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authorQuincey Koziol <koziol@hdfgroup.org>2006-09-25 22:22:14 (GMT)
committerQuincey Koziol <koziol@hdfgroup.org>2006-09-25 22:22:14 (GMT)
commitc77e39522b4ed0ac4a811dddeafbd7426014b27d (patch)
tree2f6e2a836df24bdb4a44bb9c168fce12bc2739ec /src/H5Dcontig.c
parentc439d91f811d91df590996cff2d3162c541bb1cf (diff)
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[svn-r12680] Description:
Review, revise & checkin in Peter's latest round of object copy changes, which add basic support for datasets & attributes with reference datatypes. Tested on: Linux/32 2.6 (chicago) Linux/64 2.6 (chicago2)
Diffstat (limited to 'src/H5Dcontig.c')
-rw-r--r--src/H5Dcontig.c184
1 files changed, 109 insertions, 75 deletions
diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c
index 544e092..d39c8c5 100644
--- a/src/H5Dcontig.c
+++ b/src/H5Dcontig.c
@@ -104,7 +104,7 @@ H5D_contig_create(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout /*out */ )
/* Allocate space for the contiguous data */
if (HADDR_UNDEF==(layout->u.contig.addr=H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, layout->u.contig.size)))
- HGOTO_ERROR (H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space")
+ HGOTO_ERROR(H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space")
done:
FUNC_LEAVE_NOAPI(ret_value)
@@ -212,7 +212,7 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id)
if(dset->shared->fill.buf) {
/* Allocate temporary buffer */
if ((buf=H5FL_BLK_MALLOC(non_zero_fill,bufsize))==NULL)
- HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer")
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer")
H5V_array_fill(buf, dset->shared->fill.buf, elmt_size, ptsperbuf);
@@ -232,7 +232,7 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id)
else
buf=H5FL_BLK_MALLOC(zero_fill,bufsize);
if(buf==NULL)
- HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer")
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer")
/* Indicate that a zero fill buffer was used */
non_zero_fill_f=0;
@@ -996,8 +996,8 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
-H5D_contig_copy(H5F_t *f_src, H5O_layout_t *layout_src,
- H5F_t *f_dst, H5O_layout_t *layout_dst, H5T_t *dt_src, hid_t dxpl_id)
+H5D_contig_copy(H5F_t *f_src, H5O_layout_t *layout_src, H5F_t *f_dst,
+ H5O_layout_t *layout_dst, H5T_t *dt_src, H5O_copy_t *cpy_info, hid_t dxpl_id)
{
haddr_t addr_src; /* File offset in source dataset */
haddr_t addr_dst; /* File offset in destination dataset */
@@ -1023,7 +1023,8 @@ H5D_contig_copy(H5F_t *f_src, H5O_layout_t *layout_src,
H5S_t *buf_space = NULL; /* Dataspace describing buffer */
hid_t buf_sid = -1; /* ID for buffer dataspace */
hsize_t buf_dim; /* Dimension for buffer */
- hbool_t do_conv; /* Flag to indicate that type conversion should occur */
+ hbool_t is_vlen = FALSE; /* Flag to indicate that VL type conversion should occur */
+ hbool_t fix_ref = FALSE; /* Flag to indicate that ref values should be fixed */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_contig_copy, FAIL)
@@ -1045,71 +1046,83 @@ H5D_contig_copy(H5F_t *f_src, H5O_layout_t *layout_src,
/* If there's a source datatype, set up type conversion information */
if(dt_src) {
- /* Create datatype ID for src datatype */
- if((tid_src = H5I_register(H5I_DATATYPE, dt_src)) < 0)
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype")
-
- /* create a memory copy of the variable-length datatype */
- if(NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
- if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem)) < 0)
- HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype")
-
- /* create variable-length datatype at the destinaton file */
- if(NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
- if(H5T_set_loc(dt_dst, f_dst, H5T_LOC_DISK) < 0)
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "cannot mark datatype on disk")
- if((tid_dst = H5I_register(H5I_DATATYPE, dt_dst)) < 0)
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype")
-
- /* Set up the conversion functions */
- if(NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem, NULL, NULL, dxpl_id, FALSE)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes")
- if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst, NULL, NULL, dxpl_id, FALSE)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes")
-
- /* Determine largest datatype size */
- if(0 == (src_dt_size = H5T_get_size(dt_src)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
- if(0 == (mem_dt_size = H5T_get_size(dt_mem)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
- max_dt_size = MAX(src_dt_size, mem_dt_size);
- if(0 == (dst_dt_size = H5T_get_size(dt_dst)))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
- max_dt_size = MAX(max_dt_size, dst_dt_size);
-
- /* Set maximum number of whole elements that fit in buffer */
- if(0 == (nelmts = buf_size / max_dt_size))
- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "element size too large")
-
- /* Set the number of bytes to transfer */
- src_nbytes = nelmts * src_dt_size;
- dst_nbytes = nelmts * dst_dt_size;
- mem_nbytes = nelmts * mem_dt_size;
-
- /* Adjust buffer size to be multiple of elements */
- buf_size = nelmts * max_dt_size;
-
- /* Create dataspace for number of elements in buffer */
- buf_dim = nelmts;
-
- /* Create the space and set the initial extent */
- if(NULL == (buf_space = H5S_create_simple((unsigned)1, &buf_dim, NULL)))
- HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
-
- /* Atomize */
- if((buf_sid = H5I_register(H5I_DATASPACE, buf_space)) < 0) {
- H5S_close(buf_space);
- HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID")
- } /* end if */
+ if(H5T_detect_class(dt_src, H5T_VLEN) > 0) {
+ /* Create datatype ID for src datatype */
+ if((tid_src = H5I_register(H5I_DATATYPE, dt_src)) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype")
+
+ /* create a memory copy of the variable-length datatype */
+ if(NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
+ if((tid_mem = H5I_register(H5I_DATATYPE, dt_mem)) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype")
+
+ /* create variable-length datatype at the destinaton file */
+ if(NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy")
+ if(H5T_set_loc(dt_dst, f_dst, H5T_LOC_DISK) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "cannot mark datatype on disk")
+ if((tid_dst = H5I_register(H5I_DATATYPE, dt_dst)) < 0)
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype")
+
+ /* Set up the conversion functions */
+ if(NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem, NULL, NULL, dxpl_id, FALSE)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes")
+ if(NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst, NULL, NULL, dxpl_id, FALSE)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes")
+
+ /* Determine largest datatype size */
+ if(0 == (src_dt_size = H5T_get_size(dt_src)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
+ if(0 == (mem_dt_size = H5T_get_size(dt_mem)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
+ max_dt_size = MAX(src_dt_size, mem_dt_size);
+ if(0 == (dst_dt_size = H5T_get_size(dt_dst)))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size")
+ max_dt_size = MAX(max_dt_size, dst_dt_size);
+
+ /* Set maximum number of whole elements that fit in buffer */
+ if(0 == (nelmts = buf_size / max_dt_size))
+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "element size too large")
+
+ /* Set the number of bytes to transfer */
+ src_nbytes = nelmts * src_dt_size;
+ dst_nbytes = nelmts * dst_dt_size;
+ mem_nbytes = nelmts * mem_dt_size;
+
+ /* Adjust buffer size to be multiple of elements */
+ buf_size = nelmts * max_dt_size;
+
+ /* Create dataspace for number of elements in buffer */
+ buf_dim = nelmts;
+
+ /* Create the space and set the initial extent */
+ if(NULL == (buf_space = H5S_create_simple((unsigned)1, &buf_dim, NULL)))
+ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace")
+
+ /* Atomize */
+ if((buf_sid = H5I_register(H5I_DATASPACE, buf_space)) < 0) {
+ H5S_close(buf_space);
+ HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID")
+ } /* end if */
- /* Set flag to do type conversion */
- do_conv = TRUE;
+ /* Set flag to do type conversion */
+ is_vlen = TRUE;
+ }
+ /* Check for reference datatype */
+ else if((H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) && (f_src != f_dst)) {
+ /* need to fix values of reference */
+ fix_ref = TRUE;
+
+ /* Set the number of bytes to read & write to the buffer size */
+ src_nbytes = dst_nbytes = mem_nbytes = buf_size;
+ } /* end if */
+ else
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy dataset elements")
} /* end if */
else {
/* Type conversion not necessary */
- do_conv = FALSE;
+ is_vlen = FALSE;
/* Set the number of bytes to read & write to the buffer size */
src_nbytes = dst_nbytes = mem_nbytes = buf_size;
@@ -1121,9 +1134,13 @@ H5D_contig_copy(H5F_t *f_src, H5O_layout_t *layout_src,
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for copy buffer")
/* Need extra buffer for datatype conversions, to prevent stranding/leaking memory */
- if(do_conv) {
+ if(is_vlen || fix_ref) {
if(NULL == (reclaim_buf = H5FL_BLK_MALLOC(type_conv, buf_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for copy buffer")
+
+ /* allocate temporary bkg buff for data conversion */
+ if(NULL == (bkg = H5FL_BLK_MALLOC(type_conv, buf_size)))
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for copy buffer")
} /* end if */
/* Loop over copying data */
@@ -1136,7 +1153,7 @@ H5D_contig_copy(H5F_t *f_src, H5O_layout_t *layout_src,
src_nbytes = (size_t)total_src_nbytes;
/* Adjust dataspace describing buffer */
- if(do_conv) {
+ if(is_vlen) {
/* Adjust destination & memory bytes to transfer */
nelmts = src_nbytes / src_dt_size;
dst_nbytes = nelmts * dst_dt_size;
@@ -1149,10 +1166,9 @@ H5D_contig_copy(H5F_t *f_src, H5O_layout_t *layout_src,
if(H5S_set_extent_real(buf_space, &buf_dim) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSET, FAIL, "unable to change buffer dataspace size")
} /* end if */
- else {
+ else
/* Adjust destination & memory bytes to transfer */
dst_nbytes = mem_nbytes = src_nbytes;
- } /* end else */
} /* end if */
/* Read raw data from source file */
@@ -1160,7 +1176,7 @@ H5D_contig_copy(H5F_t *f_src, H5O_layout_t *layout_src,
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to read raw data")
/* Perform datatype conversion, if necessary */
- if(do_conv) {
+ if(is_vlen) {
/* Convert from source file to memory */
if(H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0)
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed")
@@ -1168,9 +1184,8 @@ H5D_contig_copy(H5F_t *f_src, H5O_layout_t *layout_src,
/* Copy into another buffer, to reclaim memory later */
HDmemcpy(reclaim_buf, buf, mem_nbytes);
- /* allocate temporary bkg buff for data conversion */
- if(NULL == (bkg = H5FL_BLK_CALLOC(type_conv, buf_size)))
- HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for copy buffer")
+ /* Set background buffer to all zeros */
+ HDmemset(bkg, 0, buf_size);
/* Convert from memory to destination file */
if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, bkg, dxpl_id) < 0)
@@ -1180,6 +1195,25 @@ H5D_contig_copy(H5F_t *f_src, H5O_layout_t *layout_src,
if(H5D_vlen_reclaim(tid_mem, buf_space, H5P_DATASET_XFER_DEFAULT, reclaim_buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to reclaim variable-length data")
} /* end if */
+ else if(fix_ref) {
+ /* Check for expanding references */
+ if(cpy_info->expand_ref) {
+ size_t ref_count;
+
+ /* Determine # of reference elements to copy */
+ ref_count = src_nbytes / H5T_get_size(dt_src);
+
+ /* Copy the reference elements */
+ if(H5O_copy_expand_ref(f_src, buf, dxpl_id, f_dst, bkg, ref_count, H5T_get_ref_type(dt_src), cpy_info) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy reference attribute")
+
+ /* After fix ref, copy the new reference elements to the buffer to write out */
+ HDmemcpy(buf, bkg, buf_size);
+ } /* end if */
+ else
+ /* Reset value to zero */
+ HDmemset(buf, 0, src_nbytes);
+ } /* end if */
/* Write raw data to destination file */
if(H5F_block_write(f_dst, H5FD_MEM_DRAW, addr_dst, dst_nbytes, H5P_DATASET_XFER_DEFAULT, buf) < 0)