Bring SWMR-related tools changes from revise_chunks to develop.

15 files changed, 527 insertions, 18 deletions

diff --git a/tools/test/h5diff/CMakeTests.cmake b/tools/test/h5diff/CMakeTests.cmake
index 7bbff61..3687574 100644
--- a/tools/test/h5diff/CMakeTests.cmake
+++ b/tools/test/h5diff/CMakeTests.cmake
@@ -46,10 +46,15 @@
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_comp_vl_strs.h5
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_attr_v_level1.h5
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_attr_v_level2.h5
+      ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_enum_invalid_values.h5
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/compounds_array_vlen1.h5
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/compounds_array_vlen2.h5
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/non_comparables1.h5
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/non_comparables2.h5
+      ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/tmptest.he5
+      ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/tmptest2.he5
+      ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/tmpSingleSiteBethe.reference.h5
+      ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/tmpSingleSiteBethe.output.h5
       # tools/testfiles/vds
       ${HDF5_TOOLS_DIR}/testfiles/vds/1_a.h5
       ${HDF5_TOOLS_DIR}/testfiles/vds/1_b.h5
@@ -115,6 +120,7 @@
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_26.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_27.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_28.txt
+      ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_30.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_300.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_400.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_401.txt
@@ -251,6 +257,8 @@
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_710.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_80.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_90.txt
+      ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_tmp1.txt
+      ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_tmp2.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_v1.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_v2.txt
       ${HDF5_TOOLS_TEST_H5DIFF_SOURCE_DIR}/testfiles/h5diff_v3.txt
@@ -867,6 +875,15 @@ 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
 # ##############################################################################
 
@@ -1010,6 +1027,10 @@ 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
diff --git a/tools/test/h5diff/testfiles/h5diff_dset_idx1.h5 b/tools/test/h5diff/testfiles/h5diff_dset_idx1.h5
new file mode 100644
index 0000000..3252303
--- /dev/null
+++ b/tools/test/h5diff/testfiles/h5diff_dset_idx1.h5
diff --git a/tools/test/h5diff/testfiles/h5diff_dset_idx2.h5 b/tools/test/h5diff/testfiles/h5diff_dset_idx2.h5
new file mode 100644
index 0000000..db7584d
--- /dev/null
+++ b/tools/test/h5diff/testfiles/h5diff_dset_idx2.h5
diff --git a/tools/test/h5diff/testfiles/h5diff_idx.txt b/tools/test/h5diff/testfiles/h5diff_idx.txt
new file mode 100644
index 0000000..754d3ea
--- /dev/null
+++ b/tools/test/h5diff/testfiles/h5diff_idx.txt
@@ -0,0 +1,14 @@
+
+file1     file2
+---------------------------------------
+    x      x    /              
+    x      x    /dset          
+    x      x    /dset_filter   
+
+group  : </> and </>
+0 differences found
+dataset: </dset> and </dset>
+0 differences found
+dataset: </dset_filter> and </dset_filter>
+0 differences found
+EXIT CODE: 0
diff --git a/tools/test/h5format_convert/h5fc_gentest.c b/tools/test/h5format_convert/h5fc_gentest.c
index 97def9a..520e5bf 100644
--- a/tools/test/h5format_convert/h5fc_gentest.c
+++ b/tools/test/h5format_convert/h5fc_gentest.c
@@ -44,6 +44,8 @@ const char *FILENAME[] = {
 
 #define GROUP			"GROUP"
 
+#define DSET_BT1		"DSET_BT1"
+#define DSET_NDATA_BT1		"DSET_NDATA_BT1"
 #define DSET_COMPACT		"DSET_COMPACT"
 #define DSET_CONTIGUOUS		"DSET_CONTIGUOUS"
 
@@ -68,8 +70,7 @@ const char *FILENAME[] = {
 /*
  * Function: gen_non() 
  *
- * Create empty file with latest-format--this will result in v3 superbock
- * Close and re-open file with non-latest-format--v3 superblock will result in latest version support:
+ * Create a file with SWMR write+non-latest-format--this will result in v3 superbock+latest version support:
  *	1) 1 chunked dataset with extensible array chunk indexing type (without data)
  *	2) 1 chunked dataset with version 2 B-tree chunk indexing type (with data)
  * Re-open the file with write+non-latest-format and create:
@@ -82,7 +83,6 @@ gen_non(const char *fname)
 {
     hid_t	fid = -1;		/* file id */
     hid_t	fcpl = -1;		/* file creation property list */
-    hid_t	fapl = -1;		/* file access property list */
     hid_t	gid = -1;		/* group id */
     hid_t   	sid = -1;       	/* space id */
     hid_t	dcpl = -1;		/* dataset creation property id */
@@ -101,13 +101,8 @@ gen_non(const char *fname)
     if(H5Pset_istore_k(fcpl, 64) < 0)
         goto error;
 
-    if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
-	goto error;
-    if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
-	goto error;
-
     /* Create an empty file with latest-format */
-    if((fid = H5Fcreate(fname, H5F_ACC_TRUNC, fcpl, fapl)) < 0)
+    if((fid = H5Fcreate(fname, H5F_ACC_TRUNC|H5F_ACC_SWMR_WRITE, fcpl, H5P_DEFAULT)) < 0)
         goto error;
 
     /* Create a group */
@@ -172,7 +167,12 @@ gen_non(const char *fname)
         goto error;
     if(H5Gclose(gid) < 0)
         goto error;
+    if(H5Fclose(fid) < 0)
+        goto error;
 
+    /* Re-open the file with old format */
+    if((fid = H5Fopen(fname, H5F_ACC_RDWR, H5P_DEFAULT)) < 0)
+        goto error;
 
     /* Open the group */
     if((gid = H5Gopen2(fid, GROUP, H5P_DEFAULT)) < 0)
@@ -285,8 +285,6 @@ gen_non(const char *fname)
 	goto error;
     if(H5Pclose(fcpl) < 0)
 	goto error;
-    if(H5Pclose(fapl) < 0)
-        goto error;
     if(H5Fclose(fid) < 0)
         goto error;
 
@@ -773,7 +771,6 @@ error:
         H5Dclose(did2);
         H5Gclose(gid);
         H5Fclose(fid);
-        H5Pclose(fapl);
         H5Pclose(fcpl);
     } H5E_END_TRY;
 
diff --git a/tools/test/h5ls/CMakeTests.cmake b/tools/test/h5ls/CMakeTests.cmake
index 816907c..e7a5dd6 100644
--- a/tools/test/h5ls/CMakeTests.cmake
+++ b/tools/test/h5ls/CMakeTests.cmake
@@ -31,6 +31,7 @@
       ${HDF5_TOOLS_DIR}/testfiles/tstr.h5
       ${HDF5_TOOLS_DIR}/testfiles/tudlink.h5
       ${HDF5_TOOLS_DIR}/testfiles/tvldtypes1.h5
+      ${HDF5_TOOLS_DIR}/testfiles/tdset_idx.h5
   )
 
   set (LIST_OTHER_TEST_FILES
@@ -90,6 +91,7 @@
       ${HDF5_TOOLS_DIR}/testfiles/tvldtypes1.ls
       ${HDF5_TOOLS_DIR}/testfiles/tvldtypes2le.ls
       ${HDF5_TOOLS_DIR}/testfiles/tvldtypes2be.ls
+      ${HDF5_TOOLS_DIR}/testfiles/tdset_idx.ls
   )
 
   file (MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
@@ -388,3 +390,8 @@
   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)
+  
diff --git a/tools/test/h5ls/testh5ls.sh.in b/tools/test/h5ls/testh5ls.sh.in
index 0637a74..e2a72ba 100644
--- a/tools/test/h5ls/testh5ls.sh.in
+++ b/tools/test/h5ls/testh5ls.sh.in
@@ -421,7 +421,7 @@ else
 fi 
 
 # test for file with datasets that use Fixed Array chunk indices
-#echo "***skip testing tdset_idx.h5"
+echo "***skip testing tdset_idx.h5"
 TOOLTEST tdset_idx.ls 0 -w80 -d tdset_idx.h5
 
 # Clean up temporary files/directories
diff --git a/tools/test/h5repack/CMakeTests.cmake b/tools/test/h5repack/CMakeTests.cmake
index f3ef2a5..576fb58 100644
--- a/tools/test/h5repack/CMakeTests.cmake
+++ b/tools/test/h5repack/CMakeTests.cmake
@@ -57,6 +57,8 @@
       ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout3.h5
       ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testfiles/h5repack_layout.UD.h5
       ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testfiles/h5repack_named_dtypes.h5
+      ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testfiles/h5repack_nested_8bit_enum.h5
+      ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testfiles/h5repack_nested_8bit_enum_deflated.h5
       ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testfiles/h5repack_nbit.h5
       ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testfiles/h5repack_objs.h5
       ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testfiles/h5repack_refs.h5
@@ -764,6 +766,13 @@
   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
diff --git a/tools/test/h5stat/CMakeTests.cmake b/tools/test/h5stat/CMakeTests.cmake
index 201e978..39faca0 100644
--- a/tools/test/h5stat/CMakeTests.cmake
+++ b/tools/test/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
   )
 
@@ -194,6 +196,8 @@
   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/test/misc/CMakeLists.txt b/tools/test/misc/CMakeLists.txt
index db68eb1..a53fa73 100644
--- a/tools/test/misc/CMakeLists.txt
+++ b/tools/test/misc/CMakeLists.txt
@@ -27,4 +27,16 @@ INCLUDE_DIRECTORIES (${HDF5_TOOLS_DIR}/lib)
   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_TEST_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_TEST_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)
diff --git a/tools/test/misc/CMakeTests.cmake b/tools/test/misc/CMakeTests.cmake
index c041b21..9835e1e 100644
--- a/tools/test/misc/CMakeTests.cmake
+++ b/tools/test/misc/CMakeTests.cmake
@@ -177,6 +177,93 @@
         h5repart_test
   )
 
+  ###################### H5CLEAR #########################
+  # Remove any output file left over from previous test run
+  add_test (
+    NAME H5CLEAR-clearall-objects
+    COMMAND    ${CMAKE_COMMAND}
+        -E remove
+        h5clear_log_v3.h5
+        h5clear_sec2_v0.h5
+        h5clear_sec2_v2.h5
+        h5clear_sec2_v3.h5
+        latest_h5clear_log_v3.h5
+        latest_h5clear_sec2_v3.h5
+  )
+  if (NOT "${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> latest_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 ${H5_DEP_EXECUTABLES}
+        h5clear_gentest
+  )
+
+  ###################### H5MKGRP #########################
   if (HDF5_ENABLE_USING_MEMCHECKER)
     add_test (
         NAME H5MKGRP-clearall-objects
diff --git a/tools/test/misc/Makefile.am b/tools/test/misc/Makefile.am
index 4168e8c..1025a8a 100644
--- a/tools/test/misc/Makefile.am
+++ b/tools/test/misc/Makefile.am
@@ -26,12 +26,12 @@ SUBDIRS=vds
 AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 
 #test scripts and programs
-TEST_PROG=h5repart_gentest talign
-TEST_SCRIPT=testh5repart.sh testh5mkgrp.sh
+TEST_PROG=h5repart_gentest h5clear_gentest talign
+TEST_SCRIPT=testh5repart.sh testh5mkgrp.sh testh5clear.sh
 
-check_PROGRAMS=$(TEST_PROG) repart_test
+check_PROGRAMS=$(TEST_PROG) repart_test clear_open_chk
 check_SCRIPTS=$(TEST_SCRIPT)
-SCRIPT_DEPEND=../../src/misc/h5repart$(EXEEXT) ../../src/misc/h5mkgrp$(EXEEXT)
+SCRIPT_DEPEND=../../src/misc/h5repart$(EXEEXT) ../../src/misc/h5mkgrp$(EXEEXT) ../../src/misc/h5clear$(EXEEXT)
 
 # Temporary files.  *.h5 are generated by h5repart_gentest.  They should
 # copied to the testfiles/ directory if update is required. fst_family*.h5
@@ -39,7 +39,7 @@ SCRIPT_DEPEND=../../src/misc/h5repart$(EXEEXT) ../../src/misc/h5mkgrp$(EXEEXT)
 CHECK_CLEANFILES+=*.h5 ../testfiles/fst_family*.h5 ../testfiles/scd_family*.h5
 
 # These were generated by configure.  Remove them only when distclean.
-DISTCLEANFILES=testh5repart.sh
+DISTCLEANFILES=testh5repart.sh testh5clear.sh
 
 # All programs rely on hdf5 library and h5tools library
 LDADD=$(LIBH5TOOLS) $(LIBHDF5)
diff --git a/tools/test/misc/clear_open_chk.c b/tools/test/misc/clear_open_chk.c
new file mode 100644
index 0000000..f3e6ba3
--- /dev/null
+++ b/tools/test/misc/clear_open_chk.c
@@ -0,0 +1,72 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * 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 files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+#include "hdf5.h"
+#include "H5private.h"
+#include "h5tools.h"
+
+static void usage(void);
+
+static void
+usage(void)
+{
+    HDfprintf(stdout, "\n");
+    HDfprintf(stdout, "Usage error!\n");
+    HDfprintf(stdout, "Usage: clear_open_chk filename\n");
+} /* usage() */
+
+/*-------------------------------------------------------------------------
+ * Function:	main
+ *
+ * Purpose:	To open the file which has zero or nonzero status_flags in 
+ *		the superblock.
+ *
+ * Return:	0 on success
+ *		1 on failure
+ *
+ * Programmer:	Vailin Choi; July 2013
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(int argc, char *argv[])
+{
+    char *fname;	/* The HDF5 file name */
+    hid_t fid;		/* File ID */
+
+    /* Check the # of arguments */
+    if(argc != 2) {
+	usage();
+	return(EXIT_FAILURE);
+    }
+
+    /* Get the file name */
+    fname = HDstrdup(argv[1]);
+
+    /* Try opening the file */
+    if((fid = h5tools_fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t)0)) < 0) {
+	HDfprintf(stderr, "clear_open_chk: unable to open the file\n");
+	return EXIT_FAILURE;
+    }
+
+    /* Close the file */
+    if(H5Fclose(fid) < 0) {
+	HDfprintf(stderr, "clear_open_chk: cannot close the file\n");
+	return EXIT_FAILURE;
+    }
+
+    /* Return success */
+    return EXIT_SUCCESS;
+
+} /* main() */
diff --git a/tools/test/misc/h5clear_gentest.c b/tools/test/misc/h5clear_gentest.c
new file mode 100644
index 0000000..0f20c35
--- /dev/null
+++ b/tools/test/misc/h5clear_gentest.c
@@ -0,0 +1,174 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * 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 files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+#include "hdf5.h"
+#include "H5private.h"
+
+/* The HDF5 test files */
+const char *FILENAME[] = {
+    "h5clear_sec2_v3.h5",		/* 0 -- sec2 file with superblock version 3 */
+    "h5clear_log_v3.h5",		/* 1 -- log file with superblock veresion 3 */
+    "h5clear_sec2_v0.h5",		/* 2 -- sec2 file with superblock version 0 */
+    "h5clear_sec2_v2.h5"		/* 3 -- sec2 file with superblock version 2 */
+};
+
+#define KB 		1024U
+
+/*-------------------------------------------------------------------------
+ * Function:	main
+ *
+ * Purpose:	To create HDF5 files with non-zero status_flags in the superblock
+ *		via flushing and exiting without closing the library.
+ *
+ *		Due to file locking, status_flags in the superblock will be 
+ *		nonzero after H5Fcreate.  The library will clear status_flags
+ *		on file closing.  This program, after "H5Fcreate" the files,
+ *		exits without going through library closing. Thus, status_flags
+ *		for these files are not cleared.
+ *		The library will check consistency of status_flags when opening
+ *		a file with superblock >= v3 and will return error accordingly.
+ *		The library will not check status_flags when opening a file 
+ *		with < v3 superblock.
+ *
+ *		These files are used by "h5clear" to see if the tool clears
+ *		status_flags properly so users can open the files afterwards.
+ *
+ * Return:	Success:	0
+ *		Failure:	1
+ *
+ * Programmer:	Vailin Choi; July 2013
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main(void)
+{
+    hid_t fid;			/* File ID */
+    hid_t fcpl;			/* File creation property list */
+    hid_t fapl, new_fapl;	/* File access property lists */
+    char fname[512];		/* File name */
+    unsigned new_format;		/* To use latest library format or not */
+
+    /* Create a copy of the file access property list */
+    if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+	goto error;
+
+    /* Copy the file access property list */
+    if((new_fapl = H5Pcopy(fapl)) < 0)
+	goto error;
+    /* Set to latest library format */
+    if(H5Pset_libver_bounds(new_fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
+	goto error;
+
+    /* Files created within this for loop will have v3 superblock and nonzero status_flags */
+    for(new_format = FALSE; new_format <= TRUE; new_format++) {
+	hid_t fapl2, my_fapl;	/* File access property lists */
+
+	/* Set to use the appropriate file access property list */
+	if(new_format)
+	    fapl2 = new_fapl;
+	else
+	    fapl2 = fapl;
+	/*
+	 * Create a sec2 file
+	 */
+	if((my_fapl = H5Pcopy(fapl2)) < 0)
+	    goto error;
+	/* Create the file */
+	sprintf(fname, "%s%s", new_format? "latest_":"", FILENAME[0]);
+	if((fid = H5Fcreate(fname, H5F_ACC_TRUNC | (new_format ? 0 : H5F_ACC_SWMR_WRITE), H5P_DEFAULT, my_fapl)) < 0) 
+	    goto error;
+
+	/* Flush the file */
+	if(H5Fflush(fid, H5F_SCOPE_GLOBAL) < 0)
+	    goto error;
+    
+	/* Close the property list */
+	if(H5Pclose(my_fapl) < 0)
+	    goto error;
+
+	/*
+	 * Create a log file
+	 */
+	/* Create a copy of file access property list */
+	if((my_fapl = H5Pcopy(fapl2)) < 0)
+	    goto error;
+
+	/* Setup the fapl for the log driver */
+	if(H5Pset_fapl_log(my_fapl, "append.log", (unsigned long long)H5FD_LOG_ALL, (size_t)(4 * KB)) < 0)
+	    goto error;
+
+	/* Create the file */
+	sprintf(fname, "%s%s", new_format? "latest_":"", FILENAME[1]);
+	if((fid = H5Fcreate(fname, H5F_ACC_TRUNC | (new_format ? 0 : H5F_ACC_SWMR_WRITE), H5P_DEFAULT, my_fapl)) < 0) 
+	    goto error;
+
+	/* Flush the file */
+	if(H5Fflush(fid, H5F_SCOPE_GLOBAL) < 0)
+	    goto error;
+
+	/* Close the property list */
+	if(H5Pclose(my_fapl) < 0)
+	    goto error;
+
+    } /* end for */
+
+    /* 
+     * Create a sec2 file with v0 superblock but nonzero status_flags
+     */
+    if((fid = H5Fcreate(FILENAME[2], H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0) 
+	goto error;
+
+    /* Flush the file */
+    if(H5Fflush(fid, H5F_SCOPE_GLOBAL) < 0)
+	goto error;
+
+
+    /* 
+     * Create a sec2 file with v2 superblock but nonzero status_flags
+     */
+    if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
+	goto error;
+    if(H5Pset_shared_mesg_nindexes(fcpl, 1) < 0)
+        goto error;
+    if(H5Pset_shared_mesg_index(fcpl, 0, H5O_SHMESG_DTYPE_FLAG, 50) < 0)
+        goto error;
+
+    if((fid = H5Fcreate(FILENAME[3], H5F_ACC_TRUNC, fcpl, fapl)) < 0) 
+	goto error;
+
+    /* Flush the file */
+    if(H5Fflush(fid, H5F_SCOPE_GLOBAL) < 0)
+	goto error;
+
+    
+    /* Close the property lists */
+    if(H5Pclose(fapl) < 0)
+	goto error;
+    if(H5Pclose(new_fapl) < 0)
+	goto error;
+    if(H5Pclose(fcpl) < 0)
+	goto error;
+
+    fflush(stdout);
+    fflush(stderr);
+
+    /* Not going through library closing by calling _exit(0) with success */
+    HD_exit(0);
+
+error:
+
+    /* Exit with failure */
+    HD_exit(1);
+}
diff --git a/tools/test/misc/testh5clear.sh.in b/tools/test/misc/testh5clear.sh.in
new file mode 100644
index 0000000..a6836d4
--- /dev/null
+++ b/tools/test/misc/testh5clear.sh.in
@@ -0,0 +1,112 @@
+#! /bin/sh
+#
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# 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 files COPYING and Copyright.html.  COPYING can be found at the root
+# of the source code distribution tree; Copyright.html can be found at the
+# root level of an installed copy of the electronic HDF5 document set and
+# is linked from the top-level documents page.  It can also be found at
+# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
+# access to either file, you may request a copy from help@hdfgroup.org.
+#
+# Tests for the h5clear tool
+#
+srcdir=@srcdir@
+TESTNAME=h5clear
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+
+H5CLEAR=../../src/misc/h5clear
+H5CLEAR_BIN=`pwd`/$H5CLEAR        # The path of the tool binary
+
+OPENCHK=clear_open_chk        # Try opening the test file
+OPENCHK_BIN=`pwd`/$OPENCHK    # The path to the binary
+
+SUCCEED=0
+FAIL=1
+
+nerrors=0
+verbose=yes
+
+# Print a line-line message left justified in a field of 70 characters
+# beginning with the word "Testing".
+#
+TESTING() {
+   SPACES="                                                               "
+   echo "Testing $* $SPACES" | cut -c1-70 | tr -d '\012'
+}
+
+
+
+# (1)Use "clear_open_chk" to check if the file open succeeds or fails
+# $1 is the filename to open
+# $2 is the expected return from "clear_open_chk"
+# (2) Use "h5clear" to clear the status_flags in the test file
+# (3) Open the test file via "clear_open_chk"
+TOOLTEST() {
+    fname=$1
+    expected=$2
+    # (1)
+    $OPENCHK_BIN $fname 2>/dev/null
+    actual=$?
+    if test $actual -ne $expected; then
+       echo "Unexpected return from $OPENCHK"
+       nerrors=`expr $nerrors + 1`
+    fi
+    # (2)
+    TESTING $H5CLEAR $1
+    fname=$1
+    # Use "h5clear" to clear the status_flags in the test file
+    $RUNSERIAL $H5CLEAR_BIN $fname
+    if test $? -ne $SUCCEED; then
+    echo ".....$H5CLEAR: should succeed"
+    nerrors=`expr $nerrors + 1`
+    else
+    # (3) Open the test file via "clear_open_chk"
+    $OPENCHK_BIN $fname
+    if test $? -ne $SUCCEED; then
+        echo "......$OPENCHK: should succeed"
+        nerrors=`expr $nerrors + 1`
+    else
+        echo "PASSED"
+    fi
+    fi
+}
+
+##############################################################################
+##############################################################################
+###              T H E   T E S T S                                ###
+##############################################################################
+##############################################################################
+#
+# Initial file open fails
+# After "h5clear" the file, the subsequent file open succeeds
+TOOLTEST h5clear_sec2_v3.h5 $FAIL
+#
+TOOLTEST h5clear_log_v3.h5 $FAIL
+#
+TOOLTEST latest_h5clear_sec2_v3.h5 $FAIL
+#
+TOOLTEST latest_h5clear_log_v3.h5 $FAIL
+#
+#
+# File open succeeds because the library does not check status_flags for file with < v3 superblock
+TOOLTEST h5clear_sec2_v0.h5 $SUCCEED
+TOOLTEST h5clear_sec2_v2.h5 $SUCCEED
+#
+# Clean up test files
+if test -z "$HDF5_NOCLEANUP"; then
+   rm -f h5clear_*.h5 latest_h5clear*.h5
+fi
+
+if test $nerrors -eq 0 ; then
+    echo "All $TESTNAME tests passed."
+    exit $EXIT_SUCCESS
+else
+    echo "$TESTNAME tests failed with $nerrors error(s)."
+    exit $EXIT_FAILURE
+fi