diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/H5Dio.c | 24 | ||||
| -rw-r--r-- | src/H5Dmpio.c | 98 |
2 files changed, 104 insertions, 18 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c index 6e75a93..259eb06 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -289,6 +289,7 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, H5D_t *dset = NULL; const H5S_t *mem_space = NULL; const H5S_t *file_space = NULL; + char fake_char; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dread, FAIL) @@ -326,6 +327,13 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, if (!buf && H5S_GET_SELECT_NPOINTS(file_space)!=0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer") + /* If the buffer is nil, and 0 element is selected, make a fake buffer. + * This is for some MPI package like ChaMPIon on NCSA's tungsten which + * doesn't support this feature. + */ + if (!buf) + buf = &fake_char; + /* read raw data */ if (H5D_read(dset, mem_type_id, mem_space, file_space, plist_id, buf/*out*/) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data") @@ -373,6 +381,7 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, H5D_t *dset = NULL; const H5S_t *mem_space = NULL; const H5S_t *file_space = NULL; + char fake_char; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dwrite, FAIL) @@ -409,6 +418,13 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms") if(!buf && H5S_GET_SELECT_NPOINTS(file_space)!=0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer") + + /* If the buffer is nil, and 0 element is selected, make a fake buffer. + * This is for some MPI package like ChaMPIon on NCSA's tungsten which + * doesn't support this feature. + */ + if (!buf) + buf = &fake_char; /* write raw data */ if(H5D_write(dset, mem_type_id, mem_space, file_space, plist_id, buf) < 0) @@ -788,6 +804,8 @@ H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts, FUNC_ENTER_NOAPI_NOINIT(H5D_contig_read) + assert (buf); + /* Initialize storage info for this dataset */ if (dataset->shared->dcpl_cache.efl.nused > 0) HDmemcpy(&store.efl, &(dataset->shared->dcpl_cache.efl), sizeof(H5O_efl_t)); @@ -1066,6 +1084,8 @@ H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts, FUNC_ENTER_NOAPI_NOINIT(H5D_contig_write) + assert (buf); + /* Initialize storage info for this dataset */ if(dataset->shared->dcpl_cache.efl.nused > 0) HDmemcpy(&store.efl, &(dataset->shared->dcpl_cache.efl), sizeof(H5O_efl_t)); @@ -1344,6 +1364,8 @@ H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_read) + assert (buf); + /* Map elements between file and memory for each chunk*/ if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping") @@ -1734,6 +1756,8 @@ H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_write) + assert (buf); + /* Map elements between file and memory for each chunk*/ if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping") diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index 90f8974..a6981ee 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -988,6 +988,7 @@ H5D_link_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf, for ( i = 0; i< num_chunk;i++){ if (MPI_SUCCESS != (mpi_code= MPI_Type_free( chunk_mtype+i ))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code); + if (MPI_SUCCESS != (mpi_code= MPI_Type_free( chunk_ftype+i ))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code); } @@ -1014,7 +1015,7 @@ H5D_link_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf, if(H5DEBUG(D)) HDfprintf(H5DEBUG(D),"before coming to final collective IO\n"); #endif - + if(H5D_final_collective_io(io_info,&chunk_final_ftype,&chunk_final_mtype,&coll_info,buf,do_write)<0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL,"couldn't finish MPI-IO"); @@ -1059,7 +1060,6 @@ done: static herr_t H5D_multi_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf, hbool_t do_write) { - unsigned i, total_chunk; hsize_t ori_total_chunk; uint8_t *chunk_io_option; @@ -1070,6 +1070,16 @@ H5D_multi_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf, H5D_storage_t store; /* union of EFL and chunk pointer in file space */ hbool_t select_chunk; hbool_t last_io_mode_coll = TRUE; + + void *chunk = NULL; /* Pointer to the data chunk in cache */ + H5D_t *dataset=io_info->dset;/* Local pointer to dataset info */ + H5D_istore_ud1_t udata; /*B-tree pass-through */ + haddr_t caddr; /* Address of the cached chunk */ + size_t accessed_bytes; /*total accessed size in a chunk */ + unsigned idx_hint=0; /* Cache index hint */ + hbool_t dirty = TRUE; /* Flag for cache flushing */ + hbool_t relax=TRUE; /* Whether whole chunk is selected */ + herr_t ret_value = SUCCEED; #ifdef H5Dmpio_DEBUG int mpi_rank; @@ -1167,18 +1177,41 @@ H5D_multi_chunk_collective_io(H5D_io_info_t *io_info,fm_map *fm,const void *buf, if(H5D_ioinfo_make_ind(io_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to independent I/O") + /* Load the chunk into cache. But if the whole chunk is written, + * simply allocate space instead of load the chunk. */ + if(HADDR_UNDEF==(caddr = H5D_istore_get_addr(io_info, &udata))) + HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk info from skipped list"); + + if (H5D_istore_if_load(dataset, caddr)) { + accessed_bytes = chunk_info->chunk_points * H5T_get_size(dataset->shared->type); + if((do_write && (accessed_bytes != dataset->shared->layout.u.chunk.size)) || !do_write) + 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; + if(do_write) { if((io_info->ops.write)(io_info, chunk_info->chunk_points,H5T_get_size(io_info->dset->shared->type), - chunk_info->fspace,chunk_info->mspace,0, NULL, buf) < 0) + chunk_info->fspace,chunk_info->mspace,caddr,chunk, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed") } else { if((io_info->ops.read)(io_info, chunk_info->chunk_points,H5T_get_size(io_info->dset->shared->type), - chunk_info->fspace,chunk_info->mspace,0, NULL, buf) < 0) + chunk_info->fspace,chunk_info->mspace,caddr,chunk, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed") - } + } + + /* Release the cache lock on the chunk. */ + if (H5D_istore_if_load(dataset, caddr)) { + if(!do_write) dirty = FALSE; + + if(H5D_istore_unlock(io_info, dirty, idx_hint, chunk, accessed_bytes) < 0) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk") + } #else if(!last_io_mode_coll) /* using independent I/O with file setview.*/ @@ -1250,6 +1283,16 @@ H5D_multi_chunk_collective_io_no_opt(H5D_io_info_t *io_info,fm_map *fm,const voi haddr_t chunk_addr; H5SL_node_t *chunk_node; /* Current node in chunk skip list */ H5D_storage_t store; /* union of EFL and chunk pointer in file space */ + H5D_chunk_info_t *chunk_info; /* chunk information */ + hbool_t make_ind, make_coll; /* Flags to indicate that the MPI mode should change */ + + void *chunk = NULL; /* Pointer to the data chunk in cache */ + H5D_t *dataset=io_info->dset;/* Local pointer to dataset info */ + H5D_istore_ud1_t udata; /*B-tree pass-through */ + size_t accessed_bytes; /*total accessed size in a chunk */ + unsigned idx_hint=0; /* Cache index hint */ + hbool_t dirty = TRUE; /* Flag for cache flushing */ + hbool_t relax=TRUE; /* Whether whole chunk is selected */ herr_t ret_value = SUCCEED; #ifdef H5Dmpio_DEBUG @@ -1317,24 +1360,43 @@ H5D_multi_chunk_collective_io_no_opt(H5D_io_info_t *io_info,fm_map *fm,const voi if(H5D_ioinfo_make_ind(io_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to independent I/O") + if(HADDR_UNDEF==(chunk_addr = H5D_istore_get_addr(io_info, &udata))) + HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk info from skipped list"); + if(make_ind) {/*independent I/O */ - - if(do_write) { - if((io_info->ops.write)(io_info, + /* Load the chunk into cache. But if the whole chunk is written, + * simply allocate space instead of load the chunk. */ + if (H5D_istore_if_load(dataset, chunk_addr)) { + accessed_bytes = chunk_info->chunk_points * H5T_get_size(dataset->shared->type); + if((do_write && (accessed_bytes != dataset->shared->layout.u.chunk.size)) || !do_write) + 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; + + if(do_write) { + if((io_info->ops.write)(io_info, chunk_info->chunk_points,H5T_get_size(io_info->dset->shared->type), - chunk_info->fspace,chunk_info->mspace, (hsize_t)0, NULL, buf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed") - } - else { - if((io_info->ops.read)(io_info, + chunk_info->fspace,chunk_info->mspace, chunk_addr, chunk, buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed") + } else { + if((io_info->ops.read)(io_info, chunk_info->chunk_points,H5T_get_size(io_info->dset->shared->type), - chunk_info->fspace,chunk_info->mspace, (hsize_t)0, NULL, buf) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed") - } + chunk_info->fspace,chunk_info->mspace, chunk_addr, chunk, buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed") + } + + /* Release the cache lock on the chunk. */ + if (H5D_istore_if_load(dataset, chunk_addr)) { + if(!do_write) dirty = FALSE; + + if(H5D_istore_unlock(io_info, dirty, idx_hint, chunk, accessed_bytes) < 0) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk") + } } else { /*collective I/O */ - if(HADDR_UNDEF==(chunk_addr = H5D_istore_get_addr(io_info,NULL))) - HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk info from skipped list"); if(H5D_inter_collective_io(io_info,chunk_info->fspace,chunk_info->mspace, chunk_addr,buf,do_write ) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL,"couldn't finish shared collective MPI-IO"); |