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authorNeil Fortner <nfortne2@hdfgroup.org>2015-03-30 22:11:58 (GMT)
committerNeil Fortner <nfortne2@hdfgroup.org>2015-03-30 22:11:58 (GMT)
commit904c84b2a2590124713f4187a074c8d89c79b2c1 (patch)
tree35cdb038c60dbeeb6064f7b78efdfed4620cafb1 /src
parente270981617f5e1edec5318b4ed9680eb87940027 (diff)
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[svn-r26668] Fix error in H5D__virtual_read/write that prevented short circuit.
Fix off by 1 error in H5S__hyper_project_intersection algorithm. Add many tests for fixed size hyperslab I/O. Note make check still fails in h5dump test (unrelated to this checkin). Tested: ummon
Diffstat (limited to 'src')
-rw-r--r--src/H5Dvirtual.c9
-rw-r--r--src/H5Shyper.c285
2 files changed, 148 insertions, 146 deletions
diff --git a/src/H5Dvirtual.c b/src/H5Dvirtual.c
index 14efe42..698aea8 100644
--- a/src/H5Dvirtual.c
+++ b/src/H5Dvirtual.c
@@ -1,6 +1,5 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 *
@@ -473,12 +472,12 @@ H5D__virtual_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
if(H5S_select_project_intersection(file_space, mem_space, storage->list[i].virtual_select, &projected_mem_space) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCLIP, FAIL, "can't project virtual intersection onto memory space")
- /* Get number of elements in projected dataspace */
+ /* Get number of elements in projected dataspace */
if((select_nelmts = (hssize_t)H5S_GET_SELECT_NPOINTS(projected_mem_space)) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get number of elements in selection")
/* Only perform I/O if there are any elements */
- if(nelmts > 0) {
+ if(select_nelmts > 0) {
/* Open source dataset */
if(!storage->list[i].source_dset) {
/* Try to open dataset */
@@ -585,7 +584,7 @@ H5D__virtual_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "unable to get number of elements in selection")
/* Only perform I/O if there are any elements */
- if(nelmts > 0) {
+ if(select_nelmts > 0) {
/* Open source dataset, fail if cannot open */
if(!storage->list[i].source_dset) {
//VDSINC check all source datasets before any I/O
@@ -655,6 +654,8 @@ H5D__virtual_flush(H5D_t UNUSED *dset, hid_t UNUSED dxpl_id)
{
FUNC_ENTER_STATIC_NOERR
+ /* Need to decide what to do here - flush only open datasets, try to flush
+ * all, or do nothing and rely on source datasets to flush themselves? */
/* No-op for now VDSINC */
FUNC_LEAVE_NOAPI(SUCCEED)
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index f866e5d..13573e1 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -9010,48 +9010,50 @@ H5S__hyper_project_intersection(const H5S_t *src_space, const H5S_t *dst_space,
HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
sis_nelem -= nelem;
- /* Make sure all sequences are non-empty */
- if((ss_nseq > 0) && (ds_nseq > 0) && (sis_nseq > 0)) {
- /* Loop until we run out of sequences in either the source or source
- * intersect space */
- while(1) {
- if(advance_ss || (ss_off[ss_i] + ss_len[ss_i] <= sis_off[sis_i])) {
- /* Either we finished the current source sequence or the
- * sequences do not intersect. Advance source space. */
- ss_sel_off += (hsize_t)ss_len[ss_i];
- if(++ss_i == ss_nseq) {
- if(ss_nelem > 0) {
- HDassert(0 && "Checking code coverage..."); //VDSINC
- /* Try to grab more sequences from src_space */
- if(H5S_SELECT_GET_SEQ_LIST(src_space, 0u, &ss_iter, H5S_PROJECT_INTERSECT_NSEQS, ss_nelem, &ss_nseq, &nelem, ss_off, ss_len) < 0)
- HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
- HDassert(ss_len[0] > 0);
-
- /* Update ss_nelem */
- HDassert(nelem > 0);
- HDassert(nelem <= ss_nelem);
- ss_nelem -= nelem;
-
- /* Reset source space index */
- ss_i = 0;
- } /* end if */
- else
- /* There are no more sequences in src_space, so we can
- * exit the loop */
- break;
+ /* If any sequences are empty, skip the main loop */
+ if((ss_nseq == 0) || (ds_nseq == 0) || (sis_nseq == 0))
+ goto loop_end;
+
+ /* Loop until we run out of sequences in either the source or source
+ * intersect space */
+ while(1) {
+ while(advance_ss || (ss_off[ss_i] + ss_len[ss_i] <= sis_off[sis_i])) {
+ /* Either we finished the current source sequence or the
+ * sequences do not intersect. Advance source space. */
+ ss_sel_off += (hsize_t)ss_len[ss_i];
+ if(++ss_i == ss_nseq) {
+ if(ss_nelem > 0) {
+ /* Try to grab more sequences from src_space */
+ if(H5S_SELECT_GET_SEQ_LIST(src_space, 0u, &ss_iter, H5S_PROJECT_INTERSECT_NSEQS, ss_nelem, &ss_nseq, &nelem, ss_off, ss_len) < 0)
+ HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
+ HDassert(ss_len[0] > 0);
+
+ /* Update ss_nelem */
+ HDassert(nelem > 0);
+ HDassert(nelem <= ss_nelem);
+ ss_nelem -= nelem;
+
+ /* Reset source space index */
+ ss_i = 0;
} /* end if */
-
- /* Reset advance_ss */
- advance_ss = FALSE;
+ else
+ /* There are no more sequences in src_space, so we can exit
+ * the loop. Use goto instead of break so we exit the outer
+ * loop. */
+ goto loop_end;
} /* end if */
- else if(advance_sis
- || (sis_off[sis_i] + sis_len[sis_i] <= ss_off[ss_i])) {
+
+ /* Reset advance_ss */
+ advance_ss = FALSE;
+ } /* end if */
+ if(advance_sis
+ || (sis_off[sis_i] + sis_len[sis_i] <= ss_off[ss_i])) {
+ do {
/* Either we finished the current source intersect sequence or
* the sequences do not intersect. Advance source intersect
* space. */
if(++sis_i == sis_nseq) {
if(sis_nelem > 0) {
- HDassert(0 && "Checking code coverage..."); //VDSINC
/* Try to grab more sequences from src_intersect_space
*/
if(H5S_SELECT_GET_SEQ_LIST(src_intersect_space, 0u, &sis_iter, H5S_PROJECT_INTERSECT_NSEQS, sis_nelem, &sis_nseq, &nelem, sis_off, sis_len) < 0)
@@ -9068,120 +9070,122 @@ H5S__hyper_project_intersection(const H5S_t *src_space, const H5S_t *dst_space,
} /* end if */
else
/* There are no more sequences in src_intersect_space,
- * so we can exit the loop */
- break;
+ * so we can exit the loop. Use goto instead of break
+ * so we exit the outer loop. */
+ goto loop_end;
} /* end if */
+ } while(sis_off[sis_i] + sis_len[sis_i] <= ss_off[ss_i]);
- /* Reset advance_sis */
- advance_sis = FALSE;
+ /* Reset advance_sis */
+ advance_sis = FALSE;
+ } /* end if */
+ else {
+ /* Sequences intersect, add intersection to projected space */
+ /* Calculate intersection sequence in terms of offset within source
+ * selection and advance any sequences we complete */
+ if(ss_off[ss_i] >= sis_off[sis_i])
+ int_sel_off = ss_sel_off;
+ else
+ int_sel_off = sis_off[sis_i] - ss_off[ss_i] + ss_sel_off;
+ if((ss_off[ss_i] + (hsize_t)ss_len[ss_i]) <= (sis_off[sis_i]
+ + (hsize_t)sis_len[sis_i])) {
+ int_len = (size_t)((hsize_t)ss_len[ss_i] + ss_sel_off - int_sel_off);
+ advance_ss = TRUE;
} /* end if */
- else {
- /* Sequences intersect, add intersection to projected space */
- /* Calculate intersection sequence in terms of offset within
- * source selection and advance any sequences we complete */
- if(ss_off[ss_i] >= sis_off[sis_i])
- int_sel_off = ss_sel_off;
- else
- int_sel_off = sis_off[sis_i] - ss_off[ss_i] + ss_sel_off;
- if((ss_off[ss_i] + (hsize_t)ss_len[ss_i]) <= (sis_off[sis_i]
- + (hsize_t)sis_len[sis_i])) {
- int_len = (size_t)((hsize_t)ss_len[ss_i] + ss_sel_off - int_sel_off);
- advance_ss = TRUE;
- } /* end if */
- else
- int_len = (size_t)(sis_off[sis_i] + (hsize_t)sis_len[sis_i] - ss_off[ss_i] + ss_sel_off - int_sel_off);
- if((ss_off[ss_i] + (hsize_t)ss_len[ss_i]) >= (sis_off[sis_i]
- + (hsize_t)sis_len[sis_i]))
- advance_sis = TRUE;
-
- /* Project intersection sequence to destination selection */
- while(int_len > (size_t)0) {
- while(ds_sel_off + (hsize_t)ds_len[ds_i] <= int_sel_off) {
- /* Intersection is not projected to this destination
- * sequence, advance destination space */
- ds_sel_off += (hsize_t)ds_len[ds_i];
- if(++ds_i == ds_nseq) {
- HDassert(0 && "Checking code coverage..."); //VDSINC
- HDassert(ds_nelem > 0);
-
- /* Try to grab more sequences from dst_space */
- if(H5S_SELECT_GET_SEQ_LIST(dst_space, 0u, &ds_iter, H5S_PROJECT_INTERSECT_NSEQS, ds_nelem, &ds_nseq, &nelem, ds_off, ds_len) < 0)
- HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
- HDassert(ds_len[0] > 0);
-
- /* Update ss_nelem */
- HDassert(nelem > 0);
- HDassert(nelem <= ds_nelem);
- ds_nelem -= nelem;
-
- /* Reset source space index */
- ds_i = 0;
- } /* end if */
- } /* end while */
+ else
+ int_len = (size_t)(sis_off[sis_i] + (hsize_t)sis_len[sis_i] - ss_off[ss_i] + ss_sel_off - int_sel_off);
+ if((ss_off[ss_i] + (hsize_t)ss_len[ss_i]) >= (sis_off[sis_i]
+ + (hsize_t)sis_len[sis_i]))
+ advance_sis = TRUE;
+
+ /* Project intersection sequence to destination selection */
+ while(int_len > (size_t)0) {
+ while(ds_sel_off + (hsize_t)ds_len[ds_i] <= int_sel_off) {
+ /* Intersection is not projected to this destination
+ * sequence, advance destination space */
+ ds_sel_off += (hsize_t)ds_len[ds_i];
+ if(++ds_i == ds_nseq) {
+ HDassert(ds_nelem > 0);
+
+ /* Try to grab more sequences from dst_space */
+ if(H5S_SELECT_GET_SEQ_LIST(dst_space, 0u, &ds_iter, H5S_PROJECT_INTERSECT_NSEQS, ds_nelem, &ds_nseq, &nelem, ds_off, ds_len) < 0)
+ HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed")
+ HDassert(ds_len[0] > 0);
- /* Add sequence to projected space */
- HDassert(ds_sel_off <= int_sel_off);
- proj_off = ds_off[ds_i] + int_sel_off - ds_sel_off;
- proj_len = proj_len_rem = MIN(int_len, (size_t)(ds_sel_off
- + (hsize_t)ds_len[ds_i] - int_sel_off + (hsize_t)1));
-
- /* Add to span tree */
- while(proj_len_rem > (size_t)0) {
- /* Check for more than one full row (in every dim) and
- * append multiple spans at once? -NAF */
- /* Append spans in higher dimensions if we're going
- * ouside the plane of the span currently being built
- * (i.e. it's finished being built) */
- for(i = proj_rank - 1; ((i > 0)
- && (((proj_off / proj_down_dims[i])
- % proj_space->extent.size[i])
- != curr_span_dim[i - 1])); i--) {
- if(curr_span_tree[i]) {
- HDassert(prev_span[i]);
-
- /* Append complete lower dimension span tree to
- * current dimension */
- if(H5S_hyper_append_span(&prev_span[i - 1], &curr_span_tree[i - 1], curr_span_dim[i - 1], curr_span_dim[i - 1], curr_span_tree[i], NULL) < 0)
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate hyperslab span")
-
- /* Reset lower dimension's span tree and previous
- * span since we just committed it and will start
- * over with a new one */
- if(H5S_hyper_free_span_info(curr_span_tree[i]) < 0)
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't free span info")
- curr_span_tree[i] = NULL;
- prev_span[i] = NULL;
- } /* end if */
+ /* Update ss_nelem */
+ HDassert(nelem > 0);
+ HDassert(nelem <= ds_nelem);
+ ds_nelem -= nelem;
- /* Update curr_span_dim */
- curr_span_dim[i - 1] = (proj_off / proj_down_dims[i]) % proj_space->extent.size[i];
- } /* end for */
+ /* Reset source space index */
+ ds_i = 0;
+ } /* end if */
+ } /* end while */
- /* Compute bounds for new span in lowest dimension */
- low = proj_off % proj_space->extent.size[proj_rank - 1];
- span_len = MIN(proj_len_rem,
- (size_t)(proj_space->extent.size[proj_rank - 1]
- - low));
- HDassert(proj_len_rem >= span_len);
- high = low + (hsize_t)span_len - (hsize_t)1;
+ /* Add sequence to projected space */
+ HDassert(ds_sel_off <= int_sel_off);
+ proj_off = ds_off[ds_i] + int_sel_off - ds_sel_off;
+ proj_len = proj_len_rem = (size_t)MIN(int_len,
+ (size_t)(ds_sel_off + (hsize_t)ds_len[ds_i]
+ - int_sel_off));
+
+ /* Add to span tree */
+ while(proj_len_rem > (size_t)0) {
+ /* Check for more than one full row (in every dim) and
+ * append multiple spans at once? -NAF */
+ /* Append spans in higher dimensions if we're going ouside
+ * the plane of the span currently being built (i.e. it's
+ * finished being built) */
+ for(i = proj_rank - 1; ((i > 0)
+ && (((proj_off / proj_down_dims[i])
+ % proj_space->extent.size[i])
+ != curr_span_dim[i - 1])); i--) {
+ if(curr_span_tree[i]) {
+ HDassert(prev_span[i]);
+
+ /* Append complete lower dimension span tree to
+ * current dimension */
+ if(H5S_hyper_append_span(&prev_span[i - 1], &curr_span_tree[i - 1], curr_span_dim[i - 1], curr_span_dim[i - 1], curr_span_tree[i], NULL) < 0)
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate hyperslab span")
- /* Append span in lowest dimension */
- if(H5S_hyper_append_span(&prev_span[proj_rank - 1], &curr_span_tree[proj_rank - 1], low, high, NULL, NULL) < 0)
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate hyperslab span")
+ /* Reset lower dimension's span tree and previous
+ * span since we just committed it and will start
+ * over with a new one */
+ if(H5S_hyper_free_span_info(curr_span_tree[i]) < 0)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't free span info")
+ curr_span_tree[i] = NULL;
+ prev_span[i] = NULL;
+ } /* end if */
- /* Update remaining offset and length */
- proj_off += (hsize_t)span_len;
- proj_len_rem -= span_len;
- } /* end while */
+ /* Update curr_span_dim */
+ curr_span_dim[i - 1] = (proj_off / proj_down_dims[i]) % proj_space->extent.size[i];
+ } /* end for */
+
+ /* Compute bounds for new span in lowest dimension */
+ low = proj_off % proj_space->extent.size[proj_rank - 1];
+ span_len = MIN(proj_len_rem,
+ (size_t)(proj_space->extent.size[proj_rank - 1]
+ - low));
+ HDassert(proj_len_rem >= span_len);
+ high = low + (hsize_t)span_len - (hsize_t)1;
+
+ /* Append span in lowest dimension */
+ if(H5S_hyper_append_span(&prev_span[proj_rank - 1], &curr_span_tree[proj_rank - 1], low, high, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate hyperslab span")
- /* Update intersection sequence */
- int_sel_off += (hsize_t)proj_len;
- int_len -= proj_len;
+ /* Update remaining offset and length */
+ proj_off += (hsize_t)span_len;
+ proj_len_rem -= span_len;
} /* end while */
- } /* end else */
- } /* end while */
- } /* end if */
+ /* Update intersection sequence */
+ int_sel_off += (hsize_t)proj_len;
+ int_len -= proj_len;
+ } /* end while */
+ } /* end else */
+ } /* end while */
+
+loop_end:
/* Add remaining spans to span tree */
for(i = proj_rank - 1; i > 0; i--)
if(curr_span_tree[i]) {
@@ -9210,13 +9214,10 @@ H5S__hyper_project_intersection(const H5S_t *src_space, const H5S_t *dst_space,
if(H5S_hyper_rebuild(proj_space) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOUNT, FAIL, "can't rebuild hyperslab info")
} /* end if */
- else {
- HDassert(0 && "Checking code coverage..."); //VDSINC
+ else
/* If we did not add anything to proj_space, select none instead */
if(H5S_select_none(proj_space) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTDELETE, FAIL, "can't convert selection")
- } /* end else */
-
done:
/* Release source selection iterator */