Split tools into src and test - remove folders

1 files changed, 0 insertions, 1581 deletions

diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c
deleted file mode 100644
index 547f61a..0000000
--- a/tools/h5repack/h5repack_copy.c
+++ /dev/null
@@ -1,1581 +0,0 @@
-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * 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 "h5repack.h"
-#include "h5tools.h"
-#include "h5tools_utils.h"
-
-/*-------------------------------------------------------------------------
- * typedefs
- *-------------------------------------------------------------------------
- */
-
-/*-------------------------------------------------------------------------
- * globals
- *-------------------------------------------------------------------------
- */
-
-/*-------------------------------------------------------------------------
- * macros
- *-------------------------------------------------------------------------
- */
-
-/* size of buffer/# of bytes to xfer at a time when copying userblock */
-#define USERBLOCK_XFER_SIZE     512     
-
-/* check H5Dread()/H5Dwrite() error, e.g. memory allocation error inside the library. */
-#define CHECK_H5DRW_ERROR(_fun, _fail, _did, _mtid, _msid, _fsid, _pid, _buf)  {  \
-    H5E_BEGIN_TRY {  \
-        if(_fun(_did, _mtid, _msid, _fsid, _pid, _buf) < 0) {  \
-            hid_t _err_num = 0; \
-            char _msg[80]; \
-            H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &_err_num); \
-            H5Eget_msg(_err_num, NULL, _msg, (size_t)80); \
-            error_msg("%s %s -- %s\n", #_fun, "failed", _msg); \
-            HGOTO_DONE(_fail) \
-        } \
-    } H5E_END_TRY; \
-}
-
-/*-------------------------------------------------------------------------
- * local functions
- *-------------------------------------------------------------------------
- */
-static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
-		size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
-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_user_block(const char *infile, const char *outfile,
-		hsize_t size);
-#if defined (H5REPACK_DEBUG_USER_BLOCK)
-static void print_user_block(const char *filename, hid_t fid);
-#endif
-static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void *udata);
-
-/* get the major number from the error stack. */
-static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) {
-	if (err_desc)
-		*((hid_t *) udata) = err_desc->maj_num;
-
-	return 0;
-}
-
-/*-------------------------------------------------------------------------
- * 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)
-{
-    int   ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    hid_t fidin;
-    hid_t fidout = -1;
-    trav_table_t *travt = NULL;
-    hsize_t ub_size = 0; /* size of user block */
-    hid_t fcpl = H5P_DEFAULT; /* file creation property list ID */
-    hid_t fapl = H5P_DEFAULT; /* file access property list ID */
-
-    /*-------------------------------------------------------------------------
-     * open input file
-     *-------------------------------------------------------------------------
-     */
-    if ((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t) 0)) < 0) {
-        error_msg("<%s>: %s\n", fnamein, H5FOPENERROR);
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-    }
-
-    /* get user block size and file space strategy/threshold */
-    {
-        hid_t fcpl_in; /* file creation property list ID for input file */
-
-        if ((fcpl_in = H5Fget_create_plist(fidin)) < 0) {
-            error_msg("failed to retrieve file creation property list\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-
-        if (H5Pget_userblock(fcpl_in, &ub_size) < 0) {
-            error_msg("failed to retrieve userblock size\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-
-        if (!options->fs_strategy) {
-            if (H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) {
-                error_msg("failed to retrieve file space strategy\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
-        }
-
-        if (!options->fs_threshold) {
-            if (H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) {
-                error_msg("failed to retrieve file space threshold\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
-        }
-
-        if (H5Pclose(fcpl_in) < 0) {
-            error_msg("failed to close property list\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-    }
-
-    /* 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("fail to create a file creation property list\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-
-        if (ub_size > 0) {
-            if (H5Pset_userblock(fcpl, ub_size) < 0) {
-                error_msg("failed to set non-default userblock size\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
-        }
-
-        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("fail to adjust group creation parameters for root group\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
-
-            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;
-
-                        default:
-                            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("fail to set the number of shared object header message indexes\n");
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-                }
-
-                /* 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("fail to configure the specified shared object header message index\n");
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-                    } /* end if */
-                } /* end for */
-            } /* if (nindex>0) */
-
-            /* Create file access property list */
-            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
-                error_msg("Could not create file access property list\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            } /* end if */
-
-            if (H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
-                error_msg("Could not set property for using latest version of the format\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            } /* end if */
-        } /* end if */
-    } /* end if */
-#if defined (H5REPACK_DEBUG_USER_BLOCK)
-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) {
-            /* create a file creation property list */
-            if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
-                error_msg("fail to create a file creation property list\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
-        }
-
-        /* set user block size */
-        if (H5Pset_userblock(fcpl, options->ublock_size) < 0) {
-            error_msg("failed to set userblock size\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-    }
-
-    /*-------------------------------------------------------------------------
-     * set alignment options
-     *-------------------------------------------------------------------------
-     */
-    if (options->alignment > 0) {
-        /* either use the FAPL already created or create a new one */
-        if (fapl == H5P_DEFAULT) {
-            /* create a file access property list */
-            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
-                error_msg("Could not create file access property list\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
-        }
-
-        if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) {
-            error_msg("failed to set alignment\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-    }
-
-    /*-------------------------------------------------------------------------
-     * set metadata block size option
-     *-------------------------------------------------------------------------
-     */
-    if (options->meta_block_size > 0) {
-        /* either use the FAPL already created or create a new one */
-        if (fapl == H5P_DEFAULT) {
-            /* create a file access property list */
-            if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
-                error_msg("Could not create file access property list\n");
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
-        }
-
-        if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) {
-            error_msg("failed to set metadata block size\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-    }
-
-    /*-------------------------------------------------------------------------
-     * set free-space strategy options
-     *-------------------------------------------------------------------------
-     */
-
-    /* either use the FCPL already created or create a new one */
-    if (fcpl == H5P_DEFAULT) {
-        /* create a file creation property list */
-        if ((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) {
-            error_msg("fail to create a file creation property list\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-    }
-
-    /* set file space strategy and free space threshold */
-    if (H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0) {
-        error_msg("failed to set file space strategy & threshold \n");
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-    }
-
-    /*-------------------------------------------------------------------------
-     * 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("<%s>: Could not create file\n", fnameout);
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-    }
-
-    /*-------------------------------------------------------------------------
-     * write a new user block if requested
-     *-------------------------------------------------------------------------
-     */
-    if (options->ublock_size > 0) {
-        if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0) {
-            error_msg("Could not copy user block. Exiting...\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-    }
-
-    /*-------------------------------------------------------------------------
-     * get list of objects
-     *-------------------------------------------------------------------------
-     */
-
-    /* init table */
-    trav_table_init(&travt);
-
-    /* get the list of objects in the file */
-    if (h5trav_gettable(fidin, travt) < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-
-    /*-------------------------------------------------------------------------
-     * do the copy
-     *-------------------------------------------------------------------------
-     */
-    if (do_copy_objects(fidin, fidout, travt, options) < 0) {
-        error_msg("<%s>: Could not copy data to: %s\n", fnamein, fnameout);
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-    } /* 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);
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-    }
-
-    /*-------------------------------------------------------------------------
-     * close
-     *-------------------------------------------------------------------------
-     */
-
-    if (fapl > 0)
-        H5Pclose(fapl);
-
-    if (fcpl > 0)
-        H5Pclose(fcpl);
-
-    H5Fclose(fidin);
-    H5Fclose(fidout);
-
-    /* free table */
-    trav_table_free(travt);
-    travt = NULL;
-
-    /*-------------------------------------------------------------------------
-     * write only the input file user block if there is no user block file input
-     *-------------------------------------------------------------------------
-     */
-
-    if (ub_size > 0 && options->ublock_size == 0) {
-        if (copy_user_block(fnamein, fnameout, ub_size) < 0) {
-            error_msg("Could not copy user block. Exiting...\n");
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-    }
-
-    return 0;
-
-    /*-------------------------------------------------------------------------
-     * out
-     *-------------------------------------------------------------------------
-     */
-
-done:
-    H5E_BEGIN_TRY {
-        H5Pclose(fapl);
-        H5Pclose(fcpl);
-        H5Fclose(fidin);
-        H5Fclose(fidout);
-    } H5E_END_TRY;
-    if (travt)
-        trav_table_free(travt);
-
-    return ret_value;
-}
-
-/*-------------------------------------------------------------------------
- * Function: Get_hyperslab
- *
- * Purpose: Calulate a hyperslab from a dataset for higher performance.
- *          The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
- *          Return the hyperslab dimentions and size in byte.
- *
- * Return: 0 - SUCCEED, -1 FAILED
- *
- * Parameters:
- *   dcpl_id : [IN] dataset creation property.
- *   rank_dset : [IN] dataset rank
- *   dims_dset[] : [IN] dataset dimentions
- *   size_datum : [IN] size of a data element in byte
- *   dims_hslab[] : [OUT] calculated hyperslab dimentions
- *   * hslab_nbytes_p : [OUT] total byte of the hyperslab
- *
- * Programmer: Jonathan Kim
- * Date: Feburary, 2012
- * Update:
- *   The hyperslab calucation would be depend on if the dataset is chunked
- *   or not.
- *
- *   There care 3 conditions to cover:
- *   1. If chunked and a chunk fits in buffer, each chunk would be a unit of
- *      collection and the boundary would be dataset's dims.
- *   2. If chunked but a chunk doesn't fit in buffer, each data element would
- *      be a unit of collection and the boundary would be the chunk itself.
- *   3. If not chunked, each data element would be a unit of collection and
- *      the boundary would be dataset's dims.
- *
- *   The calulation starts from the last dimention (h5dump dims output).
- *
- * Note:
- *   Added for JIRA HDFFV-7862.
- *-----------------------------------------*/
-
-int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
-        size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
-{
-    int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    int k;
-    H5D_layout_t dset_layout;
-    int rank_chunk;
-    hsize_t dims_chunk[H5S_MAX_RANK];
-    hsize_t size_chunk = 1;
-    hsize_t nchunk_fit; /* number of chunks that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
-    hsize_t ndatum_fit; /* number of dataum that fits in hyperslab buffer (H5TOOLS_BUFSIZE) */
-    hsize_t chunk_dims_map[H5S_MAX_RANK]; /* mapped chunk dimentions */
-    hsize_t hs_dims_map[H5S_MAX_RANK]; /* mapped hyperslab dimentions */
-    hsize_t hslab_nbytes; /* size of hyperslab in byte */
-
-    /* init to set as size of a data element */
-    hslab_nbytes = size_datum;
-
-    /* get layout of dataset */
-    dset_layout = H5Pget_layout(dcpl_id);
-
-    /* if dataset is chunked */
-    if (dset_layout == H5D_CHUNKED) {
-        /* get chunk dims */
-        rank_chunk = H5Pget_chunk(dcpl_id, rank_dset, dims_chunk);
-        if (rank_chunk < 0)
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-
-        for (k = rank_dset; k > 0; --k)
-            size_chunk *= dims_chunk[k - 1];
-
-        /* figure out how many chunks can fit in the hyperslab buffer */
-        nchunk_fit = (H5TOOLS_BUFSIZE / size_datum) / size_chunk;
-
-        /* 1. if a chunk fit in hyperslab buffer */
-        if (nchunk_fit >= 1) {
-            /* Calulate a hyperslab that contains as many chunks that can fit
-             * in hyperslab buffer. Hyperslab will be increased starting from
-             * the last dimention of the dataset (see h5dump's dims output).
-             * The calculation boundary is dataset dims.
-             * In the loop, used mapping from a datum to a chunk to figure out
-             * chunk based hyperslab.
-             */
-            for (k = rank_dset; k > 0; --k) {
-                /* map dataset dimentions with a chunk dims */
-                chunk_dims_map[k - 1] = dims_dset[k - 1] / dims_chunk[k - 1];
-
-                /* if reminder exist, increse by 1 to cover partial edge chunks */
-                if (dims_dset[k - 1] % dims_chunk[k - 1] > 0)
-                    chunk_dims_map[k - 1]++;
-
-                /* get mapped hyperslab dims */
-                hs_dims_map[k - 1] = MIN (nchunk_fit, chunk_dims_map[k-1]);
-
-                /* prepare next round */
-                nchunk_fit = nchunk_fit / chunk_dims_map[k - 1];
-                /* if a chunk is bigger than the rest of buffer */
-                if (nchunk_fit == 0)
-                    nchunk_fit = 1;
-
-                /* get hyperslab dimentions as unmapping to actual size */
-                dims_hslab[k - 1] = MIN( (hs_dims_map[k-1] * dims_chunk[k-1]), dims_dset[k-1]);
-
-                /* calculate total size for the hyperslab */
-                hslab_nbytes *= dims_hslab[k - 1];
-            }
-        }
-        /* 2. if a chunk is bigger than hyperslab buffer */
-        else {
-            /* Calulate a hyperslab that contains as many data elements that
-             * can fit in hyperslab buffer. Hyperslab will be increased
-             * starting from the last dimention of the chunk (see h5dump's dims
-             * output).
-             * The calculation boundary is a chunk dims.
-             */
-            for (k = rank_dset; k > 0; --k) {
-                ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
-
-                /* if a datum is bigger than rest of buffer */
-                if (ndatum_fit == 0)
-                    ndatum_fit = 1;
-                /* get hyperslab dimentions within a chunk boundary */
-                dims_hslab[k - 1] = MIN (dims_chunk[k-1], ndatum_fit);
-
-                /* calculate total size for the hyperslab */
-                hslab_nbytes *= dims_hslab[k - 1];
-
-                if (hslab_nbytes <= 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-            }
-        }
-    }
-    /* 3. if dataset is not chunked */
-    else {
-        /* Calulate a hyperslab that contains as many data elements that can
-         * fit in hyperslab buffer. Hyperslab will be increased starting from
-         * the last dimention of the dataset (see h5dump's dims output).
-         * The calculation boundary is dataset dims.
-         */
-        for (k = rank_dset; k > 0; --k) {
-            ndatum_fit = H5TOOLS_BUFSIZE / hslab_nbytes;
-
-            /* if a datum is bigger than rest of buffer */
-            if (ndatum_fit == 0)
-                ndatum_fit = 1;
-            /* get hyperslab dimentions within dataset boundary */
-            dims_hslab[k - 1] = MIN(dims_dset[k - 1], ndatum_fit);
-
-            /* calculate total size for the hyperslab */
-            hslab_nbytes *= dims_hslab[k - 1];
-
-            if (hslab_nbytes <= 0)
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-        }
-    }
-
-    /* pass out the hyperslab size*/
-    *hslab_nbytes_p = hslab_nbytes;
-
-done:
-    return ret_value;
-}
-
-/*-------------------------------------------------------------------------
- * 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
- *
- * Feburary 2012:  improve Read/Write by hyperslabs for big datasets.
- * Programmer: Jonathan Kim
- *
- *  A threshold of H5TOOLS_MALLOCSIZE 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_dataset )
- *  H5Dwrite( output_dataset )
- *
- *  with all elements in the datasets selected. If the memory needed is greater than
- *  H5TOOLS_MALLOCSIZE, then the following operations are done instead:
- *
- *  1. figure out a hyperslab (dimentions) and size  (refer to Get_hyperslab()).
- *  2. Calculate the hyperslab selections as the selection is moving forward.
- *     Selection would be same as the hyperslab except for the remaining edge portion
- *     of the dataset. The code take care of the remaining portion if exist.
- *
- *-------------------------------------------------------------------------
- */
-
-int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
-		pack_opt_t *options) /* repack options */
-{
-    int   ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    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_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_in = -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 */
-    named_dt_t *named_dt_head = NULL; /* Pointer to the stack of named datatypes copied */
-    size_t msize; /* size of type */
-    hsize_t nelmts; /* number of elements in dataset */
-    H5D_space_status_t space_status; /* determines whether space has been allocated for the 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 *hslab_buf = NULL; /* hyperslab buffer for raw data */
-    int has_filter; /* current object has a filter */
-    int req_filter; /* there was a request for a filter */
-    int req_obj_layout = 0; /* request layout to current object */
-    unsigned crt_order_flags; /* group creation order flag */
-    unsigned i;
-    unsigned u;
-    int is_ref = 0;
-    htri_t is_named;
-    hbool_t limit_maxdims;
-    hsize_t size_dset;
-
-    /*-------------------------------------------------------------------------
-     * 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++) {
-        /* init variables per obj */
-        buf = NULL;
-        limit_maxdims = FALSE;
-
-        switch (travt->objs[i].type) {
-            case H5TRAV_TYPE_UNKNOWN:
-                HDassert(0);
-                break;
-
-                /*-------------------------------------------------------------------------
-                 * H5TRAV_TYPE_GROUP
-                 *-------------------------------------------------------------------------
-                 */
-            case H5TRAV_TYPE_GROUP:
-                if (options->verbose)
-                    printf(FORMAT_OBJ, "group", travt->objs[i].name);
-
-                /* open input group */
-                if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
-
-                /* get input group creation property list */
-                if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gget_create_plist failed");
-
-                /* query and set the group creation properties */
-                if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_link_creation_order failed");
-
-                /* set up group creation property list */
-                if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");
-
-                if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_creation_order failed");
-
-                /*-------------------------------------------------------------------------
-                 * 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)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
-                }
-                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)
-                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed");
-
-                    if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gcreate2 failed");
-                }
-
-                /*-------------------------------------------------------------------------
-                 * copy attrs
-                 *-------------------------------------------------------------------------
-                 */
-                if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
-
-                if (H5Pclose(gcpl_out) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-                if (H5Pclose(gcpl_in) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-                if (H5Gclose(grp_out) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
-                if (H5Gclose(grp_in) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gclose failed");
-
-                break;
-
-                /*-------------------------------------------------------------------------
-                 * H5TRAV_TYPE_DATASET
-                 *-------------------------------------------------------------------------
-                 */
-            case H5TRAV_TYPE_DATASET:
-                has_filter = 0;
-                req_filter = 0;
-
-                /* 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++)
-                    if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0)
-                        if (options->op_tbl->objs[u].filter->filtn > 0)
-                            req_filter = 1;
-
-                /* check if layout change requested individual object */
-                if (options->layout_g != H5D_LAYOUT_ERROR) {
-                    pack_info_t *pckinfo;
-
-                    /* any dataset is specified */
-                    if (options->op_tbl->nelems > 0) {
-                        /* check if object exist */
-                        pckinfo = options_get_object(travt->objs[i].name, options->op_tbl);
-                        if (pckinfo)
-                            req_obj_layout = 1;
-                    }
-                }
-
-                /* early detection of references */
-                if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
-                if ((ftype_id = H5Dget_type(dset_in)) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
-                if (H5T_REFERENCE == H5Tget_class(ftype_id))
-                    is_ref = 1;
-
-                /* Check if the datatype is committed */
-                if ((is_named = H5Tcommitted(ftype_id)) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed");
-                if (is_named)
-                    if ((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
-
-                if (H5Tclose(ftype_id) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
-                if (H5Dclose(dset_in) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
-
-                /*-------------------------------------------------------------------------
-                 * 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 || is_named) {
-
-                    int j;
-
-                    if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
-                    if ((f_space_id = H5Dget_space(dset_in)) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space failed");
-                    if ((ftype_id = H5Dget_type(dset_in)) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
-                    if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
-                    if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
-                    if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
-                    HDmemset(dims, 0, sizeof dims);
-                    if (H5Sget_simple_extent_dims(f_space_id, dims, NULL) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
-                    if (H5Dget_space_status(dset_in, &space_status) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space_status failed");
-
-                    nelmts = 1;
-                    for (j = 0; j < rank; j++)
-                        nelmts *= dims[j];
-
-                    /* wtype_id will have already been set if using a named dtype */
-                    if (!is_named) {
-                        if (options->use_native == 1)
-                            wtype_id = h5tools_get_native_type(ftype_id);
-                        else
-                            wtype_id = H5Tcopy(ftype_id);
-                    } /* end if */
-
-                    if ((msize = H5Tget_size(wtype_id)) == 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
-
-                    /* size of current dset */
-                    size_dset = nelmts * msize;
-
-                    /*-------------------------------------------------------------------------
-                     * 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_in) == 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 small size datasets (less than 1k) except
-                             * changing to COMPACT. For the reference, COMPACT is limited
-                             * by size 64K by library.
-                             */
-                            if (options->layout_g != H5D_COMPACT)
-                                if (size_dset < 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)
-                                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "apply_filters failed");
-
-                            /* only if layout change requested for entire file or
-                             * individual obj */
-                            if (options->all_layout > 0 || req_obj_layout == 1)
-                                /*-------------------------------------------------
-                                 * Unset the unlimited max dims if convert to other
-                                 * than chunk layouts, because unlimited max dims
-                                 * only can be applied to chunk layout.
-                                 * Also perform only for targeted dataset
-                                 * Also check for size limit to convert to compact
-                                 *-------------------------------------------------*/
-                                if (options->layout_g != H5D_CHUNKED) {
-                                    /* any dataset is specified */
-                                    if (options->op_tbl->nelems > 0) {
-                                        /* if current obj match specified obj */
-                                        if (options_get_object(travt->objs[i].name, options->op_tbl))
-                                            limit_maxdims = TRUE;
-                                    }
-                                    else  /* no dataset is specified */
-                                        limit_maxdims = TRUE;
-
-                                    /* if convert to COMPACT */
-                                    if (options->layout_g == H5D_COMPACT)
-                                        /* should be smaller than 64K */
-                                        if (size_dset > MAX_COMPACT_DSIZE)
-                                            limit_maxdims = FALSE;
-
-                                    /* unset unlimited max dims */
-                                    if (limit_maxdims)
-                                        H5Sset_extent_simple(f_space_id, rank, dims, NULL);
-                                }
-
-                            /*-------------------------------------------------------------------------
-                             * 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
-                             *-------------------------------------------------------------------------
-                             */
-                            dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_out, H5P_DEFAULT);
-                            if (dset_out == FAIL) {
-                                H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed");
-                                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_in, H5P_DEFAULT)) < 0)
-                                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
-                                apply_f = 0;
-                            }
-
-                            /*-------------------------------------------------------------------------
-                             * read/write
-                             *-------------------------------------------------------------------------
-                             */
-                            if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) {
-                                size_t need = (size_t)(nelmts * msize); /* bytes needed */
-
-                                /* have to read the whole dataset if there is only one element in the dataset */
-                                if (need < H5TOOLS_MALLOCSIZE)
-                                    buf = HDmalloc(need);
-
-                                if (buf != NULL) {
-                                    /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
-                                    CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
-                                    CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
-
-                                    /* Check if we have VL data in the dataset's
-                                     * datatype that must be reclaimed */
-                                    if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
-                                        if (H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
-                                            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed");
-                                }
-                                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 elements */
-                                    hsize_t elmtno; /*counter  */
-                                    int carry; /*counter carry value */
-                                    unsigned int vl_data = 0; /*contains VL datatypes */
-
-                                    /* hyperslab info */
-                                    hsize_t hslab_dims[H5S_MAX_RANK]; /*hyperslab dims */
-                                    hsize_t hslab_nbytes; /*bytes per hyperslab */
-                                    hsize_t hslab_nelmts; /*elements per hyperslab*/
-                                    hid_t hslab_space; /*hyperslab data space */
-
-                                    /* hyperslab selection info */
-                                    hsize_t hs_sel_offset[H5S_MAX_RANK];/* selection offset */
-                                    hsize_t hs_sel_count[H5S_MAX_RANK]; /* selection count */
-                                    hsize_t hs_select_nelmts; /* selected elements */
-                                    hsize_t zero[8]; /*vector of zeros */
-                                    int k;
-                                    H5D_layout_t dset_layout;
-                                    hid_t dcpl_tmp = -1; /* dataset creation property list ID */
-
-                                    /* check if we have VL data in the dataset's datatype */
-                                    if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE)
-                                        vl_data = TRUE;
-
-                                    /* check first if writing dataset is chunked,
-                                     * if so use its chunk layout for better performance. */
-                                    dset_layout = H5Pget_layout(dcpl_out);
-                                    if (dset_layout == H5D_CHUNKED)
-                                        dcpl_tmp = dcpl_out; /* writing dataset */
-                                    else { /* if reading dataset is chunked */
-                                        dset_layout = H5Pget_layout(dcpl_in);
-                                        if (dset_layout == H5D_CHUNKED)
-                                            dcpl_tmp = dcpl_in; /* reading dataset */
-                                    }
-
-                                    /* get hyperslab dims and size in byte */
-                                    if (Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
-                                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Get_hyperslab failed");
-
-                                    hslab_buf = HDmalloc((size_t)hslab_nbytes);
-
-                                    hslab_nelmts = hslab_nbytes / p_type_nbytes;
-                                    hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL);
-
-                                    /* the hyperslab selection loop */
-                                    HDmemset(hs_sel_offset, 0, sizeof hs_sel_offset);
-                                    HDmemset(zero, 0, sizeof zero);
-
-                                    for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_select_nelmts) {
-                                        if (rank > 0) {
-                                            /* calculate the hyperslab selections.
-                                             * The selection would be same as the hyperslab
-                                             * except for remaining edge portion of the dataset
-                                             * which is smaller then the hyperslab.
-                                             */
-                                            for (k = 0, hs_select_nelmts = 1; k < rank; k++) {
-                                                /* MIN() is used to get the remaining edge portion if exist.
-                                                 * "dims[k] - hs_sel_offset[k]" is remaining edge portion that is smaller then the hyperslab.*/
-                                                hs_sel_count[k] = MIN(dims[k] - hs_sel_offset[k], hslab_dims[k]);
-                                                hs_select_nelmts *= hs_sel_count[k];
-                                            }
-
-                                            if (H5Sselect_hyperslab(f_space_id, H5S_SELECT_SET, hs_sel_offset, NULL, hs_sel_count, NULL) < 0)
-                                                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
-                                            if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0)
-                                                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
-                                        }
-                                        else {
-                                            H5Sselect_all(f_space_id);
-                                            H5Sselect_all(hslab_space);
-                                            hs_select_nelmts = 1;
-                                        } /* rank */
-
-                                        /* read/write: use the macro to check error, e.g. memory allocation error inside the library. */
-                                        CHECK_H5DRW_ERROR(H5Dread, FAIL, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
-                                        CHECK_H5DRW_ERROR(H5Dwrite, FAIL, dset_out, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf);
-
-                                        /* reclaim any VL memory, if necessary */
-                                        if (vl_data)
-                                            H5Dvlen_reclaim(wtype_id, hslab_space, H5P_DEFAULT, hslab_buf);
-
-                                        /* calculate the next hyperslab offset */
-                                        for (k = rank, carry = 1; k > 0 && carry; --k) {
-                                            hs_sel_offset[k - 1] += hs_sel_count[k - 1];
-                                            /* if reached the end of a dim */
-                                            if (hs_sel_offset[k - 1] == dims[k - 1])
-                                                hs_sel_offset[k - 1] = 0;
-                                            else
-                                                carry = 0;
-                                        } /* k */
-                                    } /* elmtno */
-
-                                    H5Sclose(hslab_space);
-                                    /* free */
-                                    if (hslab_buf != NULL) {
-                                        HDfree(hslab_buf);
-                                        hslab_buf = NULL;
-                                    }
-                                } /* hyperslab read */
-                            } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
-
-                            /*-------------------------------------------------------------------------
-                             * 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) {
-                                    /* get the storage size of the output dataset */
-                                    dsize_out = H5Dget_storage_size(dset_out);
-
-                                    /* compression ratio = uncompressed size /  compressed size */
-                                    if (dsize_out != 0)
-                                        ratio = (double) dsize_in / (double) dsize_out;
-                                    print_dataset_info(dcpl_out, travt->objs[i].name, ratio, 1);
-                                }
-                                else
-                                    print_dataset_info(dcpl_in, 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, &named_dt_head, travt, options) < 0)
-                                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
-
-                            /*close */
-                            if (H5Dclose(dset_out) < 0)
-                                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
-                        }/*!H5T_REFERENCE*/
-                    }/*h5tools_canreadf*/
-
-                    /*-------------------------------------------------------------------------
-                     * close
-                     *-------------------------------------------------------------------------
-                     */
-                    if (H5Tclose(ftype_id) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
-                    if (H5Tclose(wtype_id) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
-                    if (H5Pclose(dcpl_in) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-                    if (H5Pclose(dcpl_out) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-                    if (H5Sclose(f_space_id) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
-                    if (H5Dclose(dset_in) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
-                }
-                /*-------------------------------------------------------------------------
-                 * 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)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");
-
-                    /* set options for object copy */
-                    if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_copy_object failed");
-
-                    /*-------------------------------------------------------------------------
-                     * 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 */
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Ocopy failed");
-
-                    /* close property */
-                    if (H5Pclose(pid) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
-
-                    /*-------------------------------------------------------------------------
-                     * copy attrs manually
-                     *-------------------------------------------------------------------------
-                     */
-                    if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
-                    if ((dset_out = H5Dopen2(fidout, travt->objs[i].name, H5P_DEFAULT)) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dopen2 failed");
-                    if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
-                    if (H5Dclose(dset_in) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
-                    if (H5Dclose(dset_out) < 0)
-                        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
-
-                    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)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed");
-
-                /* Copy the datatype anonymously */
-                if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, travt, options)) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
-
-                /* Link in to group structure */
-                if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcreate_hard failed");
-
-                /*-------------------------------------------------------------------------
-                 * copy attrs
-                 *-------------------------------------------------------------------------
-                 */
-                if (copy_attr(type_in, type_out, &named_dt_head, travt, options) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
-
-                if (H5Tclose(type_in) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
-                if (H5Tclose(type_out) < 0)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
-
-                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)
-                    HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcopy failed");
-
-                if (options->verbose)
-                    printf(FORMAT_OBJ, "link", travt->objs[i].name);
-                break;
-
-            default:
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found");
-        } /* switch */
-
-        /* free */
-        if (buf != NULL) {
-            HDfree(buf);
-            buf = NULL;
-        }
-    } /* i */
-
-    /* Finalize (link) the stack of named datatypes (if any) */
-    named_datatype_free(&named_dt_head, 0);
-
-    return ret_value;
-
-done:
-    H5E_BEGIN_TRY
-    {
-        H5Gclose(grp_in);
-        H5Gclose(grp_out);
-        H5Pclose(dcpl_in);
-        H5Pclose(gcpl_in);
-        H5Pclose(gcpl_out);
-        H5Sclose(f_space_id);
-        H5Dclose(dset_in);
-        H5Dclose(dset_out);
-        H5Tclose(ftype_id);
-        H5Tclose(wtype_id);
-        H5Tclose(type_in);
-        H5Tclose(type_out);
-        named_datatype_free(&named_dt_head, 1);
-    }H5E_END_TRY;
-
-    /* free */
-    if (buf != NULL)
-        HDfree(buf);
-    if (hslab_buf != NULL)
-        HDfree(hslab_buf);
-
-    return ret_value;
-}
-
-/*-------------------------------------------------------------------------
- * 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;
-
-    HDstrcpy(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) {
-            case H5Z_FILTER_NONE:
-                HDstrcat(strfilter, "NONE ");
-                break;
-
-            case H5Z_FILTER_DEFLATE:
-                HDstrcat(strfilter, "GZIP ");
-
-#if defined (PRINT_DEBUG)
-                {
-                    unsigned level = cd_values[0];
-
-                    sprintf(temp,"(%d)", level);
-                    HDstrcat(strfilter, temp);
-                }
-#endif
-                break;
-
-            case H5Z_FILTER_SZIP:
-                HDstrcat(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);
-                    HDstrcat(strfilter, temp);
-                    if (options_mask & H5_SZIP_EC_OPTION_MASK)
-                        HDstrcpy(temp, "EC) ");
-                    else if (options_mask & H5_SZIP_NN_OPTION_MASK)
-                        HDstrcpy(temp, "NN) ");
-                }
-                HDstrcat(strfilter, temp);
-#endif
-                break;
-
-            case H5Z_FILTER_SHUFFLE:
-                HDstrcat(strfilter, "SHUF ");
-                break;
-
-            case H5Z_FILTER_FLETCHER32:
-                HDstrcat(strfilter, "FLET ");
-                break;
-
-            case H5Z_FILTER_NBIT:
-                HDstrcat(strfilter, "NBIT ");
-                break;
-
-            case H5Z_FILTER_SCALEOFFSET:
-                HDstrcat(strfilter, "SCALEOFFSET ");
-                break;
-
-            default:
-                HDstrcat(strfilter, "UD ");
-                break;
-        } /* switch */
-    }/*i*/
-
-    if (!pr)
-        printf(FORMAT_OBJ, "dset", objname);
-    else {
-        char str[255], temp[28];
-
-        HDstrcpy(str, "dset     ");
-        HDstrcat(str, strfilter);
-        sprintf(temp, "  (%.3f:1)", ratio);
-        HDstrcat(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 ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    int infid = -1, outfid = -1; /* File descriptors */
-
-    /* User block must be any power of 2 equal to 512 or greater (512, 1024, 2048, etc.) */
-    HDassert(size > 0);
-
-    /* Open files */
-    if ((infid = HDopen(infile, O_RDONLY, 0)) < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
-    if ((outfid = HDopen(outfile, O_WRONLY, 0644)) < 0)
-        HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDopen failed");
-
-    /* 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)
-            HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDread failed");
-
-        /* 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 */
-                HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDwrite failed");
-            HDassert(nwritten > 0);
-            HDassert(nwritten <= nbytes);
-
-            /* Update # of bytes left & offset in buffer */
-            nbytes -= nwritten;
-            wbuf += nwritten;
-            HDassert(nbytes == 0 || wbuf < (rbuf + USERBLOCK_XFER_SIZE));
-        } /* end while */
-
-        /* Update size of userblock left to transfer */
-        size = size - (hsize_t) nread;
-    } /* end while */
-
-done:
-    if (infid > 0)
-        HDclose(infid);
-    if (outfid > 0)
-        HDclose(outfid);
-
-    return ret_value;
-}
-
-/*-------------------------------------------------------------------------
- * 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)
-{
-    int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
-    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("failed to retrieve file creation property list\n");
-        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Fget_create_plist failed");
-    }
-
-	if(H5Pget_userblock(fcpl, &ub_size) < 0) {
-		error_msg("failed to retrieve userblock size\n");
-        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pget_userblock failed");
-    }
-
-	if(H5Pclose(fcpl) < 0) {
-		error_msg("failed to close property list\n");
-        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "H5Pclose failed");
-    }
-
-	/* open file */
-	if((fh = HDopen(filename, O_RDONLY, 0)) < 0) {
-        HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "HDopen failed");
-    }
-
-	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) {
-            HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0");
-        }
-
-		/* update size of userblock left to transfer */
-		size -= nread;
-	}
-
-done:
-	if(fh > 0)
-		HDclose(fh);
-
-	return;
-}
-#endif
-