[svn-r15551] 1) There are 2 new command line parameters for h5repack. Together they allow a call to H5Pset_alignment to be made

  -t T, --threshold=T     Threshold value for H5Pset_alignment
   -a A, --alignment=A     Alignment value for H5Pset_alignment

2) bug fix
the printing of the dataset name was not done for references (verbose mode)

tested: windows, linux

7 files changed, 192 insertions, 23 deletions

diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index 73f78f6..75684fc 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -95,7 +95,7 @@ int h5repack_init (pack_opt_t *options,
 {
     int k, n;
     memset(options,0,sizeof(pack_opt_t));
-    options->threshold = 1024;
+    options->min_comp = 1024;
     options->verbose   = verbose;
         
     for ( n = 0; n < H5_REPACK_MAX_NFILTERS; n++)
@@ -427,7 +427,25 @@ static int check_options(pack_opt_t *options)
             options->ublock_filename);
         return -1;
     }
+
+
+    /*--------------------------------------------------------------------------------
+    * verify alignment options; both threshold and alignment sizes must be present
+    *---------------------------------------------------------------------------------
+    */
+#if 0
+    if ( options->alignment != 0 && options->threshold == 0 )
+    {
+        error_msg(progname, "threshold for H5Pset_alignment missing\n");
+        return -1;
+    }
     
+    if ( options->alignment == 0 && options->threshold != 0 )
+    {
+        error_msg(progname, "alignment for H5Pset_alignment missing\n");
+        return -1;
+    }
+#endif    
     
     return 0;
 }
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index e67bb97..a7b3fd9 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -25,6 +25,8 @@
 #define PFORMAT1 "%-7s %-7s %-7s"     /* chunk info, compression info, name*/
 #define MAX_NC_NAME 256               /* max length of a name */
 #define MAX_VAR_DIMS 32               /* max per variable dimensions */
+#define FORMAT_OBJ      " %-27s %s\n"   /* obj type, name */
+#define FORMAT_OBJ_ATTR "  %-27s %s\n"  /* obj type, name */
 
 /*-------------------------------------------------------------------------
  * data structures for command line options
@@ -99,7 +101,7 @@ typedef struct {
  chunk_info_t    chunk_g;     /*global chunk INFO for the ALL case */
  H5D_layout_t    layout_g;    /*global layout information for the ALL case */
  int             verbose;     /*verbose mode */
- hsize_t         threshold;   /*minimum size to compress, in bytes */
+ hsize_t         min_comp;    /*minimum size to compress, in bytes */
  int             use_native;  /*use a native type in write */  
  int             latest;      /*pack file with the latest file format */
  int             grp_compact; /* Set the maximum number of links to store as header messages in the group */
@@ -108,6 +110,8 @@ typedef struct {
                                  datatype, fill value, filter pipleline, attribute */
  const char      *ublock_filename; /* user block file name */
  int             ublock_size;      /* user block size */
+ hsize_t         threshold;        /* alignment threshold for H5Pset_alignment */
+ hsize_t         alignment ;       /* alignment for H5Pset_alignment */
 } pack_opt_t;
 
 
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index fdd93da..c4afde9 100755
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -494,6 +494,10 @@ fi
 arg="$FILE1 -u ublock.bin -b 2048"
 TOOLTEST $arg
 
+# add alignment
+arg="$FILE1 -t 1 -a 1 "
+TOOLTEST $arg
+
 
 if test $nerrors -eq 0 ; then
    echo "All $H5REPACK tests passed."
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index e9ddbe0..7f43ad0 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -31,8 +31,6 @@ extern char  *progname;
  * macros
  *-------------------------------------------------------------------------
  */
-#define FORMAT_OBJ      " %-27s %s\n"   /* obj type, name */
-#define FORMAT_OBJ_ATTR "  %-27s %s\n"  /* obj type, name */
 #define USERBLOCK_XFER_SIZE     512     /* size of buffer/# of bytes to xfer at a time when copying userblock */
 
 /*-------------------------------------------------------------------------
@@ -240,6 +238,48 @@ int copy_objects(const char* fnamein,
         
     }
 
+
+    /*-------------------------------------------------------------------------
+    * set alignment options
+    *-------------------------------------------------------------------------
+    */
+
+   
+    if (  options->alignment > 0 )
+    {
+        /* either use the FCPL already created or create a new one */
+        if (fapl != H5P_DEFAULT)
+        {
+            
+            if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
+            {
+                error_msg(progname, "failed to set alignment\n");
+                goto out;
+            }
+            
+        }
+        
+        else
+        {
+            
+            /* create a file access property list */
+            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) 
+            {
+                error_msg(progname, "Could not create file access property list\n");
+                goto out;
+            } 
+            
+            if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
+            {
+                error_msg(progname, "failed to set alignment\n");
+                goto out;
+            }
+            
+        }      
+        
+    }
+
+
     /*-------------------------------------------------------------------------
     * create the output file
     *-------------------------------------------------------------------------
@@ -588,7 +628,7 @@ int do_copy_objects(hid_t fidin,
                             dsize_in=H5Dget_storage_size(dset_in);
 
                             /* check for datasets too small */
-                            if (nelmts*msize < options->threshold )
+                            if (nelmts*msize < options->min_comp )
                                 apply_s=0;
 
                             /* apply the filter */
@@ -768,7 +808,7 @@ int do_copy_objects(hid_t fidin,
                                 if ( has_filter && apply_s == 0 )
                                     printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
                                             travt->objs[i].name,
-                                            (int)options->threshold);
+                                            (int)options->min_comp);
 
                                 if ( has_filter && apply_f == 0 )
                                     printf(" <warning: could not apply the filter to %s>\n",
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index c949732..f457f23 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -37,14 +37,14 @@ static int has_i_o = 0;
  * 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:";
+static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:t:a:";
 static struct long_options l_opts[] = {
     { "help", no_arg, 'h' },
     { "version", no_arg, 'V' },
     { "verbose", no_arg, 'v' },
     { "filter", require_arg, 'f' },
     { "layout", require_arg, 'l' },
-    { "threshold", require_arg, 'm' },
+    { "minimum", require_arg, 'm' },
     { "file", require_arg, 'e' },
     { "native", no_arg, 'n' },
     { "latest", no_arg, 'L' },
@@ -53,6 +53,8 @@ static struct long_options l_opts[] = {
     { "ssize", require_arg, 's' },
     { "ublock", require_arg, 'u' },
     { "block", require_arg, 'b' },
+    { "threshold", require_arg, 't' },
+    { "alignment", require_arg, 'a' },
     { NULL, 0, '\0' }
 };
 
@@ -87,7 +89,9 @@ static struct long_options l_opts[] = {
  *   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) 
+ *    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, char **argv)
@@ -166,10 +170,10 @@ int main(int argc, char **argv)
             
             else if (strcmp(argv[i], "-m") == 0) 
             {
-                options.threshold = parse_number(argv[i+1]);
-                if ((int)options.threshold==-1) 
+                options.min_comp = parse_number(argv[i+1]);
+                if ((int)options.min_comp<=0) 
                 {
-                    error_msg(progname, "invalid treshold size <%s>\n",argv[i+1]);
+                    error_msg(progname, "invalid minimum compress size <%s>\n",argv[i+1]);
                     exit(1);
                 }
                 ++i;
@@ -288,7 +292,6 @@ int main(int argc, char **argv)
         
     }
 
-
    
     /* pack it */
     ret=h5repack(infile,outfile,&options);
@@ -327,20 +330,24 @@ static void usage(const char *prog)
  printf("   -c L1, --compact=L1     Maximum number of links in header messages\n");
  printf("   -d L2, --indexed=L2     Minimum number of links in the indexed format\n");
  printf("   -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
- printf("   -m T, --threshold=T     Do not apply the filter to datasets smaller than T\n");
- printf("   -e M, --file=M          Name of file M with the -f and -l options\n");
+ printf("   -m M, --minimum=M       Do not apply the filter to datasets smaller than M\n");
+ 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 D, --block=D         Size of user block to be added\n");
+ printf("   -b B, --block=B         Size of user block to be added\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");
  printf("   -l LAYT, --layout=LAYT  Layout type\n");
  
  printf("\n");
 
- printf("  T - is an integer greater than 1, size of dataset in bytes \n");
- printf("  M - is a filename.\n");
- printf("  U - is a filename.\n");
+ printf("  M - is an integer greater than 1, size of dataset in bytes \n");
+ printf("  E - is a filename.\n");
  printf("  S - is an integer\n");
- printf("  D - is the user block size (any power of 2 equal to 512 or greater)\n");
+ printf("  U - is a filename.\n");
+ printf("  T - is an integer\n");
+ printf("  A - is an integer greater than zero\n");
+ printf("  B - is the user block size (any power of 2 equal to 512 or greater)\n");
  printf("  F - is the shared object header message type, any of <dspace|dtype|fill|\n");
  printf("        pline|attr>. If F is not specified, S applies to all messages\n");
 
@@ -464,10 +471,10 @@ static void parse_command_line(int argc, const char* argv[], pack_opt_t* options
 
         case 'm':
 
-            options->threshold = parse_number( opt_arg );
-            if ((int)options->threshold==-1) 
+            options->min_comp = parse_number( opt_arg );
+            if ((int)options->min_comp<=0) 
             {
-                error_msg(progname, "invalid treshold size <%s>\n", opt_arg );
+                error_msg(progname, "invalid minimum compress size <%s>\n", opt_arg );
                 exit(EXIT_FAILURE);
             }
             break;
@@ -550,6 +557,26 @@ static void parse_command_line(int argc, const char* argv[], pack_opt_t* options
             options->ublock_size = atoi( opt_arg );
             break;
 
+        case 't':
+            
+            options->threshold = atoi( opt_arg );
+            if ( options->threshold < 0 ) 
+            {
+                error_msg(progname, "invalid threshold size\n", opt_arg );
+                exit(EXIT_FAILURE);
+            }
+            break;
+
+        case 'a':
+            
+            options->alignment = atoi( opt_arg );
+            if ( options->alignment < 1 ) 
+            {
+                error_msg(progname, "invalid alignment size\n", opt_arg );
+                exit(EXIT_FAILURE);
+            }
+            break;
+
         } /* switch */
         
         
diff --git a/tools/h5repack/h5repack_refs.c b/tools/h5repack/h5repack_refs.c
index 85af317..b0428bf 100644
--- a/tools/h5repack/h5repack_refs.c
+++ b/tools/h5repack/h5repack_refs.c
@@ -192,9 +192,13 @@ int do_copy_refobjs(hid_t fidin,
                                     if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, -1) < 0)
                                         goto error;
                                     if(options->verbose)
+                                    {
+                                        
+                                        printf(FORMAT_OBJ,"dset",travt->objs[i].name );
                                         printf("object <%s> object reference created to <%s>\n",
                                             travt->objs[i].name,
                                             refname);
+                                    }
                                 } /*refname*/
                                 H5Oclose(refobj_id);
                             } /* u */
@@ -271,9 +275,13 @@ int do_copy_refobjs(hid_t fidin,
                                     if(H5Sclose(region_id) < 0)
                                         goto error;
                                     if(options->verbose)
+                                    {
+                                        
+                                        printf(FORMAT_OBJ,"dset",travt->objs[i].name );
                                         printf("object <%s> region reference created to <%s>\n",
                                             travt->objs[i].name,
                                             refname);
+                                    }
                                 } /*refname*/
                                 H5Oclose(refobj_id);
                             } /* u */
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index e7024f2..75af4f1 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -1403,6 +1403,9 @@ if (szip_can_encode) {
  *-------------------------------------------------------------------------
  */
  TESTING("    file with added userblock");
+
+#ifdef H5_HAVE_FILTER_DEFLATE
+
  if(h5repack_init(&pack_options, 0) < 0)
   GOERROR;
 
@@ -1420,7 +1423,72 @@ if (szip_can_encode) {
   GOERROR;
  if(h5repack_end(&pack_options) < 0)
   GOERROR;
+
+
+ PASSED();
+#else
+ SKIPPED();
+#endif
+
+
+/*-------------------------------------------------------------------------
+ * test file with aligment
+ *-------------------------------------------------------------------------
+ */
+ TESTING("    file with aligment");
+
+#ifdef H5_HAVE_FILTER_DEFLATE
+
+ if(h5repack_init(&pack_options, 0) < 0)
+  GOERROR;
+
+ /* add the options for aligment */
+ pack_options.alignment = 1;
+ pack_options.threshold = 1;
+ 
+ if(h5repack(FNAME8, FNAME8OUT, &pack_options) < 0)
+  GOERROR;
+ if(h5diff(FNAME8, FNAME8OUT, NULL, NULL, &diff_options) > 0)
+  GOERROR;
+ if(h5repack_verify(FNAME8OUT, &pack_options) <= 0)
+  GOERROR;
+ 
+
+ /* verify aligment */
+ {
+     hsize_t threshold;
+     hsize_t alignment;
+     hid_t fapl;
+     hid_t fid;
+     
+     if (( fid = H5Fopen(FNAME8OUT, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0 )
+         GOERROR;
+     if ((fapl = H5Fget_access_plist(fid)) < 0)
+         GOERROR;
+     if ( H5Pget_alignment(fapl, &threshold, &alignment  )  < 0)
+         GOERROR;
+     if ( threshold != 1 )
+         GOERROR;
+     if ( alignment != 1 )
+         GOERROR;
+     if ( H5Pclose(fapl) < 0)
+         GOERROR;
+     if (H5Fclose(fid) < 0)
+         GOERROR;
+     
+ }
+
+
+ if(h5repack_end(&pack_options) < 0)
+  GOERROR;
+ 
+
  PASSED();
+#else
+ SKIPPED();
+#endif
+
+