dev-zero 14/08/11 07:15:24 Added: netcdf-4.3.2-HDF5-1.8.13+-compat.patch Log: Pull patch from upstream to use HDF5 >=1.8.13 with MPI (bug #512502). (Portage version: 2.2.10/cvs/Linux x86_64, signed Manifest commit with key 0x1A5D023975B0583D!)
Revision Changes Path 1.1 sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch?rev=1.1&view=markup plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch?rev=1.1&content-type=text/plain Index: netcdf-4.3.2-HDF5-1.8.13+-compat.patch =================================================================== >From 435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8 Mon Sep 17 00:00:00 2001 From: Quincey Koziol <[email protected]> Date: Wed, 7 May 2014 08:45:15 -0500 Subject: [PATCH] Account for the HDF5 library not having the MPI-POSIX VFD configured in. --- RELEASE_NOTES.md | 2 ++ libsrc4/nc4file.c | 40 ++++++++++++++++++++++++++++++++++++++++ nc_test4/tst_nc4perf.c | 5 +++++ nc_test4/tst_parallel3.c | 5 +++++ 4 files changed, 52 insertions(+) diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index 27f228c..1a69d17 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -9,6 +9,8 @@ This file contains a high-level description of this package's evolution. Release ### 4.3.3-rc1 Released TBD +* When the NC_MPIPOSIX flag is given for parallel I/O access and the HDF5 library does not have the MPI-POSIX VFD configured in, the NC_MPIPOSIX flag is transparently aliased to the NC_MPIIO flag within the netCDF-4 library. + ## 4.3.2 Released 2014-04-23 * As part of an ongoing project, the Doxygen-generated netcdf documentation has been reorganized. The goal is to make the documentation easier to parse, and to eliminate redundant material. This project is ongoing. 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; -- 2.0.3
