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-rw-r--r--src/H5Smpio.c443
1 files changed, 406 insertions, 37 deletions
diff --git a/src/H5Smpio.c b/src/H5Smpio.c
index 77e902f..284e16f 100644
--- a/src/H5Smpio.c
+++ b/src/H5Smpio.c
@@ -43,6 +43,14 @@ 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,
@@ -131,6 +139,335 @@ H5S_mpio_none_type(MPI_Datatype *new_type, int *count, hbool_t *is_derived_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.
@@ -478,7 +815,7 @@ done:
/*-------------------------------------------------------------------------
- * Function: H5S_obtain datatype
+ * Function: H5S_obtain_datatype
*
* Purpose: Obtain an MPI derived datatype based on span-tree
* implementation
@@ -673,8 +1010,9 @@ done:
*-------------------------------------------------------------------------
*/
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)
+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 */
@@ -684,44 +1022,75 @@ H5S_mpio_space_type(const H5S_t *space, size_t elmt_size,
HDassert(space);
HDassert(elmt_size);
- /* Creat MPI type based on the kind of selection */
+ /* Create MPI type based on the kind of selection */
switch(H5S_GET_EXTENT_TYPE(space)) {
case H5S_NULL:
case H5S_SCALAR:
case H5S_SIMPLE:
- 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:
- /* not yet implemented */
- ret_value = FAIL;
- 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 */
+ /* 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: