Enable MPI builds
This commit is contained in:
Orion Poplawski
parent
a5c9892dd6
commit
b9d7608ce6
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@ -0,0 +1,17 @@
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diff -up netcdf-4.1.3/libdispatch/parallel.c.mpi netcdf-4.1.3/libdispatch/parallel.c
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--- netcdf-4.1.3/libdispatch/parallel.c.mpi 2011-06-10 07:35:00.000000000 -0600
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+++ netcdf-4.1.3/libdispatch/parallel.c 2012-02-10 10:46:18.229286019 -0700
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@@ -29,13 +29,8 @@ nc_create_par(const char *path, int cmod
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!(cmode & NC_PNETCDF))
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return NC_EINVAL;
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-#ifdef HAVE_MPI_COMM_F2C
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- comm_c = MPI_Comm_f2c(comm);
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- info_c = MPI_Info_f2c(info);
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-#else
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comm_c = (MPI_Comm)comm;
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info_c = (MPI_Info)info;
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-#endif
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data.comm = comm_c;
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data.info = info_c;
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@ -0,0 +1,32 @@
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diff -up netcdf-4.1.3/configure.postdeps netcdf-4.1.3/configure
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--- netcdf-4.1.3/configure.postdeps 2011-06-17 14:52:05.000000000 -0600
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+++ netcdf-4.1.3/configure 2012-02-07 21:41:30.207617024 -0700
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@@ -21293,15 +21293,16 @@ if { { eval echo "\"\$as_me\":${as_linen
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# Sentinel used to keep track of whether or not we are before
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# the conftest object file.
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pre_test_object_deps_done=no
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-
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+set -x
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for p in `eval "$output_verbose_link_cmd"`; do
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case ${prev}${p} in
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-L* | -R* | -l*)
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- # Some compilers place space between "-{L,R}" and the path.
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+ # Some compilers place space between "-{L,R,l}" and the path.
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# Remove the space.
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if test $p = "-L" ||
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- test $p = "-R"; then
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+ test $p = "-R" ||
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+ test $p = "-l"; then
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prev=$p
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continue
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fi
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@@ -21370,7 +21371,7 @@ if { { eval echo "\"\$as_me\":${as_linen
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esac
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done
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-
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+set +x
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# Clean up.
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rm -f a.out a.exe
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else
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219
netcdf.spec
219
netcdf.spec
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@ -1,6 +1,6 @@
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Name: netcdf
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Version: 4.1.3
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Release: 2%{?dist}
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Release: 3%{?dist}
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Summary: Libraries for the Unidata network Common Data Form
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Group: Applications/Engineering
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@ -12,6 +12,10 @@ Source0: http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-%{versio
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Patch0: netcdf-pkgconfig.patch
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#Strip FFLAGS from nc-config
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Patch1: netcdf-fflags.patch
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# Fix issue parsing mpif90 output
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Patch2: netcdf-postdeps.patch
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# Upstream patch to fix mpi issue
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Patch3: netcdf-mpi.patch
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BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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BuildRequires: gcc-gfortran, gawk
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@ -21,6 +25,29 @@ BuildRequires: zlib-devel
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%ifnarch s390 s390x %{arm}
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BuildRequires: valgrind
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%endif
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#mpiexec segfaults if ssh is not present
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#https://trac.mcs.anl.gov/projects/mpich2/ticket/1576
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BuildRequires: openssh-clients
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%global with_mpich2 1
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%global with_openmpi 1
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%if 0%{?rhel}
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%ifarch ppc64
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# No mpich2 on ppc64 in EL
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%global with_mpich2 0
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%endif
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%endif
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%ifarch s390 s390x
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# No openmpi on s390(x)
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%global with_openmpi 0
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%endif
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%if %{with_mpich2}
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%global mpi_list mpich2
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%endif
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%if %{with_openmpi}
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%global mpi_list %{?mpi_list} openmpi
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%endif
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%description
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NetCDF (network Common Data Form) is an interface for array-oriented
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@ -77,38 +104,162 @@ Requires: %{name} = %{version}-%{release}
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This package contains the netCDF static libs.
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%if %{with_mpich2}
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%package mpich2
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Summary: NetCDF mpich2 libraries
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Group: Development/Libraries
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Requires: mpich2
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BuildRequires: mpich2-devel
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BuildRequires: hdf5-mpich2-devel >= 1.8.4
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%description mpich2
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NetCDF parallel mpich2 libraries
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%package mpich2-devel
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Summary: NetCDF mpich2 development files
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Group: Development/Libraries
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Requires: %{name}-mpich2%{?_isa} = %{version}-%{release}
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Requires: mpich2
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Requires: gcc-gfortran%{_isa}
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Requires: pkgconfig
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Requires: hdf5-mpich2-devel
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Requires: libcurl-devel
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%description mpich2-devel
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NetCDF parallel mpich2 development files
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%package mpich2-static
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Summary: NetCDF mpich2 static libraries
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Group: Development/Libraries
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Requires: %{name}-mpich2-devel%{?_isa} = %{version}-%{release}
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%description mpich2-static
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NetCDF parallel mpich2 static libraries
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%endif
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%if %{with_openmpi}
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%package openmpi
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Summary: NetCDF openmpi libraries
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Group: Development/Libraries
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Requires: openmpi
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BuildRequires: openmpi-devel
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BuildRequires: hdf5-openmpi-devel >= 1.8.4
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%description openmpi
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NetCDF parallel openmpi libraries
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%package openmpi-devel
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Summary: NetCDF openmpi development files
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Group: Development/Libraries
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Requires: %{name}-openmpi%{_isa} = %{version}-%{release}
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Requires: openmpi-devel
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Requires: gcc-gfortran%{_isa}
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Requires: pkgconfig
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Requires: hdf5-openmpi-devel
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Requires: libcurl-devel
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%description openmpi-devel
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NetCDF parallel openmpi development files
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%package openmpi-static
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Summary: NetCDF openmpi static libraries
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Group: Development/Libraries
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Requires: %{name}-openmpi-devel%{?_isa} = %{version}-%{release}
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%description openmpi-static
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NetCDF parallel openmpi static libraries
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%endif
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%prep
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%setup -q
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%patch0 -p1 -b .pkgconfig
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%patch1 -p1 -b .fflags
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%patch2 -p1 -b .postdeps
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%patch3 -p1 -b .mpi
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%build
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#Do out of tree builds
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%global _configure ../configure
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#Common configure options
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%global configure_opts \\\
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--enable-shared \\\
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--enable-netcdf-4 \\\
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--enable-dap \\\
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--enable-ncgen4 \\\
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--enable-extra-example-tests \\\
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--disable-dap-remote-tests \\\
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%{nil}
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# Serial build
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export F77="gfortran"
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export FC="gfortran"
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export FFLAGS="${RPM_OPT_FLAGS}"
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export FCFLAGS="$FFLAGS"
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%configure \
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--enable-shared \
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--enable-netcdf-4 \
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--enable-dap \
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--enable-ncgen4 \
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--enable-extra-example-tests \
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--disable-dap-remote-tests
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mkdir build
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pushd build
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ln -s ../configure .
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%configure %{configure_opts}
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make %{?_smp_mflags}
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popd
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# MPI builds
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export CC=mpicc
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export CXX=mpicxx
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export F77=mpif90
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export FC=mpif90
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# netcdf gets confused about Fortran type
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export CPPFLAGS=-DpgiFortran
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for mpi in %{mpi_list}
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do
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mkdir $mpi
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pushd $mpi
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module load $mpi-%{_arch}
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ln -s ../configure .
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%configure %{configure_opts} \
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--libdir=%{_libdir}/$mpi/lib \
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--bindir=%{_libdir}/$mpi/bin \
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--sbindir=%{_libdir}/$mpi/sbin \
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--includedir=%{_includedir}/$mpi-%{_arch} \
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--datarootdir=%{_libdir}/$mpi/share \
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--mandir=%{_libdir}/$mpi/share/man \
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--enable-parallel-tests
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make %{?_smp_mflags}
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module purge
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popd
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done
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%install
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make install DESTDIR=${RPM_BUILD_ROOT}
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make -C build install DESTDIR=${RPM_BUILD_ROOT}
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mkdir -p ${RPM_BUILD_ROOT}%{_fmoddir}
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/bin/mv ${RPM_BUILD_ROOT}%{_includedir}/*.mod \
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${RPM_BUILD_ROOT}%{_fmoddir}
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/bin/rm -f ${RPM_BUILD_ROOT}%{_libdir}/*.la
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/bin/rm -f ${RPM_BUILD_ROOT}%{_infodir}/dir
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for mpi in %{mpi_list}
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do
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module load $mpi-%{_arch}
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make -C $mpi install DESTDIR=${RPM_BUILD_ROOT}
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rm $RPM_BUILD_ROOT/%{_libdir}/$mpi/lib/*.la
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module purge
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done
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%check
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make check
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make -C build check
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for mpi in mpich2 openmpi
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do
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module load $mpi-%{_arch}
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make -C $mpi check
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module purge
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done
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%clean
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@ -129,7 +280,6 @@ fi
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%files
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%defattr(-,root,root,-)
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%doc COPYRIGHT README
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%{_bindir}/nccopy
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%{_bindir}/ncdump
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@ -140,7 +290,6 @@ fi
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%{_infodir}/*
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%files devel
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%defattr(-,root,root,-)
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%{_bindir}/nc-config
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%{_includedir}/ncvalues.h
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%{_includedir}/netcdf.h
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@ -153,11 +302,55 @@ fi
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%{_mandir}/man3/*
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%files static
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%defattr(-,root,root,-)
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%{_libdir}/*.a
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%if %{with_mpich2}
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%files mpich2
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%doc COPYRIGHT README
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%{_libdir}/mpich2/bin/nccopy
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%{_libdir}/mpich2/bin/ncdump
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%{_libdir}/mpich2/bin/ncgen
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%{_libdir}/mpich2/bin/ncgen3
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%{_libdir}/mpich2/lib/*.so.*
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%doc %{_libdir}/mpich2/share/man/man1/*.1*
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%files mpich2-devel
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%{_libdir}/mpich2/bin/nc-config
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%{_includedir}/mpich2-%{_arch}
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%{_libdir}/mpich2/lib/*.so
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%{_libdir}/mpich2/lib/pkgconfig/%{name}.pc
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%doc %{_libdir}/mpich2/share/man/man3/*.3*
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%files mpich2-static
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%{_libdir}/mpich2/lib/*.a
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%endif
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%if %{with_openmpi}
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%files openmpi
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%doc COPYRIGHT README
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%{_libdir}/openmpi/bin/nccopy
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%{_libdir}/openmpi/bin/ncdump
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%{_libdir}/openmpi/bin/ncgen
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%{_libdir}/openmpi/bin/ncgen3
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%{_libdir}/openmpi/lib/*.so.*
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%doc %{_libdir}/openmpi/share/man/man1/*.1*
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%files openmpi-devel
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%{_libdir}/openmpi/bin/nc-config
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%{_includedir}/openmpi-%{_arch}
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%{_libdir}/openmpi/lib/*.so
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%{_libdir}/openmpi/lib/pkgconfig/%{name}.pc
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%doc %{_libdir}/openmpi/share/man/man3/*.3*
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%files openmpi-static
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%{_libdir}/openmpi/lib/*.a
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%endif
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%changelog
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* Wed Feb 1 2012 Orion Poplawski <orion@cora.nwra.com> - 4.1.3-3
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- Enable MPI builds
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* Thu Aug 11 2011 Peter Robinson <pbrobinson@fedoraproject.org> - 4.1.3-2
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- Add ARM to valgrind excludes
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