Split tools into src and test - add folders

6 files changed, 1230 insertions, 0 deletions

diff --git a/tools/src/h5diff/CMakeLists.txt b/tools/src/h5diff/CMakeLists.txt
new file mode 100644
index 0000000..85a24ef
--- /dev/null
+++ b/tools/src/h5diff/CMakeLists.txt
@@ -0,0 +1,67 @@
+cmake_minimum_required (VERSION 3.1.0)
+PROJECT (HDF5_TOOLS_SRC_H5DIFF)
+
+#-----------------------------------------------------------------------------
+# Setup include Directories
+#-----------------------------------------------------------------------------
+INCLUDE_DIRECTORIES (${HDF5_TOOLS_DIR}/lib)
+
+# --------------------------------------------------------------------
+# Add the h5diff executables
+# --------------------------------------------------------------------
+add_executable (h5diff
+    ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.c
+    ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_main.c
+)
+TARGET_NAMING (h5diff STATIC)
+TARGET_C_PROPERTIES (h5diff STATIC " " " ")
+target_link_libraries (h5diff  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+set_target_properties (h5diff PROPERTIES FOLDER tools)
+set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5diff")
+
+set (H5_DEP_EXECUTABLES h5diff)
+
+if (H5_HAVE_PARALLEL)
+  add_executable (ph5diff
+      ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.c
+      ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/ph5diff_main.c
+  )
+  TARGET_NAMING (ph5diff STATIC)
+  TARGET_C_PROPERTIES (ph5diff STATIC " " " ")
+  target_link_libraries (ph5diff  ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+  set_target_properties (ph5diff PROPERTIES FOLDER tools)
+  set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};ph5diff")
+endif (H5_HAVE_PARALLEL)
+
+##############################################################################
+##############################################################################
+###           I N S T A L L A T I O N                                      ###
+##############################################################################
+##############################################################################
+
+#-----------------------------------------------------------------------------
+# Rules for Installation of tools using make Install target
+#-----------------------------------------------------------------------------
+
+#INSTALL_PROGRAM_PDB (h5diff ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+
+install (
+    TARGETS
+        h5diff
+    EXPORT
+        ${HDF5_EXPORTED_TARGETS}
+    RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT toolsapplications
+)
+
+if (H5_HAVE_PARALLEL)
+
+  #INSTALL_PROGRAM_PDB (ph5diff ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+
+  install (
+      TARGETS
+          ph5diff
+      EXPORT
+          ${HDF5_EXPORTED_TARGETS}
+      RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT toolsapplications
+  )
+endif (H5_HAVE_PARALLEL)
diff --git a/tools/src/h5diff/Makefile.am b/tools/src/h5diff/Makefile.am
new file mode 100644
index 0000000..a5af3f2
--- /dev/null
+++ b/tools/src/h5diff/Makefile.am
@@ -0,0 +1,46 @@
+#
+# 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.
+##
+## Makefile.am
+## Run automake to generate a Makefile.in from this file.
+#
+# HDF5 Library Makefile(.in)
+#
+
+include $(top_srcdir)/config/commence.am
+
+# Include src and tools/lib directories
+AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
+
+# Always build and test h5diff but build and test ph5diff only if parallel
+# is enabled.
+if BUILD_PARALLEL_CONDITIONAL
+  H5PDIFF=ph5diff
+endif
+
+# Our main target, h5diff
+bin_PROGRAMS=h5diff $(H5PDIFF)
+
+# Add h5diff specific linker flags here
+h5diff_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+
+# Source files for the program
+h5diff_SOURCES=h5diff_main.c h5diff_common.c
+ph5diff_SOURCES=ph5diff_main.c h5diff_common.c
+
+# Programs depend on the main HDF5 library and tools library
+LDADD=$(LIBH5TOOLS) $(LIBHDF5)
+
+include $(top_srcdir)/config/conclude.am
+
diff --git a/tools/src/h5diff/h5diff_common.c b/tools/src/h5diff/h5diff_common.c
new file mode 100644
index 0000000..2453ffc
--- /dev/null
+++ b/tools/src/h5diff/h5diff_common.c
@@ -0,0 +1,607 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 <stdlib.h>
+#include <string.h>
+#include "H5private.h"
+#include "h5diff.h"
+#include "h5diff_common.h"
+#include "h5tools.h"
+#include "h5tools_utils.h"
+
+static int check_n_input( const char* );
+static int check_p_input( const char* );
+static int check_d_input( const char* );
+
+/*
+ * Command-line options: The user can specify short or long-named
+ * parameters.
+ */
+static const char *s_opts = "hVrv:qn:d:p:Nc";
+static struct long_options l_opts[] = {
+    { "help", no_arg, 'h' },
+    { "version", no_arg, 'V' },
+    { "report", no_arg, 'r' },
+    { "verbose", optional_arg, 'v' },
+    { "quiet", no_arg, 'q' },
+    { "count", require_arg, 'n' },
+    { "delta", require_arg, 'd' },
+    { "relative", require_arg, 'p' },
+    { "nan", no_arg, 'N' },
+    { "compare", no_arg, 'c' },
+    { "use-system-epsilon", no_arg, 'e' },
+    { "follow-symlinks", no_arg, 'l' },
+    { "no-dangling-links", no_arg, 'x' },
+    { "exclude-path", require_arg, 'E' },
+    { NULL, 0, '\0' }
+};
+
+/*-------------------------------------------------------------------------
+ * Function: check_options
+ *
+ * Purpose: parse command line input
+ *
+ *-------------------------------------------------------------------------
+ */
+static void check_options(diff_opt_t* options)
+{
+    /*--------------------------------------------------------------
+     * check for mutually exclusive options 
+     *--------------------------------------------------------------*/
+
+    /* check between -d , -p, --use-system-epsilon.
+     * These options are mutually exclusive.
+     */
+    if ((options->d + options->p + options->use_system_epsilon) > 1)
+    {
+        printf("%s error: -d, -p and --use-system-epsilon options are mutually-exclusive;\n", PROGRAMNAME);
+        printf("use no more than one.\n");
+        printf("Try '-h' or '--help' option for more information or see the %s entry in the 'HDF5 Reference Manual'.\n", PROGRAMNAME);
+        h5diff_exit(EXIT_FAILURE);
+    }
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: parse_command_line
+ *
+ * Purpose: parse command line input
+ *
+ *-------------------------------------------------------------------------
+ */
+
+void parse_command_line(int argc,
+                        const char* argv[],
+                        const char** fname1,
+                        const char** fname2,
+                        const char** objname1,
+                        const char** objname2,
+                        diff_opt_t* options)
+{
+    int i;
+    int opt;
+    struct exclude_path_list *exclude_head, *exclude_prev, *exclude_node;
+
+    /* process the command-line */
+    memset(options, 0, sizeof (diff_opt_t));
+
+    /* assume equal contents initially */
+    options->contents = 1;
+
+    /* NaNs are handled by default */
+    options->do_nans = 1;
+
+    /* not Listing objects that are not comparable */
+    options->m_list_not_cmp = 0;
+
+    /* initially no not-comparable. */
+    /**this is bad in mixing option with results**/
+    options->not_cmp=0;
+
+    /* init for exclude-path option */
+    exclude_head = NULL;
+
+    /* parse command line options */
+    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF)
+    {
+        switch ((char)opt)
+        {
+        default:
+            usage();
+            h5diff_exit(EXIT_FAILURE);
+        case 'h':
+            usage();
+            h5diff_exit(EXIT_SUCCESS);
+        case 'V':
+            print_version(h5tools_getprogname());
+            h5diff_exit(EXIT_SUCCESS);
+        case 'v':
+            options->m_verbose = 1;
+            /* This for loop is for handling style like 
+             * -v, -v1, --verbose, --verbose=1.
+             */
+            for (i = 1; i < argc; i++)
+            {                
+                /* 
+                 * short opt 
+                 */
+                if (!strcmp (argv[i], "-v"))  /* no arg */
+            {
+                    opt_ind--;
+                    options->m_verbose_level = 0;
+                    break;
+            }
+                else if (!strncmp (argv[i], "-v", (size_t)2))
+            {
+                    options->m_verbose_level = atoi(&argv[i][2]);
+                    break;
+            }    
+
+                /* 
+                 * long opt 
+                 */
+                if (!strcmp (argv[i], "--verbose"))  /* no arg */
+            {
+                    options->m_verbose_level = 0;
+                    break;
+            }
+            else if ( !strncmp (argv[i], "--verbose", (size_t)9) && argv[i][9]=='=')
+            {
+                    options->m_verbose_level = atoi(&argv[i][10]);
+                    break;
+                }
+            }
+            break;
+        case 'q':
+            /* use quiet mode; supress the message "0 differences found" */
+            options->m_quiet = 1;
+            break;
+        case 'r':
+            options->m_report = 1;
+            break;
+        case 'l':
+            options->follow_links = TRUE;
+            break;
+        case 'x':
+            options->no_dangle_links = 1;
+            break;
+        case 'E':
+            options->exclude_path = 1;
+            
+            /* create linked list of excluding objects */
+            if( (exclude_node = (struct exclude_path_list*) HDmalloc(sizeof(struct exclude_path_list))) == NULL)
+            {
+                printf("Error: lack of memory!\n");
+                h5diff_exit(EXIT_FAILURE);
+            }
+
+            /* init */
+            exclude_node->obj_path = (char*)opt_arg;
+            exclude_node->obj_type = H5TRAV_TYPE_UNKNOWN;
+            exclude_prev = exclude_head;
+            
+            if (NULL == exclude_head)            
+            {
+                exclude_head = exclude_node;
+                exclude_head->next = NULL;
+            }
+            else
+            {
+                while(NULL != exclude_prev->next)
+                    exclude_prev=exclude_prev->next;
+
+                exclude_node->next = NULL;
+                exclude_prev->next = exclude_node;
+            }            
+            break;
+        case 'd':
+            options->d=1;
+
+            if ( check_d_input( opt_arg )==-1)
+            {
+                printf("<-d %s> is not a valid option\n", opt_arg );
+                usage();
+                h5diff_exit(EXIT_FAILURE);
+            }
+            options->delta = atof( opt_arg );
+
+            /* -d 0 is the same as default */
+            if (H5_DBL_ABS_EQUAL(options->delta, (double)0.0F))
+            options->d=0;
+
+            break;
+
+        case 'p':
+
+            options->p=1;
+            if ( check_p_input( opt_arg )==-1)
+            {
+                printf("<-p %s> is not a valid option\n", opt_arg );
+                usage();
+                h5diff_exit(EXIT_FAILURE);
+            }
+            options->percent = atof( opt_arg );
+
+            /* -p 0 is the same as default */
+            if (H5_DBL_ABS_EQUAL(options->percent, (double)0.0F))
+            options->p = 0;
+
+            break;
+
+        case 'n':
+
+            options->n=1;
+            if ( check_n_input( opt_arg )==-1)
+            {
+                printf("<-n %s> is not a valid option\n", opt_arg );
+                usage();
+                h5diff_exit(EXIT_FAILURE);
+            }
+            options->count = HDstrtoull(opt_arg, NULL, 0);
+            break;
+
+        case 'N':
+            options->do_nans = 0;
+            break;
+
+        case 'c':
+            options->m_list_not_cmp = 1;
+            break;
+
+        case 'e':
+            options->use_system_epsilon = 1;
+            break;
+        }
+    }
+
+    /* check options */
+    check_options(options);
+
+    /* if exclude-path option is used, keep the exclude path list */
+    if (options->exclude_path)
+        options->exclude = exclude_head;
+
+    /* check for file names to be processed */
+    if (argc <= opt_ind || argv[ opt_ind + 1 ] == NULL)
+    {
+        error_msg("missing file names\n");
+        usage();
+        h5diff_exit(EXIT_FAILURE);
+    }
+
+    *fname1 = argv[ opt_ind ];
+    *fname2 = argv[ opt_ind + 1 ];
+    *objname1 = argv[ opt_ind + 2 ];
+
+    if ( *objname1 == NULL )
+    {
+        *objname2 = NULL;
+        return;
+    }
+
+    if ( argv[ opt_ind + 3 ] != NULL)
+    {
+        *objname2 = argv[ opt_ind + 3 ];
+    }
+    else
+    {
+        *objname2 = *objname1;
+    }
+
+
+}
+
+
+/*-------------------------------------------------------------------------
+ * Function: print_info
+ *
+ * Purpose: print several information messages after h5diff call
+ *
+ *-------------------------------------------------------------------------
+ */
+
+ void  print_info(diff_opt_t* options)
+ {
+     if (options->m_quiet || options->err_stat )
+         return;
+
+     if (options->cmn_objs==0)
+     {
+         printf("No common objects found. Files are not comparable.\n");
+         if (!options->m_verbose)
+             printf("Use -v for a list of objects.\n");
+     }
+
+     if (options->not_cmp==1)
+     {
+         if ( options->m_list_not_cmp == 0 )
+         {
+             printf("--------------------------------\n");
+             printf("Some objects are not comparable\n");
+             printf("--------------------------------\n");
+             if (options->m_verbose)
+                 printf("Use -c for a list of objects without details of differences.\n");
+             else
+                 printf("Use -c for a list of objects.\n");
+         }
+
+
+     }
+
+ }
+
+/*-------------------------------------------------------------------------
+ * Function: check_n_input
+ *
+ * Purpose: check for valid input
+ *
+ * Return: 1 for ok, -1 for fail
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: May 9, 2003
+ *
+ * Comments:
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+H5_ATTR_PURE static int
+check_n_input( const char *str )
+{
+    unsigned i;
+    char c;
+
+    for ( i = 0; i < strlen(str); i++)
+    {
+        c = str[i];
+        if ( i==0 )
+        {
+            if ( c < 49 || c > 57  ) /* ascii values between 1 and 9 */
+                return -1;
+        }
+        else
+            if ( c < 48 || c > 57  ) /* 0 also */
+                return -1;
+    }
+    return 1;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: check_p_input
+ *
+ * Purpose: check for a valid p option input
+ *
+ * Return: 1 for ok, -1 for fail
+ *
+ * Date: May 9, 2003
+ *
+ * Comments:
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+check_p_input( const char *str )
+{
+    double x;
+
+    /*
+    the atof return value on a hexadecimal input is different
+    on some systems; we do a character check for this
+    */
+    if (strlen(str)>2 && str[0]=='0' && str[1]=='x')
+        return -1;
+
+    x=atof(str);
+    if (x<0)
+        return -1;
+
+    return 1;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: check_d_input
+ *
+ * Purpose: check for a valid d option input
+ *
+ * Return: 1 for ok, -1 for fail
+ *
+ * Date: November 11, 2007
+ *
+ * Comments:
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+check_d_input( const char *str )
+{
+    double x;
+
+    /*
+    the atof return value on a hexadecimal input is different
+    on some systems; we do a character check for this
+    */
+    if (strlen(str)>2 && str[0]=='0' && str[1]=='x')
+        return -1;
+
+    x=atof(str);
+    if (x <0)
+        return -1;
+
+    return 1;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: usage
+ *
+ * Purpose: print a usage message
+ *
+ * Return: void
+ *
+ *-------------------------------------------------------------------------
+ */
+
+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("\n");
+ printf("  OPTIONS\n");
+ printf("   -h, --help\n");
+ printf("         Print a usage message and exit.\n");
+ printf("   -V, --version\n");
+ printf("         Print version number and exit.\n");
+ printf("   -r, --report\n");
+ printf("         Report mode. Print differences.\n");
+ printf("   -v --verbose\n");
+ printf("         Verbose mode. Print differences information and list of objects.\n");
+ printf("   -vN --verbose=N\n");
+ printf("         Verbose mode with level. Print differences and list of objects.\n");
+ printf("         Level of detail depends on value of N:\n");
+ printf("          0 : Identical to '-v' or '--verbose'.\n");
+ printf("          1 : All level 0 information plus one-line attribute\n");
+ printf("              status summary.\n");
+ printf("          2 : All level 1 information plus extended attribute\n");
+ printf("              status report.\n");
+ printf("   -q, --quiet\n");
+ printf("         Quiet mode. Do not produce output.\n");
+ printf("   --follow-symlinks\n");
+ printf("         Follow symbolic links (soft links and external links and compare the)\n");
+ printf("         links' target objects.\n");
+ printf("         If symbolic link(s) with the same name exist in the files being\n");
+ printf("         compared, then determine whether the target of each link is an existing\n");
+ printf("         object (dataset, group, or named datatype) or the link is a dangling\n");
+ printf("         link (a soft or external link pointing to a target object that does\n");
+ printf("         not yet exist).\n");
+ printf("         - If both symbolic links are dangling links, they are treated as being\n");
+ printf("           the same; by default, h5diff returns an exit code of 0.\n");
+ printf("           If, however, --no-dangling-links is used with --follow-symlinks,\n");
+ printf("           this situation is treated as an error and h5diff returns an\n");
+ printf("           exit code of 2.\n");
+ printf("         - If only one of the two links is a dangling link,they are treated as\n");
+ printf("           being different and h5diff returns an exit code of 1.\n");
+ printf("           If, however, --no-dangling-links is used with --follow-symlinks,\n");
+ printf("           this situation is treated as an error and h5diff returns an\n");
+ printf("           exit code of 2.\n");
+ printf("         - If both symbolic links point to existing objects, h5diff compares the\n");
+ printf("           two objects.\n");
+ printf("         If any symbolic link specified in the call to h5diff does not exist,\n");
+ printf("         h5diff treats it as an error and returns an exit code of 2.\n");
+ printf("   --no-dangling-links\n");
+ printf("         Must be used with --follow-symlinks option; otherwise, h5diff shows\n");
+ printf("         error message and returns an exit code of 2.\n");
+ printf("         Check for any symbolic links (soft links or external links) that do not\n");
+ printf("         resolve to an existing object (dataset, group, or named datatype).\n");
+ printf("         If any dangling link is found, this situation is treated as an error\n");
+ printf("         and h5diff returns an exit code of 2.\n");
+ printf("   -c, --compare\n");
+ printf("         List objects that are not comparable\n");
+ printf("   -N, --nan\n");
+ printf("         Avoid NaNs detection\n");
+ printf("   -n C, --count=C\n");
+ printf("         Print differences up to C. C must be a positive integer.\n");
+ printf("   -d D, --delta=D\n");
+ printf("         Print difference if (|a-b| > D). D must be a positive number.\n");
+ printf("         Can not use with '-p' or '--use-system-epsilon'.\n");
+ printf("   -p R, --relative=R\n");
+ printf("         Print difference if (|(a-b)/b| > R). R must be a positive number.\n");
+ printf("         Can not use with '-d' or '--use-system-epsilon'.\n");
+ printf("   --use-system-epsilon\n");
+ printf("         Print difference if (|a-b| > EPSILON), EPSILON is system defined value.\n");
+ printf("         If the system epsilon is not defined,one of the following predefined\n");
+ printf("         values will be used:\n");
+ printf("           FLT_EPSILON = 1.19209E-07 for floating-point type\n");
+ printf("           DBL_EPSILON = 2.22045E-16 for double precision type\n");
+ printf("         Can not use with '-p' or '-d'.\n");
+ printf("   --exclude-path \"path\" \n");
+ printf("         Exclude the specified path to an object when comparing files or groups.\n");
+ printf("         If a group is excluded, all member objects will also be excluded.\n");
+ printf("         The specified path is excluded wherever it occurs.\n");
+ printf("         This flexibility enables the same option to exclude either objects that\n");
+ printf("         exist only in one file or common objects that are known to differ.\n");
+ printf("\n");
+ printf("         When comparing files, \"path\" is the absolute path to the excluded;\n");
+ printf("         object; when comparing groups, \"path\" is similar to the relative\n");
+ printf("         path from the group to the excluded object. This \"path\" can be\n");
+ printf("         taken from the first section of the output of the --verbose option.\n");
+ printf("         For example, if you are comparing the group /groupA in two files and\n");
+ printf("         you want to exclude /groupA/groupB/groupC in both files, the exclude\n");
+ printf("         option would read as follows:\n");
+ printf("           --exclude-path \"/groupB/groupC\"\n");
+ printf("\n");
+ printf("         If there are multiple paths to an object, only the specified path(s)\n");
+ printf("         will be excluded; the comparison will include any path not explicitly\n");
+ printf("         excluded.\n");
+ printf("         This option can be used repeatedly to exclude multiple paths.\n");
+ printf("\n");
+
+ printf(" Modes of output:\n");
+ printf("  Default mode: print the number of differences found and where they occured\n");
+ printf("  -r Report mode: print the above plus the differences\n");
+ printf("  -v Verbose mode: print the above plus a list of objects and warnings\n");
+ printf("  -q Quiet mode: do not print output\n");
+
+ printf("\n");
+
+ printf(" File comparison:\n");
+ printf("  If no objects [obj1[ obj2]] are specified, the h5diff comparison proceeds as\n");
+ printf("  a comparison of the two files' root groups.  That is, h5diff first compares\n");
+ printf("  the names of root group members, generates a report of root group objects\n");
+ printf("  that appear in only one file or in both files, and recursively compares\n");
+ printf("  common objects.\n");
+ printf("\n");
+
+ printf(" Object comparison:\n");
+ printf("  1) Groups \n");
+ printf("      First compares the names of member objects (relative path, from the\n");
+ printf("      specified group) and generates a report of objects that appear in only\n");
+ printf("      one group or in both groups. Common objects are then compared recursively.\n");
+ printf("  2) Datasets \n");
+ printf("      Array rank and dimensions, datatypes, and data values are compared.\n");
+ printf("  3) Datatypes \n");
+ printf("      The comparison is based on the return value of H5Tequal.\n");
+ printf("  4) Symbolic links \n");
+ printf("      The paths to the target objects are compared.\n");
+ printf("      (The option --follow-symlinks overrides the default behavior when\n");
+ printf("       symbolic links are compared.).\n");
+ printf("\n");
+
+ printf(" Exit code:\n");
+ printf("  0 if no differences, 1 if differences found, 2 if error\n");
+ printf("\n");
+ printf(" Examples of use:\n");
+ printf(" 1) h5diff file1 file2 /g1/dset1 /g1/dset2\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("    Compares object '/g1/dset1' in both files\n");
+ printf("\n");
+ printf(" 3) h5diff file1 file2\n");
+ printf("    Compares all objects in both files\n");
+ printf("\n");
+ printf(" Notes:\n");
+ printf("  file1 and file2 can be the same file.\n");
+ printf("  Use h5diff file1 file1 /g1/dset1 /g1/dset2 to compare\n");
+ printf("  '/g1/dset1' and '/g1/dset2' in the same file\n");
+ printf("\n");
+}
diff --git a/tools/src/h5diff/h5diff_common.h b/tools/src/h5diff/h5diff_common.h
new file mode 100644
index 0000000..5b1317f
--- /dev/null
+++ b/tools/src/h5diff/h5diff_common.h
@@ -0,0 +1,36 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#ifndef H5DIFFCOMMON_H__
+#define H5DIFFCOMMON_H__
+
+#include "h5tools.h"
+/* Name of tool */
+#define PROGRAMNAME "h5diff"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+void usage(void);
+void parse_command_line(int argc, const char* argv[], const char** fname1, const char** fname2, const char** objname1, const char** objname2, diff_opt_t* options);
+void h5diff_exit(int status);
+void print_info(diff_opt_t* options);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* H5DIFFCOMMON_H__ */
diff --git a/tools/src/h5diff/h5diff_main.c b/tools/src/h5diff/h5diff_main.c
new file mode 100644
index 0000000..cdaca29
--- /dev/null
+++ b/tools/src/h5diff/h5diff_main.c
@@ -0,0 +1,145 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 <stdlib.h>
+#include <assert.h>
+#include <memory.h>
+#include "H5private.h"
+#include "h5diff.h"
+#include "h5diff_common.h"
+#include "h5tools.h"
+#include "h5tools_utils.h"
+
+
+/*-------------------------------------------------------------------------
+ * Function: main
+ *
+ * Purpose: h5diff main program
+ *
+ * Return: An  exit status of 0 means no differences were found, 1 means some
+ *   differences were found.
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: May 9, 2003
+ *
+ * Comments:
+ *
+ * Modifications: July 2004
+ *  Introduced the four modes:
+ *   Normal mode: print the number of differences found and where they occured
+ *   Report mode: print the above plus the differences
+ *   Verbose mode: print the above plus a list of objects and warnings
+ *   Quiet mode: do not print output
+ *
+ * November 2004: Leon Arber (larber@uiuc.edu)
+ *     Additions that allow h5diff to be run in parallel
+ *
+ * February 2005: Leon Arber (larber@uiuc.edu)
+ *   h5diff and ph5diff split into two files, one that is used
+ *   to build a serial h5diff and one used to build a parallel h5diff
+ *   Common functions have been moved to h5diff_common.c
+ *
+ * October 2005
+ *  Introduced a new field 'not_cmp' to 'diff_opt_t' that detects
+ *  if some objects are not comparable and prints the message
+ *  "Some objects are not comparable"
+ *
+ * February 2007
+ *  Added comparison for dataset regions.
+ *  Added support for reading and comparing by hyperslabs for large files.
+ *  Inclusion of a relative error formula to compare floating
+ *   point numbers in order to deal with floating point uncertainty.
+ *  Printing of dataset dimensions along with dataset name
+ *
+ *  November 19, 2007
+ *    adopted the syntax h5diff  [OPTIONS]  file1 file2  [obj1[obj2]]
+ *
+ *-------------------------------------------------------------------------
+ */
+
+
+int main(int argc, const char *argv[])
+{
+    int        ret;
+    const char *fname1 = NULL;
+    const char *fname2 = NULL;
+    const char *objname1  = NULL;
+    const char *objname2  = NULL;
+    hsize_t    nfound=0;
+    diff_opt_t options;
+
+    h5tools_setprogname(PROGRAMNAME);
+    h5tools_setstatus(EXIT_SUCCESS);
+
+    /* Initialize h5tools lib */
+    h5tools_init();
+
+    /*-------------------------------------------------------------------------
+    * process the command-line
+    *-------------------------------------------------------------------------
+    */
+    parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &options);
+
+    /*-------------------------------------------------------------------------
+    * do the diff
+    *-------------------------------------------------------------------------
+    */
+
+    nfound = h5diff(fname1,fname2,objname1,objname2,&options);
+
+    print_info(&options);
+
+   /*-------------------------------------------------------------------------
+    * exit code
+    *   1 if differences, 0 if no differences, 2 if error
+    *-------------------------------------------------------------------------
+    */
+
+    ret = (nfound == 0 ? 0 : 1 );
+
+    /* if graph difference return 1 for differences  */
+    if ( options.contents == 0 )
+        ret = 1;
+
+    /* and return 2 for error */
+    if (options.err_stat)
+        ret = 2;
+
+    return ret;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: h5diff_exit
+ *
+ * Purpose: dismiss phdiff worker processes and exit
+ *
+ * Return: none
+ *
+ * Programmer: Albert Cheng
+ * Date: Feb 6, 2005
+ *
+ * Comments:
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+H5_ATTR_NORETURN void
+h5diff_exit(int status)
+{
+    HDexit(status);
+}
+
diff --git a/tools/src/h5diff/ph5diff_main.c b/tools/src/h5diff/ph5diff_main.c
new file mode 100644
index 0000000..a26b6e9
--- /dev/null
+++ b/tools/src/h5diff/ph5diff_main.c
@@ -0,0 +1,329 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include "H5private.h"
+#include "h5diff.h"
+#include "ph5diff.h"
+#include "h5diff_common.h"
+#include "h5tools.h"
+#include "h5tools_utils.h"
+
+/* Name of tool */
+#define PROGRAMNAME "h5diff"
+
+static void ph5diff_worker(int );
+
+/*-------------------------------------------------------------------------
+ * Function: main
+ *
+ * Purpose: ph5diff main program
+ *
+ * Return: An exit status of 0 means no differences were found, 1 means some
+ *   differences were found.
+ *
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+ *
+ * Date: May 9, 2003
+ *
+ * Comments:
+ *
+ * This function drives the diff process and will do a serial or parallel diff depending
+ * on the value of the global variable g_Parallel (default is 0), set to 1 when the program
+ * is run as "ph5diff"
+ *-------------------------------------------------------------------------
+ */
+
+int main(int argc, const char *argv[])
+{
+    int        nID = 0;
+    const char *fname1 = NULL;
+    const char *fname2 = NULL;
+    const char *objname1  = NULL;
+    const char *objname2  = NULL;
+    diff_opt_t options;
+
+    h5tools_setprogname(PROGRAMNAME);
+    h5tools_setstatus(EXIT_SUCCESS);
+
+    /* Initialize h5tools lib */
+    h5tools_init();
+
+    outBuffOffset = 0;
+    g_Parallel = 1;
+
+    MPI_Init(&argc, (char***) &argv);
+
+    MPI_Comm_rank(MPI_COMM_WORLD, &nID);
+    MPI_Comm_size(MPI_COMM_WORLD, &g_nTasks);
+
+    if(g_nTasks == 1)
+    {
+        printf("Only 1 task available...doing serial diff\n");
+
+        g_Parallel = 0;
+
+        parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &options);
+
+        h5diff(fname1, fname2, objname1, objname2, &options);
+
+        print_info(&options);
+    }
+    /* Parallel h5diff */
+    else {
+
+        /* Have the manager process the command-line */
+        if(nID == 0)
+        {
+            parse_command_line(argc, argv, &fname1, &fname2, &objname1, &objname2, &options);
+
+            h5diff(fname1, fname2, objname1, objname2, &options);
+
+            MPI_Barrier(MPI_COMM_WORLD);
+
+            print_info(&options);
+            print_manager_output();
+        }
+        /* All other tasks become workers and wait for assignments. */
+        else {
+            ph5diff_worker(nID);
+
+            MPI_Barrier(MPI_COMM_WORLD);
+        } /* end else */
+
+    } /* end else */
+
+    MPI_Finalize();
+
+    return 0;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: ph5diff_worker
+ *
+ * Purpose: worker process of ph5diff
+ *
+ * Return: none
+ *
+ * Programmer: Leon Arber
+ * Date: January 2005
+ *
+ * Comments:
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+static void
+ph5diff_worker(int nID)
+{
+    hid_t file1_id = -1, file2_id = -1;
+
+    while(1)
+    {
+        MPI_Status Status;
+
+        MPI_Probe(0, MPI_ANY_TAG, MPI_COMM_WORLD, &Status);
+
+        /* Check for filenames */
+        if(Status.MPI_TAG == MPI_TAG_PARALLEL)
+        {
+            char    filenames[2][MAX_FILENAME];
+
+            /* Retrieve filenames */
+            MPI_Recv(filenames, MAX_FILENAME*2, MPI_CHAR, 0, MPI_ANY_TAG, MPI_COMM_WORLD, &Status);
+
+            /* disable error reporting */
+            H5E_BEGIN_TRY
+            {
+                /* Open the files */
+                if ((file1_id = H5Fopen (filenames[0], H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
+                {
+                    printf ("h5diff Task [%d]: <%s>: unable to open file\n", nID, filenames[0]);
+                    MPI_Abort(MPI_COMM_WORLD, 0);
+                }
+                if ((file2_id = H5Fopen (filenames[1], H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
+                {
+                    printf ("h5diff Task [%d]: <%s>: unable to open file\n", nID, filenames[1]);
+                    MPI_Abort(MPI_COMM_WORLD, 0);
+                }
+                /* enable error reporting */
+            }
+            H5E_END_TRY;
+        }
+        /* Check for work */
+        else if(Status.MPI_TAG == MPI_TAG_ARGS)
+        {
+            struct diff_mpi_args args;
+            struct diffs_found  diffs;
+            int i;
+
+            /* Make certain we've received the filenames and opened the files already */
+            if(file1_id < 0 || file2_id < 0)
+            {
+                printf("ph5diff_worker: ERROR: work received before/without filenames\n");
+                break;
+            }
+
+            /* Recv parameters for diff from manager task */
+            MPI_Recv(&args, sizeof(args), MPI_BYTE, 0, MPI_TAG_ARGS, MPI_COMM_WORLD, &Status);
+
+            /* Do the diff */
+            diffs.nfound = diff(file1_id, args.name1, file2_id, args.name2, &(args.options), &(args.argdata));
+            diffs.not_cmp = args.options.not_cmp;
+
+            /* If print buffer has something in it, request print token.*/
+            if(outBuffOffset>0)
+            {
+                MPI_Send(NULL, 0, MPI_BYTE, 0, MPI_TAG_TOK_REQUEST, MPI_COMM_WORLD);
+
+                /* Wait for print token. */
+                MPI_Recv(NULL, 0, MPI_BYTE, 0, MPI_TAG_PRINT_TOK, MPI_COMM_WORLD, &Status);
+
+                /* When get token, send all of our output to the manager task and then return the token */
+                for(i=0; i<outBuffOffset; i+=PRINT_DATA_MAX_SIZE)
+                    MPI_Send(outBuff+i, PRINT_DATA_MAX_SIZE, MPI_BYTE, 0, MPI_TAG_PRINT_DATA, MPI_COMM_WORLD);
+
+                /* An overflow file exists, so we send it's output to the manager too and then delete it */
+                if(overflow_file)
+                {
+                    char out_data[PRINT_DATA_MAX_SIZE];
+                    int tmp;
+
+                    memset(out_data, 0, PRINT_DATA_MAX_SIZE);
+                    i=0;
+
+                    rewind(overflow_file);
+                    while((tmp = getc(overflow_file)) >= 0)
+                    {
+                        *(out_data + i++) = (char)tmp;
+                        if(i==PRINT_DATA_MAX_SIZE)
+                        {
+                            MPI_Send(out_data, PRINT_DATA_MAX_SIZE, MPI_BYTE, 0, MPI_TAG_PRINT_DATA, MPI_COMM_WORLD);
+                            i=0;
+                            memset(out_data, 0, PRINT_DATA_MAX_SIZE);
+                        }
+                    }
+
+                    if(i>0)
+                        MPI_Send(out_data, PRINT_DATA_MAX_SIZE, MPI_BYTE, 0, MPI_TAG_PRINT_DATA, MPI_COMM_WORLD);
+
+                    fclose(overflow_file);
+                    overflow_file = NULL;
+                }
+
+                fflush(stdout);
+                memset(outBuff, 0, OUTBUFF_SIZE);
+                outBuffOffset = 0;
+
+                MPI_Send(&diffs, sizeof(diffs), MPI_BYTE, 0, MPI_TAG_TOK_RETURN, MPI_COMM_WORLD);
+            }
+            else
+                MPI_Send(&diffs, sizeof(diffs), MPI_BYTE, 0, MPI_TAG_DONE, MPI_COMM_WORLD);
+        }
+        /* Check for leaving */
+        else if(Status.MPI_TAG == MPI_TAG_END)
+        {
+            MPI_Recv(NULL, 0, MPI_BYTE, 0, MPI_TAG_END, MPI_COMM_WORLD, &Status);
+            break;
+        }
+        else
+        {
+            printf("ph5diff_worker: ERROR: invalid tag (%d) received\n", Status.MPI_TAG);
+            break;
+        }
+
+    }
+
+    return;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: print_manager_output
+ *
+ * Purpose: special function that prints any output accumulated by the
+ *      manager task.
+ *
+ * Return: none
+ *
+ * Programmer: Leon Arber
+ *
+ * Date: Feb 7, 2005
+ *
+ *-------------------------------------------------------------------------
+ */
+void print_manager_output(void)
+{
+    /* If there was something we buffered, let's print it now */
+    if( (outBuffOffset>0) && g_Parallel)
+    {
+        printf("%s", outBuff);
+
+        if(overflow_file)
+        {
+            int     tmp;
+            rewind(overflow_file);
+            while((tmp = getc(overflow_file)) >= 0)
+                putchar(tmp);
+            fclose(overflow_file);
+            overflow_file = NULL;
+        }
+
+        HDfflush(stdout);
+        HDmemset(outBuff, 0, OUTBUFF_SIZE);
+        outBuffOffset = 0;
+    }
+    else if( (outBuffOffset>0) && !g_Parallel)
+    {
+        HDfprintf(stderr, "h5diff error: outBuffOffset>0, but we're not in parallel!\n");
+    }
+}
+
+/*-------------------------------------------------------------------------
+ * Function: h5diff_exit
+ *
+ * Purpose: dismiss phdiff worker processes and exit
+ *
+ * Return: none
+ *
+ * Programmer: Albert Cheng
+ * Date: Feb 6, 2005
+ *
+ * Comments:
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+void h5diff_exit(int status)
+{
+    /* if in parallel mode, dismiss workers, close down MPI, then exit */
+    if(g_Parallel) {
+        if(g_nTasks > 1) {
+            phdiff_dismiss_workers();
+            MPI_Barrier(MPI_COMM_WORLD);
+        }
+        MPI_Finalize();
+        status = EXIT_SUCCESS;  /* Reset exit status, since some mpiexec commands generate output on failure status */
+    }
+
+    /* Always exit(0), since MPI implementations do weird stuff when they
+     *  receive a non-zero exit value. - QAK
+     */
+    exit(0);
+}
+