[svn-r29694] HDFFV-9756,9766,9719:

9756-fix h5diff VDS
9766-fix h5repack VDS
9719 - reconcile tools differences

24 files changed, 460 insertions, 131 deletions

diff --git a/MANIFEST b/MANIFEST
index b4b2793..70b0e58 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -2347,6 +2347,16 @@
 ./tools/h5repack/testfiles/h5repack_layout.h5.ddl
 ./tools/h5repack/testfiles/h5repack_layout.UD.h5-plugin_none.ddl
 ./tools/h5repack/testfiles/h5repack_layout.h5-plugin_test.ddl
+./tools/h5repack/testfiles/1_vds.h5-vds_dset_compa-v.ddl
+./tools/h5repack/testfiles/1_vds.h5-vds_dset_conti-v.ddl
+./tools/h5repack/testfiles/2_vds.h5-vds_null_compa-v.ddl
+./tools/h5repack/testfiles/2_vds.h5-vds_null_conti-v.ddl
+./tools/h5repack/testfiles/4_vds.h5-vds_compa_compa-v.ddl
+./tools/h5repack/testfiles/4_vds.h5-vds_compa_conti-v.ddl
+./tools/h5repack/testfiles/4_vds.h5-vds_compa-v.ddl
+./tools/h5repack/testfiles/4_vds.h5-vds_conti_compa-v.ddl
+./tools/h5repack/testfiles/4_vds.h5-vds_conti_conti-v.ddl
+./tools/h5repack/testfiles/4_vds.h5-vds_conti-v.ddl
 
 # jam utility and tests
 ./tools/h5jam/h5jam.c
diff --git a/src/H5Dint.c b/src/H5Dint.c
index 06ea1e4..9359311 100644
--- a/src/H5Dint.c
+++ b/src/H5Dint.c
@@ -530,39 +530,47 @@ H5D__get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id
 
     HDassert(dset);
 
-    /* Get the dataset's dataspace */
-    HDassert(dset->shared->space);
-
-    /* Get the total number of elements in dataset's dataspace */
-    if((snelmts = H5S_GET_EXTENT_NPOINTS(dset->shared->space)) < 0)
-        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve number of elements in dataspace")
-    nelmts = (hsize_t)snelmts;
-
-    /* Get the size of the dataset's datatype */
-    if(0 == (dt_size = H5T_GET_SIZE(dset->shared->type)))
-        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve size of datatype")
-
-    /* Compute the maximum size of the dataset in bytes */
-    full_size = nelmts * dt_size;
-
-    /* Check for overflow during multiplication */
-    if(nelmts != (full_size / dt_size))
-        HGOTO_ERROR(H5E_DATASET, H5E_OVERFLOW, FAIL, "size of dataset's storage overflowed")
-
-    /* Difficult to error check, since the error value is 0 and 0 is a valid value... :-/ */
-    if(H5D__get_storage_size(dset, dxpl_id, &space_allocated) < 0)
-        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get size of dataset's storage")
-
-    /* Decide on how much of the space is allocated */
-    if(space_allocated == 0)
-        *allocation = H5D_SPACE_STATUS_NOT_ALLOCATED;
-    else if(space_allocated == full_size)
-        *allocation = H5D_SPACE_STATUS_ALLOCATED;
+    /* Check for chunked layout */
+    if(dset->shared->layout.type == H5D_CHUNKED) {
+        /* For chunked layout set the space status by the storage size */
+        /* Get the dataset's dataspace */
+        HDassert(dset->shared->space);
+
+        /* Get the total number of elements in dataset's dataspace */
+        if((snelmts = H5S_GET_EXTENT_NPOINTS(dset->shared->space)) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve number of elements in dataspace")
+        nelmts = (hsize_t)snelmts;
+
+        /* Get the size of the dataset's datatype */
+        if(0 == (dt_size = H5T_GET_SIZE(dset->shared->type)))
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve size of datatype")
+
+        /* Compute the maximum size of the dataset in bytes */
+        full_size = nelmts * dt_size;
+
+        /* Check for overflow during multiplication */
+        if(nelmts != (full_size / dt_size))
+            HGOTO_ERROR(H5E_DATASET, H5E_OVERFLOW, FAIL, "size of dataset's storage overflowed")
+
+        /* Difficult to error check, since the error value is 0 and 0 is a valid value... :-/ */
+        if(H5D__get_storage_size(dset, dxpl_id, &space_allocated) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get size of dataset's storage")
+
+        /* Decide on how much of the space is allocated */
+        if(space_allocated == 0)
+            *allocation = H5D_SPACE_STATUS_NOT_ALLOCATED;
+        else if(space_allocated == full_size)
+            *allocation = H5D_SPACE_STATUS_ALLOCATED;
+        else 
+            *allocation = H5D_SPACE_STATUS_PART_ALLOCATED;
+    } /* end if */
     else {
-        /* Should only happen for chunked datasets currently */
-        HDassert(dset->shared->layout.type == H5D_CHUNKED);
-
-        *allocation = H5D_SPACE_STATUS_PART_ALLOCATED;
+        /* For non-chunked layouts set space status by result of is_space_alloc
+         * function */
+        if(dset->shared->layout.ops->is_space_alloc(&dset->shared->layout.storage))
+            *allocation = H5D_SPACE_STATUS_ALLOCATED;
+        else
+            *allocation = H5D_SPACE_STATUS_NOT_ALLOCATED;
     } /* end else */
 
 done:
diff --git a/test/vds.c b/test/vds.c
index 1c3dcca..50523f0 100644
--- a/test/vds.c
+++ b/test/vds.c
@@ -332,6 +332,7 @@ test_api_get_ex_dcpl(test_api_config_t config, hid_t fapl, hid_t dcpl,
 {
     hid_t       file = -1;      /* File */
     hid_t       dset = -1;      /* Virtual dataset */
+    H5D_space_status_t space_status; /* Dataset space status */
     void        *plist_buf = NULL; /* Serialized property list buffer */
     H5O_info_t  oinfo;          /* Object info struct */
     htri_t      tri_ret;
@@ -352,6 +353,12 @@ test_api_get_ex_dcpl(test_api_config_t config, hid_t fapl, hid_t dcpl,
         if((dset = H5Dcreate2(file, "vdset", H5T_NATIVE_INT, vspace, H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
             TEST_ERROR
 
+        /* Test H5Dget_space_status */
+        if(H5Dget_space_status(dset, &space_status) < 0)
+            TEST_ERROR
+        if(space_status != H5D_SPACE_STATUS_ALLOCATED)
+            TEST_ERROR
+
         /* Reopen dataset if requested */
         if(config >= TEST_API_REOPEN_DSET) {
             /* Close dataset */
@@ -401,6 +408,12 @@ test_api_get_ex_dcpl(test_api_config_t config, hid_t fapl, hid_t dcpl,
         if(oinfo.meta_size.attr.index_size != (hsize_t)0)
             TEST_ERROR
 
+        /* Test H5Dget_space_status */
+        if(H5Dget_space_status(dset, &space_status) < 0)
+            TEST_ERROR
+        if(space_status != H5D_SPACE_STATUS_ALLOCATED)
+            TEST_ERROR
+
         /* Close dataset */
         if(H5Dclose(dset) < 0)
             TEST_ERROR
diff --git a/tools/Makefile.am b/tools/Makefile.am
index bffc14d..887c0f0 100644
--- a/tools/Makefile.am
+++ b/tools/Makefile.am
@@ -24,6 +24,7 @@ include $(top_srcdir)/config/commence.am
 CONFIG=ordered
 
 # All subdirectories
-SUBDIRS=lib h5diff h5ls h5dump misc h5import h5repack h5jam h5copy h5stat h5format_convert perform
+SUBDIRS=lib h5diff h5ls h5dump misc h5import h5repack h5jam h5copy h5stat \
+	h5format_convert perform
 
 include $(top_srcdir)/config/conclude.am
diff --git a/tools/h5copy/CMakeTests.cmake b/tools/h5copy/CMakeTests.cmake
index 9002e5a..4ef49ee 100644
--- a/tools/h5copy/CMakeTests.cmake
+++ b/tools/h5copy/CMakeTests.cmake
@@ -22,7 +22,7 @@
   file (MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
 
   foreach (listfiles ${LIST_HDF5_TEST_FILES} ${LIST_OTHER_TEST_FILES})
-    GET_FILENAME_COMPONENT(fname "${listfiles}" NAME)
+    get_filename_component(fname "${listfiles}" NAME)
     set (dest "${PROJECT_BINARY_DIR}/testfiles/${fname}")
     #message (STATUS " Copying ${listfiles}")
     add_custom_command (
diff --git a/tools/h5diff/CMakeTests.cmake b/tools/h5diff/CMakeTests.cmake
index 0595edd..e58f90c 100644
--- a/tools/h5diff/CMakeTests.cmake
+++ b/tools/h5diff/CMakeTests.cmake
@@ -44,12 +44,17 @@
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_exclude3-1.h5
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_exclude3-2.h5
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_comp_vl_strs.h5
-      ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_attr_v_level1.h5
-      ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_attr_v_level2.h5
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/compounds_array_vlen1.h5
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/compounds_array_vlen2.h5
+      ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_attr_v_level1.h5
+      ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_attr_v_level2.h5
+      ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_enum_invalid_values.h5
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/non_comparables1.h5
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/non_comparables2.h5
+      ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/tmptest.he5
+      ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/tmptest2.he5
+      ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/tmpSingleSiteBethe.reference.h5
+      ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/tmpSingleSiteBethe.output.h5
       # tools/testfiles/vds
       ${HDF5_TOOLS_SRC_DIR}/testfiles/vds/1_a.h5
       ${HDF5_TOOLS_SRC_DIR}/testfiles/vds/1_b.h5
@@ -119,6 +124,7 @@
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_26.txt
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_27.txt
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_28.txt
+      ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_30.txt
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_300.txt
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_400.txt
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_401.txt
@@ -255,6 +261,8 @@
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_710.txt
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_80.txt
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_90.txt
+      ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_tmp1.txt
+      ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_tmp2.txt
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_v1.txt
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_v2.txt
       ${HDF5_TOOLS_H5DIFF_SOURCE_DIR}/testfiles/h5diff_v3.txt
@@ -267,7 +275,7 @@
   # copy test files from source to build dir
   #
   foreach (h5_tstfiles ${LIST_HDF5_TEST_FILES} ${LIST_OTHER_TEST_FILES})
-    GET_FILENAME_COMPONENT(fname "${h5_tstfiles}" NAME)
+    get_filename_component(fname "${h5_tstfiles}" NAME)
     set (dest "${PROJECT_BINARY_DIR}/testfiles/${fname}")
     #message (STATUS " Copying ${fname}")
     add_custom_command (
@@ -930,6 +938,15 @@ ADD_H5_TEST (h5diff_27 1 -v ${FILE3} ${FILE3} t1 t2)
 ADD_H5_TEST (h5diff_28 1 -v ${FILE3} ${FILE3} l1 l2)
 
 # ##############################################################################
+# # Enum value tests (may become more comprehensive in the future)
+# ##############################################################################
+
+# 3.0
+# test enum types which may have invalid values
+ADD_H5_TEST (h5diff_30 1 -v h5diff_enum_invalid_values.h5 h5diff_enum_invalid_values.h5 dset1 dset2)
+
+
+# ##############################################################################
 # # Dataset datatypes
 # ##############################################################################
 
@@ -1073,6 +1090,10 @@ ADD_H5_TEST (h5diff_631 0 -v --use-system-epsilon ${FILE1} ${FILE1} g1/fp18 g1/f
 # 7.  attributes
 # ##############################################################################
 ADD_H5_TEST (h5diff_70 1 -v ${FILE5} ${FILE6})
+# temporary test to verify HDF5-8625
+ADD_H5_TEST (h5diff_tmp1 0 tmptest2.he5 tmptest.he5)
+# temporary test to verify HDF5-8639
+ADD_H5_TEST (h5diff_tmp2 1 tmpSingleSiteBethe.output.h5 tmpSingleSiteBethe.reference.h5)
 
 # ##################################################
 #  attrs with verbose option level
@@ -1115,8 +1136,10 @@ ADD_H5_TEST (h5diff_90 0 -v ${FILE2} ${FILE2})
 ADD_H5_TEST (h5diff_100 1 -v ${FILE9} ${FILE10})
 
 # 11. floating point comparison
+# double value
 ADD_H5_TEST (h5diff_101 1 -v ${FILE1} ${FILE1} g1/d1  g1/d2)
 
+# float value
 ADD_H5_TEST (h5diff_102 1 -v ${FILE1} ${FILE1} g1/fp1 g1/fp2)
 
 # with --use-system-epsilon for double value. expect less differences
@@ -1361,7 +1384,7 @@ ADD_H5_TEST (h5diff_517 1 -v ${GRP_RECURSE1_EXT} ${GRP_RECURSE2_EXT1} /g1)
 ADD_H5_TEST (h5diff_518 0 -v --follow-symlinks ${GRP_RECURSE1_EXT} ${GRP_RECURSE2_EXT1} /g1)
 
 # ##############################################################################
-# # Exclude path (--exclude-path)
+# # Exclude objects (--exclude-path)
 # ##############################################################################
 #
 # Same structure, same names and different value.
diff --git a/tools/h5diff/testfiles/h5diff_v1.txt b/tools/h5diff/testfiles/h5diff_v1.txt
index 31a3eae..8210cf9 100644
--- a/tools/h5diff/testfiles/h5diff_v1.txt
+++ b/tools/h5diff/testfiles/h5diff_v1.txt
@@ -7,7 +7,7 @@ file1     file2
 group  : </> and </>
 0 differences found
 dataset: </vds_dset> and </vds_dset>
-Not comparable: </vds_dset> or </vds_dset> is an empty dataset
+Warning: </vds_dset> or </vds_dset> is a virtual dataset
 Not comparable: </vds_dset> has rank 3, dimensions [5x18x8], max dimensions [18446744073709551615x18x8]
 and </vds_dset> has rank 3, dimensions [6x8x14], max dimensions [18446744073709551615x8x14]
 0 differences found
diff --git a/tools/h5diff/testfiles/h5diff_v3.txt b/tools/h5diff/testfiles/h5diff_v3.txt
index 8c5d2a2..57af303 100644
--- a/tools/h5diff/testfiles/h5diff_v3.txt
+++ b/tools/h5diff/testfiles/h5diff_v3.txt
@@ -1,4 +1,4 @@
-Not comparable: </vds_dset> or </vds_dset> is an empty dataset
+Warning: </vds_dset> or </vds_dset> is a virtual dataset
 Not comparable: </vds_dset> has rank 3, dimensions [5x18x8], max dimensions [18446744073709551615x18x8]
 and </vds_dset> has rank 3, dimensions [6x8x14], max dimensions [18446744073709551615x8x14]
 EXIT CODE: 0
diff --git a/tools/h5diff/testh5diff.sh.in b/tools/h5diff/testh5diff.sh.in
index fec6035..0dfdaa2 100644
--- a/tools/h5diff/testh5diff.sh.in
+++ b/tools/h5diff/testh5diff.sh.in
@@ -120,6 +120,10 @@ $SRC_H5DIFF_TESTFILES/h5diff_attr_v_level2.h5
 $SRC_H5DIFF_TESTFILES/h5diff_enum_invalid_values.h5
 $SRC_H5DIFF_TESTFILES/non_comparables1.h5
 $SRC_H5DIFF_TESTFILES/non_comparables2.h5
+$SRC_H5DIFF_TESTFILES/tmptest.he5
+$SRC_H5DIFF_TESTFILES/tmptest2.he5
+$SRC_H5DIFF_TESTFILES/tmpSingleSiteBethe.reference.h5
+$SRC_H5DIFF_TESTFILES/tmpSingleSiteBethe.output.h5
 $SRC_TOOLS_TESTFILES/vds/1_a.h5
 $SRC_TOOLS_TESTFILES/vds/1_b.h5
 $SRC_TOOLS_TESTFILES/vds/1_c.h5
@@ -327,10 +331,9 @@ $SRC_H5DIFF_TESTFILES/h5diff_80.txt
 $SRC_H5DIFF_TESTFILES/h5diff_90.txt
 $SRC_H5DIFF_TESTFILES/h5diff_tmp1.txt
 $SRC_H5DIFF_TESTFILES/h5diff_tmp2.txt
-$SRC_H5DIFF_TESTFILES/tmptest.he5
-$SRC_H5DIFF_TESTFILES/tmptest2.he5
-$SRC_H5DIFF_TESTFILES/tmpSingleSiteBethe.reference.h5
-$SRC_H5DIFF_TESTFILES/tmpSingleSiteBethe.output.h5
+$SRC_H5DIFF_TESTFILES/h5diff_v1.txt
+$SRC_H5DIFF_TESTFILES/h5diff_v2.txt
+$SRC_H5DIFF_TESTFILES/h5diff_v3.txt
 "
 
 #
diff --git a/tools/h5dump/CMakeTests.cmake b/tools/h5dump/CMakeTests.cmake
index 9f7e2b0..7897311 100644
--- a/tools/h5dump/CMakeTests.cmake
+++ b/tools/h5dump/CMakeTests.cmake
@@ -1141,10 +1141,10 @@
   ADD_H5_TEST_N (tattr-2 0 --enable-error-stack -N /\\\\/attr1 --any_path /attr4 --any_path=/attr5 tattr.h5)
   # test for header and error messages
   ADD_H5ERR_MASK_TEST (tattr-3 1 --enable-error-stack --header -a /attr2 --attribute=/attr tattr.h5)
-  # test for displaying attributes in shared datatype (also in group and dataset)
-  ADD_H5_TEST (tnamed_dtype_attr 0 --enable-error-stack tnamed_dtype_attr.h5)
   # test for displaying at least 9 attributes on root from a be machine
   ADD_H5_TEST (tattr-4_be 0 --enable-error-stack tattr4_be.h5)
+  # test for displaying attributes in shared datatype (also in group and dataset)
+  ADD_H5_TEST (tnamed_dtype_attr 0 --enable-error-stack tnamed_dtype_attr.h5)
 
   # test for displaying soft links and user-defined links
   ADD_H5_TEST (tslink-1 0 --enable-error-stack tslink.h5)
@@ -1423,6 +1423,7 @@
   # test for dataset region references
   ADD_H5_TEST (tdatareg 0 --enable-error-stack tdatareg.h5)
   ADD_H5ERR_MASK_TEST (tdataregR 0 --enable-error-stack -R tdatareg.h5)
+  ADD_H5_TEST (tattrreg 0 --enable-error-stack tattrreg.h5)
   ADD_H5ERR_MASK_TEST (tattrregR 0 -R --enable-error-stack tattrreg.h5)
   ADD_H5_EXPORT_TEST (tbinregR tdatareg.h5 0 --enable-error-stack -d /Dataset1 -s 0 -R -y -o)
 
diff --git a/tools/h5dump/CMakeTestsPBITS.cmake b/tools/h5dump/CMakeTestsPBITS.cmake
index e76fa0e..745d5b1 100644
--- a/tools/h5dump/CMakeTestsPBITS.cmake
+++ b/tools/h5dump/CMakeTestsPBITS.cmake
@@ -86,7 +86,7 @@
   )
 
   foreach (pbits_h5_file ${HDF5_REFERENCE_TEST_PBITS})
-    GET_FILENAME_COMPONENT(fname "${pbits_h5_file}" NAME)
+    get_filename_component(fname "${pbits_h5_file}" NAME)
     set (dest "${PROJECT_BINARY_DIR}/testfiles/pbits/${fname}")
     #message (STATUS " Copying ${pbits_h5_file}")
     add_custom_command (
@@ -99,7 +99,7 @@
 
 
   foreach (ddl_pbits ${HDF5_REFERENCE_PBITS})
-    GET_FILENAME_COMPONENT(fname "${ddl_pbits}" NAME)
+    get_filename_component(fname "${ddl_pbits}" NAME)
     set (ddldest "${PROJECT_BINARY_DIR}/testfiles/pbits/${fname}")
     #message (STATUS " Copying ${ddl_pbits}")
     add_custom_command (
@@ -111,7 +111,7 @@
   endforeach (ddl_pbits ${HDF5_REFERENCE_PBITS})
 
   foreach (ddl_pbits ${HDF5_ERROR_REFERENCE_PBITS})
-    GET_FILENAME_COMPONENT(fname "${ddl_pbits}" NAME)
+    get_filename_component(fname "${ddl_pbits}" NAME)
     set (ddldest "${PROJECT_BINARY_DIR}/testfiles/pbits/${fname}")
     #message (STATUS " Copying ${ddl_pbits}")
     add_custom_command (
diff --git a/tools/h5dump/CMakeTestsVDS.cmake b/tools/h5dump/CMakeTestsVDS.cmake
index cc68896..dcb90e0 100644
--- a/tools/h5dump/CMakeTestsVDS.cmake
+++ b/tools/h5dump/CMakeTestsVDS.cmake
@@ -65,7 +65,7 @@
   )
 
   foreach (vds_h5_file ${HDF5_REFERENCE_TEST_VDS})
-    GET_FILENAME_COMPONENT(fname "${vds_h5_file}" NAME)
+    get_filename_component(fname "${vds_h5_file}" NAME)
     set (dest "${PROJECT_BINARY_DIR}/testfiles/vds/${fname}")
     #message (STATUS " Copying ${vds_h5_file}")
     add_custom_command (
@@ -78,7 +78,7 @@
 
 
   foreach (ddl_vds ${HDF5_REFERENCE_VDS})
-    GET_FILENAME_COMPONENT(fname "${ddl_vds}" NAME)
+    get_filename_component(fname "${ddl_vds}" NAME)
     set (ddldest "${PROJECT_BINARY_DIR}/testfiles/vds/${fname}")
     #message (STATUS " Copying ${ddl_vds}")
     add_custom_command (
@@ -90,7 +90,7 @@
   endforeach (ddl_vds ${HDF5_REFERENCE_VDS})
 
   foreach (ddl_vds ${HDF5_ERROR_REFERENCE_VDS})
-    GET_FILENAME_COMPONENT(fname "${ddl_vds}" NAME)
+    get_filename_component(fname "${ddl_vds}" NAME)
     set (ddldest "${PROJECT_BINARY_DIR}/testfiles/vds/${fname}")
     #message (STATUS " Copying ${ddl_vds}")
     add_custom_command (
@@ -111,7 +111,7 @@
     # If using memchecker add tests without using scripts
     if (HDF5_ENABLE_USING_MEMCHECKER)
       add_test (NAME H5DUMP-${resultfile} COMMAND $<TARGET_FILE:h5dump> ${ARGN})
-      set_tests_properties (H5DUMP-${resultfile} PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfilesvds")
+      set_tests_properties (H5DUMP-${resultfile} PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles/vds")
       if (NOT ${resultcode} STREQUAL "0")
         set_tests_properties (H5DUMP-${resultfile} PROPERTIES WILL_FAIL "true")
       endif (NOT ${resultcode} STREQUAL "0")
@@ -144,7 +144,7 @@
     # If using memchecker add tests without using scripts
     if (HDF5_ENABLE_USING_MEMCHECKER)
       add_test (NAME H5DUMP-${resultfile} COMMAND $<TARGET_FILE:h5dump> -p ${ARGN})
-      set_tests_properties (H5DUMP-${resultfile} PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfilesvds")
+      set_tests_properties (H5DUMP-${resultfile} PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles/vds")
       if (NOT ${resultcode} STREQUAL "0")
         set_tests_properties (H5DUMP-${resultfile} PROPERTIES WILL_FAIL "true")
       endif (NOT ${resultcode} STREQUAL "0")
diff --git a/tools/h5dump/CMakeTestsXML.cmake b/tools/h5dump/CMakeTestsXML.cmake
index 0a667c4..fc6cae7 100644
--- a/tools/h5dump/CMakeTestsXML.cmake
+++ b/tools/h5dump/CMakeTestsXML.cmake
@@ -128,7 +128,7 @@
   )
 
   foreach (tst_xml_h5_file ${HDF5_XML_REFERENCE_TEST_FILES})
-    GET_FILENAME_COMPONENT(fname "${tst_xml_h5_file}" NAME)
+    get_filename_component(fname "${tst_xml_h5_file}" NAME)
     set (dest "${PROJECT_BINARY_DIR}/testfiles/xml/${fname}")
     #message (STATUS " Copying ${tst_xml_h5_file}")
     add_custom_command (
@@ -140,7 +140,7 @@
   endforeach (tst_xml_h5_file ${HDF5_XML_REFERENCE_TEST_FILES})
   
   foreach (tst_xml_other_file ${HDF5_XML_REFERENCE_FILES})
-    GET_FILENAME_COMPONENT(fname "${tst_xml_other_file}" NAME)
+    get_filename_component(fname "${tst_xml_other_file}" NAME)
     set (dest "${PROJECT_BINARY_DIR}/testfiles/xml/${fname}")
     #message (STATUS " Copying ${tst_xml_other_file}")
     add_custom_command (
diff --git a/tools/h5dump/testh5dump.sh.in b/tools/h5dump/testh5dump.sh.in
index 6d481c6..944fb85 100644
--- a/tools/h5dump/testh5dump.sh.in
+++ b/tools/h5dump/testh5dump.sh.in
@@ -1034,6 +1034,8 @@ TOOLTEST tcomp-2.ddl --enable-error-stack -N /type1 --any_path /type2 --any_path
 TOOLTEST4 tcomp-3.ddl --enable-error-stack -t /#6632 -g /group2 tcompound.h5
 # test complicated compound datatype
 TOOLTEST tcomp-4.ddl --enable-error-stack tcompound_complex.h5
+# tests for bitfields and opaque data types
+TOOLTEST tbitnopaque.ddl --enable-error-stack tbitnopaque.h5
 
 #test for the nested compound type
 TOOLTEST tnestcomp-1.ddl --enable-error-stack tnestedcomp.h5
diff --git a/tools/h5ls/CMakeTests.cmake b/tools/h5ls/CMakeTests.cmake
index a42fa17..2e3d398 100644
--- a/tools/h5ls/CMakeTests.cmake
+++ b/tools/h5ls/CMakeTests.cmake
@@ -31,6 +31,7 @@
       ${HDF5_TOOLS_SRC_DIR}/testfiles/tstr.h5
       ${HDF5_TOOLS_SRC_DIR}/testfiles/tudlink.h5
       ${HDF5_TOOLS_SRC_DIR}/testfiles/tvldtypes1.h5
+      ${HDF5_TOOLS_SRC_DIR}/testfiles/tdset_idx.h5
   )
 
   set (LIST_OTHER_TEST_FILES
@@ -90,13 +91,14 @@
       ${HDF5_TOOLS_SRC_DIR}/testfiles/tvldtypes1.ls
       ${HDF5_TOOLS_SRC_DIR}/testfiles/tvldtypes2le.ls
       ${HDF5_TOOLS_SRC_DIR}/testfiles/tvldtypes2be.ls
+      ${HDF5_TOOLS_SRC_DIR}/testfiles/tdset_idx.ls
   )
 
   file (MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
 
   # copy the list of test files
   foreach (listfiles ${LIST_HDF5_TEST_FILES} ${LIST_OTHER_TEST_FILES})
-    GET_FILENAME_COMPONENT(fname "${listfiles}" NAME)
+    get_filename_component(fname "${listfiles}" NAME)
     set (dest "${PROJECT_BINARY_DIR}/testfiles/${fname}")
     #message (STATUS " Copying ${listfiles} to ${dest}")
     add_custom_command (
@@ -400,3 +402,8 @@
   else (H5_WORDS_BIGENDIAN)
     ADD_H5_TEST (tdataregle 0 -v tdatareg.h5)
   endif (H5_WORDS_BIGENDIAN)
+
+# test for file with datasets that use Fixed Array chunk indices
+#echo "***skip testing tdset_idx.h5"
+#ADD_H5_TEST (tdset_idx 0 -w80 -d tdset_idx.h5)
+  
\ No newline at end of file
diff --git a/tools/h5ls/CMakeTestsVDS.cmake b/tools/h5ls/CMakeTestsVDS.cmake
index 1ef3f20..3e85803 100644
--- a/tools/h5ls/CMakeTestsVDS.cmake
+++ b/tools/h5ls/CMakeTestsVDS.cmake
@@ -47,7 +47,7 @@
 
   # copy the list of test files
   foreach (listfiles ${LIST_HDF5_TEST_FILES} ${LIST_OTHER_TEST_FILES})
-    GET_FILENAME_COMPONENT(fname "${listfiles}" NAME)
+    get_filename_component(fname "${listfiles}" NAME)
     set (dest "${PROJECT_BINARY_DIR}/testfiles/vds/${fname}")
     #message (STATUS " Copying ${listfiles} to ${dest}")
     add_custom_command (
diff --git a/tools/h5repack/CMakeTests.cmake b/tools/h5repack/CMakeTests.cmake
index 8aee98f..1f4887f 100644
--- a/tools/h5repack/CMakeTests.cmake
+++ b/tools/h5repack/CMakeTests.cmake
@@ -57,6 +57,8 @@
       ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout3.h5
       ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.UD.h5
       ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_named_dtypes.h5
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_nested_8bit_enum.h5
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_nested_8bit_enum_deflated.h5
       ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_nbit.h5
       ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_objs.h5
       ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_refs.h5
@@ -115,10 +117,20 @@
       ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/plugin_test.h5repack_layout.h5.tst
       ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.UD.h5-plugin_none.ddl
       ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/plugin_none.h5repack_layout.UD.h5.tst
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/1_vds.h5-vds_dset_compa-v.ddl
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/1_vds.h5-vds_dset_conti-v.ddl
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/2_vds.h5-vds_null_compa-v.ddl
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/2_vds.h5-vds_null_conti-v.ddl
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/4_vds.h5-vds_compa_compa-v.ddl
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/4_vds.h5-vds_compa_conti-v.ddl
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/4_vds.h5-vds_compa-v.ddl
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/4_vds.h5-vds_conti_compa-v.ddl
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/4_vds.h5-vds_conti_conti-v.ddl
+      ${HDF5_TOOLS_H5REPACK_SOURCE_DIR}/testfiles/4_vds.h5-vds_conti-v.ddl
   )
 
   foreach (h5_file ${LIST_HDF5_TEST_FILES} ${LIST_OTHER_TEST_FILES})
-    GET_FILENAME_COMPONENT(fname "${h5_file}" NAME)
+    get_filename_component(fname "${h5_file}" NAME)
     set (dest "${PROJECT_BINARY_DIR}/testfiles/${fname}")
     #message (STATUS " Copying ${h5_file}")
     add_custom_command (
@@ -345,6 +357,41 @@
     endif ("${testtype}" STREQUAL "SKIP")
   ENDMACRO (ADD_H5_VERIFY_TEST)
 
+  MACRO (ADD_H5_VERIFY_VDS testname testtype resultcode testfile testdset testfilter)
+    if ("${testtype}" STREQUAL "SKIP")
+      if (NOT HDF5_ENABLE_USING_MEMCHECKER)
+        add_test (
+            NAME H5REPACK_VERIFY_LAYOUT-${testname}-SKIPPED
+            COMMAND ${CMAKE_COMMAND} -E echo "SKIP -d ${testdset} -pH ${PROJECT_BINARY_DIR}/testfiles/out-${testname}.${resultfile}"
+        )
+      endif (NOT HDF5_ENABLE_USING_MEMCHECKER)
+    else ("${testtype}" STREQUAL "SKIP")
+      if (NOT HDF5_ENABLE_USING_MEMCHECKER)
+        add_test (
+            NAME H5REPACK_VERIFY_LAYOUT-${testname}
+            COMMAND $<TARGET_FILE:h5repack> ${ARGN} ${PROJECT_BINARY_DIR}/testfiles/${testfile} ${PROJECT_BINARY_DIR}/testfiles/out-${testname}.${testfile}
+        )
+        set_tests_properties (H5REPACK_VERIFY_LAYOUT-${testname} PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
+        if (NOT "${last_test}" STREQUAL "")
+          set_tests_properties (H5REPACK_VERIFY_LAYOUT-${testname} PROPERTIES DEPENDS ${last_test})
+        endif (NOT "${last_test}" STREQUAL "")
+        add_test (
+            NAME H5REPACK_VERIFY_LAYOUT-${testname}_DMP
+            COMMAND "${CMAKE_COMMAND}"
+                -D "TEST_PROGRAM=$<TARGET_FILE:h5dump>"
+                -D "TEST_ARGS:STRING=-d;${testdset};-p;out-${testname}.${testfile}"
+                -D "TEST_FOLDER=${PROJECT_BINARY_DIR}/testfiles"
+                -D "TEST_OUTPUT=${testfile}-${testname}-v.out"
+                -D "TEST_EXPECT=${resultcode}"
+                -D "TEST_REFERENCE=${testfile}-${testname}-v.ddl"
+                -P "${HDF_RESOURCES_EXT_DIR}/runTest.cmake"
+        )
+        set_tests_properties (H5REPACK_VERIFY_LAYOUT-${testname}_DMP PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
+        set_tests_properties (H5REPACK_VERIFY_LAYOUT-${testname}_DMP PROPERTIES DEPENDS H5REPACK_VERIFY_LAYOUT-${testname})
+      endif (NOT HDF5_ENABLE_USING_MEMCHECKER)
+    endif ("${testtype}" STREQUAL "SKIP")
+  ENDMACRO (ADD_H5_VERIFY_VDS)
+
   MACRO (ADD_H5_TEST_META testname testfile)
       add_test (
           NAME H5REPACK_META-${testname}_N
@@ -716,6 +763,13 @@
   ADD_H5_TEST (layout "TEST" ${FILE4})
   ADD_H5_TEST (early "TEST" ${FILE5})
 
+# nested 8bit enum in both deflated and non-deflated datafiles
+  if (NOT USE_FILTER_DEFLATE)
+  ADD_H5_TEST (nested_8bit_enum "TEST" h5repack_nested_8bit_enum.h5)
+  else (NOT USE_FILTER_DEFLATE)
+  ADD_H5_TEST (nested_8bit_enum "TEST" h5repack_nested_8bit_enum_deflated.h5)
+  endif (NOT USE_FILTER_DEFLATE)
+
 # use $FILE4 to write some filters  (this file has  no filters)
 
 # gzip with individual object
@@ -1053,20 +1107,20 @@
 #########################################################
 # layout options
 #########################################################
-  ADD_H5_VERIFY_TEST (vds_dset_conti "TEST" 0 ${FILEV1} vds_dset CONTIGUOUS -l vds_dset:CONTI)
-  ADD_H5_VERIFY_TEST (vds_null_conti "TEST" 1 ${FILEV2} null CONTIGUOUS -l CONTI)
-  ADD_H5_VERIFY_TEST (vds_dset_compa "TEST" 0 ${FILEV1} vds_dset COMPACT -l vds_dset:COMPA)
-  ADD_H5_VERIFY_TEST (vds_null_compa "TEST" 1 ${FILEV2} null COMPACT -l COMPA)
+  ADD_H5_VERIFY_VDS (vds_dset_conti "TEST" 0 ${FILEV1} vds_dset CONTIGUOUS -l vds_dset:CONTI)
+  ADD_H5_VERIFY_VDS (vds_null_conti "TEST" 1 ${FILEV2} null CONTIGUOUS -l CONTI)
+  ADD_H5_VERIFY_VDS (vds_dset_compa "TEST" 0 ${FILEV1} vds_dset COMPACT -l vds_dset:COMPA)
+  ADD_H5_VERIFY_VDS (vds_null_compa "TEST" 1 ${FILEV2} null COMPACT -l COMPA)
 
 ################################################################
 # layout conversions
 ###############################################################
-  ADD_H5_VERIFY_TEST (vds_compa_conti "TEST" 0 ${FILEV4} vds_dset CONTIGUOUS -l vds_dset:CONTI)
-  ADD_H5_VERIFY_TEST (vds_compa_compa "TEST" 0 ${FILEV4} vds_dset COMPACT -l vds_dset:COMPA)
-  ADD_H5_VERIFY_TEST (vds_conti_compa "TEST" 0 ${FILEV4} vds_dset COMPACT -l vds_dset:COMPA)
-  ADD_H5_VERIFY_TEST (vds_conti_conti "TEST" 0 ${FILEV4} vds_dset CONTIGUOUS -l vds_dset:CONTI)
-  ADD_H5_VERIFY_TEST (vds_compa "TEST" 0 ${FILEV4} vds_dset COMPACT -l vds_dset:COMPA)
-  ADD_H5_VERIFY_TEST (vds_conti "TEST" 0 ${FILEV4} vds_dset CONTIGUOUS -l vds_dset:CONTI)
+  ADD_H5_VERIFY_VDS (vds_compa_conti "TEST" 0 ${FILEV4} vds_dset CONTIGUOUS -l vds_dset:CONTI)
+  ADD_H5_VERIFY_VDS (vds_compa_compa "TEST" 0 ${FILEV4} vds_dset COMPACT -l vds_dset:COMPA)
+  ADD_H5_VERIFY_VDS (vds_conti_compa "TEST" 0 ${FILEV4} vds_dset COMPACT -l vds_dset:COMPA)
+  ADD_H5_VERIFY_VDS (vds_conti_conti "TEST" 0 ${FILEV4} vds_dset CONTIGUOUS -l vds_dset:CONTI)
+  ADD_H5_VERIFY_VDS (vds_compa "TEST" 0 ${FILEV4} vds_dset COMPACT -l vds_dset:COMPA)
+  ADD_H5_VERIFY_VDS (vds_conti "TEST" 0 ${FILEV4} vds_dset CONTIGUOUS -l vds_dset:CONTI)
 
 ##############################################################################
 ###    P L U G I N  T E S T S
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index 24298d0..bb686db 100644
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -39,6 +39,8 @@ H5DUMP=../h5dump/h5dump         # The h5dump tool name
 H5DUMP_BIN=`pwd`/$H5DUMP        # The path of the h5dump tool binary
 
 RM='rm -rf'
+CMP='cmp'
+DIFF='diff -c'
 GREP='grep'
 CP='cp'
 DIRNAME='dirname'
@@ -148,6 +150,16 @@ $SRC_H5REPACK_TESTFILES/h5repack_layout.h5.ddl
 $SRC_H5REPACK_TESTFILES/h5repack_filters.h5.tst
 $SRC_H5REPACK_TESTFILES/h5repack_layout.h5-plugin_test.ddl
 $SRC_H5REPACK_TESTFILES/plugin_test.h5repack_layout.h5.tst
+$SRC_H5REPACK_TESTFILES/1_vds.h5-vds_dset_compa-v.ddl
+$SRC_H5REPACK_TESTFILES/1_vds.h5-vds_dset_conti-v.ddl
+$SRC_H5REPACK_TESTFILES/2_vds.h5-vds_null_compa-v.ddl
+$SRC_H5REPACK_TESTFILES/2_vds.h5-vds_null_conti-v.ddl
+$SRC_H5REPACK_TESTFILES/4_vds.h5-vds_compa_compa-v.ddl
+$SRC_H5REPACK_TESTFILES/4_vds.h5-vds_compa_conti-v.ddl
+$SRC_H5REPACK_TESTFILES/4_vds.h5-vds_compa-v.ddl
+$SRC_H5REPACK_TESTFILES/4_vds.h5-vds_conti_compa-v.ddl
+$SRC_H5REPACK_TESTFILES/4_vds.h5-vds_conti_conti-v.ddl
+$SRC_H5REPACK_TESTFILES/4_vds.h5-vds_conti-v.ddl
 "
 
 #
@@ -171,7 +183,7 @@ COPY_TESTFILES_TO_TESTDIR()
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
             INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-    	        $CP -f $tstfile $TESTDIR
+                $CP -f $tstfile $TESTDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -188,7 +200,7 @@ CLEAN_TESTFILES_AND_TESTDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $tstfile`
+    SDIR=`$DIRNAME $SRC_H5REPACK_TESTFILES/h5repack-help.txt`
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
@@ -321,6 +333,70 @@ VERIFY_LAYOUT_DSET()
     rm -f $layoutfile
 }
 
+#------------------------------------------
+# Verifying layouts of a dataset
+VERIFY_LAYOUT_VDS()
+{
+    layoutfile=layout-$1.$2
+    dset=$3
+    expectlayout=$4
+    infile=$2
+    outfile=out-$1.$2
+
+    expect="$TESTDIR/$2-$1-v.ddl"
+    actual="$TESTDIR/$2-$1-v.out"
+    actual_err="$TESTDIR/$2-$1-v.err"
+
+    shift
+    shift
+    shift
+    shift
+
+    TESTING  $H5REPACK $@
+    (
+        cd $TESTDIR
+        $RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
+    )
+    RET=$?
+    if [ $RET != 0 ] ; then
+        echo "*FAILED*"
+        nerrors="`expr $nerrors + 1`"
+    else
+        echo " PASSED"
+    fi
+
+    #---------------------------------
+    # check the layout from a dataset
+    VERIFY  "a dataset layout"
+    (
+        cd $TESTDIR
+        $RUNSERIAL $H5DUMP_BIN -d $dset -p $outfile
+    ) >$actual 2>$actual_err
+
+    cat $actual_err >> $actual
+
+    if [ ! -f $expect ]; then
+    # Create the expect file if it doesn't yet exist.
+     echo " CREATED"
+     cp $actual $expect
+    elif $CMP $expect $actual > /dev/null 2>&1 ; then
+     echo " PASSED"
+    else
+     echo "*FAILED*"
+     echo "    Expected result (*.ddl) differs from actual result (*.out)"
+     nerrors="`expr $nerrors + 1`"
+     test yes = "$verbose" && $DIFF $caseless $expect $actual |sed 's/^/    /'
+    fi
+
+    # Clean up output file
+    if test -z "$HDF5_NOCLEANUP"; then
+     rm -f $actual $actual_err
+    fi
+
+    # clean up tmp files
+    rm -f $outfile
+}
+
 #----------------------------------------
 # Verifying layouts from entire file
 VERIFY_LAYOUT_ALL()
@@ -469,11 +545,11 @@ TOOLTEST1()
     )
     RET=$?
     if [ $RET != 0 ] ; then
-	echo "*FAILED*"
-	nerrors="`expr $nerrors + 1`"
+    echo "*FAILED*"
+    nerrors="`expr $nerrors + 1`"
     else
-	echo " PASSED"
-	DIFFTEST $infile $outfile
+    echo " PASSED"
+    DIFFTEST $infile $outfile
     fi
     rm -f $outfile
 }
@@ -500,11 +576,11 @@ TOOLTESTV()
     ) >$actual 2>$actual_err
     RET=$?
     if [ $RET != 0 ] ; then
-	echo "*FAILED*"
-	nerrors="`expr $nerrors + 1`"
+    echo "*FAILED*"
+    nerrors="`expr $nerrors + 1`"
     else
-	echo " PASSED"
-	DIFFTEST $infile $outfile
+    echo " PASSED"
+    DIFFTEST $infile $outfile
     fi
 
     # display output compare
@@ -634,11 +710,11 @@ TOOLTEST_META()
     # verify sizes.
     MESSAGE "Verify the sizes of both output files ($size1 vs $size2)"
     if [ $size1 -lt $size2 ]; then
-    	# pass
-	echo " PASSED"
+        # pass
+    echo " PASSED"
     else
-	#fail
-	echo "*FAILED*"
+    #fail
+    echo "*FAILED*"
         nerrors="`expr $nerrors + 1`"
     fi
 
@@ -711,7 +787,7 @@ USE_FILTER_SZIP_ENCODER=`$RUNSERIAL $H5DETECTSZIP_BIN`
 fi
 
 ##############################################################################
-###			  T H E   T E S T S
+###              T H E   T E S T S
 ##############################################################################
 # prepare for test
 COPY_TESTFILES_TO_TESTDIR
@@ -1057,7 +1133,7 @@ TOOLTEST add_alignment $arg
 
 # Check repacking file with old version of layout message (should get upgraded
 #       to new version and be readable, etc.)
-TOOLTEST pgrade_layout h5repack_layouto.h5
+TOOLTEST upgrade_layout h5repack_layouto.h5
 
 # test for datum size > H5TOOLS_MALLOCSIZE
 TOOLTEST gt_mallocsize h5repack_objs.h5 -f GZIP=1
@@ -1091,20 +1167,20 @@ TOOLTEST_META meta_long h5repack_layout.h5 --metadata_block_size=8192
 #########################################################
 # layout options
 #########################################################
-VERIFY_LAYOUT_DSET vds_dset_conti 1_vds.h5 vds_dset CONTIGUOUS -l vds_dset:CONTI
+VERIFY_LAYOUT_VDS vds_dset_conti 1_vds.h5 vds_dset CONTIGUOUS -l vds_dset:CONTI
 VERIFY_LAYOUT_ALL vds_null_conti 2_vds.h5 CONTIGUOUS -l CONTI
-VERIFY_LAYOUT_DSET vds_dset_compa 1_vds.h5 vds_dset COMPACT -l vds_dset:COMPA
+VERIFY_LAYOUT_VDS vds_dset_compa 1_vds.h5 vds_dset COMPACT -l vds_dset:COMPA
 VERIFY_LAYOUT_ALL vds_null_compa 2_vds.h5 COMPACT -l COMPA
 
 ################################################################
 # layout conversions
 ###############################################################
-VERIFY_LAYOUT_DSET vds_compa_conti 4_vds.h5 vds_dset CONTIGUOUS -l vds_dset:CONTI
-VERIFY_LAYOUT_DSET vds_compa_compa 4_vds.h5 vds_dset COMPACT -l vds_dset:COMPA
-VERIFY_LAYOUT_DSET vds_conti_compa 4_vds.h5 vds_dset COMPACT -l vds_dset:COMPA
-VERIFY_LAYOUT_DSET vds_conti_conti 4_vds.h5 vds_dset CONTIGUOUS -l vds_dset:CONTI
-VERIFY_LAYOUT_DSET vds_compa 4_vds.h5 vds_dset COMPACT -l vds_dset:COMPA
-VERIFY_LAYOUT_DSET vds_conti 4_vds.h5 vds_dset CONTIGUOUS -l vds_dset:CONTI
+VERIFY_LAYOUT_VDS vds_compa_conti 4_vds.h5 vds_dset CONTIGUOUS -l vds_dset:CONTI
+VERIFY_LAYOUT_VDS vds_compa_compa 4_vds.h5 vds_dset COMPACT -l vds_dset:COMPA
+VERIFY_LAYOUT_VDS vds_conti_compa 4_vds.h5 vds_dset COMPACT -l vds_dset:COMPA
+VERIFY_LAYOUT_VDS vds_conti_conti 4_vds.h5 vds_dset CONTIGUOUS -l vds_dset:CONTI
+VERIFY_LAYOUT_VDS vds_compa 4_vds.h5 vds_dset COMPACT -l vds_dset:COMPA
+VERIFY_LAYOUT_VDS vds_conti 4_vds.h5 vds_dset CONTIGUOUS -l vds_dset:CONTI
 
 # Clean up temporary files/directories
 CLEAN_TESTFILES_AND_TESTDIR
diff --git a/tools/h5stat/CMakeTests.cmake b/tools/h5stat/CMakeTests.cmake
index 4175eb2..5d3c82e 100644
--- a/tools/h5stat/CMakeTests.cmake
+++ b/tools/h5stat/CMakeTests.cmake
@@ -25,6 +25,7 @@
       h5stat_newgrat.ddl
       h5stat_newgrat-UG.ddl
       h5stat_newgrat-UA.ddl
+      h5stat_idx.ddl
       h5stat_err1_links.ddl
       h5stat_links1.ddl
       h5stat_links2.ddl
@@ -45,6 +46,7 @@
       h5stat_filters.h5
       h5stat_tsohm.h5
       h5stat_newgrat.h5
+      h5stat_idx.h5
       h5stat_threshold.h5
   )
 
@@ -213,6 +215,8 @@
   ADD_H5_TEST (h5stat_newgrat 0 h5stat_newgrat.h5)
   ADD_H5_TEST (h5stat_newgrat-UG 0 -G h5stat_newgrat.h5)
   ADD_H5_TEST (h5stat_newgrat-UA 0 -A h5stat_newgrat.h5)
+# h5stat_idx.h5 is generated by h5stat_gentest.c
+  ADD_H5_TEST (h5stat_idx 0 h5stat_idx.h5)
 #
 # Tests for -l (--links) option on h5stat_threshold.h5: 
 #   -l 0 (incorrect threshold value)
diff --git a/tools/h5stat/h5stat_gentest.c b/tools/h5stat/h5stat_gentest.c
index 02bd136..b1ab168 100644
--- a/tools/h5stat/h5stat_gentest.c
+++ b/tools/h5stat/h5stat_gentest.c
@@ -121,10 +121,10 @@ gen_newgrat_file(const char *fname)
 	goto error;
     if(H5Dclose(did) < 0)
 	goto error;
-    if(H5Tclose(tid) < 0)
-	goto error;
     if(H5Sclose(sid) < 0)
 	goto error;
+    if(H5Tclose(tid) < 0)
+	goto error;
     if(H5Fclose(fid) < 0)
 	goto error;
 
@@ -133,15 +133,14 @@ error:
 	H5Pclose(fapl);
 	H5Pclose(fcpl);
 	H5Aclose(attr_id);
+        H5Dclose(did);
         H5Tclose(tid);
         H5Sclose(sid);
         H5Gclose(gid);
-        H5Dclose(did);
         H5Fclose(fid);
     } H5E_END_TRY;
 } /* gen_newgrat_file() */
 
-
 /*
  * Generate an HDF5 file with groups, datasets, attributes for testing the options:
  *	-l N (--links=N): Set the threshold for # of links when printing information for small groups.
diff --git a/tools/lib/h5diff_dset.c b/tools/lib/h5diff_dset.c
index b8dd0e8..63f1483 100644
--- a/tools/lib/h5diff_dset.c
+++ b/tools/lib/h5diff_dset.c
@@ -71,9 +71,7 @@ hsize_t diff_dataset( hid_t file1_id,
     if((dcpl1 = H5Dget_create_plist(did1)) < 0)
         goto error;
     if((dcpl2 = H5Dget_create_plist(did2)) < 0)
-    {
         goto error;
-    }
 
     /*-------------------------------------------------------------------------
     * check if the dataset creation property list has filters that
@@ -191,6 +189,10 @@ hsize_t diff_datasetid( hid_t did1,
     hid_t      f_tid2=-1;
     hid_t      m_tid1=-1;
     hid_t      m_tid2=-1;
+    hid_t      dcpl1 = -1;
+    hid_t      dcpl2 = -1;
+    H5D_layout_t     stl1 = -1;
+    H5D_layout_t     stl2 = -1;
     size_t     m_size1;
     size_t     m_size2;
     H5T_sign_t sign1;
@@ -260,6 +262,21 @@ hsize_t diff_datasetid( hid_t did1,
         goto error;
     }
 
+
+    /*-------------------------------------------------------------------------
+    * get the storage layout type
+    *-------------------------------------------------------------------------
+    */
+    if((dcpl1 = H5Dget_create_plist(did1)) < 0)
+        goto error;
+    if((dcpl2 = H5Dget_create_plist(did2)) < 0)
+        goto error;
+
+    if((stl1 = H5Pget_layout(dcpl1)) < 0)
+        goto error;
+    if((stl2 = H5Pget_layout(dcpl2)) < 0)
+        goto error;
+
     /*-------------------------------------------------------------------------
     * check for empty datasets
     *-------------------------------------------------------------------------
@@ -271,10 +288,18 @@ hsize_t diff_datasetid( hid_t did1,
 
     if (storage_size1==0 || storage_size2==0)
     {
-        if ( (options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
-            parallel_print("Not comparable: <%s> or <%s> is an empty dataset\n", obj1_name, obj2_name);
-        can_compare=0;
-        options->not_cmp=1;
+        if (stl1==H5D_VIRTUAL || stl2==H5D_VIRTUAL)
+        {
+            if ( (options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
+                parallel_print("Warning: <%s> or <%s> is a virtual dataset\n", obj1_name, obj2_name);
+        }
+        else
+        {
+            if ( (options->m_verbose||options->m_list_not_cmp) && obj1_name && obj2_name)
+                parallel_print("Not comparable: <%s> or <%s> is an empty dataset\n", obj1_name, obj2_name);
+            can_compare=0;
+            options->not_cmp=1;
+        }
     }
 
     /*-------------------------------------------------------------------------
@@ -329,7 +354,7 @@ hsize_t diff_datasetid( hid_t did1,
                 parallel_print("Not comparable: <%s> has sign %s ", obj1_name, get_sign(sign1));
                 parallel_print("and <%s> has sign %s\n", obj2_name, get_sign(sign2));
             }
-    
+
             can_compare=0;
             options->not_cmp=1;
         }
@@ -369,7 +394,7 @@ hsize_t diff_datasetid( hid_t did1,
         h5difftrace("upgrade the smaller memory size?\n");
 
         if (FAIL == match_up_memsize (f_tid1, f_tid2,
-                                      &m_tid1, &m_tid2, 
+                                      &m_tid1, &m_tid2,
                                       &m_size1, &m_size2))
             goto error;
 
diff --git a/tools/misc/CMakeLists.txt b/tools/misc/CMakeLists.txt
index 088dbdf..6397899 100644
--- a/tools/misc/CMakeLists.txt
+++ b/tools/misc/CMakeLists.txt
@@ -28,10 +28,17 @@ TARGET_C_PROPERTIES (h5mkgrp STATIC " " " ")
 target_link_libraries (h5mkgrp  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
 set_target_properties (h5mkgrp PROPERTIES FOLDER tools)
 
+add_executable (h5clear ${HDF5_TOOLS_MISC_SOURCE_DIR}/h5clear.c)
+TARGET_NAMING (h5clear STATIC)
+TARGET_C_PROPERTIES (h5clear STATIC " " " ")
+target_link_libraries (h5clear  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+set_target_properties (h5clear PROPERTIES FOLDER tools)
+
 set (H5_DEP_EXECUTABLES
     h5debug
     h5repart
     h5mkgrp
+    h5clear
 )
 
 #-----------------------------------------------------------------------------
@@ -63,6 +70,18 @@ if (BUILD_TESTING)
   target_link_libraries (h5repart_test ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
   set_target_properties (h5repart_test PROPERTIES FOLDER tools)
 
+  add_executable (h5clear_gentest ${HDF5_TOOLS_MISC_SOURCE_DIR}/h5clear_gentest.c)
+  TARGET_NAMING (h5clear_gentest STATIC)
+  TARGET_C_PROPERTIES (h5clear_gentest STATIC " " " ")
+  target_link_libraries (h5clear_gentest ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
+  set_target_properties (h5clear_gentest PROPERTIES FOLDER tools)
+
+  add_executable (clear_open_chk ${HDF5_TOOLS_MISC_SOURCE_DIR}/clear_open_chk.c)
+  TARGET_NAMING (clear_open_chk STATIC)
+  TARGET_C_PROPERTIES (clear_open_chk STATIC " " " ")
+  target_link_libraries (clear_open_chk ${HDF5_LIB_TARGET} ${HDF5_TOOLS_LIB_TARGET})
+  set_target_properties (clear_open_chk PROPERTIES FOLDER tools)
+
   include (CMakeTests.cmake)
 endif (BUILD_TESTING)
 
diff --git a/tools/misc/CMakeTests.cmake b/tools/misc/CMakeTests.cmake
index d28b744..1a31c92 100644
--- a/tools/misc/CMakeTests.cmake
+++ b/tools/misc/CMakeTests.cmake
@@ -4,7 +4,7 @@
 ###           T E S T I N G                                                ###
 ##############################################################################
 ##############################################################################
-  
+
   # --------------------------------------------------------------------
   # Copy all the HDF5 files from the source directory into the test directory
   # --------------------------------------------------------------------
@@ -39,7 +39,7 @@
         ARGS       -E copy_if_different ${HDF5_TOOLS_SRC_DIR}/testfiles/${h5_file} ${dest}
     )
   endforeach (h5_file ${HDF5_REFERENCE_TEST_FILES})
-  
+
   set (HDF5_MKGRP_TEST_FILES
       #h5mkgrp_help.txt
       #h5mkgrp_version
@@ -90,14 +90,14 @@
       add_test (
           NAME H5MKGRP-${resultfile}-clear-objects
           COMMAND    ${CMAKE_COMMAND}
-              -E remove 
-                  ${resultfile}.h5 
+              -E remove
+                  ${resultfile}.h5
                   ${resultfile}.out
                   ${resultfile}.out.err
       )
       set_tests_properties (H5MKGRP-${resultfile}-clear-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
     endif (NOT HDF5_ENABLE_USING_MEMCHECKER)
-      
+
     add_test (
         NAME H5MKGRP-${resultfile}
         COMMAND $<TARGET_FILE:h5mkgrp> ${resultoption} ${resultfile}.h5 ${ARGN}
@@ -132,8 +132,8 @@
       add_test (
           NAME H5MKGRP_CMP-${resultfile}-clear-objects
           COMMAND    ${CMAKE_COMMAND}
-              -E remove 
-                  ${resultfile}.h5 
+              -E remove
+                  ${resultfile}.h5
                   ${resultfile}.out
                   ${resultfile}.out.err
       )
@@ -159,11 +159,12 @@
 ##############################################################################
 ##############################################################################
 
+  ###################### H5REPART #########################
   # Remove any output file left over from previous test run
   add_test (
     NAME H5REPART-clearall-objects
     COMMAND    ${CMAKE_COMMAND}
-        -E remove 
+        -E remove
         fst_family00000.h5
         scd_family00000.h5
         scd_family00001.h5
@@ -175,7 +176,7 @@
     set_tests_properties (H5REPART-clearall-objects PROPERTIES DEPENDS ${last_test})
   endif (NOT "${last_test}" STREQUAL "")
   set (last_test "H5REPART-clearall-objects")
-  
+
   # repartition family member size to 20,000 bytes.
   add_test (NAME H5REPART-h5repart_20K COMMAND $<TARGET_FILE:h5repart> -m 20000 family_file%05d.h5 fst_family%05d.h5)
   set_tests_properties (H5REPART-h5repart_20K PROPERTIES DEPENDS H5REPART-clearall-objects)
@@ -195,50 +196,135 @@
   set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES}
         h5repart_test
   )
-  
+
+  ###################### H5CLEAR #########################
+  # Remove any output file left over from previous test run
+  add_test (
+    NAME H5CLEAR-clearall-objects
+    COMMAND    ${CMAKE_COMMAND}
+        -E remove
+        h5clear_sec2_v3.h5
+        h5clear_log_v3.h5
+        h5clear_sec2_v0.h5
+        h5clear_sec2_v2.h5
+  )
+  if (NOT "${last_test}" STREQUAL "")
+    set_tests_properties (H5CLEAR-clearall-objects PROPERTIES DEPENDS ${last_test})
+  endif (NOT "${last_test}" STREQUAL "")
+  set (last_test "H5CLEAR-clearall-objects")
+
+  # create the output files to be used.
+  add_test (NAME H5CLEAR-h5clear_gentest COMMAND $<TARGET_FILE:h5clear_gentest>)
+  set_tests_properties (H5CLEAR-h5clear_gentest PROPERTIES DEPENDS "H5CLEAR-clearall-objects")
+
+  # Initial file open fails
+  add_test (NAME H5CLEAR-clear_open_chk-sec2_v3_F COMMAND $<TARGET_FILE:clear_open_chk> h5clear_sec2_v3.h5)
+  set_tests_properties (H5CLEAR-clear_open_chk-sec2_v3_F PROPERTIES WILL_FAIL "true")
+  set_tests_properties (H5CLEAR-clear_open_chk-sec2_v3_F PROPERTIES DEPENDS H5CLEAR-h5clear_gentest)
+  # After "h5clear" the file, the subsequent file open succeeds
+  add_test (NAME H5CLEAR-h5clear-sec2_v3 COMMAND $<TARGET_FILE:h5clear> h5clear_sec2_v3.h5)
+  set_tests_properties (H5CLEAR-h5clear-sec2_v3 PROPERTIES DEPENDS H5CLEAR-clear_open_chk-sec2_v3_F)
+  add_test (NAME H5CLEAR-clear_open_chk-sec2_v3 COMMAND $<TARGET_FILE:clear_open_chk> h5clear_sec2_v3.h5)
+  set_tests_properties (H5CLEAR-clear_open_chk-sec2_v3 PROPERTIES DEPENDS H5CLEAR-h5clear-sec2_v3)
+
+  # Initial file open fails
+  add_test (NAME H5CLEAR-clear_open_chk-log_v3_F COMMAND $<TARGET_FILE:clear_open_chk> h5clear_log_v3.h5)
+  set_tests_properties (H5CLEAR-clear_open_chk-log_v3_F PROPERTIES WILL_FAIL "true")
+  set_tests_properties (H5CLEAR-clear_open_chk-log_v3_F PROPERTIES DEPENDS H5CLEAR-h5clear_gentest)
+  # After "h5clear" the file, the subsequent file open succeeds
+  add_test (NAME H5CLEAR-h5clear-log_v3 COMMAND $<TARGET_FILE:h5clear> h5clear_log_v3.h5)
+  set_tests_properties (H5CLEAR-h5clear-log_v3 PROPERTIES DEPENDS H5CLEAR-clear_open_chk-log_v3_F)
+  add_test (NAME H5CLEAR-clear_open_chk-log_v3 COMMAND $<TARGET_FILE:clear_open_chk> h5clear_log_v3.h5)
+  set_tests_properties (H5CLEAR-clear_open_chk-log_v3 PROPERTIES DEPENDS H5CLEAR-h5clear-log_v3)
+
+  # Initial file open fails
+  add_test (NAME H5CLEAR-clear_open_chk-latest_sec2_v3_F COMMAND $<TARGET_FILE:clear_open_chk> latest_h5clear_sec2_v3.h5)
+  set_tests_properties (H5CLEAR-clear_open_chk-latest_sec2_v3_F PROPERTIES WILL_FAIL "true")
+  set_tests_properties (H5CLEAR-clear_open_chk-latest_sec2_v3_F PROPERTIES DEPENDS H5CLEAR-h5clear_gentest)
+  # After "h5clear" the file, the subsequent file open succeeds
+  add_test (NAME H5CLEAR-h5clear-latest_sec2_v3 COMMAND $<TARGET_FILE:h5clear> latest_h5clear_sec2_v3.h5)
+  set_tests_properties (H5CLEAR-h5clear-latest_sec2_v3 PROPERTIES DEPENDS H5CLEAR-clear_open_chk-latest_sec2_v3_F)
+  add_test (NAME H5CLEAR-clear_open_chk-latest_sec2_v3 COMMAND $<TARGET_FILE:clear_open_chk> latest_h5clear_sec2_v3.h5)
+  set_tests_properties (H5CLEAR-clear_open_chk-latest_sec2_v3 PROPERTIES DEPENDS H5CLEAR-h5clear-latest_sec2_v3)
+
+  # Initial file open fails
+  add_test (NAME H5CLEAR-clear_open_chk-latest_log_v3_F COMMAND $<TARGET_FILE:clear_open_chk> h5clear_log_v3.h5)
+  set_tests_properties (H5CLEAR-clear_open_chk-latest_log_v3_F PROPERTIES WILL_FAIL "true")
+  set_tests_properties (H5CLEAR-clear_open_chk-latest_log_v3_F PROPERTIES DEPENDS H5CLEAR-h5clear_gentest)
+  # After "h5clear" the file, the subsequent file open succeeds
+  add_test (NAME H5CLEAR-h5clear-latest_log_v3 COMMAND $<TARGET_FILE:h5clear> latest_h5clear_log_v3.h5)
+  set_tests_properties (H5CLEAR-h5clear-latest_log_v3 PROPERTIES DEPENDS H5CLEAR-clear_open_chk-latest_log_v3_F)
+  add_test (NAME H5CLEAR-clear_open_chk-latest_log_v3 COMMAND $<TARGET_FILE:clear_open_chk> latest_h5clear_log_v3.h5)
+  set_tests_properties (H5CLEAR-clear_open_chk-latest_log_v3 PROPERTIES DEPENDS H5CLEAR-h5clear-latest_log_v3)
+
+  #
+  # File open succeeds because the library does not check status_flags for file with < v3 superblock
+  add_test (NAME H5CLEAR-clear_open_chk-sec2_v0_P COMMAND $<TARGET_FILE:clear_open_chk> h5clear_sec2_v0.h5)
+  set_tests_properties (H5CLEAR-clear_open_chk-sec2_v0_P PROPERTIES DEPENDS H5CLEAR-h5clear_gentest)
+  # After "h5clear" the file, the subsequent file open succeeds
+  add_test (NAME H5CLEAR-h5clear-sec2_v0 COMMAND $<TARGET_FILE:h5clear> h5clear_sec2_v0.h5)
+  set_tests_properties (H5CLEAR-h5clear-sec2_v0 PROPERTIES DEPENDS H5CLEAR-clear_open_chk-sec2_v0_P)
+  add_test (NAME H5CLEAR-clear_open_chk-sec2_v0 COMMAND $<TARGET_FILE:clear_open_chk> h5clear_sec2_v0.h5)
+  set_tests_properties (H5CLEAR-clear_open_chk-sec2_v0 PROPERTIES DEPENDS H5CLEAR-h5clear-sec2_v0)
+
+  #
+  # File open succeeds because the library does not check status_flags for file with < v3 superblock
+  add_test (NAME H5CLEAR-clear_open_chk-sec2_v2_P COMMAND $<TARGET_FILE:clear_open_chk> h5clear_sec2_v2.h5)
+  set_tests_properties (H5CLEAR-clear_open_chk-sec2_v2_P PROPERTIES DEPENDS H5CLEAR-h5clear_gentest)
+  # After "h5clear" the file, the subsequent file open succeeds
+  add_test (NAME H5CLEAR-h5clear-sec2_v2 COMMAND $<TARGET_FILE:h5clear> h5clear_sec2_v2.h5)
+  set_tests_properties (H5CLEAR-h5clear-sec2_v2 PROPERTIES DEPENDS H5CLEAR-clear_open_chk-sec2_v2_P)
+  add_test (NAME H5CLEAR-clear_open_chk-sec2_v2 COMMAND $<TARGET_FILE:clear_open_chk> h5clear_sec2_v2.h5)
+  set_tests_properties (H5CLEAR-clear_open_chk-sec2_v2 PROPERTIES DEPENDS H5CLEAR-h5clear-sec2_v2)
+
+  set (H5_DEP_EXECUTABLES ${H5_DEP_EXECUTABLES}
+        h5clear_gentest
+  )
+
+  ###################### H5MKGRP #########################
   if (HDF5_ENABLE_USING_MEMCHECKER)
     add_test (
         NAME H5MKGRP-clearall-objects
         COMMAND    ${CMAKE_COMMAND}
-            -E remove 
+            -E remove
                 h5mkgrp_help.out
                 h5mkgrp_help.out.err
                 h5mkgrp_version.out
                 h5mkgrp_version.out.err
-                h5mkgrp_single.h5 
+                h5mkgrp_single.h5
                 h5mkgrp_single.out
                 h5mkgrp_single.out.err
-                h5mkgrp_single_v.h5 
+                h5mkgrp_single_v.h5
                 h5mkgrp_single_v.out
                 h5mkgrp_single_v.out.err
-                h5mkgrp_single_p.h5 
+                h5mkgrp_single_p.h5
                 h5mkgrp_single_p.out
                 h5mkgrp_single_p.out.err
-                h5mkgrp_single_l.h5 
+                h5mkgrp_single_l.h5
                 h5mkgrp_single_l.out
                 h5mkgrp_single_l.out.err
-                h5mkgrp_several.h5 
+                h5mkgrp_several.h5
                 h5mkgrp_several.out
                 h5mkgrp_several.out.err
-                h5mkgrp_several_v.h5 
+                h5mkgrp_several_v.h5
                 h5mkgrp_several_v.out
                 h5mkgrp_several_v.out.err
-                h5mkgrp_several_p.h5 
+                h5mkgrp_several_p.h5
                 h5mkgrp_several_p.out
                 h5mkgrp_several_p.out.err
-                h5mkgrp_several_l.h5 
+                h5mkgrp_several_l.h5
                 h5mkgrp_several_l.out
                 h5mkgrp_several_l.out.err
-                h5mkgrp_nested_p.h5 
+                h5mkgrp_nested_p.h5
                 h5mkgrp_nested_p.out
                 h5mkgrp_nested_p.out.err
-                h5mkgrp_nested_lp.h5 
+                h5mkgrp_nested_lp.h5
                 h5mkgrp_nested_lp.out
                 h5mkgrp_nested_lp.out.err
-                h5mkgrp_nested_mult_p.h5 
+                h5mkgrp_nested_mult_p.h5
                 h5mkgrp_nested_mult_p.out
                 h5mkgrp_nested_mult_p.out.err
-                h5mkgrp_nested_mult_lp.h5 
+                h5mkgrp_nested_mult_lp.h5
                 h5mkgrp_nested_mult_lp.out
                 h5mkgrp_nested_mult_lp.out.err
     )
@@ -265,7 +351,7 @@
   ADD_H5_TEST (h5mkgrp_several_p 0 "-p" one two)
   ADD_H5_TEST (h5mkgrp_several_l 0 "-l" one two)
 
-  # Create various nested groups 
+  # Create various nested groups
   ADD_H5_TEST (h5mkgrp_nested_p 0 "-p" /one/two)
   ADD_H5_TEST (h5mkgrp_nested_lp 0 "-lp" /one/two)
   ADD_H5_TEST (h5mkgrp_nested_mult_p 0 "-p" /one/two /three/four)
diff --git a/tools/misc/Makefile.am b/tools/misc/Makefile.am
index bde6805..b4d6bac 100644
--- a/tools/misc/Makefile.am
+++ b/tools/misc/Makefile.am
@@ -29,12 +29,10 @@ AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 TEST_PROG=h5repart_gentest talign
 TEST_SCRIPT=testh5repart.sh testh5mkgrp.sh testh5clear.sh
 
-
 check_PROGRAMS=$(TEST_PROG) repart_test clear_open_chk
 check_SCRIPTS=$(TEST_SCRIPT)
 SCRIPT_DEPEND=h5repart$(EXEEXT) h5mkgrp$(EXEEXT) h5clear$(EXEEXT)
 
-
 # These are our main targets, the tools
 bin_PROGRAMS=h5debug h5repart h5mkgrp h5clear
 bin_SCRIPTS=h5redeploy