[svn-r22180] Description:

    Add new "metadata block size" command line option ('-M <x>' or
'--metadata_block_size=<x>') for h5repack.

Tested on:
    Mac OSX/64 10.7.3 (amazon) w/debug)
    (h5committest upcoming)

6 files changed, 110 insertions, 120 deletions

diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index 28d66c5..9778fdd 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -87,10 +87,12 @@ int h5repack(const char* infile,
 */
 
 int
-h5repack_init(pack_opt_t *options, int verbose, H5F_file_space_type_t strategy, hsize_t threshold)
+h5repack_init(pack_opt_t *options, int verbose, H5F_file_space_type_t strategy,
+    hsize_t threshold)
 {
     int k, n;
-    HDmemset(options,0,sizeof(pack_opt_t));
+
+    HDmemset(options, 0, sizeof(pack_opt_t));
     options->min_comp = 1024;
     options->verbose  = verbose;
 
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index 6415d3a..3907178 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -111,6 +111,7 @@ typedef struct {
                                  datatype, fill value, filter pipleline, attribute */
  const char      *ublock_filename; /* user block file name */
  hsize_t         ublock_size;      /* user block size */
+ hsize_t         meta_block_size;  /* metadata aggregation block size (for H5Pset_meta_block_size) */
  hsize_t         threshold;        /* alignment threshold for H5Pset_alignment */
  hsize_t         alignment ;       /* alignment for H5Pset_alignment */
  H5F_file_space_type_t fs_strategy;     /* File space handling strategy */
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index c1cbba1..2271f34 100644
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -801,7 +801,6 @@ TOOLTEST h5repack_refs.h5
 # the references in attribute of compund or vlen datatype 
 TOOLTEST h5repack_attr_refs.h5 
 
-
 # Add test for memory leak in attirbute. This test is verified by CTEST.   
 # 1. leak from vlen string  
 # 2. leak from compound type without reference member
@@ -809,6 +808,10 @@ TOOLTEST h5repack_attr_refs.h5
 # Note: this test is experimental for sharing test file among tools
 TOOLTEST h5diff_attr1.h5
 
+# tests for metadata block size option ('-M')
+TOOLTEST h5diff_layout.h5 -M 8192
+TOOLTEST h5diff_layout.h5 --metadata_block_size=8192
+
 if test $nerrors -eq 0 ; then
     echo "All $TESTNAME tests passed."
     exit $EXIT_SUCCESS
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 55cf932..15df639 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -132,23 +132,23 @@ int copy_objects(const char* fnamein,
             goto out;
         }
 
-  if(!options->fs_strategy)
-  {
-     if(H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0)
-     {
-    error_msg("failed to retrieve file space strategy\n");
-    goto out;
-     }
-  }
-
-  if(!options->fs_threshold)
-  {
-     if(H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0)
-     {
-    error_msg("failed to retrieve file space threshold\n");
-    goto out;
-     }
-  }
+        if(!options->fs_strategy)
+        {
+            if(H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0)
+            {
+                error_msg("failed to retrieve file space strategy\n");
+                goto out;
+            }
+        }
+
+        if(!options->fs_threshold)
+        {
+            if(H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0)
+            {
+                error_msg("failed to retrieve file space threshold\n");
+                goto out;
+            }
+        }
 
         if(H5Pclose(fcpl_in) < 0)
         {
@@ -254,135 +254,113 @@ int copy_objects(const char* fnamein,
             } /* end if */
         } /* end if */
     } /* end if */
-
-
-
-
 #if defined (H5REPACK_DEBUG_USER_BLOCK)
-    print_user_block(fnamein,fidin);
+    print_user_block(fnamein, fidin);
 #endif
 
-
     /*-------------------------------------------------------------------------
     * set the new user userblock options in the FCPL (before H5Fcreate )
     *-------------------------------------------------------------------------
     */
-
     if ( options->ublock_size > 0 )
     {
         /* either use the FCPL already created or create a new one */
-        if(fcpl != H5P_DEFAULT)
+        if(fcpl == H5P_DEFAULT)
         {
-            /* set user block size */
-            if(H5Pset_userblock(fcpl, options->ublock_size) < 0)
-            {
-                error_msg("failed to set userblock size\n");
-                goto out;
-            }
-
-        }
-
-        else
-        {
-
             /* create a file creation property list */
             if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
             {
                 error_msg("fail to create a file creation property list\n");
                 goto out;
             }
-
-            /* set user block size */
-            if(H5Pset_userblock(fcpl, options->ublock_size) < 0)
-            {
-                error_msg("failed to set userblock size\n");
-                goto out;
-            }
-
         }
 
-
-
+        /* set user block size */
+        if(H5Pset_userblock(fcpl, options->ublock_size) < 0)
+        {
+            error_msg("failed to set userblock size\n");
+            goto out;
+        }
     }
 
-
     /*-------------------------------------------------------------------------
     * set alignment options
     *-------------------------------------------------------------------------
     */
-
-
     if (  options->alignment > 0 )
     {
         /* either use the FAPL already created or create a new one */
-        if (fapl != H5P_DEFAULT)
+        if (fapl == H5P_DEFAULT)
         {
-
-            if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
+            /* create a file access property list */
+            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
             {
-                error_msg("failed to set alignment\n");
+                error_msg("Could not create file access property list\n");
                 goto out;
             }
-
         }
 
-        else
+        if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
         {
+            error_msg("failed to set alignment\n");
+            goto out;
+        }
+    }
 
+    /*-------------------------------------------------------------------------
+    * set metadata block size option
+    *-------------------------------------------------------------------------
+    */
+    if (  options->meta_block_size > 0 )
+    {
+        /* either use the FAPL already created or create a new one */
+        if (fapl == H5P_DEFAULT)
+        {
             /* create a file access property list */
             if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
             {
                 error_msg("Could not create file access property list\n");
                 goto out;
             }
-
-            if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
-            {
-                error_msg("failed to set alignment\n");
-                goto out;
-            }
-
         }
 
+        if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0)
+        {
+            error_msg("failed to set metadata block size\n");
+            goto out;
+        }
     }
 
+    /*-------------------------------------------------------------------------
+    * set free-space strategy options
+    *-------------------------------------------------------------------------
+    */
+
     /* either use the FCPL already created or create a new one */
-    if(fcpl != H5P_DEFAULT)
+    if(fcpl == H5P_DEFAULT)
     {
-  /* set file space strategy and free space threshold */
-  if(H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0)
-  {
-      error_msg("failed to set file space strategy & threshold\n");
-      goto out;
-  }
+        /* create a file creation property list */
+        if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
+        {
+            error_msg("fail to create a file creation property list\n");
+            goto out;
+        }
     }
-    else
+
+    /* set file space strategy and free space threshold */
+    if(H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0)
     {
-  /* create a file creation property list */
-  if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
-  {
-      error_msg("fail to create a file creation property list\n");
-      goto out;
-  }
-
-  /* set file space strategy and free space threshold */
-  if(H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0)
-  {
-      error_msg("failed to set file space strategy & threshold \n");
-      goto out;
-  }
+        error_msg("failed to set file space strategy & threshold \n");
+        goto out;
     }
 
     /*-------------------------------------------------------------------------
     * create the output file
     *-------------------------------------------------------------------------
     */
-
-
     if(options->verbose)
         printf("Making file <%s>...\n",fnameout);
 
-
     if((fidout = H5Fcreate(fnameout,H5F_ACC_TRUNC, fcpl, fapl)) < 0)
     {
         error_msg("<%s>: Could not create file\n", fnameout );
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index e1697ab..6004084 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -35,7 +35,7 @@ const char  *outfile = NULL;
  * Command-line options: The user can specify short or long-named
  * parameters.
  */
-static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:t:a:i:o:S:T:";
+static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:M:t:a:i:o:S:T:";
 static struct long_options l_opts[] = {
     { "help", no_arg, 'h' },
     { "version", no_arg, 'V' },
@@ -51,6 +51,7 @@ static struct long_options l_opts[] = {
     { "ssize", require_arg, 's' },
     { "ublock", require_arg, 'u' },
     { "block", require_arg, 'b' },
+    { "metadata_block_size", require_arg, 'M' },
     { "threshold", require_arg, 't' },
     { "alignment", require_arg, 'a' },
     { "infile", require_arg, 'i' },   /* -i for backward compability */
@@ -78,24 +79,6 @@ static struct long_options l_opts[] = {
  *
  * 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
- *   PVN, November 19, 2007
- *    adopted the syntax h5repack [OPTIONS]  file1 file2
- *   PVN, November 28, 2007
- *    added support for multiple global filters
- *   PVN, May 16, 2008
- *    added  backward compatibility for -i infile -o outfile
- *   PVN, August 20, 2008
- *    add a user block to repacked file (switches -u -b)
- *   PVN, August 28, 2008
- *    add options to set alignment (H5Pset_alignment) (switches -t -a)
  *-------------------------------------------------------------------------
  */
 int main(int argc, const char **argv)
@@ -115,7 +98,7 @@ int main(int argc, const char **argv)
         HDexit(EXIT_FAILURE);
 
     /* initialize options  */
-    h5repack_init(&options, 0, 0, (hsize_t)0);
+    h5repack_init(&options, 0, H5F_FILE_SPACE_DEFAULT, (hsize_t)0);
 
     parse_command_line(argc, argv, &options);
 
@@ -187,6 +170,7 @@ static void usage(const char *prog)
  printf("   -e E, --file=E          Name of file E with the -f and -l options\n");
  printf("   -u U, --ublock=U        Name of file U with user block data to be added\n");
  printf("   -b B, --block=B         Size of user block to be added\n");
+ printf("   -M A, --metadata_block_size=A  Metadata block size for H5Pset_meta_block_size\n");
  printf("   -t T, --threshold=T     Threshold value for H5Pset_alignment\n");
  printf("   -a A, --alignment=A     Alignment value for H5Pset_alignment\n");
  printf("   -f FILT, --filter=FILT  Filter type\n");
@@ -428,7 +412,6 @@ void parse_command_line(int argc, const char **argv, pack_opt_t* options)
 
             break;
 
-
         case 'u':
 
             options->ublock_filename = opt_arg;
@@ -439,6 +422,11 @@ void parse_command_line(int argc, const char **argv, pack_opt_t* options)
             options->ublock_size = (hsize_t)HDatol( opt_arg );
             break;
 
+        case 'M':
+
+            options->meta_block_size = (hsize_t)HDatol( opt_arg );
+            break;
+
         case 't':
 
             options->threshold = (hsize_t)HDatol( opt_arg );
@@ -455,7 +443,7 @@ void parse_command_line(int argc, const char **argv, pack_opt_t* options)
             break;
 
         case 'S':
-  {
+            {
             char strategy[MAX_NC_NAME];
 
             HDstrcpy(strategy, opt_arg);
@@ -472,7 +460,7 @@ void parse_command_line(int argc, const char **argv, pack_opt_t* options)
                 HDexit(EXIT_FAILURE);
             }
             break;
-        }
+            }
 
         case 'T':
 
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index 17a6190..5d72ce4 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -78,7 +78,6 @@
 #define FNAME17OUT  "h5repack_named_dtypes_out.h5"
 
 #define FNAME18     "h5repack_layout2.h5"
-#define FNAME18OUT  "h5repack_layout2_out.h5"
 
 #define FNAME_UB   "ublock.bin"
 
@@ -1561,6 +1560,25 @@ int main (void)
     PASSED();
 
     /*-------------------------------------------------------------------------
+    * test --metadata_block_size option
+    *-------------------------------------------------------------------------
+    */
+    TESTING("    metadata block size option");
+    if (h5repack_init (&pack_options, 0, fs_type, fs_size) < 0)
+        GOERROR;
+    pack_options.meta_block_size = 8192;
+    if(h5repack(FNAME1, FNAME1OUT, &pack_options) < 0)
+        GOERROR;
+    if(h5diff(FNAME1, FNAME1OUT, NULL, NULL, &diff_options) > 0)
+        GOERROR;
+    if(h5repack_verify(FNAME1, FNAME1OUT, &pack_options) <= 0)
+        GOERROR;
+    if(h5repack_end(&pack_options) < 0)
+        GOERROR;
+    PASSED();
+
+
+    /*-------------------------------------------------------------------------
     * clean temporary test files
     *-------------------------------------------------------------------------
     */
@@ -3253,7 +3271,7 @@ make_userblock(void)
 
     /* Initialize userblock data */
     for(u = 0; u < USERBLOCK_SIZE; u++)
-        ub[u] = 'a' + (u % 26);
+        ub[u] = 'a' + (char)(u % 26);
 
     /* Re-open HDF5 file, as "plain" file */
     if((fd = HDopen(FNAME16, O_WRONLY, 0644)) < 0)
@@ -3366,7 +3384,7 @@ make_userblock_file(void)
 
     /* initialize userblock data */
     for(u = 0; u < USERBLOCK_SIZE; u++)
-        ub[u] = 'a' + (u % 26);
+        ub[u] = 'a' + (char)(u % 26);
 
     /* open file */
     if((fd = HDopen(FNAME_UB,O_WRONLY|O_CREAT|O_TRUNC, 0644 )) < 0)
@@ -3842,7 +3860,7 @@ int write_dset_in(hid_t loc_id,
             int l;
 
             buf52[i][j].p = malloc((i + 1) * sizeof(int));
-            buf52[i][j].len = i + 1;
+            buf52[i][j].len = (size_t)(i + 1);
             for(l = 0; l < i + 1; l++)
             {
                 if(make_diffs)
@@ -4063,7 +4081,7 @@ int write_dset_in(hid_t loc_id,
                 int l;
 
                 buf53[i][j][k].p = malloc((i + 1) * sizeof(int));
-                buf53[i][j][k].len = i + 1;
+                buf53[i][j][k].len = (size_t)(i + 1);
                 for(l = 0; l < i + 1; l++)
                 {
                     if(make_diffs)
@@ -4854,7 +4872,7 @@ int write_attr_in(hid_t loc_id,
         {
             int l;
             buf52[i][j].p = malloc((i + 1) * sizeof(int));
-            buf52[i][j].len = i + 1;
+            buf52[i][j].len = (size_t)(i + 1);
             for (l = 0; l < i + 1; l++)
                 if (make_diffs)((int *)buf52[i][j].p)[l] = 0;
                 else ((int *)buf52[i][j].p)[l] = n++;
@@ -5320,7 +5338,7 @@ int write_attr_in(hid_t loc_id,
             {
                 int l;
                 buf53[i][j][k].p = malloc((i + 1) * sizeof(int));
-                buf53[i][j][k].len = i + 1;
+                buf53[i][j][k].len = (size_t)i + 1;
                 for (l = 0; l < i + 1; l++)
                     if (make_diffs)
                     {