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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Programmer: rky 980813
*
* Purpose: Functions to read/write directly between app buffer and file.
*
* Beware of the ifdef'ed print statements.
* I didn't make them portable.
*/
#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_ASSIGN_OVERFLOW(nelmts, snelmts, hssize_t, hsize_t);
total_bytes = (hsize_t)elmt_size * nelmts;
/* fill in the return values */
*new_type = MPI_BYTE;
H5_ASSIGN_OVERFLOW(*count, total_bytes, hsize_t, int);
*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_ASSIGN_OVERFLOW(max_elem, num_points, hsize_t, size_t);
/* Loop, while elements left in selection */
u = 0;
while(max_elem > 0) {
hsize_t off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */
size_t len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */
size_t nelem; /* Number of elements used in sequences */
size_t nseq; /* Number of sequences generated */
size_t curr_seq; /* Current sequence being worked on */
/* Get the sequences of bytes */
if(H5S_SELECT_GET_SEQ_LIST(space, 0, &sel_iter, (size_t)H5D_IO_VECTOR_SIZE, max_elem, &nseq, &nelem, off, len) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
/* Loop, while sequences left to process */
for(curr_seq = 0; curr_seq < nseq; curr_seq++) {
hsize_t curr_off; /* Current offset within sequence */
size_t curr_len; /* Length of bytes left to process in sequence */
/* Get the current offset */
curr_off = off[curr_seq];
/* Get the number of bytes in sequence */
curr_len = len[curr_seq];
/* Loop, while bytes left in sequence */
while(curr_len > 0) {
/* Set the displacement of the current point */
disp[u] = curr_off;
/* This is a memory displacement, so for each point selected,
* apply the map that was generated by the file selection */
if((*permute)[u] != num_points) {
MPI_Aint temp = disp[u];
HDmemmove(disp + (*permute)[u] + 1, disp + (*permute)[u],
(u - (*permute)[u]) * sizeof(MPI_Aint));
disp[(*permute)[u]] = temp;
} /* end if */
/* Advance to next element */
u++;
/* Increment offset in dataspace */
curr_off += elmt_size;
/* Decrement number of bytes left in sequence */
curr_len -= elmt_size;
} /* end while */
} /* end for */
/* Decrement number of elements left to process */
max_elem -= nelem;
} /* end while */
/* Create the MPI datatype for the set of element displacements */
if(H5S_mpio_create_point_datatype(elmt_size, num_points, disp, new_type) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create an MPI Datatype from point selection")
/* Set values about MPI datatype created */
*count = 1;
*is_derived_type = TRUE;
done:
/* Release selection iterator */
if(sel_iter_init)
if(H5S_SELECT_ITER_RELEASE(&sel_iter) < 0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator")
/* Free memory */
if(disp)
H5MM_free(disp);
if(*permute) {
H5MM_free(*permute);
*permute = NULL;
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* H5S_mpio_permute_type() */
/*-------------------------------------------------------------------------
* Function: H5S_mpio_hyper_type
*
* Purpose: Translate an HDF5 hyperslab selection into an MPI type.
*
* 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;
int block_length[3];
MPI_Datatype inner_type, outer_type, old_types[3];
MPI_Aint extent_len, displacement[3];
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=%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
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=%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
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]=%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
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=%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.
****************************************/
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 */
displacement[1] = d[i].start * offset[i] * elmt_size;
displacement[2] = (MPI_Aint)elmt_size * max_xtent[i];
if(MPI_SUCCESS != (mpi_code = MPI_Type_extent(outer_type, &extent_len)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_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(displacement[1] > 0 || (int)extent_len < displacement[2]) {
block_length[0] = 1;
block_length[1] = 1;
block_length[2] = 1;
displacement[0] = 0;
old_types[0] = MPI_LB;
old_types[1] = outer_type;
old_types[2] = MPI_UB;
#ifdef H5S_DEBUG
if(H5DEBUG(S))
HDfprintf(H5DEBUG(S), "%s: i=%d Extending struct type\n"
"***displacements: %ld, %ld, %ld\n",
FUNC, i, (long)displacement[0], (long)displacement[1], (long)displacement[2]);
#endif
mpi_code = MPI_Type_struct(3, /* count */
block_length, /* blocklengths */
displacement, /* displacements */
old_types, /* old types */
&inner_type); /* new type */
MPI_Type_free(&outer_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
* thru 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; /* Number of span tree nodes allocated at this level */
size_t outercount; /* 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_hindexed((int)outercount, blocklen, disp, *elmt_type, span_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_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_hvector((int)tspan->nelem, 1, stride, down_type, &inner_type[outercount]))) {
MPI_Type_free(&down_type);
HMPI_GOTO_ERROR(FAIL, "MPI_Type_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_struct((int)outercount, blocklen, disp, inner_type, span_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_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 */
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