2021-01-18 12:00:25 +08:00
|
|
|
%global with_mpich 1
|
|
|
|
|
%global with_openmpi 1
|
|
|
|
|
%if %{with_mpich}
|
|
|
|
|
%global mpi_list mpich
|
|
|
|
|
%endif
|
|
|
|
|
%if %{with_openmpi}
|
|
|
|
|
%global mpi_list %{?mpi_list} openmpi
|
|
|
|
|
%endif
|
|
|
|
|
|
2020-02-14 14:01:32 +08:00
|
|
|
Name: hdf5
|
|
|
|
|
Version: 1.8.20
|
2021-01-18 12:00:25 +08:00
|
|
|
Release: 11
|
2020-02-14 14:01:32 +08:00
|
|
|
Summary: A data model, library, and file format for storing and managing data
|
2021-01-18 12:00:25 +08:00
|
|
|
License: GPL
|
2020-02-14 14:01:32 +08:00
|
|
|
|
2020-09-15 17:16:34 +08:00
|
|
|
URL: https://portal.hdfgroup.org/display/HDF5/HDF5
|
|
|
|
|
Source0: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.20/src/hdf5-1.8.20.tar.bz2
|
2020-02-14 14:01:32 +08:00
|
|
|
|
|
|
|
|
Patch0: hdf5-LD_LIBRARY_PATH.patch
|
|
|
|
|
Patch1: hdf5-mpi.patch
|
|
|
|
|
Patch2: hdf5-ldouble-ppc64le.patch
|
2020-11-09 16:54:10 +08:00
|
|
|
Patch3: CVE-2018-17233.patch
|
|
|
|
|
Patch4: CVE-2018-17234.patch
|
|
|
|
|
Patch5: CVE-2018-17237.patch
|
|
|
|
|
Patch6: CVE-2018-17434-CVE-2018-17437.patch
|
|
|
|
|
Patch7: CVE-2018-17438.patch
|
2020-12-14 10:46:04 +08:00
|
|
|
Patch8: CVE-2017-17506.patch
|
|
|
|
|
Patch9: fix-compile-error.patch
|
|
|
|
|
Patch10: CVE-2018-17432.patch
|
|
|
|
|
Patch11: CVE-2018-17435.patch
|
|
|
|
|
Patch12: CVE-2018-13869-CVE-2018-13870.patch
|
|
|
|
|
Patch13: CVE-2018-13873.patch
|
2020-02-14 14:01:32 +08:00
|
|
|
|
|
|
|
|
BuildRequires: gcc, gcc-c++
|
|
|
|
|
BuildRequires: krb5-devel, openssl-devel, zlib-devel, gcc-gfortran, time
|
|
|
|
|
BuildRequires: automake libtool
|
|
|
|
|
BuildRequires: openssh-clients
|
|
|
|
|
BuildRequires: libaec-devel
|
|
|
|
|
|
|
|
|
|
%description
|
|
|
|
|
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. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.
|
|
|
|
|
|
|
|
|
|
%package devel
|
|
|
|
|
Summary: HDF5 development files
|
2021-01-18 12:00:25 +08:00
|
|
|
Provides: hdf5-static = %{version}-%{release}
|
|
|
|
|
Obsoletes: hdf5-static < %{version}-%{release}
|
2020-02-14 14:01:32 +08:00
|
|
|
Requires: %{name}%{?_isa} = %{version}-%{release}
|
|
|
|
|
Requires: libaec-devel%{?_isa}
|
|
|
|
|
Requires: zlib-devel%{?_isa}
|
|
|
|
|
Requires: gcc-gfortran%{?_isa}
|
|
|
|
|
|
|
|
|
|
%description devel
|
|
|
|
|
HDF5 development headers and libraries.
|
|
|
|
|
|
2021-01-18 12:00:25 +08:00
|
|
|
%if %{with_mpich}
|
|
|
|
|
%package mpich
|
|
|
|
|
Summary: HDF5 mpich libraries
|
|
|
|
|
BuildRequires: mpich-devel
|
|
|
|
|
Provides: %{name}-mpich2 = %{version}-%{release}
|
|
|
|
|
Obsoletes: %{name}-mpich2 < %{version}-%{release}
|
|
|
|
|
|
|
|
|
|
%description mpich
|
|
|
|
|
HDF5 parallel mpich libraries
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
%package mpich-devel
|
|
|
|
|
Summary: HDF5 mpich development files
|
|
|
|
|
Requires: %{name}-mpich%{?_isa} = %{version}-%{release}
|
|
|
|
|
Requires: libaec-devel%{?_isa}
|
|
|
|
|
Requires: zlib-devel%{?_isa}
|
|
|
|
|
Requires: mpich-devel%{?_isa}
|
|
|
|
|
Provides: %{name}-mpich2-devel = %{version}-%{release}
|
|
|
|
|
Obsoletes: %{name}-mpich2-devel < %{version}-%{release}
|
|
|
|
|
|
|
|
|
|
%description mpich-devel
|
|
|
|
|
HDF5 parallel mpich development files
|
|
|
|
|
|
|
|
|
|
%package mpich-static
|
|
|
|
|
Summary: HDF5 mpich static libraries
|
|
|
|
|
Requires: %{name}-mpich-devel%{?_isa} = %{version}-%{release}
|
|
|
|
|
Provides: %{name}-mpich2-static = %{version}-%{release}
|
|
|
|
|
Obsoletes: %{name}-mpich2-static < %{version}-%{release}
|
|
|
|
|
|
|
|
|
|
%description mpich-static
|
|
|
|
|
HDF5 parallel mpich static libraries
|
|
|
|
|
%endif
|
|
|
|
|
|
|
|
|
|
%if %{with_openmpi}
|
|
|
|
|
%package openmpi
|
|
|
|
|
Summary: HDF5 openmpi libraries
|
|
|
|
|
BuildRequires: openmpi-devel
|
|
|
|
|
|
|
|
|
|
%description openmpi
|
|
|
|
|
HDF5 parallel openmpi libraries
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
%package openmpi-devel
|
|
|
|
|
Summary: HDF5 openmpi development files
|
|
|
|
|
Requires: %{name}-openmpi%{?_isa} = %{version}-%{release}
|
|
|
|
|
Requires: libaec-devel%{?_isa}
|
|
|
|
|
Requires: zlib-devel%{?_isa}
|
|
|
|
|
Requires: openmpi-devel%{?_isa}
|
|
|
|
|
|
|
|
|
|
%description openmpi-devel
|
|
|
|
|
HDF5 parallel openmpi development files
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
%package openmpi-static
|
|
|
|
|
Summary: HDF5 openmpi static libraries
|
|
|
|
|
Requires: %{name}-openmpi-devel%{?_isa} = %{version}-%{release}
|
|
|
|
|
|
|
|
|
|
%description openmpi-static
|
|
|
|
|
HDF5 parallel openmpi static libraries
|
|
|
|
|
%endif
|
|
|
|
|
|
2020-02-14 14:01:32 +08:00
|
|
|
%prep
|
2020-11-09 16:54:10 +08:00
|
|
|
%autosetup -n %{name}-%{version} -p1
|
2020-02-14 14:01:32 +08:00
|
|
|
|
|
|
|
|
sed -i -e '/^STATIC_AVAILABLE=/s/=.*/=no/' */*/h5[cf]*.in
|
|
|
|
|
autoreconf -f -i
|
|
|
|
|
|
|
|
|
|
sed -e 's|-O -finline-functions|-O3 -finline-functions|g' -i config/gnu-flags
|
|
|
|
|
|
|
|
|
|
%build
|
|
|
|
|
%global _configure ../configure
|
|
|
|
|
%global configure_opts \\\
|
|
|
|
|
--disable-silent-rules \\\
|
|
|
|
|
--enable-fortran \\\
|
|
|
|
|
--enable-fortran2003 \\\
|
|
|
|
|
--enable-hl \\\
|
|
|
|
|
--enable-shared \\\
|
|
|
|
|
--with-szlib \\\
|
|
|
|
|
%{nil}
|
|
|
|
|
|
|
|
|
|
export CC=gcc
|
|
|
|
|
export CXX=g++
|
|
|
|
|
export F9X=gfortran
|
|
|
|
|
export LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed"
|
|
|
|
|
mkdir build
|
|
|
|
|
pushd build
|
|
|
|
|
ln -s ../configure .
|
|
|
|
|
%configure \
|
|
|
|
|
%{configure_opts} \
|
|
|
|
|
--enable-cxx
|
|
|
|
|
sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool
|
|
|
|
|
make LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed"
|
|
|
|
|
popd
|
|
|
|
|
|
2021-01-18 12:00:25 +08:00
|
|
|
export CC=mpicc
|
|
|
|
|
export CXX=mpicxx
|
|
|
|
|
export F9X=mpif90
|
|
|
|
|
export LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed"
|
|
|
|
|
for mpi in %{?mpi_list}
|
|
|
|
|
do
|
|
|
|
|
mkdir $mpi
|
|
|
|
|
pushd $mpi
|
|
|
|
|
module load mpi/$mpi-%{_arch}
|
|
|
|
|
ln -s ../configure .
|
|
|
|
|
%configure \
|
|
|
|
|
%{configure_opts} \
|
|
|
|
|
FCFLAGS="$FCFLAGS -I$MPI_FORTRAN_MOD_DIR" \
|
|
|
|
|
--enable-parallel \
|
|
|
|
|
--exec-prefix=%{_libdir}/$mpi \
|
|
|
|
|
--libdir=%{_libdir}/$mpi/lib \
|
|
|
|
|
--bindir=%{_libdir}/$mpi/bin \
|
|
|
|
|
--sbindir=%{_libdir}/$mpi/sbin \
|
|
|
|
|
--includedir=%{_includedir}/$mpi-%{_arch} \
|
|
|
|
|
--datarootdir=%{_libdir}/$mpi/share \
|
|
|
|
|
--mandir=%{_libdir}/$mpi/share/man
|
|
|
|
|
sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool
|
|
|
|
|
make LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed"
|
|
|
|
|
module purge
|
|
|
|
|
popd
|
|
|
|
|
done
|
|
|
|
|
|
2020-02-14 14:01:32 +08:00
|
|
|
%install
|
|
|
|
|
%make_install -C build
|
|
|
|
|
%delete_la
|
|
|
|
|
cat >h5comp <<EOF
|
|
|
|
|
#!/bin/bash
|
|
|
|
|
|
|
|
|
|
ARCH=$(uname -m)
|
|
|
|
|
|
|
|
|
|
case $ARCH in
|
|
|
|
|
x86_64 ) BITS=64;;
|
|
|
|
|
* ) BITS=32;;
|
|
|
|
|
esac
|
|
|
|
|
|
|
|
|
|
exec $0-${BITS} "$@"
|
|
|
|
|
EOF
|
|
|
|
|
mkdir -p ${RPM_BUILD_ROOT}%{_fmoddir}
|
|
|
|
|
mv ${RPM_BUILD_ROOT}%{_includedir}/*.mod ${RPM_BUILD_ROOT}%{_fmoddir}
|
2021-01-18 12:00:25 +08:00
|
|
|
|
|
|
|
|
for mpi in %{?mpi_list}
|
|
|
|
|
do
|
|
|
|
|
module load mpi/$mpi-%{_arch}
|
|
|
|
|
make -C $mpi install DESTDIR=${RPM_BUILD_ROOT}
|
|
|
|
|
rm $RPM_BUILD_ROOT/%{_libdir}/$mpi/lib/*.la
|
|
|
|
|
#Fortran modules
|
|
|
|
|
mkdir -p ${RPM_BUILD_ROOT}${MPI_FORTRAN_MOD_DIR}
|
|
|
|
|
mv ${RPM_BUILD_ROOT}%{_includedir}/${mpi}-%{_arch}/*.mod ${RPM_BUILD_ROOT}${MPI_FORTRAN_MOD_DIR}/
|
|
|
|
|
module purge
|
|
|
|
|
done
|
|
|
|
|
|
2020-02-14 14:01:32 +08:00
|
|
|
find ${RPM_BUILD_ROOT}%{_datadir} \( -name '*.[ch]*' -o -name '*.f90' \) -exec chmod -x {} +
|
|
|
|
|
|
|
|
|
|
%ifarch x86_64
|
|
|
|
|
sed -i -e s/H5pubconf.h/H5pubconf-64.h/ ${RPM_BUILD_ROOT}%{_includedir}/H5public.h
|
|
|
|
|
mv ${RPM_BUILD_ROOT}%{_includedir}/H5pubconf.h \
|
|
|
|
|
${RPM_BUILD_ROOT}%{_includedir}/H5pubconf-64.h
|
|
|
|
|
for x in h5c++ h5cc h5fc
|
|
|
|
|
do
|
|
|
|
|
mv ${RPM_BUILD_ROOT}%{_bindir}/${x} \
|
|
|
|
|
${RPM_BUILD_ROOT}%{_bindir}/${x}-64
|
|
|
|
|
install -m 0755 h5comp ${RPM_BUILD_ROOT}%{_bindir}/${x}
|
|
|
|
|
done
|
|
|
|
|
%else
|
|
|
|
|
sed -i -e s/H5pubconf.h/H5pubconf-32.h/ ${RPM_BUILD_ROOT}%{_includedir}/H5public.h
|
|
|
|
|
mv ${RPM_BUILD_ROOT}%{_includedir}/H5pubconf.h \
|
|
|
|
|
${RPM_BUILD_ROOT}%{_includedir}/H5pubconf-32.h
|
|
|
|
|
for x in h5c++ h5cc h5fc
|
|
|
|
|
do
|
|
|
|
|
mv ${RPM_BUILD_ROOT}%{_bindir}/${x} \
|
|
|
|
|
${RPM_BUILD_ROOT}%{_bindir}/${x}-32
|
|
|
|
|
install -m 0755 h5comp ${RPM_BUILD_ROOT}%{_bindir}/${x}
|
|
|
|
|
done
|
|
|
|
|
%endif
|
|
|
|
|
|
|
|
|
|
mkdir -p ${RPM_BUILD_ROOT}/%{_rpmmacrodir}
|
|
|
|
|
cat > ${RPM_BUILD_ROOT}/%{_rpmmacrodir}/macros.hdf5 <<EOF
|
|
|
|
|
# HDF5 version is
|
|
|
|
|
%%_hdf5_version %{version}
|
|
|
|
|
EOF
|
|
|
|
|
|
|
|
|
|
%check
|
|
|
|
|
make -C build check
|
|
|
|
|
%ldconfig_scriptlets
|
|
|
|
|
|
|
|
|
|
%files
|
|
|
|
|
%license COPYING
|
|
|
|
|
%doc MANIFEST README.txt release_docs/RELEASE.txt
|
|
|
|
|
%doc release_docs/HISTORY*.txt
|
|
|
|
|
%{_bindir}/gif2h5
|
|
|
|
|
%{_bindir}/h52gif
|
|
|
|
|
%{_bindir}/h5copy
|
|
|
|
|
%{_bindir}/h5debug
|
|
|
|
|
%{_bindir}/h5diff
|
|
|
|
|
%{_bindir}/h5dump
|
|
|
|
|
%{_bindir}/h5import
|
|
|
|
|
%{_bindir}/h5jam
|
|
|
|
|
%{_bindir}/h5ls
|
|
|
|
|
%{_bindir}/h5mkgrp
|
|
|
|
|
%{_bindir}/h5perf_serial
|
|
|
|
|
%{_bindir}/h5repack
|
|
|
|
|
%{_bindir}/h5repart
|
|
|
|
|
%{_bindir}/h5stat
|
|
|
|
|
%{_bindir}/h5unjam
|
|
|
|
|
%{_libdir}/*.so.10*
|
|
|
|
|
%{_libdir}/libhdf5_cpp.so.15*
|
|
|
|
|
%{_libdir}/libhdf5_hl_cpp.so.11*
|
|
|
|
|
|
|
|
|
|
%files devel
|
|
|
|
|
%{_bindir}/h5c++*
|
|
|
|
|
%{_bindir}/h5cc*
|
|
|
|
|
%{_bindir}/h5fc*
|
|
|
|
|
%{_bindir}/h5redeploy
|
|
|
|
|
%{_includedir}/*.h
|
|
|
|
|
%{_libdir}/*.so
|
|
|
|
|
%{_libdir}/*.settings
|
|
|
|
|
%{_fmoddir}/*.mod
|
|
|
|
|
%{_datadir}/hdf5_examples/
|
|
|
|
|
%{_libdir}/*.a
|
|
|
|
|
%{_rpmmacrodir}/macros.hdf5
|
|
|
|
|
|
2021-01-18 12:00:25 +08:00
|
|
|
%if %{with_mpich}
|
|
|
|
|
%files mpich
|
|
|
|
|
%license COPYING
|
|
|
|
|
%doc MANIFEST README.txt release_docs/RELEASE.txt
|
|
|
|
|
%doc release_docs/HISTORY*.txt
|
|
|
|
|
%{_libdir}/mpich/bin/gif2h5
|
|
|
|
|
%{_libdir}/mpich/bin/h52gif
|
|
|
|
|
%{_libdir}/mpich/bin/h5copy
|
|
|
|
|
%{_libdir}/mpich/bin/h5debug
|
|
|
|
|
%{_libdir}/mpich/bin/h5diff
|
|
|
|
|
%{_libdir}/mpich/bin/h5dump
|
|
|
|
|
%{_libdir}/mpich/bin/h5import
|
|
|
|
|
%{_libdir}/mpich/bin/h5jam
|
|
|
|
|
%{_libdir}/mpich/bin/h5ls
|
|
|
|
|
%{_libdir}/mpich/bin/h5mkgrp
|
|
|
|
|
%{_libdir}/mpich/bin/h5redeploy
|
|
|
|
|
%{_libdir}/mpich/bin/h5repack
|
|
|
|
|
%{_libdir}/mpich/bin/h5perf
|
|
|
|
|
%{_libdir}/mpich/bin/h5perf_serial
|
|
|
|
|
%{_libdir}/mpich/bin/h5repart
|
|
|
|
|
%{_libdir}/mpich/bin/h5stat
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%{_libdir}/mpich/bin/h5unjam
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%{_libdir}/mpich/bin/ph5diff
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%{_libdir}/mpich/lib/*.so.10*
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%files mpich-devel
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%{_includedir}/mpich-%{_arch}
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%{_fmoddir}/mpich/*.mod
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%{_libdir}/mpich/bin/h5pcc
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%{_libdir}/mpich/bin/h5pfc
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%{_libdir}/mpich/lib/lib*.so
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%{_libdir}/mpich/lib/lib*.settings
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%{_libdir}/mpich/share/hdf5_examples/
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%files mpich-static
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%{_libdir}/mpich/lib/*.a
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%endif
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%if %{with_openmpi}
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%files openmpi
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%license COPYING
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%doc MANIFEST README.txt release_docs/RELEASE.txt
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%doc release_docs/HISTORY*.txt
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%{_libdir}/openmpi/bin/gif2h5
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%{_libdir}/openmpi/bin/h52gif
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%{_libdir}/openmpi/bin/h5copy
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%{_libdir}/openmpi/bin/h5debug
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%{_libdir}/openmpi/bin/h5diff
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%{_libdir}/openmpi/bin/h5dump
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%{_libdir}/openmpi/bin/h5import
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%{_libdir}/openmpi/bin/h5jam
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%{_libdir}/openmpi/bin/h5ls
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%{_libdir}/openmpi/bin/h5mkgrp
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%{_libdir}/openmpi/bin/h5perf
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%{_libdir}/openmpi/bin/h5perf_serial
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%{_libdir}/openmpi/bin/h5redeploy
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%{_libdir}/openmpi/bin/h5repack
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%{_libdir}/openmpi/bin/h5repart
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%{_libdir}/openmpi/bin/h5stat
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%{_libdir}/openmpi/bin/h5unjam
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%{_libdir}/openmpi/bin/ph5diff
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%{_libdir}/openmpi/lib/*.so.10*
|
|
|
|
|
|
|
|
|
|
%files openmpi-devel
|
|
|
|
|
%{_includedir}/openmpi-%{_arch}
|
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|
|
|
%{_fmoddir}/openmpi/*.mod
|
|
|
|
|
%{_libdir}/openmpi/bin/h5pcc
|
|
|
|
|
%{_libdir}/openmpi/bin/h5pfc
|
|
|
|
|
%{_libdir}/openmpi/lib/lib*.so
|
|
|
|
|
%{_libdir}/openmpi/lib/lib*.settings
|
|
|
|
|
%{_libdir}/openmpi/share/hdf5_examples/
|
|
|
|
|
|
|
|
|
|
%files openmpi-static
|
|
|
|
|
%{_libdir}/openmpi/lib/*.a
|
|
|
|
|
%endif
|
|
|
|
|
|
2020-02-14 14:01:32 +08:00
|
|
|
%changelog
|
2021-01-18 12:00:25 +08:00
|
|
|
* Fri Jan 15 2021 yanan li <liyanan32@huawei.com> - 1.8.20-11
|
|
|
|
|
- add sub packages hdf5-openmpi-static, hdf5-openmpi-devel, hdf5-openmpi,
|
|
|
|
|
- hdf5-mpich-static, hdf5-mpich-devel, hdf5-mpich
|
|
|
|
|
|
2020-12-14 10:46:04 +08:00
|
|
|
* Mon Dec 14 2020 openEuler Buildteam <buildteam@openeuler.org> - 1.8.20-10
|
|
|
|
|
- fix CVE-2017-17506 CVE-2018-17432 CVE-2018-17435 CVE-2018-13869 CVE-2018-13870 CVE-2018-13873
|
|
|
|
|
|
2020-11-09 16:54:10 +08:00
|
|
|
* Mon Nov 9 2020 wangxiao <wangxiao65@huawei.com> - 1.8.20-9
|
|
|
|
|
- fix CVE-2018-17233 CVE-2018-17234 CVE-2018-17237 CVE-2018-17434 CVE-2018-17437 CVE-2018-17438
|
|
|
|
|
|
2020-09-15 17:16:34 +08:00
|
|
|
* Tue Sep 15 2020 shaoqiang kang <kangshaoqiang1@openeuler.org> - 1.8.20-8
|
|
|
|
|
- Modify source
|
|
|
|
|
|
2020-02-14 14:01:32 +08:00
|
|
|
* Tue Oct 22 2019 openEuler Buildteam <buildteam@openeuler.org> - 1.8.20-7
|
|
|
|
|
- Package init
|
