Merge pull request #1590 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:1.10/master to 1.10/masterhdf5-1_10_5

* commit '6819c11508b0610f222fe3bfe8a19f637bf4319c': (154 commits)
  CMake needs a tar.gz examples file for windows, too.
  Correct file permissions on README.txt.
  Address merge anomalies and incorrect file permissions.
  Update release date in README.txt and RELEASE.txt.
  Revisions to Platforms tested.
  Updated LT_VERS_AGE in config/lt_vers.am due to reinstatement of previously removed symbols, then ran autogen.sh to propagate so number changes and H5E_LOGFAIL_g addition to files checked in on release branch.
  Updated H5err.txt to replace a global variable that was removed during the metadata cache logging changes (to maintain binary compatibility).
  HDFFV-10552,10686 restore H5O_*1 functions
  Minor fix in h5str_sprintf for NULL region references
  Add new files to MANIFEST.
  Update so version numbers. fix 2 typos.
  Update RELEASE.txt for TRILABS-34 and remove unused sections.
  Add script for building HDF5 with CMake on HPC machines that use sbatch. Add README file for inclusion in CMake-hdf5-<version>.tar.gz file. Add updated README_HPC file with cross compile instructions.
  set version to 1.10.5-pre1. Change default build mode to production.
  Merge pull request #1560 in HDFFV/hdf5 from hdf5-1-10-documentation-only to hdf5_1_10_5
  Update HISTORY-1_10.txt and RELEASE.txt files.
  Modify RELEASE.txt in response to PR comments
  Check in files generated by autogen.sh for hdf5_1_10_5 release branch.
  Check in files generated by autogen.sh for hdf5_1_10_5 release branch. 2019/02/16.
  Code improvement
  ...

7 files changed, 140 insertions, 93 deletions

diff --git a/tools/test/h5repack/CMakeLists.txt b/tools/test/h5repack/CMakeLists.txt
index 2a168e9..890d5d2 100644
--- a/tools/test/h5repack/CMakeLists.txt
+++ b/tools/test/h5repack/CMakeLists.txt
@@ -32,45 +32,47 @@ set_target_properties (h5repacktest PROPERTIES FOLDER tools)
 #-----------------------------------------------------------------------------
 # If plugin library tests can be tested
 #-----------------------------------------------------------------------------
-set (HDF5_TOOL_PLUGIN_LIB_CORENAME         "dynlibadd")
-set (HDF5_TOOL_PLUGIN_LIB_NAME             "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_TOOL_PLUGIN_LIB_CORENAME}")
-set (HDF5_TOOL_PLUGIN_LIB_TARGET           ${HDF5_TOOL_PLUGIN_LIB_CORENAME})
-set (HDF5_TOOL_PLUGIN_LIB_VCORENAME        "dynlibvers")
-set (HDF5_TOOL_PLUGIN_LIB_VNAME            "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_TOOL_PLUGIN_LIB_VCORENAME}")
-set (HDF5_TOOL_PLUGIN_LIB_VTARGET          ${HDF5_TOOL_PLUGIN_LIB_VCORENAME})
+if (BUILD_SHARED_LIBS)
+  set (HDF5_TOOL_PLUGIN_LIB_CORENAME         "dynlibadd")
+  set (HDF5_TOOL_PLUGIN_LIB_NAME             "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_TOOL_PLUGIN_LIB_CORENAME}")
+  set (HDF5_TOOL_PLUGIN_LIB_TARGET           ${HDF5_TOOL_PLUGIN_LIB_CORENAME})
+  set (HDF5_TOOL_PLUGIN_LIB_VCORENAME        "dynlibvers")
+  set (HDF5_TOOL_PLUGIN_LIB_VNAME            "${HDF5_EXTERNAL_LIB_PREFIX}${HDF5_TOOL_PLUGIN_LIB_VCORENAME}")
+  set (HDF5_TOOL_PLUGIN_LIB_VTARGET          ${HDF5_TOOL_PLUGIN_LIB_VCORENAME})
 
-add_library (${HDF5_TOOL_PLUGIN_LIB_TARGET} SHARED dynlib_rpk.c)
-target_include_directories(${HDF5_TOOL_PLUGIN_LIB_TARGET} PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
-TARGET_C_PROPERTIES (${HDF5_TOOL_PLUGIN_LIB_TARGET} SHARED)
-target_link_libraries (${HDF5_TOOL_PLUGIN_LIB_TARGET} PRIVATE ${HDF5_TEST_LIB_TARGET})
-H5_SET_LIB_OPTIONS (${HDF5_TOOL_PLUGIN_LIB_TARGET} ${HDF5_TOOL_PLUGIN_LIB_NAME} SHARED "LIB")
+  add_library (${HDF5_TOOL_PLUGIN_LIB_TARGET} SHARED dynlib_rpk.c)
+  target_include_directories(${HDF5_TOOL_PLUGIN_LIB_TARGET} PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  TARGET_C_PROPERTIES (${HDF5_TOOL_PLUGIN_LIB_TARGET} SHARED)
+  target_link_libraries (${HDF5_TOOL_PLUGIN_LIB_TARGET} PRIVATE ${HDF5_TEST_LIB_TARGET})
+  H5_SET_LIB_OPTIONS (${HDF5_TOOL_PLUGIN_LIB_TARGET} ${HDF5_TOOL_PLUGIN_LIB_NAME} SHARED "LIB")
 
-add_library (${HDF5_TOOL_PLUGIN_LIB_VTARGET} SHARED dynlib_vrpk.c)
-target_include_directories(${HDF5_TOOL_PLUGIN_LIB_VTARGET} PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
-TARGET_C_PROPERTIES (${HDF5_TOOL_PLUGIN_LIB_VTARGET} SHARED)
-target_link_libraries (${HDF5_TOOL_PLUGIN_LIB_VTARGET} PRIVATE ${HDF5_TEST_LIB_TARGET})
-H5_SET_LIB_OPTIONS (${HDF5_TOOL_PLUGIN_LIB_VTARGET} ${HDF5_TOOL_PLUGIN_LIB_VNAME} SHARED "LIB")
+  add_library (${HDF5_TOOL_PLUGIN_LIB_VTARGET} SHARED dynlib_vrpk.c)
+  target_include_directories(${HDF5_TOOL_PLUGIN_LIB_VTARGET} PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  TARGET_C_PROPERTIES (${HDF5_TOOL_PLUGIN_LIB_VTARGET} SHARED)
+  target_link_libraries (${HDF5_TOOL_PLUGIN_LIB_VTARGET} PRIVATE ${HDF5_TEST_LIB_TARGET})
+  H5_SET_LIB_OPTIONS (${HDF5_TOOL_PLUGIN_LIB_VTARGET} ${HDF5_TOOL_PLUGIN_LIB_VNAME} SHARED "LIB")
 
-# make plugins dir
-file (MAKE_DIRECTORY "${CMAKE_BINARY_DIR}/plugins")
-#-----------------------------------------------------------------------------
-# Copy plugin library to a plugins folder
-#-----------------------------------------------------------------------------
-add_custom_command (
-    TARGET     ${HDF5_TOOL_PLUGIN_LIB_TARGET}
-    POST_BUILD
-    COMMAND    ${CMAKE_COMMAND}
-    ARGS       -E copy_if_different
-          "$<TARGET_FILE:${HDF5_TOOL_PLUGIN_LIB_TARGET}>"
-          "${CMAKE_BINARY_DIR}/plugins/$<TARGET_FILE_NAME:${HDF5_TOOL_PLUGIN_LIB_TARGET}>"
-)
-add_custom_command (
-    TARGET     ${HDF5_TOOL_PLUGIN_LIB_VTARGET}
-    POST_BUILD
-    COMMAND    ${CMAKE_COMMAND}
-    ARGS       -E copy_if_different
-          "$<TARGET_FILE:${HDF5_TOOL_PLUGIN_LIB_VTARGET}>"
-          "${CMAKE_BINARY_DIR}/plugins/$<TARGET_FILE_NAME:${HDF5_TOOL_PLUGIN_LIB_VTARGET}>"
-)
+  # make plugins dir
+  file (MAKE_DIRECTORY "${CMAKE_BINARY_DIR}/plugins")
+  #-----------------------------------------------------------------------------
+  # Copy plugin library to a plugins folder
+  #-----------------------------------------------------------------------------
+  add_custom_command (
+      TARGET     ${HDF5_TOOL_PLUGIN_LIB_TARGET}
+      POST_BUILD
+      COMMAND    ${CMAKE_COMMAND}
+      ARGS       -E copy_if_different
+            "$<TARGET_FILE:${HDF5_TOOL_PLUGIN_LIB_TARGET}>"
+            "${CMAKE_BINARY_DIR}/plugins/$<TARGET_FILE_NAME:${HDF5_TOOL_PLUGIN_LIB_TARGET}>"
+  )
+  add_custom_command (
+      TARGET     ${HDF5_TOOL_PLUGIN_LIB_VTARGET}
+      POST_BUILD
+      COMMAND    ${CMAKE_COMMAND}
+      ARGS       -E copy_if_different
+            "$<TARGET_FILE:${HDF5_TOOL_PLUGIN_LIB_VTARGET}>"
+            "${CMAKE_BINARY_DIR}/plugins/$<TARGET_FILE_NAME:${HDF5_TOOL_PLUGIN_LIB_VTARGET}>"
+  )
+endif ()
 
 include (CMakeTests.cmake)
diff --git a/tools/test/h5repack/CMakeTests.cmake b/tools/test/h5repack/CMakeTests.cmake
index a063e19..c2a2be7 100644
--- a/tools/test/h5repack/CMakeTests.cmake
+++ b/tools/test/h5repack/CMakeTests.cmake
@@ -16,39 +16,6 @@
 ##############################################################################
 ##############################################################################
 
-  if (HDF5_TEST_VFD)
-    set (VFD_LIST
-        sec2
-        stdio
-        core
-        split
-        multi
-        family
-    )
-
-    if (DIRECT_VFD)
-      set (VFD_LIST ${VFD_LIST} direct)
-    endif ()
-
-    macro (ADD_VFD_TEST vfdname resultcode)
-      add_test (
-        NAME H5REPACK-VFD-${vfdname}-h5repacktest
-        COMMAND "${CMAKE_COMMAND}"
-            -D "TEST_PROGRAM=$<TARGET_FILE:h5repacktest>"
-            -D "TEST_ARGS:STRING="
-            -D "TEST_VFD:STRING=${vfdname}"
-            -D "TEST_EXPECT=${resultcode}"
-            -D "TEST_OUTPUT=h5repacktest"
-            -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
-            -P "${HDF_RESOURCES_DIR}/vfdTest.cmake"
-      )
-      if (NOT "${last_test}" STREQUAL "")
-        set_tests_properties (H5REPACK-VFD-${vfdname}-h5repacktest PROPERTIES DEPENDS ${last_test})
-      endif ()
-      set (last_test "H5REPACK-VFD-${vfdname}-h5repacktest")
-    endmacro ()
-  endif ()
-
   # --------------------------------------------------------------------
   # Copy all the HDF5 files from the source directory into the test directory
   # --------------------------------------------------------------------
@@ -377,7 +344,8 @@
                 -D "TEST_OUTPUT=${resultfile}-${testname}.out"
                 -D "TEST_EXPECT=${resultcode}"
                 -D "TEST_MASK_ERROR=true"
-                -D "TEST_REFERENCE=${resultfile}-${testname}.tst"
+                -D "TEST_REFERENCE=${resultfile}.mty"
+                -D "TEST_ERRREF=${resultfile}-${testname}.tst"
                 -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
         )
         set_tests_properties (H5REPACK_MASK-${testname} PROPERTIES DEPENDS H5REPACK_MASK-${testname}-clear-objects)
@@ -1450,15 +1418,20 @@ ADD_H5_VERIFY_INVALIDBOUNDS (latest_latest_invalid bounds_latest_latest.h5 0 1)
 ##############################################################################
 ###    P L U G I N  T E S T S
 ##############################################################################
+if (BUILD_SHARED_LIBS)
   ADD_H5_UD_TEST (plugin_version_test 0 h5repack_layout.h5 -v -f UD=260,0,4,9,${H5_VERS_MAJOR},${H5_VERS_MINOR},${H5_VERS_RELEASE})
   ADD_H5_UD_TEST (plugin_test 0 h5repack_layout.h5 -v -f UD=257,0,1,9)
   ADD_H5_UD_TEST (plugin_none 0 h5repack_layout.UD.h5 -v -f NONE)
   # check for no parameters
   ADD_H5_UD_TEST (plugin_zero 0 h5repack_layout.h5 -v -f UD=250,0,0)
+endif ()
 
-  if (HDF5_TEST_VFD)
-    # Run test with different Virtual File Driver
-    foreach (vfd ${VFD_LIST})
-      ADD_VFD_TEST (${vfd} 0)
-    endforeach ()
-  endif ()
+##############################################################################
+##############################################################################
+###                         V F D   T E S T S                              ###
+##############################################################################
+##############################################################################
+
+if (HDF5_TEST_VFD)
+  include (CMakeVFDTests.cmake)
+endif ()
diff --git a/tools/test/h5repack/CMakeVFDTests.cmake b/tools/test/h5repack/CMakeVFDTests.cmake
new file mode 100644
index 0000000..2042f31
--- /dev/null
+++ b/tools/test/h5repack/CMakeVFDTests.cmake
@@ -0,0 +1,65 @@
+#
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+#
+
+##############################################################################
+##############################################################################
+###           T E S T I N G                                                ###
+##############################################################################
+##############################################################################
+
+    set (VFD_LIST
+        sec2
+        stdio
+        core
+        split
+        multi
+        family
+    )
+
+    if (DIRECT_VFD)
+      set (VFD_LIST ${VFD_LIST} direct)
+    endif ()
+
+##############################################################################
+##############################################################################
+###           T H E   T E S T S  M A C R O S                               ###
+##############################################################################
+##############################################################################
+
+  macro (ADD_VFD_TEST vfdname resultcode)
+    add_test (
+      NAME H5REPACK-VFD-${vfdname}-h5repacktest
+      COMMAND "${CMAKE_COMMAND}"
+          -D "TEST_PROGRAM=$<TARGET_FILE:h5repacktest>"
+          -D "TEST_ARGS:STRING="
+          -D "TEST_VFD:STRING=${vfdname}"
+          -D "TEST_EXPECT=${resultcode}"
+          -D "TEST_OUTPUT=h5repacktest"
+          -D "TEST_FOLDER=${PROJECT_BINARY_DIR}"
+          -P "${HDF_RESOURCES_DIR}/vfdTest.cmake"
+    )
+    if (NOT "${last_test}" STREQUAL "")
+      set_tests_properties (H5REPACK-VFD-${vfdname}-h5repacktest PROPERTIES DEPENDS ${last_test})
+    endif ()
+    set (last_test "H5REPACK-VFD-${vfdname}-h5repacktest")
+  endmacro ()
+
+##############################################################################
+##############################################################################
+###           T H E   T E S T S                                            ###
+##############################################################################
+##############################################################################
+
+  # Run test with different Virtual File Driver
+  foreach (vfd ${VFD_LIST})
+    ADD_VFD_TEST (${vfd} 0)
+  endforeach ()
diff --git a/tools/test/h5repack/Makefile.in b/tools/test/h5repack/Makefile.in
index 36abf80..013985e 100644
--- a/tools/test/h5repack/Makefile.in
+++ b/tools/test/h5repack/Makefile.in
@@ -591,7 +591,6 @@ MAINT = @MAINT@
 MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
 MEMORYALLOCSANITYCHECK = @MEMORYALLOCSANITYCHECK@
-METADATATRACEFILE = @METADATATRACEFILE@
 MKDIR_P = @MKDIR_P@
 MPE = @MPE@
 NM = @NM@
@@ -625,6 +624,7 @@ PAC_FORTRAN_NUM_INTEGER_KINDS = @PAC_FORTRAN_NUM_INTEGER_KINDS@
 PARALLEL = @PARALLEL@
 PARALLEL_FILTERED_WRITES = @PARALLEL_FILTERED_WRITES@
 PATH_SEPARATOR = @PATH_SEPARATOR@
+PREADWRITE = @PREADWRITE@
 PROFILING = @PROFILING@
 RANLIB = @RANLIB@
 ROOT = @ROOT@
@@ -1493,7 +1493,7 @@ build-check-p: $(LIB) $(PROGS) $(chk_TESTS)
 	    echo "**** Hint ****";                                            \
 	    echo "Parallel test files reside in the current directory"        \
 	         "by default.";                                               \
-	    echo "Set HDF5_PARAPREFIX to use another directory. E.g.,";       \
+	    echo "Set HDF5_PARAPREFIX to use another directory. e.g.,";       \
 	    echo "    HDF5_PARAPREFIX=/PFS/user/me";                          \
 	    echo "    export HDF5_PARAPREFIX";                                \
 	    echo "    make check";                                            \
diff --git a/tools/test/h5repack/h5repack.sh.in b/tools/test/h5repack/h5repack.sh.in
index b0a2f99..a36eb08 100644
--- a/tools/test/h5repack/h5repack.sh.in
+++ b/tools/test/h5repack/h5repack.sh.in
@@ -997,6 +997,7 @@ fi
 ##############################################################################
 ###              T H E   T E S T S
 ##############################################################################
+
 # prepare for test
 COPY_TESTFILES_TO_TESTDIR
 
diff --git a/tools/test/h5repack/h5repacktst.c b/tools/test/h5repack/h5repacktst.c
index f6166da..0ae570b 100644
--- a/tools/test/h5repack/h5repacktst.c
+++ b/tools/test/h5repack/h5repacktst.c
@@ -3728,7 +3728,7 @@ out:
         H5Pclose(fcpl);
         H5Fclose(fid);
     } H5E_END_TRY;
-    if(fd > 0)
+    if(fd >= 0)
         HDclose(fd);
 
     return -1;
@@ -3797,7 +3797,7 @@ out:
         H5Pclose(fcpl);
         H5Fclose(fid);
     } H5E_END_TRY;
-    if(fd > 0)
+    if(fd >= 0)
         HDclose(fd);
 
     return -1;
@@ -3838,7 +3838,7 @@ make_userblock_file(void)
 
 out:
 
-    if(fd > 0)
+    if(fd >= 0)
         HDclose(fd);
 
     return -1;
@@ -4134,13 +4134,19 @@ int write_dset_in(hid_t loc_id,
         }
 
         /* create a type larger than TEST_BUFSIZE */
-        if ((tid = H5Tarray_create2(H5T_NATIVE_DOUBLE, 1, tdims)) < 0)
+        if ((tid = H5Tarray_create2(H5T_NATIVE_DOUBLE, 1, tdims)) < 0) {
+            HDfree(dbuf);
             goto out;
+        }
         size = H5Tget_size(tid);
-        if ((sid = H5Screate_simple(1, sdims, NULL)) < 0)
+        if ((sid = H5Screate_simple(1, sdims, NULL)) < 0) {
+            HDfree(dbuf);
             goto out;
-        if ((did = H5Dcreate2(loc_id, "arrayd", tid, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+        }
+        if ((did = H5Dcreate2(loc_id, "arrayd", tid, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0) {
+            HDfree(dbuf);
             goto out;
+        }
 #if defined(WRITE_ARRAY)
         H5Dwrite(did, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, dbuf);
 #endif
@@ -4149,7 +4155,7 @@ int write_dset_in(hid_t loc_id,
         H5Dclose(did);
         H5Tclose(tid);
         H5Sclose(sid);
-        HDfree( dbuf );
+        HDfree(dbuf);
     }
 
     /*-------------------------------------------------------------------------
diff --git a/tools/test/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl b/tools/test/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl
index 55bf8fe..341a404 100644
--- a/tools/test/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl
+++ b/tools/test/h5repack/testfiles/h5repack_layout.h5-plugin_version_test.ddl
@@ -11,7 +11,7 @@ GROUP "/" {
          USER_DEFINED_FILTER {
             FILTER_ID 260
             COMMENT dynlib4
-            PARAMS { 9 1 10 4 }
+            PARAMS { 9 1 10 5 }
          }
       }
       FILLVALUE {
@@ -33,7 +33,7 @@ GROUP "/" {
          USER_DEFINED_FILTER {
             FILTER_ID 260
             COMMENT dynlib4
-            PARAMS { 9 1 10 4 }
+            PARAMS { 9 1 10 5 }
          }
       }
       FILLVALUE {
@@ -55,7 +55,7 @@ GROUP "/" {
          USER_DEFINED_FILTER {
             FILTER_ID 260
             COMMENT dynlib4
-            PARAMS { 9 1 10 4 }
+            PARAMS { 9 1 10 5 }
          }
       }
       FILLVALUE {
@@ -77,7 +77,7 @@ GROUP "/" {
          USER_DEFINED_FILTER {
             FILTER_ID 260
             COMMENT dynlib4
-            PARAMS { 9 1 10 4 }
+            PARAMS { 9 1 10 5 }
          }
       }
       FILLVALUE {
@@ -99,7 +99,7 @@ GROUP "/" {
          USER_DEFINED_FILTER {
             FILTER_ID 260
             COMMENT dynlib4
-            PARAMS { 9 1 10 4 }
+            PARAMS { 9 1 10 5 }
          }
       }
       FILLVALUE {
@@ -121,7 +121,7 @@ GROUP "/" {
          USER_DEFINED_FILTER {
             FILTER_ID 260
             COMMENT dynlib4
-            PARAMS { 9 1 10 4 }
+            PARAMS { 9 1 10 5 }
          }
       }
       FILLVALUE {
@@ -143,7 +143,7 @@ GROUP "/" {
          USER_DEFINED_FILTER {
             FILTER_ID 260
             COMMENT dynlib4
-            PARAMS { 9 1 10 4 }
+            PARAMS { 9 1 10 5 }
          }
       }
       FILLVALUE {