diff options
Diffstat (limited to 'src/H5Dio.c')
| -rw-r--r-- | src/H5Dio.c | 153 |
1 files changed, 138 insertions, 15 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index 1bf5b04..7472921 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -821,10 +821,10 @@ H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts, } else #endif - { + { if((io_info->ops.read)(io_info, (size_t)nelmts, H5T_get_size(dataset->shared->type), file_space, mem_space, - (haddr_t)0, buf/*out*/) < 0) + (haddr_t)0, NULL, buf/*out*/) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "contiguous read failed "); } @@ -926,7 +926,7 @@ H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts, || (dataset->shared->layout.type == H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) || dataset->shared->dcpl_cache.efl.nused > 0 || dataset->shared->layout.type == H5D_COMPACT); - n = H5D_select_fgath(io_info, file_space, &file_iter, smine_nelmts, tconv_buf/*out*/); + n = H5D_select_fgath(io_info, file_space, &file_iter, smine_nelmts, (haddr_t)0, NULL, tconv_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[1].gath_timer), &timer); @@ -1096,7 +1096,7 @@ H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts, { if((io_info->ops.write)(io_info, (size_t)nelmts, H5T_get_size(dataset->shared->type), file_space, mem_space, - (haddr_t)0, buf/*out*/) < 0) + (haddr_t)0, NULL, buf/*out*/) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "contiguous write failed ") } @@ -1221,9 +1221,8 @@ H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts, #ifdef H5S_DEBUG 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, + (haddr_t)0, NULL, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[0].bkg_timer), &timer); @@ -1253,7 +1252,7 @@ H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts, H5_timer_begin(&timer); #endif status = H5D_select_fscat(io_info, file_space, &file_iter, smine_nelmts, - tconv_buf); + (haddr_t)0, NULL, 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; @@ -1297,6 +1296,12 @@ done: * Programmer: Raymond Lu * Thursday, April 10, 2003 * + * Modification: + * Raymond Lu + * 20 July 2007 + * Moved H5D_istore_lock and H5D_istore_unlock to this level + * from H5D_istore_readvv to avoid frequent lock and unlock + * and to improve performance. *------------------------------------------------------------------------- */ static herr_t @@ -1320,6 +1325,7 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, size_t request_nelmts; /*requested strip mine */ hsize_t smine_start; /*strip mine start loc */ size_t n, smine_nelmts; /*elements per strip */ + size_t accessed_bytes; /*total accessed size in a chunk */ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ hbool_t mem_iter_init = FALSE; /*memory selection iteration info has been initialized */ H5S_sel_iter_t bkg_iter; /*background iteration info*/ @@ -1330,6 +1336,10 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, uint8_t *tconv_buf = NULL; /*datatype conv buffer */ uint8_t *bkg_buf = NULL; /*background buffer */ H5D_storage_t store; /*union of EFL and chunk pointer in file space */ + void *chunk = NULL; + haddr_t chunk_addr; /* Chunk address on disk */ + H5D_istore_ud1_t udata; /*B-tree pass-through */ + unsigned idx_hint=0; /* Cache index hint */ herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_read) @@ -1383,11 +1393,27 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, store.chunk.offset = chunk_info->coords; store.chunk.index = chunk_info->index; + /* Load the chunk into cache and lock it. */ + chunk_addr = H5D_istore_get_addr(io_info, &udata); + + if (H5D_istore_if_load(dataset, chunk_addr)) { + if(NULL == (chunk = H5D_istore_lock(io_info, &udata, FALSE, &idx_hint))) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk") + } else + chunk = NULL; + /* Perform the actual read operation */ if((io_info->ops.read)(io_info, chunk_info->chunk_points, H5T_get_size(dataset->shared->type), chunk_info->fspace, - chunk_info->mspace, (haddr_t)0, buf) < 0) + chunk_info->mspace, chunk_addr, chunk, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, " chunked read failed") + + /* Release the cache lock on the chunk. */ + if (H5D_istore_if_load(dataset, chunk_addr)) { + accessed_bytes = chunk_info->chunk_points * H5T_get_size(dataset->shared->type); + if(H5D_istore_unlock(io_info, FALSE, idx_hint, chunk, accessed_bytes) < 0) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk") + } /* Advance to next chunk in list */ chunk_node = H5SL_next(chunk_node); @@ -1492,6 +1518,15 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, store.chunk.offset = chunk_info->coords; store.chunk.index = chunk_info->index; + /* Load the chunk into cache and lock it. */ + chunk_addr = H5D_istore_get_addr(io_info, &udata); + + if (H5D_istore_if_load(dataset, chunk_addr)) { + if(NULL == (chunk = H5D_istore_lock(io_info, &udata, FALSE, &idx_hint))) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk") + } else + chunk = NULL; + for (smine_start=0; smine_start<chunk_info->chunk_points; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ assert(H5S_SELECT_ITER_NELMTS(&file_iter)==(chunk_info->chunk_points-smine_start)); @@ -1509,7 +1544,14 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, HDassert(((dataset->shared->layout.type == H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr)) || (dataset->shared->layout.type == H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) || dataset->shared->dcpl_cache.efl.nused > 0 || dataset->shared->layout.type == H5D_COMPACT); - n = H5D_select_fgath(io_info, chunk_info->fspace, &file_iter, smine_nelmts, tconv_buf/*out*/); + + if(chunk) { + n = H5D_select_mgath(chunk, chunk_info->fspace, &file_iter, + smine_nelmts, dxpl_cache, tconv_buf/*out*/); + } else { + n = H5D_select_fgath(io_info, chunk_info->fspace, &file_iter, smine_nelmts, + (haddr_t)0, NULL, tconv_buf/*out*/); + } #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[1].gath_timer), &timer); @@ -1577,6 +1619,13 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "scatter failed") } /* end for */ + /* Release the cache lock on the chunk. */ + if (H5D_istore_if_load(dataset, chunk_addr)) { + accessed_bytes = chunk_info->chunk_points * H5T_get_size(dataset->shared->type); + if(H5D_istore_unlock(io_info, FALSE, idx_hint, chunk, accessed_bytes) < 0) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk") + } + /* Release selection iterators */ if(file_iter_init) { if(H5S_SELECT_ITER_RELEASE(&file_iter) < 0) @@ -1636,6 +1685,12 @@ done: * Programmer: Raymond Lu * Thursday, April 10, 2003 * + * Modification: + * Raymond Lu + * 20 July 2007 + * Moved H5D_istore_lock and H5D_istore_unlock to this level + * from H5D_istore_writevv to avoid frequent lock and unlock + * and to improve performance. *------------------------------------------------------------------------- */ static herr_t @@ -1657,6 +1712,7 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, size_t max_type_size; /* Size of largest source/destination type */ size_t target_size; /*desired buffer size */ size_t request_nelmts; /*requested strip mine */ + size_t accessed_bytes; /*total accessed size in a chunk */ hsize_t smine_start; /*strip mine start loc */ size_t n, smine_nelmts; /*elements per strip */ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ @@ -1669,7 +1725,11 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, uint8_t *tconv_buf = NULL; /*datatype conv buffer */ uint8_t *bkg_buf = NULL; /*background buffer */ H5D_storage_t store; /*union of EFL and chunk pointer in file space */ - + void *chunk = NULL; + haddr_t chunk_addr; /* Chunk address on disk */ + H5D_istore_ud1_t udata; /*B-tree pass-through */ + unsigned idx_hint=0; /* Cache index hint */ + hbool_t relax=TRUE; /* Whether whole chunk is selected */ herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_write) @@ -1681,6 +1741,16 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, /* Set dataset storage for I/O info */ io_info->store=&store; +#ifdef H5_HAVE_PARALLEL + /* Additional sanity checks when operating in parallel */ + if(IS_H5FD_MPI(dataset->oloc.file)) { + if (chunk_addr==HADDR_UNDEF) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk") + if (dataset->shared->dcpl_cache.pline.nused>0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot write to chunked storage with filters in parallel") + } /* end if */ +#endif /* H5_HAVE_PARALLEL */ + /* * If there is no type conversion then write directly from the * application's buffer. This saves at least one mem-to-mem copy. @@ -1718,12 +1788,33 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, store.chunk.offset = chunk_info->coords; store.chunk.index = chunk_info->index; + /* Load the chunk into cache. But if the whole chunk is written, + * simply allocate space instead of load the chunk. */ + chunk_addr = H5D_istore_get_addr(io_info, &udata); + + if (H5D_istore_if_load(dataset, chunk_addr)) { + accessed_bytes = chunk_info->chunk_points * H5T_get_size(dataset->shared->type); + if(accessed_bytes != dataset->shared->layout.u.chunk.size) + relax=FALSE; + + if(NULL == (chunk = H5D_istore_lock(io_info, &udata, relax, &idx_hint))) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk") + } else + chunk = NULL; + /* Perform the actual read operation */ if((io_info->ops.write)(io_info, chunk_info->chunk_points, H5T_get_size(dataset->shared->type), chunk_info->fspace, - chunk_info->mspace, (haddr_t)0, buf) < 0) + chunk_info->mspace, chunk_addr, chunk, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, " chunked write failed") + /* Release the cache lock on the chunk. */ + if (H5D_istore_if_load(dataset, chunk_addr)) { + if(H5D_istore_unlock(io_info, TRUE, idx_hint, chunk, accessed_bytes) < 0) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk") + } + relax=TRUE; + /* Advance to next chunk in list */ chunk_node = H5SL_next(chunk_node); } /* end while */ @@ -1830,6 +1921,25 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, store.chunk.offset = chunk_info->coords; store.chunk.index = chunk_info->index; + /* Load the chunk into cache. But if the whole chunk is written, + * simply allocate space instead of load the chunk. */ + chunk_addr = H5D_istore_get_addr(io_info, &udata); + + if (H5D_istore_if_load(dataset, chunk_addr)) { + accessed_bytes = chunk_info->chunk_points * H5T_get_size(dataset->shared->type); + if(accessed_bytes != dataset->shared->layout.u.chunk.size) + relax=FALSE; + if(relax) { + accessed_bytes = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)*H5T_get_size(mem_type); + if(accessed_bytes != dataset->shared->layout.u.chunk.size) + relax = FALSE; + } + + if(NULL == (chunk = H5D_istore_lock(io_info, &udata, relax, &idx_hint))) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk") + } else + chunk = NULL; + for (smine_start=0; smine_start<chunk_info->chunk_points; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ assert(H5S_SELECT_ITER_NELMTS(&file_iter)==(chunk_info->chunk_points-smine_start)); @@ -1868,8 +1978,13 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif - n = H5D_select_fgath(io_info, chunk_info->fspace, &bkg_iter, smine_nelmts, - bkg_buf/*out*/); + if(chunk) { + n = H5D_select_mgath(chunk, chunk_info->fspace, &bkg_iter, + smine_nelmts, dxpl_cache, bkg_buf/*out*/); + } else { + n = H5D_select_fgath(io_info, chunk_info->fspace, &bkg_iter, smine_nelmts, + (haddr_t)0, NULL, bkg_buf/*out*/); + } #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[0].bkg_timer), &timer); @@ -1900,7 +2015,7 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, #endif status = H5D_select_fscat(io_info, chunk_info->fspace, &file_iter, smine_nelmts, - tconv_buf); + chunk_addr, chunk, tconv_buf); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[0].scat_timer), &timer); @@ -1911,6 +2026,14 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed") } /* end for */ + /* Release the cache lock on the chunk. */ + if (H5D_istore_if_load(dataset, chunk_addr)) { + accessed_bytes = chunk_info->chunk_points * H5T_get_size(dataset->shared->type); + if(H5D_istore_unlock(io_info, TRUE, idx_hint, chunk, accessed_bytes) < 0) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk") + } + relax=TRUE; + /* Release selection iterators */ if(file_iter_init) { if(H5S_SELECT_ITER_RELEASE(&file_iter) < 0) |