[svn-r16658] merge from trunk 16656

#1402 (B1) h5repack does not preserve creation order indexing. 
ISSUE : h5repack does not handle group creation order flags. 
ACTION: call H5P(g)(s)et_link_creation_order functions when handling groups, add new groups with these flags to the test generation program, and verify results in the test program. 
TEST: in the test program, function that compares property lists, added code to verify groups
DOCS: Added the note to RELEASE.txt: "h5repack now handles group creation order. PVN - 2009/4/2 - 1402".

1 files changed, 705 insertions, 678 deletions

diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
index 4e2e036..8ab5a35 100644
--- a/tools/h5repack/h5repack_copy.c
+++ b/tools/h5repack/h5repack_copy.c
@@ -1,17 +1,17 @@
 /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * 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.     *
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+* 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>
@@ -25,15 +25,15 @@ extern char  *progname;
 
 
 /*-------------------------------------------------------------------------
- * macros
- *-------------------------------------------------------------------------
- */
+* macros
+*-------------------------------------------------------------------------
+*/
 #define USERBLOCK_XFER_SIZE     512     /* size of buffer/# of bytes to xfer at a time when copying userblock */
 
 /*-------------------------------------------------------------------------
- * local functions
- *-------------------------------------------------------------------------
- */
+* local functions
+*-------------------------------------------------------------------------
+*/
 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);
@@ -43,28 +43,28 @@ static void  print_user_block(const char *filename, hid_t fid);
 #endif
 
 /*-------------------------------------------------------------------------
- * Function: copy_objects
- *
- * Purpose: duplicate all HDF5 objects in the file
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: October, 23, 2003
- *
- * Modification:
- *   Peter Cao, June 13, 2007
- *   Add "-L, --latest" and other options to pack a file with the latest file format
- *
- *   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
- *
- *-------------------------------------------------------------------------
- */
+* Function: copy_objects
+*
+* Purpose: duplicate all HDF5 objects in the file
+*
+* Return: 0, ok, -1 no
+*
+* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+*
+* Date: October, 23, 2003
+*
+* Modification:
+*   Peter Cao, June 13, 2007
+*   Add "-L, --latest" and other options to pack a file with the latest file format
+*
+*   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
+*
+*-------------------------------------------------------------------------
+*/
 
 int copy_objects(const char* fnamein,
                  const char* fnameout,
@@ -90,19 +90,19 @@ int copy_objects(const char* fnamein,
     /* get user block size */
     {
         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");
             goto out;
         } 
-        
+
         if(H5Pget_userblock(fcpl_in, &ub_size) < 0) 
         {
             error_msg(progname, "failed to retrieve userblock size\n");
             goto out;
         } 
-        
+
         if(H5Pclose(fcpl_in) < 0) 
         {
             error_msg(progname, "failed to close property list\n");
@@ -147,25 +147,27 @@ int copy_objects(const char* fnamein,
                 {
                     switch(i) 
                     {
-                        case 0:
-                            mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
-                            break;
-
-                        case 1:
-                            mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
-                            break;
-
-                        case 2:
-                            mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
-                            break;
-
-                        case 3:
-                            mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
-                            break;
-
-                        case 4:
-                            mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
-                            break;
+                    case 0:
+                        mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG;
+                        break;
+
+                    case 1:
+                        mesg_type_flags[nindex] = H5O_SHMESG_DTYPE_FLAG;
+                        break;
+
+                    case 2:
+                        mesg_type_flags[nindex] = H5O_SHMESG_FILL_FLAG;
+                        break;
+
+                    case 3:
+                        mesg_type_flags[nindex] = H5O_SHMESG_PLINE_FLAG;
+                        break;
+
+                    case 4:
+                        mesg_type_flags[nindex] = H5O_SHMESG_ATTR_FLAG;
+                        break;
+                    default:
+                        break;
                     } /* end switch */
                     min_mesg_sizes[nindex] = (unsigned)options->msg_size[i];
 
@@ -205,8 +207,8 @@ int copy_objects(const char* fnamein,
             } /* end if */
         } /* end if */
     } /* end if */
-  
-   
+
+
 
 
 #if defined (H5REPACK_DEBUG_USER_BLOCK)  
@@ -230,30 +232,30 @@ int copy_objects(const char* fnamein,
                 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;
             } 
-            
+
         }
-        
-       
-        
+
+
+
     }
 
 
@@ -262,39 +264,39 @@ int copy_objects(const char* fnamein,
     *-------------------------------------------------------------------------
     */
 
-   
+
     if (  options->alignment > 0 )
     {
         /* either use the FAPL 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;
             }
-            
+
         }      
-        
+
     }
 
 
@@ -303,18 +305,18 @@ int copy_objects(const char* fnamein,
     *-------------------------------------------------------------------------
     */
 
-    
+
     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;
     } 
 
-    
+
     /*-------------------------------------------------------------------------
     * write a new user block if requested
     *-------------------------------------------------------------------------
@@ -325,11 +327,11 @@ int copy_objects(const char* fnamein,
         {
             error_msg(progname, "Could not copy user block. Exiting...\n");
             goto out;
-            
+
         }
     }
 
-     /*-------------------------------------------------------------------------
+    /*-------------------------------------------------------------------------
     * get list of objects
     *-------------------------------------------------------------------------
     */
@@ -375,7 +377,7 @@ int copy_objects(const char* fnamein,
 
     H5Fclose(fidin);
     H5Fclose(fidout);
-    
+
     /* free table */
     trav_table_free(travt);
     travt = NULL;
@@ -391,7 +393,7 @@ int copy_objects(const char* fnamein,
         {
             error_msg(progname, "Could not copy user block. Exiting...\n");
             goto out;
-            
+
         }
     }
 
@@ -417,74 +419,74 @@ out:
 }
 
 /*-------------------------------------------------------------------------
- * Function: do_copy_objects
- *
- * Purpose: duplicate all HDF5 objects in the file
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: October, 23, 2003
- *
- * Modifications: 
- *
- *  July 2004:     Introduced the extra EC or NN option for SZIP
- *
- *  December 2004: Added a check for H5Dcreate; if the dataset cannot be created
- *                  with the requested filter, use the input one
- *
- *  October 2006:  Read/write using the file type by default.
- *
- *  October 2006:  Read by hyperslabs for big datasets.
- *
- *  A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
- *  i.e., if the memory needed to read a dataset is greater than this limit, 
- *  then hyperslab I/O is done instead of one operation I/O 
- *  For each dataset, the memory needed is calculated according to
- *
- *  memory needed = number of elements * size of each element
- *
- *  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations 
- *  are done
- *
- *  H5Dread( input_dataset1 )
- *  H5Dread( input_dataset2 )
- *
- *  with all elements in the datasets selected. If the memory needed is greater than 
- *  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
- *
- *  a strip mine is defined for each dimension k (a strip mine is defined as a 
- *  hyperslab whose size is memory manageable) according to the formula
- *
- *  (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
- *
- *  where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures 
- *  that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip 
- *  mine size k is simply defined as its dimension k, but for larger datasets the 
- *  hyperslab size is still memory manageable.
- *  a cycle is done until the number of elements in the dataset is reached. In each 
- *  iteration, two parameters are defined for the function H5Sselect_hyperslab, 
- *  the start and size of each hyperslab, according to
- *
- *  (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
- *
- *  where hyperslab_offset [k] is initially set to zero, and later incremented in 
- *  hyperslab_size[k] offsets. The reason for the operation 
- *
- *  dimension[k] - hyperslab_offset[k]
- *
- *  in (2) is that, when using the strip mine size, it assures that the "remaining" part 
- *  of the dataset that does not fill an entire strip mine is processed.
- *
- *  November 2006:  Use H5Ocopy in the copy of objects. The logic for using 
- *   H5Ocopy or not is if a change of filters or layout is requested by the user 
- *   then use read/write else use H5Ocopy. 
- *
- * May, 1, 2008: Add a printing of the compression ratio of old size / new size
- *
- *-------------------------------------------------------------------------
- */
+* Function: do_copy_objects
+*
+* Purpose: duplicate all HDF5 objects in the file
+*
+* Return: 0, ok, -1 no
+*
+* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+*
+* Date: October, 23, 2003
+*
+* Modifications: 
+*
+*  July 2004:     Introduced the extra EC or NN option for SZIP
+*
+*  December 2004: Added a check for H5Dcreate; if the dataset cannot be created
+*                  with the requested filter, use the input one
+*
+*  October 2006:  Read/write using the file type by default.
+*
+*  October 2006:  Read by hyperslabs for big datasets.
+*
+*  A threshold of H5TOOLS_MALLOCSIZE (128 MB) is the limit upon which I/O hyperslab is done
+*  i.e., if the memory needed to read a dataset is greater than this limit, 
+*  then hyperslab I/O is done instead of one operation I/O 
+*  For each dataset, the memory needed is calculated according to
+*
+*  memory needed = number of elements * size of each element
+*
+*  if the memory needed is lower than H5TOOLS_MALLOCSIZE, then the following operations 
+*  are done
+*
+*  H5Dread( input_dataset1 )
+*  H5Dread( input_dataset2 )
+*
+*  with all elements in the datasets selected. If the memory needed is greater than 
+*  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
+*
+*  a strip mine is defined for each dimension k (a strip mine is defined as a 
+*  hyperslab whose size is memory manageable) according to the formula
+*
+*  (1) strip_mine_size[k ] = MIN(dimension[k ], H5TOOLS_BUFSIZE / size of memory type)
+*
+*  where H5TOOLS_BUFSIZE is a constant currently defined as 1MB. This formula assures 
+*  that for small datasets (small relative to the H5TOOLS_BUFSIZE constant), the strip 
+*  mine size k is simply defined as its dimension k, but for larger datasets the 
+*  hyperslab size is still memory manageable.
+*  a cycle is done until the number of elements in the dataset is reached. In each 
+*  iteration, two parameters are defined for the function H5Sselect_hyperslab, 
+*  the start and size of each hyperslab, according to
+*
+*  (2) hyperslab_size [k] = MIN(dimension[k] - hyperslab_offset[k], strip_mine_size [k])
+*
+*  where hyperslab_offset [k] is initially set to zero, and later incremented in 
+*  hyperslab_size[k] offsets. The reason for the operation 
+*
+*  dimension[k] - hyperslab_offset[k]
+*
+*  in (2) is that, when using the strip mine size, it assures that the "remaining" part 
+*  of the dataset that does not fill an entire strip mine is processed.
+*
+*  November 2006:  Use H5Ocopy in the copy of objects. The logic for using 
+*   H5Ocopy or not is if a change of filters or layout is requested by the user 
+*   then use read/write else use H5Ocopy. 
+*
+* May, 1, 2008: Add a printing of the compression ratio of old size / new size
+*
+*-------------------------------------------------------------------------
+*/
 
 int do_copy_objects(hid_t fidin,
                     hid_t fidout,
@@ -495,7 +497,8 @@ int do_copy_objects(hid_t fidin,
     hid_t    grp_out=-1;        /* group ID */
     hid_t    dset_in=-1;        /* read dataset ID */
     hid_t    dset_out=-1;       /* write dataset ID */
-    hid_t    gcpl_id=-1;        /* group creation property list */
+    hid_t    gcpl_in=-1;        /* group creation property list */
+    hid_t    gcpl_out=-1;       /* group creation property list */
     hid_t    type_in=-1;        /* named type ID */
     hid_t    type_out=-1;       /* named type ID */
     hid_t    dcpl_id=-1;        /* dataset creation property list ID */
@@ -515,6 +518,7 @@ int do_copy_objects(hid_t fidin,
     void     *sm_buf=NULL;      /* buffer for raw data */
     int      has_filter;        /* current object has a filter */
     int      req_filter;        /* there was a request for a filter */
+    unsigned crt_order_flags;   /* group creation order flag */
     unsigned i;
     unsigned u;
     int      is_ref=0;
@@ -537,510 +541,532 @@ int do_copy_objects(hid_t fidin,
         buf = NULL;
         switch ( travt->objs[i].type ) 
         {
+
+        case H5TRAV_TYPE_UNKNOWN:
+            assert(0);
+            break;
             /*-------------------------------------------------------------------------
-             * H5TRAV_TYPE_GROUP
-             *-------------------------------------------------------------------------
-             */
-            case H5TRAV_TYPE_GROUP:
-                if (options->verbose)
-                    printf(FORMAT_OBJ,"group",travt->objs[i].name );
+            * H5TRAV_TYPE_GROUP
+            *-------------------------------------------------------------------------
+            */
+        case H5TRAV_TYPE_GROUP:
 
-                /*-------------------------------------------------------------------------
-                 * the root is a special case, we get an ID for the root group
-                 * and copy its attributes using that ID
-                 *-------------------------------------------------------------------------
-                 */
-                if(HDstrcmp(travt->objs[i].name, "/") == 0) 
-                {
-                    if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
-                        goto error;
-                }
-                else if (options->grp_compact>0 || options->grp_indexed>0) 
-                {
-                    /* Set up group creation property list */
-                    if((gcpl_id = H5Pcreate(H5P_GROUP_CREATE)) < 0)
-                        goto error;
+            if (options->verbose)
+            {
+                printf(FORMAT_OBJ,"group",travt->objs[i].name );
+            }
 
-                    if(H5Pset_link_phase_change(gcpl_id, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0)
-                        goto error;
+            /* open input group */
+            if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+                goto error;
 
-                    if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_id, H5P_DEFAULT)) < 0)
-                        goto error; 
-                }
-                else 
-                {
-                    if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
-                        goto error;
-                }
+            /* get input group creation property list */
+            if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
+                goto error;
 
-                if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                    goto error;
+            /* query and set the group creation properties */
+            if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
+                goto error;
 
-                /*-------------------------------------------------------------------------
-                 * copy attrs
-                 *-------------------------------------------------------------------------
-                 */
-                if(copy_attr(grp_in,grp_out,options) < 0)
+            /* set up group creation property list */
+            if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
+                goto error;
+
+            if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
+                goto error;
+
+
+            /*-------------------------------------------------------------------------
+            * the root is a special case, we get an ID for the root group
+            * and copy its attributes using that ID
+            *-------------------------------------------------------------------------
+            */
+            if(HDstrcmp(travt->objs[i].name, "/") == 0) 
+            {
+                if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0)
                     goto error;
+            }
 
-                if(gcpl_id > 0) {
-                    if(H5Pclose(gcpl_id) < 0)
+            else
+            {
+
+                if (options->grp_compact>0 || options->grp_indexed>0) 
+                {
+                    if(H5Pset_link_phase_change(gcpl_out, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0)
                         goto error;
                 }
-                if(H5Gclose(grp_out) < 0)
-                    goto error;
-                if(H5Gclose(grp_in) < 0)
+
+                if((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
                     goto error;
 
-                break;
+            }
+
+            /*-------------------------------------------------------------------------
+            * copy attrs
+            *-------------------------------------------------------------------------
+            */
+            if(copy_attr(grp_in,grp_out,options) < 0)
+                goto error;
+
+
+            if(H5Pclose(gcpl_out) < 0)
+                goto error;
+            if(H5Pclose(gcpl_in) < 0)
+                goto error;
+            if(H5Gclose(grp_out) < 0)
+                goto error;
+            if(H5Gclose(grp_in) < 0)
+                goto error;
+
+            break;
 
             /*-------------------------------------------------------------------------
-             * H5TRAV_TYPE_DATASET
-             *-------------------------------------------------------------------------
-             */
-            case H5TRAV_TYPE_DATASET:
+            * H5TRAV_TYPE_DATASET
+            *-------------------------------------------------------------------------
+            */
+        case H5TRAV_TYPE_DATASET:
+
+            has_filter = 0;
+            req_filter = 0;
 
-                has_filter = 0;
-                req_filter = 0;
+            /* check if global filters were requested */
+            if ( options->n_filter_g )
+                req_filter = 1;
 
-                /* check if global filters were requested */
-                if ( options->n_filter_g )
-                    req_filter = 1;
+            /* check if filters were requested for individual objects */
+            for( u = 0; u < options->op_tbl->nelems; u++)
+            {
+                int k; 
 
-                /* check if filters were requested for individual objects */
-                for( u = 0; u < options->op_tbl->nelems; u++)
+                for( k = 0; k < options->op_tbl->objs[u].nfilters; k++)
                 {
-                    int k; 
-                    
-                    for( k = 0; k < options->op_tbl->objs[u].nfilters; k++)
+                    if ( options->op_tbl->objs[u].filter->filtn > 0 )
                     {
-                        if ( options->op_tbl->objs[u].filter->filtn > 0 )
-                        {
-                            
-                            req_filter = 1;
-                            
-                        }
-                        
+
+                        req_filter = 1;
+
                     }
+
                 }
+            }
+
+            /* early detection of references */
+            if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+                goto error;
+            if((ftype_id = H5Dget_type(dset_in)) < 0)
+                goto error;
+            if(H5T_REFERENCE == H5Tget_class(ftype_id))
+                is_ref = 1;
+            if(H5Tclose(ftype_id) < 0)
+                goto error;
+            if(H5Dclose(dset_in) < 0)
+                goto error;
+
+
+            /*-------------------------------------------------------------------------
+            * check if we should use H5Ocopy or not
+            * if there is a request for filters/layout, we read/write the object
+            * otherwise we do a copy using H5Ocopy
+            *-------------------------------------------------------------------------
+            */
+            if ( options->op_tbl->nelems  || 
+                options->all_filter == 1 || 
+                options->all_layout == 1 || 
+                is_ref) 
+            {
+
+                int      j;
 
-                /* early detection of references */
                 if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
                     goto error;
+                if((f_space_id = H5Dget_space(dset_in)) < 0)
+                    goto error;
                 if((ftype_id = H5Dget_type(dset_in)) < 0)
                     goto error;
-                if(H5T_REFERENCE == H5Tget_class(ftype_id))
-                    is_ref = 1;
-                if(H5Tclose(ftype_id) < 0)
+                if((dcpl_id = H5Dget_create_plist(dset_in)) < 0)
                     goto error;
-                if(H5Dclose(dset_in) < 0)
+                if((dcpl_out = H5Pcopy(dcpl_id)) < 0)
+                    goto error;
+                if((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
+                    goto error;
+                HDmemset(dims, 0, sizeof dims);
+                if(H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
+                    goto error;
+                nelmts = 1;
+                for ( j = 0; j < rank; j++)
+                {
+                    nelmts *= dims[j];
+                }
+
+                if(options->use_native == 1)
+                    wtype_id = h5tools_get_native_type(ftype_id);
+                else
+                    wtype_id = H5Tcopy(ftype_id); 
+
+                if((msize = H5Tget_size(wtype_id)) == 0)
                     goto error;
-                  
 
                 /*-------------------------------------------------------------------------
-                 * check if we should use H5Ocopy or not
-                 * if there is a request for filters/layout, we read/write the object
-                 * otherwise we do a copy using H5Ocopy
-                 *-------------------------------------------------------------------------
-                 */
-                if ( options->op_tbl->nelems  || 
-                     options->all_filter == 1 || 
-                     options->all_layout == 1 || 
-                     is_ref) 
+                * check if the dataset creation property list has filters that
+                * are not registered in the current configuration
+                * 1) the external filters GZIP and SZIP might not be available
+                * 2) the internal filters might be turned off
+                *-------------------------------------------------------------------------
+                */
+                if (h5tools_canreadf((travt->objs[i].name),dcpl_id)==1)
                 {
-                    
-                    int      j;
-                   
-                    if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                        goto error;
-                    if((f_space_id = H5Dget_space(dset_in)) < 0)
-                        goto error;
-                    if((ftype_id = H5Dget_type(dset_in)) < 0)
-                        goto error;
-                    if((dcpl_id = H5Dget_create_plist(dset_in)) < 0)
-                        goto error;
-                    if((dcpl_out = H5Pcopy(dcpl_id)) < 0)
-                        goto error;
-                    if((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
-                        goto error;
-                    HDmemset(dims, 0, sizeof dims);
-                    if(H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
-                        goto error;
-                    nelmts = 1;
-                    for ( j = 0; j < rank; j++)
-                    {
-                        nelmts *= dims[j];
-                    }
+                    apply_s=1;
+                    apply_f=1;
 
-                    if(options->use_native == 1)
-                        wtype_id = h5tools_get_native_type(ftype_id);
-                    else
-                        wtype_id = H5Tcopy(ftype_id); 
-
-                    if((msize = H5Tget_size(wtype_id)) == 0)
-                        goto error;
-                      
                     /*-------------------------------------------------------------------------
-                     * check if the dataset creation property list has filters that
-                     * are not registered in the current configuration
-                     * 1) the external filters GZIP and SZIP might not be available
-                     * 2) the internal filters might be turned off
-                     *-------------------------------------------------------------------------
-                     */
-                    if (h5tools_canreadf((travt->objs[i].name),dcpl_id)==1)
+                    * references are a special case
+                    * we cannot just copy the buffers, but instead we recreate the reference
+                    * in a second traversal of the output file
+                    *-------------------------------------------------------------------------
+                    */
+                    if (H5T_REFERENCE!=H5Tget_class(wtype_id))
                     {
-                        apply_s=1;
-                        apply_f=1;
+                        /* get the storage size of the input dataset */
+                        dsize_in=H5Dget_storage_size(dset_in);
+
+                        /* check for datasets too small */
+                        if (nelmts*msize < options->min_comp )
+                            apply_s=0;
+
+                        /* apply the filter */
+                        if (apply_s) 
+                        {
+                            if (apply_filters(travt->objs[i].name,
+                                rank,
+                                dims,
+                                msize,
+                                dcpl_out,
+                                options,
+                                &has_filter) < 0)
+                                goto error;
+                        }
 
                         /*-------------------------------------------------------------------------
-                        * references are a special case
-                        * we cannot just copy the buffers, but instead we recreate the reference
-                        * in a second traversal of the output file
+                        * create the output dataset;
+                        * disable error checking in case the dataset cannot be created with the
+                        * modified dcpl; in that case use the original instead
                         *-------------------------------------------------------------------------
                         */
-                        if (H5T_REFERENCE!=H5Tget_class(wtype_id))
+                        H5E_BEGIN_TRY {
+                            dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
+                        } H5E_END_TRY;
+
+                        if(dset_out == FAIL) 
                         {
-                            /* get the storage size of the input dataset */
-                            dsize_in=H5Dget_storage_size(dset_in);
+                            if(options->verbose)
+                                printf(" warning: could not create dataset <%s>. Applying original settings\n",
+                                travt->objs[i].name);
 
-                            /* check for datasets too small */
-                            if (nelmts*msize < options->min_comp )
-                                apply_s=0;
+                            if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
+                                goto error;
+                            apply_f = 0;
+                        }
 
-                            /* apply the filter */
-                            if (apply_s) 
-                            {
-                                if (apply_filters(travt->objs[i].name,
-                                    rank,
-                                    dims,
-                                    msize,
-                                    dcpl_out,
-                                    options,
-                                    &has_filter) < 0)
-                                    goto error;
-                            }
+                        /*-------------------------------------------------------------------------
+                        * read/write
+                        *-------------------------------------------------------------------------
+                        */
+                        if (nelmts)
+                        {
+                            size_t need = (size_t)(nelmts*msize);  /* bytes needed */
+                            if ( need < H5TOOLS_MALLOCSIZE )
+                                buf = HDmalloc(need);
 
-                            /*-------------------------------------------------------------------------
-                             * create the output dataset;
-                             * disable error checking in case the dataset cannot be created with the
-                             * modified dcpl; in that case use the original instead
-                             *-------------------------------------------------------------------------
-                             */
-                            H5E_BEGIN_TRY {
-                                dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
-                            } H5E_END_TRY;
-
-                            if(dset_out == FAIL) 
+                            if (buf != NULL )
                             {
-                                if(options->verbose)
-                                     printf(" warning: could not create dataset <%s>. Applying original settings\n",
-                                            travt->objs[i].name);
-
-                                if((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT)) < 0)
+                                if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf) < 0)
                                     goto error;
-                                apply_f = 0;
-                            }
+                                if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf) < 0)
+                                    goto error;
+                            }      
 
-                            /*-------------------------------------------------------------------------
-                             * read/write
-                             *-------------------------------------------------------------------------
-                             */
-                            if (nelmts)
+                            else /* possibly not enough memory, read/write by hyperslabs */
                             {
-                                size_t need = (size_t)(nelmts*msize);  /* bytes needed */
-                                if ( need < H5TOOLS_MALLOCSIZE )
-                                    buf = HDmalloc(need);
+                                size_t        p_type_nbytes = msize; /*size of memory type */
+                                hsize_t       p_nelmts = nelmts;     /*total selected elmts */
+                                hsize_t       elmtno;                /*counter  */
+                                int           carry;                 /*counter carry value */
+                                unsigned int  vl_data = 0;           /*contains VL datatypes */
+
+                                /* stripmine info */
+                                hsize_t       sm_size[H5S_MAX_RANK]; /*stripmine size */
+                                hsize_t       sm_nbytes;             /*bytes per stripmine */
+                                hsize_t       sm_nelmts;             /*elements per stripmine*/
+                                hid_t         sm_space;              /*stripmine data space */
+
+                                /* hyperslab info */
+                                hsize_t       hs_offset[H5S_MAX_RANK];/*starting offset */
+                                hsize_t       hs_size[H5S_MAX_RANK];  /*size this pass */
+                                hsize_t       hs_nelmts;              /*elements in request */
+                                hsize_t       zero[8];                /*vector of zeros */
+                                int           k;          
+
+                                /* check if we have VL data in the dataset's datatype */
+                                if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
+                                    vl_data = TRUE;
+
+                                /*
+                                * determine the strip mine size and allocate a buffer. The strip mine is
+                                * a hyperslab whose size is manageable.
+                                */
+                                sm_nbytes = p_type_nbytes;
 
-                                if (buf != NULL )
+                                for (k = rank; k > 0; --k) 
                                 {
-                                    if (H5Dread(dset_in,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf) < 0)
-                                        goto error;
-                                    if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf) < 0)
-                                        goto error;
-                                }      
+                                    hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
+                                    if ( size == 0) /* datum size > H5TOOLS_BUFSIZE */
+                                        size = 1;
+                                    sm_size[k - 1] = MIN(dims[k - 1], size);
+                                    sm_nbytes *= sm_size[k - 1];
+                                    assert(sm_nbytes > 0);
+                                }
+                                sm_buf = HDmalloc((size_t)sm_nbytes);
+
+                                sm_nelmts = sm_nbytes / p_type_nbytes;
+                                sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
 
-                                else /* possibly not enough memory, read/write by hyperslabs */
+                                /* the stripmine loop */
+                                memset(hs_offset, 0, sizeof hs_offset);
+                                memset(zero, 0, sizeof zero);
+
+                                for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) 
                                 {
-                                    size_t        p_type_nbytes = msize; /*size of memory type */
-                                    hsize_t       p_nelmts = nelmts;     /*total selected elmts */
-                                    hsize_t       elmtno;                /*counter  */
-                                    int           carry;                 /*counter carry value */
-                                    unsigned int  vl_data = 0;           /*contains VL datatypes */
-
-                                    /* stripmine info */
-                                    hsize_t       sm_size[H5S_MAX_RANK]; /*stripmine size */
-                                    hsize_t       sm_nbytes;             /*bytes per stripmine */
-                                    hsize_t       sm_nelmts;             /*elements per stripmine*/
-                                    hid_t         sm_space;              /*stripmine data space */
-
-                                    /* hyperslab info */
-                                    hsize_t       hs_offset[H5S_MAX_RANK];/*starting offset */
-                                    hsize_t       hs_size[H5S_MAX_RANK];  /*size this pass */
-                                    hsize_t       hs_nelmts;              /*elements in request */
-                                    hsize_t       zero[8];                /*vector of zeros */
-                                    int           k;          
-
-                                    /* check if we have VL data in the dataset's datatype */
-                                    if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
-                                        vl_data = TRUE;
-
-                                    /*
-                                     * determine the strip mine size and allocate a buffer. The strip mine is
-                                     * a hyperslab whose size is manageable.
-                                     */
-                                    sm_nbytes = p_type_nbytes;
-
-                                    for (k = rank; k > 0; --k) 
-                                    {
-                                        hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
-                                        if ( size == 0) /* datum size > H5TOOLS_BUFSIZE */
-                                            size = 1;
-                                        sm_size[k - 1] = MIN(dims[k - 1], size);
-                                        sm_nbytes *= sm_size[k - 1];
-                                        assert(sm_nbytes > 0);
-                                    }
-                                    sm_buf = HDmalloc((size_t)sm_nbytes);
-
-                                    sm_nelmts = sm_nbytes / p_type_nbytes;
-                                    sm_space = H5Screate_simple(1, &sm_nelmts, NULL);
-
-                                    /* the stripmine loop */
-                                    memset(hs_offset, 0, sizeof hs_offset);
-                                    memset(zero, 0, sizeof zero);
-
-                                    for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) 
+                                    /* calculate the hyperslab size */
+                                    if (rank > 0) 
                                     {
-                                        /* calculate the hyperslab size */
-                                        if (rank > 0) 
+                                        for (k = 0, hs_nelmts = 1; k < rank; k++) 
                                         {
-                                            for (k = 0, hs_nelmts = 1; k < rank; k++) 
-                                            {
-                                                hs_size[k] = MIN(dims[k] - hs_offset[k], sm_size[k]);
-                                                hs_nelmts *= hs_size[k];
-                                            }
-
-                                            if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
-                                                goto error;
-                                            if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0)
-                                                goto error;
-                                        } 
-                                        else 
-                                        {
-                                            H5Sselect_all(f_space_id);
-                                            H5Sselect_all(sm_space);
-                                            hs_nelmts = 1;
-                                        } /* rank */
+                                            hs_size[k] = MIN(dims[k] - hs_offset[k], sm_size[k]);
+                                            hs_nelmts *= hs_size[k];
+                                        }
 
-                                        /* read/write */
-                                        if (H5Dread(dset_in, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) 
+                                        if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
                                             goto error;
-                                        if (H5Dwrite(dset_out, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) 
+                                        if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0)
                                             goto error;
+                                    } 
+                                    else 
+                                    {
+                                        H5Sselect_all(f_space_id);
+                                        H5Sselect_all(sm_space);
+                                        hs_nelmts = 1;
+                                    } /* rank */
+
+                                    /* read/write */
+                                    if (H5Dread(dset_in, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) 
+                                        goto error;
+                                    if (H5Dwrite(dset_out, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) 
+                                        goto error;
 
-                                        /* reclaim any VL memory, if necessary */
-                                        if(vl_data)
-                                            H5Dvlen_reclaim(wtype_id, sm_space, H5P_DEFAULT, sm_buf);
+                                    /* reclaim any VL memory, if necessary */
+                                    if(vl_data)
+                                        H5Dvlen_reclaim(wtype_id, sm_space, H5P_DEFAULT, sm_buf);
 
-                                        /* calculate the next hyperslab offset */
-                                        for (k = rank, carry = 1; k > 0 && carry; --k) 
-                                        {
-                                            hs_offset[k - 1] += hs_size[k - 1];
-                                            if (hs_offset[k - 1] == dims[k - 1])
-                                                hs_offset[k - 1] = 0;
-                                            else
-                                                carry = 0;
-                                        } /* k */
-                                    } /* elmtno */
-
-                                    H5Sclose(sm_space);
-                                    /* free */
-                                    if (sm_buf!=NULL)
+                                    /* calculate the next hyperslab offset */
+                                    for (k = rank, carry = 1; k > 0 && carry; --k) 
                                     {
-                                        HDfree(sm_buf);
-                                        sm_buf=NULL;
-                                    }
-                                } /* hyperslab read */
-                            }/*nelmts*/
-
-                            /*-------------------------------------------------------------------------
-                             * amount of compression used
-                             *-------------------------------------------------------------------------
-                             */
-                            if (options->verbose) 
+                                        hs_offset[k - 1] += hs_size[k - 1];
+                                        if (hs_offset[k - 1] == dims[k - 1])
+                                            hs_offset[k - 1] = 0;
+                                        else
+                                            carry = 0;
+                                    } /* k */
+                                } /* elmtno */
+
+                                H5Sclose(sm_space);
+                                /* free */
+                                if (sm_buf!=NULL)
+                                {
+                                    HDfree(sm_buf);
+                                    sm_buf=NULL;
+                                }
+                            } /* hyperslab read */
+                        }/*nelmts*/
+
+                        /*-------------------------------------------------------------------------
+                        * amount of compression used
+                        *-------------------------------------------------------------------------
+                        */
+                        if (options->verbose) 
+                        {
+                            double ratio=0;
+
+                            /* only print the compression ration if there was a filter request */
+                            if (apply_s && apply_f && req_filter)
                             {
-                                double ratio=0;
+                                hssize_t a, b;
 
-                                /* only print the compression ration if there was a filter request */
-                                if (apply_s && apply_f && req_filter)
-                                {
-                                    hssize_t a, b;
+                                /* get the storage size of the output dataset */
+                                dsize_out=H5Dget_storage_size(dset_out);
 
-                                    /* get the storage size of the output dataset */
-                                    dsize_out=H5Dget_storage_size(dset_out);
+                                /* compression ratio = uncompressed size /  compressed size */
 
-                                    /* compression ratio = uncompressed size /  compressed size */
+                                a = dsize_in; b = dsize_out;
+                                if (b!=0)
+                                    ratio = (double) a / (double) b;
 
-                                    a = dsize_in; b = dsize_out;
-                                    if (b!=0)
-                                        ratio = (double) a / (double) b;
-                                  
-                                    print_dataset_info(dcpl_out,travt->objs[i].name,ratio,1);
-                                }
-                                else
-                                    print_dataset_info(dcpl_id,travt->objs[i].name,ratio,0);
+                                print_dataset_info(dcpl_out,travt->objs[i].name,ratio,1);
+                            }
+                            else
+                                print_dataset_info(dcpl_id,travt->objs[i].name,ratio,0);
 
-                                /* print a message that the filter was not applied 
-                                (in case there was a filter)
-                                */
-                                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->min_comp);
-
-                                if ( has_filter && apply_f == 0 )
-                                    printf(" <warning: could not apply the filter to %s>\n",
-                                            travt->objs[i].name);
-
-                            } /* verbose */
-
-                            /*-------------------------------------------------------------------------
-                             * copy attrs
-                             *-------------------------------------------------------------------------
-                             */
-                            if (copy_attr(dset_in,dset_out,options) < 0)
-                                goto error;
+                            /* print a message that the filter was not applied 
+                            (in case there was a filter)
+                            */
+                            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->min_comp);
 
-                            /*close */
-                            if (H5Dclose(dset_out) < 0)
-                                goto error;
+                            if ( has_filter && apply_f == 0 )
+                                printf(" <warning: could not apply the filter to %s>\n",
+                                travt->objs[i].name);
 
-                        }/*!H5T_REFERENCE*/
-                    }/*h5tools_canreadf*/
+                        } /* verbose */
 
+                        /*-------------------------------------------------------------------------
+                        * copy attrs
+                        *-------------------------------------------------------------------------
+                        */
+                        if (copy_attr(dset_in,dset_out,options) < 0)
+                            goto error;
+
+                        /*close */
+                        if (H5Dclose(dset_out) < 0)
+                            goto error;
+
+                    }/*!H5T_REFERENCE*/
+                }/*h5tools_canreadf*/
 
-                    /*-------------------------------------------------------------------------
-                     * close
-                     *-------------------------------------------------------------------------
-                     */
-                    if (H5Tclose(ftype_id) < 0)
-                        goto error;
-                    if (H5Tclose(wtype_id) < 0)
-                        goto error;
-                    if (H5Pclose(dcpl_id) < 0)
-                        goto error;
-                    if (H5Pclose(dcpl_out) < 0)
-                        goto error;
-                    if (H5Sclose(f_space_id) < 0)
-                        goto error;
-                    if (H5Dclose(dset_in) < 0)
-                        goto error;
 
-                }
                 /*-------------------------------------------------------------------------
-                 * we do not have request for filter/chunking use H5Ocopy instead
-                 *-------------------------------------------------------------------------
-                 */
-                else 
-                {
-                    hid_t        pid;
+                * close
+                *-------------------------------------------------------------------------
+                */
+                if (H5Tclose(ftype_id) < 0)
+                    goto error;
+                if (H5Tclose(wtype_id) < 0)
+                    goto error;
+                if (H5Pclose(dcpl_id) < 0)
+                    goto error;
+                if (H5Pclose(dcpl_out) < 0)
+                    goto error;
+                if (H5Sclose(f_space_id) < 0)
+                    goto error;
+                if (H5Dclose(dset_in) < 0)
+                    goto error;
 
-                    /* create property to pass copy options */
-                    if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) 
-                        goto error;
+            }
+            /*-------------------------------------------------------------------------
+            * we do not have request for filter/chunking use H5Ocopy instead
+            *-------------------------------------------------------------------------
+            */
+            else 
+            {
+                hid_t        pid;
 
-                    /* set options for object copy */
-                    if(H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) 
-                        goto error;
+                /* create property to pass copy options */
+                if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) 
+                    goto error;
 
-                    /*-------------------------------------------------------------------------
-                     * do the copy
-                     *-------------------------------------------------------------------------
-                     */
-
-                    if(H5Ocopy(fidin,          /* Source file or group identifier */
-                            travt->objs[i].name,       /* Name of the source object to be copied */
-                            fidout,                    /* Destination file or group identifier  */
-                            travt->objs[i].name,       /* Name of the destination object  */
-                            pid,                       /* Properties which apply to the copy   */
-                            H5P_DEFAULT) < 0)            /* Properties which apply to the new hard link */              
-                        goto error;
+                /* set options for object copy */
+                if(H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) 
+                    goto error;
 
-                    /* close property */
-                    if(H5Pclose(pid) < 0)
-                        goto error;
+                /*-------------------------------------------------------------------------
+                * do the copy
+                *-------------------------------------------------------------------------
+                */
+
+                if(H5Ocopy(fidin,          /* Source file or group identifier */
+                    travt->objs[i].name,       /* Name of the source object to be copied */
+                    fidout,                    /* Destination file or group identifier  */
+                    travt->objs[i].name,       /* Name of the destination object  */
+                    pid,                       /* Properties which apply to the copy   */
+                    H5P_DEFAULT) < 0)            /* Properties which apply to the new hard link */              
+                    goto error;
 
+                /* close property */
+                if(H5Pclose(pid) < 0)
+                    goto error;
 
-                    /*-------------------------------------------------------------------------
-                     * copy attrs manually
-                     *-------------------------------------------------------------------------
-                     */
-                    if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                        goto error;
-                    if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                        goto error;
-                    if(copy_attr(dset_in, dset_out, options) < 0)
-                        goto error;
-                    if(H5Dclose(dset_in) < 0)
-                        goto error;
-                    if(H5Dclose(dset_out) < 0)
-                        goto error;
+
+                /*-------------------------------------------------------------------------
+                * copy attrs manually
+                *-------------------------------------------------------------------------
+                */
+                if((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+                    goto error;
+                if((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
+                    goto error;
+                if(copy_attr(dset_in, dset_out, options) < 0)
+                    goto error;
+                if(H5Dclose(dset_in) < 0)
+                    goto error;
+                if(H5Dclose(dset_out) < 0)
+                    goto error;
 
 
-                    if (options->verbose)
-                        printf(FORMAT_OBJ,"dset",travt->objs[i].name );
-                    
+                if (options->verbose)
+                    printf(FORMAT_OBJ,"dset",travt->objs[i].name );
 
-                } /* end do we have request for filter/chunking */
 
+            } /* end do we have request for filter/chunking */
 
-                break;
+
+            break;
 
             /*-------------------------------------------------------------------------
-             * H5TRAV_TYPE_NAMED_DATATYPE
-             *-------------------------------------------------------------------------
-             */
-            case H5TRAV_TYPE_NAMED_DATATYPE:
+            * H5TRAV_TYPE_NAMED_DATATYPE
+            *-------------------------------------------------------------------------
+            */
+        case H5TRAV_TYPE_NAMED_DATATYPE:
 
-                if(options->verbose)
-                    printf(FORMAT_OBJ, "type", travt->objs[i].name);
+            if(options->verbose)
+                printf(FORMAT_OBJ, "type", travt->objs[i].name);
 
-                if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                    goto error;
+            if((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
+                goto error;
 
-                if((type_out = H5Tcopy(type_in)) < 0)
-                    goto error;
+            if((type_out = H5Tcopy(type_in)) < 0)
+                goto error;
 
-                if((H5Tcommit2(fidout, travt->objs[i].name, type_out, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
-                    goto error;
+            if((H5Tcommit2(fidout, travt->objs[i].name, type_out, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+                goto error;
 
-                /*-------------------------------------------------------------------------
-                 * copy attrs
-                 *-------------------------------------------------------------------------
-                 */
-                if(copy_attr(type_in, type_out, options) < 0)
-                    goto error;
+            /*-------------------------------------------------------------------------
+            * copy attrs
+            *-------------------------------------------------------------------------
+            */
+            if(copy_attr(type_in, type_out, options) < 0)
+                goto error;
 
-                if(H5Tclose(type_in) < 0)
-                    goto error;
-                if(H5Tclose(type_out) < 0)
-                    goto error;
+            if(H5Tclose(type_in) < 0)
+                goto error;
+            if(H5Tclose(type_out) < 0)
+                goto error;
 
-              
 
-                break;
+
+            break;
 
 
             /*-------------------------------------------------------------------------
-             * H5TRAV_TYPE_LINK
-             * H5TRAV_TYPE_UDLINK
-             *
-             * Only handles external links; H5Lcopy will fail for other UD link types
-             * since we don't have creation or copy callbacks for them.
-             *-------------------------------------------------------------------------
-             */
-
-            case H5TRAV_TYPE_LINK:
-            case H5TRAV_TYPE_UDLINK:
+            * H5TRAV_TYPE_LINK
+            * H5TRAV_TYPE_UDLINK
+            *
+            * Only handles external links; H5Lcopy will fail for other UD link types
+            * since we don't have creation or copy callbacks for them.
+            *-------------------------------------------------------------------------
+            */
+
+        case H5TRAV_TYPE_LINK:
+        case H5TRAV_TYPE_UDLINK:
             {
 
                 if(options->verbose)
@@ -1055,8 +1081,8 @@ int do_copy_objects(hid_t fidin,
             }
             break;
 
-            default:
-                goto error;
+        default:
+            goto error;
         } /* switch */
 
         /* free */
@@ -1075,7 +1101,8 @@ error:
         H5Gclose(grp_in);
         H5Gclose(grp_out);
         H5Pclose(dcpl_id);
-        H5Pclose(gcpl_id);
+        H5Pclose(gcpl_in);
+        H5Pclose(gcpl_out);
         H5Sclose(f_space_id);
         H5Dclose(dset_in);
         H5Dclose(dset_out);
@@ -1094,21 +1121,21 @@ error:
 
 
 /*-------------------------------------------------------------------------
- * Function: copy_attr
- *
- * Purpose: copy attributes located in LOC_IN, which is obtained either from
- * loc_id = H5Gopen2( fid, name);
- * loc_id = H5Dopen2( fid, name);
- * loc_id = H5Topen2( fid, name);
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: October, 28, 2003
- *
- *-------------------------------------------------------------------------
- */
+* Function: copy_attr
+*
+* Purpose: copy attributes located in LOC_IN, which is obtained either from
+* loc_id = H5Gopen2( fid, name);
+* loc_id = H5Dopen2( fid, name);
+* loc_id = H5Topen2( fid, name);
+*
+* Return: 0, ok, -1 no
+*
+* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
+*
+* Date: October, 28, 2003
+*
+*-------------------------------------------------------------------------
+*/
 
 int copy_attr(hid_t loc_in,
               hid_t loc_out,
@@ -1129,71 +1156,71 @@ int copy_attr(hid_t loc_in,
     H5O_info_t oinfo;             /* object info */
     int        j;
     unsigned   u;
-    
+
     if(H5Oget_info(loc_in, &oinfo) < 0)
         goto error;
-    
-   /*-------------------------------------------------------------------------
+
+    /*-------------------------------------------------------------------------
     * copy all attributes
     *-------------------------------------------------------------------------
     */
-    
+
     for ( u = 0; u < (unsigned)oinfo.num_attrs; u++)
     {
-        
+
         buf=NULL;
-        
+
         /* open attribute */
         if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
             goto error;
-        
+
         /* get name */
         if (H5Aget_name( attr_id, (size_t)255, name ) < 0)
             goto error;
-        
+
         /* get the file datatype  */
         if ((ftype_id = H5Aget_type( attr_id )) < 0 )
             goto error;
-        
+
         /* get the dataspace handle  */
         if ((space_id = H5Aget_space( attr_id )) < 0 )
             goto error;
-        
+
         /* get dimensions  */
         if ( (rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0 )
             goto error;
-        
+
         nelmts=1;
         for (j=0; j<rank; j++)
             nelmts*=dims[j];
-        
+
         if (options->use_native==1)
             wtype_id = h5tools_get_native_type(ftype_id);
         else
             wtype_id = H5Tcopy(ftype_id); 
-        
+
         if ((msize=H5Tget_size(wtype_id))==0)
             goto error;
-        
-       /*-------------------------------------------------------------------------
+
+        /*-------------------------------------------------------------------------
         * object references are a special case
         * we cannot just copy the buffers, but instead we recreate the reference
         * this is done on a second sweep of the file that just copies
         * the referenced objects
         *-------------------------------------------------------------------------
         */
-        
+
         if (H5T_REFERENCE==H5Tget_class(wtype_id))
         {
             ;
         }
         else 
         {
-          /*-------------------------------------------------------------------------
-           * read to memory
-           *-------------------------------------------------------------------------
-           */
-            
+            /*-------------------------------------------------------------------------
+            * read to memory
+            *-------------------------------------------------------------------------
+            */
+
             buf = (void *)HDmalloc((size_t)(nelmts * msize));
             if(buf == NULL) {
                 error_msg(progname, "cannot read into memory\n" );
@@ -1201,46 +1228,46 @@ int copy_attr(hid_t loc_in,
             }
             if(H5Aread(attr_id, wtype_id, buf) < 0)
                 goto error;
-            
-           /*-------------------------------------------------------------------------
+
+            /*-------------------------------------------------------------------------
             * copy
             *-------------------------------------------------------------------------
             */
-            
+
             if((attr_out = H5Acreate2(loc_out, name, ftype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
                 goto error;
             if(H5Awrite(attr_out, wtype_id, buf) < 0)
                 goto error;
-            
+
             /*close*/
             if(H5Aclose(attr_out) < 0)
                 goto error;
-            
-            
+
+
             if(buf)
                 free(buf);
-            
+
         } /*H5T_REFERENCE*/
-        
-        
+
+
         if(options->verbose)
             printf(FORMAT_OBJ_ATTR, "attr", name);
-        
+
         /*-------------------------------------------------------------------------
-         * close
-         *-------------------------------------------------------------------------
-         */
-        
+        * close
+        *-------------------------------------------------------------------------
+        */
+
         if (H5Tclose(ftype_id) < 0) goto error;
         if (H5Tclose(wtype_id) < 0) goto error;
         if (H5Sclose(space_id) < 0) goto error;
         if (H5Aclose(attr_id) < 0) goto error;
-        
+
     } /* u */
-    
-    
+
+
     return 0;
-    
+
 error:
     H5E_BEGIN_TRY {
         H5Tclose(ftype_id);
@@ -1258,12 +1285,12 @@ error:
 
 
 /*-------------------------------------------------------------------------
- * Function: print_dataset_info
- *
- * Purpose: print name, filters, percentage compression of a dataset
- *
- *-------------------------------------------------------------------------
- */
+* Function: print_dataset_info
+*
+* Purpose: print name, filters, percentage compression of a dataset
+*
+*-------------------------------------------------------------------------
+*/
 static void print_dataset_info(hid_t dcpl_id,
                                char *objname,
                                double ratio,
@@ -1280,27 +1307,27 @@ static void print_dataset_info(hid_t dcpl_id,
     size_t       cd_nelmts;      /* filter client number of values */
     char         f_objname[256];    /* filter objname */
     int          i;
-    
-    
+
+
     strcpy(strfilter,"\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);
-        
+
         filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts,
             cd_values, sizeof(f_objname), f_objname, NULL);
-        
+
         switch(filtn) {
         default:
             break;
-            
+
         case H5Z_FILTER_DEFLATE:
             strcat(strfilter,"GZIP ");
-            
+
 #if defined (PRINT_DEBUG)
             {
                 unsigned level=cd_values[0];
@@ -1309,10 +1336,10 @@ static void print_dataset_info(hid_t dcpl_id,
             }
 #endif
             break;
-            
+
         case H5Z_FILTER_SZIP:
             strcat(strfilter,"SZIP ");
-            
+
 #if defined (PRINT_DEBUG)
             {
                 unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
@@ -1325,29 +1352,29 @@ static void print_dataset_info(hid_t dcpl_id,
                     strcpy(temp,"NN) ");
             }
             strcat(strfilter,temp);
-            
+
 #endif
-            
+
             break;
-            
+
         case H5Z_FILTER_SHUFFLE:
             strcat(strfilter,"SHUF ");
             break;
-            
+
         case H5Z_FILTER_FLETCHER32:
             strcat(strfilter,"FLET ");
             break;
-            
+
         case H5Z_FILTER_NBIT:
             strcat(strfilter,"NBIT ");
             break;
-            
+
         case H5Z_FILTER_SCALEOFFSET:
             strcat(strfilter,"SCALEOFFSET ");
             break;
         } /* switch */
     }/*i*/
-    
+
     if(!pr)
         printf(FORMAT_OBJ,"dset",objname );
     else
@@ -1362,18 +1389,18 @@ static void print_dataset_info(hid_t dcpl_id,
 }
 
 /*-------------------------------------------------------------------------
- * Function: copy_user_block 
- *
- * Purpose: copy user block from one file to another
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Peter Cao 
- *
- * Date: October, 25, 2007
- *
- *-------------------------------------------------------------------------
- */
+* Function: copy_user_block 
+*
+* Purpose: copy user block from one file to another
+*
+* Return: 0, ok, -1 no
+*
+* Programmer: Peter Cao 
+*
+* Date: October, 25, 2007
+*
+*-------------------------------------------------------------------------
+*/
 static int
 copy_user_block(const char *infile, const char *outfile, hsize_t size)
 {
@@ -1448,18 +1475,18 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function: print_user_block 
- *
- * Purpose: print user block
- *
- * Return: 0, ok, -1 no
- *
- * Programmer: Pedro Vicente 
- *
- * Date: August, 20, 2008
- *
- *-------------------------------------------------------------------------
- */
+* Function: print_user_block 
+*
+* Purpose: print user block
+*
+* Return: 0, ok, -1 no
+*
+* Programmer: Pedro Vicente 
+*
+* Date: August, 20, 2008
+*
+*-------------------------------------------------------------------------
+*/
 #if defined (H5REPACK_DEBUG_USER_BLOCK)  
 static 
 void print_user_block(const char *filename, hid_t fid)
@@ -1476,25 +1503,25 @@ void print_user_block(const char *filename, hid_t fid)
         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 */
@@ -1522,7 +1549,7 @@ void print_user_block(const char *filename, hid_t fid)
             goto done;
         } 
 
-       
+
         /* update size of userblock left to transfer */
         size -= nread;
     } 
@@ -1530,7 +1557,7 @@ void print_user_block(const char *filename, hid_t fid)
 done:
     if(fh > 0)
         HDclose(fh);
-  
+
 
     return;    
 }