Merge pull request #1220 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:1.10/master to 1.10/master

* commit '21eef8a98ee6949c69d79c6c4d87fc8e4e38dc29': (354 commits)
  Commit version with new release date.
  Add example packaging option and fix html5 issues
  Commit version with new release date.
  Commit files changed by autogen.sh.
  Merge pull request #1208 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to hdf5_1_10
  Merge pull request #1207 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10
  Merge pull request #1203 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10
  Commit version with new release date. Commit new generated H5version.h including #defines for H5_USE_110_API.
  Correct nested c-style comment.
  Merge pull request #1197 in HDFFV/hdf5 from ~BYRN/hdf5_merge_adb:hdf5_1_10 to hdf5_1_10
  Merge pull request #1194 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:hdf5_1_10 to hdf5_1_10
  Updated the H5Dread/write_chunk() release note.
  Added a release note for the H5Dread/write_chunk() API calls.
  Update Intel Fortran version for Windows 10.
  RELEASE.txt updates. Version change for 1.10.3 release.
  Revised entry on CVE issues
  Added notes about CVE issues
  Update version for HDF5 1.10.3 release.
  Add placeholder for performance improvement in RELEASE.txt
  updated fortran fixes
  ...

4 files changed, 27 insertions, 52 deletions

diff --git a/tools/src/h5jam/CMakeLists.txt b/tools/src/h5jam/CMakeLists.txt
index 59caf44..c455b2f 100644
--- a/tools/src/h5jam/CMakeLists.txt
+++ b/tools/src/h5jam/CMakeLists.txt
@@ -1,23 +1,20 @@
 cmake_minimum_required (VERSION 3.10)
-PROJECT (HDF5_TOOLS_SRC_H5JAM)
-
-#-----------------------------------------------------------------------------
-# Setup include Directories
-#-----------------------------------------------------------------------------
-INCLUDE_DIRECTORIES (${HDF5_TOOLS_DIR}/lib)
+project (HDF5_TOOLS_SRC_H5JAM C)
 
 # --------------------------------------------------------------------
 # Add the h5jam executables
 # --------------------------------------------------------------------
 add_executable (h5jam ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5jam.c)
-TARGET_C_PROPERTIES (h5jam STATIC " " " ")
-target_link_libraries (h5jam  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+target_include_directories(h5jam PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+TARGET_C_PROPERTIES (h5jam STATIC)
+target_link_libraries (h5jam PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
 set_target_properties (h5jam PROPERTIES FOLDER tools)
 set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5jam")
 
 add_executable (h5unjam ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5unjam.c)
-TARGET_C_PROPERTIES (h5unjam STATIC " " " ")
-target_link_libraries (h5unjam  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+target_include_directories(h5unjam PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+TARGET_C_PROPERTIES (h5unjam STATIC)
+target_link_libraries (h5unjam PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
 set_target_properties (h5unjam PROPERTIES FOLDER tools)
 set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5unjam")
 
diff --git a/tools/src/h5jam/Makefile.in b/tools/src/h5jam/Makefile.in
index 49770fe..2e21773 100644
--- a/tools/src/h5jam/Makefile.in
+++ b/tools/src/h5jam/Makefile.in
@@ -544,6 +544,7 @@ JAVA_PATH_NAME = @JAVA_PATH_NAME@
 JAVA_VERSION = @JAVA_VERSION@
 JNIFLAGS = @JNIFLAGS@
 JUNIT = @JUNIT@
+LARGE_PARALLEL_IO = @LARGE_PARALLEL_IO@
 LD = @LD@
 LDFLAGS = @LDFLAGS@
 LIBOBJS = @LIBOBJS@
@@ -591,6 +592,7 @@ PAC_FORTRAN_NATIVE_REAL_KIND = @PAC_FORTRAN_NATIVE_REAL_KIND@
 PAC_FORTRAN_NATIVE_REAL_SIZEOF = @PAC_FORTRAN_NATIVE_REAL_SIZEOF@
 PAC_FORTRAN_NUM_INTEGER_KINDS = @PAC_FORTRAN_NUM_INTEGER_KINDS@
 PARALLEL = @PARALLEL@
+PARALLEL_FILTERED_WRITES = @PARALLEL_FILTERED_WRITES@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 PROFILING = @PROFILING@
 RANLIB = @RANLIB@
diff --git a/tools/src/h5jam/h5jam.c b/tools/src/h5jam/h5jam.c
index cc5fcdc..01ba4af 100644
--- a/tools/src/h5jam/h5jam.c
+++ b/tools/src/h5jam/h5jam.c
@@ -56,11 +56,6 @@ static struct long_options l_opts[] = {
  * Purpose:     Print the usage message
  *
  * Return:      void
- *
- * Programmer:
- *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 static void
@@ -120,7 +115,6 @@ usage (const char *prog)
  * Purpose:     Shutdown and call exit()
  *
  * Return:      Does not return
- *
  *-------------------------------------------------------------------------
  */
 static void
@@ -144,13 +138,7 @@ leave(int ret)
  * Purpose:     Parse the command line for the h5dumper.
  *
  * Return:      Success:
- *
  *              Failure:    Exits program with EXIT_FAILURE value.
- *
- * Programmer:
- *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 
@@ -199,7 +187,6 @@ parse_command_line (int argc, const char *argv[])
  *
  * Return:      Success:    0
  *              Failure:    1
- *
  *-------------------------------------------------------------------------
  */
 int
@@ -238,7 +225,7 @@ main (int argc, const char *argv[])
 
     if (ub_file == NULL) {
         /* no user block */
-        error_msg("missing arguemnt for -u <user_file>.\n");
+        error_msg("missing argument for -u <user_file>.\n");
         help_ref_msg(stderr);
         leave (EXIT_FAILURE);
     }
@@ -252,7 +239,7 @@ main (int argc, const char *argv[])
     }
 
     if (input_file == NULL) {
-        error_msg("missing arguemnt for -i <HDF5 file>.\n");
+        error_msg("missing argument for -i <HDF5 file>.\n");
         help_ref_msg(stderr);
         leave (EXIT_FAILURE);
     }
@@ -419,7 +406,6 @@ main (int argc, const char *argv[])
  *
  * Return:      Success:    last byte written in the output.
  *              Failure:    Exits program with EXIT_FAILURE value.
- *
  *-------------------------------------------------------------------------
  */
 hsize_t
@@ -451,7 +437,8 @@ copy_some_to_file(int infid, int outfid, hsize_t startin, hsize_t startout,
         } /* end if */
 
         howmuch = (ssize_t)sbuf.st_size;
-    } else {
+    }
+    else {
         howmuch = limit;
     } /* end if */
 
@@ -464,7 +451,8 @@ copy_some_to_file(int infid, int outfid, hsize_t startin, hsize_t startout,
     if (howmuch > 512) {
         to = toend - 512;
         from = fromend - 512;
-    } else {
+    }
+    else {
         to = toend - howmuch;
         from = fromend - howmuch;
     } /* end if */
@@ -475,7 +463,8 @@ copy_some_to_file(int infid, int outfid, hsize_t startin, hsize_t startout,
 
         if (howmuch > 512) {
             nchars = HDread(infid, buf, (unsigned) 512);
-        } else {
+        }
+        else {
             nchars = HDread(infid, buf, (unsigned)howmuch);
         } /* end if */
 
@@ -494,7 +483,8 @@ copy_some_to_file(int infid, int outfid, hsize_t startin, hsize_t startout,
         if(howmuch > 512) {
             to -= nchars;
             from -= nchars;
-        } else {
+        }
+        else {
             to -= howmuch;
             from -= howmuch;
         } /* end if */
@@ -508,15 +498,11 @@ copy_some_to_file(int infid, int outfid, hsize_t startin, hsize_t startout,
  * Function:    compute_user_block_size
  *
  * Purpose:     Find the offset of the HDF5 header after the user block:
- *                 align at 0, 512, 1024, etc.
- *      ublock_size: the size of the user block (bytes).
+ *              align at 0, 512, 1024, etc.
+ *              ublock_size: the size of the user block (bytes).
  *
- * Return:      Success:    the location of the header == the size of the
- *        padded user block.
+ * Return:      Success:    the location of the header == the size of the padded user block.
  *              Failure:    none
- *
- * Return:      Success:    last byte written in the output.
- *              Failure:    Exits program with EXIT_FAILURE value.
  *-------------------------------------------------------------------------
  */
 H5_ATTR_CONST hsize_t
@@ -533,11 +519,12 @@ compute_user_block_size(hsize_t ublock_size)
     return where;
 } /* end compute_user_block_size() */
 
-/*
+/*-------------------------------------------------------------------------
  *  Write zeroes to fill the file from 'where' to 512, 1024, etc. bytes.
  *
  *  Sets new_where to the size of the padded file and
  *  returns SUCCEED/FAIL.
+ *-------------------------------------------------------------------------
  */
 herr_t
 write_pad(int ofile, hsize_t old_where, hsize_t *new_where)
diff --git a/tools/src/h5jam/h5unjam.c b/tools/src/h5jam/h5unjam.c
index 4e9798e..ffe2aca 100644
--- a/tools/src/h5jam/h5unjam.c
+++ b/tools/src/h5jam/h5unjam.c
@@ -56,11 +56,6 @@ static struct long_options l_opts[] = {
  * Purpose:     Print the usage message
  *
  * Return:      void
- *
- * Programmer:
- *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 static void
@@ -124,9 +119,7 @@ usage(const char *prog)
  * Purpose:     Parse the command line for the h5dumper.
  *
  * Return:      Success:    EXIT_SUCCESS;
- *
  *              Failure:    Exits function with EXIT_FAILURE value.
- *
  *-------------------------------------------------------------------------
  */
 static int
@@ -199,11 +192,6 @@ done:
  *
  * Return:      Success:    0
  *              Failure:    1
- *
- * Programmer:
- *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 int
@@ -235,7 +223,7 @@ main(int argc, const char *argv[])
 
     if (input_file == NULL) {
         /* no user block  */
-        error_msg("missing arguemnt for HDF5 file input.\n");
+        error_msg("missing argument for HDF5 file input.\n");
         help_ref_msg(stderr);
         h5tools_setstatus(EXIT_FAILURE);
         goto done;
@@ -336,11 +324,12 @@ done:
     return h5tools_getstatus();
 }
 
-/*
+/*-------------------------------------------------------------------------
  *  Copy 'how_much' bytes from the input file to the output file,
  *  starting at byte 'where' in the input file.
  *
  *  Returns 0 on success, -1 on failure.
+ *-------------------------------------------------------------------------
  */
 herr_t
 copy_to_file( FILE *infid, FILE *ofid, ssize_t _where, ssize_t show_much )