/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the COPYING file, which can be found at the root of the source code * * 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. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * Programmer: rky 980813 * * Purpose: Functions to read/write directly between app buffer and file. * */ #define H5S_PACKAGE /*suppress error about including H5Spkg */ #include "H5private.h" /* Generic Functions */ #include "H5Dprivate.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 "H5Spkg.h" /* Dataspaces */ #include "H5VMprivate.h" /* Vector and array functions */ #ifdef H5_HAVE_PARALLEL static herr_t H5S_mpio_all_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); static herr_t H5S_mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); static herr_t H5S_mpio_create_point_datatype(size_t elmt_size, hsize_t num_points, MPI_Aint *disp, MPI_Datatype *new_type); static herr_t H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type, hbool_t do_permute, hsize_t **permute_map, hbool_t *is_permuted); static herr_t H5S_mpio_permute_type(const H5S_t *space, size_t elmt_size, hsize_t **permute_map, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); static herr_t H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); static herr_t H5S_mpio_span_hyper_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type); static herr_t H5S_obtain_datatype(const hsize_t down[], H5S_hyper_span_t *span, const MPI_Datatype *elmt_type, MPI_Datatype *span_type, size_t elmt_size); #define H5S_MPIO_INITIAL_ALLOC_COUNT 256 /*------------------------------------------------------------------------- * Function: H5S_mpio_all_type * * Purpose: Translate an HDF5 "all" 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_all_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) { hsize_t total_bytes; hssize_t snelmts; /* Total number of elmts (signed) */ hsize_t nelmts; /* Total number of elmts */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT /* Check args */ HDassert(space); /* Just treat the entire extent as a block of bytes */ if ((snelmts = (hssize_t)H5S_GET_EXTENT_NPOINTS(space)) < 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection") H5_CHECKED_ASSIGN(nelmts, hsize_t, snelmts, hssize_t); total_bytes = (hsize_t)elmt_size * nelmts; /* fill in the return values */ *new_type = MPI_BYTE; H5_CHECKED_ASSIGN(*count, int, total_bytes, hsize_t); *is_derived_type = FALSE; done: FUNC_LEAVE_NOAPI(ret_value) } /* H5S_mpio_all_type() */ /*------------------------------------------------------------------------- * Function: H5S_mpio_none_type * * Purpose: Translate an HDF5 "none" 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: Quincey Koziol, October 29, 2002 * *------------------------------------------------------------------------- */ static herr_t H5S_mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) { FUNC_ENTER_NOAPI_NOINIT_NOERR /* fill in the return values */ *new_type = MPI_BYTE; *count = 0; *is_derived_type = FALSE; FUNC_LEAVE_NOAPI(SUCCEED) } /* H5S_mpio_none_type() */ /*------------------------------------------------------------------------- * Function: H5S_mpio_create_point_datatype * * Purpose: Create a derived datatype for point selections. * * Return: Non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * * Programmer: Mohamad Chaarawi * *------------------------------------------------------------------------- */ static herr_t H5S_mpio_create_point_datatype(size_t elmt_size, hsize_t num_points, MPI_Aint *disp, MPI_Datatype *new_type) { MPI_Datatype elmt_type; /* MPI datatype for individual element */ hbool_t elmt_type_created = FALSE; /* Whether the element MPI datatype was created */ int mpi_code; /* MPI error code */ int * blocks = NULL; /* Array of block sizes for MPI hindexed create call */ hsize_t u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT /* Create an MPI datatype for an element */ if (MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)elmt_size, MPI_BYTE, &elmt_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) elmt_type_created = TRUE; /* Allocate block sizes for MPI datatype call */ if (NULL == (blocks = (int *)H5MM_malloc(sizeof(int) * num_points))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of blocks") /* Would be nice to have Create_Hindexed_block to avoid this array of all ones */ for (u = 0; u < num_points; u++) blocks[u] = 1; /* Create an MPI datatype for the whole point selection */ if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)num_points, blocks, disp, elmt_type, new_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_indexed_block failed", mpi_code) /* Commit MPI datatype for later use */ if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(new_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) done: if (elmt_type_created) MPI_Type_free(&elmt_type); if (blocks) H5MM_free(blocks); FUNC_LEAVE_NOAPI(ret_value) } /* H5S_mpio_create_point_datatype() */ /*------------------------------------------------------------------------- * Function: H5S_mpio_point_type * * Purpose: Translate an HDF5 "point" selection into an MPI type. * Create a permutation array to handle out-of-order point selections. * * Return: Non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * *count how many objects of the new_type in selection * (useful if this is the buffer type for xfer) * *is_derived_type 0 if MPI primitive type, 1 if derived * *permute_map the permutation of the displacements to create * the MPI_Datatype * *is_permuted 0 if the displacements are permuted, 1 if not * * Programmer: Mohamad Chaarawi * *------------------------------------------------------------------------- */ static herr_t H5S_mpio_point_type(const H5S_t *space, size_t elmt_size, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type, hbool_t do_permute, hsize_t **permute, hbool_t *is_permuted) { MPI_Aint * disp = NULL; /* Datatype displacement for each point*/ H5S_pnt_node_t *curr = NULL; /* Current point being operated on in from the selection */ hssize_t snum_points; /* Signed number of elements in selection */ hsize_t num_points; /* Sumber of points in the selection */ hsize_t u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT /* Check args */ HDassert(space); /* Get the total number of points selected */ if ((snum_points = (hssize_t)H5S_GET_SELECT_NPOINTS(space)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements selected") num_points = (hsize_t)snum_points; /* Allocate array for element displacements */ if (NULL == (disp = (MPI_Aint *)H5MM_malloc(sizeof(MPI_Aint) * num_points))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of displacements") /* Allocate array for element permutation - returned to caller */ if (do_permute) if (NULL == (*permute = (hsize_t *)H5MM_malloc(sizeof(hsize_t) * num_points))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate permutation array") /* Iterate through list of elements */ curr = space->select.sel_info.pnt_lst->head; for (u = 0; u < num_points; u++) { /* calculate the displacement of the current point */ disp[u] = H5VM_array_offset(space->extent.rank, space->extent.size, curr->pnt); disp[u] *= elmt_size; /* This is a File Space used to set the file view, so adjust the displacements * to have them monotonically non-decreasing. * Generate the permutation array by indicating at each point being selected, * the position it will shifted in the new displacement. Example: * Suppose 4 points with corresponding are selected * Pt 1: disp=6 ; Pt 2: disp=3 ; Pt 3: disp=0 ; Pt 4: disp=4 * The permute map to sort the displacements in order will be: * point 1: map[0] = L, indicating that this point is not moved (1st point selected) * point 2: map[1] = 0, indicating that this point is moved to the first position, * since disp_pt1(6) > disp_pt2(3) * point 3: map[2] = 0, move to position 0, bec it has the lowest disp between * the points selected so far. * point 4: map[3] = 2, move the 2nd position since point 1 has a higher disp, * but points 2 and 3 have lower displacements. */ if (do_permute) { if (u > 0 && disp[u] < disp[u - 1]) { unsigned s = 0, l = u, m = u / 2; *is_permuted = TRUE; do { if (disp[u] > disp[m]) s = m + 1; else if (disp[u] < disp[m]) l = m; else break; m = s + ((l - s) / 2); } while (s < l); if (m < u) { MPI_Aint temp; temp = disp[u]; HDmemmove(disp + m + 1, disp + m, (u - m) * sizeof(MPI_Aint)); disp[m] = temp; } /* end if */ (*permute)[u] = m; } /* end if */ else (*permute)[u] = num_points; } /* end if */ /* this is a memory space, and no permutation is necessary to create the derived datatype */ else { ; /* do nothing */ } /* end else */ /* get the next point */ curr = curr->next; } /* end for */ /* Create the MPI datatype for the set of element displacements */ if (H5S_mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create an MPI Datatype from point selection") /* Set values about MPI datatype created */ *count = 1; *is_derived_type = TRUE; done: if (NULL != disp) H5MM_free(disp); /* Release the permutation buffer, if it wasn't used */ if (!(*is_permuted) && (*permute)) { H5MM_free(*permute); *permute = NULL; } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* H5S_mpio_point_type() */ /*------------------------------------------------------------------------- * Function: H5S_mpio_permute_type * * Purpose: Translate an HDF5 "all/hyper/point" selection into an MPI type, * while applying the permutation map. This function is called if * the file space selection is permuted due to out-of-order point * selection and so the memory datatype has to be permuted using the * permutation map created by the file selection. * * Note: This routine is called from H5S_mpio_space_type(), which is * called first for the file dataspace and creates * * Return: Non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * *count how many objects of the new_type in selection * (useful if this is the buffer type for xfer) * *is_derived_type 0 if MPI primitive type, 1 if derived * * Programmer: Mohamad Chaarawi * *------------------------------------------------------------------------- */ static herr_t H5S_mpio_permute_type(const H5S_t *space, size_t elmt_size, hsize_t **permute, MPI_Datatype *new_type, int *count, hbool_t *is_derived_type) { MPI_Aint * disp = NULL; /* Datatype displacement for each point*/ H5S_sel_iter_t sel_iter; /* Selection iteration info */ hbool_t sel_iter_init = FALSE; /* Selection iteration info has been initialized */ hsize_t off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */ size_t len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */ hssize_t snum_points; /* Signed number of elements in selection */ hsize_t num_points; /* Number of points in the selection */ size_t max_elem; /* Maximum number of elements allowed in sequences */ hsize_t u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT /* Check args */ HDassert(space); /* Get the total number of points selected */ if ((snum_points = (hssize_t)H5S_GET_SELECT_NPOINTS(space)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't get number of elements selected") num_points = (hsize_t)snum_points; /* Allocate array to store point displacements */ if (NULL == (disp = (MPI_Aint *)H5MM_malloc(sizeof(MPI_Aint) * num_points))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate array of displacements") /* Initialize selection iterator */ if (H5S_select_iter_init(&sel_iter, space, elmt_size) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") sel_iter_init = TRUE; /* Selection iteration info has been initialized */ /* Set the number of elements to iterate over */ H5_CHECKED_ASSIGN(max_elem, size_t, num_points, hsize_t); /* Loop, while elements left in selection */ u = 0; while (max_elem > 0) { size_t nelem; /* Number of elements used in sequences */ size_t nseq; /* Number of sequences generated */ size_t curr_seq; /* Current sequence being worked on */ /* Get the sequences of bytes */ if (H5S_SELECT_GET_SEQ_LIST(space, 0, &sel_iter, (size_t)H5D_IO_VECTOR_SIZE, max_elem, &nseq, &nelem, off, len) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "sequence length generation failed") /* Loop, while sequences left to process */ for (curr_seq = 0; curr_seq < nseq; curr_seq++) { hsize_t curr_off; /* Current offset within sequence */ size_t curr_len; /* Length of bytes left to process in sequence */ /* Get the current offset */ curr_off = off[curr_seq]; /* Get the number of bytes in sequence */ curr_len = len[curr_seq]; /* Loop, while bytes left in sequence */ while (curr_len > 0) { /* Set the displacement of the current point */ disp[u] = curr_off; /* This is a memory displacement, so for each point selected, * apply the map that was generated by the file selection */ if ((*permute)[u] != num_points) { MPI_Aint temp = disp[u]; HDmemmove(disp + (*permute)[u] + 1, disp + (*permute)[u], (u - (*permute)[u]) * sizeof(MPI_Aint)); disp[(*permute)[u]] = temp; } /* end if */ /* Advance to next element */ u++; /* Increment offset in dataspace */ curr_off += elmt_size; /* Decrement number of bytes left in sequence */ curr_len -= elmt_size; } /* end while */ } /* end for */ /* Decrement number of elements left to process */ max_elem -= nelem; } /* end while */ /* Create the MPI datatype for the set of element displacements */ if (H5S_mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create an MPI Datatype from point selection") /* Set values about MPI datatype created */ *count = 1; *is_derived_type = TRUE; done: /* Release selection iterator */ if (sel_iter_init) if (H5S_SELECT_ITER_RELEASE(&sel_iter) < 0) HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator") /* Free memory */ if (disp) H5MM_free(disp); if (*permute) { H5MM_free(*permute); *permute = NULL; } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* H5S_mpio_permute_type() */ /*------------------------------------------------------------------------- * Function: H5S_mpio_hyper_type * * Purpose: Translate 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_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 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_NOAPI_NOINIT /* Check args */ HDassert(space); HDassert(sizeof(MPI_Aint) >= sizeof(elmt_size)); /* Initialize selection iterator */ if (H5S_select_iter_init(&sel_iter, space, elmt_size) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") sel_iter_init = TRUE; /* Selection iteration info has been initialized */ /* 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; HDassert(rank <= H5S_MAX_RANK); /* within array bounds */ #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=%" PRIdHSIZE " stride=%" PRIuHSIZE " count=%" PRIuHSIZE " block=%" PRIuHSIZE " xtent=%" PRIuHSIZE, 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 if (0 == d[u].block) goto empty; if (0 == d[u].count) goto empty; if (0 == d[u].xtent) goto empty; } /* end for */ } /* end if */ else { /* Non-flattened selection */ rank = space->extent.rank; HDassert(rank <= H5S_MAX_RANK); /* within array bounds */ if (0 == rank) goto empty; #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=%" PRIdHSIZE " stride=%" PRIuHSIZE " count=%" PRIuHSIZE " block=%" PRIuHSIZE " xtent=%" PRIuHSIZE, 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 if (0 == d[u].block) goto empty; if (0 == d[u].count) goto empty; if (0 == d[u].xtent) goto empty; } /* 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]=%" PRIuHSIZE "; max_xtent[%2d]=%" PRIuHSIZE "\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]=%" PRIuHSIZE "; max_xtent[%2d]=%" PRIuHSIZE "\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=%" PRIuHSIZE "\n", i, d[i].xtent); } #endif 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) /******************************************************* * 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=%" PRIdHSIZE " count=%" PRIuHSIZE " block=%" PRIuHSIZE " stride=%" PRIuHSIZE ", xtent=%" PRIuHSIZE " max_xtent=%" PRIuHSIZE "\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. ****************************************/ 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) /**************************************** * Then build the dimension type as (start, vector type, xtent). ****************************************/ /* calculate start and extent values of this dimension */ start_disp = d[i].start * offset[i] * elmt_size; new_extent = (MPI_Aint)elmt_size * 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; HGOTO_DONE(SUCCEED); empty: /* special case: empty hyperslab */ *new_type = MPI_BYTE; *count = 0; *is_derived_type = FALSE; 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_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) { 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 down[H5S_MAX_RANK]; /* 'down' sizes for each dimension */ int mpi_code; /* MPI return code */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT /* 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); /* Create the base type for an element */ if (MPI_SUCCESS != (mpi_code = MPI_Type_contiguous((int)elmt_size, MPI_BYTE, &elmt_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code) elmt_type_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") /* Obtain derived data type */ if (H5S_obtain_datatype(down, space->select.sel_info.hslab->span_lst->head, &elmt_type, &span_type, elmt_size) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't obtain MPI derived data type") if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&span_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code) *new_type = span_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_obtain_datatype * * Purpose: Obtain an MPI derived datatype based on span-tree * implementation * * 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(const hsize_t *down, H5S_hyper_span_t *span, const MPI_Datatype *elmt_type, MPI_Datatype *span_type, size_t elmt_size) { 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 */ hbool_t span_type_valid = FALSE; /* Whether the span_type MPI datatypes is valid */ int * blocklen = NULL; MPI_Aint * disp = NULL; H5S_hyper_span_t *tspan; /* Temporary pointer to span tree node */ int mpi_code; /* MPI return status code */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT /* Sanity check */ HDassert(span); /* 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. */ if (NULL == span->down) { tspan = span; outercount = 0; while (tspan) { /* 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 */ /* Store displacement & block length */ disp[outercount] = (MPI_Aint)elmt_size * tspan->low; H5_CHECK_OVERFLOW(tspan->nelem, hsize_t, int) blocklen[outercount] = (int)tspan->nelem; tspan = tspan->next; outercount++; } /* end while */ if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed((int)outercount, blocklen, disp, *elmt_type, span_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code) span_type_valid = TRUE; } /* end if */ else { size_t u; /* Local index variable */ 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") tspan = span; outercount = 0; while (tspan) { MPI_Datatype down_type; /* Temporary MPI datatype for a span tree node's children */ MPI_Aint stride; /* Distance between inner MPI datatypes */ /* 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. */ /* Calculate the total bytes of the lower dimension */ disp[outercount] = tspan->low * (*down) * elmt_size; blocklen[outercount] = 1; /* Generate MPI datatype for next dimension down */ if (H5S_obtain_datatype(down + 1, tspan->down->head, elmt_type, &down_type, elmt_size) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't obtain MPI derived data type") /* Build the MPI datatype for this node */ stride = (*down) * elmt_size; H5_CHECK_OVERFLOW(tspan->nelem, hsize_t, int) if (MPI_SUCCESS != (mpi_code = MPI_Type_create_hvector((int)tspan->nelem, 1, stride, down_type, &inner_type[outercount]))) { MPI_Type_free(&down_type); HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hvector failed", mpi_code) } /* end if */ /* Release MPI datatype for next dimension down */ if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&down_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_free failed", mpi_code) tspan = tspan->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, span_type))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code) span_type_valid = TRUE; /* 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 */ done: /* General cleanup */ if (inner_type != NULL) { if (!inner_types_freed) { size_t u; /* Local index variable */ 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) } /* end if */ H5MM_free(inner_type); } /* end if */ if (blocklen != NULL) H5MM_free(blocklen); if (disp != NULL) H5MM_free(disp); /* Error cleanup */ if (ret_value < 0) { if (span_type_valid) if (MPI_SUCCESS != (mpi_code = MPI_Type_free(span_type))) HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code) } /* end if */ 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_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert regular 'hyperslab' selection to MPI type") } /* end if */ else { if (H5S_mpio_span_hyper_type(space, elmt_size, new_type, count, is_derived_type) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't convert irregular 'hyperslab' selection to MPI type") } /* end else */ break; case H5S_SEL_ERROR: case H5S_SEL_N: default: HDassert("unknown selection type" && 0); break; } /* end switch */ } /* end else */ break; case H5S_NO_CLASS: default: HDassert("unknown data space type" && 0); break; } /* end switch */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5S_mpio_space_type() */ #endif /* H5_HAVE_PARALLEL */