/*-------------------------------------------------------------------------
* Function: H5D_select_io
*
* Purpose: Perform I/O directly from application memory and a file
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, November 27, 2007
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_select_io(H5D_io_info_t *io_info,
size_t nelmts, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
haddr_t addr, void *chunk/*in*/,
const H5D_select_buf_t *io_buf)
{
H5S_sel_iter_t mem_iter; /* Memory selection iteration info */
hbool_t mem_iter_init = 0; /* Memory selection iteration info has been initialized */
H5S_sel_iter_t file_iter; /* File selection iteration info */
hbool_t file_iter_init = 0; /* File selection iteration info has been initialized */
hsize_t _mem_off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets in memory */
hsize_t *mem_off = NULL; /* Pointer to sequence offsets in memory */
hsize_t _file_off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets in the file */
hsize_t *file_off = NULL; /* Pointer to sequence offsets in the file */
size_t _mem_len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths in memory */
size_t *mem_len = NULL; /* Pointer to sequence lengths in memory */
size_t _file_len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths in the file */
size_t *file_len = NULL; /* Pointer to sequence lengths in the file */
size_t curr_mem_seq; /* Current memory sequence to operate on */
size_t curr_file_seq; /* Current file sequence to operate on */
size_t mem_nseq; /* Number of sequences generated in the file */
size_t file_nseq; /* Number of sequences generated in memory */
ssize_t tmp_file_len; /* Temporary number of bytes in file sequence */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_select_io, FAIL)
/* Check args */
HDassert(io_info);
HDassert(io_info->dset);
HDassert(io_info->store);
HDassert(TRUE == H5P_isa_class(io_info->dxpl_id, H5P_DATASET_XFER));
HDassert(io_buf->u.rbuf);
/* Allocate the vector I/O arrays */
if(io_info->dxpl_cache->vec_size != H5D_IO_VECTOR_SIZE) {
if(NULL == (mem_len = H5FL_SEQ_MALLOC(size_t,io_info->dxpl_cache->vec_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array")
if(NULL == (mem_off = H5FL_SEQ_MALLOC(hsize_t,io_info->dxpl_cache->vec_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array")
if(NULL == (file_len = H5FL_SEQ_MALLOC(size_t,io_info->dxpl_cache->vec_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array")
if(NULL == (file_off = H5FL_SEQ_MALLOC(hsize_t,io_info->dxpl_cache->vec_size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array")
} /* end if */
else {
/*-------------------------------------------------------------------------
* Function: H5D_compact_fill
*
* Purpose: Write fill values to a compactly stored dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* May 6, 2007
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_compact_fill(H5D_t *dset, hid_t dxpl_id)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_compact_fill, FAIL)
/* Check args */
HDassert(TRUE == H5P_isa_class(dxpl_id, H5P_DATASET_XFER));
HDassert(dset && H5D_COMPACT == dset->shared->layout.type);
HDassert(dset->shared->layout.u.compact.buf);
HDassert(dset->shared->type);
HDassert(dset->shared->space);
/* If the fill value is defined, initialize the data buffer with it */
if(dset->shared->fill.buf) {
hssize_t snpoints; /* Number of points in space (for error checking) */
size_t npoints; /* Number of points in space */
/* 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 necessary, convert fill value datatypes (which copies VL components, etc.) */
if(H5T_detect_class(dset->shared->type, H5T_VLEN) > 0) {
H5T_path_t *tpath; /* Datatype conversion path */
uint8_t *bkg_buf = NULL; /* Background conversion buffer */
H5T_t *mem_type; /* Pointer to memory datatype */
size_t mem_type_size, file_type_size; /* Size of datatype in memory and on disk */
hid_t mem_tid; /* Memory version of disk datatype */
/* 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) {
H5T_close(mem_type);
HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register memory datatype")
} /* end if */
/*-------------------------------------------------------------------------
* Function: H5D_mpio_spaces_xfer
*
* Purpose: Use MPI-IO to transfer data efficiently
* directly between app buffer and file.
*
* Return: non-negative on success, negative on failure.
*
* Programmer: rky 980813
*
* Notes:
* For collective data transfer only since this would eventually call
* H5FD_mpio_setup to do setup to eveually call MPI_File_set_view in
* H5FD_mpio_read or H5FD_mpio_write. MPI_File_set_view is a collective
* call. Letting independent data transfer use this route would result in
* hanging.
*
* The preconditions for calling this routine are located in the
* H5S_mpio_opt_possible() routine, which determines whether this routine
* can be called for a given dataset transfer.
*
* Modifications:
* rky 980918
* Added must_convert parameter to let caller know we can't optimize
* the xfer.
*
* Albert Cheng, 001123
* Include the MPI_type freeing as part of cleanup code.
*
* QAK - 2002/04/02
* Removed the must_convert parameter and move preconditions to
* H5S_mpio_opt_possible() routine
*
* QAK - 2002/06/17
* Removed 'disp' parameter from H5FD_mpio_setup routine and use the
* address of the dataset in MPI_File_set_view() calls, as necessary.
*
* QAK - 2002/06/18
* Removed 'dc_plist' parameter, since it was not used. Also, switch to
* getting the 'extra_offset' setting for each selection.
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_mpio_spaces_xfer(H5D_io_info_t *io_info, size_t elmt_size,
const H5S_t *file_space, const H5S_t *mem_space,
void *_buf /*out*/, hbool_t do_write )
{
haddr_t addr; /* Address of dataset (or selection) within file */
size_t mpi_buf_count, mpi_file_count; /* Number of "objects" to transfer */
hsize_t mpi_buf_offset, mpi_file_offset; /* Offset within dataset where selection (ie. MPI type) begins */
MPI_Datatype mpi_buf_type, mpi_file_type; /* MPI types for buffer (memory) and file */
hbool_t mbt_is_derived=0, /* Whether the buffer (memory) type is derived and needs to be free'd */
mft_is_derived=0; /* Whether the file type is derived and needs to be free'd */
hbool_t plist_is_setup=0; /* Whether the dxpl has been customized */
uint8_t *buf=(uint8_t *)_buf; /* Alias for pointer arithmetic */
int mpi_code; /* MPI return code */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT(H5D_mpio_spaces_xfer);
/* Check args */
assert (io_info);
assert (io_info->dset);
assert (file_space);
assert (mem_space);
assert (buf);
assert (IS_H5FD_MPIO(io_info->dset->ent.file));
/* Make certain we have the correct type of property list */
assert(TRUE==H5P_isa_class(io_info->dxpl_id,H5P_DATASET_XFER));
/* create the MPI buffer type */
if (H5S_mpio_space_type( mem_space, elmt_size,
/* out: */
&mpi_buf_type,
&mpi_buf_count,
&mpi_buf_offset,
&mbt_is_derived )<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't create MPI buf type");
/* create the MPI file type */
if ( H5S_mpio_space_type( file_space, elmt_size,
/* out: */
&mpi_file_type,
&mpi_file_count,
&mpi_file_offset,
&mft_is_derived )<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't create MPI file type");
/* Get the base address of the contiguous dataset or the chunk */
if(io_info->dset->shared->layout.type == H5D_CONTIGUOUS)
addr = H5D_contig_get_addr(io_info->dset) + mpi_file_offset;
else {
haddr_t chunk_addr; /* for collective chunk IO */
assert(io_info->dset->shared->layout.type == H5D_CHUNKED);
chunk_addr=H5D_istore_get_addr(io_info,NULL);
addr = H5F_BASE_ADDR(io_info->dset->ent.file) + chunk_addr + mpi_file_offset;
}
/*
* Pass buf type, file type to the file driver. Request an MPI type
* transfer (instead of an elementary byteblock transfer).
*/
if(H5FD_mpi_setup_collective(io_info->dxpl_id, mpi_buf_type, mpi_file_type)<0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set MPI-I/O properties");
plist_is_setup=1;
/* Adjust the buffer pointer to the beginning of the selection */
buf+=mpi_buf_offset;
/* transfer the data */
if (do_write) {
if (H5F_block_write(io_info->dset->ent.file, H5FD_MEM_DRAW, addr, mpi_buf_count, io_info->dxpl_id, buf) <0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,"MPI write failed");
} else {
if (H5F_block_read (io_info->dset->ent.file, H5FD_MEM_DRAW, addr, mpi_buf_count, io_info->dxpl_id, buf) <0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,"MPI read failed");
}
done:
/* Reset the dxpl settings */
if(plist_is_setup) {
if(H5FD_mpi_teardown_collective(io_info->dxpl_id)<0)
HDONE_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "unable to reset dxpl values");
} /* end if */
/* free the MPI buf and file types */
if (mbt_is_derived) {
if (MPI_SUCCESS != (mpi_code= MPI_Type_free( &mpi_buf_type )))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code);
}
if (mft_is_derived) {
if (MPI_SUCCESS != (mpi_code= MPI_Type_free( &mpi_file_type )))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code);
}
FUNC_LEAVE_NOAPI(ret_value);
} /* end H5D_mpio_spaces_xfer() */
/*-------------------------------------------------------------------------
* Function: H5D_select_fscat
*
* Purpose: Scatters dataset elements from the type conversion buffer BUF
* to the file F where the data points are arranged according to
* the file dataspace FILE_SPACE and stored according to
* LAYOUT and EFL. Each element is ELMT_SIZE bytes.
* The caller is requesting that NELMTS elements are copied.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Quincey Koziol
* Thursday, June 20, 2002
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_select_fscat (H5D_io_info_t *io_info,
const H5S_t *space, H5S_sel_iter_t *iter, size_t nelmts,
haddr_t chunk_addr, void *chunk/*in*/, const void *_buf)
{
const uint8_t *buf=_buf; /* Alias for pointer arithmetic */
hsize_t _off[H5D_IO_VECTOR_SIZE]; /* Array to store sequence offsets */
hsize_t *off=NULL; /* Pointer to sequence offsets */
hsize_t mem_off; /* Offset in memory */
size_t mem_curr_seq; /* "Current sequence" in memory */
size_t dset_curr_seq; /* "Current sequence" in dataset */
size_t _len[H5D_IO_VECTOR_SIZE]; /* Array to store sequence lengths */
size_t *len=NULL; /* Array to store sequence lengths */
size_t orig_mem_len, mem_len; /* Length of sequence in memory */
size_t nseq; /* Number of sequences generated */
size_t nelem; /* Number of elements used in sequences */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(H5D_select_fscat, FAIL);
/* Check args */
assert (io_info);
assert (space);
assert (iter);
assert (nelmts>0);
assert (_buf);
assert(TRUE==H5P_isa_class(io_info->dxpl_id,H5P_DATASET_XFER));
/* Allocate the vector I/O arrays */
if(io_info->dxpl_cache->vec_size != H5D_IO_VECTOR_SIZE) {
if((len = H5FL_SEQ_MALLOC(size_t,io_info->dxpl_cache->vec_size))==NULL)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O length vector array");
if((off = H5FL_SEQ_MALLOC(hsize_t,io_info->dxpl_cache->vec_size))==NULL)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate I/O offset vector array");
} /* end if */
else {
len=_len;
off=_off;
} /* end else */
/* Loop until all elements are written */
while(nelmts>0) {
/* Get list of sequences for selection to write */
if(H5S_SELECT_GET_SEQ_LIST(space,H5S_GET_SEQ_LIST_SORTED,iter,io_info->dxpl_cache->vec_size,nelmts,&nseq,&nelem,off,len)<0)
HGOTO_ERROR (H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed");
/* Reset the current sequence information */
mem_curr_seq=dset_curr_seq=0;
orig_mem_len=mem_len=nelem*iter->elmt_size;
mem_off=0;
/* Write sequence list out */
if((*io_info->ops.writevv)(io_info, nseq, &dset_curr_seq, len, off, (size_t)1, &mem_curr_seq, &mem_len, &mem_off, chunk_addr, chunk, buf) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error");
/* Update buffer */
buf += orig_mem_len;
/* Decrement number of elements left to process */
nelmts -= nelem;
} /* end while */
done:
if(io_info->dxpl_cache->vec_size != H5D_IO_VECTOR_SIZE) {
if(len!=NULL)
H5FL_SEQ_FREE(size_t,len);
if(off!=NULL)
H5FL_SEQ_FREE(hsize_t,off);
} /* end if */
FUNC_LEAVE_NOAPI(ret_value);
} /* H5D_select_fscat() */
