[svn-r8904] Purpose:

h5diff and h5repack changes

Description:
h5diff
introduced the following four modes of output:
 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 (h5diff always returns an exit code of 1 when differences are found)

    h5repack
     added an extra parameter for SZIP filter (coding method)
     the new syntax is
     -f SZIP=<pixels per block,coding>
     (pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN')
     Example of use:
     ./h5repack -i file1 -o file2 -f SZIP=8,NN -v

     updated usage messages, test scripts and files accordingly




Solution:

Platforms tested:
linux
AIX
solaris

Misc. update:

15 files changed, 424 insertions, 234 deletions

diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index 7ba5a6c..f9cb295 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -234,9 +234,6 @@ static int check_options(pack_opt_t *options)
 {
  int   i, k, j, has_cp=0, has_ck=0;
 
- unsigned szip_options_mask=H5_SZIP_NN_OPTION_MASK;
- unsigned szip_pixels_per_block;
-
 /*-------------------------------------------------------------------------
  * objects to layout
  *-------------------------------------------------------------------------
@@ -337,8 +334,17 @@ static int check_options(pack_opt_t *options)
    default:
     break;
    case H5Z_FILTER_SZIP:
+    {
+     
+    unsigned szip_options_mask=H5_SZIP_NN_OPTION_MASK;
+    unsigned szip_pixels_per_block;
 
     szip_pixels_per_block=pack.filter[j].cd_values[0];
+
+    if (pack.filter[j].szip_coding==0)
+     szip_options_mask=H5_SZIP_NN_OPTION_MASK;
+    else 
+     szip_options_mask=H5_SZIP_EC_OPTION_MASK;
     
     /* check szip parameters */
     if ( pack.chunk.rank!=-1 /* 
@@ -364,6 +370,7 @@ static int check_options(pack_opt_t *options)
 
     }
      
+    }
     break;
    } /* switch */
 
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index 3a3a7c0..4691a74 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -21,7 +21,9 @@
 #include "h5diff.h"
 #include "h5tools.h"
 
+#if 0
 #define CHECK_SZIP
+#endif
 
 
 #define H5FOPENERROR "unable to open file"
@@ -58,6 +60,11 @@ typedef struct {
 typedef struct {
  H5Z_filter_t filtn;               /* filter identification number */
  int          cd_values[CDVALUES]; /* filter client data values */
+ /* extra input for szip, selects the coding method
+    entropy coding method: EC=0 
+    nearest neighbor coding method: NN=1 
+ */
+ int          szip_coding;         
 } filter_info_t;
 
 /* chunk lengths along each dimension and rank */
@@ -192,17 +199,6 @@ int apply_filters(const char* name,    /* object name from traverse list */
 int has_filter(hid_t dcpl_id,
                H5Z_filter_t filtnin);
 
-int check_szip_params( unsigned bits_per_pixel, 
-                       unsigned pixels_per_block, 
-                       unsigned pixels_per_scanline, 
-                       hsize_t image_pixels);
-
-int check_szip(hid_t type_id,   /* dataset datatype */
-               int rank,        /* chunk rank */
-               hsize_t *dims,   /* chunk dims */
-               unsigned szip_options_mask /*IN*/,
-               unsigned *szip_pixels_per_block /*IN,OUT*/,
-               pack_opt_t *options);
 
 int can_read(const char* name,    /* object name from traverse list */
              hid_t dcpl_id,       /* dataset creation property list */
@@ -306,12 +302,12 @@ void write_attr_in(hid_t loc_id,
                    const char* dset_name, /* for saving reference to dataset*/
                    hid_t fid, /* for reference create */
                    int make_diffs /* flag to modify data buffers */);
-void write_null_attr(hid_t loc_id); 
 void write_dset_in(hid_t loc_id, 
                    const char* dset_name, /* for saving reference to dataset*/
                    hid_t file_id,
                    int make_diffs /* flag to modify data buffers */);
-void write_null_dset(hid_t loc_id);
+
+
 
 /*-------------------------------------------------------------------------
  * tests utils
@@ -337,6 +333,22 @@ int make_attr(hid_t loc_id,
  *-------------------------------------------------------------------------
  */
 
+#if defined (CHECK_SZIP)
+
+int check_szip_params( unsigned bits_per_pixel, 
+                       unsigned pixels_per_block, 
+                       unsigned pixels_per_scanline, 
+                       hsize_t image_pixels);
+
+int check_szip(hid_t type_id,   /* dataset datatype */
+               int rank,        /* chunk rank */
+               hsize_t *dims,   /* chunk dims */
+               unsigned szip_options_mask /*IN*/,
+               unsigned *szip_pixels_per_block /*IN,OUT*/,
+               pack_opt_t *options);
+
+
+
 typedef struct 
 {
  int compression_mode;
@@ -368,6 +380,7 @@ typedef struct
 #define NN_MODE	1
 #endif
 
+#endif /* CHECK_SZIP */
 
 
 #endif  /* H5REPACK_H__ */
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index e4d65de..98b46ba 100755
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -25,7 +25,7 @@ USE_FILTER_FLETCHER32="@USE_FILTER_FLETCHER32@"
 H5REPACK=h5repack               # The tool name
 H5REPACK_BIN=`pwd`/$H5REPACK    # The path of the tool binary
 
-H5DIFF=../h5diff/h5diff         # The h5diff tool name
+H5DIFF=../h5diff/h5diff         # The h5diff tool name 
 H5DIFF_BIN=`pwd`/$H5DIFF        # The path of the h5diff  tool binary
 
 nerrors=0
@@ -68,9 +68,9 @@ DIFFTEST()
 {
     VERIFY  $@
     if [ "`uname -s`" = "TFLOPS O/S" ]; then
-     $RUNSERIAL $H5DIFF_BIN $@
+     $RUNSERIAL $H5DIFF_BIN $@ -q
     else
-     $RUNSERIAL $H5DIFF_BIN "$@"
+     $RUNSERIAL $H5DIFF_BIN "$@" -q
     fi
     RET=$?
     if [ $RET != 0 ] ; then
@@ -151,7 +151,7 @@ else
 fi
 
 # szip with individual object
-arg="test4.h5 -f dset2:SZIP=8  -l dset2:CHUNK=20x10"
+arg="test4.h5 -f dset2:SZIP=8,EC  -l dset2:CHUNK=20x10"
 if test $USE_FILTER_SZIP_ENCODER != "yes" -o $USE_FILTER_SZIP != "yes" ; then
  SKIP $arg
 else
@@ -159,7 +159,7 @@ else
 fi
 
 # szip for all
-arg="test4.h5 -f SZIP=8"
+arg="test4.h5 -f SZIP=8,NN"
 if test $USE_FILTER_SZIP_ENCODER != "yes" -o $USE_FILTER_SZIP != "yes" ; then
  SKIP $arg
 else
@@ -200,7 +200,7 @@ else
 fi
 
 # all filters
-arg="test4.h5 -f dset2:SHUF -f dset2:FLET -f dset2:SZIP=8 -f dset2:GZIP=1 -l dset2:CHUNK=20x10"
+arg="test4.h5 -f dset2:SHUF -f dset2:FLET -f dset2:SZIP=8,NN -f dset2:GZIP=1 -l dset2:CHUNK=20x10"
 if test $USE_FILTER_SZIP_ENCODER != "yes" -o $USE_FILTER_SZIP != "yes" -o $USE_FILTER_SHUFFLE != "yes" -o $USE_FILTER_FLETCHER32 != "yes" -o $USE_FILTER_DEFLATE != "yes" ; then
  SKIP $arg
 else
@@ -285,7 +285,7 @@ fi
 
 #filter conversions
 
-arg="test_deflate.h5 -f dset_deflate:SZIP=8"
+arg="test_deflate.h5 -f dset_deflate:SZIP=8,NN"
 if test $USE_FILTER_SZIP_ENCODER != "yes" -o $USE_FILTER_SZIP != "yes" -o $USE_FILTER_DEFLATE != "yes" ; then
  SKIP $arg
 else
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 870f3c7..110069b 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -19,6 +19,110 @@
 #include "H5private.h"
 #include "h5repack.h"
 
+#if 0
+#define PRINT_DEBUG
+#endif
+
+/*-------------------------------------------------------------------------
+ * Function: print_obj
+ *
+ * Purpose: print name and filters of an object 
+ *
+ *-------------------------------------------------------------------------
+ */
+static void print_obj(hid_t dcpl_id, char *name)
+{
+ char         str[255]; 
+#if defined (PRINT_DEBUG )
+ char         temp[255];  
+#endif 
+ int          nfilters;       /* number of filters */
+ unsigned     filt_flags;     /* filter flags */
+ H5Z_filter_t filtn;          /* filter identification number */
+ unsigned     cd_values[20];  /* filter client data values */
+ size_t       cd_nelmts;      /* filter client number of values */
+ char         f_name[256];    /* filter name */
+ int          i;
+
+ strcpy(str,"\0");
+
+ /* get information about input filters */
+ if ((nfilters = H5Pget_nfilters(dcpl_id))<0) 
+  return;
+
+ for ( i=0; i<nfilters; i++)
+ {
+  cd_nelmts = NELMTS(cd_values);
+
+#ifdef H5_WANT_H5_V1_6_COMPAT
+  filtn = H5Pget_filter(dcpl_id, 
+   (unsigned)i, 
+   &filt_flags, 
+   &cd_nelmts,
+   cd_values, 
+   sizeof(f_name), 
+   f_name);
+#else
+  filtn = H5Pget_filter(dcpl_id, 
+   (unsigned)i, 
+   &filt_flags, 
+   &cd_nelmts,
+   cd_values, 
+   sizeof(f_name), 
+   f_name,
+   NULL);
+#endif /* H5_WANT_H5_V1_6_COMPAT */
+
+
+  switch (filtn)
+  {
+  default:
+   break;
+  case H5Z_FILTER_DEFLATE:
+   strcat(str,"GZIP ");
+
+#if defined (PRINT_DEBUG)
+   {
+    unsigned level=cd_values[0]; 
+    sprintf(temp,"(%d)",level);
+    strcat(str,temp);
+   }
+#endif
+
+   break;
+  case H5Z_FILTER_SZIP:
+   strcat(str,"SZIP ");
+
+#if defined (PRINT_DEBUG)
+   {
+    unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
+    unsigned ppb=cd_values[1]; 
+    sprintf(temp,"(%d,",ppb);
+    strcat(str,temp);
+    if (options_mask & H5_SZIP_EC_OPTION_MASK) 
+     strcpy(temp,"EC) ");
+    else if (options_mask & H5_SZIP_NN_OPTION_MASK) 
+     strcpy(temp,"NN) ");
+   }
+   strcat(str,temp);
+
+#endif
+
+   break;
+  case H5Z_FILTER_SHUFFLE:
+   strcat(str,"SHUF ");
+   break;
+  case H5Z_FILTER_FLETCHER32:
+   strcat(str,"FLET ");
+   break;
+  } /* switch */
+ }/*i*/
+
+ printf(" %-10s %s %s\n", "dataset",str,name );
+
+}
+
+
 /*-------------------------------------------------------------------------
  * Function: copy_objects
  *
@@ -112,46 +216,6 @@ out:
 }
 
 
-/*-------------------------------------------------------------------------
- * Function: print_obj
- *
- * Purpose: print name and filters of an object 
- *
- *-------------------------------------------------------------------------
- */
-
-
-void print_obj(pack_info_t *obj, char *name)
-{
- char str[26]; /*5x5+1*/
- int i;
-
- strcpy(str,"\0");
-
- for ( i=0; i<obj->nfilters; i++)
- {
-  switch (obj->filter[i].filtn)
-  {
-  default:
-   break;
-  case H5Z_FILTER_DEFLATE:
-   strcat(str,"GZIP ");
-   break;
-  case H5Z_FILTER_SZIP:
-   strcat(str,"SZIP ");
-   break;
-  case H5Z_FILTER_SHUFFLE:
-   strcat(str,"SHUF ");
-   break;
-  case H5Z_FILTER_FLETCHER32:
-   strcat(str,"FLET ");
-   break;
-  } /* switch */
- }/*i*/
-
- printf(" %-10s %s %s\n", "dataset",str,name );
-
-}
 
 
 /*-------------------------------------------------------------------------
@@ -262,9 +326,6 @@ int do_copy_objects(hid_t fidin,
    if ((msize=H5Tget_size(mtype_id))==0)
     goto error;
 
-   if (options->verbose)
-    print_filters(dcpl_id);
-
 /*-------------------------------------------------------------------------
  * check for external files
  *-------------------------------------------------------------------------
@@ -370,7 +431,7 @@ int do_copy_objects(hid_t fidin,
      free(buf);
 
     if (options->verbose && wrote)
-     print_obj(&obj,travt->objs[i].name );
+     print_obj(dcpl_id,travt->objs[i].name );
 
 
     
diff --git a/tools/h5repack/h5repack_filters.c b/tools/h5repack/h5repack_filters.c
index 61ef4a7..2536ced 100644
--- a/tools/h5repack/h5repack_filters.c
+++ b/tools/h5repack/h5repack_filters.c
@@ -122,8 +122,6 @@ int apply_filters(const char* name,    /* object name from traverse list */
  unsigned     aggression;     /* the deflate level */
  hsize_t      nelmts;         /* number of elements in dataset */
  size_t       size;           /* size of datatype in bytes */
- unsigned     szip_options_mask=H5_SZIP_NN_OPTION_MASK;
- unsigned     szip_pixels_per_block;
  int          i;
 
  /* check first if the object is to be filtered */
@@ -205,15 +203,23 @@ int apply_filters(const char* name,    /* object name from traverse list */
  *-------------------------------------------------------------------------
  */
   case H5Z_FILTER_SZIP:
-   szip_pixels_per_block=obj->filter[i].cd_values[0];
-
+   {
+    unsigned  options_mask;
+    unsigned  pixels_per_block;
+
+    pixels_per_block=obj->filter[i].cd_values[0];
+    if (obj->filter[i].szip_coding==0)
+     options_mask=H5_SZIP_NN_OPTION_MASK;
+    else 
+     options_mask=H5_SZIP_EC_OPTION_MASK;
+ 
 #if defined (CHECK_SZIP)
    /* check szip parameters */
    if (check_szip(type_id,
     obj->chunk.rank,
     obj->chunk.chunk_lengths,
-    szip_options_mask,
-    &szip_pixels_per_block,
+    options_mask,
+    &pixels_per_block,
     options)==1)
    {
 #endif
@@ -221,9 +227,10 @@ int apply_filters(const char* name,    /* object name from traverse list */
     /* set up for szip data */
     if(H5Pset_chunk(dcpl_id,obj->chunk.rank,obj->chunk.chunk_lengths)<0)
      return -1;
-    if (H5Pset_szip(dcpl_id, szip_options_mask, szip_pixels_per_block)<0) 
+    if (H5Pset_szip(dcpl_id,options_mask,pixels_per_block)<0) 
      return -1;
 
+
 #if defined (CHECK_SZIP)
    }
    else
@@ -234,6 +241,7 @@ int apply_filters(const char* name,    /* object name from traverse list */
 #endif
 
 
+   }
    break;
 
 /*-------------------------------------------------------------------------
@@ -269,7 +277,6 @@ out:
 }
 
 
-
 /*-------------------------------------------------------------------------
  * Function: print_filters
  *
@@ -277,7 +284,7 @@ out:
  *
  * Return: 0, ok, -1 no
  *
- * Programmer:  pvn@ncsa.uiuc.edu
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
  * Date: December 19, 2003
  *
@@ -292,7 +299,7 @@ int print_filters(hid_t dcpl_id)
  unsigned     cd_values[20];  /* filter client data values */
  size_t       cd_nelmts;      /* filter client number of values */
  size_t       cd_num;         /* filter client data counter */
- char         f_name[256];    /* filter/file name */
+ char         f_name[256];    /* filter name */
  char         s[64];          /* temporary string buffer */
  int          i;
 
@@ -338,6 +345,9 @@ int print_filters(hid_t dcpl_id)
 }
 
 
+#if defined (CHECK_SZIP)
+
+
 /*-------------------------------------------------------------------------
  * Function: check_szip
  *
@@ -353,7 +363,7 @@ int print_filters(hid_t dcpl_id)
  * Return: 1=can apply the filter
  *         0=cannot apply the filter
  *
- * Programmer:  pvn@ncsa.uiuc.edu
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
  * Date: December 23, 2003
  *
@@ -560,3 +570,6 @@ int check_szip_params( unsigned bits_per_pixel,
  return 1;
 }
 
+#endif /* CHECK_SZIP */
+
+
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index 810d30f..442af99 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -17,9 +17,25 @@
 
 static void usage(void);
 
-/*
-h5repack main program
-*/
+/*-------------------------------------------------------------------------
+ * 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
+ *
+ *-------------------------------------------------------------------------
+ */
+
 
 int main(int argc, char **argv)
 {
@@ -33,6 +49,10 @@ int main(int argc, char **argv)
 
  for ( i = 1; i < argc; i++) 
  {
+  if (strcmp(argv[i], "-h") == 0) {
+    usage();
+    exit(0);
+  }
   if (strcmp(argv[i], "-i") == 0) {
    infile = argv[++i];
   }
@@ -76,11 +96,15 @@ int main(int argc, char **argv)
   
   else if (argv[i][0] == '-') {
    usage();
+   exit(1);
   }
  }
 
  if (infile == NULL || outfile == NULL) 
+ {
   usage();
+  exit(1);
+ }
  
  /* pack it */
  ret=h5repack(infile,outfile,&options);
@@ -112,8 +136,9 @@ void usage(void)
  printf("-i input          Input HDF5 File\n");
  printf("-o output         Output HDF5 File\n");
  printf("[-h]              Print usage message\n");
+ printf("[-v]              Verbose mode. Print output (list of objects, filters, warnings)\n");
  printf("[-f 'filter']     Filter type: 'filter' is a string with the format\n");
- printf("     <list of objects> : <name of filter> <filter parameters>\n");
+ printf("     <list of objects> : <name of filter> = <filter parameters>\n");
  printf("     <list of objects> is a comma separated list of object names\n");
  printf("       meaning apply compression only to those objects.\n");
  printf("       if no object names are specified, the filter is applied to all objects\n");
@@ -124,8 +149,10 @@ void usage(void)
  printf("       FLET, to apply the HDF5 checksum filter\n");
  printf("       NONE, to remove the filter\n");
  printf("     <filter parameters> is optional compression info\n");
- printf("       GZIP, the deflation level\n");
- printf("       SZIP, the pixels per block parameter\n");
+ printf("       SHUF (no parameter)\n");
+ printf("       FLET (no parameter)\n");
+ printf("       GZIP=<deflation level> from 1-9\n");
+ printf("       SZIP=<pixels per block,coding> (pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN')\n");
  printf("[-l 'layout']     Layout type. 'layout' is a string with the format\n");
  printf("     <list of objects> : <layout type>\n");
  printf("     <list of objects> is a comma separated list of object names,\n");
@@ -143,8 +170,20 @@ void usage(void)
  printf("-m number         Do not apply the filter to objects which size in bytes is smaller than number.\n");
  printf("                  If no size is specified a minimum of 1024 bytes is assumed.\n");
  printf("\n");
-
- exit(1);
+ printf("Examples of use:\n");
+ printf("\n");
+ printf("1) h5repack -i file1 -o file2 -f GZIP=1 -v\n");
+ printf("\n");
+ printf("   Applies GZIP compression to all objects in file1 and saves the output in file2\n");
+ printf("\n");
+ printf("2) h5repack -i file1 -o file2 -f dset1:SZIP=8,NN -v\n");
+ printf("\n");
+ printf("   Applies SZIP compression only to object 'dset1'\n");
+ printf("\n");
+ printf("3) h5repack -i file1 -o file2 -l dset1,dset2:CHUNK=20x10 -v\n");
+ printf("\n");
+ printf("   Applies chunked layout to objects 'dset1' and 'dset2'\n");
+ printf("\n");
 }
 
 
diff --git a/tools/h5repack/h5repack_opttable.c b/tools/h5repack/h5repack_opttable.c
index 71cf1a8..cf76e82 100644
--- a/tools/h5repack/h5repack_opttable.c
+++ b/tools/h5repack/h5repack_opttable.c
@@ -35,7 +35,8 @@ void init_packobject(pack_info_t *obj)
  strcpy(obj->path,"\0");
  for ( j=0; j<H5_REPACK_MAX_NFILTERS; j++)
  {
-  obj->filter[j].filtn  = -1;
+  obj->filter[j].filtn        = -1;
+  obj->filter[j].szip_coding  = -1;
   for ( k=0; k<CDVALUES; k++) 
    obj->filter[j].cd_values[k] = -1;
  }
@@ -109,7 +110,7 @@ static void aux_tblinsert_layout(pack_opttbl_t *table,
 
 static int aux_inctable(pack_opttbl_t *table, int n_objs )
 {
- int i, j, k;
+ int i;
  
  table->size += n_objs;
  table->objs = (pack_info_t*)realloc(table->objs, table->size * sizeof(pack_info_t));
@@ -119,17 +120,7 @@ static int aux_inctable(pack_opttbl_t *table, int n_objs )
  }
  for (i = table->nelems; i < table->size; i++) 
  {
-  strcpy(table->objs[i].path,"\0");
-  for ( j=0; j<H5_REPACK_MAX_NFILTERS; j++)
-  {
-   table->objs[i].filter[j].filtn  = -1;
-   for ( k=0; k<CDVALUES; k++) 
-    table->objs[i].filter[j].cd_values[k] = -1;
-  }
-  table->objs[i].chunk.rank = -1;
-  table->objs[i].refobj_id = -1;
-  table->objs[i].layout = H5D_LAYOUT_ERROR;
-  table->objs[i].nfilters = 0;
+  init_packobject(&table->objs[i]);
  }
  return 0;
 }
@@ -146,7 +137,7 @@ static int aux_inctable(pack_opttbl_t *table, int n_objs )
 
 int options_table_init( pack_opttbl_t **tbl )
 {
- int i, j, k;
+ int i;
  pack_opttbl_t* table = (pack_opttbl_t*) malloc(sizeof(pack_opttbl_t));
  if (table==NULL) {
   printf("Error: not enough memory for options table\n");
@@ -163,17 +154,7 @@ int options_table_init( pack_opttbl_t **tbl )
  
  for ( i=0; i<table->size; i++) 
  {
-  strcpy(table->objs[i].path,"\0");
-  for ( j=0; j<H5_REPACK_MAX_NFILTERS; j++)
-  {
-   table->objs[i].filter[j].filtn  = -1;
-   for ( k=0; k<CDVALUES; k++) 
-    table->objs[i].filter[j].cd_values[k] = -1;
-  }
-  table->objs[i].chunk.rank = -1;
-  table->objs[i].refobj_id = -1;
-  table->objs[i].layout = H5D_LAYOUT_ERROR;
-  table->objs[i].nfilters = 0;
+  init_packobject(&table->objs[i]);
  }
  
  *tbl = table;
diff --git a/tools/h5repack/h5repack_parse.c b/tools/h5repack/h5repack_parse.c
index 96f7bce..e6974c0 100644
--- a/tools/h5repack/h5repack_parse.c
+++ b/tools/h5repack/h5repack_parse.c
@@ -56,10 +56,11 @@ obj_list_t* parse_filter(const char *str,
  unsigned    i, u;
  char        c;
  size_t      len=strlen(str);
- int         j, m, n, k, end_obj=-1, no_param=0;
+ int         j, m, n, k, l, end_obj=-1, no_param=0;
  char        sobj[MAX_NC_NAME]; 
  char        scomp[10];
  char        stype[5];
+ char        smask[3]; 
  obj_list_t* obj_list=NULL;
  unsigned    pixels_per_block;
 
@@ -132,17 +133,74 @@ obj_list_t* parse_filter(const char *str,
    if ( c=='=') {      /*one more parameter */
     scomp[k]='\0';     /*cut space */
 
-    /* here we could have 1, 2 or 3 digits  */
-    for ( m=0,u=i+1; u<len; u++,m++) {
-     c = str[u];
-     if (!isdigit(c)){
-      if (obj_list) free(obj_list);
-      printf("Input Error: Compression parameter not digit in <%s>\n",str);
-      exit(1);
-     }
-     stype[m]=c;
-    }
-    stype[m]='\0';
+     /*SZIP is a special case , it can be
+      SZIP=8,EC
+      SZIP=8,NN
+      */
+   
+    if (strcmp(scomp,"SZIP")==0)
+    {
+     l=-1; /* mask index check */
+     for ( m=0,u=i+1; u<len; u++,m++) 
+     {
+      if (str[u]==',')
+      {
+       stype[m]='\0'; /* end digit of szip */
+       l=0;  /* start EC or NN search */
+       u++;  /* skip ',' */
+      }
+      c = str[u];
+      if (!isdigit(c) && l==-1){
+       if (obj_list) free(obj_list);
+       printf("Input Error: Compression parameter not digit in <%s>\n",str);
+       exit(1);
+      }
+      if (l==-1)
+       stype[m]=c;
+      else 
+      {
+       smask[l]=c;
+       l++;
+       if (l==2)
+       {
+        smask[l]='\0';
+        i=len-1; /* end */
+        (*n_objs)--; /* we counted an extra ',' */
+        if (strcmp(smask,"NN")==0) 
+         filt->szip_coding=0;
+        else if (strcmp(smask,"EC")==0)
+         filt->szip_coding=1;
+        else
+        {
+         printf("Input Error: szip mask must be 'NN' or 'EC' \n");
+         exit(1);
+        }
+        
+       }
+      }
+      
+     }  /* u */
+    } /*if */
+    
+    else
+    {
+     /* here we could have 1 or 2 digits  */
+     for ( m=0,u=i+1; u<len; u++,m++) 
+     {
+      c = str[u];
+      if (!isdigit(c)){
+       if (obj_list) free(obj_list);
+       printf("Input Error: Compression parameter not digit in <%s>\n",str);
+       exit(1);
+      }
+      stype[m]=c;
+     } /* u */
+
+     stype[m]='\0';
+    } /*if */
+
+
+    
     filt->cd_values[j++]=atoi(stype);
     i+=m; /* jump */
    }
@@ -249,6 +307,11 @@ obj_list_t* parse_filter(const char *str,
    printf("Input Error: pixels_per_block is too large in <%s>\n",str);
    exit(1);
   }
+  if ( (strcmp(smask,"NN")!=0) && (strcmp(smask,"EC")!=0) ) {
+   if (obj_list) free(obj_list);
+   printf("Input Error: szip mask must be 'NN' or 'EC' \n");
+   exit(1);
+  }
   break;
  };
 
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index ef7f298..0db17f5 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -22,7 +22,7 @@
 static const char* MapIdToName(hid_t refobj_id, 
                                trav_table_t *travt);
 
-static void close_obj(H5G_obj_t obj_type, hid_t obj_id);
+static void close_obj(H5G_obj_t1 obj_type, hid_t obj_id);
 
 
 static int copy_refs_attr(hid_t loc_in, 
@@ -142,7 +142,6 @@ int do_copy_refobjs(hid_t fidin,
  */
    if (next==0 && h5tools_canreadf((NULL),dcpl_id)==1)
    {
-
 /*-------------------------------------------------------------------------
  * test for a valid output dataset
  *-------------------------------------------------------------------------
@@ -156,7 +155,7 @@ int do_copy_refobjs(hid_t fidin,
  */
    if (H5Tequal(mtype_id, H5T_STD_REF_OBJ)) 
    {
-    H5G_obj_t        obj_type;
+    H5G_obj_t1       obj_type;
     hid_t            refobj_id;
     hobj_ref_t       *refbuf=NULL; /* buffer for object references */
     hobj_ref_t       *buf=NULL;
@@ -231,7 +230,7 @@ int do_copy_refobjs(hid_t fidin,
  */
    else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) 
    {
-    H5G_obj_t        obj_type;
+    H5G_obj_t1       obj_type;
     hid_t            refobj_id;
     hdset_reg_ref_t  *refbuf=NULL; /* input buffer for region references */
     hdset_reg_ref_t  *buf=NULL;    /* output buffer */
@@ -528,7 +527,7 @@ static int copy_refs_attr(hid_t loc_in,
  */
    if (H5Tequal(mtype_id, H5T_STD_REF_OBJ)) 
    {
-    H5G_obj_t   obj_type;
+    H5G_obj_t1  obj_type;
     hid_t       refobj_id;
     hobj_ref_t  *refbuf=NULL;
     unsigned    k;
@@ -605,7 +604,7 @@ static int copy_refs_attr(hid_t loc_in,
  */
    else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG)) 
    {
-    H5G_obj_t        obj_type;
+    H5G_obj_t1       obj_type;
     hid_t            refobj_id;
     hdset_reg_ref_t  *refbuf=NULL; /* input buffer for region references */
     hdset_reg_ref_t  *buf=NULL;    /* output buffer */
@@ -715,7 +714,7 @@ error:
  *-------------------------------------------------------------------------
  */
 
-static void close_obj(H5G_obj_t obj_type, hid_t obj_id)
+static void close_obj(H5G_obj_t1 obj_type, hid_t obj_id)
 {
  H5E_BEGIN_TRY 
  {
diff --git a/tools/h5repack/h5repack_verify.c b/tools/h5repack/h5repack_verify.c
index 30d3c05..983371e 100644
--- a/tools/h5repack/h5repack_verify.c
+++ b/tools/h5repack/h5repack_verify.c
@@ -25,7 +25,7 @@
  *
  * Return: 1 has, 0 does not, -1 error
  *
- * Programmer: pvn@ncsa.uiuc.edu
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
  * Date: December 19, 2003
  *
@@ -99,7 +99,7 @@ int has_filter(hid_t dcpl_id,
  *
  * Return: 1 has, 0 does not, -1 error
  *
- * Programmer: pvn@ncsa.uiuc.edu
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
  * Date: December 30, 2003
  *
@@ -157,7 +157,7 @@ int has_layout(hid_t dcpl_id,
  *
  * Return: 1=filter present, 0=filter not present, -1=error
  *
- * Programmer: pvn@ncsa.uiuc.edu
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
  * Date: December 19, 2003
  *
@@ -193,11 +193,6 @@ int h5repack_verify(const char *fname,
    goto error;
   if ((dcpl_id=H5Dget_create_plist(dset_id))<0) 
    goto error;
-
-  if (options->verbose) {
-    printf(" %-10s %s\n", "dataset",name );
-    print_filters(dcpl_id);
-  }
   
 /*-------------------------------------------------------------------------
  * filter check
@@ -263,11 +258,7 @@ int h5repack_verify(const char *fname,
      goto error;
     if ((dcpl_id=H5Dget_create_plist(dset_id))<0) 
      goto error;
-    
-    if (options->verbose) {
-     printf(" %-10s %s\n", "dataset",name );
-     print_filters(dcpl_id);
-    }
+
  /*-------------------------------------------------------------------------
   * filter check
   *-------------------------------------------------------------------------
@@ -344,7 +335,7 @@ error:
  *
  * Return: 1=identical, 0=not identical, -1=error
  *
- * Programmer: pvn@ncsa.uiuc.edu
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
  * Date: December 31, 2003
  *
diff --git a/tools/h5repack/testh5repack_attr.c b/tools/h5repack/testh5repack_attr.c
index dc03415..a1dad92 100644
--- a/tools/h5repack/testh5repack_attr.c
+++ b/tools/h5repack/testh5repack_attr.c
@@ -21,7 +21,7 @@
  *
  * Purpose: write attributes in LOC_ID (dataset, group, named datatype) 
  *
- * Programmer:  pvn@ncsa.uiuc.edu
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
  * Date: November 12, 2003
  *
@@ -1028,30 +1028,5 @@ etc
  make_attr(loc_id,3,dims3,"float3D",H5T_NATIVE_FLOAT,buf83);
 }
 
-/*-------------------------------------------------------------------------
- * Function: write_null_attr
- *
- * Purpose: write null attribute in LOC_ID (dataset, group, named datatype) 
- *
- * Programmer: Raymond Lu, slu@ncsa.uiuc.edu
- *
- * Date: May 24, 2004
- *
- *-------------------------------------------------------------------------
- */
-void write_null_attr(hid_t loc_id)
-{
-     hid_t sid, attr_id;
-     int        val = 2;
-    
-     /* Create the null attribute */
-     sid = H5Screate(H5S_NULL);
-     attr_id = H5Acreate(loc_id, "null_attr", H5T_NATIVE_INT, sid, H5P_DEFAULT);
-  
-     /* Not supposed to write anything */
-     H5Awrite(attr_id, H5T_NATIVE_INT, &val);
-
-     /* Close */
-     H5Aclose(attr_id);
-     H5Sclose(sid);
-}
+
+
diff --git a/tools/h5repack/testh5repack_dset.c b/tools/h5repack/testh5repack_dset.c
index 7f6345b..57a5b27 100644
--- a/tools/h5repack/testh5repack_dset.c
+++ b/tools/h5repack/testh5repack_dset.c
@@ -617,31 +617,7 @@ void write_dset_in(hid_t loc_id,
  write_dset(loc_id,3,dims3,"float3D",H5T_NATIVE_FLOAT,buf83);
 }
 
-/*-------------------------------------------------------------------------
- * Function: write_null_dset
- *
- * Purpose: write null dataset in LOC_ID 
- *
- * Programmer: Raymond Lu, slu@ncsa.uiuc.edu
- *
- * Date: May 24, 2004
- *
- *-------------------------------------------------------------------------
- */
-void write_null_dset(hid_t loc_id)
-{
-     hid_t sid, dset_id;
-     int        val = 2;
-    
-     /* Create the null dataset */
-     sid = H5Screate(H5S_NULL);
-     dset_id  = H5Dcreate(loc_id,"null_dset",H5T_NATIVE_INT,sid,H5P_DEFAULT);
-     H5Dwrite(dset_id,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,&val);
-
-     /* Close */
-     H5Dclose(dset_id);
-     H5Sclose(sid);
-}
+
 
 /*-------------------------------------------------------------------------
  * Function: make_dset_reg_ref
diff --git a/tools/h5repack/testh5repack_main.c b/tools/h5repack/testh5repack_main.c
index 0c976f4..af19db2 100644
--- a/tools/h5repack/testh5repack_main.c
+++ b/tools/h5repack/testh5repack_main.c
@@ -29,7 +29,7 @@
  * Return: Success: zero
  *  Failure: non-zero
  *
- * Programmer:  <pvn@ncsa.uiuc.edu>
+ * Programmer:  Pedro Vicente <pvn@ncsa.uiuc.edu>
  *             January, 6, 2004
  *
  *-------------------------------------------------------------------------
@@ -58,7 +58,7 @@ int main (void)
  *     it returns RET==0 if the objects have the same data
  *-------------------------------------------------------------------------
  */
- 
+
 /*-------------------------------------------------------------------------
  * file with all kinds of dataset datatypes
  *-------------------------------------------------------------------------
@@ -178,7 +178,7 @@ int main (void)
 
  if (h5repack_init (&pack_options, 0)<0)
   TEST_ERROR;
- if (h5repack_addfilter("GZIP=9",&pack_options)<0)
+ if (h5repack_addfilter("GZIP=1",&pack_options)<0)
   TEST_ERROR;
  if (h5repack_addlayout("CHUNK=20x10",&pack_options)<0)
   TEST_ERROR;
@@ -212,7 +212,7 @@ int main (void)
  
  if (h5repack_init (&pack_options, 0)<0)
   TEST_ERROR;
- if (h5repack_addfilter("dset2:SZIP=8",&pack_options)<0)
+ if (h5repack_addfilter("dset2:SZIP=8,EC",&pack_options)<0)
   TEST_ERROR;
  if (h5repack_addlayout("dset2:CHUNK=20x10",&pack_options)<0)
   TEST_ERROR;
@@ -240,7 +240,7 @@ TESTING("    adding szip filter to all");
 #if defined (H5_HAVE_FILTER_SZIP) && defined (H5_SZIP_CAN_ENCODE)
  if (h5repack_init (&pack_options, 0)<0)
   TEST_ERROR;
- if (h5repack_addfilter("SZIP=8",&pack_options)<0)
+ if (h5repack_addfilter("SZIP=8,NN",&pack_options)<0)
   TEST_ERROR;
  if (h5repack(FNAME4,FNAME4OUT,&pack_options)<0)
   TEST_ERROR;
@@ -399,8 +399,8 @@ TESTING("    addding shuffle filter to all");
   TEST_ERROR;
 #endif
 
-#if defined (H5_HAVE_FILTER_SZIP) && defined (H5_SZIP_CAN_ENCODE)
- if (h5repack_addfilter("dset1:SZIP=8",&pack_options)<0)
+#if defined (H5_SZIP_CAN_ENCODE) &&  defined (H5_HAVE_FILTER_SZIP)
+ if (h5repack_addfilter("dset1:SZIP=8,NN",&pack_options)<0)
   TEST_ERROR;
 #endif
 
@@ -409,7 +409,6 @@ TESTING("    addding shuffle filter to all");
   TEST_ERROR;
 #endif
 
-
  if (h5repack(FNAME4,FNAME4OUT,&pack_options)<0)
   TEST_ERROR;
  if (h5diff(FNAME4,FNAME4OUT,NULL,NULL,&diff_options) == 1)
@@ -902,21 +901,26 @@ TESTING("    addding shuffle filter to all");
  SKIPPED();
 #endif
 
-
  
 /*-------------------------------------------------------------------------
- * test the NONE global option
+ * file with all filters 
+ *  dset_all
+ *  dset_deflate
+ *  dset_szip
+ *  dset_shuffle
+ *  dset_fletcher32
  *-------------------------------------------------------------------------
  */
+ 
 
-  TESTING("    removing all filters");
+ TESTING("    filter conversion from deflate to szip");
 
 #if defined (H5_HAVE_FILTER_SZIP) && defined (H5_HAVE_FILTER_DEFLATE) \
     && defined (H5_HAVE_FILTER_FLETCHER32) && defined (H5_HAVE_FILTER_SHUFFLE)
 
  if (h5repack_init (&pack_options, 0)<0)
   TEST_ERROR;
- if (h5repack_addfilter("NONE",&pack_options)<0)
+ if (h5repack_addfilter("dset_deflate:SZIP=8,NN",&pack_options)<0)
   TEST_ERROR;
  if (h5repack(FNAME11,FNAME11OUT,&pack_options)<0)
   TEST_ERROR;
@@ -931,54 +935,59 @@ TESTING("    addding shuffle filter to all");
 #else
  SKIPPED();
 #endif
- 
- TESTING("    filter conversion from deflate to szip");
-/*-------------------------------------------------------------------------
- * filter conversion from deflate to szip
- *-------------------------------------------------------------------------
- */
-#if (defined (H5_SZIP_CAN_ENCODE) && defined (H5_HAVE_FILTER_SZIP)) && defined(H5_HAVE_FILTER_DEFLATE)
+
+ TESTING("    filter conversion from szip to deflate");
+
+#if defined (H5_HAVE_FILTER_SZIP) && defined (H5_HAVE_FILTER_DEFLATE) \
+    && defined (H5_HAVE_FILTER_FLETCHER32) && defined (H5_HAVE_FILTER_SHUFFLE)
+
  if (h5repack_init (&pack_options, 0)<0)
   TEST_ERROR;
- if (h5repack_addfilter("dset_deflate:SZIP=8",&pack_options)<0)
+ if (h5repack_addfilter("dset_szip:GZIP=1",&pack_options)<0)
   TEST_ERROR;
- if (h5repack(FNAME8,FNAME8OUT,&pack_options)<0)
+ if (h5repack(FNAME11,FNAME11OUT,&pack_options)<0)
   TEST_ERROR;
- if (h5diff(FNAME8,FNAME8OUT,NULL,NULL,&diff_options) == 1)
+ if (h5diff(FNAME11,FNAME11OUT,NULL,NULL,&diff_options) == 1)
   TEST_ERROR;
- if (h5repack_verify(FNAME8OUT,&pack_options)<=0)
+ if (h5repack_verify(FNAME11OUT,&pack_options)<=0)
   TEST_ERROR;
  if (h5repack_end (&pack_options)<0)
   TEST_ERROR;
+
  PASSED();
 #else
  SKIPPED();
 #endif
 
- TESTING("    filter conversion from szip to deflate");
+  
 /*-------------------------------------------------------------------------
- * filter conversion from szip to deflate
+ * test the NONE global option
  *-------------------------------------------------------------------------
  */
-#if (defined (H5_SZIP_CAN_ENCODE) && defined (H5_HAVE_FILTER_SZIP)) && defined(H5_HAVE_FILTER_DEFLATE)
+
+  TESTING("    removing all filters");
+
+#if defined (H5_HAVE_FILTER_SZIP) && defined (H5_HAVE_FILTER_DEFLATE) \
+    && defined (H5_HAVE_FILTER_FLETCHER32) && defined (H5_HAVE_FILTER_SHUFFLE)
+
  if (h5repack_init (&pack_options, 0)<0)
   TEST_ERROR;
- if (h5repack_addfilter("dset_szip:GZIP=1",&pack_options)<0)
+ if (h5repack_addfilter("NONE",&pack_options)<0)
   TEST_ERROR;
- if (h5repack(FNAME7,FNAME7OUT,&pack_options)<0)
+ if (h5repack(FNAME11,FNAME11OUT,&pack_options)<0)
   TEST_ERROR;
- if (h5diff(FNAME7,FNAME7OUT,NULL,NULL,&diff_options) == 1)
+ if (h5diff(FNAME11,FNAME11OUT,NULL,NULL,&diff_options) == 1)
   TEST_ERROR;
- if (h5repack_verify(FNAME7OUT,&pack_options)<=0)
+ if (h5repack_verify(FNAME11OUT,&pack_options)<=0)
   TEST_ERROR;
  if (h5repack_end (&pack_options)<0)
   TEST_ERROR;
+
  PASSED();
 #else
  SKIPPED();
 #endif
-
-
+ 
   
 /*-------------------------------------------------------------------------
  * end
diff --git a/tools/h5repack/testh5repack_make.c b/tools/h5repack/testh5repack_make.c
index 249512c..b0293e3 100644
--- a/tools/h5repack/testh5repack_make.c
+++ b/tools/h5repack/testh5repack_make.c
@@ -586,7 +586,7 @@ int make_fletcher32(hid_t loc_id)
 
 
 /*-------------------------------------------------------------------------
- * checksum
+ * fletcher32
  *-------------------------------------------------------------------------
  */
 #if defined (H5_HAVE_FILTER_FLETCHER32)
@@ -625,7 +625,7 @@ out:
 /*-------------------------------------------------------------------------
  * Function: make_all
  *
- * Purpose: make a dataset with the all filters
+ * Purpose: make a file with all filters
  *
  *-------------------------------------------------------------------------
  */
@@ -683,6 +683,69 @@ int make_all(hid_t loc_id)
   goto out;
 
 /*-------------------------------------------------------------------------
+ * fletcher32
+ *-------------------------------------------------------------------------
+ */
+#if defined (H5_HAVE_FILTER_FLETCHER32)
+ /* remove the filters from the dcpl */
+ if (H5Premove_filter(dcpl,H5Z_FILTER_ALL)<0) 
+  goto out;
+ /* set the checksum filter */
+ if (H5Pset_fletcher32(dcpl)<0) 
+  goto out;
+ if (make_dset(loc_id,"dset_fletcher32",sid,dcpl,buf)<0)
+  goto out;
+#endif
+
+/*-------------------------------------------------------------------------
+ * SZIP
+ *-------------------------------------------------------------------------
+ */
+ /* Make sure encoding is enabled */
+#if defined (H5_SZIP_CAN_ENCODE) && defined (H5_HAVE_FILTER_SZIP)
+ /* remove the filters from the dcpl */
+ if (H5Premove_filter(dcpl,H5Z_FILTER_ALL)<0) 
+  goto out;
+ /* set szip data */
+ if(H5Pset_szip (dcpl,szip_options_mask,szip_pixels_per_block)<0)
+  goto out;
+ if (make_dset(loc_id,"dset_szip",sid,dcpl,buf)<0)
+  goto out;
+#endif
+
+/*-------------------------------------------------------------------------
+ * shuffle
+ *-------------------------------------------------------------------------
+ */
+#if defined (H5_HAVE_FILTER_SHUFFLE)
+ /* remove the filters from the dcpl */
+ if (H5Premove_filter(dcpl,H5Z_FILTER_ALL)<0) 
+  goto out;
+ /* set the shuffle filter */
+ if (H5Pset_shuffle(dcpl)<0) 
+  goto out;
+ if (make_dset(loc_id,"dset_shuffle",sid,dcpl,buf)<0)
+  goto out;
+#endif
+
+/*-------------------------------------------------------------------------
+ * GZIP
+ *-------------------------------------------------------------------------
+ */
+#if defined (H5_HAVE_FILTER_DEFLATE)
+ /* remove the filters from the dcpl */
+ if (H5Premove_filter(dcpl,H5Z_FILTER_ALL)<0) 
+  goto out;
+ /* set deflate data */
+ if(H5Pset_deflate(dcpl, 1)<0)
+  goto out;
+ if (make_dset(loc_id,"dset_deflate",sid,dcpl,buf)<0)
+  goto out;
+#endif
+
+
+
+/*-------------------------------------------------------------------------
  * close space and dcpl
  *-------------------------------------------------------------------------
  */
diff --git a/tools/h5repack/testh5repack_util.c b/tools/h5repack/testh5repack_util.c
index 0f7253b..f74b414 100644
--- a/tools/h5repack/testh5repack_util.c
+++ b/tools/h5repack/testh5repack_util.c
@@ -20,7 +20,7 @@
  *
  * Purpose: utility function to create and write a dataset in LOC_ID
  *
- * Programmer:  pvn@ncsa.uiuc.edu
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
  * Date: November 12, 2003
  *
@@ -60,7 +60,7 @@ int make_dset(hid_t loc_id,
  *
  * Purpose: utility function to create and write a dataset in LOC_ID
  *
- * Programmer:  pvn@ncsa.uiuc.edu
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
  * Date: November 12, 2003
  *
@@ -106,7 +106,7 @@ int write_dset( hid_t loc_id,
  *
  * Purpose: utility function to write an attribute in LOC_ID
  *
- * Programmer:  pvn@ncsa.uiuc.edu
+ * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
  *
  * Date: November 12, 2003
  *