diff options
Diffstat (limited to 'src/H5Dmpio.c')
| -rw-r--r-- | src/H5Dmpio.c | 1828 |
1 files changed, 958 insertions, 870 deletions
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index 38a6dbd..41d9bc0 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -6,7 +6,7 @@ * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * - * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. * + * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ @@ -25,24 +25,23 @@ /* Module Setup */ /****************/ -#include "H5Dmodule.h" /* This source code file is part of the H5D module */ - +#include "H5Dmodule.h" /* This source code file is part of the H5D module */ /***********/ /* Headers */ /***********/ -#include "H5private.h" /* Generic Functions */ -#include "H5CXprivate.h" /* API Contexts */ -#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 "H5CXprivate.h" /* API Contexts */ +#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 @@ -67,7 +66,7 @@ #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. *****/ @@ -77,31 +76,29 @@ */ /* Macros to represent different IO modes(NONE, Independent or collective)for multiple chunk IO case */ -#define H5D_CHUNK_IO_MODE_COL 1 +#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_REG 1 /******************/ /* 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; + haddr_t chunk_addr; H5D_chunk_info_t chunk_info; } H5D_chunk_addr_info_t; /* Rank 0 Bcast values */ typedef enum H5D_mpio_no_rank0_bcast_cause_t { - H5D_MPIO_RANK0_BCAST = 0x00, - H5D_MPIO_RANK0_NOT_H5S_ALL = 0x01, - H5D_MPIO_RANK0_NOT_CONTIGUOUS = 0x02, - H5D_MPIO_RANK0_NOT_FIXED_SIZE = 0x04, + H5D_MPIO_RANK0_BCAST = 0x00, + H5D_MPIO_RANK0_NOT_H5S_ALL = 0x01, + H5D_MPIO_RANK0_NOT_CONTIGUOUS = 0x02, + H5D_MPIO_RANK0_NOT_FIXED_SIZE = 0x04, H5D_MPIO_RANK0_GREATER_THAN_2GB = 0x08 } H5D_mpio_no_rank0_bcast_cause_t; - /* * Information about a single chunk when performing collective filtered I/O. All * of the fields of one of these structs are initialized at the start of collective @@ -186,91 +183,93 @@ typedef enum H5D_mpio_no_rank0_bcast_cause_t { * receive_buffer_array fields. */ typedef struct H5D_filtered_collective_io_info_t { - hsize_t index; - hsize_t scaled[H5O_LAYOUT_NDIMS]; - hbool_t full_overwrite; - size_t num_writers; - size_t io_size; - void *buf; - - struct { - H5F_block_t chunk_current; - H5F_block_t new_chunk; - } chunk_states; - - struct { - int original_owner; - int new_owner; - } owners; - - struct { - MPI_Request *receive_requests_array; - unsigned char **receive_buffer_array; - int num_receive_requests; - } async_info; + hsize_t index; + hsize_t scaled[H5O_LAYOUT_NDIMS]; + hbool_t full_overwrite; + size_t num_writers; + size_t io_size; + void * buf; + + struct { + H5F_block_t chunk_current; + H5F_block_t new_chunk; + } chunk_states; + + struct { + int original_owner; + int new_owner; + } owners; + + struct { + MPI_Request * receive_requests_array; + unsigned char **receive_buffer_array; + int num_receive_requests; + } async_info; } H5D_filtered_collective_io_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); -static herr_t H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, - const H5D_type_info_t *type_info, H5D_chunk_map_t *fm); -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); -static herr_t H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, - const H5D_type_info_t *type_info, H5D_chunk_map_t *fm); -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); +static herr_t H5D__multi_chunk_filtered_collective_io(H5D_io_info_t * io_info, + const H5D_type_info_t *type_info, H5D_chunk_map_t *fm); +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); +static herr_t H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, + H5D_chunk_map_t *fm); +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, - uint8_t assign_io_mode[], haddr_t chunk_addr[]); -static herr_t H5D__mpio_get_sum_chunk(const H5D_io_info_t *io_info, - const H5D_chunk_map_t *fm, int *sum_chunkf); -static herr_t H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, - const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm, - H5D_filtered_collective_io_info_t **chunk_list, size_t *num_entries); + 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, uint8_t assign_io_mode[], + haddr_t chunk_addr[]); +static herr_t H5D__mpio_get_sum_chunk(const H5D_io_info_t *io_info, const H5D_chunk_map_t *fm, + int *sum_chunkf); +static herr_t H5D__construct_filtered_io_info_list(const H5D_io_info_t * io_info, + const H5D_type_info_t * type_info, + const H5D_chunk_map_t * fm, + H5D_filtered_collective_io_info_t **chunk_list, + size_t * num_entries); #if MPI_VERSION >= 3 -static herr_t H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, - const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm, - H5D_filtered_collective_io_info_t *local_chunk_array, size_t *local_chunk_array_num_entries); +static herr_t H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t * io_info, + const H5D_type_info_t * type_info, + const H5D_chunk_map_t * fm, + H5D_filtered_collective_io_info_t *local_chunk_array, + size_t *local_chunk_array_num_entries); #endif static herr_t H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries, - size_t array_entry_size, void **gathered_array, size_t *gathered_array_num_entries, - hbool_t allgather, int root, MPI_Comm comm, int (*sort_func)(const void *, const void *)); -static herr_t H5D__mpio_filtered_collective_write_type( - H5D_filtered_collective_io_info_t *chunk_list, size_t num_entries, - MPI_Datatype *new_mem_type, hbool_t *mem_type_derived, - MPI_Datatype *new_file_type, hbool_t *file_type_derived); + size_t array_entry_size, void **gathered_array, + size_t *gathered_array_num_entries, hbool_t allgather, int root, + MPI_Comm comm, int (*sort_func)(const void *, const void *)); +static herr_t H5D__mpio_filtered_collective_write_type(H5D_filtered_collective_io_info_t *chunk_list, + size_t num_entries, MPI_Datatype *new_mem_type, + hbool_t *mem_type_derived, MPI_Datatype *new_file_type, + hbool_t *file_type_derived); static herr_t H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk_entry, - const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm); -static int H5D__cmp_chunk_addr(const void *chunk_addr_info1, const void *chunk_addr_info2); -static int H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_info_entry1, - const void *filtered_collective_io_info_entry2); + const H5D_io_info_t * io_info, + const H5D_type_info_t * type_info, + const H5D_chunk_map_t * fm); +static int H5D__cmp_chunk_addr(const void *chunk_addr_info1, const void *chunk_addr_info2); +static int H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_info_entry1, + const void *filtered_collective_io_info_entry2); #if MPI_VERSION >= 3 static int H5D__cmp_filtered_collective_io_info_entry_owner(const void *filtered_collective_io_info_entry1, - const void *filtered_collective_io_info_entry2); + const void *filtered_collective_io_info_entry2); #endif - /*********************/ /* Package Variables */ /*********************/ - /*******************/ /* Local Variables */ /*******************/ - /*------------------------------------------------------------------------- * Function: H5D__mpio_opt_possible * @@ -286,15 +285,15 @@ static int H5D__cmp_filtered_collective_io_info_entry_owner(const void *filtered *------------------------------------------------------------------------- */ 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) +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) { - H5FD_mpio_xfer_t io_xfer_mode; /* MPI I/O transfer mode */ - unsigned local_cause[2] = {0,0}; /* [0] Local reason(s) for breaking collective mode */ - /* [1] Flag if dataset is both: H5S_ALL and small */ - unsigned global_cause[2] = {0,0}; /* Global reason(s) for breaking collective mode */ - htri_t is_vl_storage; /* Whether the dataset's datatype is stored in a variable-length form */ - htri_t ret_value = SUCCEED; /* Return value */ + H5FD_mpio_xfer_t io_xfer_mode; /* MPI I/O transfer mode */ + unsigned local_cause[2] = {0, 0}; /* [0] Local reason(s) for breaking collective mode */ + /* [1] Flag if dataset is both: H5S_ALL and small */ + unsigned global_cause[2] = {0, 0}; /* Global reason(s) for breaking collective mode */ + htri_t is_vl_storage; /* Whether the dataset's datatype is stored in a variable-length form */ + htri_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -304,47 +303,46 @@ 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(H5CX_get_io_xfer_mode(&io_xfer_mode) < 0) + if (H5CX_get_io_xfer_mode(&io_xfer_mode) < 0) /* Set error flag, but keep going */ local_cause[0] |= H5D_MPIO_ERROR_WHILE_CHECKING_COLLECTIVE_POSSIBLE; - if(io_xfer_mode == H5FD_MPIO_INDEPENDENT) + if (io_xfer_mode == H5FD_MPIO_INDEPENDENT) local_cause[0] |= 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[0] |= 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[0] |= 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[0] |= 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[0] |= 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[0] |= 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[0] |= 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 - * when it it is doing disk IO. For chunking storage, mem_space will - * change for different chunks. So for chunking storage, whether we can - * use collective IO will defer until each chunk IO is reached. - */ + /* The handling of memory space is different for chunking and contiguous + * storage. For contiguous storage, mem_space and file_space won't change + * when it it is doing disk IO. For chunking storage, mem_space will + * change for different chunks. So for chunking storage, whether we can + * use collective IO will defer until each chunk IO is reached. + */ #if MPI_VERSION < 3 /* @@ -352,9 +350,8 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, * is less than 3. The functions needed (MPI_Mprobe and MPI_Imrecv) will * not be available. */ - if(io_info->op_type == H5D_IO_OP_WRITE && - io_info->dset->shared->layout.type == H5D_CHUNKED && - io_info->dset->shared->dcpl_cache.pline.nused > 0) + if (io_info->op_type == H5D_IO_OP_WRITE && io_info->dset->shared->layout.type == H5D_CHUNKED && + io_info->dset->shared->dcpl_cache.pline.nused > 0) local_cause[0] |= H5D_MPIO_PARALLEL_FILTERED_WRITES_DISABLED; #endif @@ -363,29 +360,29 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, */ /* Check to see if the process is reading the entire dataset */ - if(H5S_GET_SELECT_TYPE(file_space) != H5S_SEL_ALL) + if (H5S_GET_SELECT_TYPE(file_space) != H5S_SEL_ALL) local_cause[1] |= H5D_MPIO_RANK0_NOT_H5S_ALL; /* Only perform this optimization for contigous datasets, currently */ - else if(H5D_CONTIGUOUS != io_info->dset->shared->layout.type) + else if (H5D_CONTIGUOUS != io_info->dset->shared->layout.type) /* Flag to do a MPI_Bcast of the data from one proc instead of * having all the processes involved in the collective I/O. */ local_cause[1] |= H5D_MPIO_RANK0_NOT_CONTIGUOUS; - else if((is_vl_storage = H5T_is_vl_storage(type_info->dset_type)) < 0) + else if ((is_vl_storage = H5T_is_vl_storage(type_info->dset_type)) < 0) local_cause[0] |= H5D_MPIO_ERROR_WHILE_CHECKING_COLLECTIVE_POSSIBLE; - else if(is_vl_storage) + else if (is_vl_storage) local_cause[1] |= H5D_MPIO_RANK0_NOT_FIXED_SIZE; else { - size_t type_size; /* Size of dataset's datatype */ + size_t type_size; /* Size of dataset's datatype */ /* Retrieve the size of the dataset's datatype */ - if(0 == (type_size = H5T_GET_SIZE(type_info->dset_type))) + if (0 == (type_size = H5T_GET_SIZE(type_info->dset_type))) local_cause[0] |= H5D_MPIO_ERROR_WHILE_CHECKING_COLLECTIVE_POSSIBLE; else { - hssize_t snelmts; /* [Signed] # of elements in dataset's dataspace */ + hssize_t snelmts; /* [Signed] # of elements in dataset's dataspace */ /* Retrieve the size of the dataset's datatype */ - if((snelmts = H5S_GET_EXTENT_NPOINTS(file_space)) < 0) + if ((snelmts = H5S_GET_EXTENT_NPOINTS(file_space)) < 0) local_cause[0] |= H5D_MPIO_ERROR_WHILE_CHECKING_COLLECTIVE_POSSIBLE; else { hsize_t dset_size; @@ -393,26 +390,27 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, /* Determine dataset size */ dset_size = ((hsize_t)snelmts) * type_size; - /* If the size of the dataset is less than 2GB then do an MPI_Bcast - * of the data from one process instead of having all the processes - * involved in the collective I/O. - */ - if(dset_size > ((hsize_t)(2.0F * H5_GB) - 1)) + /* If the size of the dataset is less than 2GB then do an MPI_Bcast + * of the data from one process instead of having all the processes + * involved in the collective I/O. + */ + if (dset_size > ((hsize_t)(2.0F * H5_GB) - 1)) local_cause[1] |= H5D_MPIO_RANK0_GREATER_THAN_2GB; } /* end else */ - } /* end else */ - } /* end else */ + } /* end else */ + } /* end else */ /* Check for independent I/O */ - if(local_cause[0] & H5D_MPIO_SET_INDEPENDENT) + if (local_cause[0] & H5D_MPIO_SET_INDEPENDENT) global_cause[0] = local_cause[0]; 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, 2, MPI_UNSIGNED, MPI_BOR, io_info->comm))) + if (MPI_SUCCESS != + (mpi_code = MPI_Allreduce(local_cause, global_cause, 2, MPI_UNSIGNED, MPI_BOR, io_info->comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code) } /* end else */ @@ -421,12 +419,12 @@ H5D__mpio_opt_possible(const H5D_io_info_t *io_info, const H5S_t *file_space, H5CX_set_mpio_global_no_coll_cause(global_cause[0]); /* Set read-with-rank0-and-bcast flag if possible */ - if(global_cause[0] == 0 && global_cause[1] == 0) { + if (global_cause[0] == 0 && global_cause[1] == 0) { H5CX_set_mpio_rank0_bcast(TRUE); #ifdef H5_HAVE_INSTRUMENTED_LIBRARY H5CX_test_set_mpio_coll_rank0_bcast(TRUE); #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ - } /* end if */ + } /* end if */ /* Set the return value, based on the global cause */ ret_value = global_cause[0] > 0 ? FALSE : TRUE; @@ -435,7 +433,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D__mpio_opt_possible() */ - /*------------------------------------------------------------------------- * Function: H5D__mpio_select_read * @@ -449,22 +446,24 @@ 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->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->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 * @@ -478,23 +477,25 @@ 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->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->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__mpio_array_gatherv * @@ -524,17 +525,18 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries, - size_t array_entry_size, void **_gathered_array, size_t *_gathered_array_num_entries, - hbool_t allgather, int root, MPI_Comm comm, int (*sort_func)(const void *, const void *)) +H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries, size_t array_entry_size, + void **_gathered_array, size_t *_gathered_array_num_entries, hbool_t allgather, + int root, MPI_Comm comm, int (*sort_func)(const void *, const void *)) { - size_t gathered_array_num_entries = 0; /* The size of the newly-constructed array */ - void *gathered_array = NULL; /* The newly-constructed array returned to the caller */ - int *receive_counts_array = NULL; /* Array containing number of entries each processor is contributing */ - int *displacements_array = NULL; /* Array of displacements where each processor places its data in the final array */ - int mpi_code, mpi_rank, mpi_size; - int sendcount; - herr_t ret_value = SUCCEED; + size_t gathered_array_num_entries = 0; /* The size of the newly-constructed array */ + void * gathered_array = NULL; /* The newly-constructed array returned to the caller */ + int *receive_counts_array = NULL; /* Array containing number of entries each processor is contributing */ + int *displacements_array = + NULL; /* Array of displacements where each processor places its data in the final array */ + int mpi_code, mpi_rank, mpi_size; + int sendcount; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -547,38 +549,43 @@ H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries, /* Determine the size of the end result array by collecting the number * of entries contributed by each processor into a single total. */ - if (MPI_SUCCESS != (mpi_code = MPI_Allreduce(&local_array_num_entries, &gathered_array_num_entries, 1, MPI_INT, MPI_SUM, comm))) + if (MPI_SUCCESS != (mpi_code = MPI_Allreduce(&local_array_num_entries, &gathered_array_num_entries, 1, + MPI_INT, MPI_SUM, comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code) - /* If 0 entries resulted from the collective operation, no processor is contributing anything and there is nothing to do */ + /* If 0 entries resulted from the collective operation, no processor is contributing anything and there is + * nothing to do */ if (gathered_array_num_entries > 0) { /* - * If gathering to all processors, all processors need to allocate space for the resulting array, as well as - * the receive counts and displacements arrays for the collective MPI_Allgatherv call. Otherwise, only the - * root processor needs to allocate the space for an MPI_Gatherv call. + * If gathering to all processors, all processors need to allocate space for the resulting array, as + * well as the receive counts and displacements arrays for the collective MPI_Allgatherv call. + * Otherwise, only the root processor needs to allocate the space for an MPI_Gatherv call. */ if (allgather || (mpi_rank == root)) { if (NULL == (gathered_array = H5MM_malloc(gathered_array_num_entries * array_entry_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate gathered array") - if (NULL == (receive_counts_array = (int *) H5MM_malloc((size_t) mpi_size * sizeof(int)))) + if (NULL == (receive_counts_array = (int *)H5MM_malloc((size_t)mpi_size * sizeof(int)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive counts array") - if (NULL == (displacements_array = (int *) H5MM_malloc((size_t) mpi_size * sizeof(int)))) + if (NULL == (displacements_array = (int *)H5MM_malloc((size_t)mpi_size * sizeof(int)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive displacements array") } /* end if */ /* * If gathering to all processors, inform each processor of how many entries each other processor is * contributing to the resulting array by collecting the counts into each processor's "receive counts" - * array. Otherwise, inform only the root processor of how many entries each other processor is contributing. + * array. Otherwise, inform only the root processor of how many entries each other processor is + * contributing. */ if (allgather) { - if (MPI_SUCCESS != (mpi_code = MPI_Allgather(&local_array_num_entries, 1, MPI_INT, receive_counts_array, 1, MPI_INT, comm))) + if (MPI_SUCCESS != (mpi_code = MPI_Allgather(&local_array_num_entries, 1, MPI_INT, + receive_counts_array, 1, MPI_INT, comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code) } /* end if */ else { - if (MPI_SUCCESS != (mpi_code = MPI_Gather(&local_array_num_entries, 1, MPI_INT, receive_counts_array, 1, MPI_INT, root, comm))) + if (MPI_SUCCESS != (mpi_code = MPI_Gather(&local_array_num_entries, 1, MPI_INT, + receive_counts_array, 1, MPI_INT, root, comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Gather failed", mpi_code) } /* end else */ @@ -586,26 +593,29 @@ H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries, size_t i; /* Multiply each receive count by the size of the array entry, since the data is sent as bytes. */ - for (i = 0; i < (size_t) mpi_size; i++) - H5_CHECKED_ASSIGN(receive_counts_array[i], int, (size_t) receive_counts_array[i] * array_entry_size, size_t); + for (i = 0; i < (size_t)mpi_size; i++) + H5_CHECKED_ASSIGN(receive_counts_array[i], int, + (size_t)receive_counts_array[i] * array_entry_size, size_t); /* Set receive buffer offsets for the collective MPI_Allgatherv/MPI_Gatherv call. */ displacements_array[0] = 0; - for (i = 1; i < (size_t) mpi_size; i++) + for (i = 1; i < (size_t)mpi_size; i++) displacements_array[i] = displacements_array[i - 1] + receive_counts_array[i - 1]; } /* end if */ /* As the data is sent as bytes, calculate the true sendcount for the data. */ - H5_CHECKED_ASSIGN(sendcount, int, local_array_num_entries * array_entry_size, size_t); + H5_CHECKED_ASSIGN(sendcount, int, local_array_num_entries *array_entry_size, size_t); if (allgather) { - if (MPI_SUCCESS != (mpi_code = MPI_Allgatherv(local_array, sendcount, MPI_BYTE, - gathered_array, receive_counts_array, displacements_array, MPI_BYTE, comm))) + if (MPI_SUCCESS != + (mpi_code = MPI_Allgatherv(local_array, sendcount, MPI_BYTE, gathered_array, + receive_counts_array, displacements_array, MPI_BYTE, comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Allgatherv failed", mpi_code) } /* end if */ else { - if (MPI_SUCCESS != (mpi_code = MPI_Gatherv(local_array, sendcount, MPI_BYTE, - gathered_array, receive_counts_array, displacements_array, MPI_BYTE, root, comm))) + if (MPI_SUCCESS != + (mpi_code = MPI_Gatherv(local_array, sendcount, MPI_BYTE, gathered_array, + receive_counts_array, displacements_array, MPI_BYTE, root, comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Gatherv failed", mpi_code) } /* end else */ @@ -613,7 +623,7 @@ H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries, HDqsort(gathered_array, gathered_array_num_entries, array_entry_size, sort_func); } /* end if */ - *_gathered_array = gathered_array; + *_gathered_array = gathered_array; *_gathered_array_num_entries = gathered_array_num_entries; done: @@ -625,7 +635,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__mpio_array_gatherv() */ - /*------------------------------------------------------------------------- * Function: H5D__mpio_get_sum_chunk * @@ -640,30 +649,29 @@ 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 * @@ -679,11 +687,11 @@ 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; - herr_t ret_value = SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -691,7 +699,7 @@ H5D__contig_collective_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_ HDassert(H5FD_MPIO == H5F_DRIVER_ID(io_info->dset->oloc.file)); /* 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") /* Set the actual I/O mode property. internal_collective_io will not break to @@ -703,7 +711,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_collective_read() */ - /*------------------------------------------------------------------------- * Function: H5D__contig_collective_write * @@ -719,11 +726,11 @@ 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; - herr_t ret_value = SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE @@ -731,7 +738,7 @@ H5D__contig_collective_write(H5D_io_info_t *io_info, const H5D_type_info_t *type HDassert(H5FD_MPIO == H5F_DRIVER_ID(io_info->dset->oloc.file)); /* 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") /* Set the actual I/O mode property. internal_collective_io will not break to @@ -743,7 +750,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_collective_write() */ - /*------------------------------------------------------------------------- * Function: H5D__chunk_collective_io * @@ -781,16 +787,15 @@ 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) { 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 @@ -805,58 +810,61 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf H5CX_set_coll_metadata_read(FALSE); /* Check the optional property list for the collective chunk IO optimization option */ - if(H5CX_get_mpio_chunk_opt_mode(&chunk_opt_mode) < 0) + if (H5CX_get_mpio_chunk_opt_mode(&chunk_opt_mode) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't get chunk optimization option") - 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) + 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; /* Threshold to use single collective I/O for all chunks */ - int mpi_size; /* Number of processes in MPI job */ + unsigned one_link_chunk_io_threshold; /* Threshold 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") /* Get the chunk optimization option threshold */ - if(H5CX_get_mpio_chunk_opt_num(&one_link_chunk_io_threshold) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't get chunk optimization option threshold value") + if (H5CX_get_mpio_chunk_opt_num(&one_link_chunk_io_threshold) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, + "couldn't get chunk optimization option threshold value") /* 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 / (unsigned)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 / (unsigned)mpi_size >= one_link_chunk_io_threshold) io_option = H5D_ONE_LINK_CHUNK_IO_MORE_OPT; #ifdef H5_HAVE_INSTRUMENTED_LIBRARY else temp_not_link_io = TRUE; #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ - } /* end else */ + } /* end else */ #ifdef H5_HAVE_INSTRUMENTED_LIBRARY -{ - /*** Set collective chunk user-input optimization APIs. ***/ - if(H5D_ONE_LINK_CHUNK_IO == io_option) { - if(H5CX_test_set_mpio_coll_chunk_link_hard(0) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value") - } /* end if */ - else if(H5D_MULTI_CHUNK_IO == io_option) { - if(H5CX_test_set_mpio_coll_chunk_multi_hard(0) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value") - } /* end else-if */ - else if(H5D_ONE_LINK_CHUNK_IO_MORE_OPT == io_option) { - if(H5CX_test_set_mpio_coll_chunk_link_num_true(0) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value") - } /* end if */ - else if(temp_not_link_io) { - if(H5CX_test_set_mpio_coll_chunk_link_num_false(0) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value") - } /* end if */ -} + { + /*** Set collective chunk user-input optimization APIs. ***/ + if (H5D_ONE_LINK_CHUNK_IO == io_option) { + if (H5CX_test_set_mpio_coll_chunk_link_hard(0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value") + } /* end if */ + else if (H5D_MULTI_CHUNK_IO == io_option) { + if (H5CX_test_set_mpio_coll_chunk_multi_hard(0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value") + } /* end else-if */ + else if (H5D_ONE_LINK_CHUNK_IO_MORE_OPT == io_option) { + if (H5CX_test_set_mpio_coll_chunk_link_num_true(0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value") + } /* end if */ + else if (temp_not_link_io) { + if (H5CX_test_set_mpio_coll_chunk_link_num_false(0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value") + } /* end if */ + } #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ /* step 2: Go ahead to do IO.*/ @@ -864,37 +872,38 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf case H5D_ONE_LINK_CHUNK_IO: case H5D_ONE_LINK_CHUNK_IO_MORE_OPT: /* Check if there are any filters in the pipeline */ - if(io_info->dset->shared->dcpl_cache.pline.nused > 0) { + if (io_info->dset->shared->dcpl_cache.pline.nused > 0) { /* For now, Multi-chunk IO must be forced for parallel filtered read, * so that data can be unfiltered as it is received. There is significant * complexity in unfiltering the data when it is read all at once into a * single buffer. */ - if(io_info->op_type == H5D_IO_OP_READ) { - if(H5D__multi_chunk_filtered_collective_io(io_info, type_info, fm) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish optimized multiple filtered chunk MPI-IO") + if (io_info->op_type == H5D_IO_OP_READ) { + if (H5D__multi_chunk_filtered_collective_io(io_info, type_info, fm) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, + "couldn't finish optimized multiple filtered chunk MPI-IO") } /* end if */ - else - if(H5D__link_chunk_filtered_collective_io(io_info, type_info, fm) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish filtered linked chunk MPI-IO") + else if (H5D__link_chunk_filtered_collective_io(io_info, type_info, fm) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish filtered linked chunk MPI-IO") } /* end if */ else /* Perform unfiltered link chunk collective IO */ - if(H5D__link_chunk_collective_io(io_info, type_info, fm, sum_chunk) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish linked chunk MPI-IO") + if (H5D__link_chunk_collective_io(io_info, type_info, fm, sum_chunk) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish linked chunk MPI-IO") break; case H5D_MULTI_CHUNK_IO: /* direct request to do multi-chunk IO */ default: /* multiple chunk IO via threshold */ /* Check if there are any filters in the pipeline */ - if(io_info->dset->shared->dcpl_cache.pline.nused > 0) { - if(H5D__multi_chunk_filtered_collective_io(io_info, type_info, fm) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish optimized multiple filtered chunk MPI-IO") + if (io_info->dset->shared->dcpl_cache.pline.nused > 0) { + if (H5D__multi_chunk_filtered_collective_io(io_info, type_info, fm) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, + "couldn't finish optimized multiple filtered chunk MPI-IO") } /* end if */ else /* Perform unfiltered multi chunk collective IO */ - if(H5D__multi_chunk_collective_io(io_info, type_info, fm) < 0) - HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish optimized multiple chunk MPI-IO") + if (H5D__multi_chunk_collective_io(io_info, type_info, fm) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish optimized multiple chunk MPI-IO") break; } /* end switch */ @@ -902,7 +911,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__chunk_collective_io */ - /*------------------------------------------------------------------------- * Function: H5D__chunk_collective_read * @@ -918,22 +926,21 @@ 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 * @@ -949,22 +956,21 @@ 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 * @@ -983,26 +989,28 @@ 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) +H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm, + int sum_chunk) { H5D_chunk_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; - 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 */ - herr_t ret_value = SUCCEED; + 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; + 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 */ + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -1014,9 +1022,10 @@ H5D__link_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *typ H5CX_set_mpio_actual_io_mode(H5D_MPIO_CHUNK_COLLECTIVE); /* 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 */ @@ -1026,15 +1035,15 @@ 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; @@ -1042,11 +1051,11 @@ 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 */ @@ -1054,7 +1063,7 @@ 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, chunk_info->scaled, &udata) < 0) + if (H5D__chunk_lookup(io_info->dset, chunk_info->scaled, &udata) < 0) HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk address") ctg_store.contig.dset_addr = udata.chunk_block.offset; } /* end else */ @@ -1063,66 +1072,72 @@ 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++) { + 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 @@ -1134,46 +1149,43 @@ 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 */ @@ -1185,34 +1197,38 @@ 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 */ ctg_store.contig.dset_addr = 0; /* Set the MPI datatype */ @@ -1220,56 +1236,57 @@ 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(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__link_chunk_filtered_collective_io * @@ -1319,21 +1336,22 @@ if(H5DEBUG(D)) */ static herr_t H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5D_chunk_map_t *fm) + H5D_chunk_map_t *fm) { H5D_filtered_collective_io_info_t *chunk_list = NULL; /* The list of chunks being read/written */ - H5D_filtered_collective_io_info_t *collective_chunk_list = NULL; /* The list of chunks used during collective operations */ - H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ - MPI_Datatype mem_type = MPI_BYTE; - MPI_Datatype file_type = MPI_BYTE; - hbool_t mem_type_is_derived = FALSE; - hbool_t file_type_is_derived = FALSE; - size_t chunk_list_num_entries; - size_t collective_chunk_list_num_entries; - size_t *num_chunks_selected_array = NULL; /* Array of number of chunks selected on each process */ - size_t i; /* Local index variable */ - int mpi_rank, mpi_size, mpi_code; - herr_t ret_value = SUCCEED; + H5D_filtered_collective_io_info_t *collective_chunk_list = + NULL; /* The list of chunks used during collective operations */ + H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ + MPI_Datatype mem_type = MPI_BYTE; + MPI_Datatype file_type = MPI_BYTE; + hbool_t mem_type_is_derived = FALSE; + hbool_t file_type_is_derived = FALSE; + size_t chunk_list_num_entries; + size_t collective_chunk_list_num_entries; + size_t * num_chunks_selected_array = NULL; /* Array of number of chunks selected on each process */ + size_t i; /* Local index variable */ + int mpi_rank, mpi_size, mpi_code; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -1356,7 +1374,8 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in H5CX_set_mpio_actual_io_mode(H5D_MPIO_CHUNK_COLLECTIVE); /* Build a list of selected chunks in the collective io operation */ - if (H5D__construct_filtered_io_info_list(io_info, type_info, fm, &chunk_list, &chunk_list_num_entries) < 0) + if (H5D__construct_filtered_io_info_list(io_info, type_info, fm, &chunk_list, &chunk_list_num_entries) < + 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't construct filtered I/O info list") if (io_info->op_type == H5D_IO_OP_WRITE) { /* Filtered collective write */ @@ -1365,15 +1384,15 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in hsize_t mpi_buf_count; /* Construct chunked index info */ - index_info.f = io_info->dset->oloc.file; - index_info.pline = &(io_info->dset->shared->dcpl_cache.pline); - index_info.layout = &(io_info->dset->shared->layout.u.chunk); + index_info.f = io_info->dset->oloc.file; + index_info.pline = &(io_info->dset->shared->dcpl_cache.pline); + index_info.layout = &(io_info->dset->shared->layout.u.chunk); index_info.storage = &(io_info->dset->shared->layout.storage.u.chunk); /* Set up chunk information for insertion to chunk index */ - udata.common.layout = index_info.layout; + udata.common.layout = index_info.layout; udata.common.storage = index_info.storage; - udata.filter_mask = 0; + udata.filter_mask = 0; /* Iterate through all the chunks in the collective write operation, * updating each chunk with the data modifications from other processes, @@ -1387,8 +1406,10 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in /* Gather the new chunk sizes to all processes for a collective reallocation * of the chunks in the file. */ - if (H5D__mpio_array_gatherv(chunk_list, chunk_list_num_entries, sizeof(H5D_filtered_collective_io_info_t), - (void **) &collective_chunk_list, &collective_chunk_list_num_entries, true, 0, io_info->comm, NULL) < 0) + if (H5D__mpio_array_gatherv(chunk_list, chunk_list_num_entries, + sizeof(H5D_filtered_collective_io_info_t), + (void **)&collective_chunk_list, &collective_chunk_list_num_entries, true, + 0, io_info->comm, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather new chunk sizes") /* Collectively re-allocate the modified chunks (from each process) in the file */ @@ -1396,15 +1417,17 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in hbool_t insert; if (H5D__chunk_file_alloc(&index_info, &collective_chunk_list[i].chunk_states.chunk_current, - &collective_chunk_list[i].chunk_states.new_chunk, &insert, collective_chunk_list[i].scaled) < 0) + &collective_chunk_list[i].chunk_states.new_chunk, &insert, + collective_chunk_list[i].scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk") } /* end for */ - if (NULL == (num_chunks_selected_array = (size_t *) H5MM_malloc((size_t) mpi_size * sizeof(size_t)))) + if (NULL == (num_chunks_selected_array = (size_t *)H5MM_malloc((size_t)mpi_size * sizeof(size_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate num chunks selected array") - if (MPI_SUCCESS != (mpi_code = MPI_Allgather(&chunk_list_num_entries, 1, MPI_UNSIGNED_LONG_LONG, num_chunks_selected_array, - 1, MPI_UNSIGNED_LONG_LONG, io_info->comm))) + if (MPI_SUCCESS != + (mpi_code = MPI_Allgather(&chunk_list_num_entries, 1, MPI_UNSIGNED_LONG_LONG, + num_chunks_selected_array, 1, MPI_UNSIGNED_LONG_LONG, io_info->comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code) /* If this process has any chunks selected, create a MPI type for collectively @@ -1424,14 +1447,16 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in * of the local array. This works correctly because the array gather function guarantees * that the chunk data in the collective array is ordered in blocks by rank. */ - for (i = 0, offset = 0; i < (size_t) mpi_rank; i++) + for (i = 0, offset = 0; i < (size_t)mpi_rank; i++) offset += num_chunks_selected_array[i]; - H5MM_memcpy(chunk_list, &collective_chunk_list[offset], num_chunks_selected_array[mpi_rank] * sizeof(H5D_filtered_collective_io_info_t)); + H5MM_memcpy(chunk_list, &collective_chunk_list[offset], + num_chunks_selected_array[mpi_rank] * sizeof(H5D_filtered_collective_io_info_t)); /* Create single MPI type encompassing each selection in the dataspace */ - if (H5D__mpio_filtered_collective_write_type(chunk_list, chunk_list_num_entries, - &mem_type, &mem_type_is_derived, &file_type, &file_type_is_derived) < 0) + if (H5D__mpio_filtered_collective_write_type(chunk_list, chunk_list_num_entries, &mem_type, + &mem_type_is_derived, &file_type, + &file_type_is_derived) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADTYPE, FAIL, "couldn't create MPI link chunk I/O type") /* Override the write buffer to point to the address of the first @@ -1441,11 +1466,11 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in } /* end if */ /* We have a single, complicated MPI datatype for both memory & file */ - mpi_buf_count = (mem_type_is_derived && file_type_is_derived) ? (hsize_t) 1 : (hsize_t) 0; + mpi_buf_count = (mem_type_is_derived && file_type_is_derived) ? (hsize_t)1 : (hsize_t)0; /* Set up the base storage address for this operation */ ctg_store.contig.dset_addr = 0; /* Write address must be set to address 0 */ - io_info->store = &ctg_store; + io_info->store = &ctg_store; /* Perform I/O */ if (H5D__final_collective_io(io_info, type_info, mpi_buf_count, file_type, mem_type) < 0) @@ -1455,14 +1480,14 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in * in this iteration into the chunk index */ for (i = 0; i < collective_chunk_list_num_entries; i++) { - udata.chunk_block = collective_chunk_list[i].chunk_states.new_chunk; + udata.chunk_block = collective_chunk_list[i].chunk_states.new_chunk; udata.common.scaled = collective_chunk_list[i].scaled; - udata.chunk_idx = collective_chunk_list[i].index; + udata.chunk_idx = collective_chunk_list[i].index; if ((index_info.storage->ops->insert)(&index_info, &udata, io_info->dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk address into index") } /* end for */ - } /* end if */ + } /* end if */ done: /* Free resources used by a process which had some selection */ @@ -1488,7 +1513,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__link_chunk_filtered_collective_io() */ - /*------------------------------------------------------------------------- * Function: H5D__multi_chunk_collective_io * @@ -1507,25 +1531,27 @@ done: *------------------------------------------------------------------------- */ 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) +H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, H5D_chunk_map_t *fm) { - 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_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_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_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_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 @@ -1544,17 +1570,17 @@ 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, chunk_io_option, chunk_addr) < 0) + if (H5D__obtain_mpio_mode(io_info, fm, 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 */ H5MM_memcpy(&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 */ @@ -1562,7 +1588,7 @@ if(H5DEBUG(D)) /* Set up compact I/O info object */ H5MM_memcpy(&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 */ @@ -1572,38 +1598,39 @@ 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.scaled = chunk_info->scaled; + store.chunk.scaled = chunk_info->scaled; } /* 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; @@ -1613,7 +1640,7 @@ if(H5DEBUG(D)) * to ease switching between to mixed I/O without checking the current * value of the property. You can see the definition in H5Ppublic.h */ - actual_io_mode = (H5D_mpio_actual_io_mode_t) (actual_io_mode | H5D_MPIO_CHUNK_COLLECTIVE); + actual_io_mode = (H5D_mpio_actual_io_mode_t)(actual_io_mode | H5D_MPIO_CHUNK_COLLECTIVE); } /* end if */ else { @@ -1621,8 +1648,8 @@ if(H5DEBUG(D)) } /* end else */ /* Switch back to collective I/O */ - if(last_coll_opt_mode != H5FD_MPIO_COLLECTIVE_IO) { - if(H5CX_set_mpio_coll_opt(H5FD_MPIO_COLLECTIVE_IO) < 0) + if (last_coll_opt_mode != H5FD_MPIO_COLLECTIVE_IO) { + if (H5CX_set_mpio_coll_opt(H5FD_MPIO_COLLECTIVE_IO) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't switch to collective I/O") last_coll_opt_mode = H5FD_MPIO_COLLECTIVE_IO; } /* end if */ @@ -1631,32 +1658,33 @@ 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; /* Update the local variable tracking the actual io mode. */ - actual_io_mode = (H5D_mpio_actual_io_mode_t) (actual_io_mode | H5D_MPIO_CHUNK_INDEPENDENT); + actual_io_mode = (H5D_mpio_actual_io_mode_t)(actual_io_mode | H5D_MPIO_CHUNK_INDEPENDENT); } /* end if */ else { fspace = mspace = NULL; } /* end else */ /* Using independent I/O with file setview.*/ - if(last_coll_opt_mode != H5FD_MPIO_INDIVIDUAL_IO) { - if(H5CX_set_mpio_coll_opt(H5FD_MPIO_INDIVIDUAL_IO) < 0) + if (last_coll_opt_mode != H5FD_MPIO_INDIVIDUAL_IO) { + if (H5CX_set_mpio_coll_opt(H5FD_MPIO_INDIVIDUAL_IO) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't switch to individual I/O") last_coll_opt_mode = H5FD_MPIO_INDIVIDUAL_IO; } /* end if */ @@ -1665,28 +1693,27 @@ 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 API context. */ H5CX_set_mpio_actual_io_mode(actual_io_mode); 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__multi_chunk_filtered_collective_io * @@ -1745,23 +1772,25 @@ done: */ static herr_t H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - H5D_chunk_map_t *fm) + H5D_chunk_map_t *fm) { H5D_filtered_collective_io_info_t *chunk_list = NULL; /* The list of chunks being read/written */ - H5D_filtered_collective_io_info_t *collective_chunk_list = NULL; /* The list of chunks used during collective operations */ - H5D_storage_t store; /* union of EFL and chunk pointer in file space */ - H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */ - H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ - MPI_Datatype *file_type_array = NULL; - MPI_Datatype *mem_type_array = NULL; - hbool_t *file_type_is_derived_array = NULL; - hbool_t *mem_type_is_derived_array = NULL; - hbool_t *has_chunk_selected_array = NULL; /* Array of whether or not each process is contributing a chunk to each iteration */ - size_t chunk_list_num_entries; - size_t collective_chunk_list_num_entries; - size_t i, j; /* Local index variable */ - int mpi_rank, mpi_size, mpi_code; - herr_t ret_value = SUCCEED; + H5D_filtered_collective_io_info_t *collective_chunk_list = + NULL; /* The list of chunks used during collective operations */ + H5D_storage_t store; /* union of EFL and chunk pointer in file space */ + H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */ + H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ + MPI_Datatype *file_type_array = NULL; + MPI_Datatype *mem_type_array = NULL; + hbool_t * file_type_is_derived_array = NULL; + hbool_t * mem_type_is_derived_array = NULL; + hbool_t * has_chunk_selected_array = + NULL; /* Array of whether or not each process is contributing a chunk to each iteration */ + size_t chunk_list_num_entries; + size_t collective_chunk_list_num_entries; + size_t i, j; /* Local index variable */ + int mpi_rank, mpi_size, mpi_code; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -1784,16 +1813,17 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i H5CX_set_mpio_actual_io_mode(H5D_MPIO_CHUNK_COLLECTIVE); /* Build a list of selected chunks in the collective IO operation */ - if (H5D__construct_filtered_io_info_list(io_info, type_info, fm, &chunk_list, &chunk_list_num_entries) < 0) + if (H5D__construct_filtered_io_info_list(io_info, type_info, fm, &chunk_list, &chunk_list_num_entries) < + 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't construct filtered I/O info list") /* Set up contiguous I/O info object */ H5MM_memcpy(&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 */ - ctg_store.contig.dset_size = (hsize_t) io_info->dset->shared->layout.u.chunk.size; + ctg_store.contig.dset_size = (hsize_t)io_info->dset->shared->layout.u.chunk.size; ctg_store.contig.dset_addr = 0; /* Set dataset storage for I/O info */ @@ -1803,7 +1833,7 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i for (i = 0; i < chunk_list_num_entries; i++) if (H5D__filtered_collective_chunk_entry_io(&chunk_list[i], io_info, type_info, fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't process chunk entry") - } /* end if */ + } /* end if */ else { /* Filtered collective write */ H5D_chk_idx_info_t index_info; H5D_chunk_ud_t udata; @@ -1811,37 +1841,38 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i hsize_t mpi_buf_count; /* Construct chunked index info */ - index_info.f = io_info->dset->oloc.file; - index_info.pline = &(io_info->dset->shared->dcpl_cache.pline); - index_info.layout = &(io_info->dset->shared->layout.u.chunk); + index_info.f = io_info->dset->oloc.file; + index_info.pline = &(io_info->dset->shared->dcpl_cache.pline); + index_info.layout = &(io_info->dset->shared->layout.u.chunk); index_info.storage = &(io_info->dset->shared->layout.storage.u.chunk); /* Set up chunk information for insertion to chunk index */ - udata.common.layout = index_info.layout; + udata.common.layout = index_info.layout; udata.common.storage = index_info.storage; - udata.filter_mask = 0; + udata.filter_mask = 0; /* Retrieve the maximum number of chunks being written among all processes */ - if (MPI_SUCCESS != (mpi_code = MPI_Allreduce(&chunk_list_num_entries, &max_num_chunks, - 1, MPI_UNSIGNED_LONG_LONG, MPI_MAX, io_info->comm))) + if (MPI_SUCCESS != (mpi_code = MPI_Allreduce(&chunk_list_num_entries, &max_num_chunks, 1, + MPI_UNSIGNED_LONG_LONG, MPI_MAX, io_info->comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code) /* If no one is writing anything at all, end the operation */ - if (!(max_num_chunks > 0)) HGOTO_DONE(SUCCEED); + if (!(max_num_chunks > 0)) + HGOTO_DONE(SUCCEED); /* Allocate arrays for storing MPI file and mem types and whether or not the * types were derived. */ - if (NULL == (file_type_array = (MPI_Datatype *) H5MM_malloc(max_num_chunks * sizeof(MPI_Datatype)))) + if (NULL == (file_type_array = (MPI_Datatype *)H5MM_malloc(max_num_chunks * sizeof(MPI_Datatype)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate file type array") - if (NULL == (file_type_is_derived_array = (hbool_t *) H5MM_calloc(max_num_chunks * sizeof(hbool_t)))) + if (NULL == (file_type_is_derived_array = (hbool_t *)H5MM_calloc(max_num_chunks * sizeof(hbool_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate file type is derived array") - if (NULL == (mem_type_array = (MPI_Datatype *) H5MM_malloc(max_num_chunks * sizeof(MPI_Datatype)))) + if (NULL == (mem_type_array = (MPI_Datatype *)H5MM_malloc(max_num_chunks * sizeof(MPI_Datatype)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate mem type array") - if (NULL == (mem_type_is_derived_array = (hbool_t *) H5MM_calloc(max_num_chunks * sizeof(hbool_t)))) + if (NULL == (mem_type_is_derived_array = (hbool_t *)H5MM_calloc(max_num_chunks * sizeof(hbool_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate mem type is derived array") /* Iterate over the max number of chunks among all processes, as this process could @@ -1850,7 +1881,8 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i */ for (i = 0; i < max_num_chunks; i++) { /* Check if this process has a chunk to work on for this iteration */ - hbool_t have_chunk_to_process = (i < chunk_list_num_entries) && (mpi_rank == chunk_list[i].owners.new_owner); + hbool_t have_chunk_to_process = + (i < chunk_list_num_entries) && (mpi_rank == chunk_list[i].owners.new_owner); if (have_chunk_to_process) if (H5D__filtered_collective_chunk_entry_io(&chunk_list[i], io_info, type_info, fm) < 0) @@ -1859,8 +1891,10 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i /* Gather the new chunk sizes to all processes for a collective re-allocation * of the chunks in the file */ - if (H5D__mpio_array_gatherv(&chunk_list[i], have_chunk_to_process ? 1 : 0, sizeof(H5D_filtered_collective_io_info_t), - (void **) &collective_chunk_list, &collective_chunk_list_num_entries, true, 0, io_info->comm, NULL) < 0) + if (H5D__mpio_array_gatherv(&chunk_list[i], have_chunk_to_process ? 1 : 0, + sizeof(H5D_filtered_collective_io_info_t), + (void **)&collective_chunk_list, &collective_chunk_list_num_entries, + true, 0, io_info->comm, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather new chunk sizes") /* Participate in the collective re-allocation of all chunks modified @@ -1870,15 +1904,18 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i hbool_t insert = FALSE; if (H5D__chunk_file_alloc(&index_info, &collective_chunk_list[j].chunk_states.chunk_current, - &collective_chunk_list[j].chunk_states.new_chunk, &insert, chunk_list[j].scaled) < 0) + &collective_chunk_list[j].chunk_states.new_chunk, &insert, + chunk_list[j].scaled) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk") } /* end for */ - if (NULL == (has_chunk_selected_array = (hbool_t *) H5MM_malloc((size_t) mpi_size * sizeof(hbool_t)))) + if (NULL == + (has_chunk_selected_array = (hbool_t *)H5MM_malloc((size_t)mpi_size * sizeof(hbool_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate num chunks selected array") - if (MPI_SUCCESS != (mpi_code = MPI_Allgather(&have_chunk_to_process, 1, MPI_C_BOOL, has_chunk_selected_array, - 1, MPI_C_BOOL, io_info->comm))) + if (MPI_SUCCESS != + (mpi_code = MPI_Allgather(&have_chunk_to_process, 1, MPI_C_BOOL, has_chunk_selected_array, 1, + MPI_C_BOOL, io_info->comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code) /* If this process has a chunk to work on, create a MPI type for the @@ -1888,26 +1925,30 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i size_t offset; int mpi_type_count; - for (j = 0, offset = 0; j < (size_t) mpi_rank; j++) + for (j = 0, offset = 0; j < (size_t)mpi_rank; j++) offset += has_chunk_selected_array[j]; /* Collect the new chunk info back to the local copy, since only the record in the * collective array gets updated by the chunk re-allocation */ - H5MM_memcpy(&chunk_list[i].chunk_states.new_chunk, &collective_chunk_list[offset].chunk_states.new_chunk, sizeof(chunk_list[i].chunk_states.new_chunk)); + H5MM_memcpy(&chunk_list[i].chunk_states.new_chunk, + &collective_chunk_list[offset].chunk_states.new_chunk, + sizeof(chunk_list[i].chunk_states.new_chunk)); H5_CHECKED_ASSIGN(mpi_type_count, int, chunk_list[i].chunk_states.new_chunk.length, hsize_t); /* Create MPI memory type for writing to chunk */ - if (MPI_SUCCESS != (mpi_code = MPI_Type_contiguous(mpi_type_count, MPI_BYTE, &mem_type_array[i]))) + if (MPI_SUCCESS != + (mpi_code = MPI_Type_contiguous(mpi_type_count, MPI_BYTE, &mem_type_array[i]))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) - if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&mem_type_array[i]))) + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&mem_type_array[i]))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) mem_type_is_derived_array[i] = TRUE; /* Create MPI file type for writing to chunk */ - if (MPI_SUCCESS != (mpi_code = MPI_Type_contiguous(mpi_type_count, MPI_BYTE, &file_type_array[i]))) + if (MPI_SUCCESS != + (mpi_code = MPI_Type_contiguous(mpi_type_count, MPI_BYTE, &file_type_array[i]))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) - if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&file_type_array[i]))) + if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&file_type_array[i]))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) file_type_is_derived_array[i] = TRUE; @@ -1923,34 +1964,36 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i } /* end if */ else { mem_type_array[i] = file_type_array[i] = MPI_BYTE; - mpi_buf_count = 0; + mpi_buf_count = 0; } /* end else */ /* Perform the I/O */ - if (H5D__final_collective_io(&ctg_io_info, type_info, mpi_buf_count, file_type_array[i], mem_type_array[i]) < 0) + if (H5D__final_collective_io(&ctg_io_info, type_info, mpi_buf_count, file_type_array[i], + mem_type_array[i]) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish MPI-IO") /* Participate in the collective re-insertion of all chunks modified * in this iteration into the chunk index */ for (j = 0; j < collective_chunk_list_num_entries; j++) { - udata.chunk_block = collective_chunk_list[j].chunk_states.new_chunk; + udata.chunk_block = collective_chunk_list[j].chunk_states.new_chunk; udata.common.scaled = collective_chunk_list[j].scaled; - udata.chunk_idx = collective_chunk_list[j].index; + udata.chunk_idx = collective_chunk_list[j].index; if ((index_info.storage->ops->insert)(&index_info, &udata, io_info->dset) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk address into index") + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, + "unable to insert chunk address into index") } /* end for */ - if (collective_chunk_list){ + if (collective_chunk_list) { H5MM_free(collective_chunk_list); collective_chunk_list = NULL; } /* end if */ - if (has_chunk_selected_array){ + if (has_chunk_selected_array) { H5MM_free(has_chunk_selected_array); has_chunk_selected_array = NULL; } /* end if */ - } /* end for */ + } /* end for */ /* Free the MPI file and memory types, if they were derived */ for (i = 0; i < max_num_chunks; i++) { @@ -1962,7 +2005,7 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&mem_type_array[i]))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) } /* end for */ - } /* end else */ + } /* end else */ done: if (chunk_list) { @@ -1987,7 +2030,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__multi_chunk_filtered_collective_io() */ - /*------------------------------------------------------------------------- * Function: H5D__inter_collective_io * @@ -2002,20 +2044,20 @@ 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 */ + 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 @@ -2027,39 +2069,40 @@ 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 { @@ -2072,30 +2115,29 @@ 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 * @@ -2109,35 +2151,34 @@ 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(H5CX_set_mpi_coll_datatypes(mpi_buf_type, mpi_file_type) < 0) + if (H5CX_set_mpi_coll_datatypes(mpi_buf_type, mpi_file_type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O collective I/O datatypes") - 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 * @@ -2155,17 +2196,16 @@ if(H5DEBUG(D)) static int H5D__cmp_chunk_addr(const void *chunk_addr_info1, const void *chunk_addr_info2) { - haddr_t addr1 = HADDR_UNDEF, addr2 = HADDR_UNDEF; + haddr_t addr1 = HADDR_UNDEF, addr2 = HADDR_UNDEF; - 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__cmp_filtered_collective_io_info_entry * @@ -2183,20 +2223,23 @@ H5D__cmp_chunk_addr(const void *chunk_addr_info1, const void *chunk_addr_info2) *------------------------------------------------------------------------- */ static int -H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_info_entry1, const void *filtered_collective_io_info_entry2) +H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_info_entry1, + const void *filtered_collective_io_info_entry2) { haddr_t addr1 = HADDR_UNDEF, addr2 = HADDR_UNDEF; FUNC_ENTER_STATIC_NOERR - addr1 = ((const H5D_filtered_collective_io_info_t *) filtered_collective_io_info_entry1)->chunk_states.new_chunk.offset; - addr2 = ((const H5D_filtered_collective_io_info_t *) filtered_collective_io_info_entry2)->chunk_states.new_chunk.offset; + addr1 = ((const H5D_filtered_collective_io_info_t *)filtered_collective_io_info_entry1) + ->chunk_states.new_chunk.offset; + addr2 = ((const H5D_filtered_collective_io_info_t *)filtered_collective_io_info_entry2) + ->chunk_states.new_chunk.offset; FUNC_LEAVE_NOAPI(H5F_addr_cmp(addr1, addr2)) } /* end H5D__cmp_filtered_collective_io_info_entry() */ #if MPI_VERSION >= 3 - + /*------------------------------------------------------------------------- * Function: H5D__cmp_filtered_collective_io_info_entry_owner * @@ -2215,20 +2258,22 @@ H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_in *------------------------------------------------------------------------- */ static int -H5D__cmp_filtered_collective_io_info_entry_owner(const void *filtered_collective_io_info_entry1, const void *filtered_collective_io_info_entry2) +H5D__cmp_filtered_collective_io_info_entry_owner(const void *filtered_collective_io_info_entry1, + const void *filtered_collective_io_info_entry2) { int owner1 = -1, owner2 = -1; FUNC_ENTER_STATIC_NOERR - owner1 = ((const H5D_filtered_collective_io_info_t *) filtered_collective_io_info_entry1)->owners.original_owner; - owner2 = ((const H5D_filtered_collective_io_info_t *) filtered_collective_io_info_entry2)->owners.original_owner; + owner1 = ((const H5D_filtered_collective_io_info_t *)filtered_collective_io_info_entry1) + ->owners.original_owner; + owner2 = ((const H5D_filtered_collective_io_info_t *)filtered_collective_io_info_entry2) + ->owners.original_owner; FUNC_LEAVE_NOAPI(owner1 - owner2) } /* end H5D__cmp_filtered_collective_io_info_entry_owner() */ #endif - /*------------------------------------------------------------------------- * Function: H5D__sort_chunk * @@ -2243,8 +2288,8 @@ H5D__cmp_filtered_collective_io_info_entry_owner(const void *filtered_collective * 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 @@ -2256,24 +2301,24 @@ H5D__cmp_filtered_collective_io_info_entry_owner(const void *filtered_collective */ 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 @@ -2285,56 +2330,59 @@ 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 = (haddr_t *)H5MM_malloc(sizeof(haddr_t) * (size_t)fm->layout->u.chunk.nchunks))) + if (NULL == (total_chunk_addr_array = + (haddr_t *)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))) + 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 = (H5D_chunk_info_t *)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 = (H5D_chunk_info_t *)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, chunk_info->scaled, &udata) < 0) + if (H5D__chunk_lookup(io_info->dset, chunk_info->scaled, &udata) < 0) HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk info from skipped list") chunk_addr = udata.chunk_block.offset; } /* end if */ @@ -2342,7 +2390,7 @@ 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 */ @@ -2355,23 +2403,22 @@ 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 * @@ -2392,7 +2439,8 @@ 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: * @@ -2409,17 +2457,17 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, - uint8_t assign_io_mode[], haddr_t chunk_addr[]) +H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_chunk_map_t *fm, uint8_t assign_io_mode[], + haddr_t chunk_addr[]) { size_t 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 root; @@ -2430,91 +2478,90 @@ H5D__obtain_mpio_mode(H5D_io_info_t* io_info, H5D_chunk_map_t *fm, 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, size_t, fm->layout->u.chunk.nchunks, hsize_t); - if(H5CX_get_mpio_chunk_opt_ratio(&percent_nproc_per_chunk) < 0) + if (H5CX_get_mpio_chunk_opt_ratio(&percent_nproc_per_chunk) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't get percent nproc per chunk") /* 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 = (unsigned)mpi_size * percent_nproc_per_chunk/100; + threshold_nproc_per_chunk = (unsigned)mpi_size * percent_nproc_per_chunk / 100; /* Allocate memory */ - if(NULL == (io_mode_info = (uint8_t *)H5MM_calloc(total_chunks))) + if (NULL == (io_mode_info = (uint8_t *)H5MM_calloc(total_chunks))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate I/O mode info buffer") - if(NULL == (mergebuf = (uint8_t *)H5MM_malloc((sizeof(haddr_t) + 1) * total_chunks))) + if (NULL == (mergebuf = (uint8_t *)H5MM_malloc((sizeof(haddr_t) + 1) * total_chunks))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate mergebuf buffer") - tempbuf = mergebuf + total_chunks; - if(mpi_rank == root) - if(NULL == (recv_io_mode_info = (uint8_t *)H5MM_malloc(total_chunks * (size_t)mpi_size))) + tempbuf = mergebuf + total_chunks; + if (mpi_rank == root) + if (NULL == (recv_io_mode_info = (uint8_t *)H5MM_malloc(total_chunks * (size_t)mpi_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate recv I/O mode info buffer") /* Obtain the regularity and selection information for all chunks in this process. */ - chunk_node = H5SL_first(fm->sel_chunks); - while(chunk_node) { - chunk_info = (H5D_chunk_info_t *)H5SL_item(chunk_node); + chunk_node = H5SL_first(fm->sel_chunks); + while (chunk_node) { + chunk_info = (H5D_chunk_info_t *)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); + chunk_node = H5SL_next(chunk_node); } /* end while */ /* Gather all the information */ H5_CHECK_OVERFLOW(total_chunks, size_t, int) - if(MPI_SUCCESS != (mpi_code = MPI_Gather(io_mode_info, (int)total_chunks, MPI_BYTE, - recv_io_mode_info, (int)total_chunks, MPI_BYTE, root, comm))) + if (MPI_SUCCESS != (mpi_code = MPI_Gather(io_mode_info, (int)total_chunks, MPI_BYTE, recv_io_mode_info, + (int)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) { - size_t nproc; - unsigned* nproc_per_chunk; + if (mpi_rank == root) { + size_t nproc; + unsigned *nproc_per_chunk; /* pre-computing: calculate number of processes and regularity of the selection occupied in each chunk */ - if(NULL == (nproc_per_chunk = (unsigned*)H5MM_calloc(total_chunks * sizeof(unsigned)))) + if (NULL == (nproc_per_chunk = (unsigned *)H5MM_calloc(total_chunks * sizeof(unsigned)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate nproc_per_chunk buffer") /* calculating the chunk address */ - if(H5D__chunk_addrmap(io_info, chunk_addr) < 0) { + if (H5D__chunk_addrmap(io_info, chunk_addr) < 0) { H5MM_free(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 < (size_t)mpi_size; nproc++) { + for (nproc = 0; nproc < (size_t)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 */ H5MM_memcpy(mergebuf, assign_io_mode, total_chunks); @@ -2524,38 +2571,39 @@ 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((sizeof(haddr_t) + 1) * total_chunks > INT_MAX) + if ((sizeof(haddr_t) + 1) * total_chunks > INT_MAX) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "result overflow") - if(MPI_SUCCESS != (mpi_code = MPI_Bcast(mergebuf, (int)((sizeof(haddr_t) + 1) * total_chunks), MPI_BYTE, root, comm))) + if (MPI_SUCCESS != + (mpi_code = MPI_Bcast(mergebuf, (int)((sizeof(haddr_t) + 1) * total_chunks), MPI_BYTE, root, comm))) HMPI_GOTO_ERROR(FAIL, "MPI_BCast failed", mpi_code) H5MM_memcpy(assign_io_mode, mergebuf, total_chunks); H5MM_memcpy(chunk_addr, tempbuf, sizeof(haddr_t) * total_chunks); #ifdef H5_HAVE_INSTRUMENTED_LIBRARY -{ - hbool_t coll_op = FALSE; + { + hbool_t coll_op = FALSE; + + for (ic = 0; ic < total_chunks; ic++) + if (assign_io_mode[ic] == H5D_CHUNK_IO_MODE_COL) { + if (H5CX_test_set_mpio_coll_chunk_multi_ratio_coll(0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value") + coll_op = TRUE; + break; + } /* end if */ - for(ic = 0; ic < total_chunks; ic++) - if(assign_io_mode[ic] == H5D_CHUNK_IO_MODE_COL) { - if(H5CX_test_set_mpio_coll_chunk_multi_ratio_coll(0) < 0) + if (!coll_op) + if (H5CX_test_set_mpio_coll_chunk_multi_ratio_ind(0) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value") - coll_op = TRUE; - break; - } /* end if */ - - if(!coll_op) - if(H5CX_test_set_mpio_coll_chunk_multi_ratio_ind(0) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value") -} + } #endif done: - if(io_mode_info) + if (io_mode_info) H5MM_free(io_mode_info); - if(mergebuf) + if (mergebuf) H5MM_free(mergebuf); - if(recv_io_mode_info) { + if (recv_io_mode_info) { HDassert(mpi_rank == root); H5MM_free(recv_io_mode_info); } /* end if */ @@ -2563,7 +2611,6 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__obtain_mpio_mode() */ - /*------------------------------------------------------------------------- * Function: H5D__construct_filtered_io_info_list * @@ -2584,13 +2631,15 @@ done: */ static herr_t H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - const H5D_chunk_map_t *fm, H5D_filtered_collective_io_info_t **chunk_list, size_t *num_entries) + const H5D_chunk_map_t * fm, + H5D_filtered_collective_io_info_t **chunk_list, size_t *num_entries) { - H5D_filtered_collective_io_info_t *local_info_array = NULL; /* The list of initially selected chunks for this process */ - size_t num_chunks_selected; - size_t i; - int mpi_rank; - herr_t ret_value = SUCCEED; + H5D_filtered_collective_io_info_t *local_info_array = + NULL; /* The list of initially selected chunks for this process */ + size_t num_chunks_selected; + size_t i; + int mpi_rank; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -2607,35 +2656,37 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ if ((num_chunks_selected = H5SL_count(fm->sel_chunks))) { H5D_chunk_info_t *chunk_info; H5D_chunk_ud_t udata; - H5SL_node_t *chunk_node; + H5SL_node_t * chunk_node; hsize_t select_npoints; hssize_t chunk_npoints; - if(NULL == (local_info_array = (H5D_filtered_collective_io_info_t *) H5MM_malloc(num_chunks_selected * sizeof(H5D_filtered_collective_io_info_t)))) + if (NULL == (local_info_array = (H5D_filtered_collective_io_info_t *)H5MM_malloc( + num_chunks_selected * sizeof(H5D_filtered_collective_io_info_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate local io info array buffer") chunk_node = H5SL_first(fm->sel_chunks); - for(i = 0; chunk_node; i++) { - chunk_info = (H5D_chunk_info_t *) H5SL_item(chunk_node); + for (i = 0; chunk_node; i++) { + chunk_info = (H5D_chunk_info_t *)H5SL_item(chunk_node); /* Obtain this chunk's address */ - if(H5D__chunk_lookup(io_info->dset, chunk_info->scaled, &udata) < 0) + if (H5D__chunk_lookup(io_info->dset, chunk_info->scaled, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") - local_info_array[i].index = chunk_info->index; - local_info_array[i].chunk_states.chunk_current = local_info_array[i].chunk_states.new_chunk = udata.chunk_block; - local_info_array[i].num_writers = 0; + local_info_array[i].index = chunk_info->index; + local_info_array[i].chunk_states.chunk_current = local_info_array[i].chunk_states.new_chunk = + udata.chunk_block; + local_info_array[i].num_writers = 0; local_info_array[i].owners.original_owner = local_info_array[i].owners.new_owner = mpi_rank; - local_info_array[i].buf = NULL; + local_info_array[i].buf = NULL; - local_info_array[i].async_info.num_receive_requests = 0; - local_info_array[i].async_info.receive_buffer_array = NULL; + local_info_array[i].async_info.num_receive_requests = 0; + local_info_array[i].async_info.receive_buffer_array = NULL; local_info_array[i].async_info.receive_requests_array = NULL; H5MM_memcpy(local_info_array[i].scaled, chunk_info->scaled, sizeof(chunk_info->scaled)); - select_npoints = H5S_GET_SELECT_NPOINTS(chunk_info->mspace); - local_info_array[i].io_size = (size_t) select_npoints * type_info->src_type_size; + select_npoints = H5S_GET_SELECT_NPOINTS(chunk_info->mspace); + local_info_array[i].io_size = (size_t)select_npoints * type_info->src_type_size; /* Currently the full overwrite status of a chunk is only obtained on a per-process * basis. This means that if the total selection in the chunk, as determined by the combination @@ -2648,22 +2699,26 @@ H5D__construct_filtered_io_info_list(const H5D_io_info_t *io_info, const H5D_typ if ((chunk_npoints = H5S_GET_EXTENT_NPOINTS(chunk_info->fspace)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") local_info_array[i].full_overwrite = - (local_info_array[i].io_size >= (hsize_t) chunk_npoints * type_info->dst_type_size) ? TRUE : FALSE; + (local_info_array[i].io_size >= (hsize_t)chunk_npoints * type_info->dst_type_size) ? TRUE + : FALSE; chunk_node = H5SL_next(chunk_node); } /* end for */ - } /* end if */ + } /* end if */ /* Redistribute shared chunks to new owners as necessary */ if (io_info->op_type == H5D_IO_OP_WRITE) #if MPI_VERSION >= 3 - if (H5D__chunk_redistribute_shared_chunks(io_info, type_info, fm, local_info_array, &num_chunks_selected) < 0) + if (H5D__chunk_redistribute_shared_chunks(io_info, type_info, fm, local_info_array, + &num_chunks_selected) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to redistribute shared chunks") #else - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to redistribute shared chunks - MPI version < 3 (MPI_Mprobe and MPI_Imrecv missing)") + HGOTO_ERROR( + H5E_DATASET, H5E_WRITEERROR, FAIL, + "unable to redistribute shared chunks - MPI version < 3 (MPI_Mprobe and MPI_Imrecv missing)") #endif - *chunk_list = local_info_array; + *chunk_list = local_info_array; *num_entries = num_chunks_selected; done: @@ -2671,7 +2726,7 @@ done: } /* end H5D__construct_filtered_io_info_list() */ #if MPI_VERSION >= 3 - + /*------------------------------------------------------------------------- * Function: H5D__chunk_redistribute_shared_chunks * @@ -2713,23 +2768,27 @@ done: */ static herr_t H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, - const H5D_chunk_map_t *fm, H5D_filtered_collective_io_info_t *local_chunk_array, size_t *local_chunk_array_num_entries) + const H5D_chunk_map_t * fm, + H5D_filtered_collective_io_info_t *local_chunk_array, + size_t * local_chunk_array_num_entries) { - H5D_filtered_collective_io_info_t *shared_chunks_info_array = NULL; /* The list of all chunks selected in the operation by all processes */ - H5S_sel_iter_t *mem_iter = NULL; /* Memory iterator for H5D__gather_mem */ - unsigned char **mod_data = NULL; /* Array of chunk modification data buffers sent by a process to new chunk owners */ - MPI_Request *send_requests = NULL; /* Array of MPI_Isend chunk modification data send requests */ - MPI_Status *send_statuses = NULL; /* Array of MPI_Isend chunk modification send statuses */ - hbool_t mem_iter_init = FALSE; - size_t shared_chunks_info_array_num_entries = 0; - size_t num_send_requests = 0; - size_t *num_assigned_chunks_array = NULL; - size_t i, last_assigned_idx; - int *send_counts = NULL; - int *send_displacements = NULL; - int scatter_recvcount_int; - int mpi_rank, mpi_size, mpi_code; - herr_t ret_value = SUCCEED; + H5D_filtered_collective_io_info_t *shared_chunks_info_array = + NULL; /* The list of all chunks selected in the operation by all processes */ + H5S_sel_iter_t *mem_iter = NULL; /* Memory iterator for H5D__gather_mem */ + unsigned char **mod_data = + NULL; /* Array of chunk modification data buffers sent by a process to new chunk owners */ + MPI_Request *send_requests = NULL; /* Array of MPI_Isend chunk modification data send requests */ + MPI_Status * send_statuses = NULL; /* Array of MPI_Isend chunk modification send statuses */ + hbool_t mem_iter_init = FALSE; + size_t shared_chunks_info_array_num_entries = 0; + size_t num_send_requests = 0; + size_t * num_assigned_chunks_array = NULL; + size_t i, last_assigned_idx; + int * send_counts = NULL; + int * send_displacements = NULL; + int scatter_recvcount_int; + int mpi_rank, mpi_size, mpi_code; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -2747,58 +2806,63 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty H5CX_set_libver_bounds(NULL); if (*local_chunk_array_num_entries) - if (NULL == (send_requests = (MPI_Request *) H5MM_malloc(*local_chunk_array_num_entries * sizeof(MPI_Request)))) + if (NULL == (send_requests = + (MPI_Request *)H5MM_malloc(*local_chunk_array_num_entries * sizeof(MPI_Request)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate send requests buffer") - if (NULL == (mem_iter = (H5S_sel_iter_t *) H5MM_malloc(sizeof(H5S_sel_iter_t)))) + if (NULL == (mem_iter = (H5S_sel_iter_t *)H5MM_malloc(sizeof(H5S_sel_iter_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate memory iterator") - /* Gather every rank's list of chunks to rank 0 to allow it to perform the redistribution operation. After this - * call, the gathered list will initially be sorted in increasing order of chunk offset in the file. + /* Gather every rank's list of chunks to rank 0 to allow it to perform the redistribution operation. After + * this call, the gathered list will initially be sorted in increasing order of chunk offset in the file. */ - if (H5D__mpio_array_gatherv(local_chunk_array, *local_chunk_array_num_entries, sizeof(H5D_filtered_collective_io_info_t), - (void **) &shared_chunks_info_array, &shared_chunks_info_array_num_entries, false, 0, - io_info->comm, H5D__cmp_filtered_collective_io_info_entry) < 0) + if (H5D__mpio_array_gatherv(local_chunk_array, *local_chunk_array_num_entries, + sizeof(H5D_filtered_collective_io_info_t), (void **)&shared_chunks_info_array, + &shared_chunks_info_array_num_entries, false, 0, io_info->comm, + H5D__cmp_filtered_collective_io_info_entry) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather array") /* Rank 0 redistributes any shared chunks to new owners as necessary */ if (mpi_rank == 0) { - if (NULL == (send_counts = (int *) H5MM_calloc((size_t) mpi_size * sizeof(int)))) + if (NULL == (send_counts = (int *)H5MM_calloc((size_t)mpi_size * sizeof(int)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate send counts buffer") - if (NULL == (send_displacements = (int *) H5MM_malloc((size_t) mpi_size * sizeof(int)))) + if (NULL == (send_displacements = (int *)H5MM_malloc((size_t)mpi_size * sizeof(int)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate send displacements buffer") - if (NULL == (num_assigned_chunks_array = (size_t *) H5MM_calloc((size_t) mpi_size * sizeof(size_t)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate number of assigned chunks array") + if (NULL == (num_assigned_chunks_array = (size_t *)H5MM_calloc((size_t)mpi_size * sizeof(size_t)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "unable to allocate number of assigned chunks array") for (i = 0; i < shared_chunks_info_array_num_entries;) { H5D_filtered_collective_io_info_t chunk_entry; - haddr_t last_seen_addr = shared_chunks_info_array[i].chunk_states.chunk_current.offset; - size_t set_begin_index = i; - size_t num_writers = 0; - int new_chunk_owner = shared_chunks_info_array[i].owners.original_owner; + haddr_t last_seen_addr = shared_chunks_info_array[i].chunk_states.chunk_current.offset; + size_t set_begin_index = i; + size_t num_writers = 0; + int new_chunk_owner = shared_chunks_info_array[i].owners.original_owner; /* Process each set of duplicate entries caused by another process writing to the same chunk */ do { chunk_entry = shared_chunks_info_array[i]; - send_counts[chunk_entry.owners.original_owner] += (int) sizeof(chunk_entry); + send_counts[chunk_entry.owners.original_owner] += (int)sizeof(chunk_entry); /* The new owner of the chunk is determined by the process * writing to the chunk which currently has the least amount * of chunks assigned to it */ - if (num_assigned_chunks_array[chunk_entry.owners.original_owner] < num_assigned_chunks_array[new_chunk_owner]) + if (num_assigned_chunks_array[chunk_entry.owners.original_owner] < + num_assigned_chunks_array[new_chunk_owner]) new_chunk_owner = chunk_entry.owners.original_owner; num_writers++; - } while (++i < shared_chunks_info_array_num_entries && shared_chunks_info_array[i].chunk_states.chunk_current.offset == last_seen_addr); + } while (++i < shared_chunks_info_array_num_entries && + shared_chunks_info_array[i].chunk_states.chunk_current.offset == last_seen_addr); /* Set all of the chunk entries' "new_owner" fields */ for (; set_begin_index < i; set_begin_index++) { shared_chunks_info_array[set_begin_index].owners.new_owner = new_chunk_owner; - shared_chunks_info_array[set_begin_index].num_writers = num_writers; + shared_chunks_info_array[set_begin_index].num_writers = num_writers; } /* end for */ num_assigned_chunks_array[new_chunk_owner]++; @@ -2807,19 +2871,22 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty /* Sort the new list in order of previous owner so that each original owner of a chunk * entry gets that entry back, with the possibly newly-modified "new_owner" field */ - if(shared_chunks_info_array_num_entries > 1) + if (shared_chunks_info_array_num_entries > 1) HDqsort(shared_chunks_info_array, shared_chunks_info_array_num_entries, - sizeof(H5D_filtered_collective_io_info_t), H5D__cmp_filtered_collective_io_info_entry_owner); + sizeof(H5D_filtered_collective_io_info_t), + H5D__cmp_filtered_collective_io_info_entry_owner); send_displacements[0] = 0; - for (i = 1; i < (size_t) mpi_size; i++) + for (i = 1; i < (size_t)mpi_size; i++) send_displacements[i] = send_displacements[i - 1] + send_counts[i - 1]; } /* end if */ /* Scatter the segments of the list back to each process */ - H5_CHECKED_ASSIGN(scatter_recvcount_int, int, *local_chunk_array_num_entries * sizeof(H5D_filtered_collective_io_info_t), size_t); - if (MPI_SUCCESS != (mpi_code = MPI_Scatterv(shared_chunks_info_array, send_counts, send_displacements, - MPI_BYTE, local_chunk_array, scatter_recvcount_int, MPI_BYTE, 0, io_info->comm))) + H5_CHECKED_ASSIGN(scatter_recvcount_int, int, + *local_chunk_array_num_entries * sizeof(H5D_filtered_collective_io_info_t), size_t); + if (MPI_SUCCESS != + (mpi_code = MPI_Scatterv(shared_chunks_info_array, send_counts, send_displacements, MPI_BYTE, + local_chunk_array, scatter_recvcount_int, MPI_BYTE, 0, io_info->comm))) HMPI_GOTO_ERROR(FAIL, "unable to scatter shared chunks info buffer", mpi_code) if (shared_chunks_info_array) { @@ -2833,7 +2900,8 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty * chunks it is assigned, in order to avoid potential deadlocking issues. */ if (*local_chunk_array_num_entries) - if (NULL == (mod_data = (unsigned char **) H5MM_malloc(*local_chunk_array_num_entries * sizeof(unsigned char *)))) + if (NULL == (mod_data = (unsigned char **)H5MM_malloc(*local_chunk_array_num_entries * + sizeof(unsigned char *)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate modification data buffer array") for (i = 0, last_assigned_idx = 0; i < *local_chunk_array_num_entries; i++) { @@ -2841,50 +2909,54 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty if (mpi_rank != chunk_entry->owners.new_owner) { H5D_chunk_info_t *chunk_info = NULL; - unsigned char *mod_data_p = NULL; + unsigned char * mod_data_p = NULL; hsize_t iter_nelmts; size_t mod_data_size; /* Look up the chunk and get its file and memory dataspaces */ - if(NULL == (chunk_info = (H5D_chunk_info_t *) H5SL_search(fm->sel_chunks, &chunk_entry->index))) + if (NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_entry->index))) HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't locate chunk in skip list") /* Determine size of serialized chunk file dataspace, plus the size of * the data being written */ - if(H5S_encode(chunk_info->fspace, &mod_data_p, &mod_data_size) < 0) + if (H5S_encode(chunk_info->fspace, &mod_data_p, &mod_data_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "unable to get encoded dataspace size") iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace); H5_CHECK_OVERFLOW(iter_nelmts, hsize_t, size_t); - mod_data_size += (size_t) iter_nelmts * type_info->src_type_size; + mod_data_size += (size_t)iter_nelmts * type_info->src_type_size; - if(NULL == (mod_data[num_send_requests] = (unsigned char *) H5MM_malloc(mod_data_size))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk modification send buffer") + if (NULL == (mod_data[num_send_requests] = (unsigned char *)H5MM_malloc(mod_data_size))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "couldn't allocate chunk modification send buffer") /* Serialize the chunk's file dataspace into the buffer */ mod_data_p = mod_data[num_send_requests]; - if(H5S_encode(chunk_info->fspace, &mod_data_p, &mod_data_size) < 0) + if (H5S_encode(chunk_info->fspace, &mod_data_p, &mod_data_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "unable to encode dataspace") /* Initialize iterator for memory selection */ - if(H5S_select_iter_init(mem_iter, chunk_info->mspace, type_info->src_type_size, 0) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") + if (H5S_select_iter_init(mem_iter, chunk_info->mspace, type_info->src_type_size, 0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to initialize memory selection information") mem_iter_init = TRUE; /* Collect the modification data into the buffer */ - if(0 == H5D__gather_mem(io_info->u.wbuf, mem_iter, (size_t)iter_nelmts, mod_data_p)) + if (0 == H5D__gather_mem(io_info->u.wbuf, mem_iter, (size_t)iter_nelmts, mod_data_p)) HGOTO_ERROR(H5E_IO, H5E_CANTGATHER, FAIL, "couldn't gather from write buffer") /* Send modification data to new owner */ H5_CHECK_OVERFLOW(mod_data_size, size_t, int) H5_CHECK_OVERFLOW(chunk_entry->index, hsize_t, int) - if(MPI_SUCCESS != (mpi_code = MPI_Isend(mod_data[num_send_requests], (int) mod_data_size, MPI_BYTE, - chunk_entry->owners.new_owner, (int) chunk_entry->index, io_info->comm, &send_requests[num_send_requests]))) + if (MPI_SUCCESS != + (mpi_code = MPI_Isend(mod_data[num_send_requests], (int)mod_data_size, MPI_BYTE, + chunk_entry->owners.new_owner, (int)chunk_entry->index, io_info->comm, + &send_requests[num_send_requests]))) HMPI_GOTO_ERROR(FAIL, "MPI_Isend failed", mpi_code) - if(mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) + if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release memory selection iterator") mem_iter_init = FALSE; @@ -2897,11 +2969,14 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty MPI_Status status; size_t j; - chunk_entry->async_info.num_receive_requests = (int) chunk_entry->num_writers - 1; - if (NULL == (chunk_entry->async_info.receive_requests_array = (MPI_Request *) H5MM_malloc((size_t) chunk_entry->async_info.num_receive_requests * sizeof(MPI_Request)))) + chunk_entry->async_info.num_receive_requests = (int)chunk_entry->num_writers - 1; + if (NULL == (chunk_entry->async_info.receive_requests_array = (MPI_Request *)H5MM_malloc( + (size_t)chunk_entry->async_info.num_receive_requests * sizeof(MPI_Request)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate async requests array") - if (NULL == (chunk_entry->async_info.receive_buffer_array = (unsigned char **) H5MM_malloc((size_t) chunk_entry->async_info.num_receive_requests * sizeof(unsigned char *)))) + if (NULL == + (chunk_entry->async_info.receive_buffer_array = (unsigned char **)H5MM_malloc( + (size_t)chunk_entry->async_info.num_receive_requests * sizeof(unsigned char *)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate async receive buffers") for (j = 0; j < chunk_entry->num_writers - 1; j++) { @@ -2911,35 +2986,39 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty * from the receive queue in the process and allocating that much memory * for the asynchronous receive */ - if (MPI_SUCCESS != (mpi_code = MPI_Mprobe(MPI_ANY_SOURCE, (int) chunk_entry->index, io_info->comm, &message, &status))) + if (MPI_SUCCESS != (mpi_code = MPI_Mprobe(MPI_ANY_SOURCE, (int)chunk_entry->index, + io_info->comm, &message, &status))) HMPI_GOTO_ERROR(FAIL, "MPI_Mprobe failed", mpi_code) if (MPI_SUCCESS != (mpi_code = MPI_Get_count(&status, MPI_BYTE, &count))) HMPI_GOTO_ERROR(FAIL, "MPI_Get_count failed", mpi_code) HDassert(count >= 0); - if (NULL == (chunk_entry->async_info.receive_buffer_array[j] = (unsigned char *) H5MM_malloc((size_t) count * sizeof(char *)))) - HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate modification data receive buffer") - - if (MPI_SUCCESS != (mpi_code = MPI_Imrecv(chunk_entry->async_info.receive_buffer_array[j], count, MPI_BYTE, - &message, &chunk_entry->async_info.receive_requests_array[j]))) + if (NULL == (chunk_entry->async_info.receive_buffer_array[j] = + (unsigned char *)H5MM_malloc((size_t)count * sizeof(char *)))) + HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, + "unable to allocate modification data receive buffer") + + if (MPI_SUCCESS != (mpi_code = MPI_Imrecv( + chunk_entry->async_info.receive_buffer_array[j], count, MPI_BYTE, + &message, &chunk_entry->async_info.receive_requests_array[j]))) HMPI_GOTO_ERROR(FAIL, "MPI_Imrecv failed", mpi_code) } /* end for */ - } /* end if */ + } /* end if */ local_chunk_array[last_assigned_idx++] = local_chunk_array[i]; } /* end else */ - } /* end for */ + } /* end for */ *local_chunk_array_num_entries = last_assigned_idx; /* Wait for all async send requests to complete before returning */ if (num_send_requests) { - if (NULL == (send_statuses = (MPI_Status *) H5MM_malloc(num_send_requests * sizeof(MPI_Status)))) + if (NULL == (send_statuses = (MPI_Status *)H5MM_malloc(num_send_requests * sizeof(MPI_Status)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate send statuses buffer") H5_CHECK_OVERFLOW(num_send_requests, size_t, int); - if (MPI_SUCCESS != (mpi_code = MPI_Waitall((int) num_send_requests, send_requests, send_statuses))) + if (MPI_SUCCESS != (mpi_code = MPI_Waitall((int)num_send_requests, send_requests, send_statuses))) HMPI_GOTO_ERROR(FAIL, "MPI_Waitall failed", mpi_code) } /* end if */ @@ -2975,7 +3054,6 @@ done: } /* end H5D__chunk_redistribute_shared_chunks() */ #endif - /*------------------------------------------------------------------------- * Function: H5D__mpio_filtered_collective_write_type * @@ -2992,14 +3070,14 @@ done: *------------------------------------------------------------------------- */ static herr_t -H5D__mpio_filtered_collective_write_type(H5D_filtered_collective_io_info_t *chunk_list, - size_t num_entries, MPI_Datatype *new_mem_type, hbool_t *mem_type_derived, - MPI_Datatype *new_file_type, hbool_t *file_type_derived) +H5D__mpio_filtered_collective_write_type(H5D_filtered_collective_io_info_t *chunk_list, size_t num_entries, + MPI_Datatype *new_mem_type, hbool_t *mem_type_derived, + MPI_Datatype *new_file_type, hbool_t *file_type_derived) { - MPI_Aint *write_buf_array = NULL; /* Relative displacements of filtered chunk data buffers */ + MPI_Aint *write_buf_array = NULL; /* Relative displacements of filtered chunk data buffers */ MPI_Aint *file_offset_array = NULL; /* Chunk offsets in the file */ - int *length_array = NULL; /* Filtered Chunk lengths */ - herr_t ret_value = SUCCEED; + int * length_array = NULL; /* Filtered Chunk lengths */ + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -3012,40 +3090,46 @@ H5D__mpio_filtered_collective_write_type(H5D_filtered_collective_io_info_t *chun if (num_entries > 0) { size_t i; int mpi_code; - void *base_buf; + void * base_buf; H5_CHECK_OVERFLOW(num_entries, size_t, int); /* Allocate arrays */ - if (NULL == (length_array = (int *) H5MM_malloc((size_t) num_entries * sizeof(int)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "memory allocation failed for filtered collective write length array") - if (NULL == (write_buf_array = (MPI_Aint *) H5MM_malloc((size_t) num_entries * sizeof(MPI_Aint)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "memory allocation failed for filtered collective write buf length array") - if (NULL == (file_offset_array = (MPI_Aint *) H5MM_malloc((size_t) num_entries * sizeof(MPI_Aint)))) - HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "memory allocation failed for collective write offset array") + if (NULL == (length_array = (int *)H5MM_malloc((size_t)num_entries * sizeof(int)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "memory allocation failed for filtered collective write length array") + if (NULL == (write_buf_array = (MPI_Aint *)H5MM_malloc((size_t)num_entries * sizeof(MPI_Aint)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "memory allocation failed for filtered collective write buf length array") + if (NULL == (file_offset_array = (MPI_Aint *)H5MM_malloc((size_t)num_entries * sizeof(MPI_Aint)))) + HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "memory allocation failed for collective write offset array") /* Ensure the list is sorted in ascending order of offset in the file */ - HDqsort(chunk_list, num_entries, sizeof(H5D_filtered_collective_io_info_t), H5D__cmp_filtered_collective_io_info_entry); + HDqsort(chunk_list, num_entries, sizeof(H5D_filtered_collective_io_info_t), + H5D__cmp_filtered_collective_io_info_entry); base_buf = chunk_list[0].buf; for (i = 0; i < num_entries; i++) { /* Set up the offset in the file, the length of the chunk data, and the relative * displacement of the chunk data write buffer */ - file_offset_array[i] = (MPI_Aint) chunk_list[i].chunk_states.new_chunk.offset; - length_array[i] = (int) chunk_list[i].chunk_states.new_chunk.length; - write_buf_array[i] = (MPI_Aint) chunk_list[i].buf - (MPI_Aint) base_buf; + file_offset_array[i] = (MPI_Aint)chunk_list[i].chunk_states.new_chunk.offset; + length_array[i] = (int)chunk_list[i].chunk_states.new_chunk.length; + write_buf_array[i] = (MPI_Aint)chunk_list[i].buf - (MPI_Aint)base_buf; } /* end for */ /* Create memory MPI type */ - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int) num_entries, length_array, write_buf_array, MPI_BYTE, new_mem_type))) + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)num_entries, length_array, + write_buf_array, MPI_BYTE, new_mem_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) *mem_type_derived = TRUE; if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_mem_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) /* Create file MPI type */ - if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int) num_entries, length_array, file_offset_array, MPI_BYTE, new_file_type))) + if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)num_entries, length_array, + file_offset_array, MPI_BYTE, new_file_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) *file_type_derived = TRUE; if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_file_type))) @@ -3053,17 +3137,16 @@ H5D__mpio_filtered_collective_write_type(H5D_filtered_collective_io_info_t *chun } /* end if */ done: - if(write_buf_array) + if (write_buf_array) H5MM_free(write_buf_array); - if(file_offset_array) + if (file_offset_array) H5MM_free(file_offset_array); - if(length_array) + if (length_array) H5MM_free(length_array); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__mpio_filtered_collective_write_type() */ - /*------------------------------------------------------------------------- * Function: H5D__filtered_collective_chunk_entry_io * @@ -3081,27 +3164,28 @@ done: */ static herr_t H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk_entry, - const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, const H5D_chunk_map_t *fm) + const H5D_io_info_t *io_info, const H5D_type_info_t *type_info, + const H5D_chunk_map_t *fm) { H5D_chunk_info_t *chunk_info = NULL; - H5S_sel_iter_t *mem_iter = NULL; /* Memory iterator for H5D__scatter_mem/H5D__gather_mem */ - H5S_sel_iter_t *file_iter = NULL; - H5Z_EDC_t err_detect; /* Error detection info */ - H5Z_cb_t filter_cb; /* I/O filter callback function */ + H5S_sel_iter_t * mem_iter = NULL; /* Memory iterator for H5D__scatter_mem/H5D__gather_mem */ + H5S_sel_iter_t * file_iter = NULL; + H5Z_EDC_t err_detect; /* Error detection info */ + H5Z_cb_t filter_cb; /* I/O filter callback function */ unsigned filter_mask = 0; - hsize_t iter_nelmts; /* Number of points to iterate over for the chunk IO operation */ + hsize_t iter_nelmts; /* Number of points to iterate over for the chunk IO operation */ hssize_t extent_npoints; hsize_t true_chunk_size; - hbool_t mem_iter_init = FALSE; + hbool_t mem_iter_init = FALSE; hbool_t file_iter_init = FALSE; size_t buf_size; size_t i; - H5S_t *dataspace = NULL; /* Other process' dataspace for the chunk */ - void *tmp_gath_buf = NULL; /* Temporary gather buffer to gather into from application buffer + H5S_t * dataspace = NULL; /* Other process' dataspace for the chunk */ + void * tmp_gath_buf = NULL; /* Temporary gather buffer to gather into from application buffer before scattering out to the chunk data buffer (when writing data), or vice versa (when reading data) */ - int mpi_code; - herr_t ret_value = SUCCEED; + int mpi_code; + herr_t ret_value = SUCCEED; FUNC_ENTER_STATIC @@ -3111,18 +3195,18 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk HDassert(fm); /* Retrieve filter settings from API context */ - if(H5CX_get_err_detect(&err_detect) < 0) + if (H5CX_get_err_detect(&err_detect) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get error detection info") - if(H5CX_get_filter_cb(&filter_cb) < 0) + if (H5CX_get_filter_cb(&filter_cb) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get I/O filter callback function") /* Look up the chunk and get its file and memory dataspaces */ - if (NULL == (chunk_info = (H5D_chunk_info_t *) H5SL_search(fm->sel_chunks, &chunk_entry->index))) + if (NULL == (chunk_info = (H5D_chunk_info_t *)H5SL_search(fm->sel_chunks, &chunk_entry->index))) HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, FAIL, "can't locate chunk in skip list") if ((extent_npoints = H5S_GET_EXTENT_NPOINTS(chunk_info->fspace)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid") - true_chunk_size = (hsize_t) extent_npoints * type_info->src_type_size; + true_chunk_size = (hsize_t)extent_npoints * type_info->src_type_size; /* If the size of the filtered chunk is larger than the number of points in the * chunk file space extent times the datatype size, allocate enough space to hold the @@ -3137,7 +3221,7 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk /* If this is not a full chunk overwrite or this is a read operation, the chunk must be * read from the file and unfiltered. */ - if(!chunk_entry->full_overwrite || io_info->op_type == H5D_IO_OP_READ) { + if (!chunk_entry->full_overwrite || io_info->op_type == H5D_IO_OP_READ) { H5FD_mpio_xfer_t xfer_mode; /* Parallel transfer for this request */ chunk_entry->chunk_states.new_chunk.length = chunk_entry->chunk_states.chunk_current.length; @@ -3147,24 +3231,25 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk * this should be refactored to use collective chunk reads - JTH */ /* Get the original state of parallel I/O transfer mode */ - if(H5CX_get_io_xfer_mode(&xfer_mode) < 0) + if (H5CX_get_io_xfer_mode(&xfer_mode) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode") /* Change the xfer_mode to independent for handling the I/O */ - if(H5CX_set_io_xfer_mode(H5FD_MPIO_INDEPENDENT) < 0) + if (H5CX_set_io_xfer_mode(H5FD_MPIO_INDEPENDENT) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O transfer mode") - if(H5F_block_read(io_info->dset->oloc.file, H5FD_MEM_DRAW, chunk_entry->chunk_states.chunk_current.offset, - chunk_entry->chunk_states.new_chunk.length, chunk_entry->buf) < 0) + if (H5F_block_read(io_info->dset->oloc.file, H5FD_MEM_DRAW, + chunk_entry->chunk_states.chunk_current.offset, + chunk_entry->chunk_states.new_chunk.length, chunk_entry->buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to read raw data chunk") /* Return to the original I/O transfer mode setting */ - if(H5CX_set_io_xfer_mode(xfer_mode) < 0) + if (H5CX_set_io_xfer_mode(xfer_mode) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O transfer mode") - if(H5Z_pipeline(&io_info->dset->shared->dcpl_cache.pline, H5Z_FLAG_REVERSE, - &filter_mask, err_detect, filter_cb, (size_t *)&chunk_entry->chunk_states.new_chunk.length, - &buf_size, &chunk_entry->buf) < 0) + if (H5Z_pipeline(&io_info->dset->shared->dcpl_cache.pline, H5Z_FLAG_REVERSE, &filter_mask, err_detect, + filter_cb, (size_t *)&chunk_entry->chunk_states.new_chunk.length, &buf_size, + &chunk_entry->buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFILTER, FAIL, "couldn't unfilter chunk for modifying") } /* end if */ else { @@ -3172,10 +3257,10 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk } /* end else */ /* Initialize iterator for memory selection */ - if (NULL == (mem_iter = (H5S_sel_iter_t *) H5MM_malloc(sizeof(H5S_sel_iter_t)))) + if (NULL == (mem_iter = (H5S_sel_iter_t *)H5MM_malloc(sizeof(H5S_sel_iter_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate memory iterator") - if(H5S_select_iter_init(mem_iter, chunk_info->mspace, type_info->src_type_size, 0) < 0) + if (H5S_select_iter_init(mem_iter, chunk_info->mspace, type_info->src_type_size, 0) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") mem_iter_init = TRUE; @@ -3185,26 +3270,27 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk * from the current process, then apply any modifications from other processes. Finally, * filter the newly-updated chunk. */ - switch(io_info->op_type) { + switch (io_info->op_type) { case H5D_IO_OP_READ: - if(NULL == (file_iter = (H5S_sel_iter_t *) H5MM_malloc(sizeof(H5S_sel_iter_t)))) + if (NULL == (file_iter = (H5S_sel_iter_t *)H5MM_malloc(sizeof(H5S_sel_iter_t)))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate file iterator") - if(H5S_select_iter_init(file_iter, chunk_info->fspace, type_info->src_type_size, 0) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") + if (H5S_select_iter_init(file_iter, chunk_info->fspace, type_info->src_type_size, 0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to initialize memory selection information") file_iter_init = TRUE; iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->fspace); - if(NULL == (tmp_gath_buf = H5MM_malloc(iter_nelmts * type_info->src_type_size))) + if (NULL == (tmp_gath_buf = H5MM_malloc(iter_nelmts * type_info->src_type_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate temporary gather buffer") - if(!H5D__gather_mem(chunk_entry->buf, file_iter, (size_t) iter_nelmts, tmp_gath_buf)) + if (!H5D__gather_mem(chunk_entry->buf, file_iter, (size_t)iter_nelmts, tmp_gath_buf)) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "couldn't gather from chunk buffer") iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace); - if(H5D__scatter_mem(tmp_gath_buf, mem_iter, (size_t) iter_nelmts, io_info->u.rbuf) < 0) + if (H5D__scatter_mem(tmp_gath_buf, mem_iter, (size_t)iter_nelmts, io_info->u.rbuf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to read buffer") break; @@ -3212,20 +3298,21 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk case H5D_IO_OP_WRITE: iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace); - if(NULL == (tmp_gath_buf = H5MM_malloc(iter_nelmts * type_info->src_type_size))) + if (NULL == (tmp_gath_buf = H5MM_malloc(iter_nelmts * type_info->src_type_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate temporary gather buffer") /* Gather modification data from the application write buffer into a temporary buffer */ - if(0 == H5D__gather_mem(io_info->u.wbuf, mem_iter, (size_t) iter_nelmts, tmp_gath_buf)) + if (0 == H5D__gather_mem(io_info->u.wbuf, mem_iter, (size_t)iter_nelmts, tmp_gath_buf)) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "couldn't gather from write buffer") - if(H5S_SELECT_ITER_RELEASE(mem_iter) < 0) + if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") mem_iter_init = FALSE; /* Initialize iterator for file selection */ - if(H5S_select_iter_init(mem_iter, chunk_info->fspace, type_info->dst_type_size, 0) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information") + if (H5S_select_iter_init(mem_iter, chunk_info->fspace, type_info->dst_type_size, 0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to initialize file selection information") mem_iter_init = TRUE; iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->fspace); @@ -3233,43 +3320,45 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk /* Scatter the owner's modification data into the chunk data buffer according to * the file space. */ - if(H5D__scatter_mem(tmp_gath_buf, mem_iter, (size_t) iter_nelmts, chunk_entry->buf) < 0) + if (H5D__scatter_mem(tmp_gath_buf, mem_iter, (size_t)iter_nelmts, chunk_entry->buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to chunk data buffer") - if(H5S_SELECT_ITER_RELEASE(mem_iter) < 0) + if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") mem_iter_init = FALSE; - if(MPI_SUCCESS != (mpi_code = MPI_Waitall(chunk_entry->async_info.num_receive_requests, - chunk_entry->async_info.receive_requests_array, MPI_STATUSES_IGNORE))) + if (MPI_SUCCESS != + (mpi_code = MPI_Waitall(chunk_entry->async_info.num_receive_requests, + chunk_entry->async_info.receive_requests_array, MPI_STATUSES_IGNORE))) HMPI_GOTO_ERROR(FAIL, "MPI_Waitall failed", mpi_code) /* For each asynchronous receive call previously posted, receive the chunk modification * buffer from another rank and update the chunk data */ - for(i = 0; i < (size_t) chunk_entry->async_info.num_receive_requests; i++) { + for (i = 0; i < (size_t)chunk_entry->async_info.num_receive_requests; i++) { const unsigned char *mod_data_p; /* Decode the process' chunk file dataspace */ mod_data_p = chunk_entry->async_info.receive_buffer_array[i]; - if(NULL == (dataspace = H5S_decode(&mod_data_p))) + if (NULL == (dataspace = H5S_decode(&mod_data_p))) HGOTO_ERROR(H5E_DATASET, H5E_CANTDECODE, FAIL, "unable to decode dataspace") - if(H5S_select_iter_init(mem_iter, dataspace, type_info->dst_type_size, 0) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information") + if (H5S_select_iter_init(mem_iter, dataspace, type_info->dst_type_size, 0) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, + "unable to initialize memory selection information") mem_iter_init = TRUE; iter_nelmts = H5S_GET_SELECT_NPOINTS(dataspace); /* Update the chunk data with the received modification data */ - if(H5D__scatter_mem(mod_data_p, mem_iter, (size_t) iter_nelmts, chunk_entry->buf) < 0) + if (H5D__scatter_mem(mod_data_p, mem_iter, (size_t)iter_nelmts, chunk_entry->buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't scatter to write buffer") - if(H5S_SELECT_ITER_RELEASE(mem_iter) < 0) + if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator") mem_iter_init = FALSE; - if(dataspace) { - if(H5S_close(dataspace) < 0) + if (dataspace) { + if (H5S_close(dataspace) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't close dataspace") dataspace = NULL; } @@ -3277,14 +3366,14 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk } /* end for */ /* Filter the chunk */ - if(H5Z_pipeline(&io_info->dset->shared->dcpl_cache.pline, 0, &filter_mask, - err_detect, filter_cb, (size_t *)&chunk_entry->chunk_states.new_chunk.length, - &buf_size, &chunk_entry->buf) < 0) + if (H5Z_pipeline(&io_info->dset->shared->dcpl_cache.pline, 0, &filter_mask, err_detect, filter_cb, + (size_t *)&chunk_entry->chunk_states.new_chunk.length, &buf_size, + &chunk_entry->buf) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "output pipeline failed") #if H5_SIZEOF_SIZE_T > 4 /* Check for the chunk expanding too much to encode in a 32-bit value */ - if (chunk_entry->chunk_states.new_chunk.length > ((size_t) 0xffffffff)) + if (chunk_entry->chunk_states.new_chunk.length > ((size_t)0xffffffff)) HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length") #endif break; @@ -3314,5 +3403,4 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__filtered_collective_chunk_entry_io() */ -#endif /* H5_HAVE_PARALLEL */ - +#endif /* H5_HAVE_PARALLEL */ |