21 files changed, 864 insertions, 539 deletions

diff --git a/tools/h5diff/h5diff_common.c b/tools/h5diff/h5diff_common.c
index 898f56c..569cd00 100644
--- a/tools/h5diff/h5diff_common.c
+++ b/tools/h5diff/h5diff_common.c
@@ -475,6 +475,8 @@ int check_d_input( const char *str )
  *
  *-------------------------------------------------------------------------
  */
+
+#if defined (OLD)
 void usage(void)
 {
  printf("usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] \n");
@@ -533,6 +535,73 @@ void usage(void)
 
 }
 
+
+#else
+
+void usage(void)
+{
+ printf("usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] \n");
+ printf("  file1                    File name of the first HDF5 file\n");
+ printf("  file2                    File name of the second HDF5 file\n");
+ printf("  [obj1]                   Name of an HDF5 object, in absolute path\n");
+ printf("  [obj2]                   Name of an HDF5 object, in absolute path\n");
+
+ printf("  OPTIONS\n");
+
+ printf("   -h, --help              Print a usage message and exit\n");
+ printf("   -V, --version           Print version number and exit\n");
+ printf("   -r, --report            Report mode. Print differences\n");
+ printf("   -v, --verbose           Verbose mode. Print differences, list of objects\n");
+  
+ printf("   -q, --quiet             Quiet mode. Do not do output\n");
+ printf("   -n C, --count=C         Print differences up to C number\n");
+ printf("   -d D, --delta=D         Print difference when greater than limit D\n");
+ printf("   -p R, --relative=R      Print difference when greater than relative limit R\n");
+ 
+
+ printf("\n");
+
+ printf("  C - is a positive integer\n");
+ printf("  D - is a positive number. Compare criteria is |a - b| > D\n");
+ printf("  R - is a positive number. Compare criteria is |(b-a)/a| > R\n");
+
+ printf("\n");
+
+ printf("h5diff has four modes of output:\n");
+ printf(" Normal mode: print the number of differences found and where they occured\n");
+ printf(" Report mode: print the above plus the differences\n");
+ printf(" Verbose mode: print the above plus a list of objects and warnings\n");
+ printf(" Quiet mode: do not print output (h5diff always returns an exit code of 1 when differences are found)\n");
+ printf("\n");
+ printf("Examples of use:\n");
+ printf("\n");
+ printf("1) h5diff file1 file2 /g1/dset1 /g1/dset2\n");
+ printf("\n");
+ printf("   Compares object '/g1/dset1' in file1 with '/g1/dset2' in file2\n");
+ printf("\n");
+ printf("2) h5diff file1 file2 /g1/dset1\n");
+ printf("\n");
+ printf("   Compares object '/g1/dset1' in both files\n");
+ printf("\n");
+ printf("3) h5diff file1 file2\n");
+ printf("\n");
+ printf("   Compares all objects in both files\n");
+ printf("\n");
+ printf("Note)  file1 and file2 can be the same file. Use\n");
+ printf("\n");
+ printf("   h5diff file1 file1 /g1/dset1 /g1/dset2\n");
+ printf("\n");
+ printf("   to compare '/g1/dset1' and '/g1/dset2' in the same file\n");
+ printf("\n");
+ printf("If no objects are specified, h5diff only compares objects with the same ");
+ printf("absolute path in both files. The compare criteria is: ");
+ printf("1) datasets: numerical array differences 2) groups: name string difference ");
+ printf("3) datatypes: the return value of H5Tequal 2) links: name string difference of the linked value\n");
+
+}
+
+#endif
+
 /*-------------------------------------------------------------------------
  * Function: h5diff_exit
  *
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index 01f7c10..25a4936 100755
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -122,9 +122,9 @@ TOOLTEST()
     outfile=$path/out.$1
     shift
     if [ "`uname -s`" = "TFLOPS O/S" ]; then
-     $RUNSERIAL $H5REPACK_BIN -i $infile -o $outfile $@
+     $RUNSERIAL $H5REPACK_BIN $@ $infile $outfile
     else
-     $RUNSERIAL $H5REPACK_BIN -i $infile -o $outfile "$@"
+     $RUNSERIAL $H5REPACK_BIN "$@" $infile $outfile
     fi
 
     RET=$?
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 6c26cee..6ad97d7 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -437,6 +437,9 @@ int do_copy_objects(hid_t fidin,
              */
             case H5TRAV_TYPE_DATASET:
 
+                if (options->verbose)
+                    printf(FORMAT_OBJ,"dset",travt->objs[i].name );
+
                 has_filter = 0;
 
                 /* early detection of references */
@@ -777,6 +780,9 @@ int do_copy_objects(hid_t fidin,
              */
             case H5TRAV_TYPE_NAMED_DATATYPE:
 
+                if(options->verbose)
+                    printf(FORMAT_OBJ, "type", travt->objs[i].name);
+
                 if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
                     goto error;
 
@@ -798,8 +804,7 @@ int do_copy_objects(hid_t fidin,
                 if(H5Tclose(type_out) < 0)
                     goto error;
 
-                if(options->verbose)
-                    printf(FORMAT_OBJ, "type", travt->objs[i].name);
+              
 
                 break;
 
@@ -816,6 +821,10 @@ int do_copy_objects(hid_t fidin,
             case H5TRAV_TYPE_LINK:
             case H5TRAV_TYPE_UDLINK:
             {
+
+                if(options->verbose)
+                    printf(FORMAT_OBJ, "link", travt->objs[i].name);
+
                 if(H5Lcopy(fidin, travt->objs[i].name,fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
                     goto error;
 
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index 9c8b99f..f564b63 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -18,10 +18,404 @@
 #include "h5tools_utils.h"
 #include "h5repack.h"
 
+#if 0
+#define OLD
+#endif
+
+#if defined (OLD)
+static void usage(void);
+#else
+static void usage(const char *prog);
+#endif
+
+
 /* module-scoped variables */
 const char *progname = "h5repack";
 int d_status = EXIT_SUCCESS;
 
+/*
+ * Command-line options: The user can specify short or long-named
+ * parameters.
+ */
+static const char *s_opts = "hVvf:l:m:e:nLc:i:s:";
+static struct long_options l_opts[] = {
+    { "help", no_arg, 'h' },
+    { "version", no_arg, 'V' },
+    { "verbose", no_arg, 'v' },
+    { "filter", require_arg, 'f' },
+    { "layout", require_arg, 'l' },
+    { "threshold", require_arg, 'm' },
+    { "file", require_arg, 'e' },
+    { "native", no_arg, 'n' },
+    { "latest", no_arg, 'L' },
+    { "compact", require_arg, 'c' },
+    { "indexed", require_arg, 'i' },
+    { "ssize", require_arg, 's' },
+    { NULL, 0, '\0' }
+};
+
+/*-------------------------------------------------------------------------
+ * Function: parse_command_line
+ *
+ * Purpose: parse command line input
+ *
+ *-------------------------------------------------------------------------
+ */
+
+#if 0
+#define OLD
+#endif
+
+#if defined (OLD)
+
+
+void parse_command_line(int argc, 
+                        const char* argv[], 
+                        char** fname1, 
+                        char** fname2,
+                        pack_opt_t* options)
+{
+    
+    int i;
+    
+    if (argc<2)
+    {
+        usage();
+        exit(1);
+    }
+    
+    for ( i = 1; i < argc; i++)
+    {
+        if (strcmp(argv[i], "-h") == 0) {
+            usage();
+            exit(0);
+        }
+        else if (strcmp(argv[i], "-V") == 0) {
+            print_version(progname);
+            exit(0);
+        }
+        else if (strcmp(argv[i], "-i") == 0) {
+            *fname1 = argv[++i];
+        }
+        else if (strcmp(argv[i], "-o") == 0) {
+            *fname2 = argv[++i];
+        }
+        else if (strcmp(argv[i], "-v") == 0) {
+            options->verbose = 1;
+        }
+        else if (strcmp(argv[i], "-f") == 0) {
+            
+            /* add the -f filter option */
+            if (h5repack_addfilter(argv[i+1], options)<0)
+            {
+                error_msg(progname, "in parsing filter\n");
+                exit(1);
+            }
+            
+            /* jump to next */
+            ++i;
+        }
+        else if (strcmp(argv[i], "-l") == 0) {
+            
+            /* parse the -l layout option */
+            if (h5repack_addlayout(argv[i+1], options)<0)
+            {
+                error_msg(progname, "in parsing layout\n");
+                exit(1);
+            }
+            
+            /* jump to next */
+            ++i;
+        }
+        
+        else if (strcmp(argv[i], "-m") == 0) {
+            options->threshold = parse_number(argv[i+1]);
+            if ((int)options->threshold==-1) {
+                error_msg(progname, "invalid treshold size <%s>\n",argv[i+1]);
+                exit(1);
+            }
+            ++i;
+        }
+        
+        else if (strcmp(argv[i], "-e") == 0) {
+            read_info(argv[++i], options);
+        }
+        else if (strcmp(argv[i], "-n") == 0) {
+            options->use_native = 1;
+        }
+        
+        else if ( (strcmp(argv[i], "-L") == 0) || (strcmp(argv[i], "--latest") == 0)) {
+            options->latest = 1; 
+        }
+        
+        else if ( strncmp(argv[i], "-compact=", 9) == 0 ) {
+            options->grp_compact = atoi(argv[i]+9);
+            if (options->grp_compact>0)
+                options->latest = 1; /* must use latest format */
+        }
+        
+        else if ( strncmp(argv[i], "-indexed=", 9) == 0 ) {
+            options->grp_indexed = atoi(argv[i]+9);
+            if (options->grp_indexed>0)
+                options->latest = 1; /* must use latest format */
+        }
+        
+        else if ( strncmp(argv[i], "-ssize=", 7) == 0 ) {
+            int idx = 0;
+            int ssize = 0;
+            char *msgPtr = strchr(argv[i]+7, ':');
+            options->latest = 1; /* must use latest format */
+            if (msgPtr == NULL) {
+                ssize = atoi(argv[i]+7);
+                for (idx=0; idx<5; idx++)
+                    options->msg_size[idx] = ssize; 
+            }
+            else {
+                char msgType[10];
+                strcpy(msgType, msgPtr+1);
+                msgPtr[0] = '\0';
+                ssize = atoi(argv[i]+7);
+                if (strcmp(msgType, "dspace") == 0) {
+                    options->msg_size[0] = ssize;
+                }
+                else if (strcmp(msgType, "dtype") == 0) {
+                    options->msg_size[1] = ssize;
+                }
+                else if (strcmp(msgType, "fill") == 0) {
+                    options->msg_size[2] = ssize;
+                }
+                else if (strcmp(msgType, "pline") == 0) {
+                    options->msg_size[3] = ssize;
+                }
+                else if (strcmp(msgType, "attr") == 0) {
+                    options->msg_size[4] = ssize;
+                }
+            }
+        } /*  else if ( strncmp(argv[i], "-ssize=", 7) == 0 ) */
+        
+        else if (argv[i][0] == '-') {
+            error_msg(progname, " - is not a valid argument\n");
+            usage();
+            exit(1);
+        }
+        
+ }
+ 
+ 
+}
+
+#else
+
+void parse_command_line(int argc, 
+                        const char* argv[], 
+                        pack_opt_t* options)
+{
+    
+    int opt;
+   
+    /* parse command line options */
+    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) 
+    {
+        switch ((char)opt) 
+        {
+        case 'h':
+            usage(progname);
+            exit(EXIT_SUCCESS);
+        case 'V':
+            print_version(progname);
+            exit(EXIT_SUCCESS);
+        case 'v':
+            options->verbose = 1;
+            break;
+        case 'f':
+            
+            /* parse the -f filter option */
+            if (h5repack_addfilter( opt_arg, options)<0)
+            {
+                error_msg(progname, "in parsing filter\n");
+                exit(EXIT_FAILURE);
+            }
+            break;
+        case 'l':
+            
+            /* parse the -l layout option */
+            if (h5repack_addlayout( opt_arg, options)<0)
+            {
+                error_msg(progname, "in parsing layout\n");
+                exit(EXIT_FAILURE);
+            }
+            break;
+            
+
+        case 'm':
+
+            options->threshold = parse_number( opt_arg );
+            if ((int)options->threshold==-1) 
+            {
+                error_msg(progname, "invalid treshold size <%s>\n", opt_arg );
+                exit(EXIT_FAILURE);
+            }
+            break;
+        
+        case 'e':
+            read_info( opt_arg, options);
+            break;
+
+        case 'n':
+            options->use_native = 1;
+            break;
+        
+        case 'L':
+            options->latest = 1; 
+            break;
+        
+        case 'c':
+
+            options->grp_compact = atoi( opt_arg );
+            if (options->grp_compact>0)
+                options->latest = 1; /* must use latest format */
+            break;
+        
+        
+        case 'i':
+
+            options->grp_indexed = atoi( opt_arg );
+            if (options->grp_indexed>0)
+                options->latest = 1; /* must use latest format */
+            break;
+
+        case 's':
+
+            {
+                
+                int idx = 0;
+                int ssize = 0;
+                char *msgPtr = strchr( opt_arg, ':');
+                options->latest = 1; /* must use latest format */
+                if (msgPtr == NULL) 
+                {
+                    ssize = atoi( opt_arg );
+                    for (idx=0; idx<5; idx++)
+                        options->msg_size[idx] = ssize; 
+                }
+                else 
+                {
+                    char msgType[10];
+                    strcpy(msgType, msgPtr+1);
+                    msgPtr[0] = '\0';
+                    ssize = atoi( opt_arg );
+                    if (strcmp(msgType, "dspace") == 0) {
+                        options->msg_size[0] = ssize;
+                    }
+                    else if (strcmp(msgType, "dtype") == 0) {
+                        options->msg_size[1] = ssize;
+                    }
+                    else if (strcmp(msgType, "fill") == 0) {
+                        options->msg_size[2] = ssize;
+                    }
+                    else if (strcmp(msgType, "pline") == 0) {
+                        options->msg_size[3] = ssize;
+                    }
+                    else if (strcmp(msgType, "attr") == 0) {
+                        options->msg_size[4] = ssize;
+                    }
+                }            
+            }
+            
+            break;
+
+        } /* switch */
+        
+        
+    } /* while */
+    
+    /* check for file names to be processed */
+    if (argc <= opt_ind || argv[ opt_ind + 1 ] == NULL) 
+    {
+        error_msg(progname, "missing file names\n");
+        usage(progname);
+        exit(EXIT_FAILURE);
+    }
+    
+    
+
+ 
+ 
+}
+
+
+#endif
+
+/*-------------------------------------------------------------------------
+ * Function: main
+ *
+ * Purpose: h5repack main program
+ *
+ * Return: 1, error, 0, no error
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: May 9, 2003
+ *
+ * Comments:
+ *
+ * Modifications: 
+ *  July 2004: Introduced the extra EC or NN option for SZIP
+ *  October 2006: Added a new switch -n, that allows to write the dataset 
+ *                using a native type. The default to write is the file type.
+ *
+ * Modification:
+ *   Peter Cao, June 13, 2007
+ *   Add "-L, --latest" option to pack a file with the latest file format
+ *-------------------------------------------------------------------------
+ */
+int main(int argc, char **argv)
+{
+    char          *infile  = NULL;
+    char          *outfile = NULL;
+    pack_opt_t    options;            /*the global options */
+    int           ret;
+    
+    /* initialize options  */
+    h5repack_init (&options,0);
+
+#if defined (OLD)
+    
+    parse_command_line(argc, argv, &infile, &outfile, &options);
+    
+   
+#else
+
+    parse_command_line(argc, argv, &options);
+    
+    if ( argv[ opt_ind ] != NULL && argv[ opt_ind + 1 ] != NULL ) 
+    {
+        infile = argv[ opt_ind ];
+        outfile = argv[ opt_ind + 1 ];
+    }
+    
+    else
+    {
+        error_msg(progname, "file names missing\n");
+        usage(progname);
+        exit(EXIT_FAILURE);
+    }
+
+#endif
+    
+    /* pack it */
+    ret=h5repack(infile,outfile,&options);
+    
+    /* free tables */
+    h5repack_end(&options);
+    
+    if (ret==-1)
+        return 1;
+    else
+        return 0;
+}
+
+
 
 /*-------------------------------------------------------------------------
  * Function: usage
@@ -33,21 +427,21 @@ int d_status = EXIT_SUCCESS;
  *-------------------------------------------------------------------------
  */
 
-static
-void usage(void)
+#if defined OLD
+static void usage(void)
 {
- printf("usage: h5repack -i input -o output [-h] [-v] [-f FILTER] [-l LAYOUT] [-n] [-m size] [-e file]\n");
+ printf("usage: h5repack [-h] [-v] [-V] [-n] [-L] [-c] [-i] [-s] [-m size] [-e file] [-f FILTER] [-l LAYOUT] file1 file2\n");
  printf("\n");
- printf("-i input       Input HDF5 File\n");
- printf("-o output      Output HDF5 File\n");
+ printf("file1          Input HDF5 File\n");
+ printf("file2          Output HDF5 File\n");
  printf("[-h]           Print this message\n");
- printf("[-v]           Verbose mode\n");
+ printf("[-v]           Verbose mode, print object information\n");
  printf("[-V]           Print HDF5 version number and exit\n");
  printf("[-n]           Use a native HDF5 type when repacking. Default is the file type\n");
  printf("[-L, --latest]      Use latest version of file format to create groups, datasets and datatypes\n");
- printf("[-compact=<size>]      Set the maximum number of links to store as header messages in a group\n");
- printf("[-indexed=<size>]      Set the minimum number of links to store in the indexed format\n");
- printf("[-ssize=<size>[:<dspace|dtype|fill|pline|attr>]]      Set the shared object header message minimum size\n");
+ printf("[-c <size>, --compact=<size>]      Set the maximum number of links to store as header messages in a group\n");
+ printf("[-i <size>, --indexed=<size>]      Set the minimum number of links to store in the indexed format\n");
+ printf("[-s, --ssize=<size>[:<dspace|dtype|fill|pline|attr>]]      Set the shared object header message minimum size\n");
  printf("[-m size]      Do not apply the filter to objects smaller than size\n");
  printf("[-e file]      Name of file with the -f and -l options\n");
  printf("[-f FILTER]    Filter type\n");
@@ -116,178 +510,99 @@ void usage(void)
  printf("\n");
 }
 
-/*-------------------------------------------------------------------------
- * Function: main
- *
- * Purpose: h5repack main program
- *
- * Return: 1, error, 0, no error
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: May 9, 2003
- *
- * Comments:
- *
- * Modifications: 
- *  July 2004: Introduced the extra EC or NN option for SZIP
- *  October 2006: Added a new switch -n, that allows to write the dataset 
- *                using a native type. The default to write is the file type.
- *
- * Modification:
- *   Peter Cao, June 13, 2007
- *   Add "-L, --latest" option to pack a file with the latest file format
- *-------------------------------------------------------------------------
- */
-int main(int argc, char **argv)
-{
- char          *infile  = NULL;
- char          *outfile = NULL;
- pack_opt_t    options;            /*the global options */
- int           i, ret;
-
- /* initialize options  */
- h5repack_init (&options,0);
-
- if (argc<2)
- {
-  usage();
-  exit(1);
- }
-
- for ( i = 1; i < argc; i++)
- {
-  if (strcmp(argv[i], "-h") == 0) {
-    usage();
-    exit(0);
-  }
-  else if (strcmp(argv[i], "-V") == 0) {
-   print_version(progname);
-   exit(0);
-  }
-  else if (strcmp(argv[i], "-i") == 0) {
-   infile = argv[++i];
-  }
-  else if (strcmp(argv[i], "-o") == 0) {
-   outfile = argv[++i];
-  }
-  else if (strcmp(argv[i], "-v") == 0) {
-   options.verbose = 1;
-  }
-  else if (strcmp(argv[i], "-f") == 0) {
-
-   /* add the -f filter option */
-   if (h5repack_addfilter(argv[i+1],&options)<0)
-   {
-    error_msg(progname, "in parsing filter\n");
-    exit(1);
-   }
-
-   /* jump to next */
-   ++i;
-  }
-  else if (strcmp(argv[i], "-l") == 0) {
-
-   /* parse the -l layout option */
-   if (h5repack_addlayout(argv[i+1],&options)<0)
-   {
-    error_msg(progname, "in parsing layout\n");
-    exit(1);
-   }
-
-   /* jump to next */
-   ++i;
-  }
-
-  else if (strcmp(argv[i], "-m") == 0) {
-   options.threshold = parse_number(argv[i+1]);
-   if ((int)options.threshold==-1) {
-    error_msg(progname, "invalid treshold size <%s>\n",argv[i+1]);
-    exit(1);
-   }
-   ++i;
-  }
-
-  else if (strcmp(argv[i], "-e") == 0) {
-   read_info(argv[++i],&options);
-  }
-  else if (strcmp(argv[i], "-n") == 0) {
-   options.use_native = 1;
-  }
-
-  else if ( (strcmp(argv[i], "-L") == 0) || (strcmp(argv[i], "--latest") == 0)) {
-   options.latest = 1; 
-  }
-
-  else if ( strncmp(argv[i], "-compact=", 9) == 0 ) {
-   options.grp_compact = atoi(argv[i]+9);
-   if (options.grp_compact>0)
-    options.latest = 1; /* must use latest format */
-  }
-
-  else if ( strncmp(argv[i], "-indexed=", 9) == 0 ) {
-   options.grp_indexed = atoi(argv[i]+9);
-   if (options.grp_indexed>0)
-    options.latest = 1; /* must use latest format */
-  }
-
-  else if ( strncmp(argv[i], "-ssize=", 7) == 0 ) {
-   int idx = 0;
-   int ssize = 0;
-   char *msgPtr = strchr(argv[i]+7, ':');
-   options.latest = 1; /* must use latest format */
-   if (msgPtr == NULL) {
-    ssize = atoi(argv[i]+7);
-    for (idx=0; idx<5; idx++)
-     options.msg_size[idx] = ssize; 
-   }
-   else {
-    char msgType[10];
-    strcpy(msgType, msgPtr+1);
-    msgPtr[0] = '\0';
-    ssize = atoi(argv[i]+7);
-    if (strcmp(msgType, "dspace") == 0) {
-     options.msg_size[0] = ssize;
-    }
-    else if (strcmp(msgType, "dtype") == 0) {
-     options.msg_size[1] = ssize;
-    }
-    else if (strcmp(msgType, "fill") == 0) {
-     options.msg_size[2] = ssize;
-    }
-    else if (strcmp(msgType, "pline") == 0) {
-     options.msg_size[3] = ssize;
-    }
-    else if (strcmp(msgType, "attr") == 0) {
-     options.msg_size[4] = ssize;
-    }
-   }
-  } /*  else if ( strncmp(argv[i], "-ssize=", 7) == 0 ) */
-
-  else if (argv[i][0] == '-') {
-   error_msg(progname, " - is not a valid argument\n");
-   usage();
-   exit(1);
-  }
+#else
 
- }
-
- if (infile == NULL || outfile == NULL)
- {
-  error_msg(progname, "file names missing\n");
-  usage();
-  exit(1);
- }
+static void usage(const char *prog)
+{
+ printf("usage: %s [OPTIONS] file1 file2\n", prog);
+ printf("  file1                    Input HDF5 File\n");
+ printf("  file2                    Output HDF5 File\n");
+ printf("  OPTIONS\n");
+ printf("   -h, --help              Print a usage message and exit\n");
+ printf("   -v, --verbose           Verbose mode, print object information\n");
+ printf("   -V, --version           Print version number and exit\n");
+ printf("   -n, --native            Use a native HDF5 type when repacking\n");
+ printf("   -L, --latest            Use latest version of file format\n");
+ printf("   -c <L1>, --compact=<L1> Maximum number of links in header messages\n");
+ printf("   -i <L2>, --indexed=<L2> Minimum number of links in the indexed format\n");
+ printf("   -s <S:F>, --ssize=<S:F> Set the shared object header message minimum size\n");
+ printf("   -m T, --threshold=T     Do not apply the filter to objects smaller than T\n");
+ printf("   -e M, --file=M          Name of file M with the -f and -l options\n");
+ printf("   -f FILT, --filter=FILT  Filter type\n");
+ printf("   -l LAYT, --layout=LAYT  Layout type\n");
+ 
+ printf("\n");
 
- /* pack it */
- ret=h5repack(infile,outfile,&options);
+ printf("  T - is an integer greater than 1\n");
+ printf("  M - is a filename.\n");
+ printf("  F - is the shared object header message type, any of\n");
+ printf("        <dspace|dtype|fill|pline|attr>\n");
 
- /* free tables */
- h5repack_end(&options);
+ printf("\n");
 
- if (ret==-1)
-  return 1;
- else
-  return 0;
+ printf("  FILT - is a string with the format:\n");
+ printf("\n");
+ printf("    <list of objects>:<name of filter>=<filter parameters>\n");
+ printf("\n");
+ printf("    <list of objects> is a comma separated list of object names, meaning apply\n");
+ printf("      compression only to those objects. If no names are specified, the filter\n");
+ printf("      is applied to all objects\n");
+ printf("    <name of filter> can be:\n");
+ printf("      GZIP, to apply the HDF5 GZIP filter (GZIP compression)\n");
+ printf("      SZIP, to apply the HDF5 SZIP filter (SZIP compression)\n");
+ printf("      SHUF, to apply the HDF5 shuffle filter\n");
+ printf("      FLET, to apply the HDF5 checksum filter\n");
+ printf("      NBIT, to apply the HDF5 NBIT filter (NBIT compression)\n");
+ printf("      SOFF, to apply the HDF5 Scale/Offset filter\n");
+ printf("      NONE, to remove all filters\n");
+ printf("    <filter parameters> is optional filter parameter information\n");
+ printf("      GZIP=<deflation level> from 1-9\n");
+ printf("      SZIP=<pixels per block,coding> pixels per block is a even number in\n");
+ printf("            2-32 and coding method is either EC or NN\n");
+ printf("      SHUF (no parameter)\n");
+ printf("      FLET (no parameter)\n");
+ printf("      NBIT (no parameter)\n");
+ printf("      SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
+ printf("            is either IN or DS\n");
+ printf("      NONE (no parameter)\n");
+ printf("\n");
+ printf("  LAYT - is a string with the format:\n");
+ printf("\n");
+ printf("    <list of objects>:<layout type>=<layout parameters>\n");
+ printf("\n");
+ printf("    <list of objects> is a comma separated list of object names, meaning that\n");
+ printf("      layout information is supplied for those objects. If no names are\n");
+ printf("      specified, the layout type is applied to all objects\n");
+ printf("    <layout type> can be:\n");
+ printf("      CHUNK, to apply chunking layout\n");
+ printf("      COMPA, to apply compact layout\n");
+ printf("      CONTI, to apply continuous layout\n");
+ printf("    <layout parameters> is optional layout information\n");
+ printf("      CHUNK=DIM[xDIM...xDIM], the chunk size of each dimension\n");
+ printf("      COMPA (no parameter)\n");
+ printf("      CONTI (no parameter)\n");
+ printf("\n");
+ printf("Examples of use:\n");
+ printf("\n");
+ printf("1) h5repack -v -f GZIP=1 file1 file2\n");
+ printf("\n");
+ printf("   GZIP compression with level 1 to all objects\n");
+ printf("\n");
+ printf("2) h5repack -v -f A:SZIP=8,NN file1 file2\n");
+ printf("\n");
+ printf("   SZIP compression with 8 pixels per block and NN coding method to object A\n");
+ printf("\n");
+ printf("3) h5repack -v -l A,B:CHUNK=20x10 -f C,D,F:NONE file1 file2\n");
+ printf("\n");
+ printf("   Chunked layout, with a layout size of 20x10, to objects A and B\n");
+ printf("   and remove filters to objects C, D, F\n");
+ printf("\n");
+ printf("4) h5repack -L -c=10 -s=20:dtype file1 file2 \n");
+ printf("\n");
+ printf("   Using latest file format with maximum compact group size of 10 and\n");
+ printf("   and minimum shared datatype size of 20\n");
+ printf("\n");
 }
 
+#endif
+
diff --git a/tools/testfiles/h5diff_10.txt b/tools/testfiles/h5diff_10.txt
index 6a45339..cc20357 100644
--- a/tools/testfiles/h5diff_10.txt
+++ b/tools/testfiles/h5diff_10.txt
@@ -2,27 +2,23 @@
 Expected output for 'h5diff -h'
 #############################
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_600.txt b/tools/testfiles/h5diff_600.txt
index a1bb063..d108d9a 100644
--- a/tools/testfiles/h5diff_600.txt
+++ b/tools/testfiles/h5diff_600.txt
@@ -2,27 +2,23 @@
 Expected output for 'h5diff h5diff_basic1.h5'
 #############################
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_602.txt b/tools/testfiles/h5diff_602.txt
index b9c2b8f6..318e91b 100644
--- a/tools/testfiles/h5diff_602.txt
+++ b/tools/testfiles/h5diff_602.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -d h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/dse
 #############################
 <-d h5diff_basic1.h5> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_603.txt b/tools/testfiles/h5diff_603.txt
index efc8769..c1f1af2 100644
--- a/tools/testfiles/h5diff_603.txt
+++ b/tools/testfiles/h5diff_603.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -d -4 h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/
 #############################
 <-d -4> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_604.txt b/tools/testfiles/h5diff_604.txt
index 7f0a2a6..898e32b 100644
--- a/tools/testfiles/h5diff_604.txt
+++ b/tools/testfiles/h5diff_604.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -d 0 h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/d
 #############################
 <-d 0> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_605.txt b/tools/testfiles/h5diff_605.txt
index 5101c2d..be291ba 100644
--- a/tools/testfiles/h5diff_605.txt
+++ b/tools/testfiles/h5diff_605.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -d u h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/d
 #############################
 <-d u> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_606.txt b/tools/testfiles/h5diff_606.txt
index 9e32909..c59f386 100644
--- a/tools/testfiles/h5diff_606.txt
+++ b/tools/testfiles/h5diff_606.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -d 0x1 h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1
 #############################
 <-d 0x1> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_611.txt b/tools/testfiles/h5diff_611.txt
index 1d5e146..dc861ab 100644
--- a/tools/testfiles/h5diff_611.txt
+++ b/tools/testfiles/h5diff_611.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -r -p h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/
 #############################
 <-p h5diff_basic1.h5> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_612.txt b/tools/testfiles/h5diff_612.txt
index 47c36fb..a694dde 100644
--- a/tools/testfiles/h5diff_612.txt
+++ b/tools/testfiles/h5diff_612.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -p -4 h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/
 #############################
 <-p -4> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_613.txt b/tools/testfiles/h5diff_613.txt
index 056cbd6..4e36094 100644
--- a/tools/testfiles/h5diff_613.txt
+++ b/tools/testfiles/h5diff_613.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -p 0 h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/d
 #############################
 <-p 0> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_614.txt b/tools/testfiles/h5diff_614.txt
index 82db7f3..f0530e3 100644
--- a/tools/testfiles/h5diff_614.txt
+++ b/tools/testfiles/h5diff_614.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -p u h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/d
 #############################
 <-p u> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_615.txt b/tools/testfiles/h5diff_615.txt
index 8ff33ac..eb45442 100644
--- a/tools/testfiles/h5diff_615.txt
+++ b/tools/testfiles/h5diff_615.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -p 0x1 h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1
 #############################
 <-p 0x1> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_620.txt b/tools/testfiles/h5diff_620.txt
index 29110b9..1707bb7 100644
--- a/tools/testfiles/h5diff_620.txt
+++ b/tools/testfiles/h5diff_620.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -n h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/dse
 #############################
 <-n h5diff_basic1.h5> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_621.txt b/tools/testfiles/h5diff_621.txt
index ae7c644..39e4c48 100644
--- a/tools/testfiles/h5diff_621.txt
+++ b/tools/testfiles/h5diff_621.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -n -4 h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/
 #############################
 <-n -4> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_622.txt b/tools/testfiles/h5diff_622.txt
index 97cfda0..aff6dee 100644
--- a/tools/testfiles/h5diff_622.txt
+++ b/tools/testfiles/h5diff_622.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -n 0 h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/d
 #############################
 <-n 0> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_623.txt b/tools/testfiles/h5diff_623.txt
index 9d2a914..4d1c6fa 100644
--- a/tools/testfiles/h5diff_623.txt
+++ b/tools/testfiles/h5diff_623.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -n u h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1/d
 #############################
 <-n u> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured
diff --git a/tools/testfiles/h5diff_624.txt b/tools/testfiles/h5diff_624.txt
index 7fc9cb1..1cba110 100644
--- a/tools/testfiles/h5diff_624.txt
+++ b/tools/testfiles/h5diff_624.txt
@@ -3,27 +3,23 @@ Expected output for 'h5diff -n 0x1 h5diff_basic1.h5 h5diff_basic2.h5 g1/dset3 g1
 #############################
 <-n 0x1> is not a valid option
 usage: h5diff [OPTIONS] file1 file2 [obj1[obj2]] 
-
-file1             File name of the first HDF5 file
-file2             File name of the second HDF5 file
-[obj1]            Name of an HDF5 object, in absolute path
-[obj2]            Name of an HDF5 object, in absolute path
-[OPTIONS] are:
-[-h]              Print out this information
-[-V]              Print HDF5 library version number and exit
-[-r]              Report mode. Print differences
-[-v]              Verbose mode. Print differences, list of objects, warnings
-[-q]              Quiet mode. Do not do output
-[-n count]        Print difference up to count number
-[-d delta]        Print difference when it is greater than limit delta
-[-p relative]     Print difference when it is greater than a relative limit
-
-Items in [] are optional
-[obj1] and [obj2] are HDF5 objects (datasets, groups, datatypes or links)
-The 'count' value must be a positive integer
-The 'delta' and 'relative' values must be positive numbers
-The -d compare criteria is |a - b| > delta
-The -p compare criteria is |(b-a)/a| > relative
+  file1                    File name of the first HDF5 file
+  file2                    File name of the second HDF5 file
+  [obj1]                   Name of an HDF5 object, in absolute path
+  [obj2]                   Name of an HDF5 object, in absolute path
+  OPTIONS
+   -h, --help              Print a usage message and exit
+   -V, --version           Print version number and exit
+   -r, --report            Report mode. Print differences
+   -v, --verbose           Verbose mode. Print differences, list of objects
+   -q, --quiet             Quiet mode. Do not do output
+   -n C, --count=C         Print differences up to C number
+   -d D, --delta=D         Print difference when greater than limit D
+   -p R, --relative=R      Print difference when greater than relative limit R
+
+  C - is a positive integer
+  D - is a positive number. Compare criteria is |a - b| > D
+  R - is a positive number. Compare criteria is |(b-a)/a| > R
 
 h5diff has four modes of output:
  Normal mode: print the number of differences found and where they occured