diff options
Diffstat (limited to 'tools/h5repack/h5repack_copy.c')
| -rw-r--r-- | tools/h5repack/h5repack_copy.c | 3239 |
1 files changed, 1584 insertions, 1655 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c index 02337fd..521b9bd 100644 --- a/tools/h5repack/h5repack_copy.c +++ b/tools/h5repack/h5repack_copy.c @@ -1,36 +1,36 @@ /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * -* Copyright by The HDF Group. * -* Copyright by the Board of Trustees of the University of Illinois. * -* All rights reserved. * -* * -* This file is part of HDF5. The full HDF5 copyright notice, including * -* terms governing use, modification, and redistribution, is contained in * -* the files COPYING and Copyright.html. COPYING can be found at the root * -* of the source code distribution tree; Copyright.html can be found at the * -* root level of an installed copy of the electronic HDF5 document set and * -* is linked from the top-level documents page. It can also be found at * -* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * -* access to either file, you may request a copy from help@hdfgroup.org. * -* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + * Copyright by The HDF Group. * + * Copyright by the Board of Trustees of the University of Illinois. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the files COPYING and Copyright.html. COPYING can be found at the root * + * of the source code distribution tree; Copyright.html can be found at the * + * root level of an installed copy of the electronic HDF5 document set and * + * is linked from the top-level documents page. It can also be found at * + * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * + * access to either file, you may request a copy from help@hdfgroup.org. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #include "h5repack.h" #include "h5tools.h" #include "h5tools_utils.h" /*------------------------------------------------------------------------- -* typedefs -*------------------------------------------------------------------------- -*/ + * typedefs + *------------------------------------------------------------------------- + */ /*------------------------------------------------------------------------- -* globals -*------------------------------------------------------------------------- -*/ + * globals + *------------------------------------------------------------------------- + */ /*------------------------------------------------------------------------- -* macros -*------------------------------------------------------------------------- -*/ + * macros + *------------------------------------------------------------------------- + */ /* size of buffer/# of bytes to xfer at a time when copying userblock */ #define USERBLOCK_XFER_SIZE 512 @@ -48,1701 +48,1630 @@ } \ } 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); + * 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); +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; +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(!options->fs_strategy) - { - if(H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) - { - error_msg("failed to retrieve file space strategy\n"); - goto out; - } - } - - if(!options->fs_threshold) - { - if(H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) - { - error_msg("failed to retrieve file space threshold\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 */ + * 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 (!options->fs_strategy) { + if (H5Pget_file_space(fcpl_in, &options->fs_strategy, NULL) < 0) { + error_msg("failed to retrieve file space strategy\n"); + goto out; + } + } + + if (!options->fs_threshold) { + if (H5Pget_file_space(fcpl_in, NULL, &options->fs_threshold) < 0) { + error_msg("failed to retrieve file space threshold\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); + 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; - } - } - - /*------------------------------------------------------------------------- - * 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"); - goto out; - } - } - - /* 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"); - 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 - *------------------------------------------------------------------------- - */ + /*------------------------------------------------------------------------- + * 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; + } + } + + /*------------------------------------------------------------------------- + * 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"); + goto out; + } + } + + /* 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"); + 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; + 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; + * 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; + 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 */ + * 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(" <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) - 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; + 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( + " <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) + 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; + 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]; + * 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]; + 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; + 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"); - HDstrcpy(strfilter,"\0"); + /* get information about input filters */ + if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0) + return; - /* get information about input filters */ - if((nfilters = H5Pget_nfilters(dcpl_id)) < 0) - return; + for (i = 0; i < nfilters; i++) { + cd_nelmts = NELMTS(cd_values); - 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); - filtn = H5Pget_filter2(dcpl_id, (unsigned)i, &filt_flags, &cd_nelmts, - cd_values, sizeof(f_objname), f_objname, NULL); + switch (filtn) { - switch(filtn) { - default: - break; + case H5Z_FILTER_NONE: + HDstrcat(strfilter, "NONE "); + break; - case H5Z_FILTER_DEFLATE: - HDstrcat(strfilter,"GZIP "); + case H5Z_FILTER_DEFLATE: + HDstrcat(strfilter, "GZIP "); #if defined (PRINT_DEBUG) - { - unsigned level=cd_values[0]; - sprintf(temp,"(%d)",level); - HDstrcat(strfilter,temp); - } + { + unsigned level=cd_values[0]; + sprintf(temp,"(%d)",level); + HDstrcat(strfilter,temp); + } #endif - break; + break; - case H5Z_FILTER_SZIP: - HDstrcat(strfilter,"SZIP "); + 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); + { + 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; - } /* 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); - } + 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 */ + * 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); + if (infid > 0) + HDclose(infid); + if (outfid > 0) + HDclose(outfid); - return status; + return status; } - - /*------------------------------------------------------------------------- -* Function: print_user_block -* -* Purpose: print user block -* -* Return: 0, ok, -1 no -* -* Programmer: Pedro Vicente -* -* Date: August, 20, 2008 -* -*------------------------------------------------------------------------- -*/ + * Function: print_user_block + * + * Purpose: print user block + * + * Return: 0, ok, -1 no + * + * Programmer: Pedro Vicente + * + * Date: August, 20, 2008 + * + *------------------------------------------------------------------------- + */ #if defined (H5REPACK_DEBUG_USER_BLOCK) static void print_user_block(const char *filename, hid_t fid) { - 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; - } + 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; -done: - if(fh > 0) - HDclose(fh); + /* 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; + return; } #endif |