rpms/netcdf
3
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

Add patch for hdf5 1.8.13 support

Browse Source
This commit is contained in:
Orion Poplawski 2014-06-09 14:13:23 -06:00
parent 68b3285458
commit f619cae32e
2 changed files with 126 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

122
netcdf-mpio.patch Normal file
View File

@ -0,0 +1,122 @@
commit 435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8
Author: Quincey Koziol <quincey@koziol.cc>
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;

9
netcdf.spec
View File

@ -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 <orion@cora.nwra.com> - 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 <rel-eng@lists.fedoraproject.org> - 4.3.2-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild