[svn-r15521] #1184

Add a userblock to an HDF5 file during the repack.  The user gives  
give a filename and userblock size as command line parameters to  
h5repack and the contents of that file are stored in the  
userblock for the HDF5 file created by h5repack.

New flags to handle this -u and -b
Tested : windows, linux

6 files changed, 310 insertions, 16 deletions

diff --git a/tools/h5repack/h5repack.c b/tools/h5repack/h5repack.c
index febf7d7..3809377 100644
--- a/tools/h5repack/h5repack.c
+++ b/tools/h5repack/h5repack.c
@@ -384,8 +384,12 @@ static int check_options(pack_opt_t *options)
         is present with other objects\n");
     return -1;
     }
-    
-    /* check options for the latest format */
+
+    /*-------------------------------------------------------------------------
+    * check options for the latest format
+    *-------------------------------------------------------------------------
+    */
+
     if (options->grp_compact < 0) {
         error_msg(progname, "invalid maximum number of links to store as header messages\n");
         return -1;
@@ -404,6 +408,26 @@ static int check_options(pack_opt_t *options)
             return -1;
         }
     }
+
+
+    /*-------------------------------------------------------------------------
+    * verify new user userblock options
+    *-------------------------------------------------------------------------
+    */
+    if ( options->ublock_filename != NULL && options->ublock_size == 0 )
+    {
+        error_msg(progname, "user block size missing for file %s\n",
+            options->ublock_filename);
+        return -1;
+    }
+    
+    if ( options->ublock_filename == NULL && options->ublock_size != 0 )
+    {
+        error_msg(progname, "file name missing for user block\n",
+            options->ublock_filename);
+        return -1;
+    }
+    
     
     return 0;
 }
diff --git a/tools/h5repack/h5repack.h b/tools/h5repack/h5repack.h
index 80fb1b0..42b9bbc 100644
--- a/tools/h5repack/h5repack.h
+++ b/tools/h5repack/h5repack.h
@@ -106,6 +106,8 @@ typedef struct {
  int             grp_indexed; /* Set the minimum number of links to store in the indexed format */
  int             msg_size[8]; /* Minumum size of shared messages: dataspace, 
                                  datatype, fill value, filter pipleline, attribute */
+ const char      *ublock_filename; /* user block file name */
+ int             ublock_size;      /* user block size */
 } pack_opt_t;
 
 
diff --git a/tools/h5repack/h5repack.sh.in b/tools/h5repack/h5repack.sh.in
index 0d3c7d4..fdd93da 100755
--- a/tools/h5repack/h5repack.sh.in
+++ b/tools/h5repack/h5repack.sh.in
@@ -490,6 +490,10 @@ else
  TOOLTEST0 $arg
 fi 
 
+# add a userblock to file
+arg="$FILE1 -u ublock.bin -b 2048"
+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 73b201e..3bff946 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -23,6 +23,10 @@
 
 extern char  *progname;
 
+#if 0
+#define H5REPACK_DEBUG
+#endif
+
 /*-------------------------------------------------------------------------
  * macros
  *-------------------------------------------------------------------------
@@ -39,6 +43,7 @@ static void  print_dataset_info(hid_t dcpl_id,char *objname,double per, int pr);
 static int   do_copy_objects(hid_t fidin,hid_t fidout,trav_table_t *travt,pack_opt_t *options);
 static int   copy_attr(hid_t loc_in,hid_t loc_out,pack_opt_t *options);
 static int   copy_user_block(const char *infile, const char *outfile, hsize_t size);
+static void  print_user_block(const char *filename, hid_t fid);
 
 /*-------------------------------------------------------------------------
  * Function: copy_objects
@@ -55,10 +60,12 @@ static int   copy_user_block(const char *infile, const char *outfile, hsize_t si
  *   Peter Cao, June 13, 2007
  *   Add "-L, --latest" and other options to pack a file with the latest file format
  *
- * Modification:
  *   Peter Cao, September 25, 2007
  *   Copy user block when repacking a file
  *
+ *   Pedro Vicente, August 20, 2008
+ *   Add a user block to file if requested
+ *
  *-------------------------------------------------------------------------
  */
 
@@ -84,7 +91,7 @@ int copy_objects(const char* fnamein,
 
     /* get user block size */
     {
-        hid_t         fcpl_in;              /* File creation property list ID for input file */
+        hid_t fcpl_in; /* file creation property list ID for input file */
 
         if((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
             error_msg(progname, "failed to retrieve file creation property list\n");
@@ -182,14 +189,84 @@ int copy_objects(const char* fnamein,
             } /* end if */
         } /* end if */
     } /* end if */
+  
+   
+
+
+#if defined (H5REPACK_DEBUG)  
+    print_user_block(fnamein,fidin);
+#endif
+
+
+    /*-------------------------------------------------------------------------
+    * set the new user userblock options in the FCPL (before H5Fcreate )
+    *-------------------------------------------------------------------------
+    */
 
-    if((fidout = H5Fcreate(fnameout,H5F_ACC_TRUNC, fcpl, fapl)) < 0) {
+    if ( options->ublock_size > 0 && options->ublock_filename != NULL )
+    {
+        /* either use the FCPL already created or create a new one */
+        if(fcpl != H5P_DEFAULT)
+        {
+            /* set user block size */
+            if(H5Pset_userblock(fcpl, options->ublock_size) < 0) 
+            {
+                error_msg(progname, "failed to set userblock size\n");
+                goto out;
+            } 
+            
+        }
+        
+        else
+        {
+            
+            /* create a file creation property list */
+            if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) 
+            {
+                error_msg(progname, "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(progname, "failed to set userblock size\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(progname, "<%s>: Could not create file\n", fnameout );
         goto out;
     } /* end if */
 
-    if(options->verbose)
-        printf("Making file <%s>...\n",fnameout);
+    
+    /*-------------------------------------------------------------------------
+    * write a new user block if requested
+    *-------------------------------------------------------------------------
+    */
+    if ( options->ublock_size > 0 && options->ublock_filename != NULL )
+    {      
+        copy_user_block( options->ublock_filename, fnameout, options->ublock_size);
+    }
+
+   
 
     /* init table */
     trav_table_init(&travt);
@@ -1240,3 +1317,91 @@ done:
     return status;    
 }
 
+
+
+/*-------------------------------------------------------------------------
+ * Function: print_user_block 
+ *
+ * Purpose: print user block
+ *
+ * Return: 0, ok, -1 no
+ *
+ * Programmer: Pedro Vicente 
+ *
+ * Date: August, 20, 2008
+ *
+ *-------------------------------------------------------------------------
+ */
+static 
+void print_user_block(const char *filename, hid_t fid)
+{
+    int     fh;      /* file handle  */
+    hsize_t ub_size; /* user block size */
+    hsize_t size;    /* size read */
+    hid_t   fcpl;    /* file creation property list ID for HDF5 file */
+    int     i;
+
+    /* get user block size */  
+    if(( fcpl = H5Fget_create_plist(fid)) < 0) 
+    {
+        error_msg(progname, "failed to retrieve file creation property list\n");
+        goto done;
+    } 
+    
+    if(H5Pget_userblock(fcpl, &ub_size) < 0) 
+    {
+        error_msg(progname, "failed to retrieve userblock size\n");
+        goto done;
+    } 
+    
+    if(H5Pclose(fcpl) < 0) 
+    {
+        error_msg(progname, "failed to close property list\n");
+        goto done;
+    } 
+    
+    /* open file */
+    if((fh = HDopen(filename, O_RDONLY, 0)) < 0) 
+    {
+        goto done;
+    }
+ 
+    size = ub_size;
+
+    /* read file */
+    while(size > 0) 
+    {
+        ssize_t nread;                  /* # of bytes read */
+        char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */
+
+        /* read buffer */
+        if(size > USERBLOCK_XFER_SIZE)
+            nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
+        else
+            nread = HDread(fh, rbuf, (size_t)size);
+
+        for(i = 0; i < nread; i++) 
+        {
+
+            printf("%c ", rbuf[i]);
+
+        }
+        printf("\n");
+
+        if(nread < 0) 
+        {
+            goto done;
+        } 
+
+       
+        /* update size of userblock left to transfer */
+        size -= nread;
+    } 
+
+done:
+    if(fh > 0)
+        HDclose(fh);
+  
+
+    return;    
+}
diff --git a/tools/h5repack/h5repack_main.c b/tools/h5repack/h5repack_main.c
index d512923..db0a87b 100644
--- a/tools/h5repack/h5repack_main.c
+++ b/tools/h5repack/h5repack_main.c
@@ -37,7 +37,7 @@ 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:";
+static const char *s_opts = "hVvf:l:m:e:nLc:d:s:u:b:";
 static struct long_options l_opts[] = {
     { "help", no_arg, 'h' },
     { "version", no_arg, 'V' },
@@ -51,6 +51,8 @@ static struct long_options l_opts[] = {
     { "compact", require_arg, 'c' },
     { "indexed", require_arg, 'd' },
     { "ssize", require_arg, 's' },
+    { "ublock", require_arg, 'u' },
+    { "block", require_arg, 'b' },
     { NULL, 0, '\0' }
 };
 
@@ -84,14 +86,16 @@ static struct long_options l_opts[] = {
  *    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 file if requested (new switches -u -b) 
+ *-------------------------------------------------------------------------
  */
 int main(int argc, char **argv)
 {
     char          *infile  = NULL;
     char          *outfile = NULL;
     pack_opt_t    options;            /*the global options */
-    int           ret;
+    int           ret=-1;
     int           i;
     
     /* initialize options  */
@@ -284,7 +288,8 @@ int main(int argc, char **argv)
         
     }
 
-  
+
+   
     /* pack it */
     ret=h5repack(infile,outfile,&options);
     
@@ -324,6 +329,8 @@ static void usage(const char *prog)
  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("   -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("   -f FILT, --filter=FILT  Filter type\n");
  printf("   -l LAYT, --layout=LAYT  Layout type\n");
  
@@ -331,7 +338,9 @@ static void usage(const char *prog)
 
  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("  S - is an integer\n");
+ printf("  D - 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");
 
@@ -530,6 +539,17 @@ static void parse_command_line(int argc, const char* argv[], pack_opt_t* options
             
             break;
 
+            
+        case 'u':
+            
+            options->ublock_filename = opt_arg;
+            break;
+            
+        case 'b':
+            
+            options->ublock_size = atoi( opt_arg );
+            break;
+
         } /* switch */
         
         
diff --git a/tools/h5repack/h5repacktst.c b/tools/h5repack/h5repacktst.c
index 3796179..e7024f2 100644
--- a/tools/h5repack/h5repacktst.c
+++ b/tools/h5repack/h5repacktst.c
@@ -71,6 +71,9 @@
 #define FNAME16    "h5repack_ub.h5"
 #define FNAME16OUT "h5repack_ub_out.h5"
 
+#define FNAME_UB   "ublock.bin"
+
+
 
 const char *H5REPACK_FILENAMES[] = {
    "h5repack_big_out",
@@ -123,7 +126,8 @@ int make_attr(hid_t loc_id,int rank,hsize_t *dims,const char *attr_name,hid_t ty
 void make_dset_reg_ref(hid_t loc_id);
 int make_external(hid_t loc_id);
 static int make_userblock(void);
-static int verify_userblock(void);
+static int verify_userblock( const char* filename);
+static int make_userblock_file(void);
 
 
 /*-------------------------------------------------------------------------
@@ -1332,7 +1336,7 @@ if (szip_can_encode) {
   GOERROR;
  if(h5repack_verify(FNAME16OUT, &pack_options) <= 0)
   GOERROR;
- if(verify_userblock() < 0)
+ if(verify_userblock(FNAME16OUT) < 0)
   GOERROR;
  if(h5repack_end(&pack_options) < 0)
   GOERROR;
@@ -1394,6 +1398,32 @@ if (szip_can_encode) {
 #endif
 
 
+ /*-------------------------------------------------------------------------
+ * test file with userblock
+ *-------------------------------------------------------------------------
+ */
+ TESTING("    file with added userblock");
+ if(h5repack_init(&pack_options, 0) < 0)
+  GOERROR;
+
+ /* add the options for a user block size and user block filename */
+ pack_options.ublock_size = USERBLOCK_SIZE;
+ pack_options.ublock_filename = FNAME_UB;
+ 
+ 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;
+ if(verify_userblock(FNAME8OUT) < 0)
+  GOERROR;
+ if(h5repack_end(&pack_options) < 0)
+  GOERROR;
+ PASSED();
+
+
+
 /*-------------------------------------------------------------------------
  * clean temporary test files
  *-------------------------------------------------------------------------
@@ -1600,6 +1630,13 @@ int make_testfiles(void)
  if(make_userblock() < 0)
   goto out;
 
+ /*-------------------------------------------------------------------------
+ * create a userblock file 
+ *-------------------------------------------------------------------------
+ */
+ if(make_userblock_file() < 0)
+  goto out;
+
  return 0;
 
 out:
@@ -2879,7 +2916,7 @@ out:
  *-------------------------------------------------------------------------
  */
 static int
-verify_userblock(void)
+verify_userblock( const char* filename)
 {
     hid_t   fid = -1;
     hid_t   fcpl = -1;
@@ -2890,7 +2927,7 @@ verify_userblock(void)
     size_t  u;                  /* Local index variable */
 
     /* Open file with userblock */
-    if((fid = H5Fopen(FNAME16OUT, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
+    if((fid = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
         goto out;
 
     /* Retrieve file creation property list & userblock size */
@@ -2912,7 +2949,7 @@ verify_userblock(void)
 
 
     /* Re-open HDF5 file, as "plain" file */
-    if((fd = HDopen(FNAME16, O_RDONLY, 0)) < 0)
+    if((fd = HDopen(filename, O_RDONLY, 0)) < 0)
         goto out;
 
     /* Read userblock data */
@@ -2942,6 +2979,48 @@ out:
 
 
 /*-------------------------------------------------------------------------
+ * Function: make_userblock_file
+ *
+ * Purpose: create a file for the userblock add test
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+make_userblock_file(void)
+{
+    hid_t   fid = -1;
+    hid_t   fcpl = -1;
+    int     fd = -1;            /* File descriptor for writing userblock */
+    char    ub[USERBLOCK_SIZE]; /* User block data */
+    ssize_t nwritten;           /* # of bytes written */
+    size_t  u;                  /* Local index variable */
+
+    /* initialize userblock data */
+    for(u = 0; u < USERBLOCK_SIZE; u++)
+        ub[u] = 'a' + (u % 26);
+
+    /* open file */
+    if((fd = HDopen(FNAME_UB,O_WRONLY|O_CREAT|O_TRUNC, 0644 )) < 0)
+        goto out;
+
+    /* write userblock data */
+    nwritten = HDwrite(fd, ub, (size_t)USERBLOCK_SIZE);
+    assert(nwritten == USERBLOCK_SIZE);
+
+    /* close file */
+    HDclose(fd);
+
+    return 0;
+
+out:
+    
+    if(fd > 0)
+        HDclose(fd);
+
+    return -1;
+} 
+
+/*-------------------------------------------------------------------------
  * Function: write_dset_in
  *
  * Purpose: write datasets in LOC_ID