diff options
Diffstat (limited to 'src/H5Dcontig.c')
| -rw-r--r-- | src/H5Dcontig.c | 213 |
1 files changed, 212 insertions, 1 deletions
diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c index fd05e8c..bed70d7 100644 --- a/src/H5Dcontig.c +++ b/src/H5Dcontig.c @@ -38,6 +38,7 @@ #include "H5Fprivate.h" /* Files */ #include "H5FDprivate.h" /* File drivers */ #include "H5FLprivate.h" /* Free Lists */ +#include "H5Iprivate.h" /* IDs */ #include "H5MFprivate.h" /* File memory management */ #include "H5Oprivate.h" /* Object headers */ #include "H5Pprivate.h" /* Property lists */ @@ -75,6 +76,9 @@ H5FL_BLK_DEFINE_STATIC(non_zero_fill); /* Declare the free list to manage blocks of zero fill-value data */ H5FL_BLK_DEFINE_STATIC(zero_fill); +/* Declare extern the free list to manage blocks of type conversion data */ +H5FL_BLK_EXTERN(type_conv); + /*------------------------------------------------------------------------- * Function: H5D_contig_create @@ -130,7 +134,7 @@ H5D_contig_fill(H5D_t *dset, hid_t dxpl_id) 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=64*1024; /* Size of buffer to write */ + size_t bufsize=H5D_XFER_MAX_TEMP_BUF_DEF; /* 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 */ @@ -976,3 +980,210 @@ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_contig_writevv() */ + +/*------------------------------------------------------------------------- + * Function: H5D_contig_copy + * + * Purpose: Copy contiguous storage raw data from SRC file to DST file. + * + * Return: Non-negative on success, negative on failure. + * + * Programmer: Quincey Koziol + * Monday, November 21, 2005 + * + *------------------------------------------------------------------------- + */ +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) +{ + haddr_t addr_src; /* File offset in source dataset */ + haddr_t addr_dst; /* File offset in destination dataset */ + H5T_path_t *tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */ + H5T_t *dt_dst = NULL; /* Destination datatype */ + H5T_t *dt_mem = NULL; /* Memory datatype */ + hid_t tid_src = -1; /* Datatype ID for source datatype */ + hid_t tid_dst = -1; /* Datatype ID for destination datatype */ + hid_t tid_mem = -1; /* Datatype ID for memory datatype */ + size_t max_dt_size; /* Max. datatype size */ + size_t nelmts = 0; /* Number of elements in buffer */ + hsize_t total_nbytes; /* Total number of bytes to copy */ + size_t buf_size; /* Size of copy buffer */ + void *buf = NULL; /* Buffer for copying data */ + void *reclaim_buf = NULL; /* Buffer for reclaiming data */ + 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 */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOAPI(H5D_contig_copy, FAIL) + + /* Check args */ + HDassert(f_src); + HDassert(f_dst); + HDassert(layout_src && H5D_CONTIGUOUS == layout_src->type); + HDassert(layout_dst && H5D_CONTIGUOUS == layout_dst->type); + + /* Allocate space for destination raw data */ + if(H5D_contig_create(f_dst, dxpl_id, layout_dst) < 0) + HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to allocate contiguous storage") + + /* Set up number of bytes to copy, and initial buffer size */ + total_nbytes = layout_src->u.contig.size; + buf_size = MIN(H5D_XFER_MAX_TEMP_BUF_DEF, total_nbytes); + + /* If there's a source datatype, set up type conversion information */ + if(dt_src) { + size_t tmp_dt_size; /* Temp. atatype size */ + + /* 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 == (max_dt_size = H5T_get_size(dt_src))) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size") + if(0 == (tmp_dt_size = H5T_get_size(dt_mem))) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to determine datatype size") + max_dt_size = MAX(max_dt_size, tmp_dt_size); + if(0 == (tmp_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, tmp_dt_size); + + /* Set 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") + + /* 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; + } /* end if */ + else + /* Type conversion not necessary */ + do_conv = FALSE; + + /* Allocate space for copy buffer */ + HDassert(buf_size); + if(NULL == (buf = H5FL_BLK_MALLOC(type_conv, buf_size))) + 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(NULL == (reclaim_buf = 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 */ + addr_src = layout_src->u.contig.addr; + addr_dst = layout_dst->u.contig.addr; + while(total_nbytes > 0) { + size_t nbytes; /* Number of bytes to copy each time */ + + /* Compute number of bytes to copy for this pass */ + if(total_nbytes >= buf_size) + nbytes = buf_size; + else { + nbytes = (size_t)total_nbytes; + + /* Adjust dataspace describing buffer */ + if(do_conv) { + /* Adjust size of buffer's dataspace dimension */ + buf_dim = nelmts = nbytes / max_dt_size; + + /* Adjust size of buffer's dataspace */ + 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 */ + } /* end else */ + + /* Read raw data from source file */ + if(H5F_block_read(f_src, H5FD_MEM_DRAW, addr_src, nbytes, H5P_DATASET_XFER_DEFAULT, buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to read raw data") + + /* Perform datatype conversion, if necessary */ + if(do_conv) { + /* 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") + + /* Copy into another buffer, to reclaim memory later */ + HDmemcpy(reclaim_buf, buf, nbytes); + + /* Convert from memory to destination file */ + if(H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, NULL, dxpl_id) < 0) + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed") + } /* end if */ + + /* Write raw data to destination file */ + if(H5F_block_write(f_dst, H5FD_MEM_DRAW, addr_dst, nbytes, H5P_DATASET_XFER_DEFAULT, buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write raw data") + + /* Reclaim any space from variable length data */ + if(do_conv) { + 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 */ + + /* Adjust loop variables */ + addr_src += nbytes; + addr_dst += nbytes; + total_nbytes -= nbytes; + } /* end while */ + +done: + if(buf_sid > 0) + if(H5I_dec_ref(buf_sid) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary dataspace ID") + if(tid_src > 0) + if(H5I_dec_ref(tid_src) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") + if(tid_dst > 0) + if(H5I_dec_ref(tid_dst) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") + if(tid_mem > 0) + if(H5I_dec_ref(tid_mem) < 0) + HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") + if(buf) + H5FL_BLK_FREE(type_conv, buf); + if(reclaim_buf) + H5FL_BLK_FREE(type_conv, reclaim_buf); + + FUNC_LEAVE_NOAPI(ret_value) +} /* end H5D_contig_copy() */ + |