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authorQuincey Koziol <koziol@hdfgroup.org>2001-01-18 22:01:17 (GMT)
committerQuincey Koziol <koziol@hdfgroup.org>2001-01-18 22:01:17 (GMT)
commit7c8547ed04497b1da081f7b161c229a29bf522c8 (patch)
tree88eb2a43af575b2fc67f27aae717897fd171b53b
parente108a974a055c9ceda186860c92289b478dc2d53 (diff)
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[svn-r3302] Purpose:
Bug fix Description: Certain combinations of hyperslabs, especially those that have to be strip-mined during I/O were causing data to be incorrectly transferred. Solution: Changed the code in H5S_get_hyper_regions to be more careful about the regions of the current dimension that are valid. Sometimes, regions which had already been iterated through were being re-processed. Platforms tested: FreeBSD 4.2 (hawkwind)
-rw-r--r--src/H5D.c10
-rw-r--r--src/H5Shyper.c167
2 files changed, 111 insertions, 66 deletions
diff --git a/src/H5D.c b/src/H5D.c
index 2f50613..15f2f54 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -1823,12 +1823,18 @@ printf("%s: check 2.0, src_type_size=%d, dst_type_size=%d, target_size=%d, min_e
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
}
if (NULL==(tconv_buf=xfer_parms->tconv_buf)) {
+#ifdef QAK
+ printf("%s: check 3.1, allocating conversion buffer\n",FUNC);
+#endif
/* Allocate temporary buffer */
if((tconv_buf=H5FL_BLK_ALLOC(type_conv,target_size,0))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed for type conversion");
}
if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) {
+#ifdef QAK
+ printf("%s: check 3.2, allocating conversion buffer\n",FUNC);
+#endif
/* Allocate temporary buffer */
if((bkg_buf=H5FL_BLK_ALLOC(bkgr_conv,request_nelmts*dst_type_size,0))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
@@ -1876,6 +1882,7 @@ printf("%s: check 2.0, src_type_size=%d, dst_type_size=%d, target_size=%d, min_e
#ifdef QAK
printf("%s: check 6.0\n",FUNC);
+#ifdef QAK
{
int i;
int *b;
@@ -1889,7 +1896,8 @@ printf("%s: check 2.0, src_type_size=%d, dst_type_size=%d, target_size=%d, min_e
printf("\n");
/* } */
}
-#endif
+#endif /* QAK */
+#endif /* QAK */
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index 08cad89..e446157 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -219,7 +219,7 @@ H5S_hyper_favail (const H5S_t UNUSED *space,
assert (sel_iter);
#ifdef QAK
- printf("%s: max=%u\n",FUNC,(unsigned)max);
+ printf("%s: sel_iter->hyp.elmt_left=%u, max=%u\n",FUNC,(unsigned)sel_iter->hyp.elmt_left,(unsigned)max);
#endif /* QAK */
FUNC_LEAVE (MIN(sel_iter->hyp.elmt_left,max));
} /* H5S_hyper_favail() */
@@ -297,69 +297,83 @@ H5S_hyper_get_regions (size_t *num_regions, uintn rank, uintn dim,
printf("%s: %d - pos=%d, offset=%d\n",FUNC,i,(int)pos[i],offset!=NULL ? (int)offset[i] : 0);
#endif /* QAK */
-#ifdef QAK
- printf("%s: check 1.1, bound_count=%d, pos[%d]=%d\n",FUNC,bound_count,(int)dim,(int)pos[dim]);
-#endif /* QAK */
-
/* Iterate over the blocks which fit the position, or all of the blocks, if pos[dim]==-1 */
lo_bound_dim=lo_bounds[dim];
pos_dim=pos[dim];
off_dim=offset[dim];
- for(i=0; i<bound_count && (pos_dim<0 || pos_dim>=lo_bound_dim->bound+off_dim); i++,lo_bound_dim++) {
#ifdef QAK
-printf("%s: check 1.2, i=%d, num_reg=%d, curr_reg=%d\n",FUNC,(int)i,(int)num_reg,(int)curr_reg);
+ printf("%s: check 1.1, bound_count=%d, pos_dim=%d\n",FUNC,bound_count,(int)pos_dim);
+#endif /* QAK */
+
+ for(i=0; i<bound_count; i++,lo_bound_dim++) {
+#ifdef QAK
+ printf("%s: check 1.2, i=%d, num_reg=%d, curr_reg=%d\n",FUNC,(int)i,(int)num_reg,(int)curr_reg);
+ printf("%s: check 1.2.1, lo_bound_dim->bound=%d\n",FUNC,(int)lo_bound_dim->bound);
#endif /* QAK */
/* Check if each boundary overlaps in the higher dimensions */
node=lo_bound_dim->node;
- temp_dim=(dim-1);
- node_start=node->start+temp_dim;
- node_end=node->end+temp_dim;
- tmp_pos=pos+temp_dim;
- tmp_off=offset+temp_dim;
- while(temp_dim>=0 && *tmp_pos>=(*node_start+*tmp_off) && *tmp_pos<=(*node_end+*tmp_off)) {
- temp_dim--;
- node_start--;
- node_end--;
- tmp_pos--;
- tmp_off--;
- }
+ if(pos_dim<0 || (node->end[dim]+off_dim)>=pos_dim) {
+ temp_dim=(dim-1);
+ if(temp_dim>=0) {
+ node_start=node->start+temp_dim;
+ node_end=node->end+temp_dim;
+ tmp_pos=pos+temp_dim;
+ tmp_off=offset+temp_dim;
+ while(temp_dim>=0 && *tmp_pos>=(*node_start+*tmp_off) && *tmp_pos<=(*node_end+*tmp_off)) {
+ temp_dim--;
+ node_start--;
+ node_end--;
+ tmp_pos--;
+ tmp_off--;
+ } /* end while */
+ } /* end if */
#ifdef QAK
-printf("%s: check 1.3, i=%d, temp_dim=%d\n",FUNC,(int)i,(int)temp_dim);
+ printf("%s: check 1.3, i=%d, temp_dim=%d\n",FUNC,(int)i,(int)temp_dim);
#endif /* QAK */
- /* Yes, all previous positions match, this is a valid region */
- if(temp_dim<0) {
- /* Check if we've allocated the array yet */
- if(num_reg==0) {
- /* Allocate temporary buffer, big enough for worst case size */
- reg=H5FL_ARR_ALLOC(H5S_hyper_region_t,(hsize_t)bound_count,0);
-
- /* Initialize with first region */
- reg[num_reg].start=MAX(node->start[dim],pos[dim])+offset[dim];
- reg[num_reg].end=node->end[dim]+offset[dim];
- reg[num_reg].node=node;
+ /* Yes, all previous positions match, this is a valid region */
+ if(temp_dim<0) {
+#ifdef QAK
+ printf("%s: check 1.4, node->start[%d]=%d, node->end[%d]=%d\n",FUNC,(int)dim,(int)node->start[dim],(int)dim,(int)node->end[dim]);
+#endif /* QAK */
+ /* Check if we've allocated the array yet */
+ if(num_reg==0) {
+ /* Allocate temporary buffer, big enough for worst case size */
+ reg=H5FL_ARR_ALLOC(H5S_hyper_region_t,(hsize_t)bound_count,0);
- /* Increment the number of regions */
- num_reg++;
- curr_reg++;
- } else {
- /* Try to merge regions together in all dimensions, except the final one */
- if(dim<(rank-1) && (node->start[dim]+offset[dim])<=(reg[curr_reg].end+1)) {
- reg[curr_reg].end=MAX(node->end[dim],reg[curr_reg].end)+offset[dim];
- } else { /* no overlap with previous region, add new region */
- /* Initialize with new region */
- reg[num_reg].start=node->start[dim]+offset[dim];
+ /* Initialize with first region */
+ reg[num_reg].start=MAX(node->start[dim],pos[dim])+offset[dim];
reg[num_reg].end=node->end[dim]+offset[dim];
reg[num_reg].node=node;
- /*
- * Increment the number of regions & the current
- * region.
- */
+ /* Increment the number of regions */
num_reg++;
curr_reg++;
+ } else {
+ /* Try to merge regions together in all dimensions, except the final one */
+ if(dim<(rank-1) && (node->start[dim]+offset[dim])<=(reg[curr_reg].end+1)) {
+#ifdef QAK
+ printf("%s: check 1.4.1\n",FUNC);
+#endif /* QAK */
+ reg[curr_reg].end=MAX(node->end[dim],reg[curr_reg].end)+offset[dim];
+ } else { /* no overlap with previous region, add new region */
+#ifdef QAK
+ printf("%s: check 1.4.2\n",FUNC);
+#endif /* QAK */
+ /* Initialize with new region */
+ reg[num_reg].start=node->start[dim]+offset[dim];
+ reg[num_reg].end=node->end[dim]+offset[dim];
+ reg[num_reg].node=node;
+
+ /*
+ * Increment the number of regions & the current
+ * region.
+ */
+ num_reg++;
+ curr_reg++;
+ } /* end else */
} /* end else */
- } /* end else */
+ } /* end if */
} /* end if */
} /* end for */
@@ -471,6 +485,9 @@ H5S_hyper_block_read (H5S_hyper_node_t *node, H5S_hyper_io_info_t *io_info, hsiz
!! NOTE !! This will need to be changed for different dimension
permutations from the standard 'C' ordering!
*/
+#ifdef QAK
+ printf("%s: check 1.0, io_info->dst=%p, node->cinfo.rpos=%p, region_size=%lu, io_info->elmt_size=%lu\n",FUNC,io_info->dst,node->cinfo.rpos,(unsigned long)region_size,(unsigned long)io_info->elmt_size);
+#endif /* QAK */
HDmemcpy(io_info->dst, node->cinfo.rpos, (size_t)(region_size*io_info->elmt_size));
/*
@@ -588,6 +605,9 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
size_t num_regions; /* number of regions overlapped */
size_t i; /* Counters */
intn j;
+#ifdef QAK
+ uintn u;
+#endif /* QAK */
hsize_t num_read=0; /* Number of elements read */
const H5D_xfer_t *xfer_parms;/* Data transfer property list */
@@ -613,7 +633,7 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
io_info->space->select.sel_info.hslab.hyper_lst->lo_bounds,
io_info->iter->hyp.pos,io_info->space->select.offset))!=NULL) {
- /*
+ /*
* Check if this is the second to last dimension in dataset (Which
* means that we've got a list of the regions in the fastest changing
* dimension and should input those regions).
@@ -622,10 +642,10 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
if(dim>=0) {
printf("%s: check 2.0, rank=%d, ",
FUNC,(int)io_info->space->extent.u.simple.rank);
- printf("pos={",FUNC);
- for(j=0; j<io_info->space->extent.u.simple.rank; j++) {
- printf("%d",(int)io_info->iter->hyp.pos[j]);
- if(j<io_info->space->extent.u.simple.rank-1)
+ printf("%s: pos={",FUNC);
+ for(u=0; u<io_info->space->extent.u.simple.rank; u++) {
+ printf("%d",(int)io_info->iter->hyp.pos[u]);
+ if(u<io_info->space->extent.u.simple.rank-1)
printf(", ");
} /* end for */
printf("}\n");
@@ -633,8 +653,8 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
else
printf("%s: check 2.0, rank=%d\n",
FUNC,(int)io_info->space->extent.u.simple.rank);
- for(i=0; i<num_regions; i++)
- printf("%s: check 2.1, region #%d: start=%d, end=%d\n",
+ for(i=0; i<num_regions; i++)
+ printf("%s: check 2.1, region #%d: start=%d, end=%d\n",
FUNC,i,(int)regions[i].start,(int)regions[i].end);
#endif /* QAK */
if((uintn)(dim+2)==io_info->space->extent.u.simple.rank) {
@@ -648,7 +668,7 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
region_size=MIN((hssize_t)io_info->nelmts, (regions[i].end-regions[i].start)+1);
#ifdef QAK
- printf("%s: check 2.1.2, region=%d, region_size=%d\n",FUNC,(int)i,(int)region_size);
+ printf("%s: check 2.1.2, region=%d, region_size=%d, num_read=%lu\n",FUNC,(int)i,(int)region_size,(unsigned long)num_read);
#endif /* QAK */
/* Check if this hyperslab block is cached or could be cached */
if(!regions[i].node->cinfo.cached &&
@@ -672,7 +692,7 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
}
else {
#ifdef QAK
- printf("%s: check 2.1.5, reading block from file\n",FUNC);
+ printf("%s: check 2.1.5, reading block from file, parm_init=%d\n",FUNC,(int)parm_init);
#endif /* QAK */
/* Set up hyperslab I/O parameters which apply to all regions */
if(!parm_init) {
@@ -707,9 +727,9 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
#ifdef QAK
printf("%s: check 2.3, region #%d\n",FUNC,(int)i);
printf("pos={");
- for(j=0; j<io_info->space->extent.u.simple.rank; j++) {
- printf("%d",(int)io_info->iter->hyp.pos[j]);
- if(j<io_info->space->extent.u.simple.rank-1)
+ for(u=0; u<io_info->space->extent.u.simple.rank; u++) {
+ printf("%d",(int)io_info->iter->hyp.pos[u]);
+ if(u<io_info->space->extent.u.simple.rank-1)
printf(", ");
} /* end for */
printf("}\n");
@@ -773,7 +793,7 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
/* Step through each location in each region */
for(j=MAX(io_info->iter->hyp.pos[dim],regions[i].start); j<=regions[i].end && io_info->nelmts>0; j++) {
#ifdef QAK
- printf("%s: check 4.0, dim=%d, location=%d\n",FUNC,dim,j);
+ printf("%s: check 4.0, dim=%d, j=%d, num_read=%lu\n",FUNC,dim,j,(unsigned long)num_read);
#endif /* QAK */
/* Set the correct position we are working on */
@@ -788,13 +808,11 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
} /* end for */
#ifdef QAK
{
- intn k;
-
printf("%s: check 5.0, dim=%d, j=%d, region #%d={%d, %d}\n",FUNC,(int)dim,(int)j,(int)i,(int)regions[i].start,(int)regions[i].end);
- printf("pos={");
- for(k=0; k<io_info->space->extent.u.simple.rank; k++) {
- printf("%d",(int)io_info->iter->hyp.pos[k]);
- if(k<io_info->space->extent.u.simple.rank-1)
+ printf("%s: pos={",FUNC);
+ for(u=0; u<io_info->space->extent.u.simple.rank; u++) {
+ printf("%d",(int)io_info->iter->hyp.pos[u]);
+ if(u<io_info->space->extent.u.simple.rank-1)
printf(", ");
} /* end for */
printf("}\n");
@@ -4717,6 +4735,25 @@ H5S_generate_hyperslab (H5S_t *space, H5S_seloper_t op,
/* (Why someone would torture us this way, I don't know... -QAK :-) */
for(u=0; u<space->extent.u.simple.rank; u++)
slab[u]=count[u]*stride[u];
+#ifdef QAK
+ printf("%s: check 4.2\n",FUNC);
+ printf("%s: start = {",FUNC);
+ for(u=0; u<space->extent.u.simple.rank; u++) {
+ printf("%d",(int)start[u]);
+ if(u<(space->extent.u.simple.rank-1))
+ printf(", ");
+ else
+ printf("}\n");
+ }
+ printf("%s: slab = {",FUNC);
+ for(u=0; u<space->extent.u.simple.rank; u++) {
+ printf("%d",(int)slab[u]);
+ if(u<(space->extent.u.simple.rank-1))
+ printf(", ");
+ else
+ printf("}\n");
+ }
+#endif /* QAK */
/* Add the contiguous hyperslab to the selection */
if(H5S_hyper_node_add(&add,0,space->extent.u.simple.rank,start,(const hsize_t *)slab)<0) {