[arch-commits] Commit in hdf5-openmpi/repos (3 files)

[Bruno Pagani]

    Date: Thursday, August 23, 2018 @ 20:42:29
  Author: archange
Revision: 373480

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 373479, hdf5-openmpi/trunk/PKGBUILD)
  hdf5-openmpi/repos/community-staging-x86_64/mpi.patch
    (from rev 373479, hdf5-openmpi/trunk/mpi.patch)

-----------+
 PKGBUILD  |   79 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 mpi.patch |   18 +++++++++++++
 2 files changed, 97 insertions(+)

Copied: hdf5-openmpi/repos/community-staging-x86_64/PKGBUILD (from rev 373479, hdf5-openmpi/trunk/PKGBUILD)
===================================================================
--- community-staging-x86_64/PKGBUILD	                        (rev 0)
+++ community-staging-x86_64/PKGBUILD	2018-08-23 20:42:29 UTC (rev 373480)
@@ -0,0 +1,79 @@
+# $Id$
+# Maintainer: Ronald van Haren <ronald.archlinux.org>
+# Maintainer: Bruno Pagani <archange at archlinux.org>
+# Contributor: Stefan Husmann <stefan-husmann at t-online.de>
+# Contributor: damir <damir at archlinux.org>
+# Contributor: Tom K <tomk at runbox.com>
+# Contributor: Jed Brown <jed at 59A2.org>
+# Contributor: Simone Pezzuto <junki.gnu at gmail.com>
+
+_pkgname=hdf5
+_mpi=openmpi
+pkgname=${_pkgname}-${_mpi}
+pkgver=1.10.3
+pkgrel=1
+pkgdesc="General purpose library and file format for storing scientific data (${_mpi} version)"
+arch=('x86_64')
+url="https://www.hdfgroup.org/hdf5"
+license=('custom')
+depends=('zlib' 'libaec' 'bash' 'openmpi')
+makedepends=('cmake' 'time' 'gcc-fortran')
+provides=('hdf5' 'hdf5-cpp-fortran' "hdf5-fortran-${_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=('56c5039103c51a40e493b43c504ce982'
+         'dfa8dd50b8a7ebb3ad7249c627156cf9')
+sha256sums=('c65cdcce4724a57fd3f8da9f0d109b497be30092acb9fac634d1291190d905a9'
+            '603006358175b7a8b35fa44c484cddf45c0381cf50db4fb7c50ea5969d361eca')
+
+prepare() {
+    mkdir -p build
+
+    cd ${_pkgname}-${pkgver/_/-}
+    # FS#33343
+    patch -p1 -i ../mpi.patch
+}
+
+build() {
+    cd build
+    CXX="mpicxx" \
+    CC="mpicc" \
+    FC="mpif90" \
+    F9X="mpif90" \
+    RUNPARALLEL="mpirun" \
+    OMPI_MCA_disable_memory_allocator=1 \
+    cmake ../${_pkgname}-${pkgver/_/-} \
+        -DCMAKE_INSTALL_PREFIX=/usr \
+        -DBUILD_SHARED_LIBS=ON \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DALLOW_UNSUPPORTED=ON \
+        -DHDF5_BUILD_HL_LIB=ON \
+        -DHDF5_BUILD_CPP_LIB=ON \
+        -DHDF5_BUILD_FORTRAN=ON \
+        -DHDF5_ENABLE_PARALLEL=ON \
+        -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
+        -DHDF5_ENABLE_SZIP_SUPPORT=ON \
+        -DHDF5_ENABLE_SZIP_ENCODING=ON
+    cmake --build . --config Release
+}
+
+check() {
+    cd build
+    # Three expected test failures (https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.3/src/hdf5-1.10.3-RELEASE.txt, Known Problems):
+    #   142 - TEST_PAR_testphdf5 (Failed)
+    #   146 - TEST_PAR_t_cache_image (Timeout)
+    #   153 - TEST_PAR_t_shapesame (Failed)
+    ctest . -C Release || warning "Tests failed"
+}
+
+package() {
+    cd build
+
+    make DESTDIR="${pkgdir}" install
+
+    install -d "${pkgdir}"/usr/share/licenses/${pkgname}
+    mv "${pkgdir}"/usr/share/COPYING "${pkgdir}"/usr/share/licenses/${pkgname}/
+    rm "${pkgdir}"/usr/share/{RELEASE,USING_HDF5_CMake}.txt
+}

Copied: hdf5-openmpi/repos/community-staging-x86_64/mpi.patch (from rev 373479, hdf5-openmpi/trunk/mpi.patch)
===================================================================
--- community-staging-x86_64/mpi.patch	                        (rev 0)
+++ community-staging-x86_64/mpi.patch	2018-08-23 20:42:29 UTC (rev 373480)
@@ -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>
+