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Diffstat (limited to 'src/H5Dio.c')
| -rw-r--r-- | src/H5Dio.c | 2293 |
1 files changed, 2293 insertions, 0 deletions
diff --git a/src/H5Dio.c b/src/H5Dio.c new file mode 100644 index 0000000..51e66a3 --- /dev/null +++ b/src/H5Dio.c @@ -0,0 +1,2293 @@ +/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * Copyright by the Board of Trustees of the University of Illinois. * + * All rights reserved. * + * * + * This file is part of HDF5. The full HDF5 copyright notice, including * + * terms governing use, modification, and redistribution, is contained in * + * the files COPYING and Copyright.html. COPYING can be found at the root * + * of the source code distribution tree; Copyright.html can be found at the * + * root level of an installed copy of the electronic HDF5 document set and * + * is linked from the top-level documents page. It can also be found at * + * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * + * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ + +#define H5D_PACKAGE /*suppress error about including H5Dpkg */ + +#include "H5private.h" /* Generic Functions */ +#include "H5Dpkg.h" /* Dataset functions */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5FLprivate.h" /* Free Lists */ +#include "H5Iprivate.h" /* IDs */ +#include "H5MMprivate.h" /* Memory management */ +#include "H5Sprivate.h" /* Dataspace functions */ +#include "H5Vprivate.h" /* Vector and array functions */ + +/*#define H5D_DEBUG*/ + +/* + * The MPIO, MPIPOSIX, & FPHDF5 drivers are needed because there are + * file and places where we check for things that aren't handled by these + * drivers. + */ +#include "H5FDfphdf5.h" +#include "H5FDmpio.h" +#include "H5FDmpiposix.h" + +#ifdef H5_HAVE_PARALLEL +/* Remove this if H5R_DATASET_REGION is no longer used in this file */ +# include "H5Rpublic.h" +#endif /*H5_HAVE_PARALLEL*/ + +/* Pablo information */ +#define PABLO_MASK H5Dio_mask + +/* Local typedefs */ + +/*information for mapping between file space and memory space*/ +typedef struct fm_map { + H5S_t **fspace; /*file spaces for all chunks*/ + H5S_t **mspace; /*memory spaces for all chunks*/ + hsize_t elmt_count; /*indicate which element is being processed*/ + hsize_t nchunks; /*total number of chunks*/ + H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */ + unsigned m_ndims; /* Number of dimensions for memory dataspace */ + hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Number of chunks in each dimension */ + hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */ + hssize_t *chunk_coords; /*coordinates for all chunks*/ + H5O_layout_t *layout; /*dataset layout information*/ +} fm_map; + +/* Interface initialization */ +static int interface_initialize_g = 0; +#define INTERFACE_INIT NULL + +/* Local functions */ +static herr_t H5D_read(H5D_t *dataset, const H5T_t *mem_type, + const H5S_t *mem_space, const H5S_t *file_space, + hid_t dset_xfer_plist, void *buf/*out*/); +static herr_t H5D_write(H5D_t *dataset, const H5T_t *mem_type, + const H5S_t *mem_space, const H5S_t *file_space, + hid_t dset_xfer_plist, const void *buf); +static herr_t +H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, + const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, + H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t doing_mpio, H5FD_mpio_xfer_t xfer_mode, + hid_t src_id, hid_t dst_id, void *buf/*out*/); +static herr_t +H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, + const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, + H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t doing_mpio, H5FD_mpio_xfer_t xfer_mode, + hid_t src_id, hid_t dst_id, const void *buf); +static herr_t +H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, + const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, + H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t doing_mpio, H5FD_mpio_xfer_t xfer_mode, + hid_t src_id, hid_t dst_id, void *buf/*out*/); +static herr_t +H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, + const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, + H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t doing_mpio, H5FD_mpio_xfer_t xfer_mode, + hid_t src_id, hid_t dst_id, const void *buf); +#ifdef H5_HAVE_PARALLEL +static herr_t +H5D_io_assist_mpio(H5P_genplist_t *dx_plist, hbool_t doing_mpio, H5FD_mpio_xfer_t xfer_mode, + hbool_t *xfer_mode_changed); +#endif /*H5_HAVE_PARALLEL*/ +static herr_t +H5D_chunk_mem_file_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_space, + const H5S_t *mem_space, fm_map *fm_struct); +static herr_t H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, + hsize_t chunks[], hsize_t chunk_ptr); +static herr_t H5D_chunk_cb(void *elem, hid_t type_id, hsize_t ndims, + hssize_t *coords, void *fm); +static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, + const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id); + + +/* Declare a free list to manage blocks of single datatype element data */ +H5FL_BLK_DEFINE(type_elem); + +/* Declare a free list to manage blocks of type conversion data */ +H5FL_BLK_DEFINE(type_conv); + + +/*-------------------------------------------------------------------------- + NAME + H5Dfill + PURPOSE + Fill a selection in memory with a value + USAGE + herr_t H5Dfill(fill, fill_type, space, buf, buf_type) + const void *fill; IN: Pointer to fill value to use + hid_t fill_type_id; IN: Datatype of the fill value + void *buf; IN/OUT: Memory buffer to fill selection within + hid_t buf_type_id; IN: Datatype of the elements in buffer + hid_t space_id; IN: Dataspace describing memory buffer & + containing selection to use. + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to fill elements in a memory buffer. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + If "fill" parameter is NULL, use all zeros as fill value + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +herr_t +H5Dfill(const void *fill, hid_t fill_type_id, void *buf, hid_t buf_type_id, hid_t space_id) +{ + H5S_t *space; /* Dataspace */ + H5T_t *fill_type; /* Fill-value datatype */ + H5T_t *buf_type; /* Buffer datatype */ + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_API(H5Dfill, FAIL); + H5TRACE5("e","xixii",fill,fill_type_id,buf,buf_type_id,space_id); + + /* Check args */ + if (buf==NULL) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid buffer"); + if (NULL == (space=H5I_object_verify(space_id, H5I_DATASPACE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataspace"); + if (NULL == (fill_type=H5I_object_verify(fill_type_id, H5I_DATATYPE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype"); + if (NULL == (buf_type=H5I_object_verify(buf_type_id, H5I_DATATYPE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype"); + + /* Fill the selection in the memory buffer */ + if(H5D_fill(fill,fill_type,buf,buf_type,space, H5AC_dxpl_id)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed"); + +done: + FUNC_LEAVE_API(ret_value); +} /* H5Dfill() */ + + +/*-------------------------------------------------------------------------- + NAME + H5D_fill + PURPOSE + Fill a selection in memory with a value (internal version) + USAGE + herr_t H5D_fill(fill, fill_type, buf, buf_type, space) + const void *fill; IN: Pointer to fill value to use + H5T_t *fill_type; IN: Datatype of the fill value + void *buf; IN/OUT: Memory buffer to fill selection within + H5T_t *buf_type; IN: Datatype of the elements in buffer + H5S_t *space; IN: Dataspace describing memory buffer & + containing selection to use. + RETURNS + Non-negative on success/Negative on failure. + DESCRIPTION + Use the selection in the dataspace to fill elements in a memory buffer. + GLOBAL VARIABLES + COMMENTS, BUGS, ASSUMPTIONS + If "fill" parameter is NULL, use all zeros as fill value. If "fill_type" + parameter is NULL, use "buf_type" for the fill value datatype. + EXAMPLES + REVISION LOG +--------------------------------------------------------------------------*/ +static herr_t +H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id) +{ + H5T_path_t *tpath = NULL; /* Conversion information*/ + uint8_t *tconv_buf = NULL; /* Data type conv buffer */ + uint8_t *bkg_buf = NULL; /* Temp conversion buffer */ + hid_t src_id = -1, dst_id = -1; /* Temporary type IDs */ + size_t src_type_size; /* Size of source type */ + size_t dst_type_size; /* Size of destination type*/ + size_t buf_size; /* Desired buffer size */ + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_NOINIT(H5D_fill); + + /* Check args */ + assert(buf); + assert(buf_type); + assert(space); + + /* Check for "default" fill value */ + if(fill_type==NULL) + fill_type=buf_type; + + /* Get the memory and file datatype sizes */ + src_type_size = H5T_get_size(fill_type); + dst_type_size = H5T_get_size(buf_type); + + /* Get the maximum buffer size needed and allocate it */ + buf_size=MAX(src_type_size,dst_type_size); + if (NULL==(tconv_buf = H5FL_BLK_MALLOC(type_elem,buf_size)) || NULL==(bkg_buf = H5FL_BLK_CALLOC(type_elem,buf_size))) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed"); + + /* Copy the user's data into the buffer for conversion */ + if(fill==NULL) + HDmemset(tconv_buf,0,src_type_size); + else + HDmemcpy(tconv_buf,fill,src_type_size); + + /* Convert memory buffer into disk buffer */ + /* Set up type conversion function */ + if (NULL == (tpath = H5T_path_find(fill_type, buf_type, NULL, NULL, dxpl_id))) { + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); + } else if (!H5T_IS_NOOP(tpath)) { + if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(fill_type, H5T_COPY_ALL)))<0 || + (dst_id = H5I_register(H5I_DATATYPE, H5T_copy(buf_type, H5T_COPY_ALL)))<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); + } + + /* Perform data type conversion */ + if (H5T_convert(tpath, src_id, dst_id, (hsize_t)1, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed"); + + /* Fill the selection in the memory buffer */ + if(H5S_select_fill(tconv_buf, dst_type_size, space, buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed"); + +done: + if (tconv_buf) + H5FL_BLK_FREE(type_elem,tconv_buf); + if (bkg_buf) + H5FL_BLK_FREE(type_elem,bkg_buf); + FUNC_LEAVE_NOAPI(ret_value); +} /* H5D_fill() */ + + +/*------------------------------------------------------------------------- + * Function: H5Dread + * + * Purpose: Reads (part of) a DSET from the file into application + * memory BUF. The part of the dataset to read is defined with + * MEM_SPACE_ID and FILE_SPACE_ID. The data points are + * converted from their file type to the MEM_TYPE_ID specified. + * Additional miscellaneous data transfer properties can be + * passed to this function with the PLIST_ID argument. + * + * The FILE_SPACE_ID can be the constant H5S_ALL which indicates + * that the entire file data space is to be referenced. + * + * The MEM_SPACE_ID can be the constant H5S_ALL in which case + * the memory data space is the same as the file data space + * defined when the dataset was created. + * + * The number of elements in the memory data space must match + * the number of elements in the file data space. + * + * The PLIST_ID can be the constant H5P_DEFAULT in which + * case the default data transfer properties are used. + * + * Return: Non-negative on success/Negative on failure + * + * Errors: + * ARGS BADTYPE Not a data space. + * ARGS BADTYPE Not a data type. + * ARGS BADTYPE Not a dataset. + * ARGS BADTYPE Not xfer parms. + * ARGS BADVALUE No output buffer. + * DATASET READERROR Can't read data. + * + * Programmer: Robb Matzke + * Thursday, December 4, 1997 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, + hid_t file_space_id, hid_t plist_id, void *buf/*out*/) +{ + H5D_t *dset = NULL; + const H5T_t *mem_type = NULL; + const H5S_t *mem_space = NULL; + const H5S_t *file_space = NULL; + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_API(H5Dread, FAIL); + H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id, + plist_id,buf); + + /* check arguments */ + if (NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); + if (NULL == dset->ent.file) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); + if (NULL == (mem_type = H5I_object_verify(mem_type_id, H5I_DATATYPE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); + if (H5S_ALL != mem_space_id) { + if (NULL == (mem_space = H5I_object_verify(mem_space_id, H5I_DATASPACE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); + + /* Check for valid selection */ + if(H5S_select_valid(mem_space)!=TRUE) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); + } + if (H5S_ALL != file_space_id) { + if (NULL == (file_space = H5I_object_verify(file_space_id, H5I_DATASPACE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); + + /* Check for valid selection */ + if(H5S_select_valid(file_space)!=TRUE) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); + } + + /* Get the default dataset transfer property list if the user didn't provide one */ + if (H5P_DEFAULT == plist_id) + plist_id= H5P_DATASET_XFER_DEFAULT; + else + if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); + if (!buf) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer"); + + /* read raw data */ + if (H5D_read(dset, mem_type, mem_space, file_space, plist_id, buf/*out*/) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data"); + +done: + FUNC_LEAVE_API(ret_value); +} + + +/*------------------------------------------------------------------------- + * Function: H5Dwrite + * + * Purpose: Writes (part of) a DSET from application memory BUF to the + * file. The part of the dataset to write is defined with the + * MEM_SPACE_ID and FILE_SPACE_ID arguments. The data points + * are converted from their current type (MEM_TYPE_ID) to their + * file data type. Additional miscellaneous data transfer + * properties can be passed to this function with the + * PLIST_ID argument. + * + * The FILE_SPACE_ID can be the constant H5S_ALL which indicates + * that the entire file data space is to be referenced. + * + * The MEM_SPACE_ID can be the constant H5S_ALL in which case + * the memory data space is the same as the file data space + * defined when the dataset was created. + * + * The number of elements in the memory data space must match + * the number of elements in the file data space. + * + * The PLIST_ID can be the constant H5P_DEFAULT in which + * case the default data transfer properties are used. + * + * Return: Non-negative on success/Negative on failure + * + * Errors: + * + * Programmer: Robb Matzke + * Thursday, December 4, 1997 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +herr_t +H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, + hid_t file_space_id, hid_t plist_id, const void *buf) +{ + H5D_t *dset = NULL; + const H5T_t *mem_type = NULL; + const H5S_t *mem_space = NULL; + const H5S_t *file_space = NULL; + herr_t ret_value=SUCCEED; /* Return value */ + + FUNC_ENTER_API(H5Dwrite, FAIL); + H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id, + plist_id,buf); + + /* check arguments */ + if (NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); + if (NULL == dset->ent.file) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); + if (NULL == (mem_type = H5I_object_verify(mem_type_id, H5I_DATATYPE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); + if (H5S_ALL != mem_space_id) { + if (NULL == (mem_space = H5I_object_verify(mem_space_id, H5I_DATASPACE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); + + /* Check for valid selection */ + if (H5S_select_valid(mem_space)!=TRUE) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); + } + if (H5S_ALL != file_space_id) { + if (NULL == (file_space = H5I_object_verify(file_space_id, H5I_DATASPACE))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); + + /* Check for valid selection */ + if (H5S_select_valid(file_space)!=TRUE) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); + } + + /* Get the default dataset transfer property list if the user didn't provide one */ + if (H5P_DEFAULT == plist_id) + plist_id= H5P_DATASET_XFER_DEFAULT; + else + if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); + if (!buf) + HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer"); + + /* write raw data */ + if (H5D_write(dset, mem_type, mem_space, file_space, plist_id, buf) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data"); + +done: + FUNC_LEAVE_API(ret_value); +} + + +/*------------------------------------------------------------------------- + * Function: H5D_read + * + * Purpose: Reads (part of) a DATASET into application memory BUF. See + * H5Dread() for complete details. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Robb Matzke + * Thursday, December 4, 1997 + * + * Modifications: + * Robb Matzke, 1998-06-09 + * The data space is no longer cached in the dataset struct. + * + * Robb Matzke, 1998-08-11 + * Added timing calls around all the data space I/O functions. + * + * rky, 1998-09-18 + * Added must_convert to do non-optimized read when necessary. + * + * Quincey Koziol, 1999-07-02 + * Changed xfer_parms parameter to xfer plist parameter, so it + * could be passed to H5T_convert. + * + * Albert Cheng, 2000-11-21 + * Added the code that when it detects it is not safe to process a + * COLLECTIVE read request without hanging, it changes it to + * INDEPENDENT calls. + * + * Albert Cheng, 2000-11-27 + * Changed to use the optimized MPIO transfer for Collective calls only. + * + * Raymond Lu, 2001-10-2 + * Changed the way to retrieve property for generic property list. + * + * Raymond Lu, 2002-2-26 + * For the new fill value design, data space can either be allocated + * or not allocated at this stage. Fill value or data from space is + * returned to outgoing buffer. + * + * QAK - 2002/04/02 + * Removed the must_convert parameter and move preconditions to + * H5S_<foo>_opt_possible() routine + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, + const H5S_t *file_space, hid_t dxpl_id, void *buf/*out*/) +{ + hssize_t snelmts; /*total number of elmts (signed) */ + hsize_t nelmts; /*total number of elmts */ + H5T_path_t *tpath = NULL; /*type conversion info */ + hid_t src_id = -1, dst_id = -1;/*temporary type atoms */ + H5S_conv_t *sconv=NULL; /*space conversion funcs*/ + H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; /*xfer_mode for this request */ + hbool_t doing_mpio=0; /*This is an MPIO access */ + H5P_genplist_t *dx_plist=NULL; /* Data transfer property list */ + H5P_genplist_t *dc_plist; /* Dataset creation roperty list */ + unsigned sconv_flags=0; /* Flags for the space conversion */ + H5S_sel_type fsel_type; /* Selection type on disk */ + H5S_sel_type msel_type; /* Selection type in memory */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOINIT(H5D_read); + + /* check args */ + assert(dataset && dataset->ent.file); + assert(mem_type); + assert(buf); + + /* Get the dataset's creation property list */ + if (NULL == (dc_plist = H5I_object(dataset->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); + + /* Get the dataset transfer property list */ + if (NULL == (dx_plist = H5I_object(dxpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); + + if (!file_space) + file_space = dataset->space; + if (!mem_space) + mem_space = file_space; + if((snelmts = H5S_get_select_npoints(mem_space))<0) + HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection"); + nelmts=snelmts; + +#ifdef H5_HAVE_PARALLEL + /* Collect Parallel I/O information for possible later use */ + if (H5FD_MPIO==H5P_peek_hid_t(dx_plist,H5D_XFER_VFL_ID_NAME)) { + doing_mpio++; + xfer_mode=H5P_peek_unsigned(dx_plist, H5D_XFER_IO_XFER_MODE_NAME); + } /* end if */ + /* Collective access is not permissible without the MPIO or MPIPOSIX driver */ + if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE && + !(IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file) || IS_H5FD_FPHDF5(dataset->ent.file))) + HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPIO & MPIPOSIX drivers only"); + + /* Set the "parallel I/O possible" flag, for H5S_find() */ + if (H5S_mpi_opt_types_g && IS_H5FD_MPIO(dataset->ent.file)) { + /* Only collective write should call this since it eventually + * calls MPI_File_set_view which is a collective call. + * See H5S_mpio_spaces_xfer() for details. + */ + if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE) + sconv_flags |= H5S_CONV_PAR_IO_POSSIBLE; + } /* end if */ +#endif /*H5_HAVE_PARALLEL*/ + + /* Make certain that the number of elements in each selection is the same */ + if (nelmts!=(hsize_t)H5S_get_select_npoints(file_space)) + HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); + + /* Retrieve dataset properties */ + /* <none needed in the general case> */ + + /* If space hasn't been allocated and not using external storage, + * return fill value to buffer if fill time is upon allocation, or + * do nothing if fill time is never. If the dataset is compact and + * fill time is NEVER, there is no way to tell whether part of data + * has been overwritten. So just proceed in reading. + */ + if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT + && dataset->layout.addr==HADDR_UNDEF) { + H5O_fill_t fill; /* Fill value info */ + H5D_fill_time_t fill_time; /* When to write the fill values */ + H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ + + /* Retrieve dataset's fill-value properties */ + if(H5P_fill_value_defined(dc_plist, &fill_status)<0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined"); + if((fill_status==H5D_FILL_VALUE_DEFAULT || fill_status==H5D_FILL_VALUE_USER_DEFINED) + && H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill value"); + if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill time"); + + /* Should be impossible, but check anyway... */ + if(fill_status == H5D_FILL_VALUE_UNDEFINED && fill_time == H5D_FILL_TIME_ALLOC) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "read failed: dataset doesn't exist, no data can be read"); + + /* If we're never going to fill this dataset, just leave the junk in the user's buffer */ + if(fill_time == H5D_FILL_TIME_NEVER) + HGOTO_DONE(SUCCEED); + + /* Go fill the user's selection with the dataset's fill value */ + if(H5D_fill(fill.buf,fill.type,buf,mem_type,mem_space, dxpl_id)<0) { + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "filling buf failed"); + } else + HGOTO_DONE(SUCCEED); + } /* end if */ + + /* + * Locate the type conversion function and data space conversion + * functions, and set up the element numbering information. If a data + * type conversion is necessary then register data type atoms. Data type + * conversion is necessary if the user has set the `need_bkg' to a high + * enough value in xfer_parms since turning off data type conversion also + * turns off background preservation. + */ + if (NULL==(tpath=H5T_path_find(dataset->type, mem_type, NULL, NULL, dxpl_id))) { + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); + } else if (!H5T_IS_NOOP(tpath)) { + if ((src_id=H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0 || + (dst_id=H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); + } /* end if */ + + /* Set the storage flags for the space conversion check */ + switch(dataset->layout.type) { + case H5D_COMPACT: + sconv_flags |= H5S_CONV_STORAGE_COMPACT; + break; + + case H5D_CONTIGUOUS: + sconv_flags |= H5S_CONV_STORAGE_CONTIGUOUS; + break; + + case H5D_CHUNKED: + sconv_flags |= H5S_CONV_STORAGE_CHUNKED; + break; + + default: + assert(0 && "Unhandled layout type!"); + } /* end switch */ + + /* Get dataspace functions */ + if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags))) + HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from file to memory data space"); + + /* Get type of selection on disk & in memory */ + if((fsel_type=H5S_get_select_type(file_space))<0) + HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space"); + if((msel_type=H5S_get_select_type(mem_space))<0) + HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space"); + + /* Determine correct I/O routine to invoke */ + if((fsel_type==H5S_SEL_POINTS || msel_type==H5S_SEL_POINTS) || + dataset->layout.type!=H5D_CHUNKED) { + /* Must use "contiguous" code for point selections, + * since order of I/O accesses can be different from that of the + * other kinds of selections + */ + if(H5D_contig_read(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, dc_plist, + dx_plist, dxpl_id, doing_mpio, xfer_mode, src_id, dst_id, buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data"); + } /* end if */ + else { + if(H5D_chunk_read(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, dc_plist, + dx_plist, dxpl_id, doing_mpio, xfer_mode, src_id, dst_id, buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data"); + } /* end else */ + +done: + if (src_id >= 0) + H5I_dec_ref(src_id); + if (dst_id >= 0) + H5I_dec_ref(dst_id); + + FUNC_LEAVE_NOAPI(ret_value); +} /* end H5D_read() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_write + * + * Purpose: Writes (part of) a DATASET to a file from application memory + * BUF. See H5Dwrite() for complete details. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Robb Matzke + * Thursday, December 4, 1997 + * + * Modifications: + * Robb Matzke, 9 Jun 1998 + * The data space is no longer cached in the dataset struct. + * + * rky 980918 + * Added must_convert to do non-optimized read when necessary. + * + * Quincey Koziol, 2 July 1999 + * Changed xfer_parms parameter to xfer plist parameter, so it could + * be passed to H5T_convert + * + * Albert Cheng, 2000-11-21 + * Added the code that when it detects it is not safe to process a + * COLLECTIVE write request without hanging, it changes it to + * INDEPENDENT calls. + * + * Albert Cheng, 2000-11-27 + * Changed to use the optimized MPIO transfer for Collective calls only. + * + * Raymond Lu, 2001-10-2 + * Changed the way to retrieve property for generic property list. + * + * Raymond Lu, 2002-2-26 + * For the new fill value design, space may not be allocated until + * this function is called. Allocate and initialize space if it + * hasn't been. + * + * QAK - 2002/04/02 + * Removed the must_convert parameter and move preconditions to + * H5S_<foo>_opt_possible() routine + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, + const H5S_t *file_space, hid_t dxpl_id, const void *buf) +{ + hssize_t snelmts; /*total number of elmts (signed) */ + hsize_t nelmts; /*total number of elmts */ + H5T_path_t *tpath = NULL; /*type conversion info */ + hid_t src_id = -1, dst_id = -1;/*temporary type atoms */ + H5S_conv_t *sconv=NULL; /*space conversion funcs*/ + H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; /*xfer_mode for this request */ + hbool_t doing_mpio=0; /*This is an MPIO access */ + H5P_genplist_t *dx_plist=NULL; /* Data transfer property list */ + H5P_genplist_t *dc_plist; /* Dataset creation roperty list */ + unsigned sconv_flags=0; /* Flags for the space conversion */ + H5S_sel_type fsel_type; /* Selection type on disk */ + H5S_sel_type msel_type; /* Selection type in memory */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOINIT(H5D_write); + + /* check args */ + assert(dataset && dataset->ent.file); + assert(mem_type); + assert(buf); + + /* If MPIO, MPIPOSIX, or FPHDF5 is used, no VL datatype support yet. */ + /* This is because they use the global heap in the file and we don't */ + /* support parallel access of that yet */ + if ( (IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file) || IS_H5FD_FPHDF5(dataset->ent.file)) && + H5T_get_class(mem_type)==H5T_VLEN) + HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL datatypes yet"); + /* If MPIO, MPIPOSIX, or FPHDF5 is used, no dataset region reference datatype support yet. */ + /* This is because they use the global heap in the file and we don't */ + /* support parallel access of that yet */ + if ((IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file) || IS_H5FD_FPHDF5(dataset->ent.file)) && + H5T_get_class(mem_type)==H5T_REFERENCE && + H5T_get_ref_type(mem_type)==H5R_DATASET_REGION) + HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing region reference datatypes yet"); + + /* Check if we are allowed to write to this file */ + if (0==(H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR)) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file"); + + /* Get the dataset's creation property list */ + if (NULL == (dc_plist = H5I_object(dataset->dcpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); + + /* Get the dataset transfer property list */ + if (NULL == (dx_plist = H5I_object(dxpl_id))) + HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); + + if (!file_space) + file_space = dataset->space; + if (!mem_space) + mem_space = file_space; + if((snelmts = H5S_get_select_npoints(mem_space))<0) + HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection"); + nelmts=snelmts; + +#ifdef H5_HAVE_PARALLEL + /* Collect Parallel I/O information for possible later use */ + if (H5FD_MPIO==H5P_peek_hid_t(dx_plist,H5D_XFER_VFL_ID_NAME)) { + doing_mpio++; + xfer_mode=H5P_peek_unsigned(dx_plist, H5D_XFER_IO_XFER_MODE_NAME); + } /* end if */ + + /* Collective access is not permissible without the MPIO or MPIPOSIX driver */ + if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE && + !(IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file) || IS_H5FD_FPHDF5(dataset->ent.file))) + HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPIO driver only"); + + /* If dataset is compact, collective access is only allowed when file space + * selection is H5S_ALL */ + if(doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE + && dataset->layout.type==H5D_COMPACT) { + if(H5S_get_select_type(file_space) != H5S_SEL_ALL) + HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access to compact dataset doesn't support partial access"); + } + + /* Set the "parallel I/O possible" flag, for H5S_find() */ + if (H5S_mpi_opt_types_g && IS_H5FD_MPIO(dataset->ent.file)) { + /* Only collective write should call this since it eventually + * calls MPI_File_set_view which is a collective call. + * See H5S_mpio_spaces_xfer() for details. + */ + if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE) + sconv_flags |= H5S_CONV_PAR_IO_POSSIBLE; + } /* end if */ +#endif /*H5_HAVE_PARALLEL*/ + + /* Make certain that the number of elements in each selection is the same */ + if (nelmts!=(hsize_t)H5S_get_select_npoints(file_space)) + HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); + + /* Retrieve dataset properties */ + /* <none needed currently> */ + + /* Allocate data space and initialize it if it hasn't been. */ + if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT + && dataset->layout.addr==HADDR_UNDEF) { + hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */ + + /* Get the number of elements in file dataset's dataspace */ + if((file_nelmts=H5S_get_simple_extent_npoints(file_space))<0) + HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset"); + + /* Allocate storage */ + if(H5D_alloc_storage(dataset->ent.file,dxpl_id,dataset,H5D_ALLOC_WRITE, TRUE, (hbool_t)((hsize_t)file_nelmts==nelmts ? TRUE : FALSE))<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage"); + } /* end if */ + + /* + * Locate the type conversion function and data space conversion + * functions, and set up the element numbering information. If a data + * type conversion is necessary then register data type atoms. Data type + * conversion is necessary if the user has set the `need_bkg' to a high + * enough value in xfer_parms since turning off data type conversion also + * turns off background preservation. + */ + if (NULL==(tpath=H5T_path_find(mem_type, dataset->type, NULL, NULL, dxpl_id))) { + HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); + } else if (!H5T_IS_NOOP(tpath)) { + if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0 || + (dst_id = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); + } /* end if */ + + /* Set the storage flags for the space conversion check */ + switch(dataset->layout.type) { + case H5D_COMPACT: + sconv_flags |= H5S_CONV_STORAGE_COMPACT; + break; + + case H5D_CONTIGUOUS: + sconv_flags |= H5S_CONV_STORAGE_CONTIGUOUS; + break; + + case H5D_CHUNKED: + sconv_flags |= H5S_CONV_STORAGE_CHUNKED; + break; + + default: + assert(0 && "Unhandled layout type!"); + } /* end switch */ + + /* Get dataspace functions */ + if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags))) + HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from memory to file data space"); + + /* Get type of selection on disk & in memory */ + if((fsel_type=H5S_get_select_type(file_space))<0) + HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space"); + if((msel_type=H5S_get_select_type(mem_space))<0) + HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space"); + + /* Determine correct I/O routine to invoke */ + if((fsel_type==H5S_SEL_POINTS || msel_type==H5S_SEL_POINTS) || + dataset->layout.type!=H5D_CHUNKED) { + /* Must use "contiguous" code for point selections, + * since order of I/O accesses can be different from that of the + * other kinds of selections + */ + if(H5D_contig_write(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, dc_plist, + dx_plist, dxpl_id, doing_mpio, xfer_mode, src_id, dst_id, buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data"); + } /* end if */ + else { + if(H5D_chunk_write(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, dc_plist, + dx_plist, dxpl_id, doing_mpio, xfer_mode, src_id, dst_id, buf)<0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data"); + } /* end else */ + + /* + * Update modification time. We have to do this explicitly because + * writing to a dataset doesn't necessarily change the object header. + */ + if (H5O_touch(&(dataset->ent), FALSE, dxpl_id)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time"); + +done: + if (src_id >= 0) + H5I_dec_ref(src_id); + if (dst_id >= 0) + H5I_dec_ref(dst_id); + + FUNC_LEAVE_NOAPI(ret_value); +} /* end H5D_write() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_contig_read + * + * Purpose: Read from a contiguous dataset. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * Thursday, April 10, 2003 + * + * Modifications: + * QAK - 2003/04/17 + * Hacked on it a lot. :-) + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, + const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, + H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t +#ifndef H5_HAVE_PARALLEL + UNUSED +#endif /*H5_HAVE_PARALLEL*/ + doing_mpio, H5FD_mpio_xfer_t +#ifndef H5_HAVE_PARALLEL + UNUSED +#endif /*H5_HAVE_PARALLEL*/ + xfer_mode, + hid_t src_id, hid_t dst_id, void *buf/*out*/) +{ + herr_t status; /*function return status*/ +#ifdef H5S_DEBUG + H5_timer_t timer; +#endif + size_t src_type_size; /*size of source type */ + size_t dst_type_size; /*size of destination type*/ + size_t target_size; /*desired buffer size */ + hsize_t request_nelmts; /*requested strip mine */ + 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 bkg_iter; /*background iteration info*/ + hbool_t bkg_iter_init=0; /*background 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 */ + H5T_bkg_t need_bkg; /*type of background buf*/ + uint8_t *tconv_buf = NULL; /*data type conv buffer */ + uint8_t *bkg_buf = NULL; /*background buffer */ + hsize_t smine_start; /*strip mine start loc */ + hsize_t n, smine_nelmts; /*elements per strip */ +#ifdef H5_HAVE_PARALLEL + hbool_t xfer_mode_changed; /* Whether the transfer mode was changed */ +#endif /*H5_HAVE_PARALLEL*/ + herr_t ret_value = SUCCEED; /*return value */ + + FUNC_ENTER_NOINIT(H5D_contig_read); + + /* + * If there is no type conversion then read directly into the + * application's buffer. This saves at least one mem-to-mem copy. + */ + if (H5T_IS_NOOP(tpath)) { +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + /* Sanity check dataset, then read it */ + assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || + dataset->layout.type==H5D_COMPACT); + status = (sconv->read)(dataset->ent.file, &(dataset->layout), + dc_plist, (H5D_storage_t *)&(dataset->efl), H5T_get_size(dataset->type), + file_space, mem_space, dxpl_id, buf/*out*/); +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[1].read_timer), &timer); + sconv->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->type); + sconv->stats[1].read_ncalls++; +#endif + + /* Check return value from optimized read */ + if (status<0) { + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed"); + } else + /* direct xfer accomplished successfully */ + HGOTO_DONE(SUCCEED); + } /* end if */ + + /* + * This is the general case(type conversion). + */ + +#ifdef H5_HAVE_PARALLEL + H5D_io_assist_mpio(dx_plist, doing_mpio, xfer_mode, &xfer_mode_changed); +#endif /*H5_HAVE_PARALLEL*/ + + /* Compute element sizes and other parameters */ + src_type_size = H5T_get_size(dataset->type); + dst_type_size = H5T_get_size(mem_type); + target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME); + request_nelmts = target_size / MAX(src_type_size, dst_type_size); + + /* Figure out the strip mine size. */ + if (H5S_select_iter_init(&file_iter, file_space, src_type_size)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); + file_iter_init=1; /*file selection iteration info has been initialized */ + if (H5S_select_iter_init(&mem_iter, mem_space, dst_type_size)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); + mem_iter_init=1; /*file selection iteration info has been initialized */ + if (H5S_select_iter_init(&bkg_iter, mem_space, dst_type_size)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); + bkg_iter_init=1; /*file selection iteration info has been initialized */ + + /* Sanity check elements in temporary buffer */ + if (request_nelmts<=0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); + + /* + * Get a temporary buffer for type conversion unless the app has already + * supplied one through the xfer properties. Instead of allocating a + * buffer which is the exact size, we allocate the target size. The + * malloc() is usually less resource-intensive if we allocate/free the + * same size over and over. + */ + if (tpath->cdata.need_bkg) { + /* Retrieve the bkgr buffer property */ + if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) + HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); + need_bkg = MAX(tpath->cdata.need_bkg, need_bkg); + } else { + need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ + } /* end else */ + if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { + /* Allocate temporary buffer */ + if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); + } /* end if */ + if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { + /* Allocate background buffer */ + H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); + if((bkg_buf=H5FL_BLK_MALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); + } /* end if */ + + /* Start strip mining... */ + for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) { + /* Go figure out how many elements to read from the file */ + assert(H5S_select_iter_nelmts(&file_iter)==(nelmts-smine_start)); + smine_nelmts = MIN(request_nelmts, (nelmts-smine_start)); + + /* + * Gather the data from disk into the data type conversion + * buffer. Also gather data from application to background buffer + * if necessary. + */ +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + /* Sanity check that space is allocated, then read data from it */ + assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || + dataset->layout.type==H5D_COMPACT); + n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), + dc_plist, (H5D_storage_t *)&dataset->efl, src_type_size, file_space, + &file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/); + +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[1].gath_timer), &timer); + sconv->stats[1].gath_nbytes += n * src_type_size; + sconv->stats[1].gath_ncalls++; +#endif + if (n!=smine_nelmts) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); + + if (need_bkg) { +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + n = H5S_select_mgath(buf, dst_type_size, mem_space, &bkg_iter, + smine_nelmts, dxpl_id, bkg_buf/*out*/); +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[1].bkg_timer), &timer); + sconv->stats[1].bkg_nbytes += n * dst_type_size; + sconv->stats[1].bkg_ncalls++; +#endif + if (n!=smine_nelmts) + HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed"); + } /* end if */ + + /* + * Perform data type conversion. + */ + if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); + + /* + * Scatter the data into memory. + */ +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + status = H5S_select_mscat(tconv_buf, dst_type_size, mem_space, + &mem_iter, smine_nelmts, dxpl_id, buf/*out*/); +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[1].scat_timer), &timer); + sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size; + sconv->stats[1].scat_ncalls++; +#endif + if (status<0) + HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "scatter failed"); + + } /* end for */ + +done: +#ifdef H5_HAVE_PARALLEL + /* restore xfer_mode due to the kludge */ + if (doing_mpio && xfer_mode_changed) { +#ifdef H5D_DEBUG + if (H5DEBUG(D)) + fprintf (H5DEBUG(D), "H5D: dx->xfer_mode was COLLECTIVE, restored to INDEPENDENT\n"); +#endif + xfer_mode = H5FD_MPIO_COLLECTIVE; + if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); + } /* end if */ +#endif /*H5_HAVE_PARALLEL*/ + /* Release selection iterators */ + if(file_iter_init) + H5S_select_iter_release(&file_iter); + if(mem_iter_init) + H5S_select_iter_release(&mem_iter); + if(bkg_iter_init) + H5S_select_iter_release(&bkg_iter); + + assert(dx_plist); + if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME)) + H5FL_BLK_FREE(type_conv,tconv_buf); + if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) + H5FL_BLK_FREE(type_conv,bkg_buf); + + FUNC_LEAVE_NOAPI(ret_value); +} /* end H5D_contig_read() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_contig_write + * + * Purpose: Write to a contiguous dataset. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * Thursday, April 10, 2003 + * + * Modifications: + * QAK - 2003/04/17 + * Hacked on it a lot. :-) + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, + const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, + H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t +#ifndef H5_HAVE_PARALLEL + UNUSED +#endif /*H5_HAVE_PARALLEL*/ + doing_mpio, H5FD_mpio_xfer_t +#ifndef H5_HAVE_PARALLEL + UNUSED +#endif /*H5_HAVE_PARALLEL*/ + xfer_mode, + hid_t src_id, hid_t dst_id, const void *buf) +{ + herr_t status; /*function return status*/ +#ifdef H5S_DEBUG + H5_timer_t timer; +#endif + size_t src_type_size; /*size of source type */ + size_t dst_type_size; /*size of destination type*/ + size_t target_size; /*desired buffer size */ + hsize_t request_nelmts; /*requested strip mine */ + 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 bkg_iter; /*background iteration info*/ + hbool_t bkg_iter_init=0; /*background 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 */ + H5T_bkg_t need_bkg; /*type of background buf*/ + uint8_t *tconv_buf = NULL; /*data type conv buffer */ + uint8_t *bkg_buf = NULL; /*background buffer */ + hsize_t smine_start; /*strip mine start loc */ + hsize_t n, smine_nelmts; /*elements per strip */ +#ifdef H5_HAVE_PARALLEL + hbool_t xfer_mode_changed; /* Whether the transfer mode was changed */ +#endif /*H5_HAVE_PARALLEL*/ + herr_t ret_value = SUCCEED; /*return value */ + + FUNC_ENTER_NOINIT(H5D_contig_write); + + /* + * If there is no type conversion then write directly from the + * application's buffer. This saves at least one mem-to-mem copy. + */ + if (H5T_IS_NOOP(tpath)) { +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + status = (sconv->write)(dataset->ent.file, &(dataset->layout), + dc_plist, (H5D_storage_t *)&(dataset->efl), H5T_get_size(dataset->type), + file_space, mem_space, dxpl_id, buf); +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[0].write_timer), &timer); + sconv->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type); + sconv->stats[0].write_ncalls++; +#endif + + /* Check return value from optimized write */ + if (status<0) { + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed"); + } else + /* direct xfer accomplished successfully */ + HGOTO_DONE(SUCCEED); + } /* end if */ + + /* + * This is the general case. + */ + +#ifdef H5_HAVE_PARALLEL + H5D_io_assist_mpio(dx_plist, doing_mpio, xfer_mode, &xfer_mode_changed); +#endif /*H5_HAVE_PARALLEL*/ + + /* Compute element sizes and other parameters */ + src_type_size = H5T_get_size(mem_type); + dst_type_size = H5T_get_size(dataset->type); + target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME); + request_nelmts = target_size / MAX (src_type_size, dst_type_size); + + /* Sanity check elements in temporary buffer */ + if (request_nelmts<=0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); + + /* Figure out the strip mine size. */ + if (H5S_select_iter_init(&file_iter, file_space, dst_type_size)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); + file_iter_init=1; /*file selection iteration info has been initialized */ + if (H5S_select_iter_init(&mem_iter, mem_space, src_type_size)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); + mem_iter_init=1; /*file selection iteration info has been initialized */ + if (H5S_select_iter_init(&bkg_iter, file_space, dst_type_size)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); + bkg_iter_init=1; /*file selection iteration info has been initialized */ + + /* + * Get a temporary buffer for type conversion unless the app has already + * supplied one through the xfer properties. Instead of allocating a + * buffer which is the exact size, we allocate the target size. The + * malloc() is usually less resource-intensive if we allocate/free the + * same size over and over. + */ + if (tpath->cdata.need_bkg) { + /* Retrieve the bkgr buffer property */ + if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) + HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); + need_bkg = MAX (tpath->cdata.need_bkg, need_bkg); + } else if(H5T_detect_class(dataset->type, H5T_VLEN)) { + /* Old data is retrieved into background buffer for VL datatype. The + * data is used later for freeing heap objects. */ + need_bkg = H5T_BKG_YES; + } else { + need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ + } /* end else */ + if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { + /* Allocate temporary buffer */ + if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); + } /* end if */ + if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { + /* Allocate background buffer */ + H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); + if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); + } /* end if */ + + /* Start strip mining... */ + for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) { + /* Go figure out how many elements to read from the file */ + assert(H5S_select_iter_nelmts(&file_iter)==(nelmts-smine_start)); + smine_nelmts = MIN(request_nelmts, (nelmts-smine_start)); + + /* + * Gather data from application buffer into the data type conversion + * buffer. Also gather data from the file into the background buffer + * if necessary. + */ +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + n = H5S_select_mgath(buf, src_type_size, mem_space, &mem_iter, + smine_nelmts, dxpl_id, tconv_buf/*out*/); +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[0].gath_timer), &timer); + sconv->stats[0].gath_nbytes += n * src_type_size; + sconv->stats[0].gath_ncalls++; +#endif + if (n!=smine_nelmts) + HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed"); + + if (need_bkg) { +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), + dc_plist, (H5D_storage_t *)&(dataset->efl), dst_type_size, file_space, + &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); + +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[0].bkg_timer), &timer); + sconv->stats[0].bkg_nbytes += n * dst_type_size; + sconv->stats[0].bkg_ncalls++; +#endif + if (n!=smine_nelmts) + HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed"); + } /* end if */ + + /* + * Perform data type conversion. + */ + if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); + + /* + * Scatter the data out to the file. + */ +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + status = H5S_select_fscat(dataset->ent.file, &(dataset->layout), + dc_plist, (H5D_storage_t *)&(dataset->efl), dst_type_size, file_space, &file_iter, + smine_nelmts, dxpl_id, tconv_buf); + +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[0].scat_timer), &timer); + sconv->stats[0].scat_nbytes += smine_nelmts * dst_type_size; + sconv->stats[0].scat_ncalls++; +#endif + if (status<0) + HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed"); + } /* end for */ + +done: +#ifdef H5_HAVE_PARALLEL + /* restore xfer_mode due to the kludge */ + if (doing_mpio && xfer_mode_changed) { +#ifdef H5D_DEBUG + if (H5DEBUG(D)) + fprintf (H5DEBUG(D), "H5D: dx->xfer_mode was COLLECTIVE, restored to INDEPENDENT\n"); +#endif + xfer_mode = H5FD_MPIO_COLLECTIVE; + if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); + } /* end if */ +#endif /*H5_HAVE_PARALLEL*/ + /* Release selection iterators */ + if(file_iter_init) + H5S_select_iter_release(&file_iter); + if(mem_iter_init) + H5S_select_iter_release(&mem_iter); + if(bkg_iter_init) + H5S_select_iter_release(&bkg_iter); + + assert(dx_plist); + if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME)) + H5FL_BLK_FREE(type_conv,tconv_buf); + if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) + H5FL_BLK_FREE(type_conv,bkg_buf); + + FUNC_LEAVE_NOAPI(ret_value); +} /* end H5D_contig_write() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_chunk_read + * + * Purpose: Read from a chunked dataset. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * Thursday, April 10, 2003 + * + * Modifications: + * QAK - 2003/04/17 + * Hacked on it a lot. :-) + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, + const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, + H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t +#ifndef H5_HAVE_PARALLEL + UNUSED +#endif /*H5_HAVE_PARALLEL*/ + doing_mpio, H5FD_mpio_xfer_t +#ifndef H5_HAVE_PARALLEL + UNUSED +#endif /*H5_HAVE_PARALLEL*/ + xfer_mode, hid_t src_id, hid_t dst_id, void *buf/*out*/) +{ + fm_map fm_struct; + herr_t status; /*function return status*/ +#ifdef H5S_DEBUG + H5_timer_t timer; +#endif + size_t src_type_size; /*size of source type */ + size_t dst_type_size; /*size of destination type*/ + size_t target_size; /*desired buffer size */ + hsize_t request_nelmts; /*requested strip mine */ + hsize_t smine_start; /*strip mine start loc */ + hsize_t n, smine_nelmts; /*elements per strip */ + 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 bkg_iter; /*background iteration info*/ + hbool_t bkg_iter_init=0; /*background 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 */ + H5T_bkg_t need_bkg; /*type of background buf*/ + uint8_t *tconv_buf = NULL; /*data type conv buffer */ + uint8_t *bkg_buf = NULL; /*background buffer */ + H5D_storage_t store; /*union of EFL and chunk pointer in file space */ + hsize_t h; /* Local index variable */ +#ifdef H5_HAVE_PARALLEL + hbool_t xfer_mode_changed; /* Whether the transfer mode was changed */ +#endif /*H5_HAVE_PARALLEL*/ + herr_t ret_value = SUCCEED; /*return value */ + + FUNC_ENTER_NOINIT(H5D_chunk_read); + + /* Initialize fm_map*/ + HDmemset(&fm_struct, 0, sizeof(fm_map)); + fm_struct.layout = &(dataset->layout); + + /* Map elements between file and memory for each chunk*/ + H5D_chunk_mem_file_map(dataset, mem_type, file_space, mem_space, &fm_struct); + + /* + * If there is no type conversion then read directly into the + * application's buffer. This saves at least one mem-to-mem copy. + */ + if (H5T_IS_NOOP(tpath)) { +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + /* Sanity check dataset, then read it */ + assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || + dataset->layout.type==H5D_COMPACT); + + /*loop through each chunk, read data*/ + for(h=0; h<fm_struct.nchunks; h++) { + if(H5S_get_select_npoints(fm_struct.fspace[h]) > 0) { + /*pass in chunk's coordinates in a union. LAYOUT puts datatype size as an extra dimension, + * have to take it out.*/ + store.chunk_coords = fm_struct.chunk_coords + h*dataset->layout.ndims; + + status = (sconv->read)(dataset->ent.file, &(dataset->layout), + dc_plist, &store, H5T_get_size(dataset->type), + fm_struct.fspace[h], fm_struct.mspace[h], dxpl_id, buf/*out*/); + + /* Check return value from optimized read */ + if (status<0) + HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed"); + } /* end if */ + } /* end for */ + +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[1].read_timer), &timer); + sconv->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->type); + sconv->stats[1].read_ncalls++; +#endif + + /* direct xfer accomplished successfully */ + HGOTO_DONE(SUCCEED); + } /* end if */ + + /* + * This is the general case(type conversion). + */ + +#ifdef H5_HAVE_PARALLEL + H5D_io_assist_mpio(dx_plist, doing_mpio, xfer_mode, &xfer_mode_changed); +#endif /*H5_HAVE_PARALLEL*/ + + /* Compute element sizes and other parameters */ + src_type_size = H5T_get_size(dataset->type); + dst_type_size = H5T_get_size(mem_type); + target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME); + request_nelmts = target_size / MAX(src_type_size, dst_type_size); + + /* Sanity check elements in temporary buffer */ + if (request_nelmts<=0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); + + /* + * Get a temporary buffer for type conversion unless the app has already + * supplied one through the xfer properties. Instead of allocating a + * buffer which is the exact size, we allocate the target size. The + * malloc() is usually less resource-intensive if we allocate/free the + * same size over and over. + */ + if (tpath->cdata.need_bkg) { + /* Retrieve the bkgr buffer property */ + if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) + HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); + need_bkg = MAX(tpath->cdata.need_bkg, need_bkg); + } else { + need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ + } /* end else */ + if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { + /* Allocate temporary buffer */ + if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); + } /* end if */ + if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { + /* Allocate background buffer */ + H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); + if((bkg_buf=H5FL_BLK_MALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); + } /* end if */ + + /* Loop over all the chunks, performing I/O on each */ + for(h=0; h<fm_struct.nchunks; h++) { + hsize_t chunk_nelmts; /* Number of elements selected in current chunk */ + + /* Get the number of elements selected in this chunk */ + chunk_nelmts=H5S_get_select_npoints(fm_struct.fspace[h]); + assert(chunk_nelmts<=nelmts); + if(chunk_nelmts > 0) { + /* initialize selection iterator */ + if (H5S_select_iter_init(&file_iter, fm_struct.fspace[h], src_type_size)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); + file_iter_init=1; /*file selection iteration info has been initialized */ + if (H5S_select_iter_init(&mem_iter, fm_struct.mspace[h], dst_type_size)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); + mem_iter_init=1; /*file selection iteration info has been initialized */ + if (H5S_select_iter_init(&bkg_iter, fm_struct.mspace[h], dst_type_size)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); + bkg_iter_init=1; /*file selection iteration info has been initialized */ + + /*pass in chunk's coordinates in a union*/ + store.chunk_coords = fm_struct.chunk_coords + h*dataset->layout.ndims; + + for (smine_start=0; smine_start<chunk_nelmts; smine_start+=smine_nelmts) { + /* Go figure out how many elements to read from the file */ + assert(H5S_select_iter_nelmts(&file_iter)==(chunk_nelmts-smine_start)); + smine_nelmts = MIN(request_nelmts, (chunk_nelmts-smine_start)); + + /* + * Gather the data from disk into the data type conversion + * buffer. Also gather data from application to background buffer + * if necessary. + */ +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + /* Sanity check that space is allocated, then read data from it */ + assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || + dataset->layout.type==H5D_COMPACT); + n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), + dc_plist, &store, src_type_size, fm_struct.fspace[h], + &file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/); + +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[1].gath_timer), &timer); + sconv->stats[1].gath_nbytes += n * src_type_size; + sconv->stats[1].gath_ncalls++; +#endif + if (n!=smine_nelmts) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); + + if (need_bkg) { +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + n = H5S_select_mgath(buf, dst_type_size, fm_struct.mspace[h], &bkg_iter, + smine_nelmts, dxpl_id, bkg_buf/*out*/); +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[1].bkg_timer), &timer); + sconv->stats[1].bkg_nbytes += n * dst_type_size; + sconv->stats[1].bkg_ncalls++; +#endif + if (n!=smine_nelmts) + HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed"); + } /* end if */ + + /* + * Perform data type conversion. + */ + if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, + tconv_buf, bkg_buf, dxpl_id)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); + + /* + * Scatter the data into memory. + */ +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + status = H5S_select_mscat(tconv_buf, dst_type_size, fm_struct.mspace[h], + &mem_iter, smine_nelmts, dxpl_id, buf/*out*/); +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[1].scat_timer), &timer); + sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size; + sconv->stats[1].scat_ncalls++; +#endif + if (status<0) + HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "scatter failed"); + } /* end for */ + + /* Release selection iterators */ + if(file_iter_init) { + H5S_select_iter_release(&file_iter); + file_iter_init=0; + } /* end if */ + if(mem_iter_init) { + H5S_select_iter_release(&mem_iter); + mem_iter_init=0; + } /* end if */ + if(bkg_iter_init) { + H5S_select_iter_release(&bkg_iter); + bkg_iter_init=0; + } /* end if */ + } /* end if */ + + /*close file space and memory space for each chunk*/ + /*H5S_close(fm_struct.mspace[h]); + H5S_close(fm_struct.fspace[h]);*/ + } /* end for */ + +done: +#ifdef H5_HAVE_PARALLEL + /* restore xfer_mode due to the kludge */ + if (doing_mpio && xfer_mode_changed) { +#ifdef H5D_DEBUG + if (H5DEBUG(D)) + fprintf (H5DEBUG(D), "H5D: dx->xfer_mode was COLLECTIVE, restored to INDEPENDENT\n"); +#endif + xfer_mode = H5FD_MPIO_COLLECTIVE; + if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); + } /* end if */ +#endif /*H5_HAVE_PARALLEL*/ + + assert(dx_plist); + if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME)) + H5FL_BLK_FREE(type_conv,tconv_buf); + if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) + H5FL_BLK_FREE(type_conv,bkg_buf); + + /* Release selection iterators, if necessary */ + if(file_iter_init) + H5S_select_iter_release(&file_iter); + if(mem_iter_init) + H5S_select_iter_release(&mem_iter); + if(bkg_iter_init) + H5S_select_iter_release(&bkg_iter); + + /* Close file space and memory space for each chunk*/ + for(h=0; h<fm_struct.nchunks; h++) { + if(fm_struct.mspace[h]) + H5S_close(fm_struct.mspace[h]); + if(fm_struct.fspace[h]) + H5S_close(fm_struct.fspace[h]); + } + if(fm_struct.fspace) + H5MM_free(fm_struct.fspace); + if(fm_struct.mspace) + H5MM_free(fm_struct.mspace); + + FUNC_LEAVE_NOAPI(ret_value); +} /* H5D_chunk_read() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_chunk_write + * + * Purpose: Writes to a chunked dataset. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * Thursday, April 10, 2003 + * + * Modifications: + * QAK - 2003/04/17 + * Hacked on it a lot. :-) + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, + const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, + H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t +#ifndef H5_HAVE_PARALLEL + UNUSED +#endif /*H5_HAVE_PARALLEL*/ + doing_mpio, H5FD_mpio_xfer_t +#ifndef H5_HAVE_PARALLEL + UNUSED +#endif /*H5_HAVE_PARALLEL*/ + xfer_mode, hid_t src_id, hid_t dst_id, const void *buf) +{ + fm_map fm_struct; + herr_t status; /*function return status*/ +#ifdef H5S_DEBUG + H5_timer_t timer; +#endif + size_t src_type_size; /*size of source type */ + size_t dst_type_size; /*size of destination type*/ + size_t target_size; /*desired buffer size */ + hsize_t request_nelmts; /*requested strip mine */ + hsize_t smine_start; /*strip mine start loc */ + hsize_t n, smine_nelmts; /*elements per strip */ + 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 bkg_iter; /*background iteration info*/ + hbool_t bkg_iter_init=0; /*background 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 */ + H5T_bkg_t need_bkg; /*type of background buf*/ + uint8_t *tconv_buf = NULL; /*data type conv buffer */ + uint8_t *bkg_buf = NULL; /*background buffer */ + H5D_storage_t store; /*union of EFL and chunk pointer in file space */ + hsize_t h; /* Local index variable */ +#ifdef H5_HAVE_PARALLEL + hbool_t xfer_mode_changed; /* Whether the transfer mode was changed */ +#endif /*H5_HAVE_PARALLEL*/ + herr_t ret_value = SUCCEED; /*return value */ + + FUNC_ENTER_NOINIT(H5D_chunk_write); + + /* Initialize fm_map*/ + HDmemset(&fm_struct, 0, sizeof(fm_map)); + fm_struct.layout = &(dataset->layout); + + /* Map elements between file and memory for each chunk*/ + H5D_chunk_mem_file_map(dataset, mem_type, file_space, mem_space, &fm_struct); + + /* + * If there is no type conversion then write directly from the + * application's buffer. This saves at least one mem-to-mem copy. + */ + if (H5T_IS_NOOP(tpath)) { +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + /*loop through each chunk, write data*/ + for(h=0; h<fm_struct.nchunks; h++) { + if(H5S_get_select_npoints(fm_struct.fspace[h]) > 0) { + /*pass in chunk's coordinates in a union. LAYOUT puts datatype size as an extra dimension, + * have to take it out.*/ + store.chunk_coords = fm_struct.chunk_coords + h*dataset->layout.ndims; + + status = (sconv->write)(dataset->ent.file, &(dataset->layout), + dc_plist, &store, H5T_get_size(dataset->type), + fm_struct.fspace[h], fm_struct.mspace[h], dxpl_id, buf); + + /* Check return value from optimized write */ + if (status<0) + HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed"); + } + } + +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[0].write_timer), &timer); + sconv->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type); + sconv->stats[0].write_ncalls++; +#endif + + /* direct xfer accomplished successfully */ + HGOTO_DONE(SUCCEED); + } /* end if */ + + /* + * This is the general case(type conversion). + */ + +#ifdef H5_HAVE_PARALLEL + H5D_io_assist_mpio(dx_plist, doing_mpio, xfer_mode, &xfer_mode_changed); +#endif /*H5_HAVE_PARALLEL*/ + + /* Compute element sizes and other parameters */ + src_type_size = H5T_get_size(mem_type); + dst_type_size = H5T_get_size(dataset->type); + target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME); + request_nelmts = target_size / MAX (src_type_size, dst_type_size); + + /* Sanity check elements in temporary buffer */ + if (request_nelmts<=0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); + + /* + * Get a temporary buffer for type conversion unless the app has already + * supplied one through the xfer properties. Instead of allocating a + * buffer which is the exact size, we allocate the target size. The + * malloc() is usually less resource-intensive if we allocate/free the + * same size over and over. + */ + if (tpath->cdata.need_bkg) { + /* Retrieve the bkgr buffer property */ + if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) + HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); + need_bkg = MAX (tpath->cdata.need_bkg, need_bkg); + } else if(H5T_detect_class(dataset->type, H5T_VLEN)) { + /* Old data is retrieved into background buffer for VL datatype. The + * data is used later for freeing heap objects. */ + need_bkg = H5T_BKG_YES; + } else { + need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ + } /* end else */ + if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { + /* Allocate temporary buffer */ + if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); + } /* end if */ + if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { + /* Allocate background buffer */ + H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); + if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL) + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); + } /* end if */ + + /* Loop over all the chunks, performing I/O on each */ + for(h=0; h<fm_struct.nchunks; h++) { + hsize_t chunk_nelmts; /* Number of elements selected in current chunk */ + + /* Get the number of elements selected in this chunk */ + chunk_nelmts=H5S_get_select_npoints(fm_struct.fspace[h]); + assert(chunk_nelmts<=nelmts); + if(chunk_nelmts > 0) { + + /* initialize selection iterator */ + if (H5S_select_iter_init(&file_iter, fm_struct.fspace[h], dst_type_size)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); + file_iter_init=1; /*file selection iteration info has been initialized */ + if (H5S_select_iter_init(&mem_iter, fm_struct.mspace[h], src_type_size)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); + mem_iter_init=1; /*file selection iteration info has been initialized */ + if (H5S_select_iter_init(&bkg_iter, fm_struct.fspace[h], dst_type_size)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); + bkg_iter_init=1; /*file selection iteration info has been initialized */ + + /*pass in chunk's coordinates in a union*/ + store.chunk_coords = fm_struct.chunk_coords + h*dataset->layout.ndims; + + for (smine_start=0; smine_start<chunk_nelmts; smine_start+=smine_nelmts) { + /* Go figure out how many elements to read from the file */ + assert(H5S_select_iter_nelmts(&file_iter)==(chunk_nelmts-smine_start)); + smine_nelmts = MIN(request_nelmts, (chunk_nelmts-smine_start)); + + /* + * Gather the data from disk into the data type conversion + * buffer. Also gather data from application to background buffer + * if necessary. + */ +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + n = H5S_select_mgath(buf, src_type_size, fm_struct.mspace[h], &mem_iter, + smine_nelmts, dxpl_id, tconv_buf/*out*/); + +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[1].gath_timer), &timer); + sconv->stats[1].gath_nbytes += n * src_type_size; + sconv->stats[1].gath_ncalls++; +#endif + if (n!=smine_nelmts) + HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); + + if (need_bkg) { +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), + dc_plist, &store, dst_type_size, fm_struct.fspace[h], + &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); + +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[0].bkg_timer), &timer); + sconv->stats[0].bkg_nbytes += n * dst_type_size; + sconv->stats[0].bkg_ncalls++; +#endif + if (n!=smine_nelmts) + HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed"); + } /* end if */ + + /* + * Perform data type conversion. + */ + if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, + tconv_buf, bkg_buf, dxpl_id)<0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); + + /* + * Scatter the data out to the file. + */ +#ifdef H5S_DEBUG + H5_timer_begin(&timer); +#endif + status = H5S_select_fscat(dataset->ent.file, &(dataset->layout), + dc_plist, &store, dst_type_size, fm_struct.fspace[h], + &file_iter, smine_nelmts, dxpl_id, tconv_buf); + +#ifdef H5S_DEBUG + H5_timer_end(&(sconv->stats[0].scat_timer), &timer); + sconv->stats[0].scat_nbytes += n * dst_type_size; + sconv->stats[0].scat_ncalls++; +#endif + if (status<0) + HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed"); + } /* end for */ + + /* Release selection iterators */ + if(file_iter_init) { + H5S_select_iter_release(&file_iter); + file_iter_init=0; + } /* end if */ + if(mem_iter_init) { + H5S_select_iter_release(&mem_iter); + mem_iter_init=0; + } /* end if */ + if(bkg_iter_init) { + H5S_select_iter_release(&bkg_iter); + bkg_iter_init=0; + } /* end if */ + } /* end if */ + + /*close file space and memory space for each chunk*/ + /*H5S_close(fm_struct.mspace[h]); + H5S_close(fm_struct.fspace[h]);*/ + } /* end for */ + +done: +#ifdef H5_HAVE_PARALLEL + /* restore xfer_mode due to the kludge */ + if (doing_mpio && xfer_mode_changed) { +#ifdef H5D_DEBUG + if (H5DEBUG(D)) + fprintf (H5DEBUG(D), "H5D: dx->xfer_mode was COLLECTIVE, restored to INDEPENDENT\n"); +#endif + xfer_mode = H5FD_MPIO_COLLECTIVE; + if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); + } /* end if */ +#endif /*H5_HAVE_PARALLEL*/ + + assert(dx_plist); + if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME)) + H5FL_BLK_FREE(type_conv,tconv_buf); + if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) + H5FL_BLK_FREE(type_conv,bkg_buf); + + /* Release selection iterators, if necessary */ + if(file_iter_init) + H5S_select_iter_release(&file_iter); + if(mem_iter_init) + H5S_select_iter_release(&mem_iter); + if(bkg_iter_init) + H5S_select_iter_release(&bkg_iter); + + /* Close file space and memory space for each chunk*/ + for(h=0; h<fm_struct.nchunks; h++) { + if(fm_struct.mspace[h]) + H5S_close(fm_struct.mspace[h]); + if(fm_struct.fspace[h]) + H5S_close(fm_struct.fspace[h]); + } + if(fm_struct.fspace) + H5MM_free(fm_struct.fspace); + if(fm_struct.mspace) + H5MM_free(fm_struct.mspace); + + FUNC_LEAVE_NOAPI(ret_value); +} /* H5D_chunk_write() */ + +#ifdef H5_HAVE_PARALLEL + +/*------------------------------------------------------------------------- + * Function: H5D_io_assist_mpio + * + * Purpose: Common logic for determining if the MPI transfer mode should + * be changed. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * Thursday, April 10, 2003 + * + * Modifications: + * QAK - 2003/04/17 + * Hacked on it a lot. :-) + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_io_assist_mpio(H5P_genplist_t *dx_plist, hbool_t doing_mpio, H5FD_mpio_xfer_t xfer_mode, + hbool_t *xfer_mode_changed) +{ + herr_t ret_value = SUCCEED; /*return value */ + + FUNC_ENTER_NOINIT(H5D_io_assist_mpio); + + /* The following may not handle a collective call correctly + * since it does not ensure all processes can handle the write + * request according to the MPI collective specification. + * Do the collective request via independent mode. + */ + if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE) { + /* Kludge: change the xfer_mode to independent, handle the request, + * then xfer_mode before return. + * Better way is to get a temporary data_xfer property with + * INDEPENDENT xfer_mode and pass it downwards. + */ + xfer_mode = H5FD_MPIO_INDEPENDENT; + if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); + *xfer_mode_changed=TRUE; /* restore it before return */ +#ifdef H5D_DEBUG + if (H5DEBUG(D)) + fprintf(H5DEBUG(D), "H5D: Cannot handle this COLLECTIVE write request. Do it via INDEPENDENT calls\n"); +#endif + } /* end if */ + +done: + FUNC_LEAVE_NOAPI(ret_value); +} +#endif /*H5_HAVE_PARALLEL*/ + + +/*------------------------------------------------------------------------- + * Function: H5D_chunk_coords_assist + * + * Purpose: Compute the coords for a particular chunk (in CHUNK_PTR), + * based on the size of the dataset's dataspace (given in + * NDIMS and CHUNKS), putting the resulting chunk's coordinate + * offsets in the COORDS array. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * Thursday, April 10, 2003 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, hsize_t chunks[], hsize_t chunk_ptr) +{ + hsize_t tmp; /* Size of "down elements" in each dimension */ + size_t i, j; /* Local index variables */ + + FUNC_ENTER_NOINIT(H5D_chunk_coords_assist); + + for(i=0; i<ndims; i++) { + tmp=1; + for(j=i+1; j<ndims; j++) + tmp *= chunks[j]; + coords[i] = (hssize_t)(chunk_ptr / tmp); + chunk_ptr = chunk_ptr % tmp; + } + coords[ndims] = 0; + + FUNC_LEAVE_NOAPI(SUCCEED); +} + + +/*------------------------------------------------------------------------- + * Function: H5D_chunk_mem_file_map + * + * Purpose: Creates the mapping between elements selected in each chunk + * and the elements in the memory selection. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * Thursday, April 10, 2003 + * + * Modifications: + * QAK - 2003/04/17 + * Hacked on it a lot. :-) + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_chunk_mem_file_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_space, + const H5S_t *mem_space, fm_map *fm) +{ + H5S_t *tmp_fspace=NULL, /* Temporary file dataspace */ + *tmp_mspace=NULL; /* Temporary memory dataspace */ + hid_t f_tid=(-1); /* Temporary copy of file datatype for iteration */ + size_t elmt_size; /* Memory datatype size */ + hbool_t iter_init=0; /* Selection iteration info has been initialized */ + unsigned f_ndims; /* The number of dimensions of the file's dataspace */ + int sm_ndims; /* The number of dimensions of the memory buffer's dataspace (signed) */ + unsigned m_ndims; /* The number of dimensions of the memory buffer's dataspace */ + hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* Dimensionality of file dataspace */ + char bogus; /* "bogus" buffer to pass to selection iterator */ + unsigned u; /* Local index variable */ + hsize_t j; /* Local index variable */ + herr_t ret_value = SUCCEED; /*return value */ + + FUNC_ENTER_NOINIT(H5D_chunk_mem_file_map); + + /* Create a file space of a chunk's size, instead of whole file space*/ + if(NULL==(tmp_fspace=H5S_create_simple((dataset->layout.ndims-1),dataset->layout.dim,NULL))) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace"); + + /*make a copy of mem_space*/ + if((tmp_mspace = H5S_copy(mem_space))==NULL) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space"); + + /*de-select the file space and mem space copies*/ + if(H5S_select_none(tmp_fspace)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select file space"); + if(H5S_select_none(tmp_mspace)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select memory space"); + + /* Get dim number and dimensionality for each dataspace */ + f_ndims=dataset->layout.ndims-1; + if((sm_ndims = H5S_get_simple_extent_ndims(tmp_mspace))<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number"); + fm->m_ndims=m_ndims=sm_ndims; + + if(H5S_get_simple_extent_dims(file_space, f_dims, NULL)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality"); + + /* Decide the number of chunks in each dimension*/ + fm->nchunks = 1; + for(u=0; u<f_ndims; u++) { + fm->chunks[u] = ((f_dims[u]+dataset->layout.dim[u])-1) / dataset->layout.dim[u]; + fm->nchunks *= fm->chunks[u]; + } + + /* Compute the "down" size of 'chunks' information */ + if(H5V_array_down(f_ndims,fm->chunks,fm->down_chunks)<0) + HGOTO_ERROR (H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes"); + + /* Allocate arrays to hold each chunk's dataspace & selection, for both the + * file and memory */ + H5_CHECK_OVERFLOW((sizeof(H5S_t*)*fm->nchunks),hsize_t,size_t); + fm->fspace = (H5S_t**)H5MM_malloc((size_t)(sizeof(H5S_t*)*fm->nchunks)); + fm->mspace = (H5S_t**)H5MM_malloc((size_t)(sizeof(H5S_t*)*fm->nchunks)); + fm->elmt_count = 0; + + /* Allocate array to hold coordinates of each chunk in file's dataspace */ + H5_CHECK_OVERFLOW((sizeof(hsize_t)*fm->nchunks*(f_ndims+1)),hsize_t,size_t); + fm->chunk_coords = (hssize_t*)H5MM_malloc((size_t)(sizeof(hsize_t)*fm->nchunks*(f_ndims+1))); + + /* Make per-chunk copies of memory and chunk dataspaces + * (with each one's selection set to "none" + */ + for(j=0; j<fm->nchunks; j++) { + if((fm->mspace[j] = H5S_copy(tmp_mspace))==NULL) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space"); + if((fm->fspace[j] = H5S_copy(tmp_fspace))==NULL) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space"); + + /* Initialize chunk_coords for each chunk. each stride is the number of + * file space dimensions, with fast-growing dimension at the last + */ + H5D_chunk_coords_assist(fm->chunk_coords+j*(f_ndims+1), f_ndims, fm->chunks, j); + } + + /* Create temporary datatypes for selection iteration */ + if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0) + HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype"); + + /* Create selection iterator for memory selection */ + if((elmt_size=H5T_get_size(mem_type))==0) + HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid"); + if (H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); + iter_init=1; /* Selection iteration info has been initialized */ + + /* Build the file & memory selection for each chunk */ + if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_cb, fm)<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to iterate file space"); + + /* Clean hyperslab span "scratch" information */ + for(j=0; j<fm->nchunks; j++) { + if(H5S_hyper_reset_scratch(fm->fspace[j])<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info"); + if(H5S_hyper_reset_scratch(fm->mspace[j])<0) + HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info"); + } /* end for */ + +done: + if(iter_init) { + if (H5S_select_iter_release(&(fm->mem_iter))<0) + HDONE_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); + } + if(tmp_fspace) + H5S_close(tmp_fspace); + if(tmp_mspace) + H5S_close(tmp_mspace); + if(f_tid!=(-1)) + H5Tclose(f_tid); + + FUNC_LEAVE_NOAPI(ret_value); +} /* end H5D_chunk_mem_file_map() */ + + +/*------------------------------------------------------------------------- + * Function: H5D_chunk_cb + * + * Purpose: Callback routine for file selection iterator. Used when + * creating selections in memory and each chunk for each chunk. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * Thursday, April 10, 2003 + * + * Modifications: + * QAK - 2003/04/17 + * Hacked on it a lot. :-) + * + *------------------------------------------------------------------------- + */ +static herr_t +H5D_chunk_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_t *coords, void *_fm) +{ + fm_map *fm = (fm_map*)_fm; /* File<->memory chunk mapping info */ + hssize_t coords_in_chunk[H5O_LAYOUT_NDIMS]; /* Coordinates of element in chunk */ + hssize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */ + hsize_t chunk_idx; /* Chunk index */ + hsize_t u; /* Local index variables */ + herr_t ret_value = SUCCEED; /* Return value */ + + FUNC_ENTER_NOINIT(H5D_chunk_cb); +#ifdef QAK +{ + unsigned u; + HDfprintf(stderr,"%s: coords={",FUNC); + for(u=0; u<ndims; u++) + HDfprintf(stderr,"%Hd%s",coords[u],(u<(ndims-1)?", ":"}\n")); +} +#endif /* QAK */ + + /* Calculate the index of this chunk */ + if(H5V_chunk_index((unsigned)ndims,coords,fm->layout->dim,fm->chunks,fm->down_chunks,&chunk_idx)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index"); +#ifdef QAK +HDfprintf(stderr,"%s: chunk_idx=%Hu\n",FUNC,chunk_idx); +#endif /* QAK */ + + /*convert coords from relative to whole file space to relative to its chunk space, + *pass into H5S_select_hyperslab.*/ + for(u=0; u<ndims; u++) + coords_in_chunk[u] = coords[u] % fm->layout->dim[u]; + +#ifdef QAK +{ + unsigned u; + HDfprintf(stderr,"%s: coords_in_chunk={",FUNC); + for(u=0; u<ndims; u++) + HDfprintf(stderr,"%Hd%s",coords_in_chunk[u],(u<(ndims-1)?", ":"}\n")); +} +#endif /* QAK */ + /* Add point to file selection for chunk */ + if(H5S_hyper_add_span_element(fm->fspace[chunk_idx], (unsigned)ndims, coords_in_chunk)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element"); + + /* Get coordinates of selection iterator for memory */ + if(H5S_select_iter_coords(&fm->mem_iter,coords_in_mem)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get iterator coordinates"); + +#ifdef QAK +{ + unsigned u; + HDfprintf(stderr,"%s: coords_in_mem={",FUNC); + for(u=0; u<fm->m_ndims; u++) + HDfprintf(stderr,"%Hd%s",coords_in_mem[u],(u<(fm->m_ndims-1)?", ":"}\n")); +} +#endif /* QAK */ + /* Add point to memory selection for chunk */ + if(H5S_hyper_add_span_element(fm->mspace[chunk_idx], fm->m_ndims, coords_in_mem)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element"); + + /* Move memory selection iterator to next element in selection */ + if(H5S_select_iter_next(&fm->mem_iter,1)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTNEXT, FAIL, "unable to move to next iterator location"); + +done: + FUNC_LEAVE_NOAPI(ret_value); +} /* end H5D_chunk_cb() */ |