/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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, _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); \ goto error; \ } \ } 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(UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) { if (err_desc) *((int *) 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) { 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); goto out; } /* 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"); goto out; } if (H5Pget_userblock(fcpl_in, &ub_size) < 0) { error_msg("failed to retrieve userblock size\n"); goto out; } if (H5Pclose(fcpl_in) < 0) { error_msg("failed to close property list\n"); goto out; } } /* 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"); goto out; } if (ub_size > 0) { if (H5Pset_userblock(fcpl, ub_size) < 0) { error_msg("failed to set non-default userblock size\n"); goto out; } } 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"); goto out; } 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"); goto out; } /* 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"); goto out; } /* 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"); goto out; } /* 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"); goto out; } /* 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"); goto out; } } /* set user block size */ if (H5Pset_userblock(fcpl, options->ublock_size) < 0) { error_msg("failed to set userblock size\n"); goto out; } } /*------------------------------------------------------------------------- * 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"); goto out; } } if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) { error_msg("failed to set alignment\n"); goto out; } } /*------------------------------------------------------------------------- * 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"); goto out; } } if (H5Pset_meta_block_size(fapl, options->meta_block_size) < 0) { error_msg("failed to set metadata block size\n"); goto out; } } /*------------------------------------------------------------------------- * create the output file *------------------------------------------------------------------------- */ if (options->verbose) printf("Making file <%s>...\n", fnameout); if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0) { error_msg("<%s>: Could not create file\n", fnameout); goto out; } /*------------------------------------------------------------------------- * 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"); goto out; } } /*------------------------------------------------------------------------- * get list of objects *------------------------------------------------------------------------- */ /* 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("<%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; } /*------------------------------------------------------------------------- * 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"); goto out; } } 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: 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 status = 0; 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) { status = -1; goto out; } 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) { status = -1; goto out; } } } } /* 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) { status = -1; goto out; } } } /* pass out the hyperslab size*/ *hslab_nbytes_p = hslab_nbytes; out: return status; } /*------------------------------------------------------------------------- * 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 */ { 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) goto error; /* get input group creation property list */ if ((gcpl_in = H5Gget_create_plist(grp_in)) < 0) goto error; /* query and set the group creation properties */ if (H5Pget_link_creation_order(gcpl_in, &crt_order_flags) < 0) goto error; /* set up group creation property list */ if ((gcpl_out = H5Pcreate(H5P_GROUP_CREATE)) < 0) goto error; if (H5Pset_link_creation_order(gcpl_out, crt_order_flags) < 0) goto error; /*------------------------------------------------------------------------- * the root is a special case, we get an ID for the root group * and copy its attributes using that ID *------------------------------------------------------------------------- */ if (HDstrcmp(travt->objs[i].name, "/") == 0) { if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) goto error; } else { if (options->grp_compact > 0 || options->grp_indexed > 0) { if (H5Pset_link_phase_change(gcpl_out, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0) goto error; } if ((grp_out = H5Gcreate2(fidout, travt->objs[i].name, H5P_DEFAULT, gcpl_out, H5P_DEFAULT)) < 0) goto error; } /*------------------------------------------------------------------------- * copy attrs *------------------------------------------------------------------------- */ if (copy_attr(grp_in, grp_out, &named_dt_head, travt, options) < 0) goto error; if (H5Pclose(gcpl_out) < 0) goto error; if (H5Pclose(gcpl_in) < 0) goto error; if (H5Gclose(grp_out) < 0) goto error; if (H5Gclose(grp_in) < 0) goto error; break; /*------------------------------------------------------------------------- * H5TRAV_TYPE_DATASET *------------------------------------------------------------------------- */ case H5TRAV_TYPE_DATASET: 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) goto error; if ((ftype_id = H5Dget_type(dset_in)) < 0) goto error; if (H5T_REFERENCE == H5Tget_class(ftype_id)) is_ref = 1; /* Check if the datatype is committed */ if ((is_named = H5Tcommitted(ftype_id)) < 0) goto error; if (is_named) if ((wtype_id = copy_named_datatype(ftype_id, fidout, &named_dt_head, travt, options)) < 0) goto error; 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 || is_named) { 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_in = H5Dget_create_plist(dset_in)) < 0) goto error; if ((dcpl_out = H5Pcopy(dcpl_in)) < 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; if (H5Dget_space_status(dset_in, &space_status) < 0) goto error; 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) goto error; /* 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) goto error; } /* 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 *------------------------------------------------------------------------- */ 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_in, H5P_DEFAULT)) < 0) goto error; 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, dset_in, wtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf); CHECK_H5DRW_ERROR(H5Dwrite, 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) 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 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) goto error; 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) goto error; if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0) goto error; } 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, dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf); CHECK_H5DRW_ERROR(H5Dwrite, 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( " \n", travt->objs[i].name, (int) options->min_comp); if (has_filter && apply_f == 0) printf( " \n", travt->objs[i].name); } /* verbose */ /*------------------------------------------------------------------------- * copy attrs *------------------------------------------------------------------------- */ if (copy_attr(dset_in, dset_out, &named_dt_head, travt, 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_in) < 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, &named_dt_head, travt, 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; /* Copy the datatype anonymously */ if ((type_out = copy_named_datatype(type_in, fidout, &named_dt_head, travt, options)) < 0) goto error; /* Link in to group structure */ if (H5Lcreate_hard(type_out, ".", fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0) goto error; /*------------------------------------------------------------------------- * copy attrs *------------------------------------------------------------------------- */ if (copy_attr(type_in, type_out, &named_dt_head, travt, 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 */ /* Finalize (link) the stack of named datatypes (if any) */ named_datatype_free(&named_dt_head, 0); return 0; error: 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 -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; 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 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.) */ HDassert(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 */ 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 status; } /*------------------------------------------------------------------------- * 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 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"); goto done; } if(H5Pget_userblock(fcpl, &ub_size) < 0) { error_msg("failed to retrieve userblock size\n"); goto done; } if(H5Pclose(fcpl) < 0) { error_msg("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; } #endif