diff options
Diffstat (limited to 'tools/h5repack/h5repack_copy.c')
| -rw-r--r-- | tools/h5repack/h5repack_copy.c | 234 |
1 files changed, 117 insertions, 117 deletions
diff --git a/tools/h5repack/h5repack_copy.c b/tools/h5repack/h5repack_copy.c index 77c03d2..f95db63 100644 --- a/tools/h5repack/h5repack_copy.c +++ b/tools/h5repack/h5repack_copy.c @@ -55,7 +55,7 @@ static hid_t copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named trav_table_t *travt, pack_opt_t *options); static int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err); static int copy_user_block(const char *infile, const char *outfile, hsize_t size); -#if defined (H5REPACK_DEBUG_USER_BLOCK) +#if defined (H5REPACK_DEBUG_USER_BLOCK) static void print_user_block(const char *filename, hid_t fid); #endif @@ -98,7 +98,7 @@ int copy_objects(const char* fnamein, * open input file *------------------------------------------------------------------------- */ - if((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t)0)) < 0) + if((fidin = h5tools_fopen(fnamein, H5F_ACC_RDONLY, H5P_DEFAULT, NULL, NULL, (size_t)0)) < 0) { error_msg(progname, "<%s>: %s\n", fnamein, H5FOPENERROR ); goto out; @@ -108,17 +108,17 @@ int copy_objects(const char* fnamein, { hid_t fcpl_in; /* file creation property list ID for input file */ - if((fcpl_in = H5Fget_create_plist(fidin)) < 0) + if((fcpl_in = H5Fget_create_plist(fidin)) < 0) { error_msg(progname, "failed to retrieve file creation property list\n"); goto out; - } + } - if(H5Pget_userblock(fcpl_in, &ub_size) < 0) + if(H5Pget_userblock(fcpl_in, &ub_size) < 0) { error_msg(progname, "failed to retrieve userblock size\n"); goto out; - } + } if(!options->fs_strategy) { @@ -138,49 +138,49 @@ int copy_objects(const char* fnamein, } } - if(H5Pclose(fcpl_in) < 0) + if(H5Pclose(fcpl_in) < 0) { error_msg(progname, "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) + if(options->latest || ub_size > 0) { /* Create file creation property list */ - if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) + if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { error_msg(progname, "fail to create a file creation property list\n"); goto out; - } + } if(ub_size > 0) { - if(H5Pset_userblock(fcpl, ub_size) < 0) + if(H5Pset_userblock(fcpl, ub_size) < 0) { error_msg(progname, "failed to set non-default userblock size\n"); goto out; - } + } } - if(options->latest) + 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) + if(H5Pset_link_phase_change(fcpl, (unsigned)options->grp_compact, (unsigned)options->grp_indexed) < 0) { error_msg(progname, "fail to adjust group creation parameters for root group\n"); goto out; - } + } - for(i = 0; i < 5; i++) + for(i = 0; i < 5; i++) { - if(options->msg_size[i] > 0) + if(options->msg_size[i] > 0) { - switch(i) + switch(i) { case 0: mesg_type_flags[nindex] = H5O_SHMESG_SDSPACE_FLAG; @@ -210,16 +210,16 @@ int copy_objects(const char* fnamein, } /* end if */ } /* end for */ - if(nindex > 0) + if(nindex > 0) { - if(H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) + if(H5Pset_shared_mesg_nindexes(fcpl, nindex) < 0) { error_msg(progname, "fail to set the number of shared object header message indexes\n"); goto out; - } + } /* msg_size[0]=dataspace, 1=datatype, 2=file value, 3=filter pipleline, 4=attribute */ - for(i = 0; i < (nindex - 1); i++) + for(i = 0; i < (nindex - 1); i++) { if(H5Pset_shared_mesg_index(fcpl, i, mesg_type_flags[i], min_mesg_sizes[i]) < 0) { error_msg(progname, "fail to configure the specified shared object header message index\n"); @@ -229,13 +229,13 @@ int copy_objects(const char* fnamein, } /* if (nindex>0) */ /* Create file access property list */ - if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) + if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { error_msg(progname, "Could not create file access property list\n"); goto out; } /* end if */ - if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) + if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) { error_msg(progname, "Could not set property for using latest version of the format\n"); goto out; @@ -246,7 +246,7 @@ int copy_objects(const char* fnamein, -#if defined (H5REPACK_DEBUG_USER_BLOCK) +#if defined (H5REPACK_DEBUG_USER_BLOCK) print_user_block(fnamein,fidin); #endif @@ -262,11 +262,11 @@ int copy_objects(const char* fnamein, if(fcpl != H5P_DEFAULT) { /* set user block size */ - if(H5Pset_userblock(fcpl, options->ublock_size) < 0) + if(H5Pset_userblock(fcpl, options->ublock_size) < 0) { error_msg(progname, "failed to set userblock size\n"); goto out; - } + } } @@ -274,18 +274,18 @@ int copy_objects(const char* fnamein, { /* create a file creation property list */ - if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) + if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { error_msg(progname, "fail to create a file creation property list\n"); goto out; - } + } /* set user block size */ - if(H5Pset_userblock(fcpl, options->ublock_size) < 0) + if(H5Pset_userblock(fcpl, options->ublock_size) < 0) { error_msg(progname, "failed to set userblock size\n"); goto out; - } + } } @@ -318,11 +318,11 @@ int copy_objects(const char* fnamein, { /* create a file access property list */ - if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) + if ((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0) { error_msg(progname, "Could not create file access property list\n"); goto out; - } + } if (H5Pset_alignment(fapl, options->threshold, options->alignment) < 0) { @@ -330,7 +330,7 @@ int copy_objects(const char* fnamein, goto out; } - } + } } @@ -338,27 +338,27 @@ int copy_objects(const char* fnamein, if(fcpl != H5P_DEFAULT) { /* set file space strategy and free space threshold */ - if(H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0) + if(H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0) { error_msg(progname, "failed to set file space strategy & threshold\n"); goto out; - } + } } else { /* create a file creation property list */ - if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) + if((fcpl = H5Pcreate(H5P_FILE_CREATE)) < 0) { error_msg(progname, "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) + if(H5Pset_file_space(fcpl, options->fs_strategy, options->fs_threshold) < 0) { error_msg(progname, "failed to set file space strategy & threshold \n"); goto out; - } + } } /*------------------------------------------------------------------------- @@ -371,11 +371,11 @@ int copy_objects(const char* fnamein, printf("Making file <%s>...\n",fnameout); - if((fidout = H5Fcreate(fnameout,H5F_ACC_TRUNC, fcpl, fapl)) < 0) + if((fidout = H5Fcreate(fnameout,H5F_ACC_TRUNC, fcpl, fapl)) < 0) { error_msg(progname, "<%s>: Could not create file\n", fnameout ); goto out; - } + } /*------------------------------------------------------------------------- @@ -383,7 +383,7 @@ int copy_objects(const char* fnamein, *------------------------------------------------------------------------- */ if ( options->ublock_size > 0 ) - { + { if ( copy_user_block( options->ublock_filename, fnameout, options->ublock_size) < 0 ) { error_msg(progname, "Could not copy user block. Exiting...\n"); @@ -408,7 +408,7 @@ int copy_objects(const char* fnamein, * do the copy *------------------------------------------------------------------------- */ - if(do_copy_objects(fidin, fidout, travt, options) < 0) + if(do_copy_objects(fidin, fidout, travt, options) < 0) { error_msg(progname, "<%s>: Could not copy data to: %s\n", fnamein, fnameout); goto out; @@ -419,11 +419,11 @@ int copy_objects(const char* fnamein, * and create hard links *------------------------------------------------------------------------- */ - if ( do_copy_refobjs(fidin, fidout, travt, options) < 0 ) + if ( do_copy_refobjs(fidin, fidout, travt, options) < 0 ) { printf("h5repack: <%s>: Could not copy data to: %s\n", fnamein, fnameout); goto out; - } + } /*------------------------------------------------------------------------- * close @@ -466,7 +466,7 @@ int copy_objects(const char* fnamein, */ out: - H5E_BEGIN_TRY + H5E_BEGIN_TRY { H5Pclose(fapl); H5Pclose(fcpl); @@ -490,7 +490,7 @@ out: * * Date: October, 23, 2003 * -* Modifications: +* Modifications: * * July 2004: Introduced the extra EC or NN option for SZIP * @@ -502,47 +502,47 @@ out: * 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 +* 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 +* 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 +* 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 +* 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 +* 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, +* 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 +* 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 +* 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. +* 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 * @@ -591,18 +591,18 @@ int do_copy_objects(hid_t fidin, *------------------------------------------------------------------------- */ - if (options->verbose) + if (options->verbose) { printf("-----------------------------------------\n"); printf(" Type Filter (Compression) Name\n"); printf("-----------------------------------------\n"); } - for ( i = 0; i < travt->nobjs; i++) + for ( i = 0; i < travt->nobjs; i++) { buf = NULL; - switch ( travt->objs[i].type ) + switch ( travt->objs[i].type ) { case H5TRAV_TYPE_UNKNOWN: @@ -644,7 +644,7 @@ int do_copy_objects(hid_t fidin, * and copy its attributes using that ID *------------------------------------------------------------------------- */ - if(HDstrcmp(travt->objs[i].name, "/") == 0) + if(HDstrcmp(travt->objs[i].name, "/") == 0) { if ((grp_out = H5Gopen2(fidout, "/", H5P_DEFAULT)) < 0) goto error; @@ -653,7 +653,7 @@ int do_copy_objects(hid_t fidin, else { - if (options->grp_compact>0 || options->grp_indexed>0) + 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; @@ -699,7 +699,7 @@ int do_copy_objects(hid_t fidin, /* check if filters were requested for individual objects */ for( u = 0; u < options->op_tbl->nelems; u++) { - int k; + int k; for( k = 0; k < options->op_tbl->objs[u].nfilters; k++) { @@ -740,11 +740,11 @@ int do_copy_objects(hid_t fidin, * otherwise we do a copy using H5Ocopy *------------------------------------------------------------------------- */ - if ( options->op_tbl->nelems || - options->all_filter == 1 || - options->all_layout == 1 || + if ( options->op_tbl->nelems || + options->all_filter == 1 || + options->all_layout == 1 || is_ref || - is_named) + is_named) { int j; @@ -809,7 +809,7 @@ int do_copy_objects(hid_t fidin, apply_s=0; /* apply the filter */ - if (apply_s) + if (apply_s) { if (apply_filters(travt->objs[i].name, rank, @@ -831,7 +831,7 @@ int do_copy_objects(hid_t fidin, 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(dset_out == FAIL) { if(options->verbose) printf(" warning: could not create dataset <%s>. Applying original settings\n", @@ -858,7 +858,7 @@ int do_copy_objects(hid_t fidin, goto error; if (H5Dwrite(dset_out,wtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf) < 0) goto error; - } + } else /* possibly not enough memory, read/write by hyperslabs */ { @@ -879,7 +879,7 @@ int do_copy_objects(hid_t fidin, hsize_t hs_size[H5S_MAX_RANK]; /*size this pass */ hsize_t hs_nelmts; /*elements in request */ hsize_t zero[8]; /*vector of zeros */ - int k; + int k; /* check if we have VL data in the dataset's datatype */ if (H5Tdetect_class(wtype_id, H5T_VLEN) == TRUE) @@ -891,7 +891,7 @@ int do_copy_objects(hid_t fidin, */ sm_nbytes = p_type_nbytes; - for (k = rank; k > 0; --k) + for (k = rank; k > 0; --k) { hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes; if ( size == 0) /* datum size > H5TOOLS_BUFSIZE */ @@ -909,12 +909,12 @@ int do_copy_objects(hid_t fidin, memset(hs_offset, 0, sizeof hs_offset); memset(zero, 0, sizeof zero); - for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) + for (elmtno = 0; elmtno < p_nelmts; elmtno += hs_nelmts) { /* calculate the hyperslab size */ - if (rank > 0) + if (rank > 0) { - for (k = 0, hs_nelmts = 1; k < rank; k++) + for (k = 0, hs_nelmts = 1; k < rank; k++) { hs_size[k] = MIN(dims[k] - hs_offset[k], sm_size[k]); hs_nelmts *= hs_size[k]; @@ -924,8 +924,8 @@ int do_copy_objects(hid_t fidin, goto error; if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0) goto error; - } - else + } + else { H5Sselect_all(f_space_id); H5Sselect_all(sm_space); @@ -933,9 +933,9 @@ int do_copy_objects(hid_t fidin, } /* rank */ /* read/write */ - if (H5Dread(dset_in, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) + if (H5Dread(dset_in, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) goto error; - if (H5Dwrite(dset_out, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) + if (H5Dwrite(dset_out, wtype_id, sm_space, f_space_id, H5P_DEFAULT, sm_buf) < 0) goto error; /* reclaim any VL memory, if necessary */ @@ -943,7 +943,7 @@ int do_copy_objects(hid_t fidin, H5Dvlen_reclaim(wtype_id, sm_space, H5P_DEFAULT, sm_buf); /* calculate the next hyperslab offset */ - for (k = rank, carry = 1; k > 0 && carry; --k) + for (k = rank, carry = 1; k > 0 && carry; --k) { hs_offset[k - 1] += hs_size[k - 1]; if (hs_offset[k - 1] == dims[k - 1]) @@ -967,7 +967,7 @@ int do_copy_objects(hid_t fidin, * amount of compression used *------------------------------------------------------------------------- */ - if (options->verbose) + if (options->verbose) { double ratio=0; @@ -986,7 +986,7 @@ int do_copy_objects(hid_t fidin, else print_dataset_info(dcpl_id,travt->objs[i].name,ratio,0); - /* print a message that the filter was not applied + /* print a message that the filter was not applied (in case there was a filter) */ if ( has_filter && apply_s == 0 ) @@ -1037,16 +1037,16 @@ int do_copy_objects(hid_t fidin, * we do not have request for filter/chunking use H5Ocopy instead *------------------------------------------------------------------------- */ - else + else { hid_t pid; /* create property to pass copy options */ - if ( (pid = H5Pcreate(H5P_OBJECT_COPY)) < 0) + 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) + if(H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0) goto error; /*------------------------------------------------------------------------- @@ -1059,7 +1059,7 @@ int do_copy_objects(hid_t fidin, 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 */ + H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */ goto error; /* close property */ @@ -1320,7 +1320,7 @@ int copy_attr(hid_t loc_in, { ; } - else + else { /*------------------------------------------------------------------------- * read to memory @@ -1626,13 +1626,13 @@ error: /*------------------------------------------------------------------------- -* Function: copy_user_block +* Function: copy_user_block * * Purpose: copy user block from one file to another * * Return: 0, ok, -1 no * -* Programmer: Peter Cao +* Programmer: Peter Cao * * Date: October, 25, 2007 * @@ -1706,26 +1706,26 @@ done: if(outfid > 0) HDclose(outfid); - return status; + return status; } /*------------------------------------------------------------------------- -* Function: print_user_block +* Function: print_user_block * * Purpose: print user block * * Return: 0, ok, -1 no * -* Programmer: Pedro Vicente +* Programmer: Pedro Vicente * * Date: August, 20, 2008 * *------------------------------------------------------------------------- */ -#if defined (H5REPACK_DEBUG_USER_BLOCK) -static +#if defined (H5REPACK_DEBUG_USER_BLOCK) +static void print_user_block(const char *filename, hid_t fid) { int fh; /* file handle */ @@ -1734,27 +1734,27 @@ void print_user_block(const char *filename, hid_t fid) hid_t fcpl; /* file creation property list ID for HDF5 file */ int i; - /* get user block size */ - if(( fcpl = H5Fget_create_plist(fid)) < 0) + /* get user block size */ + if(( fcpl = H5Fget_create_plist(fid)) < 0) { error_msg(progname, "failed to retrieve file creation property list\n"); goto done; - } + } - if(H5Pget_userblock(fcpl, &ub_size) < 0) + if(H5Pget_userblock(fcpl, &ub_size) < 0) { error_msg(progname, "failed to retrieve userblock size\n"); goto done; - } + } - if(H5Pclose(fcpl) < 0) + if(H5Pclose(fcpl) < 0) { error_msg(progname, "failed to close property list\n"); goto done; - } + } /* open file */ - if((fh = HDopen(filename, O_RDONLY, 0)) < 0) + if((fh = HDopen(filename, O_RDONLY, 0)) < 0) { goto done; } @@ -1762,7 +1762,7 @@ void print_user_block(const char *filename, hid_t fid) size = ub_size; /* read file */ - while(size > 0) + while(size > 0) { ssize_t nread; /* # of bytes read */ char rbuf[USERBLOCK_XFER_SIZE]; /* buffer for reading */ @@ -1773,7 +1773,7 @@ void print_user_block(const char *filename, hid_t fid) else nread = HDread(fh, rbuf, (size_t)size); - for(i = 0; i < nread; i++) + for(i = 0; i < nread; i++) { printf("%c ", rbuf[i]); @@ -1781,22 +1781,22 @@ void print_user_block(const char *filename, hid_t fid) } printf("\n"); - if(nread < 0) + if(nread < 0) { goto done; - } + } /* update size of userblock left to transfer */ size -= nread; - } + } done: if(fh > 0) HDclose(fh); - return; + return; } #endif |