From f619cae32e35204ccf5a1dad0826d5a23c648982 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Mon, 9 Jun 2014 14:13:23 -0600 Subject: [PATCH] Add patch for hdf5 1.8.13 support --- netcdf-mpio.patch | 122 ++++++++++++++++++++++++++++++++++++++++++++++ netcdf.spec | 9 ++-- 2 files changed, 126 insertions(+), 5 deletions(-) create mode 100644 netcdf-mpio.patch diff --git a/netcdf-mpio.patch b/netcdf-mpio.patch new file mode 100644 index 0000000..395b3be --- /dev/null +++ b/netcdf-mpio.patch @@ -0,0 +1,122 @@ +commit 435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8 +Author: Quincey Koziol +Date: Wed May 7 08:45:15 2014 -0500 + + Account for the HDF5 library not having the MPI-POSIX VFD configured in. + +diff --git a/libsrc4/nc4file.c b/libsrc4/nc4file.c +index ec3bb0c..5c957be 100644 +--- a/libsrc4/nc4file.c ++++ b/libsrc4/nc4file.c +@@ -308,12 +308,21 @@ nc4_create_file(const char *path, int cmode, MPI_Comm comm, MPI_Info info, + if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0) + BAIL(NC_EPARINIT); + } ++#ifdef USE_PARALLEL_POSIX + else /* MPI/POSIX */ + { + LOG((4, "creating parallel file with MPI/posix")); + if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0) + BAIL(NC_EPARINIT); + } ++#else /* USE_PARALLEL_POSIX */ ++ /* Should not happen! Code in NC4_create/NC4_open should alias the ++ * NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not ++ * available in HDF5. -QAK ++ */ ++ else /* MPI/POSIX */ ++ BAIL(NC_EPARINIT); ++#endif /* USE_PARALLEL_POSIX */ + + /* Keep copies of the MPI Comm & Info objects */ + if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm)) +@@ -465,6 +474,17 @@ NC4_create(const char* path, int cmode, size_t initialsz, int basepe, + ) + return NC_EINVAL; + ++#ifndef USE_PARALLEL_POSIX ++/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias ++ * the NC_MPIPOSIX flag to NC_MPIIO. -QAK ++ */ ++ if(cmode & NC_MPIPOSIX) ++ { ++ cmode &= ~NC_MPIPOSIX; ++ cmode |= NC_MPIIO; ++ } ++#endif /* USE_PARALLEL_POSIX */ ++ + cmode |= NC_NETCDF4; + + /* Apply default create format. */ +@@ -2168,12 +2188,21 @@ nc4_open_file(const char *path, int mode, MPI_Comm comm, + if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0) + BAIL(NC_EPARINIT); + } ++#ifdef USE_PARALLEL_POSIX + else /* MPI/POSIX */ + { + LOG((4, "opening parallel file with MPI/posix")); + if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0) + BAIL(NC_EPARINIT); + } ++#else /* USE_PARALLEL_POSIX */ ++ /* Should not happen! Code in NC4_create/NC4_open should alias the ++ * NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not ++ * available in HDF5. -QAK ++ */ ++ else /* MPI/POSIX */ ++ BAIL(NC_EPARINIT); ++#endif /* USE_PARALLEL_POSIX */ + + /* Keep copies of the MPI Comm & Info objects */ + if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm)) +@@ -2640,6 +2669,17 @@ NC4_open(const char *path, int mode, int basepe, size_t *chunksizehintp, + (mode & NC_MPIIO && mode & NC_MPIPOSIX)) + return NC_EINVAL; + ++#ifndef USE_PARALLEL_POSIX ++/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias ++ * the NC_MPIPOSIX flag to NC_MPIIO. -QAK ++ */ ++ if(mode & NC_MPIPOSIX) ++ { ++ mode &= ~NC_MPIPOSIX; ++ mode |= NC_MPIIO; ++ } ++#endif /* USE_PARALLEL_POSIX */ ++ + + /* Depending on the type of file, open it. */ + +diff --git a/nc_test4/tst_nc4perf.c b/nc_test4/tst_nc4perf.c +index 47af70e..3528b82 100644 +--- a/nc_test4/tst_nc4perf.c ++++ b/nc_test4/tst_nc4perf.c +@@ -244,6 +244,11 @@ int test_pio_4d(size_t cache_size, int facc_type, int access_flag, MPI_Comm comm + return 0; + } + ++/* Note: When the MPI-POSIX VFD is not compiled in to HDF5, the NC_MPIPOSIX ++ * flag will be aliased to the NC_MPIIO flag within the library, and ++ * therefore this test will exercise the aliasing, with the MPI-IO VFD, ++ * under that configuration. -QAK ++ */ + #define NUM_MODES 2 + #define NUM_FACC 2 + #define NUM_CHUNK_COMBOS_2D 3 +diff --git a/nc_test4/tst_parallel3.c b/nc_test4/tst_parallel3.c +index 27f9c98..9fa534f 100644 +--- a/nc_test4/tst_parallel3.c ++++ b/nc_test4/tst_parallel3.c +@@ -129,6 +129,11 @@ int main(int argc, char **argv) + if (mpi_rank == 0) + SUMMARIZE_ERR; + ++/* Note: When the MPI-POSIX VFD is not compiled in to HDF5, the NC_MPIPOSIX ++ * flag will be aliased to the NC_MPIIO flag within the library, and ++ * therefore this test will exercise the aliasing, with the MPI-IO VFD, ++ * under that configuration. -QAK ++ */ + if (mpi_rank == 0) + printf("*** Testing parallel IO for raw-data with MPIPOSIX-IO (driver)..."); + facc_type = NC_NETCDF4|NC_MPIPOSIX; diff --git a/netcdf.spec b/netcdf.spec index b934ce2..a918cf6 100644 --- a/netcdf.spec +++ b/netcdf.spec @@ -11,6 +11,8 @@ Source0: https://github.com/Unidata/netcdf-c/archive/v%{version}.tar.gz#/ #Source0: http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-%{version}.tar.gz # Use pkgconfig in nc-config to avoid multi-lib issues Patch0: netcdf-pkgconfig.patch +# Upstream patch to support hdf5 1.8.13 mpio change +Patch1: netcdf-mpio.patch BuildRequires: chrpath BuildRequires: doxygen @@ -181,10 +183,7 @@ NetCDF parallel openmpi static libraries %prep %setup -q -n %{name}-c-%{version} %patch0 -p1 -b .pkgconfig -%if 0%{?fedora} >= 21 -# No mpi-posix in hdf5 1.8.13 -sed -i -e 's/^.*USE_PARALLEL_POSIX.*$/:/' configure -%endif +%patch1 -p1 -b .mpio %build @@ -333,7 +332,7 @@ done %changelog * Mon Jun 9 2014 Orion Poplawski - 4.3.2-3 -- Rebuild for hdf5 1.8.13 +- Rebuild for hdf5 1.8.13, add patch for support * Sat Jun 07 2014 Fedora Release Engineering - 4.3.2-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild