diff options
Diffstat (limited to 'src/H5Dmpio.c')
| -rw-r--r-- | src/H5Dmpio.c | 1180 |
1 files changed, 592 insertions, 588 deletions
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index 4e5a121..de60f6c 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -27,21 +27,20 @@ #define H5D_PACKAGE /* suppress error about including H5Dpkg */ - /***********/ /* Headers */ /***********/ -#include "H5private.h" /* Generic Functions */ -#include "H5Dpkg.h" /* Datasets */ -#include "H5Eprivate.h" /* Error handling */ -#include "H5Fprivate.h" /* File access */ -#include "H5FDprivate.h" /* File drivers */ -#include "H5Iprivate.h" /* IDs */ -#include "H5MMprivate.h" /* Memory management */ -#include "H5Oprivate.h" /* Object headers */ -#include "H5Pprivate.h" /* Property lists */ -#include "H5Sprivate.h" /* Dataspaces */ -#include "H5VMprivate.h" /* Vector */ +#include "H5private.h" /* Generic Functions */ +#include "H5Dpkg.h" /* Datasets */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5Fprivate.h" /* File access */ +#include "H5FDprivate.h" /* File drivers */ +#include "H5Iprivate.h" /* IDs */ +#include "H5MMprivate.h" /* Memory management */ +#include "H5Oprivate.h" /* Object headers */ +#include "H5Pprivate.h" /* Property lists */ +#include "H5Sprivate.h" /* Dataspaces */ +#include "H5VMprivate.h" /* Vector */ #ifdef H5_HAVE_PARALLEL @@ -66,7 +65,7 @@ #define H5D_OBTAIN_ALL_CHUNK_ADDR_COL 2 /* Macros to define the default ratio of obtaining all chunk addresses for one linked-chunk IO case */ -#define H5D_ALL_CHUNK_ADDR_THRES_COL 30 +#define H5D_ALL_CHUNK_ADDR_THRES_COL 30 #define H5D_ALL_CHUNK_ADDR_THRES_COL_NUM 10000 /***** Macros for multi-chunk collective IO case. *****/ @@ -76,66 +75,58 @@ */ /* Macros to represent different IO modes(NONE, Independent or collective)for multiple chunk IO case */ -#define H5D_CHUNK_IO_MODE_IND 0 -#define H5D_CHUNK_IO_MODE_COL 1 +#define H5D_CHUNK_IO_MODE_IND 0 +#define H5D_CHUNK_IO_MODE_COL 1 /* Macros to represent the regularity of the selection for multiple chunk IO case. */ -#define H5D_CHUNK_SELECT_REG 1 -#define H5D_CHUNK_SELECT_IRREG 2 -#define H5D_CHUNK_SELECT_NONE 0 - +#define H5D_CHUNK_SELECT_REG 1 +#define H5D_CHUNK_SELECT_IRREG 2 +#define H5D_CHUNK_SELECT_NONE 0 /******************/ /* Local Typedefs */ /******************/ /* Combine chunk address and chunk info into a struct for better performance. */ typedef struct H5D_chunk_addr_info_t { - haddr_t chunk_addr; - H5D_chunk_info_t chunk_info; + haddr_t chunk_addr; + H5D_chunk_info_t chunk_info; } H5D_chunk_addr_info_t; - /********************/ /* Local Prototypes */ /********************/ -static herr_t H5D__chunk_collective_io(H5D_io_info_t *io_info, - const H5D_type_info_t *type_info, H5D_chunk_map_t *fm); -static herr_t H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, - const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, - H5P_genplist_t *dx_plist); -static herr_t H5D__link_chunk_collective_io(H5D_io_info_t *io_info, - const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, int sum_chunk, - H5P_genplist_t *dx_plist); -static herr_t H5D__inter_collective_io(H5D_io_info_t *io_info, - const H5D_type_info_t *type_info, const H5S_t *file_space, - const H5S_t *mem_space); -static herr_t H5D__final_collective_io(H5D_io_info_t *io_info, - const H5D_type_info_t *type_info, hsize_t nelmts, MPI_Datatype *mpi_file_type, - MPI_Datatype *mpi_buf_type); +static herr_t H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, + H5D_chunk_map_t *fm); +static herr_t H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, + H5D_chunk_map_t *fm, H5P_genplist_t *dx_plist); +static herr_t H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, + H5D_chunk_map_t *fm, int sum_chunk, H5P_genplist_t *dx_plist); +static herr_t H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, + const H5S_t *file_space, const H5S_t *mem_space); +static herr_t H5D__final_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, + hsize_t nelmts, MPI_Datatype *mpi_file_type, + MPI_Datatype *mpi_buf_type); static herr_t H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, - H5D_chunk_addr_info_t chunk_addr_info_array[], int many_chunk_opt); -static herr_t H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm, - H5P_genplist_t *dx_plist, uint8_t assign_io_mode[], haddr_t chunk_addr[]); + H5D_chunk_addr_info_t chunk_addr_info_array[], int many_chunk_opt); +static herr_t H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm, H5P_genplist_t *dx_plist, + uint8_t assign_io_mode[], haddr_t chunk_addr[]); static herr_t H5D__ioinfo_xfer_mode(H5D_io_info_t *io_info, H5P_genplist_t *dx_plist, - H5FD_mpio_xfer_t xfer_mode); + H5FD_mpio_xfer_t xfer_mode); static herr_t H5D__ioinfo_coll_opt_mode(H5D_io_info_t *io_info, H5P_genplist_t *dx_plist, - H5FD_mpio_collective_opt_t coll_opt_mode); -static herr_t H5D__mpio_get_min_chunk(const H5D_io_info_t *io_info, - const H5D_chunk_map_t *fm, int *min_chunkf); -static herr_t H5D__mpio_get_sum_chunk(const H5D_io_info_t *io_info, - const H5D_chunk_map_t *fm, int *sum_chunkf); - + H5FD_mpio_collective_opt_t coll_opt_mode); +static herr_t H5D__mpio_get_min_chunk(const H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, + int *min_chunkf); +static herr_t H5D__mpio_get_sum_chunk(const H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, + int *sum_chunkf); /*********************/ /* Package Variables */ /*********************/ - /*******************/ /* Local Variables */ /*******************/ - /*------------------------------------------------------------------------- * Function: H5D__mpio_opt_possible * @@ -151,13 +142,12 @@ static herr_t H5D__mpio_get_sum_chunk(const H5D_io_info_t *io_info, *------------------------------------------------------------------------- */ htri_t -H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, - const H5S_t *mem_space, const H5D_type_info_t *type_info, - const H5D_chunk_map_t *fm, H5P_genplist_t *dx_plist) +H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, const H5S_t *mem_space, + const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm, H5P_genplist_t *dx_plist) { - int local_cause = 0; /* Local reason(s) for breaking collective mode */ - int global_cause = 0; /* Global reason(s) for breaking collective mode */ - htri_t ret_value; /* Return value */ + int local_cause = 0; /* Local reason(s) for breaking collective mode */ + int global_cause = 0; /* Global reason(s) for breaking collective mode */ + htri_t ret_value; /* Return value */ FUNC_ENTER_PACKAGE @@ -167,36 +157,35 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, HDassert(file_space); HDassert(type_info); - /* For independent I/O, get out quickly and don't try to form consensus */ - if(io_info->dxpl_cache->xfer_mode == H5FD_MPIO_INDEPENDENT) + if (io_info->dxpl_cache->xfer_mode == H5FD_MPIO_INDEPENDENT) local_cause |= H5D_MPIO_SET_INDEPENDENT; /* Optimized MPI types flag must be set */ /* (based on 'HDF5_MPI_OPT_TYPES' environment variable) */ - if(!H5FD_mpi_opt_types_g) + if (!H5FD_mpi_opt_types_g) local_cause |= H5D_MPIO_MPI_OPT_TYPES_ENV_VAR_DISABLED; /* 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; /* 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; /* 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)))) + 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)))) local_cause |= H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES; /* Dataset storage must be contiguous or chunked */ - if(!(io_info->dset->shared->layout.type == H5D_CONTIGUOUS || - io_info->dset->shared->layout.type == H5D_CHUNKED)) + if (!(io_info->dset->shared->layout.type == H5D_CONTIGUOUS || + io_info->dset->shared->layout.type == H5D_CHUNKED)) local_cause |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET; /* 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 @@ -207,29 +196,30 @@ 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 && - io_info->dset->shared->dcpl_cache.pline.nused > 0) + if (io_info->dset->shared->layout.type == H5D_CHUNKED && + io_info->dset->shared->dcpl_cache.pline.nused > 0) local_cause |= H5D_MPIO_FILTERS; /* Check for independent I/O */ - if(local_cause & H5D_MPIO_SET_INDEPENDENT) + if (local_cause & H5D_MPIO_SET_INDEPENDENT) global_cause = local_cause; else { - int mpi_code; /* MPI error code */ + int mpi_code; /* MPI error code */ /* Form consensus opinion among all processes about whether to perform * collective I/O */ - if(MPI_SUCCESS != (mpi_code = MPI_Allreduce(&local_cause, &global_cause, 1, MPI_INT, MPI_BOR, io_info->comm))) + if (MPI_SUCCESS != + (mpi_code = MPI_Allreduce(&local_cause, &global_cause, 1, MPI_INT, MPI_BOR, io_info->comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code) } /* end else */ /* 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) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set local no collective cause property") + if (H5P_set(dx_plist, H5D_MPIO_LOCAL_NO_COLLECTIVE_CAUSE_NAME, &local_cause) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set local no collective cause property") /* Write the global value of no-collective-cause to the DXPL. */ - if(H5P_set(dx_plist, H5D_MPIO_GLOBAL_NO_COLLECTIVE_CAUSE_NAME, &global_cause) < 0) + if (H5P_set(dx_plist, H5D_MPIO_GLOBAL_NO_COLLECTIVE_CAUSE_NAME, &global_cause) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set global no collective cause property") /* Set the return value, based on the global cause */ @@ -239,7 +229,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D__mpio_opt_possible() */ - /*------------------------------------------------------------------------- * Function: H5D__mpio_select_read * @@ -253,22 +242,24 @@ done: */ herr_t H5D__mpio_select_read(const H5D_io_info_t *io_info, const H5D_type_info_t H5_ATTR_UNUSED *type_info, - hsize_t mpi_buf_count, const H5S_t H5_ATTR_UNUSED *file_space, const H5S_t H5_ATTR_UNUSED *mem_space) + hsize_t mpi_buf_count, const H5S_t H5_ATTR_UNUSED *file_space, + const H5S_t H5_ATTR_UNUSED *mem_space) { - const H5D_contig_storage_t *store_contig = &(io_info->store->contig); /* Contiguous storage info for this I/O operation */ + const H5D_contig_storage_t *store_contig = + &(io_info->store->contig); /* Contiguous storage info for this I/O operation */ herr_t ret_value = SUCCEED; FUNC_ENTER_PACKAGE H5_CHECK_OVERFLOW(mpi_buf_count, hsize_t, size_t); - if(H5F_block_read(io_info->dset->oloc.file, H5FD_MEM_DRAW, store_contig->dset_addr, (size_t)mpi_buf_count, io_info->dxpl_id, io_info->u.rbuf) < 0) + if (H5F_block_read(io_info->dset->oloc.file, H5FD_MEM_DRAW, store_contig->dset_addr, + (size_t)mpi_buf_count, io_info->dxpl_id, io_info->u.rbuf) < 0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "can't finish collective parallel read") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__mpio_select_read() */ - /*------------------------------------------------------------------------- * Function: H5D__mpio_select_write * @@ -282,23 +273,25 @@ done: */ herr_t H5D__mpio_select_write(const H5D_io_info_t *io_info, const H5D_type_info_t H5_ATTR_UNUSED *type_info, - hsize_t mpi_buf_count, const H5S_t H5_ATTR_UNUSED *file_space, const H5S_t H5_ATTR_UNUSED *mem_space) + hsize_t mpi_buf_count, const H5S_t H5_ATTR_UNUSED *file_space, + const H5S_t H5_ATTR_UNUSED *mem_space) { - const H5D_contig_storage_t *store_contig = &(io_info->store->contig); /* Contiguous storage info for this I/O operation */ + const H5D_contig_storage_t *store_contig = + &(io_info->store->contig); /* Contiguous storage info for this I/O operation */ herr_t ret_value = SUCCEED; FUNC_ENTER_PACKAGE /*OKAY: CAST DISCARDS CONST QUALIFIER*/ H5_CHECK_OVERFLOW(mpi_buf_count, hsize_t, size_t); - if(H5F_block_write(io_info->dset->oloc.file, H5FD_MEM_DRAW, store_contig->dset_addr, (size_t)mpi_buf_count, io_info->dxpl_id, io_info->u.wbuf) < 0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "can't finish collective parallel write") + if (H5F_block_write(io_info->dset->oloc.file, H5FD_MEM_DRAW, store_contig->dset_addr, + (size_t)mpi_buf_count, io_info->dxpl_id, io_info->u.wbuf) < 0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "can't finish collective parallel write") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__mpio_select_write() */ - /*------------------------------------------------------------------------- * Function: H5D__ioinfo_xfer_mode * @@ -312,29 +305,28 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__ioinfo_xfer_mode(H5D_io_info_t *io_info, H5P_genplist_t *dx_plist, - H5FD_mpio_xfer_t xfer_mode) +H5D__ioinfo_xfer_mode(H5D_io_info_t *io_info, H5P_genplist_t *dx_plist, H5FD_mpio_xfer_t xfer_mode) { - herr_t ret_value = SUCCEED; /* return value */ + herr_t ret_value = SUCCEED; /* return value */ FUNC_ENTER_STATIC /* Change the xfer_mode */ io_info->dxpl_cache->xfer_mode = xfer_mode; - if(H5P_set(dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &io_info->dxpl_cache->xfer_mode) < 0) + if (H5P_set(dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &io_info->dxpl_cache->xfer_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode") /* Change the "single I/O" function pointers */ - if(xfer_mode == H5FD_MPIO_INDEPENDENT) { + if (xfer_mode == H5FD_MPIO_INDEPENDENT) { /* Set the pointers to the original, non-MPI-specific routines */ - io_info->io_ops.single_read = io_info->orig.io_ops.single_read; + io_info->io_ops.single_read = io_info->orig.io_ops.single_read; io_info->io_ops.single_write = io_info->orig.io_ops.single_write; } /* end if */ else { HDassert(xfer_mode == H5FD_MPIO_COLLECTIVE); /* Set the pointers to the MPI-specific routines */ - io_info->io_ops.single_read = H5D__mpio_select_read; + io_info->io_ops.single_read = H5D__mpio_select_read; io_info->io_ops.single_write = H5D__mpio_select_write; } /* end else */ @@ -342,7 +334,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__ioinfo_xfer_mode() */ - /*------------------------------------------------------------------------- * Function: H5D__ioinfo_coll_opt_mode * @@ -358,22 +349,21 @@ done: */ static herr_t H5D__ioinfo_coll_opt_mode(H5D_io_info_t *io_info, H5P_genplist_t *dx_plist, - H5FD_mpio_collective_opt_t coll_opt_mode) + H5FD_mpio_collective_opt_t coll_opt_mode) { - herr_t ret_value = SUCCEED; /* return value */ + herr_t ret_value = SUCCEED; /* return value */ FUNC_ENTER_STATIC /* Change the optimal xfer_mode */ io_info->dxpl_cache->coll_opt_mode = coll_opt_mode; - if(H5P_set(dx_plist, H5D_XFER_MPIO_COLLECTIVE_OPT_NAME, &io_info->dxpl_cache->coll_opt_mode) < 0) + if (H5P_set(dx_plist, H5D_XFER_MPIO_COLLECTIVE_OPT_NAME, &io_info->dxpl_cache->coll_opt_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__ioinfo_coll_opt_mode() */ - /*------------------------------------------------------------------------- * Function: H5D__mpio_get_min_chunk * @@ -388,11 +378,10 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__mpio_get_min_chunk(const H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, - int *min_chunkf) +H5D__mpio_get_min_chunk(const H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, int *min_chunkf) { - int num_chunkf; /* Number of chunks to iterate over */ - int mpi_code; /* MPI return code */ + int num_chunkf; /* Number of chunks to iterate over */ + int mpi_code; /* MPI return code */ herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -401,14 +390,14 @@ H5D__mpio_get_min_chunk(const H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, num_chunkf = H5SL_count(fm->sel_chunks); /* Determine the minimum # of chunks for all processes */ - if(MPI_SUCCESS != (mpi_code = MPI_Allreduce(&num_chunkf, min_chunkf, 1, MPI_INT, MPI_MIN, io_info->comm))) + if (MPI_SUCCESS != + (mpi_code = MPI_Allreduce(&num_chunkf, min_chunkf, 1, MPI_INT, MPI_MIN, io_info->comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code) done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__mpio_get_min_chunk() */ - /*------------------------------------------------------------------------- * Function: H5D__mpio_get_sum_chunk * @@ -423,30 +412,29 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__mpio_get_sum_chunk(const H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, - int *sum_chunkf) +H5D__mpio_get_sum_chunk(const H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, int *sum_chunkf) { - int num_chunkf; /* Number of chunks to iterate over */ + int num_chunkf; /* Number of chunks to iterate over */ size_t ori_num_chunkf; - int mpi_code; /* MPI return code */ + int mpi_code; /* MPI return code */ herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC /* Get the number of chunks to perform I/O on */ - num_chunkf = 0; + num_chunkf = 0; ori_num_chunkf = H5SL_count(fm->sel_chunks); H5_CHECKED_ASSIGN(num_chunkf, int, ori_num_chunkf, size_t); /* Determine the summation of number of chunks for all processes */ - if(MPI_SUCCESS != (mpi_code = MPI_Allreduce(&num_chunkf, sum_chunkf, 1, MPI_INT, MPI_SUM, io_info->comm))) + if (MPI_SUCCESS != + (mpi_code = MPI_Allreduce(&num_chunkf, sum_chunkf, 1, MPI_INT, MPI_SUM, io_info->comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code) done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__mpio_get_sum_chunk() */ - /*------------------------------------------------------------------------- * Function: H5D__contig_collective_read * @@ -462,12 +450,12 @@ done: */ herr_t H5D__contig_collective_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - hsize_t H5_ATTR_UNUSED nelmts, const H5S_t *file_space, const H5S_t *mem_space, - H5D_chunk_map_t H5_ATTR_UNUSED *fm) + hsize_t H5_ATTR_UNUSED nelmts, const H5S_t *file_space, const H5S_t *mem_space, + H5D_chunk_map_t H5_ATTR_UNUSED *fm) { H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_CONTIGUOUS_COLLECTIVE; - H5P_genplist_t *dx_plist; /* Pointer to DXPL */ - herr_t ret_value = SUCCEED; /* Return value */ + H5P_genplist_t * dx_plist; /* Pointer to DXPL */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -476,24 +464,23 @@ H5D__contig_collective_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_ HDassert(TRUE == H5P_isa_class(io_info->dxpl_id, H5P_DATASET_XFER)); /* Call generic internal collective I/O routine */ - if(H5D__inter_collective_io(io_info, type_info, file_space, mem_space) < 0) + if (H5D__inter_collective_io(io_info, type_info, file_space, mem_space) < 0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "couldn't finish shared collective MPI-IO") /* Obtain the data transfer properties */ - if(NULL == (dx_plist = H5I_object(io_info->dxpl_id))) + if (NULL == (dx_plist = H5I_object(io_info->dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data transfer property list") /* Set the actual I/O mode property. internal_collective_io will not break to * independent I/O, so we set it here. */ - if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0) + if (H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual io mode property") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_collective_read() */ - /*------------------------------------------------------------------------- * Function: H5D__contig_collective_write * @@ -509,12 +496,12 @@ done: */ herr_t H5D__contig_collective_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - hsize_t H5_ATTR_UNUSED nelmts, const H5S_t *file_space, const H5S_t *mem_space, - H5D_chunk_map_t H5_ATTR_UNUSED *fm) + hsize_t H5_ATTR_UNUSED nelmts, const H5S_t *file_space, const H5S_t *mem_space, + H5D_chunk_map_t H5_ATTR_UNUSED *fm) { H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_CONTIGUOUS_COLLECTIVE; - H5P_genplist_t *dx_plist; /* Pointer to DXPL */ - herr_t ret_value = SUCCEED; /* Return value */ + H5P_genplist_t * dx_plist; /* Pointer to DXPL */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -523,24 +510,23 @@ H5D__contig_collective_write(H5D_io_info_t *io_info, const H5D_type_info_t *type HDassert(TRUE == H5P_isa_class(io_info->dxpl_id, H5P_DATASET_XFER)); /* Call generic internal collective I/O routine */ - if(H5D__inter_collective_io(io_info, type_info, file_space, mem_space) < 0) + if (H5D__inter_collective_io(io_info, type_info, file_space, mem_space) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "couldn't finish shared collective MPI-IO") /* Obtain the data transfer properties */ - if(NULL == (dx_plist = H5I_object(io_info->dxpl_id))) + if (NULL == (dx_plist = H5I_object(io_info->dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data transfer property list") /* Set the actual I/O mode property. internal_collective_io will not break to * independent I/O, so we set it here. */ - if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0) + if (H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual io mode property") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_collective_write() */ - /*------------------------------------------------------------------------- * Function: H5D__chunk_collective_io * @@ -578,17 +564,16 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5D_chunk_map_t *fm) +H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm) { - H5P_genplist_t *dx_plist; /* Pointer to DXPL */ + H5P_genplist_t * dx_plist; /* Pointer to DXPL */ H5FD_mpio_chunk_opt_t chunk_opt_mode; - int io_option = H5D_MULTI_CHUNK_IO_MORE_OPT; - int sum_chunk = -1; + int io_option = H5D_MULTI_CHUNK_IO_MORE_OPT; + int sum_chunk = -1; #ifdef H5_HAVE_INSTRUMENTED_LIBRARY - htri_t temp_not_link_io = FALSE; + htri_t temp_not_link_io = FALSE; #endif - herr_t ret_value = SUCCEED; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -599,31 +584,33 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf HDassert(fm); /* Obtain the data transfer properties */ - if(NULL == (dx_plist = H5I_object(io_info->dxpl_id))) + if (NULL == (dx_plist = H5I_object(io_info->dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file access property list") /* Check the optional property list on what to do with collective chunk IO. */ chunk_opt_mode = H5P_peek_unsigned(dx_plist, H5D_XFER_MPIO_CHUNK_OPT_HARD_NAME); - if(H5FD_MPIO_CHUNK_ONE_IO == chunk_opt_mode) - io_option = H5D_ONE_LINK_CHUNK_IO; /*no opt*/ + if (H5FD_MPIO_CHUNK_ONE_IO == chunk_opt_mode) + io_option = H5D_ONE_LINK_CHUNK_IO; /*no opt*/ /* direct request to multi-chunk-io */ - else if(H5FD_MPIO_CHUNK_MULTI_IO == chunk_opt_mode) - io_option = H5D_MULTI_CHUNK_IO; + else if (H5FD_MPIO_CHUNK_MULTI_IO == chunk_opt_mode) + io_option = H5D_MULTI_CHUNK_IO; /* via default path. branch by num threshold */ else { - unsigned one_link_chunk_io_threshold; /* Threshhold to use single collective I/O for all chunks */ - int mpi_size; /* Number of processes in MPI job */ + unsigned one_link_chunk_io_threshold; /* Threshhold to use single collective I/O for all chunks */ + int mpi_size; /* Number of processes in MPI job */ - if(H5D__mpio_get_sum_chunk(io_info, fm, &sum_chunk) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSWAP, FAIL, "unable to obtain the total chunk number of all processes"); - if((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) + if (H5D__mpio_get_sum_chunk(io_info, fm, &sum_chunk) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSWAP, FAIL, + "unable to obtain the total chunk number of all processes"); + if ((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi size") one_link_chunk_io_threshold = H5P_peek_unsigned(dx_plist, H5D_XFER_MPIO_CHUNK_OPT_NUM_NAME); /* step 1: choose an IO option */ - /* If the average number of chunk per process is greater than a threshold, we will do one link chunked IO. */ - if((unsigned)sum_chunk / mpi_size >= one_link_chunk_io_threshold) + /* If the average number of chunk per process is greater than a threshold, we will do one link chunked + * IO. */ + if ((unsigned)sum_chunk / mpi_size >= one_link_chunk_io_threshold) io_option = H5D_ONE_LINK_CHUNK_IO_MORE_OPT; #ifdef H5_HAVE_INSTRUMENTED_LIBRARY else @@ -632,63 +619,63 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf } /* end else */ #ifdef H5_HAVE_INSTRUMENTED_LIBRARY -{ - H5P_genplist_t *plist; /* Property list pointer */ - htri_t check_prop; - int new_value; - - /* Get the dataset transfer property list */ - if(NULL == (plist = (H5P_genplist_t *)H5I_object(io_info->dxpl_id))) - HGOTO_ERROR(H5E_IO, H5E_BADTYPE, FAIL, "not a dataset transfer property list") - - /*** Test collective chunk user-input optimization APIs. ***/ - check_prop = H5P_exist_plist(plist, H5D_XFER_COLL_CHUNK_LINK_HARD_NAME); - if(check_prop > 0) { - if(H5D_ONE_LINK_CHUNK_IO == io_option) { - new_value = 0; - if(H5P_set(plist, H5D_XFER_COLL_CHUNK_LINK_HARD_NAME, &new_value) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value") - } /* end if */ - } /* end if */ - check_prop = H5P_exist_plist(plist, H5D_XFER_COLL_CHUNK_MULTI_HARD_NAME); - if(check_prop > 0) { - if(H5D_MULTI_CHUNK_IO == io_option) { - new_value = 0; - if(H5P_set(plist, H5D_XFER_COLL_CHUNK_MULTI_HARD_NAME, &new_value) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value") - } /* end if */ - } /* end if */ - check_prop = H5P_exist_plist(plist, H5D_XFER_COLL_CHUNK_LINK_NUM_TRUE_NAME); - if(check_prop > 0) { - if(H5D_ONE_LINK_CHUNK_IO_MORE_OPT == io_option) { - new_value = 0; - if(H5P_set(plist, H5D_XFER_COLL_CHUNK_LINK_NUM_TRUE_NAME, &new_value) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value") - } /* end if */ - } /* end if */ - check_prop = H5P_exist_plist(plist, H5D_XFER_COLL_CHUNK_LINK_NUM_FALSE_NAME); - if(check_prop > 0) { - if(temp_not_link_io) { - new_value = 0; - if(H5P_set(plist, H5D_XFER_COLL_CHUNK_LINK_NUM_FALSE_NAME, &new_value) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value") - } /* end if */ - } /* end if */ -} + { + H5P_genplist_t *plist; /* Property list pointer */ + htri_t check_prop; + int new_value; + + /* Get the dataset transfer property list */ + if (NULL == (plist = (H5P_genplist_t *)H5I_object(io_info->dxpl_id))) + HGOTO_ERROR(H5E_IO, H5E_BADTYPE, FAIL, "not a dataset transfer property list") + + /*** Test collective chunk user-input optimization APIs. ***/ + check_prop = H5P_exist_plist(plist, H5D_XFER_COLL_CHUNK_LINK_HARD_NAME); + if (check_prop > 0) { + if (H5D_ONE_LINK_CHUNK_IO == io_option) { + new_value = 0; + if (H5P_set(plist, H5D_XFER_COLL_CHUNK_LINK_HARD_NAME, &new_value) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value") + } /* end if */ + } /* end if */ + check_prop = H5P_exist_plist(plist, H5D_XFER_COLL_CHUNK_MULTI_HARD_NAME); + if (check_prop > 0) { + if (H5D_MULTI_CHUNK_IO == io_option) { + new_value = 0; + if (H5P_set(plist, H5D_XFER_COLL_CHUNK_MULTI_HARD_NAME, &new_value) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value") + } /* end if */ + } /* end if */ + check_prop = H5P_exist_plist(plist, H5D_XFER_COLL_CHUNK_LINK_NUM_TRUE_NAME); + if (check_prop > 0) { + if (H5D_ONE_LINK_CHUNK_IO_MORE_OPT == io_option) { + new_value = 0; + if (H5P_set(plist, H5D_XFER_COLL_CHUNK_LINK_NUM_TRUE_NAME, &new_value) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value") + } /* end if */ + } /* end if */ + check_prop = H5P_exist_plist(plist, H5D_XFER_COLL_CHUNK_LINK_NUM_FALSE_NAME); + if (check_prop > 0) { + if (temp_not_link_io) { + new_value = 0; + if (H5P_set(plist, H5D_XFER_COLL_CHUNK_LINK_NUM_FALSE_NAME, &new_value) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTSET, FAIL, "unable to set property value") + } /* end if */ + } /* end if */ + } #endif /* step 2: Go ahead to do IO.*/ - if(H5D_ONE_LINK_CHUNK_IO == io_option || H5D_ONE_LINK_CHUNK_IO_MORE_OPT == io_option) { - if(H5D__link_chunk_collective_io(io_info, type_info, fm, sum_chunk, dx_plist) < 0) + if (H5D_ONE_LINK_CHUNK_IO == io_option || H5D_ONE_LINK_CHUNK_IO_MORE_OPT == io_option) { + if (H5D__link_chunk_collective_io(io_info, type_info, fm, sum_chunk, dx_plist) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish linked chunk MPI-IO") } /* end if */ /* direct request to multi-chunk-io */ - else if(H5D_MULTI_CHUNK_IO == io_option) { - if(H5D__multi_chunk_collective_io(io_info, type_info, fm, dx_plist) < 0) + else if (H5D_MULTI_CHUNK_IO == io_option) { + if (H5D__multi_chunk_collective_io(io_info, type_info, fm, dx_plist) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish optimized multiple chunk MPI-IO") - } /* end if */ + } /* end if */ else { /* multiple chunk IO via threshold */ - if(H5D__multi_chunk_collective_io(io_info, type_info, fm, dx_plist) < 0) + if (H5D__multi_chunk_collective_io(io_info, type_info, fm, dx_plist) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish optimized multiple chunk MPI-IO") } /* end else */ @@ -696,7 +683,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_collective_io */ - /*------------------------------------------------------------------------- * Function: H5D__chunk_collective_read * @@ -712,22 +698,21 @@ done: */ herr_t H5D__chunk_collective_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - hsize_t H5_ATTR_UNUSED nelmts, const H5S_t H5_ATTR_UNUSED *file_space, const H5S_t H5_ATTR_UNUSED *mem_space, - H5D_chunk_map_t *fm) + hsize_t H5_ATTR_UNUSED nelmts, const H5S_t H5_ATTR_UNUSED *file_space, + const H5S_t H5_ATTR_UNUSED *mem_space, H5D_chunk_map_t *fm) { - herr_t ret_value = SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Call generic selection operation */ - if(H5D__chunk_collective_io(io_info, type_info, fm) < 0) + if (H5D__chunk_collective_io(io_info, type_info, fm) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_collective_read() */ - /*------------------------------------------------------------------------- * Function: H5D__chunk_collective_write * @@ -743,22 +728,21 @@ done: */ herr_t H5D__chunk_collective_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - hsize_t H5_ATTR_UNUSED nelmts, const H5S_t H5_ATTR_UNUSED *file_space, const H5S_t H5_ATTR_UNUSED *mem_space, - H5D_chunk_map_t *fm) + hsize_t H5_ATTR_UNUSED nelmts, const H5S_t H5_ATTR_UNUSED *file_space, + const H5S_t H5_ATTR_UNUSED *mem_space, H5D_chunk_map_t *fm) { - herr_t ret_value = SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Call generic selection operation */ - if(H5D__chunk_collective_io(io_info, type_info, fm) < 0) + if (H5D__chunk_collective_io(io_info, type_info, fm) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_collective_write() */ - /*------------------------------------------------------------------------- * Function: H5D__link_chunk_collective_io * @@ -782,45 +766,48 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5D_chunk_map_t *fm, int sum_chunk, H5P_genplist_t *dx_plist) +H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, + int sum_chunk, H5P_genplist_t *dx_plist) { H5D_chunk_addr_info_t *chunk_addr_info_array = NULL; - MPI_Datatype chunk_final_mtype; /* Final memory MPI datatype for all chunks with seletion */ - hbool_t chunk_final_mtype_is_derived = FALSE; - MPI_Datatype chunk_final_ftype; /* Final file MPI datatype for all chunks with seletion */ - hbool_t chunk_final_ftype_is_derived = FALSE; - H5D_storage_t ctg_store; /* Storage info for "fake" contiguous dataset */ - size_t total_chunks; - haddr_t *total_chunk_addr_array = NULL; - MPI_Datatype *chunk_mtype = NULL; - MPI_Datatype *chunk_ftype = NULL; - MPI_Aint *chunk_disp_array = NULL; - MPI_Aint *chunk_mem_disp_array = NULL; - hbool_t *chunk_mft_is_derived_array = NULL; /* Flags to indicate each chunk's MPI file datatype is derived */ - hbool_t *chunk_mbt_is_derived_array = NULL; /* Flags to indicate each chunk's MPI memory datatype is derived */ - int *chunk_mpi_file_counts = NULL; /* Count of MPI file datatype for each chunk */ - int *chunk_mpi_mem_counts = NULL; /* Count of MPI memory datatype for each chunk */ - int mpi_code; /* MPI return code */ + MPI_Datatype chunk_final_mtype; /* Final memory MPI datatype for all chunks with seletion */ + hbool_t chunk_final_mtype_is_derived = FALSE; + MPI_Datatype chunk_final_ftype; /* Final file MPI datatype for all chunks with seletion */ + hbool_t chunk_final_ftype_is_derived = FALSE; + H5D_storage_t ctg_store; /* Storage info for "fake" contiguous dataset */ + size_t total_chunks; + haddr_t * total_chunk_addr_array = NULL; + MPI_Datatype * chunk_mtype = NULL; + MPI_Datatype * chunk_ftype = NULL; + MPI_Aint * chunk_disp_array = NULL; + MPI_Aint * chunk_mem_disp_array = NULL; + hbool_t * chunk_mft_is_derived_array = + NULL; /* Flags to indicate each chunk's MPI file datatype is derived */ + hbool_t *chunk_mbt_is_derived_array = + NULL; /* Flags to indicate each chunk's MPI memory datatype is derived */ + int *chunk_mpi_file_counts = NULL; /* Count of MPI file datatype for each chunk */ + int *chunk_mpi_mem_counts = NULL; /* Count of MPI memory datatype for each chunk */ + int mpi_code; /* MPI return code */ H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode = H5D_MPIO_LINK_CHUNK; - H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_CHUNK_COLLECTIVE; - herr_t ret_value = SUCCEED; + H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_CHUNK_COLLECTIVE; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC /* Set the actual-chunk-opt-mode property. */ - if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0) + if (H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual chunk opt mode property") /* Set the actual-io-mode property. * Link chunk I/O does not break to independent, so can set right away */ - if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0) + if (H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual io mode property") /* Get the sum # of chunks, if not already available */ - if(sum_chunk < 0) { - if(H5D__mpio_get_sum_chunk(io_info, fm, &sum_chunk) < 0) - HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSWAP, FAIL, "unable to obtain the total chunk number of all processes"); + if (sum_chunk < 0) { + if (H5D__mpio_get_sum_chunk(io_info, fm, &sum_chunk) < 0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSWAP, FAIL, + "unable to obtain the total chunk number of all processes"); } /* end if */ /* Retrieve total # of chunks in dataset */ @@ -830,15 +817,15 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ * the dataset. [This sometimes is used by developers who want the * equivalent of compressed contiguous datasets - QAK] */ - if(total_chunks == 1) { - H5SL_node_t *chunk_node; /* Pointer to chunk node for selection */ - H5S_t *fspace; /* Dataspace describing chunk & selection in it */ - H5S_t *mspace; /* Dataspace describing selection in memory corresponding to this chunk */ + if (total_chunks == 1) { + H5SL_node_t *chunk_node; /* Pointer to chunk node for selection */ + H5S_t * fspace; /* Dataspace describing chunk & selection in it */ + H5S_t * mspace; /* Dataspace describing selection in memory corresponding to this chunk */ /* Check for this process having selection in this chunk */ chunk_node = H5SL_first(fm->sel_chunks); - if(chunk_node == NULL) { + if (chunk_node == NULL) { /* Set the dataspace info for I/O to NULL, this process doesn't have any I/O to perform */ fspace = mspace = NULL; @@ -846,11 +833,11 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ ctg_store.contig.dset_addr = 0; } /* end if */ else { - H5D_chunk_ud_t udata; /* User data for querying chunk info */ - H5D_chunk_info_t *chunk_info; /* Info for chunk in skiplist */ + H5D_chunk_ud_t udata; /* User data for querying chunk info */ + H5D_chunk_info_t *chunk_info; /* Info for chunk in skiplist */ /* Get the chunk info, for the selection in the chunk */ - if(NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_item(chunk_node))) + if (NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_item(chunk_node))) HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk info from skip list") /* Set the dataspace info for I/O */ @@ -858,8 +845,8 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ mspace = chunk_info->mspace; /* Look up address of 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_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk address") ctg_store.contig.dset_addr = udata.addr; } /* end else */ @@ -868,69 +855,75 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ io_info->store = &ctg_store; #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"before inter_collective_io for total chunk = 1 \n"); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "before inter_collective_io for total chunk = 1 \n"); #endif /* Perform I/O */ - if(H5D__inter_collective_io(io_info, type_info, fspace, mspace) < 0) + if (H5D__inter_collective_io(io_info, type_info, fspace, mspace) < 0) HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't finish shared collective MPI-IO") } /* end if */ else { - hsize_t mpi_buf_count; /* Number of MPI types */ - size_t num_chunk; /* Number of chunks for this process */ - size_t u; /* Local index variable */ + hsize_t mpi_buf_count; /* Number of MPI types */ + size_t num_chunk; /* Number of chunks for this process */ + size_t u; /* Local index variable */ /* Get the number of chunks with a selection */ num_chunk = H5SL_count(fm->sel_chunks); H5_CHECK_OVERFLOW(num_chunk, size_t, int); #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"total_chunks = %Zu, num_chunk = %Zu\n", total_chunks, num_chunk); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "total_chunks = %Zu, num_chunk = %Zu\n", total_chunks, num_chunk); #endif /* Set up MPI datatype for chunks selected */ - if(num_chunk) { + if (num_chunk) { /* Allocate chunking information */ - if(NULL == (chunk_addr_info_array = (H5D_chunk_addr_info_t *)H5MM_malloc(num_chunk * sizeof(H5D_chunk_addr_info_t)))) + if (NULL == (chunk_addr_info_array = + (H5D_chunk_addr_info_t *)H5MM_malloc(num_chunk * sizeof(H5D_chunk_addr_info_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk array buffer") - if(NULL == (chunk_mtype = (MPI_Datatype *)H5MM_malloc(num_chunk * sizeof(MPI_Datatype)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk memory datatype buffer") - if(NULL == (chunk_ftype = (MPI_Datatype *)H5MM_malloc(num_chunk * sizeof(MPI_Datatype)))) + if (NULL == (chunk_mtype = (MPI_Datatype *)H5MM_malloc(num_chunk * sizeof(MPI_Datatype)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "couldn't allocate chunk memory datatype buffer") + if (NULL == (chunk_ftype = (MPI_Datatype *)H5MM_malloc(num_chunk * sizeof(MPI_Datatype)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk file datatype buffer") - if(NULL == (chunk_disp_array = (MPI_Aint *)H5MM_malloc(num_chunk * sizeof(MPI_Aint)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk file displacement buffer") - if(NULL == (chunk_mem_disp_array = (MPI_Aint *)H5MM_calloc(num_chunk * sizeof(MPI_Aint)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk memory displacement buffer") - if(NULL == (chunk_mpi_mem_counts = (int *)H5MM_calloc(num_chunk * sizeof(int)))) + if (NULL == (chunk_disp_array = (MPI_Aint *)H5MM_malloc(num_chunk * sizeof(MPI_Aint)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "couldn't allocate chunk file displacement buffer") + if (NULL == (chunk_mem_disp_array = (MPI_Aint *)H5MM_calloc(num_chunk * sizeof(MPI_Aint)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "couldn't allocate chunk memory displacement buffer") + if (NULL == (chunk_mpi_mem_counts = (int *)H5MM_calloc(num_chunk * sizeof(int)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk memory counts buffer") - if(NULL == (chunk_mpi_file_counts = (int *)H5MM_calloc(num_chunk * sizeof(int)))) + if (NULL == (chunk_mpi_file_counts = (int *)H5MM_calloc(num_chunk * sizeof(int)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk file counts buffer") - if(NULL == (chunk_mbt_is_derived_array = (hbool_t *)H5MM_calloc(num_chunk * sizeof(hbool_t)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk memory is derived datatype flags buffer") - if(NULL == (chunk_mft_is_derived_array = (hbool_t *)H5MM_calloc(num_chunk * sizeof(hbool_t)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk file is derived datatype flags buffer") + if (NULL == (chunk_mbt_is_derived_array = (hbool_t *)H5MM_calloc(num_chunk * sizeof(hbool_t)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "couldn't allocate chunk memory is derived datatype flags buffer") + if (NULL == (chunk_mft_is_derived_array = (hbool_t *)H5MM_calloc(num_chunk * sizeof(hbool_t)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "couldn't allocate chunk file is derived datatype flags buffer") #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"before sorting the chunk address \n"); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "before sorting the chunk address \n"); #endif /* Sort the chunk address */ - if(H5D__sort_chunk(io_info, fm, chunk_addr_info_array, sum_chunk) < 0) + if (H5D__sort_chunk(io_info, fm, chunk_addr_info_array, sum_chunk) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSWAP, FAIL, "unable to sort chunk address") ctg_store.contig.dset_addr = chunk_addr_info_array[0].chunk_addr; #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"after sorting the chunk address \n"); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "after sorting the chunk address \n"); #endif /* Obtain MPI derived datatype from all individual chunks */ - for(u = 0; u < num_chunk; u++) { - 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 + for (u = 0; u < num_chunk; u++) { + 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; @@ -939,46 +932,43 @@ if(H5DEBUG(D)) * 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], /* 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) + if (H5S_mpio_space_type(chunk_addr_info_array[u].chunk_info.fspace, 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") /* Sanity check */ - if(is_permuted) + 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]), - 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) + 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]), 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) + if (is_permuted) HDassert(!permute_map); /* Chunk address relative to the first chunk */ @@ -990,46 +980,51 @@ if(H5DEBUG(D)) } /* end for */ /* Create final MPI derived datatype for the file */ - if(MPI_SUCCESS != (mpi_code = MPI_Type_create_struct((int)num_chunk, chunk_mpi_file_counts, chunk_disp_array, chunk_ftype, &chunk_final_ftype))) + if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_struct((int)num_chunk, chunk_mpi_file_counts, chunk_disp_array, + chunk_ftype, &chunk_final_ftype))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code) - if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&chunk_final_ftype))) + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&chunk_final_ftype))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) chunk_final_ftype_is_derived = TRUE; /* Create final MPI derived datatype for memory */ - if(MPI_SUCCESS != (mpi_code = MPI_Type_create_struct((int)num_chunk, chunk_mpi_mem_counts, chunk_mem_disp_array, chunk_mtype, &chunk_final_mtype))) + if (MPI_SUCCESS != + (mpi_code = MPI_Type_create_struct((int)num_chunk, chunk_mpi_mem_counts, chunk_mem_disp_array, + chunk_mtype, &chunk_final_mtype))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code) - if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&chunk_final_mtype))) + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&chunk_final_mtype))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) chunk_final_mtype_is_derived = TRUE; /* Free the file & memory MPI datatypes for each chunk */ - for(u = 0; u < num_chunk; u++) { - if(chunk_mbt_is_derived_array[u]) - if(MPI_SUCCESS != (mpi_code = MPI_Type_free(chunk_mtype + u))) + for (u = 0; u < num_chunk; u++) { + if (chunk_mbt_is_derived_array[u]) + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(chunk_mtype + u))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) - if(chunk_mft_is_derived_array[u]) - if(MPI_SUCCESS != (mpi_code = MPI_Type_free(chunk_ftype + u))) + if (chunk_mft_is_derived_array[u]) + if (MPI_SUCCESS != (mpi_code = MPI_Type_free(chunk_ftype + u))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) } /* end for */ /* We have a single, complicated MPI datatype for both memory & file */ - mpi_buf_count = (hsize_t)1; - } /* end if */ - else { /* no selection at all for this process */ + mpi_buf_count = (hsize_t)1; + } /* end if */ + else { /* no selection at all for this process */ /* Allocate chunking information */ - if(NULL == (total_chunk_addr_array = (haddr_t *)H5MM_malloc(sizeof(haddr_t) * total_chunks))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate total chunk address arraybuffer") + if (NULL == (total_chunk_addr_array = (haddr_t *)H5MM_malloc(sizeof(haddr_t) * total_chunks))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "couldn't allocate total chunk address arraybuffer") /* Retrieve chunk address map */ - if(H5D__chunk_addrmap(io_info, total_chunk_addr_array) < 0) + if (H5D__chunk_addrmap(io_info, total_chunk_addr_array) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address") /* Get chunk with lowest address */ ctg_store.contig.dset_addr = HADDR_MAX; - for(u = 0; u < total_chunks; u++) - if(total_chunk_addr_array[u] < ctg_store.contig.dset_addr) + for (u = 0; u < total_chunks; u++) + if (total_chunk_addr_array[u] < ctg_store.contig.dset_addr) ctg_store.contig.dset_addr = total_chunk_addr_array[u]; HDassert(ctg_store.contig.dset_addr != HADDR_MAX); @@ -1038,58 +1033,59 @@ if(H5DEBUG(D)) chunk_final_mtype = MPI_BYTE; /* No chunks selected for this process */ - mpi_buf_count = (hsize_t)0; + mpi_buf_count = (hsize_t)0; } /* end else */ #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"before coming to final collective IO\n"); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "before coming to final collective IO\n"); #endif /* Set up the base storage address for this chunk */ io_info->store = &ctg_store; /* Perform final collective I/O operation */ - if(H5D__final_collective_io(io_info, type_info, mpi_buf_count, &chunk_final_ftype, &chunk_final_mtype) < 0) + if (H5D__final_collective_io(io_info, type_info, mpi_buf_count, &chunk_final_ftype, + &chunk_final_mtype) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish MPI-IO") } /* end else */ done: #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"before freeing memory inside H5D_link_collective_io ret_value = %d\n", ret_value); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "before freeing memory inside H5D_link_collective_io ret_value = %d\n", + ret_value); #endif /* Release resources */ - if(total_chunk_addr_array) + if (total_chunk_addr_array) H5MM_xfree(total_chunk_addr_array); - if(chunk_addr_info_array) + if (chunk_addr_info_array) H5MM_xfree(chunk_addr_info_array); - if(chunk_mtype) + if (chunk_mtype) H5MM_xfree(chunk_mtype); - if(chunk_ftype) + if (chunk_ftype) H5MM_xfree(chunk_ftype); - if(chunk_disp_array) + if (chunk_disp_array) H5MM_xfree(chunk_disp_array); - if(chunk_mem_disp_array) + if (chunk_mem_disp_array) H5MM_xfree(chunk_mem_disp_array); - if(chunk_mpi_mem_counts) + if (chunk_mpi_mem_counts) H5MM_xfree(chunk_mpi_mem_counts); - if(chunk_mpi_file_counts) + if (chunk_mpi_file_counts) H5MM_xfree(chunk_mpi_file_counts); - if(chunk_mbt_is_derived_array) + if (chunk_mbt_is_derived_array) H5MM_xfree(chunk_mbt_is_derived_array); - if(chunk_mft_is_derived_array) + if (chunk_mft_is_derived_array) H5MM_xfree(chunk_mft_is_derived_array); /* Free the MPI buf and file types, if they were derived */ - if(chunk_final_mtype_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&chunk_final_mtype))) + if (chunk_final_mtype_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&chunk_final_mtype))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) - if(chunk_final_ftype_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&chunk_final_ftype))) + if (chunk_final_ftype_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&chunk_final_ftype))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__link_chunk_collective_io */ - /*------------------------------------------------------------------------- * Function: H5D__multi_chunk_collective_io * @@ -1114,32 +1110,37 @@ if(H5DEBUG(D)) *------------------------------------------------------------------------- */ static herr_t -H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5D_chunk_map_t *fm, H5P_genplist_t *dx_plist) +H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, + H5P_genplist_t *dx_plist) { - H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */ - H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ - H5D_io_info_t cpt_io_info; /* Compact I/O info object */ - H5D_storage_t cpt_store; /* Chunk storage information as compact dataset */ - hbool_t cpt_dirty; /* Temporary placeholder for compact storage "dirty" flag */ - uint8_t *chunk_io_option = NULL; - haddr_t *chunk_addr = NULL; - H5D_storage_t store; /* union of EFL and chunk pointer in file space */ - H5FD_mpio_xfer_t last_xfer_mode = H5FD_MPIO_COLLECTIVE; /* Last parallel transfer for this request (H5D_XFER_IO_XFER_MODE_NAME) */ - H5FD_mpio_collective_opt_t last_coll_opt_mode = H5FD_MPIO_COLLECTIVE_IO; /* Last parallel transfer with independent IO or collective IO with this mode */ - size_t total_chunk; /* Total # of chunks in dataset */ + H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */ + H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ + H5D_io_info_t cpt_io_info; /* Compact I/O info object */ + H5D_storage_t cpt_store; /* Chunk storage information as compact dataset */ + hbool_t cpt_dirty; /* Temporary placeholder for compact storage "dirty" flag */ + uint8_t * chunk_io_option = NULL; + haddr_t * chunk_addr = NULL; + H5D_storage_t store; /* union of EFL and chunk pointer in file space */ + H5FD_mpio_xfer_t last_xfer_mode = + H5FD_MPIO_COLLECTIVE; /* Last parallel transfer for this request (H5D_XFER_IO_XFER_MODE_NAME) */ + H5FD_mpio_collective_opt_t last_coll_opt_mode = + H5FD_MPIO_COLLECTIVE_IO; /* Last parallel transfer with independent IO or collective IO with this mode + */ + size_t total_chunk; /* Total # of chunks in dataset */ #ifdef H5Dmpio_DEBUG int mpi_rank; #endif - size_t u; /* Local index variable */ - H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode = H5D_MPIO_MULTI_CHUNK; /* actual chunk optimization mode */ - H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_NO_COLLECTIVE; /* Local variable for tracking the I/O mode used. */ - herr_t ret_value = SUCCEED; + size_t u; /* Local index variable */ + H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode = + H5D_MPIO_MULTI_CHUNK; /* actual chunk optimization mode */ + H5D_mpio_actual_io_mode_t actual_io_mode = + H5D_MPIO_NO_COLLECTIVE; /* Local variable for tracking the I/O mode used. */ + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC /* Set the actual chunk opt mode property */ - if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0) + if (H5P_set(dx_plist, H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, &actual_chunk_opt_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual chunk opt mode property") #ifdef H5Dmpio_DEBUG @@ -1154,17 +1155,17 @@ H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *ty chunk_io_option = (uint8_t *)H5MM_calloc(total_chunk); chunk_addr = (haddr_t *)H5MM_calloc(total_chunk * sizeof(haddr_t)); #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "total_chunk %Zu\n", total_chunk); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "total_chunk %Zu\n", total_chunk); #endif /* Obtain IO option for each chunk */ - if(H5D__obtain_mpio_mode(io_info, fm, dx_plist, chunk_io_option, chunk_addr) < 0) + if (H5D__obtain_mpio_mode(io_info, fm, dx_plist, chunk_io_option, chunk_addr) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTRECV, FAIL, "unable to obtain MPIO mode") /* Set up contiguous I/O info object */ HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); - ctg_io_info.store = &ctg_store; + ctg_io_info.store = &ctg_store; ctg_io_info.layout_ops = *H5D_LOPS_CONTIG; /* Initialize temporary contiguous storage info */ @@ -1172,7 +1173,7 @@ if(H5DEBUG(D)) /* Set up compact I/O info object */ HDmemcpy(&cpt_io_info, io_info, sizeof(cpt_io_info)); - cpt_io_info.store = &cpt_store; + cpt_io_info.store = &cpt_store; cpt_io_info.layout_ops = *H5D_LOPS_COMPACT; /* Initialize temporary compact storage info */ @@ -1182,39 +1183,40 @@ if(H5DEBUG(D)) io_info->store = &store; /* Loop over _all_ the chunks */ - for(u = 0; u < total_chunk; u++) { - H5D_chunk_info_t *chunk_info; /* Chunk info for current chunk */ - H5S_t *fspace; /* Dataspace describing chunk & selection in it */ - H5S_t *mspace; /* Dataspace describing selection in memory corresponding to this chunk */ + for (u = 0; u < total_chunk; u++) { + H5D_chunk_info_t *chunk_info; /* Chunk info for current chunk */ + H5S_t * fspace; /* Dataspace describing chunk & selection in it */ + H5S_t * mspace; /* Dataspace describing selection in memory corresponding to this chunk */ #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"mpi_rank = %d, chunk index = %Zu\n", mpi_rank, u); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "mpi_rank = %d, chunk index = %Zu\n", mpi_rank, u); #endif /* Get the chunk info for this chunk, if there are elements selected */ chunk_info = fm->select_chunk[u]; /* Set the storage information for chunks with selections */ - if(chunk_info) { + if (chunk_info) { HDassert(chunk_info->index == u); /* Pass in chunk's coordinates in a union. */ - store.chunk.offset = chunk_info->coords; - store.chunk.index = chunk_info->index; + store.chunk.offset = chunk_info->coords; + store.chunk.index = chunk_info->index; } /* end if */ /* Collective IO for this chunk, * Note: even there is no selection for this process, the process still * needs to contribute MPI NONE TYPE. */ - if(chunk_io_option[u] == H5D_CHUNK_IO_MODE_COL) { + if (chunk_io_option[u] == H5D_CHUNK_IO_MODE_COL) { #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"inside collective chunk IO mpi_rank = %d, chunk index = %Zu\n", mpi_rank, u); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "inside collective chunk IO mpi_rank = %d, chunk index = %Zu\n", + mpi_rank, u); #endif /* Set the file & memory dataspaces */ - if(chunk_info) { + if (chunk_info) { fspace = chunk_info->fspace; mspace = chunk_info->mspace; @@ -1232,13 +1234,13 @@ if(H5DEBUG(D)) } /* end else */ /* Switch back to collective I/O */ - if(last_xfer_mode != H5FD_MPIO_COLLECTIVE) { - if(H5D__ioinfo_xfer_mode(io_info, dx_plist, H5FD_MPIO_COLLECTIVE) < 0) + if (last_xfer_mode != H5FD_MPIO_COLLECTIVE) { + if (H5D__ioinfo_xfer_mode(io_info, dx_plist, H5FD_MPIO_COLLECTIVE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to collective I/O") last_xfer_mode = H5FD_MPIO_COLLECTIVE; } /* end if */ - if(last_coll_opt_mode != H5FD_MPIO_COLLECTIVE_IO) { - if(H5D__ioinfo_coll_opt_mode(io_info, dx_plist, H5FD_MPIO_COLLECTIVE_IO) < 0) + if (last_coll_opt_mode != H5FD_MPIO_COLLECTIVE_IO) { + if (H5D__ioinfo_coll_opt_mode(io_info, dx_plist, H5FD_MPIO_COLLECTIVE_IO) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to collective I/O") last_coll_opt_mode = H5FD_MPIO_COLLECTIVE_IO; } /* end if */ @@ -1247,19 +1249,20 @@ if(H5DEBUG(D)) ctg_store.contig.dset_addr = chunk_addr[u]; /* Perform the I/O */ - if(H5D__inter_collective_io(&ctg_io_info, type_info, fspace, mspace) < 0) + if (H5D__inter_collective_io(&ctg_io_info, type_info, fspace, mspace) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish shared collective MPI-IO") - } /* end if */ - else { /* possible independent IO for this chunk */ + } /* end if */ + else { /* possible independent IO for this chunk */ #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"inside independent IO mpi_rank = %d, chunk index = %Zu\n", mpi_rank, u); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "inside independent IO mpi_rank = %d, chunk index = %Zu\n", mpi_rank, + u); #endif HDassert(chunk_io_option[u] == 0); /* Set the file & memory dataspaces */ - if(chunk_info) { + if (chunk_info) { fspace = chunk_info->fspace; mspace = chunk_info->mspace; @@ -1271,8 +1274,8 @@ if(H5DEBUG(D)) } /* end else */ /* Using independent I/O with file setview.*/ - if(last_coll_opt_mode != H5FD_MPIO_INDIVIDUAL_IO) { - if(H5D__ioinfo_coll_opt_mode(io_info, dx_plist, H5FD_MPIO_INDIVIDUAL_IO) < 0) + if (last_coll_opt_mode != H5FD_MPIO_INDIVIDUAL_IO) { + if (H5D__ioinfo_coll_opt_mode(io_info, dx_plist, H5FD_MPIO_INDIVIDUAL_IO) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to individual I/O") last_coll_opt_mode = H5FD_MPIO_INDIVIDUAL_IO; } /* end if */ @@ -1281,29 +1284,28 @@ if(H5DEBUG(D)) ctg_store.contig.dset_addr = chunk_addr[u]; /* Perform the I/O */ - if(H5D__inter_collective_io(&ctg_io_info, type_info, fspace, mspace) < 0) + if (H5D__inter_collective_io(&ctg_io_info, type_info, fspace, mspace) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish shared collective MPI-IO") #ifdef H5D_DEBUG - if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"after inter collective IO\n"); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "after inter collective IO\n"); #endif } /* end else */ - } /* end for */ + } /* end for */ /* Write the local value of actual io mode to the DXPL. */ - if(H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0) + if (H5P_set(dx_plist, H5D_MPIO_ACTUAL_IO_MODE_NAME, &actual_io_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "couldn't set actual io mode property") done: - if(chunk_io_option) + if (chunk_io_option) H5MM_xfree(chunk_io_option); - if(chunk_addr) + if (chunk_addr) H5MM_xfree(chunk_addr); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__multi_chunk_collective_io */ - /*------------------------------------------------------------------------- * Function: H5D__inter_collective_io * @@ -1318,23 +1320,23 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - const H5S_t *file_space, const H5S_t *mem_space) +H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, const H5S_t *file_space, + const H5S_t *mem_space) { - int mpi_buf_count; /* # of MPI types */ - hbool_t mbt_is_derived = FALSE; - hbool_t mft_is_derived = FALSE; - MPI_Datatype mpi_file_type, mpi_buf_type; - int mpi_code; /* MPI return code */ - herr_t ret_value = SUCCEED; /* return value */ + int mpi_buf_count; /* # of MPI types */ + hbool_t mbt_is_derived = FALSE; + hbool_t mft_is_derived = FALSE; + MPI_Datatype mpi_file_type, mpi_buf_type; + int mpi_code; /* MPI return code */ + herr_t ret_value = SUCCEED; /* return value */ FUNC_ENTER_STATIC - 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 + 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; @@ -1343,39 +1345,40 @@ H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf * 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) + 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") /* Sanity check */ - if(is_permuted) + 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) + 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) + if (is_permuted) HDassert(!permute_map); } /* end if */ else { @@ -1388,30 +1391,30 @@ H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf } /* end else */ #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"before final collective IO \n"); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "before final collective IO \n"); #endif /* Perform final collective I/O operation */ - if(H5D__final_collective_io(io_info, type_info, (hsize_t)mpi_buf_count, &mpi_file_type, &mpi_buf_type) < 0) + if (H5D__final_collective_io(io_info, type_info, (hsize_t)mpi_buf_count, &mpi_file_type, &mpi_buf_type) < + 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish collective MPI-IO") done: /* Free the MPI buf and file types, if they were derived */ - if(mbt_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&mpi_buf_type))) + if (mbt_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&mpi_buf_type))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) - if(mft_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&mpi_file_type))) + if (mft_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&mpi_file_type))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"before leaving inter_collective_io ret_value = %d\n",ret_value); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "before leaving inter_collective_io ret_value = %d\n", ret_value); #endif FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__inter_collective_io() */ - /*------------------------------------------------------------------------- * Function: H5D__final_collective_io * @@ -1425,35 +1428,34 @@ if(H5DEBUG(D)) *------------------------------------------------------------------------- */ static herr_t -H5D__final_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - hsize_t mpi_buf_count, MPI_Datatype *mpi_file_type, MPI_Datatype *mpi_buf_type) +H5D__final_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t mpi_buf_count, + MPI_Datatype *mpi_file_type, MPI_Datatype *mpi_buf_type) { - herr_t ret_value = SUCCEED; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC /* Pass buf type, file type to the file driver. */ - if(H5FD_mpi_setup_collective(io_info->dxpl_id, mpi_buf_type, mpi_file_type) < 0) + if (H5FD_mpi_setup_collective(io_info->dxpl_id, mpi_buf_type, mpi_file_type) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set MPI-I/O properties") - if(io_info->op_type == H5D_IO_OP_WRITE) { - if((io_info->io_ops.single_write)(io_info, type_info, mpi_buf_count, NULL, NULL) < 0) + if (io_info->op_type == H5D_IO_OP_WRITE) { + if ((io_info->io_ops.single_write)(io_info, type_info, mpi_buf_count, NULL, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed") } /* end if */ else { - if((io_info->io_ops.single_read)(io_info, type_info, mpi_buf_count, NULL, NULL) < 0) + if ((io_info->io_ops.single_read)(io_info, type_info, mpi_buf_count, NULL, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed") } /* end else */ done: #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D),"ret_value before leaving final_collective_io=%d\n",ret_value); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "ret_value before leaving final_collective_io=%d\n", ret_value); #endif - FUNC_LEAVE_NOAPI(ret_value) + FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__final_collective_io */ - /*------------------------------------------------------------------------- * Function: H5D__cmp_chunk_addr * @@ -1471,17 +1473,16 @@ if(H5DEBUG(D)) static int H5D__cmp_chunk_addr(const void *chunk_addr_info1, const void *chunk_addr_info2) { - haddr_t addr1, addr2; + haddr_t addr1, addr2; - FUNC_ENTER_STATIC_NOERR + FUNC_ENTER_STATIC_NOERR - addr1 = ((const H5D_chunk_addr_info_t *)chunk_addr_info1)->chunk_addr; - addr2 = ((const H5D_chunk_addr_info_t *)chunk_addr_info2)->chunk_addr; + addr1 = ((const H5D_chunk_addr_info_t *)chunk_addr_info1)->chunk_addr; + addr2 = ((const H5D_chunk_addr_info_t *)chunk_addr_info2)->chunk_addr; - FUNC_LEAVE_NOAPI(H5F_addr_cmp(addr1, addr2)) + FUNC_LEAVE_NOAPI(H5F_addr_cmp(addr1, addr2)) } /* end H5D__cmp_chunk_addr() */ - /*------------------------------------------------------------------------- * Function: H5D__sort_chunk * @@ -1496,8 +1497,8 @@ H5D__cmp_chunk_addr(const void *chunk_addr_info1, const void *chunk_addr_info2) * Parameters: * Input: H5D_io_info_t* io_info, * H5D_chunk_map_t *fm(global chunk map struct) - * Input/Output: H5D_chunk_addr_info_t chunk_addr_info_array[] : array to store chunk address and information - * many_chunk_opt : flag to optimize the way to obtain chunk addresses + * Input/Output: H5D_chunk_addr_info_t chunk_addr_info_array[] : array to store chunk address + *and information many_chunk_opt : flag to optimize the way to obtain chunk addresses * for many chunks * * Return: Non-negative on success/Negative on failure @@ -1509,24 +1510,24 @@ H5D__cmp_chunk_addr(const void *chunk_addr_info1, const void *chunk_addr_info2) */ static herr_t H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, - H5D_chunk_addr_info_t chunk_addr_info_array[], int sum_chunk) + H5D_chunk_addr_info_t chunk_addr_info_array[], int sum_chunk) { - H5SL_node_t *chunk_node; /* Current node in chunk skip list */ - H5D_chunk_info_t *chunk_info; /* Current chunking info. of this node. */ - haddr_t chunk_addr; /* Current chunking address of this node */ - haddr_t *total_chunk_addr_array = NULL; /* The array of chunk address for the total number of chunk */ - hbool_t do_sort = FALSE; /* Whether the addresses need to be sorted */ - int bsearch_coll_chunk_threshold; - int many_chunk_opt = H5D_OBTAIN_ONE_CHUNK_ADDR_IND; - int mpi_size; /* Number of MPI processes */ - int mpi_code; /* MPI return code */ - int i; /* Local index variable */ - herr_t ret_value = SUCCEED; /* Return value */ + H5SL_node_t * chunk_node; /* Current node in chunk skip list */ + H5D_chunk_info_t *chunk_info; /* Current chunking info. of this node. */ + haddr_t chunk_addr; /* Current chunking address of this node */ + haddr_t *total_chunk_addr_array = NULL; /* The array of chunk address for the total number of chunk */ + hbool_t do_sort = FALSE; /* Whether the addresses need to be sorted */ + int bsearch_coll_chunk_threshold; + int many_chunk_opt = H5D_OBTAIN_ONE_CHUNK_ADDR_IND; + int mpi_size; /* Number of MPI processes */ + int mpi_code; /* MPI return code */ + int i; /* Local index variable */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Retrieve # of MPI processes */ - if((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) + if ((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi size") /* Calculate the actual threshold to obtain all chunk addresses collectively @@ -1538,57 +1539,60 @@ H5D__sort_chunk(H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, * for each process. */ bsearch_coll_chunk_threshold = (sum_chunk * 100) / ((int)fm->layout->u.chunk.nchunks * mpi_size); - if((bsearch_coll_chunk_threshold > H5D_ALL_CHUNK_ADDR_THRES_COL) - && ((sum_chunk / mpi_size) >= H5D_ALL_CHUNK_ADDR_THRES_COL_NUM)) + if ((bsearch_coll_chunk_threshold > H5D_ALL_CHUNK_ADDR_THRES_COL) && + ((sum_chunk / mpi_size) >= H5D_ALL_CHUNK_ADDR_THRES_COL_NUM)) many_chunk_opt = H5D_OBTAIN_ALL_CHUNK_ADDR_COL; #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "many_chunk_opt= %d\n", many_chunk_opt); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "many_chunk_opt= %d\n", many_chunk_opt); #endif /* If we need to optimize the way to obtain the chunk address */ - if(many_chunk_opt != H5D_OBTAIN_ONE_CHUNK_ADDR_IND) { + if (many_chunk_opt != H5D_OBTAIN_ONE_CHUNK_ADDR_IND) { int mpi_rank; #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "Coming inside H5D_OBTAIN_ALL_CHUNK_ADDR_COL\n"); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "Coming inside H5D_OBTAIN_ALL_CHUNK_ADDR_COL\n"); #endif /* Allocate array for chunk addresses */ - if(NULL == (total_chunk_addr_array = H5MM_malloc(sizeof(haddr_t) * (size_t)fm->layout->u.chunk.nchunks))) + if (NULL == + (total_chunk_addr_array = H5MM_malloc(sizeof(haddr_t) * (size_t)fm->layout->u.chunk.nchunks))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate memory chunk address array") /* Retrieve all the chunk addresses with process 0 */ - if((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0) + if ((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0) HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi rank") - if(mpi_rank == 0) { - if(H5D__chunk_addrmap(io_info, total_chunk_addr_array) < 0) + if (mpi_rank == 0) { + if (H5D__chunk_addrmap(io_info, total_chunk_addr_array) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address") } /* end if */ /* Broadcasting the MPI_IO option info. and chunk address info. */ - if(MPI_SUCCESS != (mpi_code = MPI_Bcast(total_chunk_addr_array, (int)(sizeof(haddr_t) * fm->layout->u.chunk.nchunks), MPI_BYTE, (int)0, io_info->comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_BCast failed", mpi_code) + if (MPI_SUCCESS != (mpi_code = MPI_Bcast(total_chunk_addr_array, + (int)(sizeof(haddr_t) * fm->layout->u.chunk.nchunks), + MPI_BYTE, (int)0, io_info->comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_BCast failed", mpi_code) } /* end if */ /* Start at first node in chunk skip list */ i = 0; - if(NULL == (chunk_node = H5SL_first(fm->sel_chunks))) - HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk node from skipped list") + if (NULL == (chunk_node = H5SL_first(fm->sel_chunks))) + HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk node from skipped list") /* Iterate over all chunks for this process */ - while(chunk_node) { - if(NULL == (chunk_info = H5SL_item(chunk_node))) - HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL,"couldn't get chunk info from skipped list") + while (chunk_node) { + if (NULL == (chunk_info = H5SL_item(chunk_node))) + HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk info from skipped list") - if(many_chunk_opt == H5D_OBTAIN_ONE_CHUNK_ADDR_IND) { - H5D_chunk_ud_t udata; /* User data for querying chunk info */ + if (many_chunk_opt == H5D_OBTAIN_ONE_CHUNK_ADDR_IND) { + H5D_chunk_ud_t udata; /* User data for querying chunk info */ /* Get address of 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_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk info from skipped list") chunk_addr = udata.addr; } /* end if */ @@ -1596,7 +1600,7 @@ if(H5DEBUG(D)) chunk_addr = total_chunk_addr_array[chunk_info->index]; /* Check if chunk addresses are not in increasing order in the file */ - if(i > 0 && chunk_addr < chunk_addr_info_array[i - 1].chunk_addr) + if (i > 0 && chunk_addr < chunk_addr_info_array[i - 1].chunk_addr) do_sort = TRUE; /* Set the address & info for this chunk */ @@ -1609,23 +1613,22 @@ if(H5DEBUG(D)) } /* end while */ #ifdef H5D_DEBUG -if(H5DEBUG(D)) - HDfprintf(H5DEBUG(D), "before Qsort\n"); + if (H5DEBUG(D)) + HDfprintf(H5DEBUG(D), "before Qsort\n"); #endif - if(do_sort) { + if (do_sort) { size_t num_chunks = H5SL_count(fm->sel_chunks); HDqsort(chunk_addr_info_array, num_chunks, sizeof(chunk_addr_info_array[0]), H5D__cmp_chunk_addr); } /* end if */ done: - if(total_chunk_addr_array) + if (total_chunk_addr_array) H5MM_xfree(total_chunk_addr_array); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__sort_chunk() */ - /*------------------------------------------------------------------------- * Function: H5D__obtain_mpio_mode * @@ -1646,7 +1649,8 @@ done: * c) Build MPI derived datatype to combine "chunk address" and "assign_io" information * in order to do MPI Bcast only once * d) MPI Bcast the IO mode and chunk address information for each chunk. - * 4) Each process then retrieves IO mode and chunk address information to assign_io_mode and chunk_addr. + * 4) Each process then retrieves IO mode and chunk address information to assign_io_mode and + *chunk_addr. * * Parameters: * @@ -1663,109 +1667,109 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, - H5P_genplist_t *dx_plist, uint8_t assign_io_mode[], haddr_t chunk_addr[]) +H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm, H5P_genplist_t *dx_plist, + uint8_t assign_io_mode[], haddr_t chunk_addr[]) { int total_chunks; unsigned percent_nproc_per_chunk, threshold_nproc_per_chunk; - uint8_t* io_mode_info = NULL; - uint8_t* recv_io_mode_info = NULL; - uint8_t* mergebuf = NULL; - uint8_t* tempbuf; - H5SL_node_t* chunk_node; - H5D_chunk_info_t* chunk_info; + uint8_t * io_mode_info = NULL; + uint8_t * recv_io_mode_info = NULL; + uint8_t * mergebuf = NULL; + uint8_t * tempbuf; + H5SL_node_t * chunk_node; + H5D_chunk_info_t *chunk_info; int mpi_size, mpi_rank; MPI_Comm comm; int ic, root; int mpi_code; - hbool_t mem_cleanup = FALSE; + hbool_t mem_cleanup = FALSE; #ifdef H5_HAVE_INSTRUMENTED_LIBRARY - int new_value; + int new_value; htri_t check_prop; #endif - herr_t ret_value = SUCCEED; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC /* Assign the rank 0 to the root */ - root = 0; - comm = io_info->comm; + root = 0; + comm = io_info->comm; /* Obtain the number of process and the current rank of the process */ - if((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0) + if ((mpi_rank = H5F_mpi_get_rank(io_info->dset->oloc.file)) < 0) HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi rank") - if((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) + if ((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0) HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi size") /* Setup parameters */ H5_CHECKED_ASSIGN(total_chunks, int, fm->layout->u.chunk.nchunks, hsize_t); percent_nproc_per_chunk = H5P_peek_unsigned(dx_plist, H5D_XFER_MPIO_CHUNK_OPT_RATIO_NAME); /* if ratio is 0, perform collective io */ - if(0 == percent_nproc_per_chunk) { - if(H5D__chunk_addrmap(io_info, chunk_addr) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address"); - for(ic = 0; ic < total_chunks; ic++) - assign_io_mode[ic] = H5D_CHUNK_IO_MODE_COL; + if (0 == percent_nproc_per_chunk) { + if (H5D__chunk_addrmap(io_info, chunk_addr) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address"); + for (ic = 0; ic < total_chunks; ic++) + assign_io_mode[ic] = H5D_CHUNK_IO_MODE_COL; HGOTO_DONE(SUCCEED) } /* end if */ - threshold_nproc_per_chunk = mpi_size * percent_nproc_per_chunk/100; + threshold_nproc_per_chunk = mpi_size * percent_nproc_per_chunk / 100; /* Allocate memory */ - io_mode_info = (uint8_t *)H5MM_calloc(total_chunks); - mergebuf = H5MM_malloc((sizeof(haddr_t) + 1) * total_chunks); - tempbuf = mergebuf + total_chunks; - if(mpi_rank == root) + io_mode_info = (uint8_t *)H5MM_calloc(total_chunks); + mergebuf = H5MM_malloc((sizeof(haddr_t) + 1) * total_chunks); + tempbuf = mergebuf + total_chunks; + if (mpi_rank == root) recv_io_mode_info = (uint8_t *)H5MM_malloc(total_chunks * mpi_size); - mem_cleanup = TRUE; + mem_cleanup = TRUE; /* Obtain the regularity and selection information for all chunks in this process. */ - chunk_node = H5SL_first(fm->sel_chunks); - while(chunk_node) { - chunk_info = H5SL_item(chunk_node); + chunk_node = H5SL_first(fm->sel_chunks); + while (chunk_node) { + chunk_info = H5SL_item(chunk_node); - io_mode_info[chunk_info->index] = H5D_CHUNK_SELECT_REG; /* this chunk is selected and is "regular" */ - chunk_node = H5SL_next(chunk_node); + io_mode_info[chunk_info->index] = H5D_CHUNK_SELECT_REG; /* this chunk is selected and is "regular" */ + chunk_node = H5SL_next(chunk_node); } /* end while */ /* Gather all the information */ - if(MPI_SUCCESS != (mpi_code = MPI_Gather(io_mode_info, total_chunks, MPI_BYTE, recv_io_mode_info, total_chunks, MPI_BYTE, root, comm))) + if (MPI_SUCCESS != (mpi_code = MPI_Gather(io_mode_info, total_chunks, MPI_BYTE, recv_io_mode_info, + total_chunks, MPI_BYTE, root, comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Gather failed", mpi_code) /* Calculate the mode for IO(collective, independent or none) at root process */ - if(mpi_rank == root) { - int nproc; - int* nproc_per_chunk; + if (mpi_rank == root) { + int nproc; + int *nproc_per_chunk; /* pre-computing: calculate number of processes and regularity of the selection occupied in each chunk */ - nproc_per_chunk = (int*)H5MM_calloc(total_chunks * sizeof(int)); + nproc_per_chunk = (int *)H5MM_calloc(total_chunks * sizeof(int)); /* calculating the chunk address */ - if(H5D__chunk_addrmap(io_info, chunk_addr) < 0) { + if (H5D__chunk_addrmap(io_info, chunk_addr) < 0) { HDfree(nproc_per_chunk); HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address") } /* end if */ /* checking for number of process per chunk and regularity of the selection*/ - for(nproc = 0; nproc < mpi_size; nproc++) { + for (nproc = 0; nproc < mpi_size; nproc++) { uint8_t *tmp_recv_io_mode_info = recv_io_mode_info + (nproc * total_chunks); /* Calculate the number of process per chunk and adding irregular selection option */ - for(ic = 0; ic < total_chunks; ic++, tmp_recv_io_mode_info++) { - if(*tmp_recv_io_mode_info != 0) { + for (ic = 0; ic < total_chunks; ic++, tmp_recv_io_mode_info++) { + if (*tmp_recv_io_mode_info != 0) { nproc_per_chunk[ic]++; } /* end if */ - } /* end for */ - } /* end for */ + } /* end for */ + } /* end for */ /* Calculating MPIO mode for each chunk (collective, independent, none) */ - for(ic = 0; ic < total_chunks; ic++) { - if(nproc_per_chunk[ic] > MAX(1, threshold_nproc_per_chunk)) { + for (ic = 0; ic < total_chunks; ic++) { + if (nproc_per_chunk[ic] > MAX(1, threshold_nproc_per_chunk)) { assign_io_mode[ic] = H5D_CHUNK_IO_MODE_COL; } /* end if */ - } /* end for */ - + } /* end for */ /* merge buffer io_mode info and chunk addr into one */ HDmemcpy(mergebuf, assign_io_mode, total_chunks); @@ -1775,60 +1779,60 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, } /* end if */ /* Broadcasting the MPI_IO option info. and chunk address info. */ - if(MPI_SUCCESS != (mpi_code = MPI_Bcast(mergebuf, ((sizeof(haddr_t) + 1) * total_chunks), MPI_BYTE, root, comm))) + if (MPI_SUCCESS != + (mpi_code = MPI_Bcast(mergebuf, ((sizeof(haddr_t) + 1) * total_chunks), MPI_BYTE, root, comm))) HMPI_GOTO_ERROR(FAIL, "MPI_BCast failed", mpi_code) HDmemcpy(assign_io_mode, mergebuf, total_chunks); HDmemcpy(chunk_addr, tempbuf, sizeof(haddr_t) * total_chunks); #ifdef H5_HAVE_INSTRUMENTED_LIBRARY -{ - H5P_genplist_t *plist; /* Property list pointer */ + { + H5P_genplist_t *plist; /* Property list pointer */ + + /* Get the dataset transfer property list */ + if (NULL == (plist = (H5P_genplist_t *)H5I_object(io_info->dxpl_id))) + HGOTO_ERROR(H5E_IO, H5E_BADTYPE, FAIL, "not a dataset transfer property list") + + check_prop = H5P_exist_plist(plist, H5D_XFER_COLL_CHUNK_MULTI_RATIO_COLL_NAME); + if (check_prop > 0) { + for (ic = 0; ic < total_chunks; ic++) { + if (assign_io_mode[ic] == H5D_CHUNK_IO_MODE_COL) { + new_value = 0; + if (H5P_set(plist, H5D_XFER_COLL_CHUNK_MULTI_RATIO_COLL_NAME, &new_value) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to set property value") + break; + } /* end if */ + } /* end for */ + } /* end if */ - /* Get the dataset transfer property list */ - if(NULL == (plist = (H5P_genplist_t *)H5I_object(io_info->dxpl_id))) - HGOTO_ERROR(H5E_IO, H5E_BADTYPE, FAIL, "not a dataset transfer property list") + check_prop = H5P_exist_plist(plist, H5D_XFER_COLL_CHUNK_MULTI_RATIO_IND_NAME); + if (check_prop > 0) { + int temp_count = 0; - check_prop = H5P_exist_plist(plist, H5D_XFER_COLL_CHUNK_MULTI_RATIO_COLL_NAME); - if(check_prop > 0) { - for(ic = 0; ic < total_chunks; ic++) { - if(assign_io_mode[ic] == H5D_CHUNK_IO_MODE_COL) { + for (ic = 0; ic < total_chunks; ic++) { + if (assign_io_mode[ic] == H5D_CHUNK_IO_MODE_COL) { + temp_count++; + break; + } /* end if */ + } /* end for */ + if (temp_count == 0) { new_value = 0; - if(H5P_set(plist, H5D_XFER_COLL_CHUNK_MULTI_RATIO_COLL_NAME, &new_value) < 0) + if (H5P_set(plist, H5D_XFER_COLL_CHUNK_MULTI_RATIO_IND_NAME, &new_value) < 0) HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to set property value") - break; } /* end if */ - } /* end for */ - } /* end if */ - - check_prop = H5P_exist_plist(plist, H5D_XFER_COLL_CHUNK_MULTI_RATIO_IND_NAME); - if(check_prop > 0) { - int temp_count = 0; - - for(ic = 0; ic < total_chunks; ic++) { - if(assign_io_mode[ic] == H5D_CHUNK_IO_MODE_COL) { - temp_count++; - break; - } /* end if */ - } /* end for */ - if(temp_count == 0) { - new_value = 0; - if(H5P_set(plist, H5D_XFER_COLL_CHUNK_MULTI_RATIO_IND_NAME, &new_value) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to set property value") - } /* end if */ - } /* end if */ -} + } /* end if */ + } #endif done: - if(mem_cleanup) { + if (mem_cleanup) { HDfree(io_mode_info); HDfree(mergebuf); - if(mpi_rank == root) + if (mpi_rank == root) HDfree(recv_io_mode_info); } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__obtain_mpio_mode() */ -#endif /* H5_HAVE_PARALLEL */ - +#endif /* H5_HAVE_PARALLEL */ |