@ + # include <stddef.h> + #endif + #ifdef H5_HAVE_PARALLEL ++# define OMPI_SKIP_MPICXX /* Make sure that cxx specific headers are not included */ ++# define MPICH_SKIP_MPICXX + # include <mpi.h> + #ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already */ + # include <mpio.h> +