Merging pull request from gsjaardema, see #335 for more information.

CMakeLists.txt

@@ -627,6 +627,9 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
       ENDIF()
 
     ENDIF(MSVC)
+    IF(NOT HDF5_C_LIBRARY)
+      SET(HDF5_C_LIBRARY hdf5)
+    ENDIF()
   ENDIF(HDF5_C_LIBRARY AND HDF5_HL_LIBRARY AND HDF5_INCLUDE_DIR)
 
   ###
@@ -636,8 +639,8 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
     # Find out if HDF5 was built with parallel support.
     # Do that by checking for the targets H5Pget_fapl_mpiposx and
     # H5Pget_fapl_mpio in ${HDF5_LIB}.
-    CHECK_LIBRARY_EXISTS(hdf5 H5Pget_fapl_mpiposix "" HDF5_IS_PARALLEL_MPIPOSIX)
-    CHECK_LIBRARY_EXISTS(hdf5 H5Pget_fapl_mpio "" HDF5_IS_PARALLEL_MPIO)
+    CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY} H5Pget_fapl_mpiposix "" HDF5_IS_PARALLEL_MPIPOSIX)
+    CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY} H5Pget_fapl_mpio "" HDF5_IS_PARALLEL_MPIO)
     IF(HDF5_IS_PARALLEL_MPIPOSIX OR HDF5_IS_PARALLEL_MPIO)
       SET(HDF5_PARALLEL ON)
     ELSE()
@@ -653,11 +656,13 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
       SET(USE_PARALLEL_POSIX ON)
     ENDIF()
 
+    #Check to see if HDF5 library has collective metadata APIs, (HDF5 >= 1.10.0)
+    CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY} H5Pset_all_coll_metadata_ops "" HDF5_HAS_COLL_METADATA_OPS)
+
     OPTION(ENABLE_DYNAMIC_LOADING "Enable Dynamic Loading" ON)
     IF(ENABLE_DYNAMIC_LOADING)
       SET(USE_LIBDL ON CACHE BOOL "")
     ENDIF()
-    SET(HDF5_C_LIBRARY hdf5)
   ENDIF(NOT MSVC)
 
   # Make sure the user has built the library with zlib support.

config.h.cmake.in

@@ -60,6 +60,9 @@
 /* Define to 1 if you have the <ctype.h> header file. */
 #cmakedefine HAVE_CTYPE_H 1
 
+/* Define to 1 if you have hdf5_coll_metadata_ops */
+#cmakedefine HDF5_HAS_COLL_METADATA_OPS 1
+
 /* Is CURLINFO_RESPONSE_CODE defined */
 #cmakedefine HAVE_CURLINFO_RESPONSE_CODE 1
 

configure.ac

@@ -924,7 +924,7 @@ if test "x$enable_netcdf_4" = xyes; then
    [AC_MSG_ERROR([Can't find or link to the hdf5 high-level. Use --disable-netcdf-4, or see config.log for errors.])])
 
    AC_CHECK_HEADERS([hdf5.h], [], [AC_MSG_ERROR([Compiling a test with HDF5 failed.  Either hdf5.h cannot be found, or config.log should be checked for other reason.])])
-   AC_CHECK_FUNCS([H5Pget_fapl_mpiposix H5Pget_fapl_mpio H5Pset_deflate H5Z_SZIP H5free_memory H5Pset_libver_bounds])
+   AC_CHECK_FUNCS([H5Pget_fapl_mpiposix H5Pget_fapl_mpio H5Pset_deflate H5Z_SZIP H5free_memory H5Pset_libver_bounds H5Pset_all_coll_metadata_ops])
 
    # The user may have parallel HDF5 based on MPI POSIX.
    if test "x$ac_cv_func_H5Pget_fapl_mpiposix" = xyes; then
@@ -936,6 +936,11 @@ if test "x$enable_netcdf_4" = xyes; then
       AC_DEFINE([USE_PARALLEL_MPIO], [1], [if true, compile in parallel netCDF-4 based on MPI/IO])
    fi
 
+   # Check to see if HDF5 library has collective metadata APIs, (HDF5 >= 1.10.0)
+   if test "x$ac_cv_func_H5Pset_all_coll_metadata_ops" = xyes; then
+      AC_DEFINE([HDF5_HAS_COLL_METADATA_OPS], [1], [if true, use collective metadata ops in parallel netCDF-4])
+   fi
+
    # If parallel is available in hdf5, enable it in the C code. Also add some stuff to netcdf.h.
    hdf5_parallel=no
    if test "x$ac_cv_func_H5Pget_fapl_mpio" = xyes -o "x$ac_cv_func_H5Pget_fapl_mpiposix" = xyes; then

libsrc4/nc4file.c

@@ -446,6 +446,11 @@ nc4_create_file(const char *path, int cmode, MPI_Comm comm, MPI_Info info,
       BAIL(NC_EHDFERR);
 
    /* Create the file. */
+#ifdef HDF5_HAS_COLL_METADATA_OPS
+   H5Pset_all_coll_metadata_ops(fapl_id, 1 );
+   H5Pset_coll_metadata_write(fapl_id, 1);
+#endif
+
    if ((nc4_info->hdfid = H5Fcreate(path, flags, fcpl_id, fapl_id)) < 0)
         /*Change the return error from NC_EFILEMETADATA to
           System error EACCES because that is the more likely problem */
@@ -2315,6 +2320,9 @@ nc4_open_file(const char *path, int mode, void* parameters, NC *nc)
    /* The NetCDF-3.x prototype contains an mode option NC_SHARE for
       multiple processes accessing the dataset concurrently.  As there
       is no HDF5 equivalent, NC_SHARE is treated as NC_NOWRITE. */
+#ifdef HDF5_HAS_COLL_METADATA_OPS
+   H5Pset_all_coll_metadata_ops(fapl_id, 1 );
+#endif
    if(inmemory) {
        if((nc4_info->hdfid = H5LTopen_file_image(meminfo->memory,meminfo->size,
 			H5LT_FILE_IMAGE_DONT_COPY|H5LT_FILE_IMAGE_DONT_RELEASE