diff options
Diffstat (limited to 'src/H5Dcontig.c')
| -rw-r--r-- | src/H5Dcontig.c | 184 |
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) |