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author | Quincey Koziol <koziol@hdfgroup.org> | 2014-03-07 19:12:20 (GMT) |
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committer | Quincey Koziol <koziol@hdfgroup.org> | 2014-03-07 19:12:20 (GMT) |
commit | ac0ef34a4132dcf8c27eb6731cb2686acc593205 (patch) | |
tree | 2efe1bf4d516206f806ae74016e921a3a42ee58a | |
parent | e367f64e24b95876d7c2673c7181aa12533d3f31 (diff) | |
download | hdf5-ac0ef34a4132dcf8c27eb6731cb2686acc593205.zip hdf5-ac0ef34a4132dcf8c27eb6731cb2686acc593205.tar.gz hdf5-ac0ef34a4132dcf8c27eb6731cb2686acc593205.tar.bz2 |
[svn-r24769] Description:
Check in Mohamad's changes to support collective I/O on point selections,
along with some other minor cleanups.
Tested on:
Mac OSX/64 10.9.2 (amazon) w/parallel & serial
(h5committest forthcoming)
-rw-r--r-- | MANIFEST | 1 | ||||
-rw-r--r-- | hl/src/H5DO.c | 122 | ||||
-rw-r--r-- | hl/src/H5DOprivate.h | 37 | ||||
-rw-r--r-- | src/H5Dchunk.c | 84 | ||||
-rw-r--r-- | src/H5Dcompact.c | 2 | ||||
-rw-r--r-- | src/H5Dcontig.c | 2 | ||||
-rw-r--r-- | src/H5Dint.c | 8 | ||||
-rw-r--r-- | src/H5Dio.c | 31 | ||||
-rw-r--r-- | src/H5Dmpio.c | 129 | ||||
-rw-r--r-- | src/H5Dpkg.h | 16 | ||||
-rw-r--r-- | src/H5Dprivate.h | 3 | ||||
-rw-r--r-- | src/H5Pdxpl.c | 9 | ||||
-rw-r--r-- | src/H5Smpio.c | 443 | ||||
-rw-r--r-- | src/H5Sprivate.h | 13 | ||||
-rw-r--r-- | src/H5Sselect.c | 53 | ||||
-rw-r--r-- | src/H5private.h | 4 | ||||
-rw-r--r-- | testpar/t_coll_chunk.c | 401 | ||||
-rw-r--r-- | testpar/t_dset.c | 406 | ||||
-rw-r--r-- | testpar/testphdf5.h | 19 |
19 files changed, 1382 insertions, 401 deletions
@@ -2246,7 +2246,6 @@ ./hl/src/Makefile.am ./hl/src/Makefile.in ./hl/src/H5DO.c -./hl/src/H5DOprivate.h ./hl/src/H5DOpublic.h ./hl/src/H5DS.c ./hl/src/H5DSprivate.h diff --git a/hl/src/H5DO.c b/hl/src/H5DO.c index 9cfd8c1..99dbd93 100644 --- a/hl/src/H5DO.c +++ b/hl/src/H5DO.c @@ -18,8 +18,14 @@ #include <assert.h> #include <stdio.h> -#include "H5DOprivate.h" +/* High-level library internal header file */ +#include "H5HLprivate2.h" +/* public LT prototypes */ +#include "H5DOpublic.h" + + + /*------------------------------------------------------------------------- * Function: H5DOwrite_chunk * @@ -30,108 +36,64 @@ * Programmer: Raymond Lu * 30 July 2012 * - * Modifications: *------------------------------------------------------------------------- */ herr_t H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, size_t data_size, const void *buf) { - hbool_t created_dxpl = FALSE; - herr_t ret_value = SUCCEED; /* Return value */ + hbool_t created_dxpl = FALSE; /* Whether we created a DXPL */ + hbool_t do_direct_write = TRUE; /* Flag for direct writes */ + uint32_t data_size_32; /* Chunk data size (limited to 32-bits currently) */ + herr_t ret_value = FAIL; /* Return value */ - if(dset_id < 0) { - ret_value = FAIL; + /* Check arguments */ + if(dset_id < 0) goto done; - } - - if(!buf) { - ret_value = FAIL; + if(!buf) goto done; - } - - if(!offset) { - ret_value = FAIL; + if(!offset) goto done; - } - - if(!data_size) { - ret_value = FAIL; + if(!data_size) + goto done; + data_size_32 = (uint32_t)data_size; + if(data_size != (size_t)data_size_32) goto done; - } + /* If the user passed in a default DXPL, create one to pass to H5Dwrite() */ if(H5P_DEFAULT == dxpl_id) { - if((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0) { - ret_value = FAIL; + if((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0) goto done; - } - created_dxpl = TRUE; - } + } /* end if */ - if(H5DO_write_chunk(dset_id, dxpl_id, filters, offset, data_size, buf) < 0) { - ret_value = FAIL; + /* Set direct write parameters */ + if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &do_direct_write) < 0) goto done; - } - -done: - if(created_dxpl) { - if(H5Pclose(dxpl_id) < 0) - ret_value = FAIL; - } - - return ret_value; -} - -/*------------------------------------------------------------------------- - * Function: H5DO_write_chunk - * - * Purpose: Private function for H5DOwrite_chunk - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Raymond Lu - * 30 July 2012 - * - * Modifications: - *------------------------------------------------------------------------- - */ -herr_t -H5DO_write_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, - size_t data_size, const void *buf) -{ - hbool_t do_direct_write = TRUE; - herr_t ret_value = SUCCEED; /* Return value */ - - if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &do_direct_write) < 0) { - ret_value = FAIL; + if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &filters) < 0) goto done; - } - - if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &filters) < 0) { - ret_value = FAIL; + if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, &offset) < 0) goto done; - } - - if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, &offset) < 0) { - ret_value = FAIL; + if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &data_size_32) < 0) goto done; - } - if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &data_size) < 0) { - ret_value = FAIL; + /* Write chunk */ + if(H5Dwrite(dset_id, 0, H5S_ALL, H5S_ALL, dxpl_id, buf) < 0) goto done; - } - if(H5Dwrite(dset_id, 0, H5S_ALL, H5S_ALL, dxpl_id, buf) < 0) { - ret_value = FAIL; - goto done; - } + /* Indicate success */ + ret_value = SUCCEED; done: - do_direct_write = FALSE; - if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &do_direct_write) < 0) - ret_value = FAIL; + if(created_dxpl) { + if(H5Pclose(dxpl_id) < 0) + ret_value = FAIL; + } /* end if */ + else + /* Reset the direct write flag on user DXPL */ + if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &do_direct_write) < 0) + ret_value = FAIL; + + return(ret_value); +} /* end H5DOwrite_chunk() */ - return ret_value; -} diff --git a/hl/src/H5DOprivate.h b/hl/src/H5DOprivate.h deleted file mode 100644 index fcea585..0000000 --- a/hl/src/H5DOprivate.h +++ /dev/null @@ -1,37 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by The HDF Group. * - * Copyright by the Board of Trustees of the University of Illinois. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from help@hdfgroup.org. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -#ifndef _H5DOprivate_H -#define _H5DOprivate_H - -/* High-level library internal header file */ -#include "H5HLprivate2.h" - -/* public LT prototypes */ -#include "H5DOpublic.h" - -/*------------------------------------------------------------------------- - * Private functions - *------------------------------------------------------------------------- - */ - -H5_HLDLL herr_t H5DO_write_chunk(hid_t dset_id, - hid_t dxpl_id, - uint32_t filters, - const hsize_t *offset, - size_t data_size, - const void *buf); - -#endif diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index e834aa3..92db446 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -164,10 +164,18 @@ typedef struct H5D_chunk_it_ud4_t { /* Callback info for nonexistent readvv operation */ typedef struct H5D_chunk_readvv_ud_t { unsigned char *rbuf; /* Read buffer to initialize */ - H5D_t *dset; /* Dataset to operate on */ + const H5D_t *dset; /* Dataset to operate on */ hid_t dxpl_id; /* DXPL for operation */ } H5D_chunk_readvv_ud_t; +/* Callback info for file selection iteration */ +typedef struct H5D_chunk_file_iter_ud_t { + H5D_chunk_map_t *fm; /* File->memory chunk mapping info */ +#ifdef H5_HAVE_PARALLEL + const H5D_io_info_t *io_info; /* I/O info for operation */ +#endif /* H5_HAVE_PARALLEL */ +} H5D_chunk_file_iter_ud_t; + /********************/ /* Local Prototypes */ @@ -297,7 +305,7 @@ H5FL_BLK_DEFINE_STATIC(chunk); */ herr_t H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, hsize_t *offset, - size_t data_size, const void *buf) + uint32_t data_size, const void *buf) { const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */ H5D_chunk_ud_t udata; /* User data for querying chunk info */ @@ -329,8 +337,7 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, hsiz HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't get chunk index") /* Find out the file address of the chunk */ - if(H5D__chunk_lookup(dset, dxpl_id, offset, chunk_idx, - &udata) < 0) + if(H5D__chunk_lookup(dset, dxpl_id, offset, chunk_idx, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") udata.filter_mask = filters; @@ -685,7 +692,7 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t *fm) { - H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */ + const H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */ const H5T_t *mem_type = type_info->mem_type; /* Local pointer to memory datatype */ H5S_t *tmp_mspace = NULL; /* Temporary memory dataspace */ hssize_t old_offset[H5O_LAYOUT_NDIMS]; /* Old selection offset */ @@ -698,7 +705,6 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf H5S_sel_type fsel_type; /* Selection type on disk */ char bogus; /* "bogus" buffer to pass to selection iterator */ unsigned u; /* Local index variable */ - hbool_t sel_hyper_flag; herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC @@ -796,6 +802,8 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create chunk selections for single element") } /* end if */ else { + hbool_t sel_hyper_flag; /* Whether file selection is a hyperslab */ + /* Initialize skip list for chunk selections */ if(NULL == dataset->shared->cache.chunk.sel_chunks) { if(NULL == (dataset->shared->cache.chunk.sel_chunks = H5SL_create(H5SL_TYPE_HSIZE, NULL))) @@ -843,12 +851,20 @@ H5D__chunk_io_init(const H5D_io_info_t *io_info, const H5D_type_info_t *type_inf } /* end while */ } /* end if */ else { + H5D_chunk_file_iter_ud_t udata; /* User data for iteration */ + /* Create temporary datatypes for selection iteration */ if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL), FALSE)) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype") + /* Initialize the user data */ + udata.fm = fm; +#ifdef H5_HAVE_PARALLEL + udata.io_info = io_info; +#endif /* H5_HAVE_PARALLEL */ + /* Spaces might not be the same shape, iterate over the file selection directly */ - if(H5S_select_iterate(&bogus, f_tid, file_space, H5D__chunk_file_cb, fm) < 0) + if(H5S_select_iterate(&bogus, f_tid, file_space, H5D__chunk_file_cb, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") /* Reset "last chunk" info */ @@ -1265,7 +1281,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t /* Add temporary chunk to the list of chunks */ /* Allocate the file & memory chunk information */ - if (NULL==(new_chunk_info = H5FL_MALLOC (H5D_chunk_info_t))) { + if (NULL==(new_chunk_info = H5FL_MALLOC(H5D_chunk_info_t))) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") } /* end if */ @@ -1276,7 +1292,7 @@ H5D__create_chunk_file_map_hyper(H5D_chunk_map_t *fm, const H5D_io_info_t new_chunk_info->index=chunk_index; #ifdef H5_HAVE_PARALLEL - /* store chunk selection information */ + /* Store chunk selection information, for multi-chunk I/O */ if(io_info->using_mpi_vfd) fm->select_chunk[chunk_index] = new_chunk_info; #endif /* H5_HAVE_PARALLEL */ @@ -1476,9 +1492,10 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_fm) +H5D__chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_udata) { - H5D_chunk_map_t *fm = (H5D_chunk_map_t *)_fm; /* File<->memory chunk mapping info */ + H5D_chunk_file_iter_ud_t *udata = (H5D_chunk_file_iter_ud_t *)_udata; /* User data for operation */ + H5D_chunk_map_t *fm = udata->fm; /* File<->memory chunk mapping info */ H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */ hsize_t coords_in_chunk[H5O_LAYOUT_NDIMS]; /* Coordinates of element in chunk */ hsize_t chunk_index; /* Chunk index */ @@ -1496,7 +1513,7 @@ H5D__chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, cons /* If the chunk index is the same as the last chunk index we used, * get the cached info to operate on. */ - chunk_info=fm->last_chunk_info; + chunk_info = fm->last_chunk_info; } /* end if */ else { /* If the chunk index is not the same as the last chunk index we used, @@ -1553,14 +1570,20 @@ H5D__chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, cons } /* end if */ } /* end if */ +#ifdef H5_HAVE_PARALLEL + /* Store chunk selection information, for collective multi-chunk I/O */ + if(udata->io_info->using_mpi_vfd) + fm->select_chunk[chunk_index] = chunk_info; +#endif /* H5_HAVE_PARALLEL */ + /* Update the "last chunk seen" information */ - fm->last_index=chunk_index; - fm->last_chunk_info=chunk_info; + fm->last_index = chunk_index; + fm->last_chunk_info = chunk_info; } /* end else */ - /* Get the coordinates of the element in the chunk */ + /* Get the offset of the element within the chunk */ for(u = 0; u < fm->f_ndims; u++) - coords_in_chunk[u] = coords[u] % fm->layout->u.chunk.dim[u]; + coords_in_chunk[u] = coords[u] - chunk_info->coords[u]; /* Add point to file selection for chunk */ if(H5S_select_elements(chunk_info->fspace, H5S_SELECT_APPEND, (size_t)1, coords_in_chunk) < 0) @@ -1669,8 +1692,8 @@ done: htri_t H5D__chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr, hbool_t write_op) { - const H5D_t *dataset = io_info->dset; - htri_t ret_value = FAIL; + const H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */ + htri_t ret_value = FAIL; /* Return value */ FUNC_ENTER_PACKAGE @@ -1815,8 +1838,7 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, chunk_info = H5D_CHUNK_GET_NODE_INFO(fm, chunk_node); /* Get the info for the chunk in the file */ - if(H5D__chunk_lookup(io_info->dset, io_info->dxpl_id, - chunk_info->coords, chunk_info->index, &udata) < 0) + if(H5D__chunk_lookup(io_info->dset, io_info->dxpl_id, chunk_info->coords, chunk_info->index, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") /* Check for non-existant chunk & skip it if appropriate */ @@ -1945,8 +1967,7 @@ H5D__chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, /* Load the chunk into cache. But if the whole chunk is written, * simply allocate space instead of load the chunk. */ - if(H5D__chunk_lookup(io_info->dset, io_info->dxpl_id, chunk_info->coords, - chunk_info->index, &udata) < 0) + if(H5D__chunk_lookup(io_info->dset, io_info->dxpl_id, chunk_info->coords, chunk_info->index, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") if((cacheable = H5D__chunk_cacheable(io_info, udata.addr, TRUE)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't tell if chunk is cacheable") @@ -2296,7 +2317,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__chunk_create(H5D_t *dset /*in,out*/, hid_t dxpl_id) +H5D__chunk_create(const H5D_t *dset /*in,out*/, hid_t dxpl_id) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ herr_t ret_value = SUCCEED; /* Return value */ @@ -2777,7 +2798,7 @@ void * H5D__chunk_lock(const H5D_io_info_t *io_info, H5D_chunk_ud_t *udata, hbool_t relax) { - H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ + const H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ const H5O_pline_t *pline = &(dset->shared->dcpl_cache.pline); /* I/O pipeline info - always equal to the pline passed to H5D__chunk_alloc */ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */ const H5O_fill_t *fill = &(dset->shared->dcpl_cache.fill); /* Fill value info */ @@ -3216,7 +3237,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, +H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, hsize_t old_dim[]) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ @@ -3417,8 +3438,7 @@ H5D__chunk_allocate(H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, &chunk_idx) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't get chunk index") - if(H5D__chunk_lookup(dset, dxpl_id, chunk_offset, chunk_idx, - &udata) < 0) + if(H5D__chunk_lookup(dset, dxpl_id, chunk_offset, chunk_idx, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") HDassert(!H5F_addr_defined(udata.addr)); @@ -3583,7 +3603,7 @@ static herr_t H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata) { const H5D_io_info_t *io_info = udata->io_info; /* Local pointer to I/O info */ - H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ + const H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset's layout */ unsigned rank = udata->common.layout->ndims - 1; /* Dataset rank */ const hsize_t *chunk_offset = io_info->store->chunk.offset; /* Chunk offset */ @@ -3605,8 +3625,7 @@ H5D__chunk_prune_fill(H5D_chunk_it_ud1_t *udata) H5_ASSIGN_OVERFLOW(chunk_size, layout->u.chunk.size, uint32_t, size_t); /* Get the info for the chunk in the file */ - if(H5D__chunk_lookup(dset, io_info->dxpl_id, chunk_offset, - io_info->store->chunk.index, &chk_udata) < 0) + if(H5D__chunk_lookup(dset, io_info->dxpl_id, chunk_offset, io_info->store->chunk.index, &chk_udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") /* If this chunk does not exist in cache or on disk, no need to do anything @@ -4015,8 +4034,7 @@ H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim) #endif /* NDEBUG */ /* Check if the chunk exists in cache or on disk */ - if(H5D__chunk_lookup(dset, dxpl_id, chunk_offset, - chk_io_info.store->chunk.index, &chk_udata) < 0) + if(H5D__chunk_lookup(dset, dxpl_id, chunk_offset, chk_io_info.store->chunk.index, &chk_udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk") /* Evict the entry from the cache if present, but do not flush @@ -4155,7 +4173,7 @@ herr_t H5D__chunk_addrmap(const H5D_io_info_t *io_info, haddr_t chunk_addr[]) { H5D_chk_idx_info_t idx_info; /* Chunked index info */ - H5D_t *dset = io_info->dset; /* Local pointer to dataset info */ + const H5D_t *dset = io_info->dset; /* Local pointer to dataset info */ H5D_chunk_it_ud2_t udata; /* User data for iteration callback */ herr_t ret_value = SUCCEED; /* Return value */ diff --git a/src/H5Dcompact.c b/src/H5Dcompact.c index 0b34c07..789beab 100644 --- a/src/H5Dcompact.c +++ b/src/H5Dcompact.c @@ -117,7 +117,7 @@ H5FL_BLK_EXTERN(type_conv); *------------------------------------------------------------------------- */ herr_t -H5D__compact_fill(H5D_t *dset, hid_t dxpl_id) +H5D__compact_fill(const H5D_t *dset, hid_t dxpl_id) { H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */ hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */ diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c index 69db7d4..8d4cd02 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -192,7 +192,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__contig_fill(H5D_t *dset, hid_t dxpl_id) +H5D__contig_fill(const H5D_t *dset, hid_t dxpl_id) { H5D_io_info_t ioinfo; /* Dataset I/O info */ H5D_storage_t store; /* Union of storage info for dataset */ diff --git a/src/H5Dint.c b/src/H5Dint.c index bc24c4f..15f5df7 100644 --- a/src/H5Dint.c +++ b/src/H5Dint.c @@ -66,7 +66,7 @@ static herr_t H5D__init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space static herr_t H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset, hid_t dapl_id); static herr_t H5D__open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id); -static herr_t H5D__init_storage(H5D_t *dataset, hbool_t full_overwrite, +static herr_t H5D__init_storage(const H5D_t *dataset, hbool_t full_overwrite, hsize_t old_dim[], hid_t dxpl_id); @@ -1578,7 +1578,7 @@ H5D_typeof(const H5D_t *dset) *------------------------------------------------------------------------- */ herr_t -H5D__alloc_storage(H5D_t *dset/*in,out*/, hid_t dxpl_id, H5D_time_alloc_t time_alloc, +H5D__alloc_storage(const H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc, hbool_t full_overwrite, hsize_t old_dim[]) { H5F_t *f = dset->oloc.file; /* The dataset's file pointer */ @@ -1741,7 +1741,7 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__init_storage(H5D_t *dset, hbool_t full_overwrite, hsize_t old_dim[], +H5D__init_storage(const H5D_t *dset, hbool_t full_overwrite, hsize_t old_dim[], hid_t dxpl_id) { herr_t ret_value = SUCCEED; /* Return value */ @@ -2357,7 +2357,7 @@ done: *------------------------------------------------------------------------- */ herr_t -H5D__mark(H5D_t *dataset, hid_t UNUSED dxpl_id, unsigned flags) +H5D__mark(const H5D_t *dataset, hid_t UNUSED dxpl_id, unsigned flags) { herr_t ret_value = SUCCEED; /* Return value */ diff --git a/src/H5Dio.c b/src/H5Dio.c index 9b2f8ff..2687c5f 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -59,7 +59,11 @@ static herr_t H5D__pre_write(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_i hid_t file_space_id, hid_t dxpl_id, const void *buf); /* Setup/teardown routines */ -static herr_t H5D__ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache, +static herr_t H5D__ioinfo_init(H5D_t *dset, +#ifndef H5_HAVE_PARALLEL +const +#endif /* H5_HAVE_PARALLEL */ + H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, const H5D_type_info_t *type_info, H5D_storage_t *store, H5D_io_info_t *io_info); static herr_t H5D__typeinfo_init(const H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache, @@ -275,14 +279,15 @@ H5D__pre_write(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, if(NULL == (plist = (H5P_genplist_t *)H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list") + /* Retrieve the 'direct write' flag */ if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &direct_write) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting flag for direct chunk write") /* Direct chunk write */ if(direct_write) { - uint32_t direct_filters = 0; + uint32_t direct_filters; hsize_t *direct_offset; - size_t direct_datasize = 0; + uint32_t direct_datasize; int ndims = 0; hsize_t dims[H5O_LAYOUT_NDIMS]; hsize_t internal_offset[H5O_LAYOUT_NDIMS]; @@ -291,12 +296,11 @@ H5D__pre_write(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, if(H5D_CHUNKED != dset->shared->layout.type) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset") + /* Retrieve parameters for direct chunk write */ if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &direct_filters) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting filter info for direct chunk write") - if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, &direct_offset) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting offset info for direct chunk write") - if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &direct_datasize) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting data size for direct chunk write") @@ -305,7 +309,7 @@ H5D__pre_write(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, if((ndims = H5S_get_simple_extent_dims(dset->shared->space, dims, NULL)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve dataspace extent dims") - for(i=0; i<ndims; i++) { + for(i = 0; i < ndims; i++) { /* Make sure the offset doesn't exceed the dataset's dimensions */ if(direct_offset[i] > dims[i]) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset") @@ -315,7 +319,7 @@ H5D__pre_write(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary") internal_offset[i] = direct_offset[i]; - } + } /* end for */ /* Terminate the offset with a zero */ internal_offset[ndims] = 0; @@ -323,7 +327,8 @@ H5D__pre_write(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, /* write raw data */ if(H5D__chunk_direct_write(dset, dxpl_id, direct_filters, internal_offset, direct_datasize, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write chunk directly") - } else { /* Normal write */ + } /* end if */ + else { /* Normal write */ const H5S_t *mem_space = NULL; const H5S_t *file_space = NULL; char fake_char; @@ -472,7 +477,7 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, /* Attempt to construct projected dataspace for memory dataspace */ if(H5S_select_construct_projection(mem_space, &projected_mem_space, - (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, &adj_buf, type_info.dst_type_size) < 0) + (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, (const void **)&adj_buf, type_info.dst_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to construct projected memory dataspace") HDassert(projected_mem_space); HDassert(adj_buf); @@ -698,7 +703,7 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, /* Attempt to construct projected dataspace for memory dataspace */ if(H5S_select_construct_projection(mem_space, &projected_mem_space, - (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, &adj_buf, type_info.src_type_size) < 0) + (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, (const void **)&adj_buf, type_info.src_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to construct projected memory dataspace") HDassert(projected_mem_space); HDassert(adj_buf); @@ -825,7 +830,11 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, +H5D__ioinfo_init(H5D_t *dset, +#ifndef H5_HAVE_PARALLEL +const +#endif /* H5_HAVE_PARALLEL */ + H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, const H5D_type_info_t *type_info, H5D_storage_t *store, H5D_io_info_t *io_info) { FUNC_ENTER_STATIC_NOERR diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index 3b5bb30..684f510 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -183,42 +183,30 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, /* Optimized MPI types flag must be set and it must be collective IO */ /* (Don't allow parallel I/O for the MPI-posix driver, since it doesn't do real collective I/O) */ if(!(H5S_mpi_opt_types_g && io_info->dxpl_cache->xfer_mode == H5FD_MPIO_COLLECTIVE - && !IS_H5FD_MPIPOSIX(io_info->dset->oloc.file))) { + && !IS_H5FD_MPIPOSIX(io_info->dset->oloc.file))) local_cause |= H5D_MPIO_SET_MPIPOSIX; - } /* end if */ /* Don't allow collective operations if datatype conversions need to happen */ - if(!type_info->is_conv_noop) { + if(!type_info->is_conv_noop) local_cause |= H5D_MPIO_DATATYPE_CONVERSION; - } /* end if */ /* Don't allow collective operations if data transform operations should occur */ - if(!type_info->is_xform_noop) { + if(!type_info->is_xform_noop) local_cause |= H5D_MPIO_DATA_TRANSFORMS; - } /* end if */ /* Check whether these are both simple or scalar dataspaces */ if(!((H5S_SIMPLE == H5S_GET_EXTENT_TYPE(mem_space) || H5S_SCALAR == H5S_GET_EXTENT_TYPE(mem_space)) - && (H5S_SIMPLE == H5S_GET_EXTENT_TYPE(file_space) || H5S_SCALAR == H5S_GET_EXTENT_TYPE(file_space)))) { + && (H5S_SIMPLE == H5S_GET_EXTENT_TYPE(file_space) || H5S_SCALAR == H5S_GET_EXTENT_TYPE(file_space)))) local_cause |= H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES; - } /* end if */ - - /* Can't currently handle point selections */ - if(H5S_SEL_POINTS == H5S_GET_SELECT_TYPE(mem_space) - || H5S_SEL_POINTS == H5S_GET_SELECT_TYPE(file_space)) { - local_cause |= H5D_MPIO_POINT_SELECTIONS; - } /* end if */ /* Dataset storage must be contiguous or chunked */ if(!(io_info->dset->shared->layout.type == H5D_CONTIGUOUS || - io_info->dset->shared->layout.type == H5D_CHUNKED)) { + io_info->dset->shared->layout.type == H5D_CHUNKED)) local_cause |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET; - } /* end if */ /* check if external-file storage is used */ - if (io_info->dset->shared->dcpl_cache.efl.nused > 0) { + if(io_info->dset->shared->dcpl_cache.efl.nused > 0) local_cause |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET; - } /* The handling of memory space is different for chunking and contiguous * storage. For contiguous storage, mem_space and file_space won't change @@ -228,11 +216,9 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, */ /* Don't allow collective operations if filters need to be applied */ - if(io_info->dset->shared->layout.type == H5D_CHUNKED) { - if(io_info->dset->shared->dcpl_cache.pline.nused > 0) { - local_cause |= H5D_MPIO_FILTERS; - } /* end if */ - } /* end if */ + if(io_info->dset->shared->layout.type == H5D_CHUNKED && + io_info->dset->shared->dcpl_cache.pline.nused > 0) + local_cause |= H5D_MPIO_FILTERS; /* Form consensus opinion among all processes about whether to perform * collective I/O @@ -242,7 +228,6 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, ret_value = global_cause > 0 ? FALSE : TRUE; - done: /* Write the local value of no-collective-cause to the DXPL. */ if(H5P_set(dx_plist, H5D_MPIO_LOCAL_NO_COLLECTIVE_CAUSE_NAME, &local_cause) < 0) @@ -946,15 +931,58 @@ if(H5DEBUG(D)) /* Obtain MPI derived datatype from all individual chunks */ for(u = 0; u < num_chunk; u++) { - /* Disk MPI derived datatype */ + hsize_t *permute_map = NULL; /* array that holds the mapping from the old, + out-of-order displacements to the in-order + displacements of the MPI datatypes of the + point selection of the file space */ + hbool_t is_permuted = FALSE; + + /* Obtain disk and memory MPI derived datatype */ + /* NOTE: The permute_map array can be allocated within H5S_mpio_space_type + * and will be fed into the next call to H5S_mpio_space_type + * where it will be freed. + */ if(H5S_mpio_space_type(chunk_addr_info_array[u].chunk_info.fspace, - type_info->src_type_size, &chunk_ftype[u], &chunk_mpi_file_counts[u], &(chunk_mft_is_derived_array[u])) < 0) + type_info->src_type_size, + &chunk_ftype[u], /* OUT: datatype created */ + &chunk_mpi_file_counts[u], /* OUT */ + &(chunk_mft_is_derived_array[u]), /* OUT */ + TRUE, /* this is a file space, + so permute the + datatype if the point + selections are out of + order */ + &permute_map,/* OUT: a map to indicate the + permutation of points + selected in case they + are out of order */ + &is_permuted /* OUT */) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create MPI file type") - - /* Buffer MPI derived datatype */ + /* Sanity check */ + if(is_permuted) + HDassert(permute_map); if(H5S_mpio_space_type(chunk_addr_info_array[u].chunk_info.mspace, - type_info->dst_type_size, &chunk_mtype[u], &chunk_mpi_mem_counts[u], &(chunk_mbt_is_derived_array[u])) < 0) + type_info->dst_type_size, &chunk_mtype[u], + &chunk_mpi_mem_counts[u], + &(chunk_mbt_is_derived_array[u]), + FALSE, /* this is a memory + space, so if the file + space is not + permuted, there is no + need to permute the + datatype if the point + selections are out of + order*/ + &permute_map, /* IN: the permutation map + generated by the + file_space selection + and applied to the + memory selection */ + &is_permuted /* IN */) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create MPI buf type") + /* Sanity check */ + if(is_permuted) + HDassert(!permute_map); /* Chunk address relative to the first chunk */ chunk_addr_info_array[u].chunk_addr -= ctg_store.contig.dset_addr; @@ -1309,12 +1337,51 @@ H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf if((file_space != NULL) && (mem_space != NULL)) { int mpi_file_count; /* Number of file "objects" to transfer */ + hsize_t *permute_map = NULL; /* array that holds the mapping from the old, + out-of-order displacements to the in-order + displacements of the MPI datatypes of the + point selection of the file space */ + hbool_t is_permuted = FALSE; /* Obtain disk and memory MPI derived datatype */ - if(H5S_mpio_space_type(file_space, type_info->src_type_size, &mpi_file_type, &mpi_file_count, &mft_is_derived) < 0) + /* NOTE: The permute_map array can be allocated within H5S_mpio_space_type + * and will be fed into the next call to H5S_mpio_space_type + * where it will be freed. + */ + if(H5S_mpio_space_type(file_space, type_info->src_type_size, + &mpi_file_type, &mpi_file_count, &mft_is_derived, /* OUT: datatype created */ + TRUE, /* this is a file space, so + permute the datatype if the + point selection is out of + order */ + &permute_map, /* OUT: a map to indicate + the permutation of + points selected in + case they are out of + order */ + &is_permuted /* OUT */) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create MPI file type") - if(H5S_mpio_space_type(mem_space, type_info->src_type_size, &mpi_buf_type, &mpi_buf_count, &mbt_is_derived) < 0) + /* Sanity check */ + if(is_permuted) + HDassert(permute_map); + if(H5S_mpio_space_type(mem_space, type_info->src_type_size, + &mpi_buf_type, &mpi_buf_count, &mbt_is_derived, /* OUT: datatype created */ + FALSE, /* this is a memory space, so if + the file space is not + permuted, there is no need to + permute the datatype if the + point selections are out of + order*/ + &permute_map /* IN: the permutation map + generated by the + file_space selection + and applied to the + memory selection */, + &is_permuted /* IN */) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create MPI buffer type") + /* Sanity check */ + if(is_permuted) + HDassert(!permute_map); } /* end if */ else { /* For non-selection, participate with a none MPI derived datatype, the count is 0. */ diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index 7e6eb4b..c3cee61 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -187,7 +187,7 @@ typedef enum H5D_io_op_type_t { } H5D_io_op_type_t; typedef struct H5D_io_info_t { - H5D_t *dset; /* Pointer to dataset being operated on */ + const H5D_t *dset; /* Pointer to dataset being operated on */ #ifndef H5_HAVE_PARALLEL const #endif /* H5_HAVE_PARALLEL */ @@ -531,7 +531,7 @@ H5_DLL H5D_t *H5D__create_named(const H5G_loc_t *loc, const char *name, hid_t dapl_id, hid_t dxpl_id); H5_DLL herr_t H5D__get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id); -H5_DLL herr_t H5D__alloc_storage(H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc, +H5_DLL herr_t H5D__alloc_storage(const H5D_t *dset, hid_t dxpl_id, H5D_time_alloc_t time_alloc, hbool_t full_overwrite, hsize_t old_dim[]); H5_DLL herr_t H5D__get_storage_size(H5D_t *dset, hid_t dxpl_id, hsize_t *storage_size); H5_DLL haddr_t H5D__get_offset(const H5D_t *dset); @@ -544,7 +544,7 @@ H5_DLL herr_t H5D__check_filters(H5D_t *dataset); H5_DLL herr_t H5D__set_extent(H5D_t *dataset, const hsize_t *size, hid_t dxpl_id); H5_DLL herr_t H5D__get_dxpl_cache(hid_t dxpl_id, H5D_dxpl_cache_t **cache); H5_DLL herr_t H5D__flush_sieve_buf(H5D_t *dataset, hid_t dxpl_id); -H5_DLL herr_t H5D__mark(H5D_t *dataset, hid_t dxpl_id, unsigned flags); +H5_DLL herr_t H5D__mark(const H5D_t *dataset, hid_t dxpl_id, unsigned flags); H5_DLL herr_t H5D__flush_real(H5D_t *dataset, hid_t dxpl_id); /* Internal I/O routines */ @@ -586,7 +586,7 @@ H5_DLL herr_t H5D__layout_oh_write(H5D_t *dataset, hid_t dxpl_id, H5O_t *oh, H5_DLL herr_t H5D__contig_alloc(H5F_t *f, hid_t dxpl_id, H5O_storage_contig_t *storage); H5_DLL hbool_t H5D__contig_is_space_alloc(const H5O_storage_t *storage); -H5_DLL herr_t H5D__contig_fill(H5D_t *dset, hid_t dxpl_id); +H5_DLL herr_t H5D__contig_fill(const H5D_t *dset, hid_t dxpl_id); H5_DLL herr_t H5D__contig_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t *fm); @@ -603,7 +603,7 @@ H5_DLL herr_t H5D__contig_delete(H5F_t *f, hid_t dxpl_id, /* Functions that operate on chunked dataset storage */ H5_DLL htri_t H5D__chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr, hbool_t write_op); -H5_DLL herr_t H5D__chunk_create(H5D_t *dset /*in,out*/, hid_t dxpl_id); +H5_DLL herr_t H5D__chunk_create(const H5D_t *dset /*in,out*/, hid_t dxpl_id); H5_DLL herr_t H5D__chunk_set_info(const H5D_t *dset); H5_DLL herr_t H5D__chunk_init(H5F_t *f, hid_t dxpl_id, const H5D_t *dset, hid_t dapl_id); @@ -616,7 +616,7 @@ H5_DLL herr_t H5D__chunk_unlock(const H5D_io_info_t *io_info, const H5D_chunk_ud_t *udata, hbool_t dirty, void *chunk, uint32_t naccessed); H5_DLL herr_t H5D__chunk_allocated(H5D_t *dset, hid_t dxpl_id, hsize_t *nbytes); -H5_DLL herr_t H5D__chunk_allocate(H5D_t *dset, hid_t dxpl_id, +H5_DLL herr_t H5D__chunk_allocate(const H5D_t *dset, hid_t dxpl_id, hbool_t full_overwrite, hsize_t old_dim[]); H5_DLL herr_t H5D__chunk_prune_by_extent(H5D_t *dset, hid_t dxpl_id, const hsize_t *old_dim); @@ -634,12 +634,14 @@ H5_DLL herr_t H5D__chunk_dump_index(H5D_t *dset, hid_t dxpl_id, FILE *stream); H5_DLL herr_t H5D__chunk_dest(H5F_t *f, hid_t dxpl_id, H5D_t *dset); H5_DLL herr_t H5D__chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_t *oh, H5O_storage_t *store); +H5_DLL herr_t H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, + hsize_t *offset, uint32_t data_size, const void *buf); #ifdef H5D_CHUNK_DEBUG H5_DLL herr_t H5D__chunk_stats(const H5D_t *dset, hbool_t headers); #endif /* H5D_CHUNK_DEBUG */ /* Functions that operate on compact dataset storage */ -H5_DLL herr_t H5D__compact_fill(H5D_t *dset, hid_t dxpl_id); +H5_DLL herr_t H5D__compact_fill(const H5D_t *dset, hid_t dxpl_id); H5_DLL herr_t H5D__compact_copy(H5F_t *f_src, H5O_storage_compact_t *storage_src, H5F_t *f_dst, H5O_storage_compact_t *storage_dst, H5T_t *src_dtype, H5O_copy_t *cpy_info, hid_t dxpl_id); diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h index 7adc231..d4ecedc 100644 --- a/src/H5Dprivate.h +++ b/src/H5Dprivate.h @@ -175,8 +175,5 @@ H5_DLL herr_t H5D_chunk_idx_reset(H5O_storage_chunk_t *storage, hbool_t reset_ad H5_DLL herr_t H5D_btree_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent, int fwidth, unsigned ndims); -H5_DLL herr_t H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters, - hsize_t *offset, size_t data_size, const void *buf); - #endif /* _H5Dprivate_H */ diff --git a/src/H5Pdxpl.c b/src/H5Pdxpl.c index b5d688b..472700a 100644 --- a/src/H5Pdxpl.c +++ b/src/H5Pdxpl.c @@ -165,7 +165,7 @@ #define H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_DEF 0 #define H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_SIZE sizeof(hsize_t *) #define H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_DEF NULL -#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_SIZE sizeof(size_t) +#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_SIZE sizeof(uint32_t) #define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF 0 /******************/ @@ -267,7 +267,7 @@ static const void *H5D_def_xfer_xform_g = H5D_XFER_XFORM_DEF; /* Defaul static const hbool_t H5D_def_direct_chunk_flag_g = H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_DEF; /* Default value for the flag of direct chunk write */ static const uint32_t H5D_def_direct_chunk_filters_g = H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_DEF; /* Default value for the filters of direct chunk write */ static const hsize_t *H5D_def_direct_chunk_offset_g = H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_DEF; /* Default value for the offset of direct chunk write */ -static const size_t H5D_def_direct_chunk_datasize_g = H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF; /* Default value for the datasize of direct chunk write */ +static const uint32_t H5D_def_direct_chunk_datasize_g = H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF; /* Default value for the datasize of direct chunk write */ /*------------------------------------------------------------------------- @@ -1493,8 +1493,9 @@ H5Pset_btree_ratios(hid_t plist_id, double left, double middle, H5TRACE4("e", "iddd", plist_id, left, middle, right); /* Check arguments */ - if(left < 0.0 || left > 1.0 || middle < 0.0 || middle > 1.0 || - right < 0.0 || right > 1.0) + if(left < (double)0.0f || left > (double)1.0f + || middle < (double)0.0f || middle > (double)1.0f + || right < (double)0.0f || right > (double)1.0f) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "split ratio must satisfy 0.0<=X<=1.0") /* Get the plist structure */ diff --git a/src/H5Smpio.c b/src/H5Smpio.c index 77e902f..284e16f 100644 --- a/src/H5Smpio.c +++ b/src/H5Smpio.c @@ -43,6 +43,14 @@ static herr_t H5S_mpio_all_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); static herr_t H5S_mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); +static herr_t H5S_mpio_create_point_datatype(size_t elmt_size, hsize_t num_points, + MPI_Aint *disp, MPI_Datatype *new_type); +static herr_t H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, + MPI_Datatype *new_type, int *count, hbool_t *is_derived_type, + hbool_t do_permute, hsize_t **permute_map, hbool_t *is_permuted); +static herr_t H5S_mpio_permute_type(const H5S_t *space, size_t elmt_size, + hsize_t **permute_map, MPI_Datatype *new_type, int *count, + hbool_t *is_derived_type); static herr_t H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); static herr_t H5S_mpio_span_hyper_type(const H5S_t *space, size_t elmt_size, @@ -131,6 +139,335 @@ H5S_mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) /*------------------------------------------------------------------------- + * Function: H5S_mpio_create_point_datatype + * + * Purpose: Create a derived datatype for point selections. + * + * Return: non-negative on success, negative on failure. + * + * Outputs: *new_type the MPI type corresponding to the selection + * + * Programmer: Mohamad Chaarawi + * + *------------------------------------------------------------------------- + */ +static herr_t +H5S_mpio_create_point_datatype (size_t elmt_size, hsize_t num_points, + MPI_Aint *disp, MPI_Datatype *new_type) +{ + MPI_Datatype elmt_type; /* MPI datatype for individual element */ + hbool_t elmt_type_created = FALSE; /* Whether the element MPI datatype was created */ + int mpi_code; /* MPI error code */ + int *blocks = NULL; /* Array of block sizes for MPI hindexed create call */ + hsize_t u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT + + /* Create an MPI datatype for an element */ + if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)elmt_size, MPI_BYTE, &elmt_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) + elmt_type_created = TRUE; + + /* Allocate block sizes for MPI datatype call */ + if(NULL == (blocks = (int *)H5MM_malloc(sizeof(int) * num_points))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") + + /* Would be nice to have Create_Hindexed_block to avoid this array of all ones */ + for(u = 0; u < num_points; u++) + blocks[u] = 1; + + /* Create an MPI datatype for the whole point selection */ + if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)num_points, blocks, disp, elmt_type, new_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_indexed_block failed", mpi_code) + + /* Commit MPI datatype for later use */ + if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type))) + HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) + +done: + if(elmt_type_created) + MPI_Type_free(&elmt_type); + if(blocks) + H5MM_free(blocks); + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5S_mpio_create_point_datatype() */ + + +/*------------------------------------------------------------------------- + * Function: H5S_mpio_point_type + * + * Purpose: Translate an HDF5 "point" selection into an MPI type. + * Create a permutation array to handle out-of-order point selections. + * + * Return: non-negative on success, negative on failure. + * + * Outputs: *new_type the MPI type corresponding to the selection + * *count how many objects of the new_type in selection + * (useful if this is the buffer type for xfer) + * *is_derived_type 0 if MPI primitive type, 1 if derived + * *permute_map the permutation of the displacements to create + * the MPI_Datatype + * *is_permuted 0 if the displacements are permuted, 1 if not + * + * Programmer: Mohamad Chaarawi + * + *------------------------------------------------------------------------- + */ +static herr_t +H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, + int *count, hbool_t *is_derived_type, hbool_t do_permute, hsize_t **permute, + hbool_t *is_permuted) +{ + MPI_Aint *disp = NULL; /* Datatype displacement for each point*/ + H5S_pnt_node_t *curr = NULL; /* Current point being operated on in from the selection */ + hssize_t snum_points; /* Signed number of elements in selection */ + hsize_t num_points; /* Sumber of points in the selection */ + hsize_t u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT + + /* Check args */ + HDassert(space); + + /* Get the total number of points selected */ + if((snum_points = (hssize_t)H5S_GET_SELECT_NPOINTS(space)) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements selected") + num_points = (hsize_t)snum_points; + + /* Allocate array for element displacements */ + if(NULL == (disp = (MPI_Aint *)H5MM_malloc(sizeof(MPI_Aint) * num_points))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of displacements") + + /* Allocate array for element permutation - returned to caller */ + if(do_permute) + if(NULL == (*permute = (hsize_t *)H5MM_malloc(sizeof(hsize_t) * num_points))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate permutation array") + + /* Iterate through list of elements */ + curr = space->select.sel_info.pnt_lst->head; + for(u = 0 ; u < num_points ; u++) { + /* calculate the displacement of the current point */ + disp[u] = H5VM_array_offset(space->extent.rank, space->extent.size, curr->pnt); + disp[u] *= elmt_size; + + /* This is a File Space used to set the file view, so adjust the displacements + * to have them monotonically non-decreasing. + * Generate the permutation array by indicating at each point being selected, + * the position it will shifted in the new displacement. Example: + * Suppose 4 points with corresponding are selected + * Pt 1: disp=6 ; Pt 2: disp=3 ; Pt 3: disp=0 ; Pt 4: disp=4 + * The permute map to sort the displacements in order will be: + * point 1: map[0] = L, indicating that this point is not moved (1st point selected) + * point 2: map[1] = 0, indicating that this point is moved to the first position, + * since disp_pt1(6) > disp_pt2(3) + * point 3: map[2] = 0, move to position 0, bec it has the lowest disp between + * the points selected so far. + * point 4: map[3] = 2, move the 2nd position since point 1 has a higher disp, + * but points 2 and 3 have lower displacements. + */ + if(do_permute) { + if(u > 0 && disp[u] < disp[u - 1]) { + unsigned s = 0, l = u, m = u / 2; + + *is_permuted = TRUE; + do { + if(disp[u] > disp[m]) + s = m + 1; + else if(disp[u] < disp[m]) + l = m; + else + break; + m = s + ((l - s) / 2); + } while(s < l); + + if(m < u) { + MPI_Aint temp; + + temp = disp[u]; + HDmemmove(disp + m + 1, disp + m, (u - m) * sizeof(MPI_Aint)); + disp[m] = temp; + } /* end if */ + (*permute)[u] = m; + } /* end if */ + else + (*permute)[u] = num_points; + } /* end if */ + /* this is a memory space, and no permutation is necessary to create + the derived datatype */ + else { + ;/* do nothing */ + } /* end else */ + + /* get the next point */ + curr = curr->next; + } /* end for */ + + /* Create the MPI datatype for the set of element displacements */ + if(H5S_mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create an MPI Datatype from point selection") + + /* Set values about MPI datatype created */ + *count = 1; + *is_derived_type = TRUE; + +done: + if(NULL != disp) + H5MM_free(disp); + + /* Release the permutation buffer, if it wasn't used */ + if(!(*is_permuted) && (*permute)) { + H5MM_free(*permute); + *permute = NULL; + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5S_mpio_point_type() */ + + +/*------------------------------------------------------------------------- + * Function: H5S_mpio_permute_type + * + * Purpose: Translate an HDF5 "all/hyper/point" selection into an MPI type, + * while applying the permutation map. This function is called if + * the file space selection is permuted due to out-of-order point + * selection and so the memory datatype has to be permuted using the + * permutation map created by the file selection. + * + * Note: This routine is called from H5S_mpio_space_type(), which is + * called first for the file dataspace and creates + * + * Return: non-negative on success, negative on failure. + * + * Outputs: *new_type the MPI type corresponding to the selection + * *count how many objects of the new_type in selection + * (useful if this is the buffer type for xfer) + * *is_derived_type 0 if MPI primitive type, 1 if derived + * + * Programmer: Mohamad Chaarawi + * + *------------------------------------------------------------------------- + */ +static herr_t +H5S_mpio_permute_type(const H5S_t *space, size_t elmt_size, hsize_t **permute, + MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) +{ + MPI_Aint *disp = NULL; /* Datatype displacement for each point*/ + H5S_sel_iter_t sel_iter; /* Selection iteration info */ + hbool_t sel_iter_init = FALSE; /* Selection iteration info has been initialized */ + hsize_t off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */ + size_t len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */ + hssize_t snum_points; /* Signed number of elements in selection */ + hsize_t num_points; /* Number of points in the selection */ + size_t max_elem; /* Maximum number of elements allowed in sequences */ + hsize_t u; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI_NOINIT + + /* Check args */ + HDassert(space); + + /* Get the total number of points selected */ + if((snum_points = (hssize_t)H5S_GET_SELECT_NPOINTS(space)) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements selected") + num_points = (hsize_t)snum_points; + + /* Allocate array to store point displacements */ + if(NULL == (disp = (MPI_Aint *)H5MM_malloc(sizeof(MPI_Aint) * num_points))) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of displacements") + + /* Initialize selection iterator */ + if(H5S_select_iter_init(&sel_iter, space, elmt_size) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") + sel_iter_init = TRUE; /* Selection iteration info has been initialized */ + + /* Set the number of elements to iterate over */ + H5_ASSIGN_OVERFLOW(max_elem, num_points, hsize_t, size_t); + + /* Loop, while elements left in selection */ + u = 0; + while(max_elem > 0) { + hsize_t off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */ + size_t len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */ + size_t nelem; /* Number of elements used in sequences */ + size_t nseq; /* Number of sequences generated */ + size_t curr_seq; /* Current sequence being worked on */ + + /* Get the sequences of bytes */ + if(H5S_SELECT_GET_SEQ_LIST(space, 0, &sel_iter, (size_t)H5D_IO_VECTOR_SIZE, max_elem, &nseq, &nelem, off, len) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "sequence length generation failed") + + /* Loop, while sequences left to process */ + for(curr_seq = 0; curr_seq < nseq; curr_seq++) { + hsize_t curr_off; /* Current offset within sequence */ + size_t curr_len; /* Length of bytes left to process in sequence */ + + /* Get the current offset */ + curr_off = off[curr_seq]; + + /* Get the number of bytes in sequence */ + curr_len = len[curr_seq]; + + /* Loop, while bytes left in sequence */ + while(curr_len > 0) { + /* Set the displacement of the current point */ + disp[u] = curr_off; + + /* This is a memory displacement, so for each point selected, + * apply the map that was generated by the file selection */ + if((*permute)[u] != num_points) { + MPI_Aint temp = disp[u]; + + HDmemmove(disp + (*permute)[u] + 1, disp + (*permute)[u], + (u - (*permute)[u]) * sizeof(MPI_Aint)); + disp[(*permute)[u]] = temp; + } /* end if */ + + /* Advance to next element */ + u++; + + /* Increment offset in dataspace */ + curr_off += elmt_size; + + /* Decrement number of bytes left in sequence */ + curr_len -= elmt_size; + } /* end while */ + } /* end for */ + + /* Decrement number of elements left to process */ + max_elem -= nelem; + } /* end while */ + + /* Create the MPI datatype for the set of element displacements */ + if(H5S_mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create an MPI Datatype from point selection") + + /* Set values about MPI datatype created */ + *count = 1; + *is_derived_type = TRUE; + +done: + /* Release selection iterator */ + if(sel_iter_init) + if(H5S_SELECT_ITER_RELEASE(&sel_iter) < 0) + HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator") + + /* Free memory */ + if(disp) + H5MM_free(disp); + if(*permute) { + H5MM_free(*permute); + *permute = NULL; + } /* end if */ + + FUNC_LEAVE_NOAPI(ret_value) +} /* H5S_mpio_permute_type() */ + + +/*------------------------------------------------------------------------- * Function: H5S_mpio_hyper_type * * Purpose: Translate an HDF5 hyperslab selection into an MPI type. @@ -478,7 +815,7 @@ done: /*------------------------------------------------------------------------- - * Function: H5S_obtain datatype + * Function: H5S_obtain_datatype * * Purpose: Obtain an MPI derived datatype based on span-tree * implementation @@ -673,8 +1010,9 @@ done: *------------------------------------------------------------------------- */ herr_t -H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, - MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) +H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, + int *count, hbool_t *is_derived_type, hbool_t do_permute, hsize_t **permute_map, + hbool_t *is_permuted) { herr_t ret_value = SUCCEED; /* Return value */ @@ -684,44 +1022,75 @@ H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, HDassert(space); HDassert(elmt_size); - /* Creat MPI type based on the kind of selection */ + /* Create MPI type based on the kind of selection */ switch(H5S_GET_EXTENT_TYPE(space)) { case H5S_NULL: case H5S_SCALAR: case H5S_SIMPLE: - switch(H5S_GET_SELECT_TYPE(space)) { - case H5S_SEL_NONE: - if(H5S_mpio_none_type(new_type, count, is_derived_type) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert 'none' selection to MPI type") - break; - - case H5S_SEL_ALL: - if(H5S_mpio_all_type(space, elmt_size, new_type, count, is_derived_type) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert 'all' selection to MPI type") - break; - - case H5S_SEL_POINTS: - /* not yet implemented */ - ret_value = FAIL; - break; - - case H5S_SEL_HYPERSLABS: - if((H5S_SELECT_IS_REGULAR(space) == TRUE)) { - if(H5S_mpio_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert regular 'hyperslab' selection to MPI type") - } /* end if */ - else { - if(H5S_mpio_span_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert irregular 'hyperslab' selection to MPI type") - } /* end else */ - break; - - case H5S_SEL_ERROR: - case H5S_SEL_N: - default: - HDassert("unknown selection type" && 0); - break; - } /* end switch */ + /* If the file space has been permuted previously due to + * out-of-order point selection, then permute this selection which + * should be a memory selection to match the file space permutation. + */ + if(TRUE == *is_permuted) { + switch(H5S_GET_SELECT_TYPE(space)) { + case H5S_SEL_NONE: + if(H5S_mpio_none_type(new_type, count, is_derived_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert 'none' selection to MPI type") + break; + + case H5S_SEL_ALL: + case H5S_SEL_POINTS: + case H5S_SEL_HYPERSLABS: + /* Sanity check */ + HDassert(!do_permute); + + if(H5S_mpio_permute_type(space, elmt_size, permute_map, new_type, count, is_derived_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert 'all' selection to MPI type") + break; + + case H5S_SEL_ERROR: + case H5S_SEL_N: + default: + HDassert("unknown selection type" && 0); + break; + } /* end switch */ + } /* end if */ + /* the file space is not permuted, so do a regular selection */ + else { + switch(H5S_GET_SELECT_TYPE(space)) { + case H5S_SEL_NONE: + if(H5S_mpio_none_type(new_type, count, is_derived_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert 'none' selection to MPI type") + break; + + case H5S_SEL_ALL: + if(H5S_mpio_all_type(space, elmt_size, new_type, count, is_derived_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert 'all' selection to MPI type") + break; + + case H5S_SEL_POINTS: + if(H5S_mpio_point_type(space, elmt_size, new_type, count, is_derived_type, do_permute, permute_map, is_permuted) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert 'point' selection to MPI type") + break; + + case H5S_SEL_HYPERSLABS: + if((H5S_SELECT_IS_REGULAR(space) == TRUE)) { + if(H5S_mpio_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert regular 'hyperslab' selection to MPI type") + } /* end if */ + else { + if(H5S_mpio_span_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert irregular 'hyperslab' selection to MPI type") + } /* end else */ + break; + + case H5S_SEL_ERROR: + case H5S_SEL_N: + default: + HDassert("unknown selection type" && 0); + break; + } /* end switch */ + } /* end else */ break; case H5S_NO_CLASS: diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index 0e67af1..be8a28f 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -272,12 +272,13 @@ H5_DLL herr_t H5S_select_iter_release(H5S_sel_iter_t *sel_iter); /* (Defined in H5S.c) */ H5_DLLVAR hbool_t H5S_mpi_opt_types_g; -H5_DLL herr_t -H5S_mpio_space_type( const H5S_t *space, size_t elmt_size, - /* out: */ - MPI_Datatype *new_type, - int *count, - hbool_t *is_derived_type ); +H5_DLL herr_t H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, + /* out: */ MPI_Datatype *new_type, + int *count, + hbool_t *is_derived_type, + hbool_t do_permute, + hsize_t **permute_map, + hbool_t * is_permuted); #endif /* H5_HAVE_PARALLEL */ #endif /* _H5Sprivate_H */ diff --git a/src/H5Sselect.c b/src/H5Sselect.c index 44688b6..2cb4b38 100644 --- a/src/H5Sselect.c +++ b/src/H5Sselect.c @@ -34,8 +34,8 @@ /* Local functions */ #ifdef LATER -static herr_t H5S_select_iter_block (const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end); -static htri_t H5S_select_iter_has_next_block (const H5S_sel_iter_t *iter); +static herr_t H5S_select_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end); +static htri_t H5S_select_iter_has_next_block(const H5S_sel_iter_t *iter); static herr_t H5S_select_iter_next_block(H5S_sel_iter_t *iter); #endif /* LATER */ @@ -922,7 +922,7 @@ H5S_select_iter_init(H5S_sel_iter_t *sel_iter, const H5S_t *space, size_t elmt_s REVISION LOG --------------------------------------------------------------------------*/ herr_t -H5S_select_iter_coords (const H5S_sel_iter_t *sel_iter, hsize_t *coords) +H5S_select_iter_coords(const H5S_sel_iter_t *sel_iter, hsize_t *coords) { herr_t ret_value; /* return value */ @@ -964,7 +964,7 @@ H5S_select_iter_coords (const H5S_sel_iter_t *sel_iter, hsize_t *coords) REVISION LOG --------------------------------------------------------------------------*/ static herr_t -H5S_select_iter_block (const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) +H5S_select_iter_block(const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) { herr_t ret_value; /* return value */ @@ -1004,7 +1004,7 @@ H5S_select_iter_block (const H5S_sel_iter_t *iter, hsize_t *start, hsize_t *end) REVISION LOG --------------------------------------------------------------------------*/ hsize_t -H5S_select_iter_nelmts (const H5S_sel_iter_t *sel_iter) +H5S_select_iter_nelmts(const H5S_sel_iter_t *sel_iter) { hsize_t ret_value; /* return value */ @@ -1043,7 +1043,7 @@ H5S_select_iter_nelmts (const H5S_sel_iter_t *sel_iter) REVISION LOG --------------------------------------------------------------------------*/ static htri_t -H5S_select_iter_has_next_block (const H5S_sel_iter_t *iter) +H5S_select_iter_has_next_block(const H5S_sel_iter_t *iter) { herr_t ret_value; /* return value */ @@ -1217,24 +1217,13 @@ H5S_select_iterate(void *buf, hid_t type_id, const H5S_t *space, H5D_operator_t H5T_t *dt; /* Datatype structure */ H5S_sel_iter_t iter; /* Selection iteration info */ hbool_t iter_init = FALSE; /* Selection iteration info has been initialized */ - uint8_t *loc; /* Current element location in buffer */ - hsize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of element in dataspace */ hssize_t nelmts; /* Number of elements in selection */ hsize_t space_size[H5O_LAYOUT_NDIMS]; /* Dataspace size */ - hsize_t off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */ - hsize_t curr_off; /* Current offset within sequence */ - hsize_t tmp_off; /* Temporary offset within sequence */ - size_t len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */ - size_t curr_len; /* Length of bytes left to process in sequence */ - size_t nseq; /* Number of sequences generated */ - size_t curr_seq; /* Current sequnce being worked on */ - size_t nelem; /* Number of elements used in sequences */ size_t max_elem; /* Maximum number of elements allowed in sequences */ size_t elmt_size; /* Datatype size */ unsigned ndims; /* Number of dimensions in dataspace */ - int i; /* Local Index variable */ - herr_t user_ret=0; /* User's return value */ - herr_t ret_value=SUCCEED; /* Return value */ + herr_t user_ret = 0; /* User's return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(FAIL) @@ -1274,12 +1263,21 @@ H5S_select_iterate(void *buf, hid_t type_id, const H5S_t *space, H5D_operator_t /* Loop, while elements left in selection */ while(max_elem > 0 && user_ret == 0) { + hsize_t off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */ + size_t len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */ + size_t nelem; /* Number of elements used in sequences */ + size_t nseq; /* Number of sequences generated */ + size_t curr_seq; /* Current sequence being worked on */ + /* Get the sequences of bytes */ if(H5S_SELECT_GET_SEQ_LIST(space, 0, &iter, (size_t)H5D_IO_VECTOR_SIZE, max_elem, &nseq, &nelem, off, len) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed") /* Loop, while sequences left to process */ - for(curr_seq=0; curr_seq<nseq && user_ret==0; curr_seq++) { + for(curr_seq = 0; curr_seq < nseq && user_ret == 0; curr_seq++) { + hsize_t curr_off; /* Current offset within sequence */ + size_t curr_len; /* Length of bytes left to process in sequence */ + /* Get the current offset */ curr_off = off[curr_seq]; @@ -1288,6 +1286,11 @@ H5S_select_iterate(void *buf, hid_t type_id, const H5S_t *space, H5D_operator_t /* Loop, while bytes left in sequence */ while(curr_len > 0 && user_ret == 0) { + hsize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of element in dataspace */ + hsize_t tmp_off; /* Temporary offset within sequence */ + uint8_t *loc; /* Current element location in buffer */ + int i; /* Local Index variable */ + /* Compute the coordinate from the offset */ for(i = (int)ndims, tmp_off = curr_off; i >= 0; i--) { coords[i] = tmp_off % space_size[i]; @@ -1298,22 +1301,22 @@ H5S_select_iterate(void *buf, hid_t type_id, const H5S_t *space, H5D_operator_t loc = (unsigned char *)buf + curr_off; /* Call user's callback routine */ - user_ret=(*op)(loc,type_id,ndims,coords,operator_data); + user_ret = (*op)(loc, type_id, ndims, coords, operator_data); /* Increment offset in dataspace */ - curr_off+=elmt_size; + curr_off += elmt_size; /* Decrement number of bytes left in sequence */ - curr_len-=elmt_size; + curr_len -= elmt_size; } /* end while */ } /* end for */ /* Decrement number of elements left to process */ - max_elem-=nelem; + max_elem -= nelem; } /* end while */ /* Set return value */ - ret_value=user_ret; + ret_value = user_ret; done: /* Release selection iterator */ diff --git a/src/H5private.h b/src/H5private.h index 0e6ff1e..26ccf57 100644 --- a/src/H5private.h +++ b/src/H5private.h @@ -439,8 +439,8 @@ /* * Maximum & minimum values for our typedefs. */ -#define HSIZET_MAX ((hsize_t)ULLONG_MAX) -#define HSSIZET_MAX ((hssize_t)LLONG_MAX) +#define HSIZET_MAX ((hsize_t)ULLONG_MAX) +#define HSSIZET_MAX ((hssize_t)LLONG_MAX) #define HSSIZET_MIN (~(HSSIZET_MAX)) /* diff --git a/testpar/t_coll_chunk.c b/testpar/t_coll_chunk.c index 5dac36f..61b25f8 100644 --- a/testpar/t_coll_chunk.c +++ b/testpar/t_coll_chunk.c @@ -16,6 +16,9 @@ #include "testphdf5.h" #include "H5Dprivate.h" +#define HYPER 1 +#define POINT 2 +#define ALL 3 /* some commonly used routines for collective chunk IO tests*/ @@ -23,14 +26,17 @@ static void ccslab_set(int mpi_rank,int mpi_size,hsize_t start[],hsize_t count[] hsize_t stride[],hsize_t block[],int mode); static void ccdataset_fill(hsize_t start[],hsize_t count[], - hsize_t stride[],hsize_t block[],DATATYPE*dataset); + hsize_t stride[],hsize_t block[],DATATYPE*dataset, + int mem_selection); static void ccdataset_print(hsize_t start[],hsize_t block[],DATATYPE*dataset); static int ccdataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], - hsize_t block[], DATATYPE *dataset, DATATYPE *original); + hsize_t block[], DATATYPE *dataset, DATATYPE *original, + int mem_selection); -static void coll_chunktest(const char* filename,int chunk_factor,int select_factor,int api_option); +static void coll_chunktest(const char* filename, int chunk_factor, int select_factor, + int api_option, int file_selection, int mem_selection, int mode); /*------------------------------------------------------------------------- @@ -73,7 +79,15 @@ coll_chunk1(void) { const char *filename = GetTestParameters(); - coll_chunktest(filename, 1, BYROW_CONT, API_NONE); + coll_chunktest(filename, 1, BYROW_CONT, API_NONE, HYPER, HYPER, OUT_OF_ORDER); + coll_chunktest(filename, 1, BYROW_CONT, API_NONE, HYPER, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 1, BYROW_CONT, API_NONE, POINT, ALL, OUT_OF_ORDER); + coll_chunktest(filename, 1, BYROW_CONT, API_NONE, POINT, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 1, BYROW_CONT, API_NONE, POINT, HYPER, OUT_OF_ORDER); + + coll_chunktest(filename, 1, BYROW_CONT, API_NONE, POINT, ALL, IN_ORDER); + coll_chunktest(filename, 1, BYROW_CONT, API_NONE, POINT, POINT, IN_ORDER); + coll_chunktest(filename, 1, BYROW_CONT, API_NONE, POINT, HYPER, IN_ORDER); } @@ -117,7 +131,15 @@ coll_chunk2(void) { const char *filename = GetTestParameters(); - coll_chunktest(filename, 1, BYROW_DISCONT, API_NONE); + coll_chunktest(filename, 1, BYROW_DISCONT, API_NONE, HYPER, HYPER, OUT_OF_ORDER); + coll_chunktest(filename, 1, BYROW_DISCONT, API_NONE, HYPER, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 1, BYROW_DISCONT, API_NONE, POINT, ALL, OUT_OF_ORDER); + coll_chunktest(filename, 1, BYROW_DISCONT, API_NONE, POINT, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 1, BYROW_DISCONT, API_NONE, POINT, HYPER, OUT_OF_ORDER); + + coll_chunktest(filename, 1, BYROW_DISCONT, API_NONE, POINT, ALL, IN_ORDER); + coll_chunktest(filename, 1, BYROW_DISCONT, API_NONE, POINT, POINT, IN_ORDER); + coll_chunktest(filename, 1, BYROW_DISCONT, API_NONE, POINT, HYPER, IN_ORDER); } @@ -164,7 +186,15 @@ coll_chunk3(void) int mpi_size; MPI_Comm_size(MPI_COMM_WORLD, &mpi_size); - coll_chunktest(filename, mpi_size, BYROW_CONT, API_NONE); + coll_chunktest(filename, mpi_size, BYROW_CONT, API_NONE, HYPER, HYPER, OUT_OF_ORDER); + coll_chunktest(filename, mpi_size, BYROW_CONT, API_NONE, HYPER, POINT, OUT_OF_ORDER); + coll_chunktest(filename, mpi_size, BYROW_CONT, API_NONE, POINT, ALL, OUT_OF_ORDER); + coll_chunktest(filename, mpi_size, BYROW_CONT, API_NONE, POINT, POINT, OUT_OF_ORDER); + coll_chunktest(filename, mpi_size, BYROW_CONT, API_NONE, POINT, HYPER, OUT_OF_ORDER); + + coll_chunktest(filename, mpi_size, BYROW_CONT, API_NONE, POINT, ALL, IN_ORDER); + coll_chunktest(filename, mpi_size, BYROW_CONT, API_NONE, POINT, POINT, IN_ORDER); + coll_chunktest(filename, mpi_size, BYROW_CONT, API_NONE, POINT, HYPER, IN_ORDER); } /*------------------------------------------------------------------------- @@ -208,7 +238,15 @@ coll_chunk4(void) { const char *filename = GetTestParameters(); - coll_chunktest(filename, 1, BYROW_SELECTNONE, API_NONE); + coll_chunktest(filename, 1, BYROW_SELECTNONE, API_NONE, HYPER, HYPER, OUT_OF_ORDER); + coll_chunktest(filename, 1, BYROW_SELECTNONE, API_NONE, HYPER, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 1, BYROW_SELECTNONE, API_NONE, POINT, ALL, OUT_OF_ORDER); + coll_chunktest(filename, 1, BYROW_SELECTNONE, API_NONE, POINT, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 1, BYROW_SELECTNONE, API_NONE, POINT, HYPER, OUT_OF_ORDER); + + coll_chunktest(filename, 1, BYROW_SELECTNONE, API_NONE, POINT, ALL, IN_ORDER); + coll_chunktest(filename, 1, BYROW_SELECTNONE, API_NONE, POINT, POINT, IN_ORDER); + coll_chunktest(filename, 1, BYROW_SELECTNONE, API_NONE, POINT, HYPER, IN_ORDER); } /*------------------------------------------------------------------------- @@ -252,7 +290,15 @@ coll_chunk5(void) { const char *filename = GetTestParameters(); - coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_HARD); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_HARD, HYPER, HYPER, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_HARD, HYPER, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_HARD, POINT, ALL, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_HARD, POINT, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_HARD, POINT, HYPER, OUT_OF_ORDER); + + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_HARD, POINT, ALL, IN_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_HARD, POINT, POINT, IN_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_HARD, POINT, HYPER, IN_ORDER); } /*------------------------------------------------------------------------- @@ -298,7 +344,15 @@ coll_chunk6(void) { const char *filename = GetTestParameters(); - coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_HARD); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_HARD, HYPER, HYPER, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_HARD, HYPER, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_HARD, POINT, ALL, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_HARD, POINT, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_HARD, POINT, HYPER, OUT_OF_ORDER); + + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_HARD, POINT, ALL, IN_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_HARD, POINT, POINT, IN_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_HARD, POINT, HYPER, IN_ORDER); } /*------------------------------------------------------------------------- @@ -342,7 +396,15 @@ coll_chunk7(void) { const char *filename = GetTestParameters(); - coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_TRUE); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_TRUE, HYPER, HYPER, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_TRUE, HYPER, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_TRUE, POINT, ALL, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_TRUE, POINT, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_TRUE, POINT, HYPER, OUT_OF_ORDER); + + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_TRUE, POINT, ALL, IN_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_TRUE, POINT, POINT, IN_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_TRUE, POINT, HYPER, IN_ORDER); } /*------------------------------------------------------------------------- @@ -386,7 +448,15 @@ coll_chunk8(void) { const char *filename = GetTestParameters(); - coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_FALSE); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_FALSE, HYPER, HYPER, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_FALSE, HYPER, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_FALSE, POINT, ALL, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_FALSE, POINT, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_FALSE, POINT, HYPER, OUT_OF_ORDER); + + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_FALSE, POINT, ALL, IN_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_FALSE, POINT, POINT, IN_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_LINK_FALSE, POINT, HYPER, IN_ORDER); } /*------------------------------------------------------------------------- @@ -430,7 +500,15 @@ coll_chunk9(void) { const char *filename = GetTestParameters(); - coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_COLL); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_COLL, HYPER, HYPER, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_COLL, HYPER, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_COLL, POINT, ALL, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_COLL, POINT, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_COLL, POINT, HYPER, OUT_OF_ORDER); + + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_COLL, POINT, ALL, IN_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_COLL, POINT, POINT, IN_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTUNBALANCE, API_MULTI_COLL, POINT, HYPER, IN_ORDER); } /*------------------------------------------------------------------------- @@ -474,7 +552,15 @@ coll_chunk10(void) { const char *filename = GetTestParameters(); - coll_chunktest(filename, 4, BYROW_SELECTINCHUNK, API_MULTI_IND); + coll_chunktest(filename, 4, BYROW_SELECTINCHUNK, API_MULTI_IND, HYPER, HYPER, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTINCHUNK, API_MULTI_IND, HYPER, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTINCHUNK, API_MULTI_IND, POINT, ALL, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTINCHUNK, API_MULTI_IND, POINT, POINT, OUT_OF_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTINCHUNK, API_MULTI_IND, POINT, HYPER, OUT_OF_ORDER); + + coll_chunktest(filename, 4, BYROW_SELECTINCHUNK, API_MULTI_IND, POINT, ALL, IN_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTINCHUNK, API_MULTI_IND, POINT, POINT, IN_ORDER); + coll_chunktest(filename, 4, BYROW_SELECTINCHUNK, API_MULTI_IND, POINT, HYPER, IN_ORDER); } @@ -505,14 +591,16 @@ coll_chunk10(void) *------------------------------------------------------------------------- */ - static void coll_chunktest(const char* filename, int chunk_factor, int select_factor, - int api_option) + int api_option, + int file_selection, + int mem_selection, + int mode) { - hid_t file,dataset, file_dataspace; + hid_t file, dataset, file_dataspace, mem_dataspace; hid_t acc_plist,xfer_plist,crp_plist; hsize_t dims[RANK], chunk_dims[RANK]; @@ -532,6 +620,11 @@ coll_chunktest(const char* filename, MPI_Comm comm = MPI_COMM_WORLD; MPI_Info info = MPI_INFO_NULL; + size_t num_points; /* for point selection */ + hsize_t *coords =NULL; /* for point selection */ + hsize_t current_dims; /* for point selection */ + int i; + /* set up MPI parameters */ MPI_Comm_size(comm,&mpi_size); MPI_Comm_rank(comm,&mpi_rank); @@ -551,7 +644,6 @@ coll_chunktest(const char* filename, dims[0] = SPACE_DIM1*mpi_size; dims[1] = SPACE_DIM2; - /* allocate memory for data buffer */ data_array1 = (int *)HDmalloc(dims[0] * dims[1] * sizeof(int)); VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); @@ -559,9 +651,25 @@ coll_chunktest(const char* filename, /* set up dimensions of the slab this process accesses */ ccslab_set(mpi_rank, mpi_size, start, count, stride, block, select_factor); + /* set up the coords array selection */ + num_points = block[0] * block[1] * count[0] * count[1]; + coords = (hsize_t *)HDmalloc(num_points * RANK * sizeof(hsize_t)); + VRFY((coords != NULL), "coords malloc succeeded"); + point_set(start, count, stride, block, num_points, coords, mode); + file_dataspace = H5Screate_simple(2, dims, NULL); VRFY((file_dataspace >= 0), "file dataspace created succeeded"); + if(ALL != mem_selection) { + mem_dataspace = H5Screate_simple(2, dims, NULL); + VRFY((mem_dataspace >= 0), "mem dataspace created succeeded"); + } + else { + current_dims = num_points; + mem_dataspace = H5Screate_simple (1, ¤t_dims, NULL); + VRFY((mem_dataspace >= 0), "mem_dataspace create succeeded"); + } + crp_plist = H5Pcreate(H5P_DATASET_CREATE); VRFY((crp_plist >= 0),""); @@ -569,25 +677,67 @@ coll_chunktest(const char* filename, chunk_dims[0] = dims[0]/chunk_factor; /* to decrease the testing time, maintain bigger chunk size */ - (chunk_factor == 1) ? (chunk_dims[1] = SPACE_DIM2) : (chunk_dims[1] = SPACE_DIM2/2); status = H5Pset_chunk(crp_plist, 2, chunk_dims); VRFY((status >= 0),"chunk creation property list succeeded"); dataset = H5Dcreate2(file, DSET_COLLECTIVE_CHUNK_NAME, H5T_NATIVE_INT, - file_dataspace, H5P_DEFAULT, crp_plist, H5P_DEFAULT); + file_dataspace, H5P_DEFAULT, crp_plist, H5P_DEFAULT); VRFY((dataset >= 0),"dataset created succeeded"); status = H5Pclose(crp_plist); VRFY((status >= 0), ""); /*put some trivial data in the data array */ - ccdataset_fill(start, stride, count,block, data_array1); + ccdataset_fill(start, stride, count,block, data_array1, mem_selection); + MESG("data_array initialized"); - status = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, - count, block); - VRFY((status >= 0),"hyperslab selection succeeded"); + switch (file_selection) { + case HYPER: + status = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((status >= 0),"hyperslab selection succeeded"); + break; + + case POINT: + if (num_points) { + status = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords); + VRFY((status >= 0),"Element selection succeeded"); + } + else { + status = H5Sselect_none(file_dataspace); + VRFY((status >= 0),"none selection succeeded"); + } + break; + + case ALL: + status = H5Sselect_all(file_dataspace); + VRFY((status >= 0), "H5Sselect_all succeeded"); + break; + } + + switch (mem_selection) { + case HYPER: + status = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((status >= 0),"hyperslab selection succeeded"); + break; + + case POINT: + if (num_points) { + status = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords); + VRFY((status >= 0),"Element selection succeeded"); + } + else { + status = H5Sselect_none(mem_dataspace); + VRFY((status >= 0),"none selection succeeded"); + } + break; + + case ALL: + status = H5Sselect_all(mem_dataspace); + VRFY((status >= 0), "H5Sselect_all succeeded"); + break; + } /* set up the collective transfer property list */ xfer_plist = H5Pcreate(H5P_DATASET_XFER); @@ -604,33 +754,39 @@ coll_chunktest(const char* filename, case API_LINK_HARD: status = H5Pset_dxpl_mpio_chunk_opt(xfer_plist,H5FD_MPIO_CHUNK_ONE_IO); VRFY((status>= 0),"collective chunk optimization succeeded"); - break; + break; + case API_MULTI_HARD: status = H5Pset_dxpl_mpio_chunk_opt(xfer_plist,H5FD_MPIO_CHUNK_MULTI_IO); VRFY((status>= 0),"collective chunk optimization succeeded "); - break; + break; + case API_LINK_TRUE: status = H5Pset_dxpl_mpio_chunk_opt_num(xfer_plist,2); VRFY((status>= 0),"collective chunk optimization set chunk number succeeded"); - break; + break; + case API_LINK_FALSE: status = H5Pset_dxpl_mpio_chunk_opt_num(xfer_plist,6); VRFY((status>= 0),"collective chunk optimization set chunk number succeeded"); - break; + break; + case API_MULTI_COLL: status = H5Pset_dxpl_mpio_chunk_opt_num(xfer_plist,8);/* make sure it is using multi-chunk IO */ VRFY((status>= 0),"collective chunk optimization set chunk number succeeded"); status = H5Pset_dxpl_mpio_chunk_opt_ratio(xfer_plist,50); VRFY((status>= 0),"collective chunk optimization set chunk ratio succeeded"); - break; + break; + case API_MULTI_IND: status = H5Pset_dxpl_mpio_chunk_opt_num(xfer_plist,8);/* make sure it is using multi-chunk IO */ VRFY((status>= 0),"collective chunk optimization set chunk number succeeded"); status = H5Pset_dxpl_mpio_chunk_opt_ratio(xfer_plist,100); VRFY((status>= 0),"collective chunk optimization set chunk ratio succeeded"); - break; + break; + default: - ; + ; } #ifdef H5_HAVE_INSTRUMENTED_LIBRARY @@ -641,44 +797,42 @@ coll_chunktest(const char* filename, status = H5Pinsert2(xfer_plist, H5D_XFER_COLL_CHUNK_LINK_HARD_NAME, H5D_XFER_COLL_CHUNK_SIZE, &prop_value, NULL, NULL, NULL, NULL, NULL, NULL); VRFY((status >= 0),"testing property list inserted succeeded"); - - break; + break; case API_MULTI_HARD: prop_value = H5D_XFER_COLL_CHUNK_DEF; status = H5Pinsert2(xfer_plist, H5D_XFER_COLL_CHUNK_MULTI_HARD_NAME, H5D_XFER_COLL_CHUNK_SIZE, &prop_value, NULL, NULL, NULL, NULL, NULL, NULL); VRFY((status >= 0),"testing property list inserted succeeded"); - break; + break; case API_LINK_TRUE: prop_value = H5D_XFER_COLL_CHUNK_DEF; status = H5Pinsert2(xfer_plist, H5D_XFER_COLL_CHUNK_LINK_NUM_TRUE_NAME, H5D_XFER_COLL_CHUNK_SIZE, &prop_value, NULL, NULL, NULL, NULL, NULL, NULL); VRFY((status >= 0),"testing property list inserted succeeded"); - - break; + break; case API_LINK_FALSE: prop_value = H5D_XFER_COLL_CHUNK_DEF; status = H5Pinsert2(xfer_plist, H5D_XFER_COLL_CHUNK_LINK_NUM_FALSE_NAME, H5D_XFER_COLL_CHUNK_SIZE, &prop_value, NULL, NULL, NULL, NULL, NULL, NULL); VRFY((status >= 0),"testing property list inserted succeeded"); - break; + break; case API_MULTI_COLL: prop_value = H5D_XFER_COLL_CHUNK_DEF; status = H5Pinsert2(xfer_plist, H5D_XFER_COLL_CHUNK_MULTI_RATIO_COLL_NAME, H5D_XFER_COLL_CHUNK_SIZE, &prop_value, NULL, NULL, NULL, NULL, NULL, NULL); VRFY((status >= 0),"testing property list inserted succeeded"); - break; + break; case API_MULTI_IND: prop_value = H5D_XFER_COLL_CHUNK_DEF; status = H5Pinsert2(xfer_plist, H5D_XFER_COLL_CHUNK_MULTI_RATIO_IND_NAME, H5D_XFER_COLL_CHUNK_SIZE, &prop_value, NULL, NULL, NULL, NULL, NULL, NULL); VRFY((status >= 0),"testing property list inserted succeeded"); - break; + break; default: ; @@ -687,7 +841,7 @@ coll_chunktest(const char* filename, #endif /* write data collectively */ - status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, file_dataspace, + status = H5Dwrite(dataset, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((status >= 0),"dataset write succeeded"); @@ -698,32 +852,38 @@ coll_chunktest(const char* filename, status = H5Pget(xfer_plist,H5D_XFER_COLL_CHUNK_LINK_HARD_NAME,&prop_value); VRFY((status >= 0),"testing property list get succeeded"); VRFY((prop_value == 0),"API to set LINK COLLECTIVE IO directly succeeded"); - break; + break; + case API_MULTI_HARD: status = H5Pget(xfer_plist,H5D_XFER_COLL_CHUNK_MULTI_HARD_NAME,&prop_value); VRFY((status >= 0),"testing property list get succeeded"); VRFY((prop_value == 0),"API to set MULTI-CHUNK COLLECTIVE IO optimization succeeded"); - break; + break; + case API_LINK_TRUE: status = H5Pget(xfer_plist,H5D_XFER_COLL_CHUNK_LINK_NUM_TRUE_NAME,&prop_value); VRFY((status >= 0),"testing property list get succeeded"); VRFY((prop_value == 0),"API to set LINK COLLECTIVE IO succeeded"); - break; + break; + case API_LINK_FALSE: status = H5Pget(xfer_plist,H5D_XFER_COLL_CHUNK_LINK_NUM_FALSE_NAME,&prop_value); VRFY((status >= 0),"testing property list get succeeded"); VRFY((prop_value == 0),"API to set LINK IO transferring to multi-chunk IO succeeded"); - break; + break; + case API_MULTI_COLL: status = H5Pget(xfer_plist,H5D_XFER_COLL_CHUNK_MULTI_RATIO_COLL_NAME,&prop_value); VRFY((status >= 0),"testing property list get succeeded"); VRFY((prop_value == 0),"API to set MULTI-CHUNK COLLECTIVE IO with optimization succeeded"); - break; + break; + case API_MULTI_IND: status = H5Pget(xfer_plist,H5D_XFER_COLL_CHUNK_MULTI_RATIO_IND_NAME,&prop_value); VRFY((status >= 0),"testing property list get succeeded"); VRFY((prop_value == 0),"API to set MULTI-CHUNK IO transferring to independent IO succeeded"); - break; + break; + default: ; } @@ -739,12 +899,15 @@ coll_chunktest(const char* filename, status = H5Sclose(file_dataspace); VRFY((status >= 0),""); + status = H5Sclose(mem_dataspace); + VRFY((status >= 0),""); + + status = H5Fclose(file); VRFY((status >= 0),""); if (data_array1) HDfree(data_array1); - /* Use collective read to verify the correctness of collective write. */ /* allocate memory for data buffer */ @@ -771,15 +934,68 @@ coll_chunktest(const char* filename, /* set up dimensions of the slab this process accesses */ ccslab_set(mpi_rank, mpi_size, start, count, stride, block, select_factor); - /* obtain the file dataspace*/ + /* obtain the file and mem dataspace*/ file_dataspace = H5Dget_space (dataset); VRFY((file_dataspace >= 0), ""); - status=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); - VRFY((status >= 0), ""); + if (ALL != mem_selection) { + mem_dataspace = H5Dget_space (dataset); + VRFY((mem_dataspace >= 0), ""); + } + else { + current_dims = num_points; + mem_dataspace = H5Screate_simple (1, ¤t_dims, NULL); + VRFY((mem_dataspace >= 0), "mem_dataspace create succeeded"); + } + + switch (file_selection) { + case HYPER: + status = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((status >= 0),"hyperslab selection succeeded"); + break; + + case POINT: + if (num_points) { + status = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords); + VRFY((status >= 0),"Element selection succeeded"); + } + else { + status = H5Sselect_none(file_dataspace); + VRFY((status >= 0),"none selection succeeded"); + } + break; + + case ALL: + status = H5Sselect_all(file_dataspace); + VRFY((status >= 0), "H5Sselect_all succeeded"); + break; + } + + switch (mem_selection) { + case HYPER: + status = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((status >= 0),"hyperslab selection succeeded"); + break; + + case POINT: + if (num_points) { + status = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords); + VRFY((status >= 0),"Element selection succeeded"); + } + else { + status = H5Sselect_none(mem_dataspace); + VRFY((status >= 0),"none selection succeeded"); + } + break; + + case ALL: + status = H5Sselect_all(mem_dataspace); + VRFY((status >= 0), "H5Sselect_all succeeded"); + break; + } /* fill dataset with test data */ - ccdataset_fill(start, stride,count,block, data_origin1); + ccdataset_fill(start, stride,count,block, data_origin1, mem_selection); xfer_plist = H5Pcreate (H5P_DATASET_XFER); VRFY((xfer_plist >= 0),""); @@ -790,13 +1006,12 @@ coll_chunktest(const char* filename, VRFY((status>= 0),"set independent IO collectively succeeded"); } - - status = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, file_dataspace, + status = H5Dread(dataset, H5T_NATIVE_INT, mem_dataspace, file_dataspace, xfer_plist, data_array1); VRFY((status >=0),"dataset read succeeded"); /* verify the read data with original expected data */ - status = ccdataset_vrfy(start, count, stride, block, data_array1, data_origin1); + status = ccdataset_vrfy(start, count, stride, block, data_array1, data_origin1, mem_selection); if (status) nerrors++; status = H5Pclose(xfer_plist); @@ -804,15 +1019,21 @@ coll_chunktest(const char* filename, /* close dataset collectively */ status=H5Dclose(dataset); - VRFY((status >= 0), ""); + VRFY((status >= 0), "H5Dclose"); /* release all IDs created */ - H5Sclose(file_dataspace); + status = H5Sclose(file_dataspace); + VRFY((status >= 0),"H5Sclose"); + + status = H5Sclose(mem_dataspace); + VRFY((status >= 0),"H5Sclose"); /* close the file collectively */ - H5Fclose(file); + status = H5Fclose(file); + VRFY((status >= 0),"H5Fclose"); /* release data buffers */ + if (coords) free(coords); if (data_array1) HDfree(data_array1); if (data_origin1) HDfree(data_origin1); @@ -933,12 +1154,12 @@ ccdataset_fill(hsize_t start[], hsize_t stride[], hsize_t count[], hsize_t block[], - DATATYPE * dataset) + DATATYPE * dataset, + int mem_selection) { DATATYPE *dataptr = dataset; DATATYPE *tmptr; - hsize_t i,j,k1,k2; - + hsize_t i,j,k1,k2,k=0; /* put some trivial data in the data_array */ tmptr = dataptr; @@ -950,10 +1171,16 @@ ccdataset_fill(hsize_t start[], for(k2 = 0; k2 < count[1]; k2++) { for(j = 0;j < block[1]; j++) { - dataptr = tmptr + ((start[0]+k1*stride[0]+i)*SPACE_DIM2+ - start[1]+k2*stride[1]+j); + if (ALL != mem_selection) { + dataptr = tmptr + ((start[0]+k1*stride[0]+i)*SPACE_DIM2+ + start[1]+k2*stride[1]+j); + } + else { + dataptr = tmptr + k; + k++; + } - *dataptr = (DATATYPE)(k1+k2+i+j); + *dataptr = (DATATYPE)(k1+k2+i+j); } } } @@ -1000,9 +1227,10 @@ ccdataset_vrfy(hsize_t start[], hsize_t stride[], hsize_t block[], DATATYPE *dataset, - DATATYPE *original) + DATATYPE *original, + int mem_selection) { - hsize_t i, j,k1,k2; + hsize_t i, j,k1,k2,k=0; int vrfyerrs; DATATYPE *dataptr,*oriptr; @@ -1020,26 +1248,31 @@ ccdataset_vrfy(hsize_t start[], vrfyerrs = 0; - for (k1 = 0; k1 < count[0];k1++) { - for(i = 0;i < block[0];i++) { - for(k2 = 0; k2<count[1];k2++) { - for(j=0;j<block[1];j++) { - - dataptr = dataset + ((start[0]+k1*stride[0]+i)*SPACE_DIM2+ - start[1]+k2*stride[1]+j); - oriptr = original + ((start[0]+k1*stride[0]+i)*SPACE_DIM2+ - start[1]+k2*stride[1]+j); - - if (*dataptr != *oriptr){ - if (vrfyerrs++ < MAX_ERR_REPORT || VERBOSE_MED){ - printf("Dataset Verify failed at [%lu][%lu]: expect %d, got %d\n", - (unsigned long)i, (unsigned long)j, - *(original), *(dataset)); - } - } - } - } - } + for (k1=0;k1<count[0];k1++) { + for(i=0;i<block[0];i++) { + for(k2=0; k2<count[1];k2++) { + for(j=0;j<block[1];j++) { + if (ALL != mem_selection) { + dataptr = dataset + ((start[0]+k1*stride[0]+i)*SPACE_DIM2+ + start[1]+k2*stride[1]+j); + oriptr = original + ((start[0]+k1*stride[0]+i)*SPACE_DIM2+ + start[1]+k2*stride[1]+j); + } + else { + dataptr = dataset + k; + oriptr = original + k; + k++; + } + if (*dataptr != *oriptr){ + if (vrfyerrs++ < MAX_ERR_REPORT || VERBOSE_MED){ + printf("Dataset Verify failed at [%lu][%lu]: expect %d, got %d\n", + (unsigned long)i, (unsigned long)j, + *(original), *(dataset)); + } + } + } + } + } } if (vrfyerrs > MAX_ERR_REPORT && !VERBOSE_MED) printf("[more errors ...]\n"); diff --git a/testpar/t_dset.c b/testpar/t_dset.c index 246d2d9..3929ff3 100644 --- a/testpar/t_dset.c +++ b/testpar/t_dset.c @@ -118,6 +118,54 @@ if(VERBOSE_MED){ } } +/* + * Setup the coordinates for point selection. + */ +void point_set(hsize_t start[], + hsize_t count[], + hsize_t stride[], + hsize_t block[], + size_t num_points, + hsize_t coords[], + int order) +{ + hsize_t i,j, k = 0, m ,n, s1 ,s2; + + HDcompile_assert(RANK == 2); + + if(OUT_OF_ORDER == order) + k = (num_points * RANK) - 1; + else if(IN_ORDER == order) + k = 0; + + s1 = start[0]; + s2 = start[1]; + + for(i = 0 ; i < count[0]; i++) + for(j = 0 ; j < count[1]; j++) + for(m = 0 ; m < block[0]; m++) + for(n = 0 ; n < block[1]; n++) + if(OUT_OF_ORDER == order) { + coords[k--] = s2 + (stride[1] * j) + n; + coords[k--] = s1 + (stride[0] * i) + m; + } + else if(IN_ORDER == order) { + coords[k++] = s1 + stride[0] * i + m; + coords[k++] = s2 + stride[1] * j + n; + } + + if(VERBOSE_MED) { + printf("start[]=(%lu, %lu), count[]=(%lu, %lu), stride[]=(%lu, %lu), block[]=(%lu, %lu), total datapoints=%lu\n", + (unsigned long)start[0], (unsigned long)start[1], (unsigned long)count[0], (unsigned long)count[1], + (unsigned long)stride[0], (unsigned long)stride[1], (unsigned long)block[0], (unsigned long)block[1], + (unsigned long)(block[0] * block[1] * count[0] * count[1])); + k = 0; + for(i = 0; i < num_points ; i++) { + printf("(%d, %d)\n", (int)coords[k], (int)coords[k + 1]); + k += 2; + } + } +} /* * Fill the dataset with trivial data for testing. @@ -501,7 +549,8 @@ dataset_writeAll(void) hid_t sid; /* Dataspace ID */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ - hid_t dataset1, dataset2, dataset3, dataset4; /* Dataset ID */ + hid_t dataset1, dataset2, dataset3, dataset4; /* Dataset ID */ + hid_t dataset5, dataset6, dataset7; /* Dataset ID */ hid_t datatype; /* Datatype ID */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ hsize_t dims[RANK]; /* dataset dim sizes */ @@ -512,6 +561,11 @@ dataset_writeAll(void) hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ + size_t num_points = dim1; /* for point selection */ + hsize_t coords [RANK*dim1]; /* for point selection */ + hsize_t current_dims; /* for point selection */ + int i; + herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; @@ -573,6 +627,13 @@ dataset_writeAll(void) dataset3 = H5Dcreate2(fid, DATASETNAME3, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); VRFY((dataset3 >= 0), "H5Dcreate2 succeeded"); + dataset5 = H5Dcreate2(fid, DATASETNAME7, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + VRFY((dataset5 >= 0), "H5Dcreate2 succeeded"); + dataset6 = H5Dcreate2(fid, DATASETNAME8, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + VRFY((dataset6 >= 0), "H5Dcreate2 succeeded"); + dataset7 = H5Dcreate2(fid, DATASETNAME9, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); + VRFY((dataset7 >= 0), "H5Dcreate2 succeeded"); + /* release 2-D space ID created */ H5Sclose(sid); @@ -827,8 +888,6 @@ dataset_writeAll(void) VRFY((ret>= 0),"set independent IO collectively succeeded"); } - - /* write data collectively */ MESG("writeAll with scalar dataspace"); ret = H5Dwrite(dataset4, H5T_NATIVE_INT, mem_dataspace, file_dataspace, @@ -846,6 +905,137 @@ dataset_writeAll(void) H5Sclose(mem_dataspace); H5Pclose(xfer_plist); + + if(data_array1) free(data_array1); + data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); + VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); + + block[0] = 1; + block[1] = dim1; + stride[0] = 1; + stride[1] = dim1; + count[0] = 1; + count[1] = 1; + start[0] = dim0/mpi_size * mpi_rank; + start[1] = 0; + + dataset_fill(start, block, data_array1); + MESG("data_array initialized"); + if(VERBOSE_MED){ + MESG("data_array created"); + dataset_print(start, block, data_array1); + } + + /* Dataset5: point selection in File - Hyperslab selection in Memory*/ + /* create a file dataspace independently */ + point_set (start, count, stride, block, num_points, coords, OUT_OF_ORDER); + file_dataspace = H5Dget_space (dataset5); + VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); + ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords); + VRFY((ret >= 0), "H5Sselect_elements succeeded"); + + start[0] = 0; + start[1] = 0; + mem_dataspace = H5Dget_space (dataset5); + VRFY((mem_dataspace >= 0), "H5Dget_space succeeded"); + ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); + + /* set up the collective transfer properties list */ + xfer_plist = H5Pcreate (H5P_DATASET_XFER); + VRFY((xfer_plist >= 0), ""); + ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + VRFY((ret >= 0), "H5Pcreate xfer succeeded"); + if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { + ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); + VRFY((ret>= 0),"set independent IO collectively succeeded"); + } + + /* write data collectively */ + ret = H5Dwrite(dataset5, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + xfer_plist, data_array1); + VRFY((ret >= 0), "H5Dwrite dataset5 succeeded"); + + /* release all temporary handles. */ + H5Sclose(file_dataspace); + H5Sclose(mem_dataspace); + H5Pclose(xfer_plist); + + /* Dataset6: point selection in File - Point selection in Memory*/ + /* create a file dataspace independently */ + start[0] = dim0/mpi_size * mpi_rank; + start[1] = 0; + point_set (start, count, stride, block, num_points, coords, OUT_OF_ORDER); + file_dataspace = H5Dget_space (dataset6); + VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); + ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords); + VRFY((ret >= 0), "H5Sselect_elements succeeded"); + + start[0] = 0; + start[1] = 0; + point_set (start, count, stride, block, num_points, coords, IN_ORDER); + mem_dataspace = H5Dget_space (dataset6); + VRFY((mem_dataspace >= 0), "H5Dget_space succeeded"); + ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords); + VRFY((ret >= 0), "H5Sselect_elements succeeded"); + + /* set up the collective transfer properties list */ + xfer_plist = H5Pcreate (H5P_DATASET_XFER); + VRFY((xfer_plist >= 0), ""); + ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + VRFY((ret >= 0), "H5Pcreate xfer succeeded"); + if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { + ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); + VRFY((ret>= 0),"set independent IO collectively succeeded"); + } + + /* write data collectively */ + ret = H5Dwrite(dataset6, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + xfer_plist, data_array1); + VRFY((ret >= 0), "H5Dwrite dataset6 succeeded"); + + /* release all temporary handles. */ + H5Sclose(file_dataspace); + H5Sclose(mem_dataspace); + H5Pclose(xfer_plist); + + /* Dataset7: point selection in File - All selection in Memory*/ + /* create a file dataspace independently */ + start[0] = dim0/mpi_size * mpi_rank; + start[1] = 0; + point_set (start, count, stride, block, num_points, coords, IN_ORDER); + file_dataspace = H5Dget_space (dataset7); + VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); + ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords); + VRFY((ret >= 0), "H5Sselect_elements succeeded"); + + current_dims = num_points; + mem_dataspace = H5Screate_simple (1, ¤t_dims, NULL); + VRFY((mem_dataspace >= 0), "mem_dataspace create succeeded"); + + ret = H5Sselect_all(mem_dataspace); + VRFY((ret >= 0), "H5Sselect_all succeeded"); + + /* set up the collective transfer properties list */ + xfer_plist = H5Pcreate (H5P_DATASET_XFER); + VRFY((xfer_plist >= 0), ""); + ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + VRFY((ret >= 0), "H5Pcreate xfer succeeded"); + if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { + ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); + VRFY((ret>= 0),"set independent IO collectively succeeded"); + } + + /* write data collectively */ + ret = H5Dwrite(dataset7, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + xfer_plist, data_array1); + VRFY((ret >= 0), "H5Dwrite dataset7 succeeded"); + + /* release all temporary handles. */ + H5Sclose(file_dataspace); + H5Sclose(mem_dataspace); + H5Pclose(xfer_plist); + /* * All writes completed. Close datasets collectively */ @@ -856,7 +1046,13 @@ dataset_writeAll(void) ret = H5Dclose(dataset3); VRFY((ret >= 0), "H5Dclose3 succeeded"); ret = H5Dclose(dataset4); - VRFY((ret >= 0), "H5Dclose3 succeeded"); + VRFY((ret >= 0), "H5Dclose4 succeeded"); + ret = H5Dclose(dataset5); + VRFY((ret >= 0), "H5Dclose5 succeeded"); + ret = H5Dclose(dataset6); + VRFY((ret >= 0), "H5Dclose6 succeeded"); + ret = H5Dclose(dataset7); + VRFY((ret >= 0), "H5Dclose7 succeeded"); /* close the file collectively */ H5Fclose(fid); @@ -882,7 +1078,7 @@ dataset_readAll(void) hid_t xfer_plist; /* Dataset transfer properties list */ hid_t file_dataspace; /* File dataspace ID */ hid_t mem_dataspace; /* memory dataspace ID */ - hid_t dataset1, dataset2; /* Dataset ID */ + hid_t dataset1, dataset2, dataset5, dataset6, dataset7; /* Dataset ID */ hbool_t use_gpfs = FALSE; /* Use GPFS hints */ DATATYPE *data_array1 = NULL; /* data buffer */ DATATYPE *data_origin1 = NULL; /* expected data buffer */ @@ -892,6 +1088,11 @@ dataset_readAll(void) hsize_t count[RANK], stride[RANK]; /* for hyperslab setting */ hsize_t block[RANK]; /* for hyperslab setting */ + size_t num_points = dim1; /* for point selection */ + hsize_t coords [RANK*dim0*dim1]; /* for point selection */ + hsize_t current_dims; /* for point selection */ + int i,j,k; + herr_t ret; /* Generic return value */ int mpi_size, mpi_rank; @@ -939,6 +1140,14 @@ dataset_readAll(void) dataset2 = H5Dopen2(fid, DATASETNAME2, H5P_DEFAULT); VRFY((dataset2 >= 0), "H5Dopen2 2 succeeded"); + /* open another dataset collectively */ + dataset5 = H5Dopen2(fid, DATASETNAME7, H5P_DEFAULT); + VRFY((dataset5 >= 0), "H5Dopen2 5 succeeded"); + dataset6 = H5Dopen2(fid, DATASETNAME8, H5P_DEFAULT); + VRFY((dataset6 >= 0), "H5Dopen2 6 succeeded"); + dataset7 = H5Dopen2(fid, DATASETNAME9, H5P_DEFAULT); + VRFY((dataset7 >= 0), "H5Dopen2 7 succeeded"); + /* * Set up dimensions of the slab this process accesses. */ @@ -1077,6 +1286,162 @@ dataset_readAll(void) H5Sclose(mem_dataspace); H5Pclose(xfer_plist); + if(data_array1) free(data_array1); + if(data_origin1) free(data_origin1); + data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); + VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); + data_origin1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); + VRFY((data_origin1 != NULL), "data_origin1 malloc succeeded"); + + block[0] = 1; + block[1] = dim1; + stride[0] = 1; + stride[1] = dim1; + count[0] = 1; + count[1] = 1; + start[0] = dim0/mpi_size * mpi_rank; + start[1] = 0; + + dataset_fill(start, block, data_origin1); + MESG("data_array initialized"); + if(VERBOSE_MED){ + MESG("data_array created"); + dataset_print(start, block, data_origin1); + } + + /* Dataset5: point selection in memory - Hyperslab selection in file*/ + /* create a file dataspace independently */ + file_dataspace = H5Dget_space (dataset5); + VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); + ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block); + VRFY((ret >= 0), "H5Sset_hyperslab succeeded"); + + start[0] = 0; + start[1] = 0; + point_set (start, count, stride, block, num_points, coords, OUT_OF_ORDER); + mem_dataspace = H5Dget_space (dataset5); + VRFY((mem_dataspace >= 0), "H5Dget_space succeeded"); + ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords); + VRFY((ret >= 0), "H5Sselect_elements succeeded"); + + /* set up the collective transfer properties list */ + xfer_plist = H5Pcreate (H5P_DATASET_XFER); + VRFY((xfer_plist >= 0), ""); + ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + VRFY((ret >= 0), "H5Pcreate xfer succeeded"); + if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { + ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); + VRFY((ret>= 0),"set independent IO collectively succeeded"); + } + + /* read data collectively */ + ret = H5Dread(dataset5, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + xfer_plist, data_array1); + VRFY((ret >= 0), "H5Dread dataset5 succeeded"); + + + ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); + if(ret) nerrors++; + + /* release all temporary handles. */ + H5Sclose(file_dataspace); + H5Sclose(mem_dataspace); + H5Pclose(xfer_plist); + + + if(data_array1) free(data_array1); + data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); + VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); + + /* Dataset6: point selection in File - Point selection in Memory*/ + /* create a file dataspace independently */ + start[0] = dim0/mpi_size * mpi_rank; + start[1] = 0; + point_set (start, count, stride, block, num_points, coords, IN_ORDER); + file_dataspace = H5Dget_space (dataset6); + VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); + ret = H5Sselect_elements(file_dataspace, H5S_SELECT_SET, num_points, coords); + VRFY((ret >= 0), "H5Sselect_elements succeeded"); + + start[0] = 0; + start[1] = 0; + point_set (start, count, stride, block, num_points, coords, OUT_OF_ORDER); + mem_dataspace = H5Dget_space (dataset6); + VRFY((mem_dataspace >= 0), "H5Dget_space succeeded"); + ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords); + VRFY((ret >= 0), "H5Sselect_elements succeeded"); + + /* set up the collective transfer properties list */ + xfer_plist = H5Pcreate (H5P_DATASET_XFER); + VRFY((xfer_plist >= 0), ""); + ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + VRFY((ret >= 0), "H5Pcreate xfer succeeded"); + if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { + ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); + VRFY((ret>= 0),"set independent IO collectively succeeded"); + } + + /* read data collectively */ + ret = H5Dread(dataset6, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + xfer_plist, data_array1); + VRFY((ret >= 0), "H5Dread dataset6 succeeded"); + + ret = dataset_vrfy(start, count, stride, block, data_array1, data_origin1); + if(ret) nerrors++; + + /* release all temporary handles. */ + H5Sclose(file_dataspace); + H5Sclose(mem_dataspace); + H5Pclose(xfer_plist); + + if(data_array1) free(data_array1); + data_array1 = (DATATYPE *)malloc(dim0*dim1*sizeof(DATATYPE)); + VRFY((data_array1 != NULL), "data_array1 malloc succeeded"); + + /* Dataset7: point selection in memory - All selection in file*/ + /* create a file dataspace independently */ + file_dataspace = H5Dget_space (dataset7); + VRFY((file_dataspace >= 0), "H5Dget_space succeeded"); + ret = H5Sselect_all(file_dataspace); + VRFY((ret >= 0), "H5Sselect_all succeeded"); + + num_points = dim0 * dim1; + k=0; + for (i=0 ; i<dim0; i++) { + for (j=0 ; j<dim1; j++) { + coords[k++] = i; + coords[k++] = j; + } + } + mem_dataspace = H5Dget_space (dataset7); + VRFY((mem_dataspace >= 0), "H5Dget_space succeeded"); + ret = H5Sselect_elements(mem_dataspace, H5S_SELECT_SET, num_points, coords); + VRFY((ret >= 0), "H5Sselect_elements succeeded"); + + /* set up the collective transfer properties list */ + xfer_plist = H5Pcreate (H5P_DATASET_XFER); + VRFY((xfer_plist >= 0), ""); + ret = H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE); + VRFY((ret >= 0), "H5Pcreate xfer succeeded"); + if(dxfer_coll_type == DXFER_INDEPENDENT_IO) { + ret = H5Pset_dxpl_mpio_collective_opt(xfer_plist,H5FD_MPIO_INDIVIDUAL_IO); + VRFY((ret>= 0),"set independent IO collectively succeeded"); + } + + /* read data collectively */ + ret = H5Dread(dataset7, H5T_NATIVE_INT, mem_dataspace, file_dataspace, + xfer_plist, data_array1); + VRFY((ret >= 0), "H5Dread dataset7 succeeded"); + + start[0] = dim0/mpi_size * mpi_rank; + start[1] = 0; + ret = dataset_vrfy(start, count, stride, block, data_array1+(dim0/mpi_size * dim1 * mpi_rank), data_origin1); + if(ret) nerrors++; + + /* release all temporary handles. */ + H5Sclose(file_dataspace); + H5Sclose(mem_dataspace); + H5Pclose(xfer_plist); /* * All reads completed. Close datasets collectively @@ -1085,6 +1450,12 @@ dataset_readAll(void) VRFY((ret >= 0), "H5Dclose1 succeeded"); ret = H5Dclose(dataset2); VRFY((ret >= 0), "H5Dclose2 succeeded"); + ret = H5Dclose(dataset5); + VRFY((ret >= 0), "H5Dclose5 succeeded"); + ret = H5Dclose(dataset6); + VRFY((ret >= 0), "H5Dclose6 succeeded"); + ret = H5Dclose(dataset7); + VRFY((ret >= 0), "H5Dclose7 succeeded"); /* close the file collectively */ H5Fclose(fid); @@ -3073,9 +3444,6 @@ actual_io_mode_tests(void) { * TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES: * Test for NULL dataspace as the cause of breaking collective I/O. * - * TEST_POINT_SELECTIONS: - * Test for selecting elements of dataspce as the cause of breaking collective I/O. - * * TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT: * Test for Compact layout as the cause of breaking collective I/O. * @@ -3247,12 +3615,6 @@ test_no_collective_cause_mode(int selection_mode) no_collective_cause_global_expected |= H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES; } - if (selection_mode & TEST_POINT_SELECTIONS ) { - test_name = "Broken Collective I/O - Point Selection"; - no_collective_cause_local_expected |= H5D_MPIO_POINT_SELECTIONS; - no_collective_cause_global_expected |= H5D_MPIO_POINT_SELECTIONS; - } - if (selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT || selection_mode & TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL) { test_name = "Broken Collective I/O - No CONTI or CHUNKED Dataset"; @@ -3311,17 +3673,6 @@ test_no_collective_cause_mode(int selection_mode) VRFY((mem_space >= 0), "mem_space created"); } - if (selection_mode & TEST_POINT_SELECTIONS) { - coord[0][0] = 0; coord[0][1] = 0; - coord[1][0] = 1; coord[1][1] = 1; - ret = H5Sselect_elements (file_space, H5S_SELECT_SET, NELM, (const hsize_t *)coord); - VRFY((ret >= 0), "H5Sselect_elements succeeded"); - - ret = H5Sselect_elements (mem_space, H5S_SELECT_SET, NELM, (const hsize_t *)coord); - VRFY((ret >= 0), "H5Sselect_elements succeeded"); - } - - /* Get the number of elements in the selection */ length = dim0 * dim1; @@ -3437,7 +3788,7 @@ test_no_collective_cause_mode(int selection_mode) * have the correct values. * * NOTE: - * This is a temprary function. + * This is a temporary function. * test_no_collective_cause_mode(TEST_FILTERS) will replace this when * H5Dcreate and H5write support for mpio and filter feature. * @@ -3688,7 +4039,6 @@ no_collective_cause_tests(void) test_no_collective_cause_mode (TEST_DATA_TRANSFORMS); test_no_collective_cause_mode (TEST_SET_MPIPOSIX); test_no_collective_cause_mode (TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES); - test_no_collective_cause_mode (TEST_POINT_SELECTIONS); test_no_collective_cause_mode (TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT); test_no_collective_cause_mode (TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL); #ifdef H5_HAVE_FILTER_FLETCHER32 @@ -3704,7 +4054,7 @@ no_collective_cause_tests(void) */ test_no_collective_cause_mode (TEST_SET_MPIPOSIX | TEST_DATATYPE_CONVERSION); test_no_collective_cause_mode (TEST_DATATYPE_CONVERSION | TEST_DATA_TRANSFORMS); - test_no_collective_cause_mode (TEST_DATATYPE_CONVERSION | TEST_DATA_TRANSFORMS | TEST_POINT_SELECTIONS); + test_no_collective_cause_mode (TEST_SET_MPIPOSIX | TEST_DATATYPE_CONVERSION | TEST_DATA_TRANSFORMS); return; } diff --git a/testpar/testphdf5.h b/testpar/testphdf5.h index 15ff884..0b39160 100644 --- a/testpar/testphdf5.h +++ b/testpar/testphdf5.h @@ -45,6 +45,13 @@ enum H5TEST_COLL_CHUNK_API {API_NONE=0,API_LINK_HARD, #define DATASETNAME4 "Data4" #define DATASETNAME5 "Data5" #define DATASETNAME6 "Data6" +#define DATASETNAME7 "Data7" +#define DATASETNAME8 "Data8" +#define DATASETNAME9 "Data9" + +/* point selection order */ +#define IN_ORDER 1 +#define OUT_OF_ORDER 2 /* Hyperslab layout styles */ #define BYROW 1 /* divide into slabs of rows */ @@ -181,13 +188,12 @@ enum H5TEST_COLL_CHUNK_API {API_NONE=0,API_LINK_HARD, #define TEST_DATA_TRANSFORMS 0x008 #define TEST_SET_MPIPOSIX 0x010 #define TEST_NOT_SIMPLE_OR_SCALAR_DATASPACES 0x020 -#define TEST_POINT_SELECTIONS 0x040 -#define TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT 0x080 -#define TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL 0x100 -#define TEST_FILTERS 0x200 +#define TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_COMPACT 0x040 +#define TEST_NOT_CONTIGUOUS_OR_CHUNKED_DATASET_EXTERNAL 0x080 +#define TEST_FILTERS 0x100 /* TEST_FILTERS will take place of this after supporting mpio + filter for * H5Dcreate and H5Dwrite */ -#define TEST_FILTERS_READ 0x400 +#define TEST_FILTERS_READ 0x200 /* Don't erase these lines, they are put here for debugging purposes */ /* @@ -296,5 +302,6 @@ hid_t create_faccess_plist(MPI_Comm comm, MPI_Info info, int l_facc_type, hbool_ MPI_Offset h5_mpi_get_file_size(const char *filename, MPI_Comm comm, MPI_Info info); int dataset_vrfy(hsize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], DATATYPE *dataset, DATATYPE *original); - +void point_set (hsize_t start[], hsize_t count[], hsize_t stride[], hsize_t block[], + size_t num_points, hsize_t coords[], int order); #endif /* PHDF5TEST_H */ |