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author | Quincey Koziol <koziol@hdfgroup.org> | 1998-07-10 17:54:19 (GMT) |
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committer | Quincey Koziol <koziol@hdfgroup.org> | 1998-07-10 17:54:19 (GMT) |
commit | b7f334adb4acec6ff0171b8dda6f9873d8c67bb5 (patch) | |
tree | 74e271bf28a0277206d4d438d9752fa50a6794a8 /src/H5Shyper.c | |
parent | f87dbef4ca00da7bb9b89faf3d982156878c600d (diff) | |
download | hdf5-b7f334adb4acec6ff0171b8dda6f9873d8c67bb5.zip hdf5-b7f334adb4acec6ff0171b8dda6f9873d8c67bb5.tar.gz hdf5-b7f334adb4acec6ff0171b8dda6f9873d8c67bb5.tar.bz2 |
[svn-r480] Fixed an ugly bug by teaching the recursive hyperslab I/O code how to resume
when a buffer gets full. Also removed the check for disallowing zero-dim
extents on unlimited dimension datasets, per user's request.
Diffstat (limited to 'src/H5Shyper.c')
-rw-r--r-- | src/H5Shyper.c | 178 |
1 files changed, 119 insertions, 59 deletions
diff --git a/src/H5Shyper.c b/src/H5Shyper.c index 757b21c..0c9371e 100644 --- a/src/H5Shyper.c +++ b/src/H5Shyper.c @@ -73,8 +73,10 @@ H5S_hyper_init (const struct H5O_layout_t __unused__ *layout, /* Initialize the number of points to iterate over */ sel_iter->hyp.elmt_left=space->select.num_elem; - /* Start at the origin of the array */ - sel_iter->hyp.pos = H5MM_calloc(space->extent.u.simple.rank*sizeof(hssize_t)); + /* Allocate the position & initialize to invalid location */ + sel_iter->hyp.pos = H5MM_malloc(space->extent.u.simple.rank*sizeof(hssize_t)); + sel_iter->hyp.pos[0]=(-1); + H5V_array_fill(sel_iter->hyp.pos,sel_iter->hyp.pos,sizeof(hssize_t),space->extent.u.simple.rank); FUNC_LEAVE (SUCCEED); } /* H5S_hyper_init() */ @@ -102,6 +104,9 @@ H5S_hyper_favail (const H5S_t __unused__ *space, const H5S_sel_iter_t *sel_iter, assert (space && H5S_SEL_HYPERSLABS==space->select.type); assert (sel_iter); +#ifdef QAK +printf("%s: max=%d\n",FUNC,(int)max); +#endif /* QAK */ FUNC_LEAVE (MIN(sel_iter->hyp.elmt_left,max)); } /* H5S_hyper_favail() */ @@ -142,6 +147,8 @@ H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, #ifdef QAK printf("%s: check 1.0, dim=%d\n",FUNC,dim); +for(i=0; i<2; i++) + printf("%s: %d - pos=%d\n",FUNC,i,(int)pos[i]); #endif /* QAK */ /* Check if we need to generate a list of regions for the 0th dim. */ @@ -150,34 +157,37 @@ printf("%s: check 1.0, dim=%d\n",FUNC,dim); printf("%s: check 1.1, bound_count=%d\n",FUNC,bound_count); #endif /* QAK */ for(i=0; i<bound_count; i++) { - /* Check if we've allocated the array yet */ - if(num_reg==0) { - /* Allocate array */ - ret_value=H5MM_malloc(sizeof(H5S_hyper_region_t)); - - /* Initialize with first region */ - ret_value[0].start=lo_bounds[0][i].bound; - ret_value[0].end=hi_bounds[0][i].bound; - - /* Increment the number of regions */ - num_reg++; - } else { - /* Check if we should merge this region into the current region */ - if(lo_bounds[0][i].bound<ret_value[curr_reg].end) - ret_value[curr_reg].end=MAX(hi_bounds[0][i].bound,ret_value[curr_reg].end); - else { /* no overlap with previous region, add new region */ - /* Enlarge array */ - ret_value=H5MM_realloc(ret_value,sizeof(H5S_hyper_region_t)*(num_reg+1)); - - /* Initialize with new region */ - ret_value[num_reg].start=lo_bounds[0][i].bound; - ret_value[num_reg].end=hi_bounds[0][i].bound; - - /* Increment the number of regions & the current region */ + /* Skip past already iterated regions */ + if(pos[0]==(-1) || (pos[0]>=lo_bounds[0][i].bound && pos[0]<=hi_bounds[0][i].bound)) { + /* Check if we've allocated the array yet */ + if(num_reg==0) { + /* Allocate array */ + ret_value=H5MM_malloc(sizeof(H5S_hyper_region_t)); + + /* Initialize with first region */ + ret_value[0].start=MAX(lo_bounds[0][i].bound,pos[0]); + ret_value[0].end=hi_bounds[0][i].bound; + + /* Increment the number of regions */ num_reg++; - curr_reg++; + } else { + /* Check if we should merge this region into the current region */ + if(lo_bounds[0][i].bound<ret_value[curr_reg].end) + ret_value[curr_reg].end=MAX(hi_bounds[0][i].bound,ret_value[curr_reg].end); + else { /* no overlap with previous region, add new region */ + /* Enlarge array */ + ret_value=H5MM_realloc(ret_value,sizeof(H5S_hyper_region_t)*(num_reg+1)); + + /* Initialize with new region */ + ret_value[num_reg].start=lo_bounds[0][i].bound; + ret_value[num_reg].end=hi_bounds[0][i].bound; + + /* Increment the number of regions & the current region */ + num_reg++; + curr_reg++; + } /* end else */ } /* end else */ - } /* end else */ + } /* end if */ } /* end for */ } else { /* Generate list of regions based on the current position */ #ifdef QAK @@ -200,7 +210,7 @@ printf("%s: check 2.0, bound_count=%d\n",FUNC,bound_count); ret_value=H5MM_malloc(sizeof(H5S_hyper_region_t)); /* Initialize with first region */ - ret_value[0].start=lo_bounds[next_dim][i].bound; + ret_value[0].start=MAX(lo_bounds[next_dim][i].bound,pos[next_dim]); ret_value[0].end=hi_bounds[next_dim][i].bound; /* Increment the number of regions */ @@ -258,6 +268,7 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) { hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ + hsize_t region_size; /* Size of lowest region */ hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ H5S_hyper_region_t *regions; /* Pointer to array of hyperslab nodes overlapped */ size_t num_regions; /* number of regions overlapped */ @@ -305,11 +316,12 @@ for(i=0; i<num_regions; i++) HDmemset (zero, 0, fhyper_info->layout->ndims*sizeof(*zero)); /* perform I/O on data from regions */ - for(i=0; i<num_regions; i++) { + for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { #ifdef QAK -printf("%s: check 2.1, i=%d\n",FUNC,(int)i); +printf("%s: check 2.2, i=%d\n",FUNC,(int)i); #endif /* QAK */ - hsize[fhyper_info->space->extent.u.simple.rank-1]=(regions[i].end-regions[i].start)+1; + region_size=MIN(fhyper_info->nelmts,(regions[i].end-regions[i].start)+1); + hsize[fhyper_info->space->extent.u.simple.rank-1]=region_size; file_offset[fhyper_info->space->extent.u.simple.rank-1]=regions[i].start; /* @@ -322,17 +334,28 @@ printf("%s: check 2.1, i=%d\n",FUNC,(int)i); HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error"); } #ifdef QAK -printf("%s: check 2.2\n",FUNC); +printf("%s: check 2.3, region #%d\n",FUNC,(int)i); +for(j=0; j<fhyper_info->space->extent.u.simple.rank; j++) + printf("%s: %d - pos=%d\n",FUNC,j,(int)fhyper_info->iter->hyp.pos[j]); #endif /* QAK */ /* Advance the pointer in the buffer */ - fhyper_info->dst=((uint8 *)fhyper_info->dst)+((regions[i].end-regions[i].start)+1)*fhyper_info->elmt_size; + fhyper_info->dst=((uint8 *)fhyper_info->dst)+region_size*fhyper_info->elmt_size; /* Increment the number of elements read */ - num_read+=(regions[i].end-regions[i].start)+1; + num_read+=region_size; + + /* Decrement the buffer left */ + fhyper_info->nelmts-=region_size; + + /* Set the next position to start at */ + if(region_size==(hsize_t)((regions[i].end-regions[i].start)+1)) + fhyper_info->iter->hyp.pos[dim+1]=(-1); + else + fhyper_info->iter->hyp.pos[dim+1]=regions[i].start+region_size; /* Decrement the iterator count */ - fhyper_info->iter->hyp.elmt_left-=(regions[i].end-regions[i].start)+1; + fhyper_info->iter->hyp.elmt_left-=region_size; } /* end for */ } else { /* recurse on each region to next dimension down */ #ifdef QAK @@ -343,9 +366,9 @@ printf("%s: check 3.0, num_regions=%d\n",FUNC,(int)num_regions); dim++; /* Step through each region in this dimension */ - for(i=0; i<num_regions; i++) { + for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { /* Step through each location in each region */ - for(j=regions[i].start; j<=regions[i].end; j++) { + for(j=regions[i].start; j<=regions[i].end && fhyper_info->nelmts>0; j++) { #ifdef QAK printf("%s: check 4.0, dim=%d, location=%d\n",FUNC,dim,j); #endif /* QAK */ @@ -483,6 +506,7 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) { hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ + hsize_t region_size; /* Size of lowest region */ hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ H5S_hyper_region_t *regions; /* Pointer to array of hyperslab nodes overlapped */ size_t num_regions; /* number of regions overlapped */ @@ -521,8 +545,9 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) HDmemset (zero, 0, fhyper_info->layout->ndims*sizeof(*zero)); /* perform I/O on data from regions */ - for(i=0; i<num_regions; i++) { - hsize[fhyper_info->space->extent.u.simple.rank-1]=(regions[i].end-regions[i].start)+1; + for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { + region_size=MIN(fhyper_info->nelmts,(regions[i].end-regions[i].start)+1); + hsize[fhyper_info->space->extent.u.simple.rank-1]=region_size; file_offset[fhyper_info->space->extent.u.simple.rank-1]=regions[i].start; /* @@ -536,13 +561,22 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) } /* Advance the pointer in the buffer */ - fhyper_info->src=((const uint8 *)fhyper_info->src)+((regions[i].end-regions[i].start)+1)*fhyper_info->elmt_size; + fhyper_info->src=((const uint8 *)fhyper_info->src)+region_size*fhyper_info->elmt_size; /* Increment the number of elements read */ - num_written+=(regions[i].end-regions[i].start)+1; + num_written+=region_size; + + /* Decrement the buffer left */ + fhyper_info->nelmts-=region_size; + + /* Set the next position to start at */ + if(region_size==(hsize_t)((regions[i].end-regions[i].start)+1)) + fhyper_info->iter->hyp.pos[dim+1]=(-1); + else + fhyper_info->iter->hyp.pos[dim+1]=regions[i].start+region_size; /* Decrement the iterator count */ - fhyper_info->iter->hyp.elmt_left-=(regions[i].end-regions[i].start)+1; + fhyper_info->iter->hyp.elmt_left-=region_size; } /* end for */ } else { /* recurse on each region to next dimension down */ @@ -550,9 +584,9 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) dim++; /* Step through each region in this dimension */ - for(i=0; i<num_regions; i++) { + for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { /* Step through each location in each region */ - for(j=regions[i].start; j<=regions[i].end; j++) { + for(j=regions[i].start; j<=regions[i].end && fhyper_info->nelmts>0; j++) { /* Set the correct position we are working on */ fhyper_info->iter->hyp.pos[dim]=j; @@ -679,6 +713,7 @@ H5S_hyper_mread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) hsize_t mem_size[H5O_LAYOUT_NDIMS]; /*size of memory buffer*/ hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in memory*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ + hsize_t region_size; /* Size of lowest region */ hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ H5S_hyper_region_t *regions; /* Pointer to array of hyperslab nodes overlapped */ size_t num_regions; /* number of regions overlapped */ @@ -731,11 +766,12 @@ for(i=0; i<num_regions; i++) HDmemset (zero, 0, (fhyper_info->space->extent.u.simple.rank+1)*sizeof(*zero)); /* perform I/O on data from regions */ - for(i=0; i<num_regions; i++) { + for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { #ifdef QAK printf("%s: check 2.1, i=%d\n",FUNC,(int)i); #endif /* QAK */ - hsize[fhyper_info->space->extent.u.simple.rank-1]=(regions[i].end-regions[i].start)+1; + region_size=MIN(fhyper_info->nelmts,(regions[i].end-regions[i].start)+1); + hsize[fhyper_info->space->extent.u.simple.rank-1]=region_size; mem_offset[fhyper_info->space->extent.u.simple.rank-1]=regions[i].start; /* @@ -748,13 +784,22 @@ printf("%s: check 2.1, i=%d\n",FUNC,(int)i); } /* Advance the pointer in the buffer */ - fhyper_info->dst=((uint8 *)fhyper_info->dst)+((regions[i].end-regions[i].start)+1)*fhyper_info->elmt_size; + fhyper_info->dst=((uint8 *)fhyper_info->dst)+region_size*fhyper_info->elmt_size; /* Increment the number of elements read */ - num_read+=(regions[i].end-regions[i].start)+1; + num_read+=region_size; + + /* Decrement the buffer left */ + fhyper_info->nelmts-=region_size; + + /* Set the next position to start at */ + if(region_size==(hsize_t)((regions[i].end-regions[i].start)+1)) + fhyper_info->iter->hyp.pos[dim+1]=(-1); + else + fhyper_info->iter->hyp.pos[dim+1]=regions[i].start+region_size; /* Decrement the iterator count */ - fhyper_info->iter->hyp.elmt_left-=(regions[i].end-regions[i].start)+1; + fhyper_info->iter->hyp.elmt_left-=region_size; } /* end for */ } else { /* recurse on each region to next dimension down */ #ifdef QAK @@ -765,9 +810,9 @@ printf("%s: check 3.0, num_regions=%d\n",FUNC,(int)num_regions); dim++; /* Step through each region in this dimension */ - for(i=0; i<num_regions; i++) { + for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { /* Step through each location in each region */ - for(j=regions[i].start; j<=regions[i].end; j++) { + for(j=regions[i].start; j<=regions[i].end && fhyper_info->nelmts>0; j++) { #ifdef QAK printf("%s: check 4.0, dim=%d, location=%d\n",FUNC,dim,j); #endif /* QAK */ @@ -913,6 +958,7 @@ H5S_hyper_mwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) hsize_t mem_size[H5O_LAYOUT_NDIMS]; /*size of memory buffer*/ hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ + hsize_t region_size; /* Size of lowest region */ hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ H5S_hyper_region_t *regions; /* Pointer to array of hyperslab nodes overlapped */ size_t num_regions; /* number of regions overlapped */ @@ -966,8 +1012,9 @@ for(i=0; i<num_regions; i++) printf("%s: check 3.0\n",FUNC); #endif /* QAK */ /* perform I/O on data from regions */ - for(i=0; i<num_regions; i++) { - hsize[fhyper_info->space->extent.u.simple.rank-1]=(regions[i].end-regions[i].start)+1; + for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { + region_size=MIN(fhyper_info->nelmts,(regions[i].end-regions[i].start)+1); + hsize[fhyper_info->space->extent.u.simple.rank-1]=region_size; mem_offset[fhyper_info->space->extent.u.simple.rank-1]=regions[i].start; /* @@ -980,13 +1027,22 @@ printf("%s: check 3.0\n",FUNC); } /* Advance the pointer in the buffer */ - fhyper_info->src=((const uint8 *)fhyper_info->src)+((regions[i].end-regions[i].start)+1)*fhyper_info->elmt_size; + fhyper_info->src=((const uint8 *)fhyper_info->src)+region_size*fhyper_info->elmt_size; /* Increment the number of elements read */ - num_read+=(regions[i].end-regions[i].start)+1; + num_read+=region_size; + + /* Decrement the buffer left */ + fhyper_info->nelmts-=region_size; + + /* Set the next position to start at */ + if(region_size==(hsize_t)((regions[i].end-regions[i].start)+1)) + fhyper_info->iter->hyp.pos[dim+1]=(-1); + else + fhyper_info->iter->hyp.pos[dim+1]=regions[i].start+region_size; /* Decrement the iterator count */ - fhyper_info->iter->hyp.elmt_left-=(regions[i].end-regions[i].start)+1; + fhyper_info->iter->hyp.elmt_left-=region_size; } /* end for */ } else { /* recurse on each region to next dimension down */ @@ -994,9 +1050,9 @@ printf("%s: check 3.0\n",FUNC); dim++; /* Step through each region in this dimension */ - for(i=0; i<num_regions; i++) { + for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { /* Step through each location in each region */ - for(j=regions[i].start; j<=regions[i].end; j++) { + for(j=regions[i].start; j<=regions[i].end && fhyper_info->nelmts>0; j++) { /* Set the correct position we are working on */ fhyper_info->iter->hyp.pos[dim]=j; @@ -1013,6 +1069,7 @@ printf("%s: check 3.0\n",FUNC); FUNC_LEAVE (num_read); } /* H5S_hyper_mwrite() */ + /*------------------------------------------------------------------------- * Function: H5S_hyper_mscat * @@ -1214,6 +1271,9 @@ printf("%s: check 2.0\n",FUNC); #endif /* QAK */ /* Set boundary on new node */ for(i=0,elem_count=1; i<space->extent.u.simple.rank; i++) { +#ifdef QAK +printf("%s: check 2.1, %d: start=%d, size=%d, elem_count=%d\n",FUNC,(int)i,(int)start[i],(int)size[i],(int)elem_count); +#endif /* QAK */ slab->start[i]=start[i]; slab->end[i]=start[i]+size[i]-1; elem_count*=size[i]; |