Bring SWMR-related tools changes from revise_chunks to develop.

24 files changed, 813 insertions, 20 deletions

diff --git a/tools/lib/h5tools.h b/tools/lib/h5tools.h
index ed93a46..38739c8 100644
--- a/tools/lib/h5tools.h
+++ b/tools/lib/h5tools.h
@@ -203,6 +203,10 @@ typedef struct h5tools_dump_header_t {
 
 } h5tools_dump_header_t;
 
+/* Forward declaration (see declaration in h5tools_str.c) */
+struct H5LD_memb_t;
+
+
 /*
  * Information about how to format output.
  */
@@ -338,12 +342,16 @@ typedef struct h5tool_format_t {
      *
      *   end:       a string to print after we reach the last element of
      *              each compound type. prints out before the suf.
+     *
+     *   listv:    h5watch: vector containing info about the list of compound fields to be printed.
      */
     const char  *cmpd_name;
     const char  *cmpd_sep;
     const char  *cmpd_pre;
     const char  *cmpd_suf;
     const char  *cmpd_end;
+    const struct H5LD_memb_t * const *cmpd_listv;
+
 
     /*
      * Fields associated with vlen data types.
@@ -516,6 +524,7 @@ typedef struct h5tools_context_t {
     hsize_t acc[H5S_MAX_RANK];        /* accumulator position */
     hsize_t pos[H5S_MAX_RANK];        /* matrix position */
     hsize_t sm_pos;                   /* current stripmine element position */
+    struct H5LD_memb_t **cmpd_listv;  /* h5watch: vector containing info about the list of compound fields to be printed */
 } h5tools_context_t;
 
 typedef struct subset_d {
diff --git a/tools/lib/h5tools_dump.c b/tools/lib/h5tools_dump.c
index cae3107..67585d1 100644
--- a/tools/lib/h5tools_dump.c
+++ b/tools/lib/h5tools_dump.c
@@ -61,6 +61,7 @@ NULL, /*fmt_ullong */
 "{", /*cmpd_pre */
 "}", /*cmpd_suf */
 "\n", /*cmpd_end */
+NULL, /* cmpd_listv */
 
 ", ", /*vlen_sep */
 "(", /*vlen_pre */
@@ -1485,6 +1486,9 @@ h5tools_dump_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_co
         H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
     ctx->size_last_dim = total_size[ctx->ndims - 1];
 
+    /* Set the compound datatype field list for display */
+    ctx->cmpd_listv = info->cmpd_listv;
+
     h5tools_display_simple_subset(stream, info, ctx, dset, p_type, sset, f_space, total_size);
 
 CATCH
diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
index a0a78f5..358e993 100644
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -29,6 +29,15 @@
 #include "h5tools_ref.h"
 #include "h5tools_str.h"        /*function prototypes       */
 
+/* Copied from hl/src/H5LDprivate.h */
+/* Info about the list of comma-separated compound fields */
+typedef struct H5LD_memb_t {
+   size_t tot_offset;
+   size_t last_tsize;
+   hid_t last_tid;
+   char **names;
+} H5LD_memb_t;
+
 /*
  * If REPEAT_VERBOSE is defined then character strings will be printed so
  * that repeated character sequences like "AAAAAAAAAA" are displayed as
@@ -730,6 +739,9 @@ h5tools_str_indent(h5tools_str_t *str, const h5tool_format_t *info,
  *  PVN, 28 March 2006
  *  added H5T_NATIVE_LDOUBLE case
  *
+ *  Vailin Choi; August 2010
+ *	Modified to handle printing of selected compound fields for h5watch.
+ *
  *  Raymond Lu, 2011-09-01
  *  CLANG compiler complained about the line (about 800):
  *    tempint = (tempint >> packed_data_offset) & packed_data_mask;
@@ -1024,7 +1036,57 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai
                 break;
 
             case H5T_COMPOUND:
-                {
+                if(ctx->cmpd_listv) { /* there is <list_of_fields> */
+                    int save_indent_level;  	/* The indentation level */
+                    size_t curr_field;          /* Current field to display */
+                    int i = 0, x = 0; 		/* Local index variable */
+                    H5LD_memb_t **listv;  	/* Vector of information for <list_of_fields> */
+
+                    listv = ctx->cmpd_listv;	    
+                    ctx->cmpd_listv = NULL;
+
+                    h5tools_str_append(str, "%s", OPT(info->cmpd_pre, "{"));
+
+                    /* 
+                     * Go through the vector containing info about the comma-separated list of
+                     * compound fields and then members in each field: 
+                     *	   put in "{", "}", ",", member name and value accordingly.
+                     */
+                    save_indent_level = ctx->indent_level;
+                    for(curr_field = 0; listv[curr_field] != NULL; curr_field++) {
+                        if (curr_field)
+                            h5tools_str_append(str, "%s", OPT(info->cmpd_sep, ", "OPTIONAL_LINE_BREAK));
+                        else 
+                            h5tools_str_append(str, "%s", OPT(info->cmpd_end, ""));
+
+                        if(info->arr_linebreak)
+                            h5tools_str_indent(str, info, ctx);
+                        
+                        /* Process members of each field */
+                        for(i = 0; listv[curr_field]->names[i] != NULL; i++) {
+                            h5tools_str_append(str, OPT(info->cmpd_name, ""), listv[curr_field]->names[i]);
+                            if(i) {
+                                ctx->indent_level++;
+                                h5tools_str_append(str, "%s", OPT(info->cmpd_pre, "{"));
+                            }
+                        }
+                        h5tools_str_sprint(str, info, container, listv[curr_field]->last_tid, cp_vp + listv[curr_field]->tot_offset, ctx);
+                        if(ctx->indent_level > 0)
+                            for(x = ctx->indent_level; x > 0; x--)
+                                h5tools_str_append(str, "%s", OPT(info->cmpd_suf, "}"));
+                        ctx->indent_level = save_indent_level;
+                    }
+
+
+                    if(info->arr_linebreak) {
+                        h5tools_str_append(str, "%s", OPT(info->cmpd_end, ""));
+                        h5tools_str_indent(str, info, ctx);
+                    }
+                    h5tools_str_append(str, "%s", OPT(info->cmpd_suf, "}"));
+
+                    ctx->cmpd_listv = info->cmpd_listv;
+
+                } else {
                     unsigned nmembs;
                     unsigned j;
 
diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c
index 41f3914..5290c3d 100644
--- a/tools/src/h5dump/h5dump_xml.c
+++ b/tools/src/h5dump/h5dump_xml.c
@@ -69,6 +69,7 @@ static h5tool_format_t         xml_dataformat = {
     "",             /*cmpd_pre */
     "",             /*cmpd_suf */
     "",             /*cmpd_end */
+    "",             /*cmpd_listv */
 
     " ",            /*vlen_sep */
     " ",            /*vlen_pre */
diff --git a/tools/src/h5ls/h5ls.c b/tools/src/h5ls/h5ls.c
index a032f08..88bab20 100644
--- a/tools/src/h5ls/h5ls.c
+++ b/tools/src/h5ls/h5ls.c
@@ -70,6 +70,7 @@ static h5tool_format_t         ls_dataformat = {
         "{", /*cmpd_pre */
         "}", /*cmpd_suf */
         "", /*cmpd_end */
+        NULL, /* cmpd_listv */
 
         ",", /*vlen_sep */
         "(", /*vlen_pre */
diff --git a/tools/src/misc/CMakeLists.txt b/tools/src/misc/CMakeLists.txt
index 6fcff9c..0bda701 100644
--- a/tools/src/misc/CMakeLists.txt
+++ b/tools/src/misc/CMakeLists.txt
@@ -31,10 +31,18 @@ target_link_libraries (h5mkgrp  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
 set_target_properties (h5mkgrp PROPERTIES FOLDER tools)
 set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5mkgrp")
 
+add_executable (h5clear ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5clear.c)
+TARGET_NAMING (h5clear STATIC)
+TARGET_C_PROPERTIES (h5clear STATIC " " " ")
+target_link_libraries (h5clear  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+set_target_properties (h5clear PROPERTIES FOLDER tools)
+set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5clear")
+
 set (H5_DEP_EXECUTABLES
     h5debug
     h5repart
     h5mkgrp
+    h5clear
 )
 
 #-----------------------------------------------------------------------------
diff --git a/tools/src/misc/Makefile.am b/tools/src/misc/Makefile.am
index c069e9a..ad3dae9b 100644
--- a/tools/src/misc/Makefile.am
+++ b/tools/src/misc/Makefile.am
@@ -24,13 +24,14 @@ include $(top_srcdir)/config/commence.am
 AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 
 # These are our main targets, the tools
-bin_PROGRAMS=h5debug h5repart h5mkgrp
+bin_PROGRAMS=h5debug h5repart h5mkgrp h5clear
 bin_SCRIPTS=h5redeploy
 
 # Add h5debug, h5repart, and h5mkgrp specific linker flags here
 h5debug_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 h5repart_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 h5mkgrp_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+h5clear_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # Tell automake to clean h5redeploy script
 CLEANFILES=h5redeploy
diff --git a/tools/src/misc/h5clear.c b/tools/src/misc/h5clear.c
new file mode 100644
index 0000000..0be4f8f
--- /dev/null
+++ b/tools/src/misc/h5clear.c
@@ -0,0 +1,137 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Programmer:  
+ *
+ * Purpose:	
+ */
+
+#include "hdf5.h"
+#include "H5private.h"
+#include "h5tools.h"
+#include "h5tools_utils.h"
+
+/* Name of tool */
+#define PROGRAMNAME 	"h5clear"
+
+/* Make this private property (defined in H5Fprivate.h) available to h5clear. */
+#define H5F_ACS_CLEAR_STATUS_FLAGS_NAME            "clear_status_flags"
+
+/*-------------------------------------------------------------------------
+ * Function:    leave
+ *
+ * Purpose:     Close the tools library and exit
+ *
+ * Return:   	Does not return
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+leave(int ret)
+{
+    h5tools_close();
+    HDexit(ret);
+
+} /* leave() */
+
+/*-------------------------------------------------------------------------
+ * Function: 	usage
+ *
+ * Purpose: 	Prints a usage message
+ *
+ * Return: 	void
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+usage(void)
+{
+    HDfprintf(stdout, "usage: h5clear filename\n");
+
+} /* usage() */
+
+
+
+/*-------------------------------------------------------------------------
+ * Function:	main
+ *
+ * Purpose:	
+ *
+ * Return:	Success:
+ *		Failure:
+ *
+ * Programmer:	
+ *
+ *-------------------------------------------------------------------------
+ */
+int
+main (int argc, char *argv[])
+{
+    char *fname;		/* File name */
+    hbool_t clear = TRUE;  	/* To clear the status_flags in the file's superblock */
+    hid_t fapl = -1;   		/* File access property list */
+    hid_t fid = -1;		/* File ID */
+
+    h5tools_setprogname(PROGRAMNAME);
+    h5tools_setstatus(EXIT_SUCCESS);
+    
+    /* Disable the HDF5 library's error reporting */
+    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
+
+    /* initialize h5tools lib */
+    h5tools_init();
+
+    /* Check for the # of arguments */
+    if(argc != 2) {
+        usage();
+        leave(EXIT_FAILURE);
+    }
+
+    /* Duplicate the file name */
+    fname = HDstrdup(argv[opt_ind]);
+
+    /* Get a copy of the file access property list */
+    if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+        error_msg("H5Pcreate\n");
+        exit(EXIT_FAILURE);
+    }
+
+    /* Set to clear the status_flags in the file's superblock */
+    /* This is a private property used by h5clear only */
+    if(H5Pset(fapl, H5F_ACS_CLEAR_STATUS_FLAGS_NAME, &clear) < 0) {
+	error_msg("H5Pset\n");
+	exit(EXIT_FAILURE);
+    }
+
+    if((fid = h5tools_fopen(fname, H5F_ACC_RDWR, fapl, NULL, NULL, (size_t)0)) < 0) {
+	error_msg("h5tools_fopen\n");
+	exit(EXIT_FAILURE);
+    }
+
+    /* Close the file */
+    if(H5Fclose(fid) < 0) {
+	error_msg("H5Fclose\n");
+	exit(EXIT_FAILURE);
+    }
+
+    /* CLose the property list */
+    if(H5Pclose(fapl) < 0) {
+	error_msg("H5Pclose\n");
+	exit(EXIT_FAILURE);
+    }
+
+    return EXIT_SUCCESS;
+} /* main() */
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
diff --git a/tools/testfiles/tdset_idx.ddl b/tools/testfiles/tdset_idx.ddl
new file mode 100644
index 0000000..65d9f44
--- /dev/null
+++ b/tools/testfiles/tdset_idx.ddl
@@ -0,0 +1,61 @@
+#############################
+Expected output for 'h5dump -p -H tdset_idx.h5'
+#############################
+HDF5 "tdset_idx.h5" {
+GROUP "/" {
+   DATASET "dset_btree" {
+      DATATYPE  H5T_STD_I32LE
+      DATASPACE  SIMPLE { ( 20, 10 ) / ( 200, 100 ) }
+      STORAGE_LAYOUT {
+         CHUNKED ( 5, 5 )
+         SIZE 800
+       }
+      FILTERS {
+         NONE
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0      
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_INCR
+      }
+   }
+   DATASET "dset_filter" {
+      DATATYPE  H5T_STD_I32LE
+      DATASPACE  SIMPLE { ( 20, 10 ) / ( 20, 10 ) }
+      STORAGE_LAYOUT {
+         CHUNKED ( 5, 5 )
+         SIZE 200 (4.000:1 COMPRESSION)
+       }
+      FILTERS {
+         COMPRESSION DEFLATE { LEVEL 9 }
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0      
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_INCR
+      }
+   }
+   DATASET "dset_fixed" {
+      DATATYPE  H5T_STD_I32LE
+      DATASPACE  SIMPLE { ( 20, 10 ) / ( 20, 10 ) }
+      STORAGE_LAYOUT {
+         CHUNKED ( 5, 5 )
+         SIZE 800
+       }
+      FILTERS {
+         NONE
+      }
+      FILLVALUE {
+         FILL_TIME H5D_FILL_TIME_IFSET
+         VALUE  0      
+      }
+      ALLOCATION_TIME {
+         H5D_ALLOC_TIME_INCR
+      }
+   }
+}
+}