Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…

…evelop-tools-move

.github/workflows/linux-nvhpc.yml

@@ -50,7 +50,7 @@ jobs:
           export OMPI_FC=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin/nvfortran
           export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/cuda/12.2/lib64:/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/lib
           export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/comm_libs/openmpi4/bin:/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/compilers/bin:$PATH        
-          cmake -B build  -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF -DHDF5_ENABLE_PARALLEL:BOOL=ON -DHDF5_BUILD_FORTRAN:BOOL=ON 
+          cmake -B build  -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF -DHDF5_ENABLE_PARALLEL:BOOL=ON -DHDF5_BUILD_FORTRAN:BOOL=ON
           cat build/CMakeCache.txt
           cmake --build build
           ctest --test-dir build --output-on-failure        

.github/workflows/main-auto-par.yml

@@ -54,6 +54,7 @@ jobs:
             --with-default-api-version=v114 \
             --enable-shared \
             --enable-parallel \
+            --enable-subfiling-vfd \
             --disable-cxx \
             --disable-fortran \
             --disable-java \
@@ -111,6 +112,7 @@ jobs:
             --with-default-api-version=v114 \
             --enable-shared \
             --enable-parallel \
+            --enable-subfiling-vfd \
             --disable-cxx \
             --disable-fortran \
             --disable-java \

c++/src/H5DcreatProp.cpp

@@ -368,7 +368,7 @@ DSetCreatPropList::setFilter(H5Z_filter_t filter_id, unsigned int flags, size_t
 ///\exception   H5::PropListIException
 ///\par Description
 ///             Deletes a filter from the dataset creation property list;
-///             deletes all filters if \a filter_id is \c H5Z_FILTER_NONE.
+///             deletes all filters if \a filter_id is \c H5Z_FILTER_ALL.
 //--------------------------------------------------------------------------
 void
 DSetCreatPropList::removeFilter(H5Z_filter_t filter_id) const

configure.ac

@@ -4206,6 +4206,11 @@ AC_CONFIG_FILES([Makefile
                  hl/fortran/examples/run-hlfortran-ex.sh])
 
 AC_CONFIG_FILES([utils/subfiling_vfd/h5fuse.sh], [chmod +x utils/subfiling_vfd/h5fuse.sh])
+if test -n "$TESTPARALLEL"; then
+  if test "X$SUBFILING_VFD" = "Xyes"; then
+    AC_CONFIG_LINKS([testpar/h5fuse.sh:utils/subfiling_vfd/h5fuse.sh])
+  fi
+fi
 
 AC_CONFIG_COMMANDS([.classes], [], [$MKDIR_P java/src/.classes;
                 $MKDIR_P java/test/.classes;

doxygen/Doxyfile.in

@@ -913,35 +913,6 @@ USE_HTAGS              = NO
 
 VERBATIM_HEADERS       = NO
 
-# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
-# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
-# cost of reduced performance. This can be particularly helpful with template
-# rich C++ code for which doxygen's built-in parser lacks the necessary type
-# information.
-# Note: The availability of this option depends on whether or not doxygen was
-# generated with the -Duse_libclang=ON option for CMake.
-# The default value is: NO.
-
-CLANG_ASSISTED_PARSING = NO
-
-# If clang assisted parsing is enabled you can provide the compiler with command
-# line options that you would normally use when invoking the compiler. Note that
-# the include paths will already be set by doxygen for the files and directories
-# specified with INPUT and INCLUDE_PATH.
-# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
-
-CLANG_OPTIONS          =
-
-# If clang assisted parsing is enabled you can provide the clang parser with the
-# path to the compilation database (see:
-# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) used when the files
-# were built. This is equivalent to specifying the "-p" option to a clang tool,
-# such as clang-check. These options will then be passed to the parser.
-# Note: The availability of this option depends on whether or not doxygen was
-# generated with the -Duse_libclang=ON option for CMake.
-
-CLANG_DATABASE_PATH    =
-
 #---------------------------------------------------------------------------
 # Configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
@@ -1080,15 +1051,6 @@ HTML_COLORSTYLE_SAT    = 100
 
 HTML_COLORSTYLE_GAMMA  = 80
 
-# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-# page will contain the date and time when the page was generated. Setting this
-# to YES can help to show when doxygen was last run and thus if the
-# documentation is up to date.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_TIMESTAMP         = YES
-
 # If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
 # documentation will contain a main index with vertical navigation menus that
 # are dynamically created via JavaScript. If disabled, the navigation index will

doxygen/dox/ExamplesAPI.dox

@@ -7,7 +7,7 @@ Navigate back: \ref index "Main" / \ref GettingStarted
 The C, FORTRAN and Java examples below point to the examples in the hdf5-examples github repository. Examples for older versions of HDF5
 are handled by setting the appropriate USE_API_xxx definition. HDF5-1.6 examples are in a "16"-named subdirectory.
 
-The Java examples are in the HDF5-1.10 source code, and the Java Object package examples are in the HDFView source.
+The Java examples are in the develop source code, and the Java Object package examples are in the HDFView source.
 <em>Please note that you must comment out the "package" statement at the top when downloading a Java Object example individually.</em>
 
 The MATLAB and Python examples were generously provided by a user and are not tested.

fortran/src/H5Aff.F90

@@ -1131,6 +1131,9 @@ END FUNCTION H5Aopen_by_idx
     attr_id = INT(H5Aopen_by_idx(loc_id, c_obj_name, INT(idx_type, C_INT), INT(order, C_INT), n, &
          aapl_id_default, lapl_id_default), HID_T)
 
+    hdferr = 0
+    IF(attr_id.LT.0) hdferr = -1
+
   END SUBROUTINE h5aopen_by_idx_f
 
 !>

fortran/testpar/CMakeTests.cmake

@@ -16,4 +16,4 @@
 ##############################################################################
 ##############################################################################
 add_test (NAME MPI_TEST_FORT_parallel_test COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:parallel_test> ${MPIEXEC_POSTFLAGS})
-add_test (NAME MPI_TEST_FORT_subfiling_test COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:subfiling_test> ${MPIEXEC_POSTFLAGS})
+add_test (NAME MPI_TEST_FORT_subfiling_test COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:subfiling_test> ${MPIEXEC_POSTFLAGS})

java/src/hdf/hdf5lib/H5.java

@@ -8607,7 +8607,7 @@ public synchronized static native boolean H5Pall_filters_avail(long dcpl_id)
      * @ingroup JH5P
      *
      * H5Premove_filter deletes a filter from the dataset creation property list;
-     *                  deletes all filters if filter is H5Z_FILTER_NONE
+     *                  deletes all filters if filter is H5Z_FILTER_ALL
      *
      * @param obj_id
      *            IN: Property list identifier.

release_docs/RELEASE.txt

@@ -240,6 +240,10 @@ New Features
 
     Fortran Library:
     ----------------
+
+    - Fixed an uninitialized error return value for hdferr
+      to return the error state of the h5aopen_by_idx_f API.
+
     - Added h5pget_vol_cap_flags_f and related Fortran VOL
       capability definitions.
 

src/H5FDsubfiling/H5FDioc.c

@@ -32,6 +32,8 @@
 #include "H5MMprivate.h"  /* Memory management        */
 #include "H5Pprivate.h"   /* Property lists           */
 
+#define CANBE_UNUSED(X) (void)(X)
+
 /* The driver identification number, initialized at runtime */
 static hid_t H5FD_IOC_g = H5I_INVALID_HID;
 
@@ -1223,6 +1225,7 @@ H5FD__ioc_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS
     H5FD_IOC_LOG_CALL(__func__);
 
     assert(file && file->pub.cls);
+    CANBE_UNUSED(file);
     assert(buf);
 
     /* Check for overflow conditions */

src/H5FDsubfiling/H5FDsubfile_int.c

@@ -347,6 +347,7 @@ H5FD__subfiling__get_real_eof(hid_t context_id, int64_t *logical_eof_ptr)
 
         assert(ioc_rank >= 0);
         assert(ioc_rank < n_io_concentrators);
+        CANBE_UNUSED(ioc_rank);
         assert(sf_eofs[i] == -1);
 
         sf_eofs[i] = recv_msg[(3 * i) + 1];

src/H5FDsubfiling/H5FDsubfiling_priv.h

@@ -63,4 +63,6 @@ H5_DLL herr_t H5FD__subfiling__get_real_eof(hid_t context_id, int64_t *logical_e
 }
 #endif
 
+#define CANBE_UNUSED(X) (void)(X)
+
 #endif /* H5FDsubfiling_priv_H */

src/H5FDsubfiling/H5subfiling_common.c

@@ -1365,7 +1365,8 @@ init_app_layout(sf_topology_t *app_topology, MPI_Comm comm, MPI_Comm node_comm)
         if (app_layout->layout[i].node_local_rank == 0)
             app_layout->node_count++;
 
-    assert(app_layout->node_count > 0);
+    if (app_layout->node_count <= 0)
+        H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_CANTGET, FAIL, "node count less than or equal to zero");
 
     if (NULL ==
         (app_layout->node_ranks = malloc((size_t)app_layout->node_count * sizeof(*app_layout->node_ranks))))

src/H5Pocpl.c

@@ -1001,7 +1001,7 @@ H5P_filter_in_pline(H5P_genplist_t *plist, H5Z_filter_t id)
  * Function: H5Premove_filter
  *
  * Purpose: Deletes a filter from the dataset creation property list;
- *  deletes all filters if FILTER is H5Z_FILTER_NONE
+ *  deletes all filters if FILTER is H5Z_FILTER_ALL
  *
  * Return: Non-negative on success/Negative on failure
  *

src/H5Z.c

@@ -1568,7 +1568,7 @@ H5Z_all_filters_avail(const H5O_pline_t *pline)
  * Function: H5Z_delete
  *
  * Purpose:  Delete filter FILTER from pipeline PLINE;
- *           deletes all filters if FILTER is H5Z_FILTER_NONE
+ *           deletes all filters if FILTER is H5Z_FILTER_ALL
  *
  * Return:   Non-negative on success
  *           Negative on failure

test/testframe.c

@@ -167,7 +167,7 @@ TestUsage(void)
     print_func("verbose   controls the amount of information displayed\n");
     print_func("exclude   to exclude tests by name\n");
     print_func("only      to name tests which should be run\n");
-    print_func("begin     start at the name of the test givin\n");
+    print_func("begin     start at the name of the test given\n");
     print_func("summary   prints a summary of test results at the end\n");
     print_func("cleanoff  does not delete *.hdf files after execution of tests\n");
     print_func("help      print out this information\n");

testpar/t_init_term.c

@@ -37,11 +37,9 @@ main(int argc, char **argv)
 
     MPI_Finalize();
 
-    nerrors += GetTestNumErrs();
-
     /* test if we can initialize the library with MPI being finalized
        and create a file serially */
-    H5open();
+    VRFY((H5open() >= 0), "H5open succeeded");
 
     if (mpi_rank == 0) {
         char  filename[1024];
@@ -54,7 +52,7 @@ main(int argc, char **argv)
         file_id = -1;
     }
 
-    H5close();
+    VRFY((H5close() >= 0), "H5close succeeded");
 
     if (MAINPROCESS) {
         if (0 == nerrors)

testpar/t_pread.c

@@ -36,7 +36,7 @@ const char *FILENAMES[NFILENAME + 1] = {"reloc_t_pread_data_file", "reloc_t_prea
 
 bool               pass             = true;
 static const char *random_hdf5_text = "Now is the time for all first-time-users of HDF5 to read their \
-manual or go thru the tutorials!\n\
+manual or go through the tutorials!\n\
 While you\'re at it, now is also the time to read up on MPI-IO.";
 
 static const char *hitchhiker_quote = "A common mistake that people make when trying to design something\n\
@@ -359,7 +359,7 @@ generate_test_file(MPI_Comm comm, int mpi_rank, int group_id)
 
     /* Add a userblock to the head of the datafile.
      * We will use this to for a functional test of the
-     * file open optimization.  This is superblock
+     * file open optimization.  This superblock
      * relocation is done by the rank 0 process associated
      * with the communicator being used.  For test 1, we
      * utilize MPI_COMM_WORLD, so group_rank 0 is the
@@ -464,7 +464,7 @@ generate_test_file(MPI_Comm comm, int mpi_rank, int group_id)
  *
  *              The global MPI rank is used for reading and
  *              writing data for process specific data in the
- *              dataset.  We do this rather simplisticly, i.e.
+ *              dataset.  We do this rather simplistically, i.e.
  *               rank 0:  writes/reads 0-9999
  *               rank 1:  writes/reads 1000-1999
  *               rank 2:  writes/reads 2000-2999
@@ -1032,7 +1032,7 @@ test_parallel_read(MPI_Comm comm, int mpi_rank, int mpi_size, int group_id)
  *
  *              The test consists of creating two separate HDF datasets
  *              in which random text is inserted at the start of each
- *              file using the 'j5jam' application.  This forces the
+ *              file using the 'h5jam' application.  This forces the
  *              HDF5 file superblock to a non-zero offset.
  *              Having created the two independent files, we create two
  *              non-overlapping MPI groups, each of which is then tasked
@@ -1055,13 +1055,13 @@ main(int argc, char **argv)
     MPI_Comm group_comm = MPI_COMM_NULL;
 
     /* I don't believe that argv[0] can ever be NULL.
-     * It should thus be safe to dup and save as a check
-     * for cmake testing. Note that in our Cmake builds,
+     * It should thus be safe to duplicate and save as a check
+     * for CMake testing. Note that in our CMake builds,
      * all executables are located in the same directory.
      * We assume (but we'll check) that the h5jam utility
      * is in the directory as this executable.  If that
      * isn't true, then we can use a relative path that
-     * should be valid for the autotools environment.
+     * should be valid for the Autotools environment.
      */
     test_argv0 = strdup(argv[0]);