1449 lines
61 KiB
C
1449 lines
61 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the COPYING file, which can be found at the root of the source code *
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* distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. *
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* If you do not have access to either file, you may request a copy from *
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* help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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/*
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* Programmer: rky 980813
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*
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* Purpose: Create MPI data types for HDF5 selections.
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*
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*/
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/****************/
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/* Module Setup */
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/****************/
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#include "H5Smodule.h" /* This source code file is part of the H5S module */
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/***********/
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/* Headers */
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/***********/
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#include "H5private.h" /* Generic Functions */
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#include "H5Dprivate.h" /* Datasets */
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#include "H5Eprivate.h" /* Error handling */
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#include "H5FLprivate.h" /* Free Lists */
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#include "H5MMprivate.h" /* Memory management */
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#include "H5Spkg.h" /* Dataspaces */
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#include "H5VMprivate.h" /* Vector and array functions */
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#ifdef H5_HAVE_PARALLEL
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/****************/
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/* Local Macros */
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/****************/
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#define H5S_MPIO_INITIAL_ALLOC_COUNT 256
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/*******************/
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/* Local Variables */
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/*******************/
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/******************/
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/* Local Typedefs */
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/******************/
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/* Node in linked list of MPI data types created during traversal of irregular hyperslab selection */
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typedef struct H5S_mpio_mpitype_node_t {
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MPI_Datatype type; /* MPI Datatype */
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struct H5S_mpio_mpitype_node_t *next; /* Pointer to next node in list */
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} H5S_mpio_mpitype_node_t;
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/* List to track MPI data types generated during traversal of irregular hyperslab selection */
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typedef struct H5S_mpio_mpitype_list_t {
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H5S_mpio_mpitype_node_t *head; /* Pointer to head of list */
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H5S_mpio_mpitype_node_t *tail; /* Pointer to tail of list */
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} H5S_mpio_mpitype_list_t;
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/********************/
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/* Local Prototypes */
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/********************/
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static herr_t H5S__mpio_all_type(const H5S_t *space, size_t elmt_size,
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MPI_Datatype *new_type, int *count, hbool_t *is_derived_type);
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static herr_t H5S__mpio_none_type(MPI_Datatype *new_type, int *count,
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hbool_t *is_derived_type);
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static herr_t H5S__mpio_create_point_datatype(size_t elmt_size, hsize_t num_points,
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MPI_Aint *disp, MPI_Datatype *new_type);
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static herr_t H5S__mpio_point_type(const H5S_t *space, size_t elmt_size,
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MPI_Datatype *new_type, int *count, hbool_t *is_derived_type,
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hbool_t do_permute, hsize_t **permute_map, hbool_t *is_permuted);
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static herr_t H5S__mpio_permute_type(const H5S_t *space, size_t elmt_size,
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hsize_t **permute_map, MPI_Datatype *new_type, int *count,
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hbool_t *is_derived_type);
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static herr_t H5S__mpio_reg_hyper_type(const H5S_t *space, size_t elmt_size,
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MPI_Datatype *new_type, int *count, hbool_t *is_derived_type);
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static herr_t H5S__mpio_span_hyper_type(const H5S_t *space, size_t elmt_size,
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MPI_Datatype *new_type, int *count, hbool_t *is_derived_type);
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static herr_t H5S__release_datatype(H5S_mpio_mpitype_list_t *type_list);
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static herr_t H5S__obtain_datatype(H5S_hyper_span_info_t *spans, const hsize_t *down,
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size_t elmt_size, const MPI_Datatype *elmt_type, MPI_Datatype *span_type,
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H5S_mpio_mpitype_list_t *type_list, unsigned op_info_i, uint64_t op_gen);
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/*****************************/
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/* Library Private Variables */
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/*****************************/
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/*********************/
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/* Package Variables */
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/*********************/
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/* Declare a free list to manage the H5S_mpio_mpitype_node_t struct */
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H5FL_DEFINE_STATIC(H5S_mpio_mpitype_node_t);
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/*-------------------------------------------------------------------------
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* Function: H5S__mpio_all_type
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*
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* Purpose: Translate an HDF5 "all" selection into an MPI type.
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*
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* Return: Non-negative on success, negative on failure.
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*
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* Outputs: *new_type the MPI type corresponding to the selection
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* *count how many objects of the new_type in selection
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* (useful if this is the buffer type for xfer)
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* *is_derived_type 0 if MPI primitive type, 1 if derived
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*
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* Programmer: rky 980813
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*
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*-------------------------------------------------------------------------
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*/
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static herr_t
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H5S__mpio_all_type(const H5S_t *space, size_t elmt_size,
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MPI_Datatype *new_type, int *count, hbool_t *is_derived_type)
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{
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hsize_t total_bytes;
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hssize_t snelmts; /* Total number of elmts (signed) */
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hsize_t nelmts; /* Total number of elmts */
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hsize_t bigio_count; /* Transition point to create derived type */
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herr_t ret_value = SUCCEED; /* Return value */
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FUNC_ENTER_STATIC
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/* Check args */
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HDassert(space);
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/* Just treat the entire extent as a block of bytes */
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if((snelmts = (hssize_t)H5S_GET_EXTENT_NPOINTS(space)) < 0)
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HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection")
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H5_CHECKED_ASSIGN(nelmts, hsize_t, snelmts, hssize_t);
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total_bytes = (hsize_t)elmt_size * nelmts;
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bigio_count = H5_mpi_get_bigio_count();
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/* Verify that the size can be expressed as a 32 bit integer */
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if(bigio_count >= total_bytes) {
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/* fill in the return values */
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*new_type = MPI_BYTE;
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H5_CHECKED_ASSIGN(*count, int, total_bytes, hsize_t);
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*is_derived_type = FALSE;
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}
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else {
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/* Create a LARGE derived datatype for this transfer */
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if(H5_mpio_create_large_type(total_bytes, 0, MPI_BYTE, new_type) < 0)
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HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create a large datatype from the all selection")
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*count = 1;
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*is_derived_type = TRUE;
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}
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done:
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FUNC_LEAVE_NOAPI(ret_value)
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} /* H5S__mpio_all_type() */
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/*-------------------------------------------------------------------------
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* Function: H5S__mpio_none_type
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*
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* Purpose: Translate an HDF5 "none" selection into an MPI type.
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*
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* Return: Non-negative on success, negative on failure.
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*
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* Outputs: *new_type the MPI type corresponding to the selection
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* *count how many objects of the new_type in selection
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* (useful if this is the buffer type for xfer)
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* *is_derived_type 0 if MPI primitive type, 1 if derived
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*
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* Programmer: Quincey Koziol, October 29, 2002
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*
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*-------------------------------------------------------------------------
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*/
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static herr_t
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H5S__mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_type)
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{
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FUNC_ENTER_STATIC_NOERR
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/* fill in the return values */
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*new_type = MPI_BYTE;
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*count = 0;
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*is_derived_type = FALSE;
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FUNC_LEAVE_NOAPI(SUCCEED)
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} /* H5S__mpio_none_type() */
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/*-------------------------------------------------------------------------
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* Function: H5S__mpio_create_point_datatype
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*
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* Purpose: Create a derived datatype for point selections.
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*
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* Return: Non-negative on success, negative on failure.
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*
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* Outputs: *new_type the MPI type corresponding to the selection
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*
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* Programmer: Mohamad Chaarawi
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*
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*-------------------------------------------------------------------------
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*/
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static herr_t
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H5S__mpio_create_point_datatype(size_t elmt_size, hsize_t num_points,
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MPI_Aint *disp, MPI_Datatype *new_type)
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{
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MPI_Datatype elmt_type; /* MPI datatype for individual element */
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hbool_t elmt_type_created = FALSE; /* Whether the element MPI datatype was created */
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int *inner_blocks = NULL; /* Arrays for MPI datatypes when "large" datatype needed */
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MPI_Aint *inner_disps = NULL;
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MPI_Datatype *inner_types = NULL;
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#if MPI_VERSION < 3
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int *blocks = NULL; /* Array of block sizes for MPI hindexed create call */
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hsize_t u; /* Local index variable */
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#endif
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hsize_t bigio_count; /* Transition point to create derived type */
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int mpi_code; /* MPI error code */
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herr_t ret_value = SUCCEED; /* Return value */
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FUNC_ENTER_STATIC
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/* Create an MPI datatype for an element */
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if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)elmt_size, MPI_BYTE, &elmt_type)))
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HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code)
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elmt_type_created = TRUE;
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bigio_count = H5_mpi_get_bigio_count();
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/* Check whether standard or BIGIO processing will be employeed */
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if(bigio_count >= num_points) {
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#if MPI_VERSION >= 3
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/* Create an MPI datatype for the whole point selection */
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if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed_block((int)num_points, 1, disp, elmt_type, new_type)))
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HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_indexed_block failed", mpi_code)
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#else
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/* Allocate block sizes for MPI datatype call */
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if(NULL == (blocks = (int *)H5MM_malloc(sizeof(int) * num_points)))
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HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks")
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for(u = 0; u < num_points; u++)
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blocks[u] = 1;
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/* Create an MPI datatype for the whole point selection */
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if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)num_points, blocks, disp, elmt_type, new_type)))
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HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
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#endif
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/* Commit MPI datatype for later use */
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if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type)))
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HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
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}
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else {
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/* use LARGE_DATATYPE::
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* We'll create an hindexed_block type for every 2G point count and then combine
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* those and any remaining points into a single large datatype.
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*/
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int total_types, i;
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int remaining_points;
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int num_big_types;
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hsize_t leftover;
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/* Calculate how many Big MPI datatypes are needed to represent the buffer */
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num_big_types = (int)(num_points / bigio_count);
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leftover = (hsize_t)num_points - (hsize_t)num_big_types * (hsize_t)bigio_count;
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H5_CHECKED_ASSIGN(remaining_points, int, leftover, hsize_t);
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total_types = (int)(remaining_points) ? (num_big_types + 1) : num_big_types;
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/* Allocate array if MPI derived types needed */
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if(NULL == (inner_types = (MPI_Datatype *)H5MM_malloc((sizeof(MPI_Datatype) * (size_t)total_types))))
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HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks")
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if(NULL == (inner_blocks = (int *)H5MM_malloc(sizeof(int) * (size_t)total_types)))
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HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks")
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if(NULL == (inner_disps = (MPI_Aint *)H5MM_malloc(sizeof(MPI_Aint) * (size_t)total_types)))
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HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks")
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#if MPI_VERSION < 3
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/* Allocate block sizes for MPI datatype call */
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if(NULL == (blocks = (int *)H5MM_malloc(sizeof(int) * bigio_count)))
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HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks")
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for(u = 0; u < bigio_count; u++)
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blocks[u] = 1;
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#endif
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for(i = 0; i < num_big_types; i++) {
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#if MPI_VERSION >= 3
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if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed_block((int)bigio_count,
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1, &disp[(hsize_t)i*bigio_count], elmt_type, &inner_types[i])))
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HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code);
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#else
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if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)bigio_count,
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blocks, &disp[i*bigio_count], elmt_type, &inner_types[i])))
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HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
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#endif
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inner_blocks[i] = 1;
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inner_disps[i] = 0;
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} /* end for*/
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if(remaining_points) {
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#if MPI_VERSION >= 3
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if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed_block(remaining_points,
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1, &disp[(hsize_t)num_big_types*bigio_count], elmt_type, &inner_types[num_big_types])))
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HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed_block failed", mpi_code);
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#else
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if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)remaining_points,
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blocks, &disp[num_big_types*bigio_count], elmt_type, &inner_types[num_big_types])))
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HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
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#endif
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inner_blocks[num_big_types] = 1;
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inner_disps[num_big_types] = 0;
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}
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if(MPI_SUCCESS != (mpi_code = MPI_Type_create_struct(total_types,
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inner_blocks, inner_disps, inner_types, new_type)))
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HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct", mpi_code);
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for(i = 0; i < total_types; i++)
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MPI_Type_free(&inner_types[i]);
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/* Commit MPI datatype for later use */
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if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type)))
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HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
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} /* end else */
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done:
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if(elmt_type_created)
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MPI_Type_free(&elmt_type);
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#if MPI_VERSION < 3
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if(blocks)
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H5MM_free(blocks);
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#endif
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if(inner_types)
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H5MM_free(inner_types);
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if(inner_blocks)
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H5MM_free(inner_blocks);
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if(inner_disps)
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H5MM_free(inner_disps);
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FUNC_LEAVE_NOAPI(ret_value)
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} /* H5S__mpio_create_point_datatype() */
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/*-------------------------------------------------------------------------
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* Function: H5S__mpio_point_type
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*
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* Purpose: Translate an HDF5 "point" selection into an MPI type.
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* Create a permutation array to handle out-of-order point selections.
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*
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* Return: Non-negative on success, negative on failure.
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*
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* Outputs: *new_type the MPI type corresponding to the selection
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* *count how many objects of the new_type in selection
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* (useful if this is the buffer type for xfer)
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* *is_derived_type 0 if MPI primitive type, 1 if derived
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* *permute_map the permutation of the displacements to create
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* the MPI_Datatype
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* *is_permuted 0 if the displacements are permuted, 1 if not
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*
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* Programmer: Mohamad Chaarawi
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*
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*-------------------------------------------------------------------------
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*/
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static herr_t
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H5S__mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type,
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int *count, hbool_t *is_derived_type, hbool_t do_permute, hsize_t **permute,
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hbool_t *is_permuted)
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{
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MPI_Aint *disp = NULL; /* Datatype displacement for each point*/
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H5S_pnt_node_t *curr = NULL; /* Current point being operated on in from the selection */
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hssize_t snum_points; /* Signed number of elements in selection */
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hsize_t num_points; /* Sumber of points in the selection */
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hsize_t u; /* Local index variable */
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herr_t ret_value = SUCCEED; /* Return value */
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FUNC_ENTER_STATIC
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/* Check args */
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HDassert(space);
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/* Get the total number of points selected */
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if((snum_points = (hssize_t)H5S_GET_SELECT_NPOINTS(space)) < 0)
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HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements selected")
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num_points = (hsize_t)snum_points;
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/* Allocate array for element displacements */
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if(NULL == (disp = (MPI_Aint *)H5MM_malloc(sizeof(MPI_Aint) * num_points)))
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HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of displacements")
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/* Allocate array for element permutation - returned to caller */
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if(do_permute)
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if(NULL == (*permute = (hsize_t *)H5MM_malloc(sizeof(hsize_t) * num_points)))
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HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate permutation array")
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/* Iterate through list of elements */
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curr = space->select.sel_info.pnt_lst->head;
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for(u = 0 ; u < num_points ; u++) {
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/* Calculate the displacement of the current point */
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hsize_t disp_tmp = H5VM_array_offset(space->extent.rank, space->extent.size, curr->pnt);
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if(disp_tmp > LONG_MAX) /* Maximum value of type long */
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HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "disp overflow")
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disp[u] = (MPI_Aint)disp_tmp;
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disp[u] *= (MPI_Aint)elmt_size;
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/* This is a File Space used to set the file view, so adjust the displacements
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||
* to have them monotonically non-decreasing.
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* Generate the permutation array by indicating at each point being selected,
|
||
* the position it will shifted in the new displacement. Example:
|
||
* Suppose 4 points with corresponding are selected
|
||
* Pt 1: disp=6 ; Pt 2: disp=3 ; Pt 3: disp=0 ; Pt 4: disp=4
|
||
* The permute map to sort the displacements in order will be:
|
||
* point 1: map[0] = L, indicating that this point is not moved (1st point selected)
|
||
* point 2: map[1] = 0, indicating that this point is moved to the first position,
|
||
* since disp_pt1(6) > disp_pt2(3)
|
||
* point 3: map[2] = 0, move to position 0, bec it has the lowest disp between
|
||
* the points selected so far.
|
||
* point 4: map[3] = 2, move the 2nd position since point 1 has a higher disp,
|
||
* but points 2 and 3 have lower displacements.
|
||
*/
|
||
if(do_permute) {
|
||
if(u > 0 && disp[u] < disp[u - 1]) {
|
||
hsize_t s = 0, l = u, m = u / 2;
|
||
|
||
*is_permuted = TRUE;
|
||
do {
|
||
if(disp[u] > disp[m])
|
||
s = m + 1;
|
||
else if(disp[u] < disp[m])
|
||
l = m;
|
||
else
|
||
break;
|
||
m = s + ((l - s) / 2);
|
||
} while(s < l);
|
||
|
||
if(m < u) {
|
||
MPI_Aint temp;
|
||
|
||
temp = disp[u];
|
||
HDmemmove(disp + m + 1, disp + m, (u - m) * sizeof(MPI_Aint));
|
||
disp[m] = temp;
|
||
} /* end if */
|
||
(*permute)[u] = m;
|
||
} /* end if */
|
||
else
|
||
(*permute)[u] = num_points;
|
||
} /* end if */
|
||
/* this is a memory space, and no permutation is necessary to create
|
||
the derived datatype */
|
||
else {
|
||
; /* do nothing */
|
||
} /* end else */
|
||
|
||
/* get the next point */
|
||
curr = curr->next;
|
||
} /* end for */
|
||
|
||
/* Create the MPI datatype for the set of element displacements */
|
||
if(H5S__mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create an MPI Datatype from point selection")
|
||
|
||
/* Set values about MPI datatype created */
|
||
*count = 1;
|
||
*is_derived_type = TRUE;
|
||
|
||
done:
|
||
if(NULL != disp)
|
||
H5MM_free(disp);
|
||
|
||
/* Release the permutation buffer, if it wasn't used */
|
||
if(!(*is_permuted) && (*permute)) {
|
||
H5MM_free(*permute);
|
||
*permute = NULL;
|
||
} /* end if */
|
||
|
||
FUNC_LEAVE_NOAPI(ret_value)
|
||
} /* H5S__mpio_point_type() */
|
||
|
||
|
||
/*-------------------------------------------------------------------------
|
||
* Function: H5S__mpio_permute_type
|
||
*
|
||
* Purpose: Translate an HDF5 "all/hyper/point" selection into an MPI type,
|
||
* while applying the permutation map. This function is called if
|
||
* the file space selection is permuted due to out-of-order point
|
||
* selection and so the memory datatype has to be permuted using the
|
||
* permutation map created by the file selection.
|
||
*
|
||
* Note: This routine is called from H5S_mpio_space_type(), which is
|
||
* called first for the file dataspace and creates
|
||
*
|
||
* Return: Non-negative on success, negative on failure.
|
||
*
|
||
* Outputs: *new_type the MPI type corresponding to the selection
|
||
* *count how many objects of the new_type in selection
|
||
* (useful if this is the buffer type for xfer)
|
||
* *is_derived_type 0 if MPI primitive type, 1 if derived
|
||
*
|
||
* Programmer: Mohamad Chaarawi
|
||
*
|
||
*-------------------------------------------------------------------------
|
||
*/
|
||
static herr_t
|
||
H5S__mpio_permute_type(const H5S_t *space, size_t elmt_size, hsize_t **permute,
|
||
MPI_Datatype *new_type, int *count, hbool_t *is_derived_type)
|
||
{
|
||
MPI_Aint *disp = NULL; /* Datatype displacement for each point*/
|
||
H5S_sel_iter_t sel_iter; /* Selection iteration info */
|
||
hbool_t sel_iter_init = FALSE; /* Selection iteration info has been initialized */
|
||
hssize_t snum_points; /* Signed number of elements in selection */
|
||
hsize_t num_points; /* Number of points in the selection */
|
||
size_t max_elem; /* Maximum number of elements allowed in sequences */
|
||
hsize_t u; /* Local index variable */
|
||
herr_t ret_value = SUCCEED; /* Return value */
|
||
|
||
FUNC_ENTER_STATIC
|
||
|
||
/* Check args */
|
||
HDassert(space);
|
||
|
||
/* Get the total number of points selected */
|
||
if((snum_points = (hssize_t)H5S_GET_SELECT_NPOINTS(space)) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements selected")
|
||
num_points = (hsize_t)snum_points;
|
||
|
||
/* Allocate array to store point displacements */
|
||
if(NULL == (disp = (MPI_Aint *)H5MM_malloc(sizeof(MPI_Aint) * num_points)))
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of displacements")
|
||
|
||
/* Initialize selection iterator */
|
||
if(H5S_select_iter_init(&sel_iter, space, elmt_size, 0) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
|
||
sel_iter_init = TRUE; /* Selection iteration info has been initialized */
|
||
|
||
/* Set the number of elements to iterate over */
|
||
H5_CHECKED_ASSIGN(max_elem, size_t, num_points, hsize_t);
|
||
|
||
/* Loop, while elements left in selection */
|
||
u = 0;
|
||
while(max_elem > 0) {
|
||
hsize_t off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */
|
||
size_t len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */
|
||
size_t nelem; /* Number of elements used in sequences */
|
||
size_t nseq; /* Number of sequences generated */
|
||
size_t curr_seq; /* Current sequence being worked on */
|
||
|
||
/* Get the sequences of bytes */
|
||
if(H5S_SELECT_ITER_GET_SEQ_LIST(&sel_iter, (size_t)H5D_IO_VECTOR_SIZE, max_elem, &nseq, &nelem, off, len) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
|
||
|
||
/* Loop, while sequences left to process */
|
||
for(curr_seq = 0; curr_seq < nseq; curr_seq++) {
|
||
hsize_t curr_off; /* Current offset within sequence */
|
||
size_t curr_len; /* Length of bytes left to process in sequence */
|
||
|
||
/* Get the current offset */
|
||
curr_off = off[curr_seq];
|
||
|
||
/* Get the number of bytes in sequence */
|
||
curr_len = len[curr_seq];
|
||
|
||
/* Loop, while bytes left in sequence */
|
||
while(curr_len > 0) {
|
||
/* Set the displacement of the current point */
|
||
if(curr_off > LONG_MAX)
|
||
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "curr_off overflow")
|
||
disp[u] = (MPI_Aint)curr_off;
|
||
|
||
/* This is a memory displacement, so for each point selected,
|
||
* apply the map that was generated by the file selection */
|
||
if((*permute)[u] != num_points) {
|
||
MPI_Aint temp = disp[u];
|
||
|
||
HDmemmove(disp + (*permute)[u] + 1, disp + (*permute)[u],
|
||
(u - (*permute)[u]) * sizeof(MPI_Aint));
|
||
disp[(*permute)[u]] = temp;
|
||
} /* end if */
|
||
|
||
/* Advance to next element */
|
||
u++;
|
||
|
||
/* Increment offset in dataspace */
|
||
curr_off += elmt_size;
|
||
|
||
/* Decrement number of bytes left in sequence */
|
||
curr_len -= elmt_size;
|
||
} /* end while */
|
||
} /* end for */
|
||
|
||
/* Decrement number of elements left to process */
|
||
max_elem -= nelem;
|
||
} /* end while */
|
||
|
||
/* Create the MPI datatype for the set of element displacements */
|
||
if(H5S__mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create an MPI Datatype from point selection")
|
||
|
||
/* Set values about MPI datatype created */
|
||
*count = 1;
|
||
*is_derived_type = TRUE;
|
||
|
||
done:
|
||
/* Release selection iterator */
|
||
if(sel_iter_init)
|
||
if(H5S_SELECT_ITER_RELEASE(&sel_iter) < 0)
|
||
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
|
||
|
||
/* Free memory */
|
||
if(disp)
|
||
H5MM_free(disp);
|
||
if(*permute) {
|
||
H5MM_free(*permute);
|
||
*permute = NULL;
|
||
} /* end if */
|
||
|
||
FUNC_LEAVE_NOAPI(ret_value)
|
||
} /* H5S__mpio_permute_type() */
|
||
|
||
|
||
/*-------------------------------------------------------------------------
|
||
* Function: H5S__mpio_reg_hyper_type
|
||
*
|
||
* Purpose: Translate a regular HDF5 hyperslab selection into an MPI type.
|
||
*
|
||
* Return: Non-negative on success, negative on failure.
|
||
*
|
||
* Outputs: *new_type the MPI type corresponding to the selection
|
||
* *count how many objects of the new_type in selection
|
||
* (useful if this is the buffer type for xfer)
|
||
* *is_derived_type 0 if MPI primitive type, 1 if derived
|
||
*
|
||
* Programmer: rky 980813
|
||
*
|
||
*-------------------------------------------------------------------------
|
||
*/
|
||
static herr_t
|
||
H5S__mpio_reg_hyper_type(const H5S_t *space, size_t elmt_size,
|
||
MPI_Datatype *new_type, int *count, hbool_t *is_derived_type)
|
||
{
|
||
H5S_sel_iter_t sel_iter; /* Selection iteration info */
|
||
hbool_t sel_iter_init = FALSE; /* Selection iteration info has been initialized */
|
||
|
||
struct dim { /* less hassle than malloc/free & ilk */
|
||
hssize_t start;
|
||
hsize_t strid;
|
||
hsize_t block;
|
||
hsize_t xtent;
|
||
hsize_t count;
|
||
} d[H5S_MAX_RANK];
|
||
|
||
hsize_t bigio_count; /* Transition point to create derived type */
|
||
hsize_t offset[H5S_MAX_RANK];
|
||
hsize_t max_xtent[H5S_MAX_RANK];
|
||
H5S_hyper_dim_t *diminfo; /* [rank] */
|
||
unsigned rank;
|
||
MPI_Datatype inner_type, outer_type;
|
||
MPI_Aint extent_len, start_disp, new_extent;
|
||
MPI_Aint lb; /* Needed as an argument for MPI_Type_get_extent */
|
||
unsigned u; /* Local index variable */
|
||
int i; /* Local index variable */
|
||
int mpi_code; /* MPI return code */
|
||
herr_t ret_value = SUCCEED;
|
||
|
||
FUNC_ENTER_STATIC
|
||
|
||
/* Check args */
|
||
HDassert(space);
|
||
HDassert(sizeof(MPI_Aint) >= sizeof(elmt_size));
|
||
|
||
bigio_count = H5_mpi_get_bigio_count();
|
||
/* Initialize selection iterator */
|
||
if(H5S_select_iter_init(&sel_iter, space, elmt_size, 0) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator")
|
||
sel_iter_init = TRUE; /* Selection iteration info has been initialized */
|
||
|
||
/* Abbreviate args */
|
||
diminfo = sel_iter.u.hyp.diminfo;
|
||
HDassert(diminfo);
|
||
|
||
/* Make a local copy of the dimension info so we can operate with them */
|
||
|
||
/* Check if this is a "flattened" regular hyperslab selection */
|
||
if(sel_iter.u.hyp.iter_rank != 0 && sel_iter.u.hyp.iter_rank < space->extent.rank) {
|
||
/* Flattened selection */
|
||
rank = sel_iter.u.hyp.iter_rank;
|
||
#ifdef H5S_DEBUG
|
||
if(H5DEBUG(S))
|
||
HDfprintf(H5DEBUG(S), "%s: Flattened selection\n",FUNC);
|
||
#endif
|
||
for(u = 0; u < rank; ++u) {
|
||
H5_CHECK_OVERFLOW(diminfo[u].start, hsize_t, hssize_t)
|
||
d[u].start = (hssize_t)diminfo[u].start + sel_iter.u.hyp.sel_off[u];
|
||
d[u].strid = diminfo[u].stride;
|
||
d[u].block = diminfo[u].block;
|
||
d[u].count = diminfo[u].count;
|
||
d[u].xtent = sel_iter.u.hyp.size[u];
|
||
|
||
#ifdef H5S_DEBUG
|
||
if(H5DEBUG(S)) {
|
||
HDfprintf(H5DEBUG(S), "%s: start=%Hd stride=%Hu count=%Hu block=%Hu xtent=%Hu",
|
||
FUNC, d[u].start, d[u].strid, d[u].count, d[u].block, d[u].xtent);
|
||
if(u == 0)
|
||
HDfprintf(H5DEBUG(S), " rank=%u\n", rank);
|
||
else
|
||
HDfprintf(H5DEBUG(S), "\n");
|
||
}
|
||
#endif
|
||
|
||
/* Sanity check */
|
||
HDassert(d[u].block > 0);
|
||
HDassert(d[u].count > 0);
|
||
HDassert(d[u].xtent > 0);
|
||
} /* end for */
|
||
} /* end if */
|
||
else {
|
||
/* Non-flattened selection */
|
||
rank = space->extent.rank;
|
||
#ifdef H5S_DEBUG
|
||
if(H5DEBUG(S))
|
||
HDfprintf(H5DEBUG(S),"%s: Non-flattened selection\n",FUNC);
|
||
#endif
|
||
for(u = 0; u < rank; ++u) {
|
||
H5_CHECK_OVERFLOW(diminfo[u].start, hsize_t, hssize_t)
|
||
d[u].start = (hssize_t)diminfo[u].start + space->select.offset[u];
|
||
d[u].strid = diminfo[u].stride;
|
||
d[u].block = diminfo[u].block;
|
||
d[u].count = diminfo[u].count;
|
||
d[u].xtent = space->extent.size[u];
|
||
|
||
#ifdef H5S_DEBUG
|
||
if(H5DEBUG(S)) {
|
||
HDfprintf(H5DEBUG(S), "%s: start=%Hd stride=%Hu count=%Hu block=%Hu xtent=%Hu",
|
||
FUNC, d[u].start, d[u].strid, d[u].count, d[u].block, d[u].xtent);
|
||
if(u == 0)
|
||
HDfprintf(H5DEBUG(S), " rank=%u\n", rank);
|
||
else
|
||
HDfprintf(H5DEBUG(S), "\n");
|
||
}
|
||
#endif
|
||
|
||
/* Sanity check */
|
||
HDassert(d[u].block > 0);
|
||
HDassert(d[u].count > 0);
|
||
HDassert(d[u].xtent > 0);
|
||
} /* end for */
|
||
} /* end else */
|
||
|
||
/**********************************************************************
|
||
Compute array "offset[rank]" which gives the offsets for a multi-
|
||
dimensional array with dimensions "d[i].xtent" (i=0,1,...,rank-1).
|
||
**********************************************************************/
|
||
offset[rank - 1] = 1;
|
||
max_xtent[rank - 1] = d[rank - 1].xtent;
|
||
#ifdef H5S_DEBUG
|
||
if(H5DEBUG(S)) {
|
||
i = ((int)rank) - 1;
|
||
HDfprintf(H5DEBUG(S), " offset[%2d]=%Hu; max_xtent[%2d]=%Hu\n", i, offset[i], i, max_xtent[i]);
|
||
}
|
||
#endif
|
||
for(i = ((int)rank) - 2; i >= 0; --i) {
|
||
offset[i] = offset[i + 1] * d[i + 1].xtent;
|
||
max_xtent[i] = max_xtent[i + 1] * d[i].xtent;
|
||
#ifdef H5S_DEBUG
|
||
if(H5DEBUG(S))
|
||
HDfprintf(H5DEBUG(S), " offset[%2d]=%Hu; max_xtent[%2d]=%Hu\n", i, offset[i], i, max_xtent[i]);
|
||
#endif
|
||
} /* end for */
|
||
|
||
/* Create a type covering the selected hyperslab.
|
||
* Multidimensional dataspaces are stored in row-major order.
|
||
* The type is built from the inside out, going from the
|
||
* fastest-changing (i.e., inner) dimension * to the slowest (outer).
|
||
*/
|
||
|
||
/*******************************************************
|
||
* Construct contig type for inner contig dims:
|
||
*******************************************************/
|
||
#ifdef H5S_DEBUG
|
||
if(H5DEBUG(S)) {
|
||
HDfprintf(H5DEBUG(S), "%s: Making contig type %Zu MPI_BYTEs\n", FUNC, elmt_size);
|
||
for(i = ((int)rank) - 1; i >= 0; --i)
|
||
HDfprintf(H5DEBUG(S), "d[%d].xtent=%Hu \n", i, d[i].xtent);
|
||
}
|
||
#endif
|
||
|
||
/* LARGE_DATATYPE::
|
||
* Check if the number of elements to form the inner type fits into a 32 bit integer.
|
||
* If yes then just create the innertype with MPI_Type_contiguous.
|
||
* Otherwise create a compound datatype by iterating as many times as needed
|
||
* for the innertype to be created.
|
||
*/
|
||
if(bigio_count >= elmt_size) {
|
||
/* Use a single MPI datatype that has a 32 bit size */
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)elmt_size, MPI_BYTE, &inner_type)))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code)
|
||
}
|
||
else
|
||
/* Create the compound datatype for this operation (> 2GB) */
|
||
if(H5_mpio_create_large_type(elmt_size, 0, MPI_BYTE, &inner_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create a large inner datatype in hyper selection")
|
||
|
||
/*******************************************************
|
||
* Construct the type by walking the hyperslab dims
|
||
* from the inside out:
|
||
*******************************************************/
|
||
for(i = ((int)rank) - 1; i >= 0; --i) {
|
||
#ifdef H5S_DEBUG
|
||
if(H5DEBUG(S))
|
||
HDfprintf(H5DEBUG(S), "%s: Dimension i=%d \n"
|
||
"start=%Hd count=%Hu block=%Hu stride=%Hu, xtent=%Hu max_xtent=%d\n",
|
||
FUNC, i, d[i].start, d[i].count, d[i].block, d[i].strid, d[i].xtent, max_xtent[i]);
|
||
#endif
|
||
|
||
#ifdef H5S_DEBUG
|
||
if(H5DEBUG(S))
|
||
HDfprintf(H5DEBUG(S), "%s: i=%d Making vector-type \n", FUNC,i);
|
||
#endif
|
||
/****************************************
|
||
* Build vector type of the selection.
|
||
****************************************/
|
||
if(bigio_count >= d[i].count &&
|
||
bigio_count >= d[i].block && bigio_count >= d[i].strid) {
|
||
/* All the parameters fit into 32 bit integers so create the vector type normally */
|
||
mpi_code = MPI_Type_vector((int)(d[i].count), /* count */
|
||
(int)(d[i].block), /* blocklength */
|
||
(int)(d[i].strid), /* stride */
|
||
inner_type, /* old type */
|
||
&outer_type); /* new type */
|
||
|
||
MPI_Type_free(&inner_type);
|
||
if(mpi_code != MPI_SUCCESS)
|
||
HMPI_GOTO_ERROR(FAIL, "couldn't create MPI vector type", mpi_code)
|
||
}
|
||
else {
|
||
/* Things get a bit more complicated and require LARGE_DATATYPE processing
|
||
* There are two MPI datatypes that need to be created:
|
||
* 1) an internal contiguous block; and
|
||
* 2) a collection of elements where an element is a contiguous block(1).
|
||
* Remember that the input arguments to the MPI-IO functions use integer
|
||
* values to represent element counts. We ARE allowed however, in the
|
||
* more recent MPI implementations to use constructed datatypes whereby
|
||
* the total number of bytes in a transfer could be :
|
||
* (2GB-1)number_of_blocks * the_datatype_extent.
|
||
*/
|
||
|
||
MPI_Aint stride_in_bytes, inner_extent;
|
||
MPI_Datatype block_type;
|
||
|
||
/* Create a contiguous datatype inner_type x number of BLOCKS.
|
||
* Again we need to check that the number of BLOCKS can fit into
|
||
* a 32 bit integer */
|
||
if(bigio_count < d[i].block) {
|
||
if(H5_mpio_create_large_type(d[i].block, 0, inner_type, &block_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create a large block datatype in hyper selection")
|
||
}
|
||
else
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)d[i].block, inner_type, &block_type)))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code)
|
||
|
||
/* As of version 4.0, OpenMPI now turns off MPI-1 API calls by default,
|
||
* so we're using the MPI-2 version even though we don't need the lb
|
||
* value.
|
||
*/
|
||
{
|
||
MPI_Aint unused_lb_arg;
|
||
MPI_Type_get_extent(inner_type, &unused_lb_arg, &inner_extent);
|
||
}
|
||
stride_in_bytes = inner_extent * (MPI_Aint)d[i].strid;
|
||
|
||
/* If the element count is larger than what a 32 bit integer can hold,
|
||
* we call the large type creation function to handle that
|
||
*/
|
||
if(bigio_count < d[i].count) {
|
||
if(H5_mpio_create_large_type(d[i].count, stride_in_bytes, block_type, &outer_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create a large outer datatype in hyper selection")
|
||
}
|
||
/* otherwise a regular create_hvector will do */
|
||
else
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hvector((int)d[i].count, /* count */
|
||
1, /* blocklength */
|
||
stride_in_bytes, /* stride in bytes*/
|
||
block_type, /* old type */
|
||
&outer_type))) /* new type */
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code)
|
||
|
||
MPI_Type_free(&block_type);
|
||
MPI_Type_free(&inner_type);
|
||
} /* end else */
|
||
|
||
/****************************************
|
||
* Then build the dimension type as (start, vector type, xtent).
|
||
****************************************/
|
||
|
||
/* Calculate start and extent values of this dimension */
|
||
/* Check if value overflow to cast to type MPI_Aint */
|
||
if(d[i].start > LONG_MAX || offset[i] > LONG_MAX || elmt_size > LONG_MAX)
|
||
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "result overflow")
|
||
start_disp = (MPI_Aint)d[i].start * (MPI_Aint)offset[i] * (MPI_Aint)elmt_size;
|
||
|
||
if(max_xtent[i] > LONG_MAX)
|
||
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "max_xtent overflow")
|
||
new_extent = (MPI_Aint)elmt_size * (MPI_Aint)max_xtent[i];
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_get_extent(outer_type, &lb, &extent_len)))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_get_extent failed", mpi_code)
|
||
|
||
/*************************************************
|
||
* Restructure this datatype ("outer_type")
|
||
* so that it still starts at 0, but its extent
|
||
* is the full extent in this dimension.
|
||
*************************************************/
|
||
if(start_disp > 0 || extent_len < new_extent) {
|
||
MPI_Datatype interm_type;
|
||
int block_len = 1;
|
||
|
||
HDassert(0 == lb);
|
||
|
||
mpi_code = MPI_Type_create_hindexed(1, &block_len, &start_disp, outer_type, &interm_type);
|
||
MPI_Type_free(&outer_type);
|
||
if(mpi_code != MPI_SUCCESS)
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
|
||
|
||
mpi_code = MPI_Type_create_resized(interm_type, lb, new_extent, &inner_type);
|
||
MPI_Type_free(&interm_type);
|
||
if(mpi_code != MPI_SUCCESS)
|
||
HMPI_GOTO_ERROR(FAIL, "couldn't resize MPI vector type", mpi_code)
|
||
} /* end if */
|
||
else
|
||
inner_type = outer_type;
|
||
} /* end for */
|
||
/******************************************
|
||
* End of loop, walking through dimensions.
|
||
*******************************************/
|
||
|
||
/* At this point inner_type is actually the outermost type, even for 0-trip loop */
|
||
*new_type = inner_type;
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type)))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
|
||
|
||
/* fill in the remaining return values */
|
||
*count = 1; /* only have to move one of these suckers! */
|
||
*is_derived_type = TRUE;
|
||
|
||
done:
|
||
/* Release selection iterator */
|
||
if(sel_iter_init)
|
||
if(H5S_SELECT_ITER_RELEASE(&sel_iter) < 0)
|
||
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
|
||
|
||
#ifdef H5S_DEBUG
|
||
if(H5DEBUG(S))
|
||
HDfprintf(H5DEBUG(S), "Leave %s, count=%ld is_derived_type=%t\n", FUNC, *count, *is_derived_type);
|
||
#endif
|
||
FUNC_LEAVE_NOAPI(ret_value)
|
||
} /* end H5S__mpio_reg_hyper_type() */
|
||
|
||
|
||
/*-------------------------------------------------------------------------
|
||
* Function: H5S__mpio_span_hyper_type
|
||
*
|
||
* Purpose: Translate an HDF5 irregular hyperslab selection into an
|
||
MPI type.
|
||
*
|
||
* Return: Non-negative on success, negative on failure.
|
||
*
|
||
* Outputs: *new_type the MPI type corresponding to the selection
|
||
* *count how many objects of the new_type in selection
|
||
* (useful if this is the buffer type for xfer)
|
||
* *is_derived_type 0 if MPI primitive type, 1 if derived
|
||
*
|
||
* Programmer: kyang
|
||
*
|
||
*-------------------------------------------------------------------------
|
||
*/
|
||
static herr_t
|
||
H5S__mpio_span_hyper_type(const H5S_t *space, size_t elmt_size,
|
||
MPI_Datatype *new_type, int *count, hbool_t *is_derived_type)
|
||
{
|
||
H5S_mpio_mpitype_list_t type_list; /* List to track MPI data types created */
|
||
MPI_Datatype elmt_type; /* MPI datatype for an element */
|
||
hbool_t elmt_type_is_derived = FALSE; /* Whether the element type has been created */
|
||
MPI_Datatype span_type; /* MPI datatype for overall span tree */
|
||
hsize_t bigio_count; /* Transition point to create derived type */
|
||
hsize_t down[H5S_MAX_RANK]; /* 'down' sizes for each dimension */
|
||
uint64_t op_gen; /* Operation generation value */
|
||
int mpi_code; /* MPI return code */
|
||
herr_t ret_value = SUCCEED; /* Return value */
|
||
|
||
FUNC_ENTER_STATIC
|
||
|
||
/* Check args */
|
||
HDassert(space);
|
||
HDassert(space->extent.size);
|
||
HDassert(space->select.sel_info.hslab->span_lst);
|
||
HDassert(space->select.sel_info.hslab->span_lst->head);
|
||
|
||
bigio_count = H5_mpi_get_bigio_count();
|
||
/* Create the base type for an element */
|
||
if(bigio_count >= elmt_size) {
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)elmt_size, MPI_BYTE, &elmt_type)))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code)
|
||
}
|
||
else
|
||
if(H5_mpio_create_large_type(elmt_size, 0, MPI_BYTE, &elmt_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create a large element datatype in span_hyper selection")
|
||
elmt_type_is_derived = TRUE;
|
||
|
||
/* Compute 'down' sizes for each dimension */
|
||
if(H5VM_array_down(space->extent.rank, space->extent.size, down) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGETSIZE, FAIL, "couldn't compute 'down' dimension sizes")
|
||
|
||
/* Acquire an operation generation value for creating MPI datatypes */
|
||
op_gen = H5S__hyper_get_op_gen();
|
||
|
||
/* Obtain derived MPI data type */
|
||
/* Always use op_info[0] since we own this op_info, so there can be no
|
||
* simultaneous operations */
|
||
type_list.head = type_list.tail = NULL;
|
||
if(H5S__obtain_datatype(space->select.sel_info.hslab->span_lst, down, elmt_size, &elmt_type, &span_type, &type_list, 0, op_gen) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't obtain MPI derived data type")
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_dup(span_type, new_type)))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type)))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
|
||
|
||
/* Release MPI data types generated during span tree traversal */
|
||
if(H5S__release_datatype(&type_list) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "couldn't release MPI derived data type")
|
||
|
||
/* fill in the remaining return values */
|
||
*count = 1;
|
||
*is_derived_type = TRUE;
|
||
|
||
done:
|
||
/* Release resources */
|
||
if(elmt_type_is_derived)
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_free(&elmt_type)))
|
||
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
|
||
|
||
FUNC_LEAVE_NOAPI(ret_value)
|
||
} /* end H5S__mpio_span_hyper_type() */
|
||
|
||
|
||
/*-------------------------------------------------------------------------
|
||
* Function: H5S__release_datatype
|
||
*
|
||
* Purpose: Release the MPI derived datatypes for span-tree hyperslab selection
|
||
*
|
||
* Return: Non-negative on success, negative on failure.
|
||
*
|
||
* Programmer: Quincey Koziol, February 2, 2019
|
||
*
|
||
*-------------------------------------------------------------------------
|
||
*/
|
||
static herr_t
|
||
H5S__release_datatype(H5S_mpio_mpitype_list_t *type_list)
|
||
{
|
||
H5S_mpio_mpitype_node_t *curr; /* Pointer to head of list */
|
||
herr_t ret_value = SUCCEED; /* Return value */
|
||
|
||
FUNC_ENTER_STATIC
|
||
|
||
/* Sanity check */
|
||
HDassert(type_list);
|
||
|
||
/* Iterate over the list, freeing the MPI data types */
|
||
curr = type_list->head;
|
||
while(curr) {
|
||
H5S_mpio_mpitype_node_t *next; /* Pointer to next node in list */
|
||
int mpi_code; /* MPI return status code */
|
||
|
||
/* Release the MPI data type for this span tree */
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_free(&curr->type)))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
|
||
|
||
/* Get pointer to next node in list */
|
||
next = curr->next;
|
||
|
||
/* Free the current node */
|
||
curr = H5FL_FREE(H5S_mpio_mpitype_node_t, curr);
|
||
|
||
/* Advance to next node */
|
||
curr = next;
|
||
} /* end while */
|
||
|
||
done:
|
||
FUNC_LEAVE_NOAPI(ret_value)
|
||
} /* end H5S__release_datatype() */
|
||
|
||
|
||
/*-------------------------------------------------------------------------
|
||
* Function: H5S__obtain_datatype
|
||
*
|
||
* Purpose: Obtain an MPI derived datatype for span-tree hyperslab selection
|
||
*
|
||
* Return: Non-negative on success, negative on failure.
|
||
*
|
||
* Outputs: *span_type the MPI type corresponding to the selection
|
||
*
|
||
* Programmer: kyang
|
||
*
|
||
*-------------------------------------------------------------------------
|
||
*/
|
||
static herr_t
|
||
H5S__obtain_datatype(H5S_hyper_span_info_t *spans, const hsize_t *down,
|
||
size_t elmt_size, const MPI_Datatype *elmt_type, MPI_Datatype *span_type,
|
||
H5S_mpio_mpitype_list_t *type_list, unsigned op_info_i, uint64_t op_gen)
|
||
{
|
||
H5S_hyper_span_t *span; /* Hyperslab span to iterate with */
|
||
hsize_t bigio_count; /* Transition point to create derived type */
|
||
size_t alloc_count = 0; /* Number of span tree nodes allocated at this level */
|
||
size_t outercount = 0; /* Number of span tree nodes at this level */
|
||
MPI_Datatype *inner_type = NULL;
|
||
hbool_t inner_types_freed = FALSE; /* Whether the inner_type MPI datatypes have been freed */
|
||
int *blocklen = NULL;
|
||
MPI_Aint *disp = NULL;
|
||
size_t u; /* Local index variable */
|
||
int mpi_code; /* MPI return status code */
|
||
herr_t ret_value = SUCCEED; /* Return value */
|
||
|
||
FUNC_ENTER_STATIC
|
||
|
||
/* Sanity check */
|
||
HDassert(spans);
|
||
HDassert(type_list);
|
||
|
||
bigio_count = H5_mpi_get_bigio_count();
|
||
/* Check if we've visited this span tree before */
|
||
if(spans->op_info[op_info_i].op_gen != op_gen) {
|
||
H5S_mpio_mpitype_node_t *type_node; /* Pointer to new node in MPI data type list */
|
||
|
||
/* Allocate the initial displacement & block length buffers */
|
||
alloc_count = H5S_MPIO_INITIAL_ALLOC_COUNT;
|
||
if(NULL == (disp = (MPI_Aint *)H5MM_malloc(alloc_count * sizeof(MPI_Aint))))
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of displacements")
|
||
if(NULL == (blocklen = (int *)H5MM_malloc(alloc_count * sizeof(int))))
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of block lengths")
|
||
|
||
/* If this is the fastest changing dimension, it is the base case for derived datatype. */
|
||
span = spans->head;
|
||
if(NULL == span->down) {
|
||
hbool_t large_block = FALSE; /* Wether the block length is larger than 32 bit integer */
|
||
|
||
outercount = 0;
|
||
while(span) {
|
||
hsize_t nelmts; /* # of elements covered by current span */
|
||
|
||
/* Check if we need to increase the size of the buffers */
|
||
if(outercount >= alloc_count) {
|
||
MPI_Aint *tmp_disp; /* Temporary pointer to new displacement buffer */
|
||
int *tmp_blocklen; /* Temporary pointer to new block length buffer */
|
||
|
||
/* Double the allocation count */
|
||
alloc_count *= 2;
|
||
|
||
/* Re-allocate the buffers */
|
||
if(NULL == (tmp_disp = (MPI_Aint *)H5MM_realloc(disp, alloc_count * sizeof(MPI_Aint))))
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of displacements")
|
||
disp = tmp_disp;
|
||
if(NULL == (tmp_blocklen = (int *)H5MM_realloc(blocklen, alloc_count * sizeof(int))))
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of block lengths")
|
||
blocklen = tmp_blocklen;
|
||
} /* end if */
|
||
|
||
/* Compute the number of elements to attempt in this span */
|
||
nelmts = (span->high - span->low) + 1;
|
||
|
||
/* Store displacement & block length */
|
||
disp[outercount] = (MPI_Aint)elmt_size * (MPI_Aint)span->low;
|
||
H5_CHECK_OVERFLOW(nelmts, hsize_t, int)
|
||
blocklen[outercount] = (int)nelmts;
|
||
|
||
if(bigio_count < (hsize_t)blocklen[outercount])
|
||
large_block = TRUE; /* at least one block type is large, so set this flag to true */
|
||
|
||
span = span->next;
|
||
outercount++;
|
||
} /* end while */
|
||
|
||
/* Everything fits into integers, so cast them and use hindexed */
|
||
if(bigio_count >= outercount && large_block == FALSE) {
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)outercount, blocklen, disp, *elmt_type, &spans->op_info[op_info_i].u.down_type)))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
|
||
} /* end if */
|
||
else { /* LARGE_DATATYPE:: Something doesn't fit into a 32 bit integer */
|
||
for(u = 0 ; u < outercount; u++) {
|
||
MPI_Datatype temp_type = MPI_DATATYPE_NULL;
|
||
|
||
/* create the block type from elmt_type while checking the 32 bit int limit */
|
||
if((hsize_t)(blocklen[u]) > bigio_count) {
|
||
if(H5_mpio_create_large_type((hsize_t)blocklen[u], 0, *elmt_type, &temp_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create a large element datatype in span_hyper selection")
|
||
} /* end if */
|
||
else
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)blocklen[u], *elmt_type, &temp_type)))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code)
|
||
|
||
/* Combine the current datatype that is created with this current block type */
|
||
if(0 == u) /* first iteration, there is no combined datatype yet */
|
||
spans->op_info[op_info_i].u.down_type = temp_type;
|
||
else {
|
||
int bl[2] = {1, 1};
|
||
MPI_Aint ds[2] = {disp[u - 1], disp[u]};
|
||
MPI_Datatype dt[2] = {spans->op_info[op_info_i].u.down_type, temp_type};
|
||
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_struct(2, /* count */
|
||
bl, /* blocklength */
|
||
ds, /* stride in bytes*/
|
||
dt, /* old type */
|
||
&spans->op_info[op_info_i].u.down_type))) /* new type */
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code)
|
||
|
||
/* Release previous temporary datatype */
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_free(&temp_type)))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
|
||
} /* end else */
|
||
} /* end for */
|
||
} /* end else (LARGE_DATATYPE::) */
|
||
} /* end if */
|
||
else {
|
||
MPI_Aint stride; /* Distance between inner MPI datatypes */
|
||
|
||
if(NULL == (inner_type = (MPI_Datatype *)H5MM_malloc(alloc_count * sizeof(MPI_Datatype))))
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of inner MPI datatypes")
|
||
|
||
/* Calculate the total bytes of the lower dimension */
|
||
stride = (MPI_Aint)(*down) * (MPI_Aint)elmt_size;
|
||
|
||
/* Loop over span nodes */
|
||
outercount = 0;
|
||
while(span) {
|
||
MPI_Datatype down_type; /* Temporary MPI datatype for a span tree node's children */
|
||
hsize_t nelmts; /* # of elements covered by current span */
|
||
|
||
/* Check if we need to increase the size of the buffers */
|
||
if(outercount >= alloc_count) {
|
||
MPI_Aint *tmp_disp; /* Temporary pointer to new displacement buffer */
|
||
int *tmp_blocklen; /* Temporary pointer to new block length buffer */
|
||
MPI_Datatype *tmp_inner_type; /* Temporary pointer to inner MPI datatype buffer */
|
||
|
||
/* Double the allocation count */
|
||
alloc_count *= 2;
|
||
|
||
/* Re-allocate the buffers */
|
||
if(NULL == (tmp_disp = (MPI_Aint *)H5MM_realloc(disp, alloc_count * sizeof(MPI_Aint))))
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of displacements")
|
||
disp = tmp_disp;
|
||
if(NULL == (tmp_blocklen = (int *)H5MM_realloc(blocklen, alloc_count * sizeof(int))))
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of block lengths")
|
||
blocklen = tmp_blocklen;
|
||
if(NULL == (tmp_inner_type = (MPI_Datatype *)H5MM_realloc(inner_type, alloc_count * sizeof(MPI_Datatype))))
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of inner MPI datatypes")
|
||
inner_type = tmp_inner_type;
|
||
} /* end if */
|
||
|
||
/* Displacement should be in byte and should have dimension information */
|
||
/* First using MPI Type vector to build derived data type for this span only */
|
||
/* Need to calculate the disp in byte for this dimension. */
|
||
disp[outercount] = (MPI_Aint)span->low * stride;
|
||
blocklen[outercount] = 1;
|
||
|
||
/* Generate MPI datatype for next dimension down */
|
||
if(H5S__obtain_datatype(span->down, down + 1, elmt_size, elmt_type, &down_type, type_list, op_info_i, op_gen) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't obtain MPI derived data type")
|
||
|
||
/* Compute the number of elements to attempt in this span */
|
||
nelmts = (span->high - span->low) + 1;
|
||
|
||
/* Build the MPI datatype for this node */
|
||
H5_CHECK_OVERFLOW(nelmts, hsize_t, int)
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hvector((int)nelmts, 1, stride, down_type, &inner_type[outercount])))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code)
|
||
|
||
span = span->next;
|
||
outercount++;
|
||
} /* end while */
|
||
|
||
/* Building the whole vector datatype */
|
||
H5_CHECK_OVERFLOW(outercount, size_t, int)
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_struct((int)outercount, blocklen, disp, inner_type, &spans->op_info[op_info_i].u.down_type)))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code)
|
||
|
||
/* Release inner node types */
|
||
for(u = 0; u < outercount; u++)
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_free(&inner_type[u])))
|
||
HMPI_GOTO_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
|
||
inner_types_freed = TRUE;
|
||
} /* end else */
|
||
|
||
/* Allocate space for the MPI data type list node */
|
||
if(NULL == (type_node = H5FL_MALLOC(H5S_mpio_mpitype_node_t)))
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate MPI data type list node")
|
||
|
||
/* Set up MPI type node */
|
||
type_node->type = spans->op_info[op_info_i].u.down_type;
|
||
type_node->next = NULL;
|
||
|
||
/* Add MPI type node to list */
|
||
if(type_list->head == NULL)
|
||
type_list->head = type_list->tail = type_node;
|
||
else {
|
||
type_list->tail->next = type_node;
|
||
type_list->tail = type_node;
|
||
} /* end else */
|
||
|
||
/* Remember that we've visited this span tree */
|
||
spans->op_info[op_info_i].op_gen = op_gen;
|
||
} /* end else */
|
||
|
||
/* Return MPI data type for span tree */
|
||
*span_type = spans->op_info[op_info_i].u.down_type;
|
||
|
||
done:
|
||
/* General cleanup */
|
||
if(inner_type != NULL) {
|
||
if(!inner_types_freed)
|
||
for(u = 0; u < outercount; u++)
|
||
if(MPI_SUCCESS != (mpi_code = MPI_Type_free(&inner_type[u])))
|
||
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
|
||
H5MM_free(inner_type);
|
||
} /* end if */
|
||
if(blocklen != NULL)
|
||
H5MM_free(blocklen);
|
||
if(disp != NULL)
|
||
H5MM_free(disp);
|
||
|
||
FUNC_LEAVE_NOAPI(ret_value)
|
||
} /* end H5S__obtain_datatype() */
|
||
|
||
|
||
/*-------------------------------------------------------------------------
|
||
* Function: H5S_mpio_space_type
|
||
*
|
||
* Purpose: Translate an HDF5 dataspace selection into an MPI type.
|
||
* Currently handle only hyperslab and "all" selections.
|
||
*
|
||
* Return: Non-negative on success, negative on failure.
|
||
*
|
||
* Outputs: *new_type the MPI type corresponding to the selection
|
||
* *count how many objects of the new_type in selection
|
||
* (useful if this is the buffer type for xfer)
|
||
* *is_derived_type 0 if MPI primitive type, 1 if derived
|
||
*
|
||
* Programmer: rky 980813
|
||
*
|
||
*-------------------------------------------------------------------------
|
||
*/
|
||
herr_t
|
||
H5S_mpio_space_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type,
|
||
int *count, hbool_t *is_derived_type, hbool_t do_permute, hsize_t **permute_map,
|
||
hbool_t *is_permuted)
|
||
{
|
||
herr_t ret_value = SUCCEED; /* Return value */
|
||
|
||
FUNC_ENTER_NOAPI_NOINIT
|
||
|
||
/* Check args */
|
||
HDassert(space);
|
||
HDassert(elmt_size);
|
||
|
||
/* Create MPI type based on the kind of selection */
|
||
switch(H5S_GET_EXTENT_TYPE(space)) {
|
||
case H5S_NULL:
|
||
case H5S_SCALAR:
|
||
case H5S_SIMPLE:
|
||
/* If the file space has been permuted previously due to
|
||
* out-of-order point selection, then permute this selection which
|
||
* should be a memory selection to match the file space permutation.
|
||
*/
|
||
if(TRUE == *is_permuted) {
|
||
switch(H5S_GET_SELECT_TYPE(space)) {
|
||
case H5S_SEL_NONE:
|
||
if(H5S__mpio_none_type(new_type, count, is_derived_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert 'none' selection to MPI type")
|
||
break;
|
||
|
||
case H5S_SEL_ALL:
|
||
case H5S_SEL_POINTS:
|
||
case H5S_SEL_HYPERSLABS:
|
||
/* Sanity check */
|
||
HDassert(!do_permute);
|
||
|
||
if(H5S__mpio_permute_type(space, elmt_size, permute_map, new_type, count, is_derived_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert 'all' selection to MPI type")
|
||
break;
|
||
|
||
case H5S_SEL_ERROR:
|
||
case H5S_SEL_N:
|
||
default:
|
||
HDassert("unknown selection type" && 0);
|
||
break;
|
||
} /* end switch */
|
||
} /* end if */
|
||
/* the file space is not permuted, so do a regular selection */
|
||
else {
|
||
switch(H5S_GET_SELECT_TYPE(space)) {
|
||
case H5S_SEL_NONE:
|
||
if(H5S__mpio_none_type(new_type, count, is_derived_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert 'none' selection to MPI type")
|
||
break;
|
||
|
||
case H5S_SEL_ALL:
|
||
if(H5S__mpio_all_type(space, elmt_size, new_type, count, is_derived_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert 'all' selection to MPI type")
|
||
break;
|
||
|
||
case H5S_SEL_POINTS:
|
||
if(H5S__mpio_point_type(space, elmt_size, new_type, count, is_derived_type, do_permute, permute_map, is_permuted) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert 'point' selection to MPI type")
|
||
break;
|
||
|
||
case H5S_SEL_HYPERSLABS:
|
||
if((H5S_SELECT_IS_REGULAR(space) == TRUE)) {
|
||
if(H5S__mpio_reg_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert regular 'hyperslab' selection to MPI type")
|
||
} /* end if */
|
||
else
|
||
if(H5S__mpio_span_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0)
|
||
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert irregular 'hyperslab' selection to MPI type")
|
||
break;
|
||
|
||
case H5S_SEL_ERROR:
|
||
case H5S_SEL_N:
|
||
default:
|
||
HDassert("unknown selection type" && 0);
|
||
break;
|
||
} /* end switch */
|
||
} /* end else */
|
||
break;
|
||
|
||
case H5S_NO_CLASS:
|
||
default:
|
||
HDassert("unknown dataspace type" && 0);
|
||
break;
|
||
} /* end switch */
|
||
|
||
done:
|
||
FUNC_LEAVE_NOAPI(ret_value)
|
||
} /* end H5S_mpio_space_type() */
|
||
|
||
#endif /* H5_HAVE_PARALLEL */
|
||
|