path: root/tools/h5repack/h5repack_copy.c

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * 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://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html.  If you do not have     *
 * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
#include "h5repack.h"


extern char  *progname;


#define PER(A,B) { per = 0;                                       \
                   if (A!=0)                                      \
                    per = (float)fabs(1-( (float)B / (float)A )); \
                 }

#define FORMAT_OBJ      " %-21s %s\n"  /* obj type, name */
#define FORMAT_OBJ_ATTR "  %-21s %s\n"  /* obj type, name */


static
int do_hardlinks(hid_t fidout,trav_table_t *travt);

/*-------------------------------------------------------------------------
 * Function: print_dataset_info
 *
 * Purpose: print name, filters, percentage compression of a dataset
 *
 *-------------------------------------------------------------------------
 */
static void print_dataset_info(hid_t dcpl_id,
                               char *objname,
                               float per)
{
 char         strfilter[255];
#if defined (PRINT_DEBUG )
 char         temp[255];
#endif
 int          nfilters;       /* number of filters */
 unsigned     filt_flags;     /* filter flags */
 H5Z_filter_t filtn;          /* filter identification number */
 unsigned     cd_values[20];  /* filter client data values */
 size_t       cd_nelmts;      /* filter client number of values */
 char         f_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);

#ifdef H5_WANT_H5_V1_6_COMPAT
  filtn = H5Pget_filter(dcpl_id,
   (unsigned)i,
   &filt_flags,
   &cd_nelmts,
   cd_values,
   sizeof(f_objname),
   f_objname);
#else
  filtn = H5Pget_filter(dcpl_id,
   (unsigned)i,
   &filt_flags,
   &cd_nelmts,
   cd_values,
   sizeof(f_objname),
   f_objname,
   NULL);
#endif /* H5_WANT_H5_V1_6_COMPAT */


  switch (filtn)
  {
  default:
   break;
  case H5Z_FILTER_DEFLATE:
   strcat(strfilter,"GZIP ");

#if defined (PRINT_DEBUG)
   {
    unsigned level=cd_values[0];
    sprintf(temp,"(%d)",level);
    strcat(strfilter,temp);
   }
#endif

   break;
  case H5Z_FILTER_SZIP:
   strcat(strfilter,"SZIP ");

#if defined (PRINT_DEBUG)
   {
    unsigned options_mask=cd_values[0]; /* from dcpl, not filt*/
    unsigned ppb=cd_values[1];
    sprintf(temp,"(%d,",ppb);
    strcat(strfilter,temp);
    if (options_mask & H5_SZIP_EC_OPTION_MASK)
     strcpy(temp,"EC) ");
    else if (options_mask & H5_SZIP_NN_OPTION_MASK)
     strcpy(temp,"NN) ");
   }
   strcat(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 (strcmp(strfilter,"\0")==0)
  printf(FORMAT_OBJ,"dset",objname );
 else
 {
  char str[255], temp[20];
  strcpy(str,"dset  ");
  strcat(str,strfilter);
  sprintf(temp,"(%.2f%%)",per);
  strcat(str,temp);
  printf(FORMAT_OBJ,str,objname);
 }
}

/*-------------------------------------------------------------------------
 * 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
 *
 *-------------------------------------------------------------------------
 */

int copy_objects(const char* fnamein,
                 const char* fnameout,
                 pack_opt_t *options)
{
 hid_t         fidin;
 hid_t         fidout=-1;
 trav_table_t  *travt=NULL;

/*-------------------------------------------------------------------------
 * open the files
 *-------------------------------------------------------------------------
 */
 if ((fidin=h5tools_fopen(fnamein, NULL, NULL, 0))<0 ){
  error_msg(progname, "<%s>: %s\n", fnamein, H5FOPENERROR );
  goto out;
 }
 if ((fidout=H5Fcreate(fnameout,H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT))<0 ){
  error_msg(progname, "<%s>: Could not create file\n", fnameout );
  goto out;
 }

 if (options->verbose)
  printf("Making file <%s>...\n",fnameout);

 /* init table */
 trav_table_init(&travt);

 /* get the list of objects in the file */
 if (h5trav_gettable(fidin,travt)<0)
  goto out;

/*-------------------------------------------------------------------------
 * do the copy
 *-------------------------------------------------------------------------
 */
 if(do_copy_objects(fidin,fidout,travt,options)<0) {
  error_msg(progname, "<%s>: Could not copy data to: %s\n", fnamein, fnameout);
  goto out;
 }

/*-------------------------------------------------------------------------
 * create hard links
 *-------------------------------------------------------------------------
 */

 if(do_hardlinks(fidout,travt)<0) {
  error_msg(progname, "<%s>: Could not copy data to: %s\n", fnamein, fnameout);
  goto out;
 }

 /* free table */
 trav_table_free(travt);

/*-------------------------------------------------------------------------
 * close
 *-------------------------------------------------------------------------
 */

 H5Fclose(fidin);
 H5Fclose(fidout);
 return 0;

/*-------------------------------------------------------------------------
 * out
 *-------------------------------------------------------------------------
 */

out:
 H5E_BEGIN_TRY {
  H5Fclose(fidin);
  H5Fclose(fidout);
 } H5E_END_TRY;
 if (travt)
  trav_table_free(travt);

 return -1;
}

/*-------------------------------------------------------------------------
 * 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.
 *                 Read/write by hyperslabs for big datasets.
 *
 *-------------------------------------------------------------------------
 */

int do_copy_objects(hid_t fidin,
                    hid_t fidout,
                    trav_table_t *travt,
                    pack_opt_t *options) /* repack options */
{
 hid_t    grp_in=-1;         /* group ID */
 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    type_in=-1;        /* named type ID */
 hid_t    type_out=-1;       /* named type ID */
 hid_t    dcpl_id=-1;        /* dataset creation property list ID */
 hid_t    dcpl_out=-1;       /* dataset creation property list ID */
 hid_t    f_space_id=-1;     /* file space ID */
 hid_t    ftype_id=-1;       /* file type ID */
 hid_t    wtype_id=-1;       /* read/write type ID */
 size_t   msize;          /* size of type */
 hsize_t  nelmts;         /* number of elements in dataset */
 int      rank;           /* rank of dataset */
 hsize_t  dims[H5S_MAX_RANK];/* dimensions of dataset */
 hsize_t  dsize_in;       /* input dataset size before filter */
 hsize_t  dsize_out;      /* output dataset size after filter */
 int      next;           /* external files */
 int      apply_s;        /* flag for apply filter to small dataset sizes */
 int      apply_f;        /* flag for apply filter to return error on H5Dcreate */
 float    per;            /* percent utilization of storage */
 void     *buf=NULL;      /* buffer for raw data */
 void     *sm_buf=NULL;   /* buffer for raw data */
 int      i, j;
 int      nfilters;       /* number of filters in DCPL */
 H5D_layout_t layout;

/*-------------------------------------------------------------------------
 * copy the suppplied object list
 *-------------------------------------------------------------------------
 */

 if (options->verbose) {
  printf("-----------------------------------------\n");
  printf(" Type  Filter (Ratio)  Name\n");
  printf("-----------------------------------------\n");
 }

 for ( i = 0; i < travt->nobjs; i++)
 {

  buf = NULL;
  switch ( travt->objs[i].type )
  {
/*-------------------------------------------------------------------------
 * H5G_GROUP
 *-------------------------------------------------------------------------
 */
  case H5G_GROUP:
   if (options->verbose)
    printf(FORMAT_OBJ,"group",travt->objs[i].name );

   if ((grp_out=H5Gcreate(fidout,travt->objs[i].name, 0))<0)
    goto error;

   if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0)
    goto error;

   /*-------------------------------------------------------------------------
    * copy attrs
    *-------------------------------------------------------------------------
    */
   if (copy_attr(grp_in,grp_out,options)<0)
    goto error;

   if (H5Gclose(grp_out)<0)
    goto error;
   if (H5Gclose(grp_in)<0)
    goto error;


   break;

/*-------------------------------------------------------------------------
 * H5G_DATASET
 *-------------------------------------------------------------------------
 */
  case H5G_DATASET:
  
/*-------------------------------------------------------------------------
 * early check for filters or a non default layout
 *-------------------------------------------------------------------------
 */
   if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
    goto error;
   if ((dcpl_id=H5Dget_create_plist(dset_in))<0)
     goto error;
    
   /* get information about input filters */
   if ((nfilters = H5Pget_nfilters(dcpl_id))<0)
    goto error;
   if ((layout = H5Pget_layout(dcpl_id))<0)
    goto error;

   if (H5Dclose(dset_in)<0)
     goto error;
   if (H5Pclose(dcpl_id)<0)
     goto error;
   
/*-------------------------------------------------------------------------
 * check if we should use H5Ocopy or not
 * if the DCPL has filters or a non default layout, we read/write the object
 * otherwise we do a copy using H5Ocopy
 *-------------------------------------------------------------------------
 */
 
   if (nfilters || layout!=H5D_CONTIGUOUS 
      /* does the dcpl has filters or non default layout ? */ 
       ||
       options->op_tbl->nelems
       /* do we have input request for filter/chunking */ 
       ||
       options->all_filter==1 || options->all_layout==1
       )
   {
    if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<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];
    
    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 for external files
     *-------------------------------------------------------------------------
     */
    if ((next=H5Pget_external_count (dcpl_id))<0)
     goto error;
    
    if (next)
     fprintf(stderr," <warning: %s has external files, ignoring read...>\n",
     travt->objs[i].name );
    
     /*-------------------------------------------------------------------------
     * 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 (next==0 && h5tools_canreadf((travt->objs[i].name),dcpl_id)==1)
    {
     apply_s=1;
     apply_f=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)))
     {
      /* get the storage size of the input dataset */
      dsize_in=H5Dget_storage_size(dset_in);
      
      /* check for datasets too small */
      if (nelmts*msize < options->threshold )
       apply_s=0;
      
      /* apply the filter */
      if (apply_s){
       if (apply_filters(travt->objs[i].name,rank,dims,dcpl_out,options)<0)
        goto error;
      }
      
     /*-------------------------------------------------------------------------
      * 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=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_out);
      } H5E_END_TRY;
      if (dset_out==FAIL)
      {
       if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,wtype_id,f_space_id,dcpl_id))<0)
        goto error;
       apply_f=0;
      }
      
     /*-------------------------------------------------------------------------
      * read/write
      *-------------------------------------------------------------------------
      */
      if (nelmts)
      {
       size_t need = (size_t)(nelmts*msize);  /* bytes needed */
       if ( need < H5TOOLS_MALLOCSIZE )
        buf = HDmalloc(need);
       
       if (buf != NULL )
       {
        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;
       }      
       
       else /* possibly not enough memory, read/write by hyperslabs */
        
       {
        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 */
        
        /* 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 (i = rank; i > 0; --i) {
         sm_size[i - 1] = MIN(dims[i - 1], H5TOOLS_BUFSIZE / sm_nbytes);
         sm_nbytes *= sm_size[i - 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) 
         {
          for (i = 0, hs_nelmts = 1; i < rank; i++) 
          {
           hs_size[i] = MIN(dims[i] - hs_offset[i], sm_size[i]);
           hs_nelmts *= hs_size[i];
          }
          
          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 */
         
         /* 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);
         
         /* calculate the next hyperslab offset */
         for (i = rank, carry = 1; i > 0 && carry; --i) 
         {
          hs_offset[i - 1] += hs_size[i - 1];
          if (hs_offset[i - 1] == dims[i - 1])
           hs_offset[i - 1] = 0;
          else
           carry = 0;
         } /* i */
        } /* 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) 
     {
      if (apply_s && apply_f)
      {
       /* get the storage size of the input dataset */
       dsize_out=H5Dget_storage_size(dset_out);
       PER((hssize_t)dsize_in,(hssize_t)dsize_out);
       print_dataset_info(dcpl_out,travt->objs[i].name,per*(float)100.0);
      }
      else
       print_dataset_info(dcpl_id,travt->objs[i].name,0);
     }
     
     if (apply_s==0 && options->verbose)
      printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n",
      travt->objs[i].name,
      (int)options->threshold);
     
     if (apply_f==0 && options->verbose)
      printf(" <warning: could not apply the filter to %s>\n",
      travt->objs[i].name);
     
     /*-------------------------------------------------------------------------
      * copy attrs
      *-------------------------------------------------------------------------
      */
     if (copy_attr(dset_in,dset_out,options)<0)
      goto error;
     
     /*close */
     if (H5Dclose(dset_out)<0)
      goto error;
     
    }/*H5T_STD_REF_OBJ*/
   }/*can_read*/
   
   
   /*-------------------------------------------------------------------------
    * 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;
     
     /* 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;
     
     /* close property */
     if (H5Pclose(pid)<0)
      goto error;
     
    } /* end do we have request for filter/chunking */


   break;

/*-------------------------------------------------------------------------
 * H5G_TYPE
 *-------------------------------------------------------------------------
 */
  case H5G_TYPE:

   if ((type_in = H5Topen (fidin,travt->objs[i].name))<0)
    goto error;

   if ((type_out = H5Tcopy(type_in))<0)
    goto error;

   if ((H5Tcommit(fidout,travt->objs[i].name,type_out))<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 (options->verbose)
    printf(FORMAT_OBJ,"type",travt->objs[i].name );

   break;


/*-------------------------------------------------------------------------
 * H5G_LINK
 * H5G_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 H5G_LINK:
  case H5G_UDLINK:
   {
    if(H5Lcopy(fidin, travt->objs[i].name,fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
        goto error;

    if (options->verbose)
     printf(FORMAT_OBJ,"link",travt->objs[i].name );

   }
   break;

  default:
   goto error;
  } /* switch */

  /* free */
  if (buf!=NULL)
  {
   HDfree(buf);
   buf=NULL;
  }

 } /* i */

/*-------------------------------------------------------------------------
 * the root is a special case, we get an ID for the root group
 * and copy its attributes using that ID
 *-------------------------------------------------------------------------
 */

 if ((grp_out = H5Gopen(fidout,"/"))<0)
  goto error;

 if ((grp_in  = H5Gopen(fidin,"/"))<0)
  goto error;

 if (copy_attr(grp_in,grp_out,options)<0)
  goto error;

 if (H5Gclose(grp_out)<0)
  goto error;
 if (H5Gclose(grp_in)<0)
  goto error;

 return 0;

error:
 H5E_BEGIN_TRY {
  H5Gclose(grp_in);
  H5Gclose(grp_out);
  H5Pclose(dcpl_id);
  H5Sclose(f_space_id);
  H5Dclose(dset_in);
  H5Dclose(dset_out);
  H5Tclose(ftype_id);
  H5Tclose(wtype_id);
  H5Tclose(type_in);
  H5Tclose(type_out);
  /* free */
  if (buf!=NULL)
  {
   HDfree(buf);
   buf=NULL;
  }
  if (sm_buf!=NULL)
  {
   HDfree(sm_buf);
   sm_buf=NULL;
  }
 } H5E_END_TRY;
 return -1;

}


/*-------------------------------------------------------------------------
 * Function: copy_attr
 *
 * Purpose: copy attributes located in LOC_IN, which is obtained either from
 * loc_id = H5Gopen( fid, name);
 * loc_id = H5Dopen( fid, name);
 * loc_id = H5Topen( 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,
              pack_opt_t *options
              )
{
 hid_t      attr_id=-1;      /* attr ID */
 hid_t      attr_out=-1;     /* attr ID */
 hid_t      space_id=-1;     /* space ID */
 hid_t      ftype_id=-1;     /* file type ID */
 hid_t      wtype_id=-1;     /* read/write type ID */
 size_t     msize;        /* size of type */
 void       *buf=NULL;    /* data buffer */
 hsize_t    nelmts;       /* number of elements in dataset */
 int        rank;         /* rank of dataset */
 hsize_t    dims[H5S_MAX_RANK];/* dimensions of dataset */
 char       name[255];
 int        n, j;
 unsigned   u;

 if ((n = H5Aget_num_attrs(loc_in))<0)
  goto error;

 for ( u = 0; u < (unsigned)n; u++)
 {

  /* set data buffer to NULL each iteration
     we might not use it in the case of references
   */
   buf=NULL;
/*-------------------------------------------------------------------------
 * open
 *-------------------------------------------------------------------------
 */
  /* open attribute */
  if ((attr_id = H5Aopen_idx(loc_in, u))<0)
   goto error;

  /* get name */
  if (H5Aget_name( attr_id, 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 ( ! H5Tequal(wtype_id, H5T_STD_REF_OBJ))
  {
 /*-------------------------------------------------------------------------
  * read to memory
  *-------------------------------------------------------------------------
  */

   buf=(void *) HDmalloc((unsigned)(nelmts*msize));
   if ( buf==NULL){
    error_msg(progname, "cannot read into memory\n" );
    goto error;
   }
   if (H5Aread(attr_id,wtype_id,buf)<0)
    goto error;

   /*-------------------------------------------------------------------------
    * copy
    *-------------------------------------------------------------------------
    */

   if ((attr_out=H5Acreate(loc_out,name,ftype_id,space_id,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_STD_REF_OBJ*/


  if (options->verbose)
   printf(FORMAT_OBJ_ATTR, "attr", name);

/*-------------------------------------------------------------------------
 * 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);
  H5Tclose(wtype_id);
  H5Sclose(space_id);
  H5Aclose(attr_id);
  H5Aclose(attr_out);
  if (buf)
    free(buf);
 } H5E_END_TRY;
 return -1;
}

/*-------------------------------------------------------------------------
 * Function: do_hardlinks
 *
 * Purpose: duplicate hard links
 *
 * Return: 0, ok, -1 no
 *
 * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
 *
 * Date: December, 10, 2003
 *
 *-------------------------------------------------------------------------
 */

static
int do_hardlinks(hid_t fidout,trav_table_t *travt)
{
 int i, j;

 for ( i = 0; i < travt->nobjs; i++)
 {
  switch ( travt->objs[i].type )
  {
  case H5G_GROUP:

   if (travt->objs[i].nlinks)
   {
    for ( j=0; j<travt->objs[i].nlinks; j++)
    {
      if (H5Glink(fidout,
      H5L_TYPE_HARD,
      travt->objs[i].name,
      travt->objs[i].links[j].new_name)<0)
      return -1;
    }
   }

   break;

  case H5G_DATASET:

   if (travt->objs[i].nlinks)
   {
    for ( j=0; j<travt->objs[i].nlinks; j++){
     if (H5Glink(fidout,
      H5L_TYPE_HARD,
      travt->objs[i].name,
      travt->objs[i].links[j].new_name)<0)
      return -1;
    }
   }

   break;

  case H5G_TYPE:
  case H5G_LINK:
  case H5G_UDLINK:

   /*nothing to do */
   break;

  default:

   break;
  }
 }

 return 0;

}