summaryrefslogtreecommitdiffstats
path: root/src/H5Shyper.c
diff options
context:
space:
mode:
Diffstat (limited to 'src/H5Shyper.c')
-rw-r--r--src/H5Shyper.c144
1 files changed, 94 insertions, 50 deletions
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index 65cc9fd..336536b 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -7,14 +7,18 @@
*
* Purpose: Hyperslab selection data space I/O functions.
*/
+
+#define H5S_PACKAGE /*suppress error about including H5Spkg */
+
#include <H5private.h>
#include <H5Dprivate.h>
#include <H5Eprivate.h>
+#include <H5Fprivate.h>
#include <H5FLprivate.h> /*Free Lists */
#include <H5Iprivate.h>
#include <H5MMprivate.h>
#include <H5Pprivate.h>
-#include <H5Sprivate.h>
+#include <H5Spkg.h>
#include <H5Vprivate.h>
/* Interface initialization */
@@ -585,13 +589,13 @@ H5S_hyper_fread (intn dim, H5S_hyper_io_info_t *io_info)
size_t i; /* Counters */
intn j;
size_t num_read=0; /* Number of elements read */
- const H5F_xfer_t *xfer_parms;/* Data transfer property list */
+ const H5D_xfer_t *xfer_parms;/* Data transfer property list */
FUNC_ENTER (H5S_hyper_fread, 0);
assert(io_info);
if (H5P_DEFAULT==io_info->dxpl_id) {
- xfer_parms = &H5F_xfer_dflt;
+ xfer_parms = &H5D_xfer_dflt;
} else {
xfer_parms = H5I_object(io_info->dxpl_id);
assert(xfer_parms);
@@ -934,17 +938,19 @@ H5S_hyper_fread_opt (H5F_t *f, const struct H5O_layout_t *layout,
const H5S_t *file_space, H5S_sel_iter_t *file_iter,
size_t nelmts, hid_t dxpl_id, void *_buf/*out*/)
{
- hsize_t hsize[H5O_LAYOUT_NDIMS]; /* Hyperslab size */
- hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */
hssize_t offset[H5O_LAYOUT_NDIMS]; /* Offset on disk */
+ hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */
hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary block count */
hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary block offset */
uint8_t *buf=(uint8_t *)_buf; /* Alias for pointer arithmetic */
intn fast_dim; /* Rank of the fastest changing dimension for the dataspace */
intn temp_dim; /* Temporary rank holder */
+ hsize_t acc; /* Accumulator */
+ size_t buf_off; /* Buffer offset for copying memory */
intn i; /* Counters */
intn ndims; /* Number of dimensions of dataset */
uintn actual_read; /* The actual number of elements to read in */
+ uintn actual_bytes; /* The actual number of bytes to copy */
size_t num_read=0; /* Number of elements read */
FUNC_ENTER (H5S_hyper_fread_opt, 0);
@@ -965,15 +971,13 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
/* Set the rank of the fastest changing dimension */
fast_dim=file_space->extent.u.simple.rank-1;
-
- /* Set up the hyperslab and 'zero' arrays */
ndims=file_space->extent.u.simple.rank;
- /* initialize hyperslab size and offset in memory buffer */
- for(i=0; i<(ndims+1); i++) {
- hsize[i]=1; /* hyperslab size is 1, except for last element */
- zero[i]=0; /* memory offset is 0 */
+
+ /* initialize row sizes for each dimension */
+ for(i=(ndims-1),acc=1; i>=0; i--) {
+ slab[i]=acc*elmt_size;
+ acc*=file_space->extent.u.simple.size[i];
} /* end for */
- hsize[ndims] = elmt_size;
/* Check if we stopped in the middle of a sequence of elements */
if((file_iter->hyp.pos[fast_dim]-file_space->select.sel_info.hslab.diminfo[fast_dim].start)%file_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0) {
@@ -987,9 +991,7 @@ printf("%s: Check 1.0\n",FUNC);
/* Make certain that we don't read too many */
actual_read=MIN(leftover,nelmts);
-
- /* Set the hyperslab size in the fastest changing dimension to read in */
- hsize[fast_dim]=actual_read;
+ actual_bytes=actual_read*elmt_size;
/* Copy the location of the point to get */
HDmemcpy(offset, file_iter->hyp.pos,ndims*sizeof(hssize_t));
@@ -999,9 +1001,13 @@ printf("%s: Check 1.0\n",FUNC);
for(i=0; i<ndims; i++)
offset[i] += file_space->select.offset[i];
- /* Read in the rest of the sequence, if possible */
- if (H5F_arr_read(f, dxpl_id, layout, pline, fill, efl, hsize,
- hsize, zero, offset, buf/*out*/)<0) {
+ /* Compute the initial buffer offset */
+ for(i=0,buf_off=0; i<ndims; i++)
+ buf_off+=offset[i]*slab[i];
+
+ /* Read in the rest of the sequence */
+ if (H5F_seq_read(f, dxpl_id, layout, pline, fill, efl, file_space,
+ elmt_size, actual_bytes, 0, buf_off, buf/*out*/)<0) {
HRETURN_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error");
}
@@ -1053,9 +1059,15 @@ printf("%s: Check 2.0\n",FUNC);
tmp_block[i] = (file_iter->hyp.pos[i]-file_space->select.sel_info.hslab.diminfo[i].start)/file_space->select.sel_info.hslab.diminfo[i].stride;
} /* end for */
+ /* Compute the initial buffer offset */
+ for(i=0,buf_off=0; i<ndims; i++)
+ buf_off+=offset[i]*slab[i];
+
/* Set the number of elements to read each time */
actual_read=file_space->select.sel_info.hslab.diminfo[fast_dim].block;
- hsize[fast_dim]=actual_read;
+
+ /* Set the number of actual bytes */
+ actual_bytes=actual_read*elmt_size;
#ifdef QAK
printf("%s: actual_read=%d\n",FUNC,(int)actual_read);
for(i=0; i<file_space->extent.u.simple.rank; i++)
@@ -1071,7 +1083,7 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
/* Check if we are running out of room in the buffer */
if((actual_read+num_read)>nelmts) {
actual_read=nelmts-num_read;
- hsize[fast_dim]=actual_read;
+ actual_bytes=actual_read*elmt_size;
} /* end if */
#ifdef QAK
@@ -1080,9 +1092,9 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
printf("%s: tmp_count[%d]=%d, offset[%d]=%d\n",FUNC,(int)i,(int)tmp_count[i],(int)i,(int)offset[i]);
#endif /* QAK */
- /* Read in the sequence, if possible */
- if (H5F_arr_read(f, dxpl_id, layout, pline, fill, efl, hsize,
- hsize, zero, offset, buf/*out*/)<0) {
+ /* Read in the sequence */
+ if (H5F_seq_read(f, dxpl_id, layout, pline, fill, efl, file_space,
+ elmt_size, actual_bytes, 0, buf_off, buf/*out*/)<0) {
HRETURN_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error");
}
@@ -1103,10 +1115,12 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
/* Check for partial block read! */
if(actual_read<file_space->select.sel_info.hslab.diminfo[fast_dim].block) {
offset[temp_dim]+=actual_read;
+ buf_off+=actual_bytes;
break;
} /* end if */
else {
offset[temp_dim]+=file_space->select.sel_info.hslab.diminfo[temp_dim].stride; /* reset the offset in the fastest dimension */
+ buf_off+=slab[temp_dim]*file_space->select.sel_info.hslab.diminfo[temp_dim].stride;
tmp_count[temp_dim]++;
} /* end else */
@@ -1116,11 +1130,16 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
else {
tmp_count[temp_dim]=0; /* reset back to the beginning of the line */
offset[temp_dim]=file_space->select.sel_info.hslab.diminfo[temp_dim].start+file_space->select.offset[temp_dim];
+
+ /* Re-compute the initial buffer offset */
+ for(i=0,buf_off=0; i<ndims; i++)
+ buf_off+=offset[i]*slab[i];
} /* end else */
} /* end if */
else {
/* Move to the next row in the curent dimension */
offset[temp_dim]++;
+ buf_off+=slab[temp_dim];
tmp_block[temp_dim]++;
/* If this block is still in the range of blocks to output for the dimension, break out of loop */
@@ -1129,6 +1148,7 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
else {
/* Move to the next block in the current dimension */
offset[temp_dim]+=(file_space->select.sel_info.hslab.diminfo[temp_dim].stride-file_space->select.sel_info.hslab.diminfo[temp_dim].block);
+ buf_off+=(file_space->select.sel_info.hslab.diminfo[temp_dim].stride-file_space->select.sel_info.hslab.diminfo[temp_dim].block)*slab[temp_dim];
tmp_block[temp_dim]=0;
tmp_count[temp_dim]++;
@@ -1139,6 +1159,10 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
tmp_count[temp_dim]=0; /* reset back to the beginning of the line */
tmp_block[temp_dim]=0;
offset[temp_dim]=file_space->select.sel_info.hslab.diminfo[temp_dim].start+file_space->select.offset[temp_dim];
+
+ /* Re-compute the initial buffer offset */
+ for(i=0,buf_off=0; i<ndims; i++)
+ buf_off+=offset[i]*slab[i];
}
} /* end else */
} /* end else */
@@ -1273,13 +1297,13 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_io_info_t *io_info)
size_t i; /* Counters */
intn j;
size_t num_written=0; /* Number of elements read */
- const H5F_xfer_t *xfer_parms; /* Data transfer properties */
+ const H5D_xfer_t *xfer_parms; /* Data transfer properties */
FUNC_ENTER (H5S_hyper_fwrite, 0);
assert(io_info);
if (H5P_DEFAULT==io_info->dxpl_id) {
- xfer_parms = &H5F_xfer_dflt;
+ xfer_parms = &H5D_xfer_dflt;
} else {
xfer_parms = H5I_object(io_info->dxpl_id);
assert(xfer_parms);
@@ -1434,18 +1458,20 @@ H5S_hyper_fwrite_opt (H5F_t *f, const struct H5O_layout_t *layout,
const H5S_t *file_space, H5S_sel_iter_t *file_iter,
size_t nelmts, hid_t dxpl_id, const void *_buf)
{
- hsize_t hsize[H5O_LAYOUT_NDIMS]; /* Hyperslab size */
- hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */
hssize_t offset[H5O_LAYOUT_NDIMS]; /* Offset on disk */
+ hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */
hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary block count */
hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary block offset */
const uint8_t *buf=(const uint8_t *)_buf; /* Alias for pointer arithmetic */
intn fast_dim; /* Rank of the fastest changing dimension for the dataspace */
intn temp_dim; /* Temporary rank holder */
+ hsize_t acc; /* Accumulator */
+ size_t buf_off; /* Buffer offset for copying memory */
intn i; /* Counters */
intn ndims; /* Number of dimensions of dataset */
- uintn actual_write; /* The actual number of elements to read in */
- size_t num_write=0; /* Number of elements read */
+ uintn actual_write; /* The actual number of elements to read in */
+ uintn actual_bytes; /* The actual number of bytes to copy */
+ size_t num_write=0; /* Number of elements read */
FUNC_ENTER (H5S_hyper_fwrite_opt, 0);
@@ -1465,15 +1491,13 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
/* Set the rank of the fastest changing dimension */
fast_dim=file_space->extent.u.simple.rank-1;
-
- /* Set up the hyperslab and 'zero' arrays */
ndims=file_space->extent.u.simple.rank;
- /* initialize hyperslab size and offset in memory buffer */
- for(i=0; i<(int)(ndims+1); i++) {
- hsize[i]=1; /* hyperslab size is 1, except for last element */
- zero[i]=0; /* memory offset is 0 */
+
+ /* initialize row sizes for each dimension */
+ for(i=(ndims-1),acc=1; i>=0; i--) {
+ slab[i]=acc*elmt_size;
+ acc*=file_space->extent.u.simple.size[i];
} /* end for */
- hsize[ndims] = elmt_size;
/* Check if we stopped in the middle of a sequence of elements */
if((file_iter->hyp.pos[fast_dim]-file_space->select.sel_info.hslab.diminfo[fast_dim].start)%file_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0) {
@@ -1487,9 +1511,7 @@ printf("%s: Check 1.0\n",FUNC);
/* Make certain that we don't write too many */
actual_write=MIN(leftover,nelmts);
-
- /* Set the hyperslab size in the fastest changing dimension to write in */
- hsize[fast_dim]=actual_write;
+ actual_bytes=actual_write*elmt_size;
/* Copy the location of the point to get */
HDmemcpy(offset, file_iter->hyp.pos,ndims*sizeof(hssize_t));
@@ -1499,10 +1521,14 @@ printf("%s: Check 1.0\n",FUNC);
for(i=0; i<ndims; i++)
offset[i] += file_space->select.offset[i];
- /* Read in the rest of the sequence, if possible */
- if (H5F_arr_write(f, dxpl_id, layout, pline, fill, efl, hsize,
- hsize, zero, offset, buf)<0) {
- HRETURN_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "write error");
+ /* Compute the initial buffer offset */
+ for(i=0,buf_off=0; i<ndims; i++)
+ buf_off+=offset[i]*slab[i];
+
+ /* Read in the rest of the sequence */
+ if (H5F_seq_write(f, dxpl_id, layout, pline, fill, efl, file_space,
+ elmt_size, actual_bytes, 0, buf_off, buf)<0) {
+ HRETURN_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error");
}
/* Increment the offset of the buffer */
@@ -1553,9 +1579,15 @@ printf("%s: Check 2.0\n",FUNC);
tmp_block[i] = (file_iter->hyp.pos[i]-file_space->select.sel_info.hslab.diminfo[i].start)/file_space->select.sel_info.hslab.diminfo[i].stride;
} /* end for */
+ /* Compute the initial buffer offset */
+ for(i=0,buf_off=0; i<ndims; i++)
+ buf_off+=offset[i]*slab[i];
+
/* Set the number of elements to write each time */
actual_write=file_space->select.sel_info.hslab.diminfo[fast_dim].block;
- hsize[fast_dim]=actual_write;
+
+ /* Set the number of actual bytes */
+ actual_bytes=actual_write*elmt_size;
#ifdef QAK
printf("%s: actual_write=%d\n",FUNC,(int)actual_write);
for(i=0; i<file_space->extent.u.simple.rank; i++)
@@ -1571,7 +1603,7 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
/* Check if we are running out of room in the buffer */
if((actual_write+num_write)>nelmts) {
actual_write=nelmts-num_write;
- hsize[fast_dim]=actual_write;
+ actual_bytes=actual_write*elmt_size;
} /* end if */
#ifdef QAK
@@ -1580,10 +1612,10 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
printf("%s: tmp_count[%d]=%d, offset[%d]=%d\n",FUNC,(int)i,(int)tmp_count[i],(int)i,(int)offset[i]);
#endif /* QAK */
- /* Read in the sequence, if possible */
- if (H5F_arr_write(f, dxpl_id, layout, pline, fill, efl, hsize,
- hsize, zero, offset, buf)<0) {
- HRETURN_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "write error");
+ /* Read in the sequence */
+ if (H5F_seq_write(f, dxpl_id, layout, pline, fill, efl, file_space,
+ elmt_size, actual_bytes, 0, buf_off, buf)<0) {
+ HRETURN_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error");
}
/* Increment the offset of the buffer */
@@ -1603,10 +1635,12 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
/* Check for partial block write! */
if(actual_write<file_space->select.sel_info.hslab.diminfo[fast_dim].block) {
offset[temp_dim]+=actual_write;
+ buf_off+=actual_bytes;
break;
} /* end if */
else {
offset[temp_dim]+=file_space->select.sel_info.hslab.diminfo[temp_dim].stride; /* reset the offset in the fastest dimension */
+ buf_off+=slab[temp_dim]*file_space->select.sel_info.hslab.diminfo[temp_dim].stride;
tmp_count[temp_dim]++;
} /* end else */
@@ -1616,11 +1650,16 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
else {
tmp_count[temp_dim]=0; /* reset back to the beginning of the line */
offset[temp_dim]=file_space->select.sel_info.hslab.diminfo[temp_dim].start+file_space->select.offset[temp_dim];
+
+ /* Re-compute the initial buffer offset */
+ for(i=0,buf_off=0; i<ndims; i++)
+ buf_off+=offset[i]*slab[i];
} /* end else */
} /* end if */
else {
/* Move to the next row in the curent dimension */
offset[temp_dim]++;
+ buf_off+=slab[temp_dim];
tmp_block[temp_dim]++;
/* If this block is still in the range of blocks to output for the dimension, break out of loop */
@@ -1629,6 +1668,7 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
else {
/* Move to the next block in the current dimension */
offset[temp_dim]+=(file_space->select.sel_info.hslab.diminfo[temp_dim].stride-file_space->select.sel_info.hslab.diminfo[temp_dim].block);
+ buf_off+=(file_space->select.sel_info.hslab.diminfo[temp_dim].stride-file_space->select.sel_info.hslab.diminfo[temp_dim].block)*slab[temp_dim];
tmp_block[temp_dim]=0;
tmp_count[temp_dim]++;
@@ -1639,6 +1679,10 @@ for(i=0; i<file_space->extent.u.simple.rank; i++)
tmp_count[temp_dim]=0; /* reset back to the beginning of the line */
tmp_block[temp_dim]=0;
offset[temp_dim]=file_space->select.sel_info.hslab.diminfo[temp_dim].start+file_space->select.offset[temp_dim];
+
+ /* Re-compute the initial buffer offset */
+ for(i=0,buf_off=0; i<ndims; i++)
+ buf_off+=offset[i]*slab[i];
}
} /* end else */
} /* end else */
@@ -1922,7 +1966,7 @@ H5S_hyper_mread_opt (const void *_buf, size_t elmt_size,
uintn actual_bytes; /* The actual number of bytes to copy */
size_t num_read=0; /* Number of elements read */
- FUNC_ENTER (H5S_hyper_fread_opt, 0);
+ FUNC_ENTER (H5S_hyper_mread_opt, 0);
#ifdef QAK
printf("%s: Called!\n",FUNC);
generated by cgit v0.12 at 2024-07-21 19:15:42 (GMT)