Hdf5 1 12 parallel compression merge (#1529)

* Fix the function cast error in H5Dchunk.c and activate (#1170)

`-Werror=cast-function-type`.  Again.

* Parallel Compression improvements (#1302)

* Fix for parallel compression examples on Windows (#1459)

* Parallel compression adjustments for HDF5 1.12

* Committing clang-format changes

Co-authored-by: David Young <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

CMakeLists.txt

@@ -708,10 +708,14 @@ if (HDF5_ENABLE_PARALLEL)
 
     # Used by Parallel Compression feature
     set (PARALLEL_FILTERED_WRITES ON)
-    CHECK_SYMBOL_EXISTS (MPI_Mprobe "mpi.h" H5_HAVE_MPI_Mprobe)
-    CHECK_SYMBOL_EXISTS (MPI_Imrecv "mpi.h" H5_HAVE_MPI_Imrecv)
-    if (NOT H5_HAVE_MPI_Mprobe OR NOT H5_HAVE_MPI_Imrecv)
-      message (WARNING "The MPI_Mprobe and/or MPI_Imrecv functions could not be located.
+    CHECK_SYMBOL_EXISTS (MPI_Ibarrier "mpi.h" H5_HAVE_MPI_Ibarrier)
+    CHECK_SYMBOL_EXISTS (MPI_Issend "mpi.h" H5_HAVE_MPI_Issend)
+    CHECK_SYMBOL_EXISTS (MPI_Iprobe "mpi.h" H5_HAVE_MPI_Iprobe)
+    CHECK_SYMBOL_EXISTS (MPI_Irecv "mpi.h" H5_HAVE_MPI_Irecv)
+    if (H5_HAVE_MPI_Ibarrier AND H5_HAVE_MPI_Issend AND H5_HAVE_MPI_Iprobe AND H5_HAVE_MPI_Irecv)
+      set (H5_HAVE_PARALLEL_FILTERED_WRITES 1)
+    else ()
+      message (WARNING "The MPI_Ibarrier/MPI_Issend/MPI_Iprobe/MPI_Irecv functions could not be located.
                Parallel writes of filtered data will be disabled.")
       set (PARALLEL_FILTERED_WRITES OFF)
     endif ()

MANIFEST

@@ -320,6 +320,8 @@
 ./examples/h5_ref2reg_deprec.c
 ./examples/h5_shared_mesg.c
 ./examples/ph5example.c
+./examples/ph5_filtered_writes.c
+./examples/ph5_filtered_writes_no_sel.c
 ./examples/h5_vds.c
 ./examples/h5_vds-exc.c
 ./examples/h5_vds-exclim.c

config/cmake/H5pubconf.h.in

@@ -307,6 +307,9 @@
 /* Define if we have parallel support */
 #cmakedefine H5_HAVE_PARALLEL @H5_HAVE_PARALLEL@
 
+/* Define if we have support for writing to filtered datasets in parallel */
+#cmakedefine H5_HAVE_PARALLEL_FILTERED_WRITES @H5_HAVE_PARALLEL_FILTERED_WRITES@
+
 /* Define if both pread and pwrite exist. */
 #cmakedefine H5_HAVE_PREADWRITE @H5_HAVE_PREADWRITE@
 

config/gnu-warnings/error-8

@@ -1,7 +1,4 @@
-# NOTE: src/ files are not compatible with these warnings as errors
-#     src/H5Dchunk.c
-#       -Werror=cast-function-type
--Wcast-function-type
+-Werror=cast-function-type
 #
 # For GCC 8, promote maybe-initialized warnings to an error.  GCC 8
 # reports 0 maybe-uninitialized warnings where earlier versions

configure.ac

@@ -3098,28 +3098,31 @@ if test -n "$PARALLEL"; then
   fi
 
   ## ----------------------------------------------------------------------
-  ## Check for the MPI-3 functions necessary for the Parallel Compression
+  ## Check for the MPI functions necessary for the Parallel Compression
   ## feature. If these are not present, issue a warning that Parallel
   ## Compression will be disabled.
   ##
-  AC_MSG_CHECKING([for MPI_Mprobe and MPI_Imrecv functions])
+  AC_MSG_CHECKING([for MPI_Ibarrier/MPI_Issend/MPI_Iprobe/MPI_Irecv functions])
 
   AC_LINK_IFELSE(
       [AC_LANG_PROGRAM(
           [[
               #include <mpi.h>
           ]],
           [[
-              MPI_Message message;
+              int flag;
               MPI_Init(0, (void *) 0);
-              MPI_Mprobe(0, 0, 0, &message, (void *) 0);
-              MPI_Imrecv((void *) 0, 0, 0, (void *) 0, (void *) 0);
+              MPI_Ibarrier(0, (void *) 0);
+              MPI_Issend((void *) 0, 0, 0, 0, 0, 0, (void *) 0);
+              MPI_Iprobe(0, 0, 0, &flag, (void *) 0);
+              MPI_Irecv((void *) 0, 0, 0, 0, 0, 0, (void *) 0);
           ]]
       )],
       [AC_MSG_RESULT([yes])
-       PARALLEL_FILTERED_WRITES=yes],
+       PARALLEL_FILTERED_WRITES=yes
+       AC_DEFINE([HAVE_PARALLEL_FILTERED_WRITES], [1], [Define if we have support for writing to filtered datasets in parallel])],
       [AC_MSG_RESULT([no])
-       AC_MSG_WARN([A simple MPI program using the MPI_Mprobe and MPI_Imrecv functions could not be compiled and linked.
+       AC_MSG_WARN([A simple MPI program using the MPI_Ibarrier, MPI_Issend, MPI_Iprobe and MPI_Irecv functions could not be compiled and linked.
                     Parallel writes of filtered data will be disabled.])
        PARALLEL_FILTERED_WRITES=no]
   )

examples/CMakeLists.txt

@@ -42,6 +42,14 @@ set (examples
     h5_vds-percival-unlim-maxmin
 )
 
+if (H5_HAVE_PARALLEL)
+  set (parallel_examples
+    ph5example
+    ph5_filtered_writes
+    ph5_filtered_writes_no_sel
+  )
+endif ()
+
 foreach (example ${examples})
   add_executable (${example} ${HDF5_EXAMPLES_SOURCE_DIR}/${example}.c)
   target_include_directories (${example} PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
@@ -63,23 +71,25 @@ foreach (example ${examples})
 endforeach ()
 
 if (H5_HAVE_PARALLEL)
-  add_executable (ph5example ${HDF5_EXAMPLES_SOURCE_DIR}/ph5example.c)
-  target_include_directories (ph5example PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
-  if (NOT BUILD_SHARED_LIBS)
-    TARGET_C_PROPERTIES (ph5example STATIC)
-    target_link_libraries (ph5example PRIVATE ${HDF5_LIB_TARGET} ${MPI_C_LIBRARIES})
-  else ()
-    TARGET_C_PROPERTIES (ph5example SHARED)
-    target_link_libraries (ph5example PRIVATE ${HDF5_LIBSH_TARGET} ${MPI_C_LIBRARIES})
-  endif ()
-  set_target_properties (ph5example PROPERTIES FOLDER examples)
+  foreach (parallel_example ${parallel_examples})
+    add_executable (${parallel_example} ${HDF5_EXAMPLES_SOURCE_DIR}/${parallel_example}.c)
+    target_include_directories (${parallel_example} PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+    if (NOT BUILD_SHARED_LIBS)
+      TARGET_C_PROPERTIES (${parallel_example} STATIC)
+      target_link_libraries (${parallel_example} PRIVATE ${HDF5_LIB_TARGET} ${MPI_C_LIBRARIES})
+    else ()
+      TARGET_C_PROPERTIES (${parallel_example} SHARED)
+      target_link_libraries (${parallel_example} PRIVATE ${HDF5_LIBSH_TARGET} ${MPI_C_LIBRARIES})
+    endif ()
+    set_target_properties (${parallel_example} PROPERTIES FOLDER examples)
 
-  #-----------------------------------------------------------------------------
-  # Add Target to clang-format
-  #-----------------------------------------------------------------------------
-  if (HDF5_ENABLE_FORMATTERS)
-    clang_format (HDF5_EXAMPLES_ph5example_FORMAT ph5example)
-  endif ()
+    #-----------------------------------------------------------------------------
+    # Add Target to clang-format
+    #-----------------------------------------------------------------------------
+    if (HDF5_ENABLE_FORMATTERS)
+      clang_format (HDF5_EXAMPLES_${parallel_example}_FORMAT ${parallel_example})
+    endif ()
+  endforeach ()
 endif ()
 
 if (BUILD_TESTING AND HDF5_TEST_EXAMPLES)

examples/CMakeTests.cmake

@@ -101,22 +101,26 @@ if (H5_HAVE_PARALLEL AND HDF5_TEST_PARALLEL AND NOT WIN32)
   # Ensure that 24 is a multiple of the number of processes.
   # The number 24 corresponds to SPACE1_DIM1 and SPACE1_DIM2 defined in ph5example.c
   math(EXPR NUMPROCS "24 / ((24 + ${MPIEXEC_MAX_NUMPROCS} - 1) / ${MPIEXEC_MAX_NUMPROCS})")
-  if (HDF5_ENABLE_USING_MEMCHECKER)
-    add_test (NAME MPI_TEST_EXAMPLES-ph5example COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:ph5example> ${MPIEXEC_POSTFLAGS})
-  else ()
-    add_test (NAME MPI_TEST_EXAMPLES-ph5example COMMAND "${CMAKE_COMMAND}"
-        -D "TEST_PROGRAM=${MPIEXEC_EXECUTABLE};${MPIEXEC_NUMPROC_FLAG};${NUMPROCS};${MPIEXEC_PREFLAGS};$<TARGET_FILE:ph5example>;${MPIEXEC_POSTFLAGS}"
-        -D "TEST_ARGS:STRING="
-        -D "TEST_EXPECT=0"
-        -D "TEST_OUTPUT=ph5example.out"
-        -D "TEST_REFERENCE:STRING=PHDF5 tests finished with no errors"
-        -D "TEST_FILTER:STRING=PHDF5 tests finished with no errors"
-        -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
-        -P "${HDF_RESOURCES_EXT_DIR}/grepTest.cmake"
-    )
-  endif ()
-  if (last_test)
-    set_tests_properties (MPI_TEST_EXAMPLES-ph5example PROPERTIES DEPENDS ${last_test})
-  endif ()
-  set (last_test "MPI_TEST_EXAMPLES-ph5example")
+
+  foreach (parallel_example ${parallel_examples})
+    if (HDF5_ENABLE_USING_MEMCHECKER)
+      add_test (NAME MPI_TEST_EXAMPLES-${parallel_example} COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:${parallel_example}> ${MPIEXEC_POSTFLAGS})
+    else ()
+      add_test (NAME MPI_TEST_EXAMPLES-${parallel_example} COMMAND "${CMAKE_COMMAND}"
+          -D "TEST_PROGRAM=${MPIEXEC_EXECUTABLE};${MPIEXEC_NUMPROC_FLAG};${NUMPROCS};${MPIEXEC_PREFLAGS};$<TARGET_FILE:${parallel_example}>;${MPIEXEC_POSTFLAGS}"
+          -D "TEST_ARGS:STRING="
+          -D "TEST_EXPECT=0"
+          -D "TEST_SKIP_COMPARE=TRUE"
+          -D "TEST_OUTPUT=${parallel_example}.out"
+          -D "TEST_REFERENCE:STRING=PHDF5 example finished with no errors"
+          #-D "TEST_FILTER:STRING=PHDF5 tests finished with no errors"
+          -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
+          -P "${HDF_RESOURCES_EXT_DIR}/grepTest.cmake"
+      )
+    endif ()
+    if (last_test)
+      set_tests_properties (MPI_TEST_EXAMPLES-${parallel_example} PROPERTIES DEPENDS ${last_test})
+    endif ()
+    set (last_test "MPI_TEST_EXAMPLES-${parallel_example}")
+  endforeach ()
 endif ()

examples/Makefile.am

@@ -20,7 +20,7 @@
 include $(top_srcdir)/config/commence.am
 
 if BUILD_PARALLEL_CONDITIONAL
-  EXAMPLE_PROG_PARA = ph5example
+  EXAMPLE_PROG_PARA = ph5example ph5_filtered_writes ph5_filtered_writes_no_sel
 endif
 
 INSTALL_SCRIPT_FILES = run-c-ex.sh
@@ -50,7 +50,7 @@ INSTALL_FILES = h5_write.c h5_read.c h5_extend_write.c h5_chunk_read.c h5_compou
             h5_group.c h5_select.c h5_attribute.c h5_mount.c h5_drivers.c \
             h5_reference_deprec.c h5_ref_extern.c h5_ref_compat.c h5_ref2reg_deprec.c \
             h5_extlink.c h5_elink_unix2win.c h5_shared_mesg.c h5_debug_trace.c \
-            ph5example.c \
+            ph5example.c ph5_filtered_writes.c ph5_filtered_writes_no_sel.c \
             h5_vds.c h5_vds-exc.c h5_vds-exclim.c h5_vds-eiger.c h5_vds-simpleIO.c \
             h5_vds-percival.c h5_vds-percival-unlim.c h5_vds-percival-unlim-maxmin.c
 
@@ -119,6 +119,8 @@ h5_reference_deprec: $(srcdir)/h5_reference_deprec.c
 h5_ref2reg_deprec: $(srcdir)/h5_ref2reg_deprec.c
 h5_drivers: $(srcdir)/h5_drivers.c
 ph5example: $(srcdir)/ph5example.c
+ph5_filtered_writes: $(srcdir)/ph5_filtered_writes.c
+ph5_filtered_writes_no_sel: $(srcdir)/ph5_filtered_writes_no_sel.c 
 h5_dtransform: $(srcdir)/h5_dtransform.c
 h5_extlink: $(srcdir)/h5_extlink.c $(EXTLINK_DIRS)
 h5_elink_unix2win: $(srcdir)/h5_elink_unix2win.c $(EXTLINK_DIRS)