diff options
Diffstat (limited to 'src/H5Dcontig.c')
| -rw-r--r-- | src/H5Dcontig.c | 171 |
1 files changed, 134 insertions, 37 deletions
diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c index 6cdee41..e4329ff 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -129,24 +129,31 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id) { H5D_storage_t store; /* Union of storage info for dataset */ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ - H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */ + H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */ hssize_t snpoints; /* Number of points in space (for error checking) */ size_t npoints; /* Number of points in space */ size_t ptsperbuf; /* Maximum # of points which fit in the buffer */ size_t elmt_size; /* Size of each element */ size_t bufsize = H5D_TEMP_BUF_SIZE; /* Size of buffer to write */ - size_t size; /* Current # of points to write */ hsize_t offset; /* Offset of dataset */ void *buf = NULL; /* Buffer for fill value writing */ #ifdef H5_HAVE_PARALLEL - MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */ - int mpi_rank=(-1); /* This process's rank */ + MPI_Comm mpi_comm = MPI_COMM_NULL; /* MPI communicator for file */ + int mpi_rank = (-1); /* This process's rank */ int mpi_code; /* MPI return code */ hbool_t blocks_written = FALSE; /* Flag to indicate that chunk was actually written */ hbool_t using_mpi = FALSE; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */ #endif /* H5_HAVE_PARALLEL */ - int non_zero_fill_f = (-1); /* Indicate that a non-zero fill-value was used */ - herr_t ret_value = SUCCEED; /* Return value */ + htri_t non_zero_fill_f = (-1); /* Indicate that a non-zero fill-value was used */ + H5T_path_t *fill_to_mem_tpath; /* Datatype conversion path for converting the fill value to the memory buffer */ + H5T_path_t *mem_to_dset_tpath; /* Datatype conversion path for converting the memory buffer to the dataset elements */ + uint8_t *bkg_buf = NULL; /* Background conversion buffer */ + H5T_t *mem_type = NULL; /* Pointer to memory datatype */ + size_t mem_type_size, file_type_size; /* Size of datatype in memory and on disk */ + hid_t mem_tid = (-1); /* Memory version of disk datatype */ + size_t bkg_buf_size; /* Size of background buffer */ + hbool_t has_vlen_fill_type = FALSE; /* Whether the datatype for the fill value has a variable-length component */ + herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_contig_fill, FAIL) @@ -156,6 +163,7 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id) HDassert(H5F_addr_defined(dset->shared->layout.u.contig.addr)); HDassert(dset->shared->layout.u.contig.size > 0); HDassert(dset->shared->space); + HDassert(dset->shared->type); #ifdef H5_HAVE_PARALLEL /* Retrieve MPI parameters */ @@ -185,46 +193,82 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id) #endif /* H5_HAVE_PARALLEL */ /* Initialize storage info for this dataset */ - store.contig.dset_addr=dset->shared->layout.u.contig.addr; - store.contig.dset_size=dset->shared->layout.u.contig.size; - - /* Get size of elements */ - elmt_size = H5T_get_size(dset->shared->type); - HDassert(elmt_size > 0); + store.contig.dset_addr = dset->shared->layout.u.contig.addr; + store.contig.dset_size = dset->shared->layout.u.contig.size; /* Get the number of elements in the dataset's dataspace */ snpoints = H5S_GET_EXTENT_NPOINTS(dset->shared->space); HDassert(snpoints >= 0); H5_ASSIGN_OVERFLOW(npoints, snpoints, hssize_t, size_t); - /* If fill value is not library default, use it to set the element size */ - if(dset->shared->dcpl_cache.fill.buf) - elmt_size = dset->shared->dcpl_cache.fill.size; - - /* - * Fill the entire current extent with the fill value. We can do - * this quite efficiently by making sure we copy the fill value - * in relatively large pieces. - */ - ptsperbuf = MAX(1, bufsize / elmt_size); - bufsize = ptsperbuf * elmt_size; - /* Fill the buffer with the user's fill value */ if(dset->shared->dcpl_cache.fill.buf) { - /* Allocate temporary buffer */ - if(NULL == (buf = H5FL_BLK_MALLOC(non_zero_fill, bufsize))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer") + /* Indicate that a non-zero fill buffer will be used */ + non_zero_fill_f = TRUE; + + /* Detect whether the datatype has a VL component */ + has_vlen_fill_type = H5T_detect_class(dset->shared->type, H5T_VLEN); + + /* If necessary, convert fill value datatypes (which copies VL components, etc.) */ + if(has_vlen_fill_type) { + /* Create temporary datatype for conversion operation */ + if(NULL == (mem_type = H5T_copy(dset->shared->type, H5T_COPY_REOPEN))) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, FAIL, "unable to copy file datatype") + if((mem_tid = H5I_register(H5I_DATATYPE, mem_type)) < 0) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype") + + /* Retrieve sizes of memory & file datatypes */ + mem_type_size = H5T_get_size(mem_type); + HDassert(mem_type_size > 0); + file_type_size = H5T_get_size(dset->shared->type); + HDassert(file_type_size == (size_t)dset->shared->dcpl_cache.fill.size); + + /* If fill value is not library default, use it to set the element size */ + elmt_size = MAX(mem_type_size, file_type_size); + + /* Compute the number of elements that fit within a buffer to write */ + ptsperbuf = MIN(npoints, MAX(1, bufsize / elmt_size)); + bufsize = MAX(bufsize, ptsperbuf * elmt_size); + + /* Allocate temporary buffer */ + if(NULL == (buf = H5FL_BLK_MALLOC(non_zero_fill, bufsize))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer") + + /* Get the datatype conversion path for this operation */ + if(NULL == (fill_to_mem_tpath = H5T_path_find(dset->shared->type, mem_type, NULL, NULL, dxpl_id, FALSE))) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and dst datatypes") + + /* Allocate a background buffer, if necessary */ + bkg_buf_size = ptsperbuf * elmt_size; + if(H5T_path_bkg(fill_to_mem_tpath) && NULL == (bkg_buf = H5FL_BLK_MALLOC(type_conv, bkg_buf_size))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") + + /* Get the inverse datatype conversion path for this operation */ + if(NULL == (mem_to_dset_tpath = H5T_path_find(mem_type, dset->shared->type, NULL, NULL, dxpl_id, FALSE))) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to convert between src and dst datatypes") + + /* Allocate the background buffer, if necessary */ + if(H5T_path_bkg(mem_to_dset_tpath) && NULL == (bkg_buf = H5FL_BLK_MALLOC(type_conv, bkg_buf_size))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed") + } /* end if */ + else { + /* If fill value is not library default, use it to set the element size */ + elmt_size = dset->shared->dcpl_cache.fill.size; + + /* Compute the number of elements that fit within a buffer to write */ + ptsperbuf = MIN(npoints, MAX(1, bufsize / elmt_size)); + bufsize = MAX(bufsize, ptsperbuf * elmt_size); - H5V_array_fill(buf, dset->shared->dcpl_cache.fill.buf, elmt_size, ptsperbuf); + /* Allocate temporary buffer */ + if(NULL == (buf = H5FL_BLK_MALLOC(non_zero_fill, bufsize))) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer") - /* Indicate that a non-zero fill buffer was used */ - non_zero_fill_f = 1; + /* Replicate the fill value into the cached buffer */ + H5V_array_fill(buf, dset->shared->dcpl_cache.fill.buf, elmt_size, ptsperbuf); + } /* end else */ } /* end if */ else { /* Fill the buffer with the default fill value */ - htri_t buf_avail; - - /* Check if there is an already zeroed out buffer available */ - buf_avail = H5FL_BLK_AVAIL(zero_fill, bufsize); + htri_t buf_avail = H5FL_BLK_AVAIL(zero_fill, bufsize); /* Check if there is an already zeroed out buffer available */ HDassert(buf_avail != FAIL); /* Allocate temporary buffer (zeroing it if no buffer is available) */ @@ -235,16 +279,59 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id) if(buf == NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer") + /* Retrieve size of elements */ + elmt_size = H5T_get_size(dset->shared->type); + HDassert(elmt_size > 0); + + /* Compute the number of elements that fit within a buffer to write */ + ptsperbuf = MIN(npoints, MAX(1, bufsize / elmt_size)); + /* Indicate that a zero fill buffer was used */ - non_zero_fill_f = 0; + non_zero_fill_f = FALSE; } /* end else */ /* Start at the beginning of the dataset */ offset = 0; + /* + * Fill the entire current extent with the fill value. We can do + * this quite efficiently by making sure we copy the fill value + * in relatively large pieces. + */ + /* Loop through writing the fill value to the dataset */ while(npoints > 0) { - size = MIN(ptsperbuf, npoints) * elmt_size; + size_t curr_points; /* Number of elements to write on this iteration of the loop */ + size_t size; /* Size of buffer to write */ + + /* Compute # of elements and buffer size to write for this iteration */ + curr_points = MIN(ptsperbuf, npoints); + size = curr_points * elmt_size; + + /* Check for VL datatype & non-default fill value */ + if(has_vlen_fill_type) { + /* Make a copy of the (disk-based) fill value into the buffer */ + HDmemcpy(buf, dset->shared->dcpl_cache.fill.buf, file_type_size); + + /* Reset the background buffer, if necessary */ + if(H5T_path_bkg(fill_to_mem_tpath)) + HDmemset(bkg_buf, 0, bkg_buf_size); + + /* Type convert the dataset buffer, to copy any VL components */ + if(H5T_convert(fill_to_mem_tpath, dset->shared->type_id, mem_tid, (size_t)1, (size_t)0, (size_t)0, buf, bkg_buf, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed") + + /* Replicate the fill value into the cached buffer */ + H5V_array_fill(buf, buf, mem_type_size, curr_points); + + /* Reset the background buffer, if necessary */ + if(H5T_path_bkg(mem_to_dset_tpath)) + HDmemset(bkg_buf, 0, bkg_buf_size); + + /* Type convert the dataset buffer, to copy any VL components */ + if(H5T_convert(mem_to_dset_tpath, mem_tid, dset->shared->type_id, curr_points, (size_t)0, (size_t)0, buf, bkg_buf, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed") + } /* end if */ #ifdef H5_HAVE_PARALLEL /* Check if this file is accessed with an MPI-capable file driver */ @@ -267,7 +354,7 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id) } /* end else */ #endif /* H5_HAVE_PARALLEL */ - npoints -= MIN(ptsperbuf, npoints); + npoints -= curr_points; offset += size; } /* end while */ @@ -294,6 +381,16 @@ done: H5FL_BLK_FREE(zero_fill, buf); } /* end if */ + /* Free other resources for vlen fill values */ + if(has_vlen_fill_type) { + if(mem_tid > 0) + H5I_dec_ref(mem_tid); + else if(mem_type) + H5T_close(mem_type); + if(bkg_buf) + H5FL_BLK_FREE(type_conv, bkg_buf); + } /* end if */ + FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_contig_fill() */ |