diff options
Diffstat (limited to 'src/H5Dio.c')
| -rw-r--r-- | src/H5Dio.c | 363 |
1 files changed, 321 insertions, 42 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index b494596..9b0102f 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -77,6 +77,12 @@ static herr_t H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, hid_t src_id, hid_t dst_id, const void *buf); +static herr_t H5D_compound_opt_read(hsize_t nelmts, const H5S_t *mem_space, + H5S_sel_iter_t *iter, const H5D_dxpl_cache_t *dxpl_cache, + hid_t src_id, hid_t dst_id, H5T_subset_t subset, void *data_buf, + void *user_buf/*out*/); +static herr_t H5D_compound_opt_write(hsize_t nelmts, hid_t src_id, hid_t dst_id, + void *data_buf); #ifdef H5_HAVE_PARALLEL static herr_t H5D_ioinfo_term(H5D_io_info_t *io_info); @@ -116,6 +122,13 @@ H5FL_BLK_DEFINE(type_conv); /* Declare a free list to manage the H5D_chunk_info_t struct */ H5FL_DEFINE_STATIC(H5D_chunk_info_t); +/* Declare a free list to manage sequences of size_t */ +H5FL_SEQ_DEFINE_STATIC(size_t); + +/* Declare a free list to manage sequences of hsize_t */ +H5FL_SEQ_DEFINE_STATIC(hsize_t); + + /*-------------------------------------------------------------------------- NAME @@ -1167,6 +1180,23 @@ H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts, if (n!=smine_nelmts) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed") + /* If the source and destination are compound types and subset of each other + * and no conversion is needed, copy the data directly into user's buffer and + * bypass the rest of steps. This optimization is for Chicago company */ + if(H5T_SUBSET_SRC==H5T_path_compound_subset(tpath)) { + if(H5D_compound_opt_read(smine_nelmts, mem_space, &mem_iter, dxpl_cache, + src_id, dst_id, H5T_SUBSET_SRC, tconv_buf, buf /*out*/)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed") + + continue; + } else if(H5T_SUBSET_DST==H5T_path_compound_subset(tpath)) { + if(H5D_compound_opt_read(smine_nelmts, mem_space, &mem_iter, dxpl_cache, + src_id, dst_id, H5T_SUBSET_DST, tconv_buf, buf /*out*/)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed") + + continue; + } + if (H5T_BKG_YES==need_bkg) { #ifdef H5S_DEBUG H5_timer_begin(&timer); @@ -1421,33 +1451,44 @@ H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts, if (n!=smine_nelmts) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed") - if (H5T_BKG_YES==need_bkg) { + /* If the source and destination are compound types and the destination is + * is a subset of the source and no conversion is needed, copy the data + * directly into user's buffer and bypass the rest of steps. If the source + * is a subset of the destination, the optimization is done in conversion + * function H5T_conv_struct_opt to protect the background data. This + * optimization is for Chicago company */ + if(H5T_SUBSET_DST==H5T_path_compound_subset(tpath)) { + if(H5D_compound_opt_write(smine_nelmts, src_id, dst_id, tconv_buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed") + } else { + if (H5T_BKG_YES==need_bkg) { #ifdef H5S_DEBUG - H5_timer_begin(&timer); + H5_timer_begin(&timer); #endif - n = H5D_select_fgath(io_info, - file_space, &bkg_iter, smine_nelmts, - bkg_buf/*out*/); + n = H5D_select_fgath(io_info, + file_space, &bkg_iter, smine_nelmts, + bkg_buf/*out*/); #ifdef H5S_DEBUG - H5_timer_end(&(io_info->stats->stats[0].bkg_timer), &timer); - io_info->stats->stats[0].bkg_nbytes += n * dst_type_size; - io_info->stats->stats[0].bkg_ncalls++; + H5_timer_end(&(io_info->stats->stats[0].bkg_timer), &timer); + io_info->stats->stats[0].bkg_nbytes += n * dst_type_size; + io_info->stats->stats[0].bkg_ncalls++; #endif - if (n!=smine_nelmts) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed") - } /* end if */ + if (n!=smine_nelmts) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed") + } /* end if */ - /* - * Perform datatype conversion. - */ - if(H5T_convert(tpath, src_id, dst_id, smine_nelmts, (size_t)0, (size_t)0, tconv_buf, bkg_buf, io_info->dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed") + /* + * Perform datatype conversion. + */ + if(H5T_convert(tpath, src_id, dst_id, smine_nelmts, (size_t)0, (size_t)0, tconv_buf, bkg_buf, io_info->dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed") - /* Do the data transform after the type conversion (since we're using dataset->shared->type). */ - if(!H5Z_xform_noop(dxpl_cache->data_xform_prop)) - if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, dataset->shared->type) < 0) + /* Do the data transform after the type conversion (since we're using dataset->shared->type). */ + if(!H5Z_xform_noop(dxpl_cache->data_xform_prop)) + if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, dataset->shared->type) < 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform") + } /* * Scatter the data out to the file. @@ -1455,9 +1496,8 @@ H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts, #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif - status = H5D_select_fscat(io_info, - file_space, &file_iter, smine_nelmts, - tconv_buf); + status = H5D_select_fscat(io_info, file_space, &file_iter, smine_nelmts, + tconv_buf); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[0].scat_timer), &timer); io_info->stats->stats[0].scat_nbytes += smine_nelmts * dst_type_size; @@ -1723,6 +1763,23 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, if(n != smine_nelmts) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed") + /* If the source and destination are compound types and subset of each other + * and no conversion is needed, copy the data directly into user's buffer and + * bypass the rest of steps. This optimization is for Chicago company */ + if(H5T_SUBSET_SRC==H5T_path_compound_subset(tpath)) { + if(H5D_compound_opt_read(smine_nelmts, chunk_info->mspace, &mem_iter, dxpl_cache, + src_id, dst_id, H5T_SUBSET_SRC, tconv_buf, buf /*out*/)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed") + + continue; + } else if(H5T_SUBSET_DST==H5T_path_compound_subset(tpath)) { + if(H5D_compound_opt_read(smine_nelmts, chunk_info->mspace, &mem_iter, dxpl_cache, + src_id, dst_id, H5T_SUBSET_DST, tconv_buf, buf /*out*/)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed") + + continue; + } + if(H5T_BKG_YES == need_bkg) { #ifdef H5S_DEBUG H5_timer_begin(&timer); @@ -2041,33 +2098,43 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, if (n!=smine_nelmts) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed") - if (H5T_BKG_YES==need_bkg) { + /* If the source and destination are compound types and the destination is + * is a subset of the source and no conversion is needed, copy the data + * directly into user's buffer and bypass the rest of steps. If the source + * is a subset of the destination, the optimization is done in conversion + * function H5T_conv_struct_opt to protect the background data. This + * optimization is for Chicago company */ + if(H5T_SUBSET_DST==H5T_path_compound_subset(tpath)) { + if(H5D_compound_opt_write(smine_nelmts, src_id, dst_id, tconv_buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed") + } else { + if (H5T_BKG_YES==need_bkg) { #ifdef H5S_DEBUG - H5_timer_begin(&timer); + H5_timer_begin(&timer); #endif - n = H5D_select_fgath(io_info, - chunk_info->fspace, &bkg_iter, smine_nelmts, - bkg_buf/*out*/); + n = H5D_select_fgath(io_info, chunk_info->fspace, &bkg_iter, smine_nelmts, + bkg_buf/*out*/); #ifdef H5S_DEBUG - H5_timer_end(&(io_info->stats->stats[0].bkg_timer), &timer); - io_info->stats->stats[0].bkg_nbytes += n * dst_type_size; - io_info->stats->stats[0].bkg_ncalls++; + H5_timer_end(&(io_info->stats->stats[0].bkg_timer), &timer); + io_info->stats->stats[0].bkg_nbytes += n * dst_type_size; + io_info->stats->stats[0].bkg_ncalls++; #endif - if (n!=smine_nelmts) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed") - } /* end if */ + if (n!=smine_nelmts) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed") + } /* end if */ - /* - * Perform datatype conversion. - */ - if(H5T_convert(tpath, src_id, dst_id, smine_nelmts, (size_t)0, (size_t)0, tconv_buf, bkg_buf, io_info->dxpl_id) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed") + /* + * Perform datatype conversion. + */ + if(H5T_convert(tpath, src_id, dst_id, smine_nelmts, (size_t)0, (size_t)0, tconv_buf, bkg_buf, io_info->dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "datatype conversion failed") - /* Do the data transform after the type conversion (since we're using dataset->shared->type) */ - if(!H5Z_xform_noop(dxpl_cache->data_xform_prop)) - if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, dataset->shared->type) < 0) - HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform") + /* Do the data transform after the type conversion (since we're using dataset->shared->type) */ + if(!H5Z_xform_noop(dxpl_cache->data_xform_prop)) + if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, dataset->shared->type) < 0) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform") + } /* * Scatter the data out to the file. @@ -2138,6 +2205,218 @@ done: /*------------------------------------------------------------------------- + * Function: H5D_compound_opt_read + * + * Purpose: A shortcut optimization for the Chicago company for + * a special optimization case when the source and + * destination members are a subset of each other, and + * the order is the same, and no conversion is needed. + * For example: + * struct source { struct destination { + * TYPE1 A; --> TYPE1 A; + * TYPE2 B; --> TYPE2 B; + * TYPE3 C; --> TYPE3 C; + * }; TYPE4 D; + * TYPE5 E; + * }; + * or + * struct destination { struct source { + * TYPE1 A; --> TYPE1 A; + * TYPE2 B; --> TYPE2 B; + * TYPE3 C; --> TYPE3 C; + * }; TYPE4 D; + * TYPE5 E; + * }; + * The optimization is simply moving data to the appropriate + * places in the buffer. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * 11 June 2007 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_compound_opt_read(hsize_t nelmts, const H5S_t *space, + H5S_sel_iter_t *iter, const H5D_dxpl_cache_t *dxpl_cache, + hid_t src_id, hid_t dst_id, H5T_subset_t subset, + void *data_buf, void *user_buf/*out*/) +{ + uint8_t *dbuf = (uint8_t *)data_buf; /*cast for pointer arithmetic */ + uint8_t *ubuf = (uint8_t *)user_buf; /*cast for pointer arithmetic */ + uint8_t *xdbuf; + uint8_t *xubuf; + + hsize_t _off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */ + hsize_t *off=NULL; /* Pointer to sequence offsets */ + size_t _len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */ + size_t *len=NULL; /* Pointer to sequence lengths */ + size_t nseq; /* Number of sequences generated */ + size_t curr_off; /* offset of bytes left to process in sequence */ + size_t curr_seq; /* Current sequence being processed */ + size_t curr_len; /* Length of bytes left to process in sequence */ + size_t curr_nelmts; /* number of elements to process in sequence */ + size_t i; + + H5T_t *src, *dst; + size_t src_stride, dst_stride, type_size; + size_t elmtno; /*element counter */ + + herr_t ret_value = SUCCEED; /*return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_compound_opt_read) + + /* Check args */ + assert (data_buf); + assert (user_buf); + assert (space); + assert (iter); + assert (nelmts>0); + + /* Allocate the vector I/O arrays */ + if(dxpl_cache->vec_size != H5D_IO_VECTOR_SIZE) { + if((len = H5FL_SEQ_MALLOC(size_t,dxpl_cache->vec_size))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array"); + if((off = H5FL_SEQ_MALLOC(hsize_t,dxpl_cache->vec_size))==NULL) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array"); + } /* end if */ + else { + len=_len; + off=_off; + } /* end else */ + + if (NULL == (src = H5I_object(src_id)) || NULL == (dst = H5I_object(dst_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); + + src_stride = H5T_get_size(src); + dst_stride = H5T_get_size(dst); + + if(H5T_SUBSET_SRC == subset) + type_size = src_stride; + else if(H5T_SUBSET_DST == subset) + type_size = dst_stride; + + xdbuf = dbuf; + + /* Loop until all elements are written */ + while(nelmts>0) { + /* Get list of sequences for selection to write */ + if(H5S_SELECT_GET_SEQ_LIST(space,0,iter,dxpl_cache->vec_size,nelmts,&nseq,&elmtno,off,len)<0) + HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, 0, "sequence length generation failed"); + + /* Loop, while sequences left to process */ + for(curr_seq=0; curr_seq<nseq; curr_seq++) { + /* Get the number of bytes and offset in sequence */ + curr_len=len[curr_seq]; + curr_off=off[curr_seq]; + + /* Decide the number of elements and position in the buffer. */ + curr_nelmts = curr_len/dst_stride; + xubuf = ubuf + curr_off; + + /* Copy the data into the right place. */ + for(i=0; i<curr_nelmts; i++) { + HDmemmove(xubuf, xdbuf, type_size); + + /* Update pointers */ + xdbuf += src_stride; + xubuf += dst_stride; + } + + } /* end for */ + + /* Decrement number of elements left to process */ + nelmts -= elmtno; + } /* end while */ + +done: + if(dxpl_cache->vec_size != H5D_IO_VECTOR_SIZE) { + if(len!=NULL) + H5FL_SEQ_FREE(size_t,len); + if(off!=NULL) + H5FL_SEQ_FREE(hsize_t,off); + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_compound_opt_read() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_compound_opt_write + * + * Purpose: A shortcut optimization for the Chicago company for + * a special optimization case when the source and + * destination members are a subset of each other, and + * the order is the same, and no conversion is needed. + * For example: + * struct source { struct destination { + * TYPE1 A; --> TYPE1 A; + * TYPE2 B; --> TYPE2 B; + * TYPE3 C; --> TYPE3 C; + * }; TYPE4 D; + * TYPE5 E; + * }; + * or + * struct destination { struct source { + * TYPE1 A; --> TYPE1 A; + * TYPE2 B; --> TYPE2 B; + * TYPE3 C; --> TYPE3 C; + * }; TYPE4 D; + * TYPE5 E; + * }; + * The optimization is simply moving data to the appropriate + * places in the buffer. + * + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * 11 June 2007 + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_compound_opt_write(hsize_t nelmts, hid_t src_id, hid_t dst_id, void *data_buf) +{ + uint8_t *dbuf = (uint8_t *)data_buf; /*cast for pointer arithmetic */ + uint8_t *xsbuf, *xdbuf; + size_t i; + H5T_t *src, *dst; + size_t src_stride, dst_stride; + herr_t ret_value = SUCCEED; /*return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_compound_opt_write) + + /* Check args */ + assert (data_buf); + assert (nelmts>0); + + if (NULL == (src = H5I_object(src_id)) || NULL == (dst = H5I_object(dst_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); + + src_stride = H5T_get_size(src); + dst_stride = H5T_get_size(dst); + + xsbuf = dbuf; + xdbuf = dbuf; + + /* Loop until all elements are written */ + for(i=0; i<nelmts; i++) { + HDmemmove(xdbuf, xsbuf, dst_stride); + + /* Update pointers */ + xsbuf += src_stride; + xdbuf += dst_stride; + } + +done: + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_compound_opt_write() */ + + +/*------------------------------------------------------------------------- * Function: H5D_create_chunk_map * * Purpose: Creates the mapping between elements selected in each chunk |