path: root/tools/h5repack/h5repack_copy.c

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
 * 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>
#include <stdio.h>
#include "h5repack.h"
#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"

extern char  *progname;

#if 0
#define H5REPACK_DEBUG
#endif

/*-------------------------------------------------------------------------
 * macros
 *-------------------------------------------------------------------------
 */
#define USERBLOCK_XFER_SIZE     512     /* size of buffer/# of bytes to xfer at a time when copying userblock */

/*-------------------------------------------------------------------------
 * 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);
static int   copy_user_block(const char *infile, const char *outfile, hsize_t size);
static void  print_user_block(const char *filename, hid_t fid);

/*-------------------------------------------------------------------------
 * Function: copy_objects
 *
 * 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,
                 pack_opt_t *options)
{
    hid_t         fidin;
    hid_t         fidout = -1;
    trav_table_t  *travt = NULL;
    hsize_t       ub_size = 0;                  /* Size of user block */
    hid_t         fapl = H5P_DEFAULT;           /* File access property list ID */
    hid_t         fcpl = H5P_DEFAULT;           /* File creation property list ID */

    /*-------------------------------------------------------------------------
    * open the files
    *-------------------------------------------------------------------------
    */
    if((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t)0)) < 0) {
        error_msg(progname, "<%s>: %s\n", fnamein, H5FOPENERROR );
        goto out;
    }

    /* 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;
        } /* end if */

        if(H5Pget_userblock(fcpl_in, &ub_size) < 0) {
            error_msg(progname, "failed to retrieve userblock size\n");
            goto out;
        } /* end if */

        if(H5Pclose(fcpl_in) < 0) {
            error_msg(progname, "failed to close property list\n");
            goto out;
        } /* end if */
    } /* end block */

    /* Check if we need to create a non-default file creation property list */
    if(options->latest || ub_size > 0) {
        /* Create 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;
        }  /* end if */

        if(ub_size > 0)
            if(H5Pset_userblock(fcpl, ub_size) < 0) {
                error_msg(progname, "failed to set non-default userblock size\n");
                goto out;
            } /* end if */

        if(options->latest) {
            unsigned i = 0, nindex = 0, mesg_type_flags[5], min_mesg_sizes[5];

            /* Adjust group creation parameters for root group */
            /* (So that it is created in "dense storage" form) */
            if(H5Pset_link_phase_change(fcpl, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0) {
                error_msg(progname, "fail to adjust group creation parameters for root group\n");
                goto out;
            } /* end if */

            for(i = 0; i < 5; i++) {
                if(options->msg_size[i] > 0) {
                    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;
                    } /* end switch */
                    min_mesg_sizes[nindex] = (unsigned)options->msg_size[i];

                    nindex++;
                } /* end if */
            } /* end for */

            if(nindex > 0) {
                if(H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) {
                    error_msg(progname, "fail to set the number of shared object header message indexes\n");
                    goto out;
                } /* end if */

                /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */
                for(i = 0; i < (nindex - 1); i++) {
                    if(H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) {
                        error_msg(progname, "fail to configure the specified shared object header message index\n");
                        goto out;
                    } /* end if */
                } /* end for */
            } /* if (nindex>0) */

            /* Create file access property list */
            if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
                error_msg(progname, "Could not create file access property list\n");
                goto out;
            } /* end if */

            if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
                error_msg(progname, "Could not set property for using latest version of the format\n");
                goto out;
            } /* end if */
        } /* end if */
    } /* end if */




#if defined (H5REPACK_DEBUG)
    print_user_block(fnamein,fidin);
#endif


    /*-------------------------------------------------------------------------
    * set the new user userblock options in the FCPL (before H5Fcreate )
    *-------------------------------------------------------------------------
    */

    if ( options->ublock_size > 0 )
    {
        /* either use the FCPL already created or create a new one */
        if(fcpl != H5P_DEFAULT)
        {
            /* set user block size */
            if(H5Pset_userblock(fcpl, options->ublock_size) < 0)
            {
                error_msg(progname, "failed to set userblock size\n");
                goto out;
            }

        }

        else
        {

            /* create a file creation property list */
            if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0)
            {
                error_msg(progname, "fail to create a file creation property list\n");
                goto out;
            }

            /* set user block size */
            if(H5Pset_userblock(fcpl, options->ublock_size) < 0)
            {
                error_msg(progname, "failed to set userblock size\n");
                goto out;
            }

        }



    }


    /*-------------------------------------------------------------------------
    * set alignment options
    *-------------------------------------------------------------------------
    */


    if (  options->alignment > 0 )
    {
        /* either use the FCPL already created or create a new one */
        if (fapl != H5P_DEFAULT)
        {

            if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
            {
                error_msg(progname, "failed to set alignment\n");
                goto out;
            }

        }

        else
        {

            /* create a file access property list */
            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
            {
                error_msg(progname, "Could not create file access property list\n");
                goto out;
            }

            if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0)
            {
                error_msg(progname, "failed to set alignment\n");
                goto out;
            }

        }

    }


    /*-------------------------------------------------------------------------
    * create the output file
    *-------------------------------------------------------------------------
    */


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


    if((fidout = H5Fcreate(fnameout,H5F_ACC_TRUNC, fcpl, fapl)) < 0)
    {
        error_msg(progname, "<%s>: Could not create file\n", fnameout );
        goto out;
    } /* end if */


    /*-------------------------------------------------------------------------
    * write a new user block if requested
    *-------------------------------------------------------------------------
    */
    if ( options->ublock_size > 0  )
    {
        copy_user_block( options->ublock_filename, fnameout, options->ublock_size);
    }



    /* 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;
    } /* end if */

    /*-------------------------------------------------------------------------
    * do the copy of referenced objects
    * and create hard links
    *-------------------------------------------------------------------------
    */
    if(do_copy_refobjs(fidin, fidout, travt, options) < 0) {
        printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout);
        goto out;
    } /* end if */

    /* free table */
    trav_table_free(travt);


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

    if(fapl > 0)
        H5Pclose(fapl);

    if(fcpl > 0)
        H5Pclose(fcpl);

    H5Fclose(fidin);
    H5Fclose(fidout);

    /* write only the input file user block if there is no user block file input */
    if(ub_size > 0 && options->ublock_size == 0)
        copy_user_block(fnamein, fnameout, ub_size);

    return 0;

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

out:
    H5E_BEGIN_TRY {
        H5Pclose(fapl);
        H5Pclose(fcpl);
        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.
 *
 *  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,
                    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    gcpl_id=-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 */
    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      apply_s;           /* flag for apply filter to small dataset sizes */
    int      apply_f;           /* flag for apply filter to return error on H5Dcreate */
    void     *buf=NULL;         /* buffer for raw data */
    void     *sm_buf=NULL;      /* buffer for raw data */
    int      has_filter;        /* current object has a filter */
    unsigned i;
    int      is_ref=0;

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

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

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

        buf = NULL;
        switch ( travt->objs[i].type ) {
            /*-------------------------------------------------------------------------
             * H5TRAV_TYPE_GROUP
             *-------------------------------------------------------------------------
             */
            case H5TRAV_TYPE_GROUP:
                if (options->verbose)
                    printf(FORMAT_OBJ,"group",travt->objs[i].name );

                /*-------------------------------------------------------------------------
                 * 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(H5Pset_link_phase_change(gcpl_id, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 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;
                }

                if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
                    goto error;

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

                if(gcpl_id > 0) {
                    if(H5Pclose(gcpl_id) < 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:

                has_filter = 0;

                /* 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;

                    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];

                    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)
                    {
                        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->min_comp )
                                apply_s=0;

                            /* apply the filter */
                            if (apply_s) {
                                if (apply_filters(travt->objs[i].name,rank,dims,dcpl_out,options,&has_filter) < 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 = 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(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)
                                    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 */
                                    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) {
                                        sm_size[k - 1] = MIN(dims[k - 1], H5TOOLS_BUFSIZE / sm_nbytes);
                                        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)
                                        {
                                            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 */

                                        /* 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 (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)
                                    {
                                        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 */
                                if (apply_s && apply_f && has_filter)
                                {
                                    hssize_t a, b;

                                    /* get the storage size of the output dataset */
                                    dsize_out=H5Dget_storage_size(dset_out);

                                    /* compression ratio = uncompressed size /  compressed size */

                                    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 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;

                            /*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;

                    /* create property to pass copy options */
                    if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0)
                        goto error;

                    /* set options for object copy */
                    if(H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 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;


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


                } /* end do we have request for filter/chunking */


                break;

            /*-------------------------------------------------------------------------
             * H5TRAV_TYPE_NAMED_DATATYPE
             *-------------------------------------------------------------------------
             */
            case H5TRAV_TYPE_NAMED_DATATYPE:

                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_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;

                /*-------------------------------------------------------------------------
                 * 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;



                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:
            {

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

                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 */

    return 0;

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


/*-------------------------------------------------------------------------
 * 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,
              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];
    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
           *-------------------------------------------------------------------------
           */

            buf = (void *)HDmalloc((size_t)(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 = 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
         *-------------------------------------------------------------------------
         */

        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: 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,
                               int pr)
{
    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);

        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];
                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(!pr)
        printf(FORMAT_OBJ,"dset",objname );
    else
    {
        char str[255], temp[20];
        strcpy(str,"dset     ");
        strcat(str,strfilter);
        sprintf(temp,"  (%.3f:1)",ratio);
        strcat(str,temp);
        printf(FORMAT_OBJ,str,objname);
    }
}

/*-------------------------------------------------------------------------
 * 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)
{
    int infid = -1, outfid = -1;        /* File descriptors */
    int status = 0;                     /* Return value */

    /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
    assert(size > 0);

    /* Open files */
    if((infid = HDopen(infile, O_RDONLY, 0)) < 0) {
        status = -1;
        goto done;
    }
    if((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0) {
        status = -1;
        goto done;
    }

    /* Copy the userblock from the input file to the output file */
    while(size > 0) {
        ssize_t nread, nbytes;                  /* # of bytes transfered, etc. */
        char rbuf[USERBLOCK_XFER_SIZE];         /* Buffer for reading */
        const char *wbuf;                       /* Pointer into buffer, for writing */

        /* Read buffer from source file */
        if(size > USERBLOCK_XFER_SIZE)
            nread = HDread(infid, rbuf, (size_t)USERBLOCK_XFER_SIZE);
        else
            nread = HDread(infid, rbuf, (size_t)size);
        if(nread < 0) {
            status = -1;
            goto done;
        } /* end if */

        /* Write buffer to destination file */
        /* (compensating for interrupted writes & checking for errors, etc.) */
        nbytes = nread;
        wbuf = rbuf;
        while(nbytes > 0) {
            ssize_t nwritten;        /* # of bytes written */

            do {
                nwritten = HDwrite(outfid, wbuf, (size_t)nbytes);
            } while(-1 == nwritten && EINTR == errno);
            if(-1 == nwritten) { /* error */
                status = -1;
                goto done;
            } /* end if */
            assert(nwritten > 0);
            assert(nwritten <= nbytes);

            /* Update # of bytes left & offset in buffer */
            nbytes -= nwritten;
            wbuf += nwritten;
            assert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
        } /* end while */

        /* Update size of userblock left to transfer */
        size -= nread;
    } /* end while */

done:
    if(infid > 0)
        HDclose(infid);
    if(outfid > 0)
        HDclose(outfid);

    return status;
}



/*-------------------------------------------------------------------------
 * Function: print_user_block
 *
 * Purpose: print user block
 *
 * Return: 0, ok, -1 no
 *
 * Programmer: Pedro Vicente
 *
 * Date: August, 20, 2008
 *
 *-------------------------------------------------------------------------
 */
static
void print_user_block(const char *filename, hid_t fid)
{
    int     fh;      /* file handle  */
    hsize_t ub_size; /* user block size */
    hsize_t size;    /* size read */
    hid_t   fcpl;    /* file creation property list ID for HDF5 file */
    int     i;

    /* get user block size */
    if(( fcpl = H5Fget_create_plist(fid)) < 0)
    {
        error_msg(progname, "failed to retrieve file creation property list\n");
        goto done;
    }

    if(H5Pget_userblock(fcpl, &ub_size) < 0)
    {
        error_msg(progname, "failed to retrieve userblock size\n");
        goto done;
    }

    if(H5Pclose(fcpl) < 0)
    {
        error_msg(progname, "failed to close property list\n");
        goto done;
    }

    /* open file */
    if((fh = HDopen(filename, O_RDONLY, 0)) < 0)
    {
        goto done;
    }

    size = ub_size;

    /* read file */
    while(size > 0)
    {
        ssize_t nread;                  /* # of bytes read */
        char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */

        /* read buffer */
        if(size > USERBLOCK_XFER_SIZE)
            nread = HDread(fh, rbuf, (size_t)USERBLOCK_XFER_SIZE);
        else
            nread = HDread(fh, rbuf, (size_t)size);

        for(i = 0; i < nread; i++)
        {

            printf("%c ", rbuf[i]);

        }
        printf("\n");

        if(nread < 0)
        {
            goto done;
        }


        /* update size of userblock left to transfer */
        size -= nread;
    }

done:
    if(fh > 0)
        HDclose(fh);


    return;
}