diff options
Diffstat (limited to 'src')
-rw-r--r-- | src/H5Dmpio.c | 302 | ||||
-rw-r--r-- | src/H5Dprivate.h | 2 | ||||
-rw-r--r-- | src/H5FDcore.c | 2 | ||||
-rw-r--r-- | src/H5FDdirect.c | 9 | ||||
-rw-r--r-- | src/H5FDfamily.c | 4 | ||||
-rw-r--r-- | src/H5FDlog.c | 18 | ||||
-rw-r--r-- | src/H5FDmpio.c | 4 | ||||
-rw-r--r-- | src/H5FDmpiposix.c | 4 | ||||
-rw-r--r-- | src/H5Pocpl.c | 5 | ||||
-rw-r--r-- | src/H5Ppublic.h | 3 | ||||
-rw-r--r-- | src/H5detect.c | 21 | ||||
-rw-r--r-- | src/H5public.h | 4 | ||||
-rw-r--r-- | src/H5trace.c | 4 | ||||
-rw-r--r-- | src/Makefile.in | 2 |
14 files changed, 92 insertions, 292 deletions
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index c2d964e..900ad6a 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -105,10 +105,9 @@ static herr_t H5D__chunk_collective_io(H5D_io_info_t *io_info, static herr_t H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, H5P_genplist_t *dx_plist); -static herr_t H5D__multi_chunk_collective_io_no_opt(H5D_io_info_t *io_info, - const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, H5P_genplist_t *dx_plist); static herr_t H5D__link_chunk_collective_io(H5D_io_info_t *io_info, - const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, int sum_chunk); + const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, int sum_chunk, + H5P_genplist_t *dx_plist); static herr_t H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, const H5S_t *file_space, const H5S_t *mem_space); @@ -586,6 +585,12 @@ done: * Programmer: Muqun Yang * Monday, Feb. 13th, 2006 * + * Modification: + * - Refctore to remove multi-chunk-without-opimization feature and update for + * multi-chunk-io accordingly + * Programmer: Jonathan Kim + * Date: 2012-10-10 + * *------------------------------------------------------------------------- */ static herr_t @@ -594,8 +599,6 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf { H5P_genplist_t *dx_plist; /* Pointer to DXPL */ H5FD_mpio_chunk_opt_t chunk_opt_mode; - H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode; - H5D_mpio_actual_io_mode_t actual_io_mode; int io_option = H5D_MULTI_CHUNK_IO_MORE_OPT; int sum_chunk = -1; #ifdef H5_HAVE_INSTRUMENTED_LIBRARY @@ -617,10 +620,12 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf /* Check the optional property list on what to do with collective chunk IO. */ chunk_opt_mode = (H5FD_mpio_chunk_opt_t)H5P_peek_unsigned(dx_plist, H5D_XFER_MPIO_CHUNK_OPT_HARD_NAME); - if(chunk_opt_mode == H5FD_MPIO_CHUNK_ONE_IO) + if(H5FD_MPIO_CHUNK_ONE_IO == chunk_opt_mode) io_option = H5D_ONE_LINK_CHUNK_IO; /*no opt*/ - else if(chunk_opt_mode == H5FD_MPIO_CHUNK_MULTI_IO) - io_option = H5D_MULTI_CHUNK_IO; /*no opt */ + /* direct request to multi-chunk-io */ + else if(H5FD_MPIO_CHUNK_MULTI_IO == chunk_opt_mode) + io_option = H5D_MULTI_CHUNK_IO; + /* via default path. branch by num threshold */ else { unsigned one_link_chunk_io_threshold; /* Threshhold to use single collective I/O for all chunks */ int mpi_size; /* Number of processes in MPI job */ @@ -649,7 +654,7 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf /*** Test collective chunk user-input optimization APIs. ***/ check_prop = H5Pexist(io_info->dxpl_id, H5D_XFER_COLL_CHUNK_LINK_HARD_NAME); if(check_prop > 0) { - if(io_option == H5D_ONE_LINK_CHUNK_IO) { + if(H5D_ONE_LINK_CHUNK_IO == io_option) { new_value = 0; if(H5Pset(io_info->dxpl_id, H5D_XFER_COLL_CHUNK_LINK_HARD_NAME, &new_value) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value") @@ -657,7 +662,7 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf } /* end if */ check_prop = H5Pexist(io_info->dxpl_id, H5D_XFER_COLL_CHUNK_MULTI_HARD_NAME); if(check_prop > 0) { - if(io_option == H5D_MULTI_CHUNK_IO) { + if(H5D_MULTI_CHUNK_IO == io_option) { new_value = 0; if(H5Pset(io_info->dxpl_id, H5D_XFER_COLL_CHUNK_MULTI_HARD_NAME, &new_value) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value") @@ -665,7 +670,7 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf } /* end if */ check_prop = H5Pexist(io_info->dxpl_id, H5D_XFER_COLL_CHUNK_LINK_NUM_TRUE_NAME); if(check_prop > 0) { - if(io_option == H5D_ONE_LINK_CHUNK_IO_MORE_OPT) { + if(H5D_ONE_LINK_CHUNK_IO_MORE_OPT == io_option) { new_value = 0; if(H5Pset(io_info->dxpl_id, H5D_XFER_COLL_CHUNK_LINK_NUM_TRUE_NAME, &new_value) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value") @@ -682,39 +687,16 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf #endif /* step 2: Go ahead to do IO.*/ - if(io_option == H5D_ONE_LINK_CHUNK_IO || io_option == H5D_ONE_LINK_CHUNK_IO_MORE_OPT) { - /* set the actual io mode properties to the correct values for link chunk io. - * Link chunk I/O does not break to independent, so we can set the actual_io mode - * as well as the optimisation mode. */ - actual_chunk_opt_mode = H5D_MPIO_LINK_CHUNK; - actual_io_mode = H5D_MPIO_CHUNK_COLLECTIVE; - - /* Set the actual chunk opt mode property. */ - if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual chunk opt mode property") - - if(H5D__link_chunk_collective_io(io_info, type_info, fm, sum_chunk) < 0) + if(H5D_ONE_LINK_CHUNK_IO == io_option || H5D_ONE_LINK_CHUNK_IO_MORE_OPT == io_option) { + if(H5D__link_chunk_collective_io(io_info, type_info, fm, sum_chunk, dx_plist) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish linked chunk MPI-IO") - - /* Set the actual io mode property. */ - if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual io mode property") } /* end if */ - else - if(io_option == H5D_MULTI_CHUNK_IO) { - /* Set the actual chunk opt mode property */ - actual_chunk_opt_mode = H5D_MPIO_MULTI_CHUNK_NO_OPT; - if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual chunk opt mode property") - - if(H5D__multi_chunk_collective_io_no_opt(io_info, type_info, fm, dx_plist) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish multiple chunk MPI-IO") + /* direct request to multi-chunk-io */ + else if(H5D_MULTI_CHUNK_IO == io_option) { + if(H5D__multi_chunk_collective_io(io_info, type_info, fm, dx_plist) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish optimized multiple chunk MPI-IO") } /* end if */ - else { /*multiple chunk IOs with opt */ - actual_chunk_opt_mode = H5D_MPIO_MULTI_CHUNK; - if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual chunk opt mode property") - + else { /* multiple chunk IO via threshold */ if(H5D__multi_chunk_collective_io(io_info, type_info, fm, dx_plist) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish optimized multiple chunk MPI-IO") } /* end else */ @@ -801,11 +783,16 @@ done: * Programmer: Muqun Yang * Monday, Feb. 13th, 2006 * + * Modification: + * - Set H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME and H5D_MPIO_ACTUAL_IO_MODE_NAME + * dxpl in this. + * Programmer: Jonathan Kim + * Date: 2012-10-10 *------------------------------------------------------------------------- */ static herr_t H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5D_chunk_map_t *fm, int sum_chunk) + H5D_chunk_map_t *fm, int sum_chunk, H5P_genplist_t *dx_plist) { H5D_chunk_addr_info_t *chunk_addr_info_array = NULL; MPI_Datatype chunk_final_mtype; /* Final memory MPI datatype for all chunks with seletion */ @@ -824,10 +811,21 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ int *chunk_mpi_file_counts = NULL; /* Count of MPI file datatype for each chunk */ int *chunk_mpi_mem_counts = NULL; /* Count of MPI memory datatype for each chunk */ int mpi_code; /* MPI return code */ + H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode = H5D_MPIO_LINK_CHUNK; + H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_CHUNK_COLLECTIVE; herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC + /* Set the actual-chunk-opt-mode property. */ + if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual chunk opt mode property") + + /* Set the actual-io-mode property. + * Link chunk I/O does not break to independent, so can set right away */ + if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual io mode property") + /* Get the sum # of chunks, if not already available */ if(sum_chunk < 0) { if(H5D__mpio_get_sum_chunk(io_info, fm, &sum_chunk) < 0) @@ -1075,6 +1073,12 @@ if(H5DEBUG(D)) * Programmer: Muqun Yang * Monday, Feb. 13th, 2006 * + * Modification: + * - Set H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME dxpl in this to go along with + * setting H5D_MPIO_ACTUAL_IO_MODE_NAME dxpl at the bottom. + * Programmer: Jonathan Kim + * Date: 2012-10-10 + * *------------------------------------------------------------------------- */ static herr_t @@ -1096,11 +1100,16 @@ H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *ty int mpi_rank; #endif size_t u; /* Local index variable */ + H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode = H5D_MPIO_MULTI_CHUNK; /* actual chunk optimization mode */ H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_NO_COLLECTIVE; /* Local variable for tracking the I/O mode used. */ herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC + /* Set the actual chunk opt mode property */ + if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual chunk opt mode property") + #ifdef H5Dmpio_DEBUG mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file); #endif @@ -1263,210 +1272,6 @@ done: } /* end H5D__multi_chunk_collective_io */ -/*------------------------------------------------------------------------- - * Function: H5D__multi_chunk_collective_io_no_opt - * - * Purpose: To do collective IO without any optimization per chunk base - * The internal independent IO inside HDF5 cannot handle - * non-contiguous(or with holes) storage efficiently. - * Under this case, the one independent IO call may consist of - * many small disk IOs. So we may use independent IO with derived datatype - * to replace the independent IO when we find this chunk is not good to - * do collective IO. However, according to our performance study, - * this approach may not overcome the overhead caused by MPI gather/scatter. - * So we decide to leave the original collective IO per chunk approach as - * an option for users. NO MPI gather/scatter calls are used. - * HDF5 will try to collective IO if possible. - * If users choose to use - * H5Pset_dxpl_mpio_chunk_opt(dxpl_id,H5FD_MPIO_OPT_MULTI_IO), - * this function will be called. - * The HDF5 library won't do any IO management but leave it to MPI-IO to figure - * out. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Muqun Yang - * Monday, Feb. 13th, 2006 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D__multi_chunk_collective_io_no_opt(H5D_io_info_t *io_info, - const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, H5P_genplist_t *dx_plist) -{ - H5SL_node_t *chunk_node; /* Current node in chunk skip list */ - H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */ - H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ - H5D_io_info_t cpt_io_info; /* Compact I/O info object */ - H5D_storage_t cpt_store; /* Chunk storage information as compact dataset */ - hbool_t cpt_dirty; /* Temporary placeholder for compact storage "dirty" flag */ - int min_chunk = -1; /* Minimum # of chunks all processes will operate on */ - int count_chunk; /* How many chunks have we operated on? */ - H5D_storage_t store; /* union of EFL and chunk pointer in file space */ - H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_NO_COLLECTIVE; /*Local variable for tracking the I/O modes used. */ - herr_t ret_value = SUCCEED; - - FUNC_ENTER_STATIC - -#ifdef H5D_DEBUG -if(H5DEBUG(D)) { - int mpi_rank; - - mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file); - HDfprintf(H5DEBUG(D), "Rank %d: coming to multi_chunk_collective_io_no_opt\n", mpi_rank); -} -#endif - - /* Set up contiguous I/O info object */ - HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); - ctg_io_info.store = &ctg_store; - ctg_io_info.layout_ops = *H5D_LOPS_CONTIG; - - /* Initialize temporary contiguous storage info */ - ctg_store.contig.dset_size = (hsize_t)io_info->dset->shared->layout.u.chunk.size; - - /* Set up compact I/O info object */ - HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); - cpt_io_info.store = &cpt_store; - cpt_io_info.layout_ops = *H5D_LOPS_COMPACT; - - /* Initialize temporary compact storage info */ - cpt_store.compact.dirty = &cpt_dirty; - - /* Set dataset storage for I/O info */ - io_info->store = &store; - - /* Get the min. # of chunks */ - if(H5D__mpio_get_min_chunk(io_info, fm, &min_chunk) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get minimum number of chunk") - HDassert(min_chunk >= 0); - - /* Get first node in chunk skip list */ - chunk_node = H5SL_first(fm->sel_chunks); - count_chunk = 0; - - /* Iterate through chunks to be operated on */ - while(chunk_node) { - H5D_chunk_info_t *chunk_info; /* chunk information */ - H5D_chunk_ud_t udata; /* B-tree pass-through */ - hbool_t make_ind, make_coll; /* Flags to indicate that the MPI mode should change */ - - /* Get the actual chunk information from the skip list node */ - chunk_info = H5SL_item(chunk_node); - - /* Pass in chunk's coordinates in a union. */ - store.chunk.offset = chunk_info->coords; - store.chunk.index = chunk_info->index; - - /* Reset flags for changing parallel I/O mode */ - make_ind = make_coll = FALSE; - - count_chunk++; - - /* If the number of chunk is greater than minimum number of chunk, - * Do independent read. - */ - if(count_chunk > min_chunk) - /* Switch to independent I/O (permanently) */ - make_ind = TRUE; - - /* Retrieve the chunk's address */ - if(H5D__chunk_lookup(io_info->dset, io_info->dxpl_id, chunk_info->coords, - chunk_info->index, &udata) < 0) - HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk info from skipped list") - - /* Independent I/O */ - if(make_ind) { - void *chunk; /* Pointer to the data chunk in cache */ - H5D_io_info_t *chk_io_info; /* Pointer to I/O info object for this chunk */ - uint32_t accessed_bytes = 0; /* Total accessed size in a chunk */ - htri_t cacheable; /* Whether the chunk is cacheable */ - - /* Switch to independent I/O */ - if(H5D__ioinfo_xfer_mode(io_info, dx_plist, H5FD_MPIO_INDEPENDENT) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to independent I/O") - - /* Update the local variable tracking the dxpl's actual io mode */ - actual_io_mode = actual_io_mode | H5D_MPIO_CHUNK_INDEPENDENT; - - /* Load the chunk into cache and lock it. */ - if((cacheable = H5D__chunk_cacheable(io_info, udata.addr, - io_info->op_type == H5D_IO_OP_WRITE)) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable") - if(cacheable) { - hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */ - - /* Compute # of bytes accessed in chunk */ - accessed_bytes = chunk_info->chunk_points * type_info->src_type_size; - - /* Determine if we will access all the data in the chunk */ - if(((io_info->op_type == H5D_IO_OP_WRITE) && (accessed_bytes != ctg_store.contig.dset_size)) - || (io_info->op_type != H5D_IO_OP_WRITE)) - entire_chunk = FALSE; - - /* Lock the chunk into the cache */ - if(NULL == (chunk = H5D__chunk_lock(io_info, &udata, entire_chunk))) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk") - - /* Set up the storage buffer information for this chunk */ - cpt_store.compact.buf = chunk; - - /* Point I/O info at contiguous I/O info for this chunk */ - chk_io_info = &cpt_io_info; - } /* end if */ - else { - /* Set up the storage address information for this chunk */ - ctg_store.contig.dset_addr = udata.addr; - - /* No chunk cached */ - chunk = NULL; - - /* Point I/O info at temporary I/O info for this chunk */ - chk_io_info = &ctg_io_info; - } /* end else */ - - if(io_info->op_type == H5D_IO_OP_WRITE) { - if((io_info->io_ops.single_write)(chk_io_info, type_info, - (hsize_t)chunk_info->chunk_points, chunk_info->fspace, chunk_info->mspace) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed") - } /* end if */ - else { - if((io_info->io_ops.single_read)(chk_io_info, type_info, - (hsize_t)chunk_info->chunk_points, chunk_info->fspace, chunk_info->mspace) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed") - } /* end ese */ - - /* Release the cache lock on the chunk. */ - if(chunk) - if(H5D__chunk_unlock(io_info, &udata, (io_info->op_type == H5D_IO_OP_WRITE), chunk, accessed_bytes) < 0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk") - } /* end if */ - else { /*collective I/O */ - /* Set up the storage address information for this chunk */ - ctg_store.contig.dset_addr = udata.addr; - - /* Update the local variable tracking the dxpl's actual io Mode. */ - actual_io_mode = actual_io_mode | H5D_MPIO_CHUNK_COLLECTIVE; - - if(H5D__inter_collective_io(&ctg_io_info, type_info, chunk_info->fspace, chunk_info->mspace) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL,"couldn't finish shared collective MPI-IO") - } /* end else */ - - if(make_coll) - if(H5D__ioinfo_xfer_mode(io_info, dx_plist, H5FD_MPIO_COLLECTIVE) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to independent I/O") - - /* Get the next chunk node in the skip list */ - chunk_node = H5SL_next(chunk_node); - } /* end while */ - - /* Write the local value of actual io mode to the DXPL. */ - if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual io mode property") - -done: - FUNC_LEAVE_NOAPI(ret_value) -} /* end H5D__multi_chunk_collective_io_no_opt */ /*------------------------------------------------------------------------- @@ -1794,7 +1599,6 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, { int total_chunks; unsigned percent_nproc_per_chunk, threshold_nproc_per_chunk; - H5FD_mpio_chunk_opt_t chunk_opt_mode; uint8_t* io_mode_info = NULL; uint8_t* recv_io_mode_info = NULL; uint8_t* mergebuf = NULL; @@ -1827,8 +1631,8 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, /* Setup parameters */ H5_ASSIGN_OVERFLOW(total_chunks, fm->layout->u.chunk.nchunks, hsize_t, int); percent_nproc_per_chunk = H5P_peek_unsigned(dx_plist, H5D_XFER_MPIO_CHUNK_OPT_RATIO_NAME); - chunk_opt_mode = (H5FD_mpio_chunk_opt_t)H5P_peek_unsigned(dx_plist, H5D_XFER_MPIO_CHUNK_OPT_HARD_NAME); - if((chunk_opt_mode == H5FD_MPIO_CHUNK_MULTI_IO) || (percent_nproc_per_chunk == 0)) { + /* if ratio is 0, perform collective io */ + if(0 == percent_nproc_per_chunk) { if(H5D__chunk_addrmap(io_info, chunk_addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address"); for(ic = 0; ic < total_chunks; ic++) diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h index 9adf6a5..1e2b91d 100644 --- a/src/H5Dprivate.h +++ b/src/H5Dprivate.h @@ -87,8 +87,6 @@ #define H5D_XFER_COLL_CHUNK_LINK_NUM_FALSE_NAME "coll_chunk_link_false" #define H5D_XFER_COLL_CHUNK_MULTI_RATIO_COLL_NAME "coll_chunk_multi_coll" #define H5D_XFER_COLL_CHUNK_MULTI_RATIO_IND_NAME "coll_chunk_multi_ind" -#define H5D_XFER_COLL_CHUNK_LINK_TO_MULTI "coll_chunk_link_mul"/* Internal transferring from link to multiple chunk */ -#define H5D_XFER_COLL_CHUNK_LINK_TO_MULTI_OPT "coll_chunk_link_mul_opt"/* Internal transferring from link opt to multiple chunk opt*/ /* Definitions for all collective chunk instrumentation properties */ #define H5D_XFER_COLL_CHUNK_SIZE sizeof(unsigned) diff --git a/src/H5FDcore.c b/src/H5FDcore.c index 932e2af..07f4551 100644 --- a/src/H5FDcore.c +++ b/src/H5FDcore.c @@ -481,7 +481,7 @@ H5FD_core_open(const char *name, unsigned flags, hid_t fapl_id, * default value. But if the file access property list was zero then use * the default value instead. */ - file->increment = (fa->increment>0) ? fa->increment : H5FD_CORE_INCREMENT; + file->increment = (fa->increment > 0) ? fa->increment : H5FD_CORE_INCREMENT; /* If save data in backing store. */ file->backing_store = fa->backing_store; diff --git a/src/H5FDdirect.c b/src/H5FDdirect.c index 4721a44..9715bc1 100644 --- a/src/H5FDdirect.c +++ b/src/H5FDdirect.c @@ -533,7 +533,8 @@ H5FD_direct_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxadd /* Get the driver specific information */ if(NULL == (plist = H5P_object_verify(fapl_id,H5P_FILE_ACCESS))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a file access property list") - fa = H5P_get_driver_info(plist); + if(NULL == (fa = (H5FD_direct_fapl_t *)H5P_get_driver_info(plist))) + HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, NULL, "bad VFL driver info") file->fd = fd; H5_ASSIGN_OVERFLOW(file->eof,sb.st_size,h5_stat_size_t,haddr_t); @@ -562,9 +563,9 @@ H5FD_direct_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxadd * is to handle correctly the case that the file is in a different file system * than the one where the program is running. */ - buf1 = (int*)HDmalloc(sizeof(int)); - if (HDposix_memalign(&buf2, file->fa.mboundary, file->fa.fbsize) != 0) - HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, NULL, "HDposix_memalign failed") + buf1 = (int *)HDmalloc(sizeof(int)); + if(HDposix_memalign(&buf2, file->fa.mboundary, file->fa.fbsize) != 0) + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, NULL, "HDposix_memalign failed") if(o_flags & O_CREAT) { if(write(file->fd, (void*)buf1, sizeof(int))<0) { diff --git a/src/H5FDfamily.c b/src/H5FDfamily.c index f051269..dc535a2 100644 --- a/src/H5FDfamily.c +++ b/src/H5FDfamily.c @@ -675,8 +675,8 @@ H5FD_family_open(const char *name, unsigned flags, hid_t fapl_id, if(NULL == (plist = (H5P_genplist_t *)H5I_object(fapl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a file access property list") - fa = (H5FD_family_fapl_t *)H5P_get_driver_info(plist); - HDassert(fa); + if(NULL == (fa = (H5FD_family_fapl_t *)H5P_get_driver_info(plist))) + HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, NULL, "bad VFL driver info") /* Check for new family file size. It's used by h5repart only. */ if(H5P_exist_plist(plist, H5F_ACS_FAMILY_NEWSIZE_NAME) > 0) { diff --git a/src/H5FDlog.c b/src/H5FDlog.c index 6a2425c..9f4abd3 100644 --- a/src/H5FDlog.c +++ b/src/H5FDlog.c @@ -529,8 +529,8 @@ H5FD_log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr) /* Get the driver specific information */ if(NULL == (plist = H5P_object_verify(fapl_id, H5P_FILE_ACCESS))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a file access property list") - fa = (H5FD_log_fapl_t *)H5P_get_driver_info(plist); - HDassert(fa); + if(NULL == (fa = (H5FD_log_fapl_t *)H5P_get_driver_info(plist))) + HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, NULL, "bad VFL driver info") #ifdef H5_HAVE_GETTIMEOFDAY if(fa->flags & H5FD_LOG_TIME_OPEN) @@ -644,9 +644,9 @@ H5FD_log_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr) #ifdef H5_HAVE_GETTIMEOFDAY if(file->fa.flags & H5FD_LOG_TIME_OPEN) - HDfprintf(file->logfp, "Open took: (%f s)\n", (double)open_timeval_diff.tv_sec + ((double)open_timeval_diff.tv_usec / (double)1000000.0)); + HDfprintf(file->logfp, "Open took: (%f s)\n", (double)open_timeval_diff.tv_sec + ((double)open_timeval_diff.tv_usec / (double)1000000.0f)); if(file->fa.flags & H5FD_LOG_TIME_STAT) - HDfprintf(file->logfp, "Stat took: (%f s)\n", (double)stat_timeval_diff.tv_sec + ((double)stat_timeval_diff.tv_usec / (double)1000000.0)); + HDfprintf(file->logfp, "Stat took: (%f s)\n", (double)stat_timeval_diff.tv_sec + ((double)stat_timeval_diff.tv_usec / (double)1000000.0f)); #endif /* H5_HAVE_GETTIMEOFDAY */ } /* end if */ @@ -734,7 +734,7 @@ H5FD_log_close(H5FD_t *_file) timeval_diff.tv_usec += 1000000; timeval_diff.tv_sec--; } /* end if */ - HDfprintf(file->logfp, "Close took: (%f s)\n", (double)timeval_diff.tv_sec + ((double)timeval_diff.tv_usec / (double)1000000.0)); + HDfprintf(file->logfp, "Close took: (%f s)\n", (double)timeval_diff.tv_sec + ((double)timeval_diff.tv_usec / (double)1000000.0f)); } /* end if */ #endif /* H5_HAVE_GETTIMEOFDAY */ @@ -1195,7 +1195,7 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t UNUSED dxpl_id, haddr_t addr timeval_diff.tv_usec += 1000000; timeval_diff.tv_sec--; } /* end if */ - time_diff = (double)timeval_diff.tv_sec + ((double)timeval_diff.tv_usec / (double)1000000.0); + time_diff = (double)timeval_diff.tv_sec + ((double)timeval_diff.tv_usec / (double)1000000.0f); HDfprintf(file->logfp, " (%f s)\n", time_diff); /* Add to total seek time */ @@ -1284,7 +1284,7 @@ H5FD_log_read(H5FD_t *_file, H5FD_mem_t type, hid_t UNUSED dxpl_id, haddr_t addr timeval_diff.tv_usec += 1000000; timeval_diff.tv_sec--; } /* end if */ - time_diff = (double)timeval_diff.tv_sec + ((double)timeval_diff.tv_usec / (double)1000000.0); + time_diff = (double)timeval_diff.tv_sec + ((double)timeval_diff.tv_usec / (double)1000000.0f); HDfprintf(file->logfp, " (%f s)\n", time_diff); /* Add to total read time */ @@ -1401,7 +1401,7 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t UNUSED dxpl_id, haddr_t add timeval_diff.tv_usec += 1000000; timeval_diff.tv_sec--; } /* end if */ - time_diff = (double)timeval_diff.tv_sec + ((double)timeval_diff.tv_usec / (double)1000000.0); + time_diff = (double)timeval_diff.tv_sec + ((double)timeval_diff.tv_usec / (double)1000000.0f); HDfprintf(file->logfp, " (%f s)\n", time_diff); /* Add to total seek time */ @@ -1487,7 +1487,7 @@ H5FD_log_write(H5FD_t *_file, H5FD_mem_t type, hid_t UNUSED dxpl_id, haddr_t add timeval_diff.tv_usec += 1000000; timeval_diff.tv_sec--; } /* end if */ - time_diff = (double)timeval_diff.tv_sec + ((double)timeval_diff.tv_usec / (double)1000000.0); + time_diff = (double)timeval_diff.tv_sec + ((double)timeval_diff.tv_usec / (double)1000000.0f); HDfprintf(file->logfp, " (%f s)\n", time_diff); /* Add to total write time */ diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c index cac101b..2db77c9 100644 --- a/src/H5FDmpio.c +++ b/src/H5FDmpio.c @@ -1013,8 +1013,8 @@ H5FD_mpio_open(const char *name, unsigned flags, hid_t fapl_id, _fa.info = MPI_INFO_NULL; /*default*/ fa = &_fa; } else { - fa = (const H5FD_mpio_fapl_t *)H5P_get_driver_info(plist); - assert(fa); + if(NULL == (fa = (const H5FD_mpio_fapl_t *)H5P_get_driver_info(plist))) + HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, NULL, "bad VFL driver info") } /* Duplicate communicator and Info object for use by this file. */ diff --git a/src/H5FDmpiposix.c b/src/H5FDmpiposix.c index 0d0b839..092cd24 100644 --- a/src/H5FDmpiposix.c +++ b/src/H5FDmpiposix.c @@ -600,8 +600,8 @@ H5FD_mpiposix_open(const char *name, unsigned flags, hid_t fapl_id, fa = &_fa; } /* end if */ else { - fa = H5P_get_driver_info(plist); - HDassert(fa); + if(NULL == (fa = (const H5FD_mpiposix_fapl_t *)H5P_get_driver_info(plist))) + HGOTO_ERROR(H5E_PLIST, H5E_BADVALUE, NULL, "bad VFL driver info") } /* end else */ /* Duplicate the communicator for use by this file. */ diff --git a/src/H5Pocpl.c b/src/H5Pocpl.c index 6e20963..d8ddfee 100644 --- a/src/H5Pocpl.c +++ b/src/H5Pocpl.c @@ -1514,9 +1514,12 @@ H5P__ocrt_pipeline_dec(const void **_pp, void *_value) UINT64DECODE_VAR(*pp, enc_value, enc_size); filter.cd_nelmts = (size_t)enc_value; - if(filter.cd_nelmts) + if(filter.cd_nelmts) { if(NULL == (filter.cd_values = (unsigned *)H5MM_malloc(sizeof(unsigned) * filter.cd_nelmts))) HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, FAIL, "memory allocation failed for cd_values") + } /* end if */ + else + filter.cd_values = NULL; /* decode values */ for(v = 0; v < filter.cd_nelmts; v++) diff --git a/src/H5Ppublic.h b/src/H5Ppublic.h index 507bbb6..6b17e0b 100644 --- a/src/H5Ppublic.h +++ b/src/H5Ppublic.h @@ -131,8 +131,7 @@ typedef enum H5D_mpio_actual_chunk_opt_mode_t { */ H5D_MPIO_NO_CHUNK_OPTIMIZATION = 0, H5D_MPIO_LINK_CHUNK, - H5D_MPIO_MULTI_CHUNK, - H5D_MPIO_MULTI_CHUNK_NO_OPT + H5D_MPIO_MULTI_CHUNK } H5D_mpio_actual_chunk_opt_mode_t; typedef enum H5D_mpio_actual_io_mode_t { diff --git a/src/H5detect.c b/src/H5detect.c index 87a4fd5..d6f6a3b 100644 --- a/src/H5detect.c +++ b/src/H5detect.c @@ -120,7 +120,7 @@ static void print_results(int nd, detected_t *d, int na, malign_t *m); static void iprint(detected_t *); static int byte_cmp(int, const void *, const void *); static int bit_cmp(int, int *, volatile void *, volatile void *); -static void fix_order(int, int, int, int *, const char **); +static void fix_order(int, int, int *, const char **); static int imp_bit(int, int *, volatile void *, volatile void *); static unsigned long find_bias(int, int, int *, void *); static void precision (detected_t*); @@ -293,7 +293,7 @@ precision (detected_t *d) #define DETECT_F(TYPE,VAR,INFO) { \ volatile TYPE _v1, _v2, _v3; \ unsigned char _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \ - int _i, _j, _first = (-1), _last = (-1); \ + int _i, _j, _last = (-1); \ char *_mesg; \ \ memset(&INFO, 0, sizeof(INFO)); \ @@ -315,15 +315,11 @@ precision (detected_t *d) memcpy(_buf3, (const void *)&_v3, sizeof(TYPE)); \ _j = byte_cmp(sizeof(TYPE), &_buf3, &_buf1); \ if(_j >= 0) { \ - if(0 == _i || INFO.perm[_i - 1] != _j) { \ - INFO.perm[_i] = _j; \ - _last = _i; \ - if(_first < 0) \ - _first = _i; \ - } \ + INFO.perm[_i] = _j; \ + _last = _i; \ } \ } \ - fix_order(sizeof(TYPE), _first, _last, INFO.perm, (const char**)&_mesg); \ + fix_order(sizeof(TYPE), _last, INFO.perm, (const char**)&_mesg); \ \ if(!strcmp(_mesg, "VAX")) \ INFO.is_vax = TRUE; \ @@ -973,11 +969,11 @@ bit_cmp(int nbytes, int *perm, volatile void *_a, volatile void *_b) *------------------------------------------------------------------------- */ static void -fix_order(int n, int first, int last, int *perm, const char **mesg) +fix_order(int n, int last, int *perm, const char **mesg) { int i; - if (first + 1 < last) { + if (last > 1) { /* * We have at least three points to consider. */ @@ -998,6 +994,9 @@ fix_order(int n, int first, int last, int *perm, const char **mesg) } else { /* * Bi-endian machines like VAX. + * (NOTE: This is not an actual determination of the VAX-endianess. + * It could have some other endianess and fall into this + * case - JKM & QAK) */ assert(0 == n % 2); if (mesg) *mesg = "VAX"; diff --git a/src/H5public.h b/src/H5public.h index 88e514d..5d9e3ef 100644 --- a/src/H5public.h +++ b/src/H5public.h @@ -75,10 +75,10 @@ extern "C" { /* Version numbers */ #define H5_VERS_MAJOR 1 /* For major interface/format changes */ #define H5_VERS_MINOR 9 /* For minor interface/format changes */ -#define H5_VERS_RELEASE 132 /* For tweaks, bug-fixes, or development */ +#define H5_VERS_RELEASE 136 /* For tweaks, bug-fixes, or development */ #define H5_VERS_SUBRELEASE "" /* For pre-releases like snap0 */ /* Empty string for real releases. */ -#define H5_VERS_INFO "HDF5 library version: 1.9.132" /* Full version string */ +#define H5_VERS_INFO "HDF5 library version: 1.9.136" /* Full version string */ #define H5check() H5check_version(H5_VERS_MAJOR,H5_VERS_MINOR, \ H5_VERS_RELEASE) diff --git a/src/H5trace.c b/src/H5trace.c index 2dab8ec..92736d4 100644 --- a/src/H5trace.c +++ b/src/H5trace.c @@ -612,10 +612,6 @@ H5_trace(const double *returning, const char *func, const char *type, ...) fprintf(out, "H5D_MPIO_MULTI_CHUNK"); break; - case H5D_MPIO_MULTI_CHUNK_NO_OPT: - fprintf(out, "H5D_MPIO_MULTI_CHUNK_NO_OPT"); - break; - default: fprintf(out, "%ld", (long)chunk_opt_mode); break; diff --git a/src/Makefile.in b/src/Makefile.in index c673bcf..fc89be5 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -522,7 +522,7 @@ CHECK_CLEANFILES = *.chkexe *.chklog *.clog # Add libtool shared library version numbers to the HDF5 library # See libtool versioning documentation online. LT_VERS_INTERFACE = 6 -LT_VERS_REVISION = 122 +LT_VERS_REVISION = 126 LT_VERS_AGE = 0 H5detect_CFLAGS = -g $(AM_CFLAGS) |