/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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 "H5SLprivate.h" /* Skip lists */ #include "H5Vprivate.h" /* Vector and array functions */ /*#define H5D_DEBUG*/ #ifdef H5_HAVE_PARALLEL /* Remove this if H5R_DATASET_REGION is no longer used in this file */ # include "H5Rpublic.h" #endif /*H5_HAVE_PARALLEL*/ /* Local macros */ #define H5D_DEFAULT_SKIPLIST_HEIGHT 8 /* Local typedefs */ /* Information for mapping between file space and memory space */ /* Structure holding information about a chunk's selection for mapping */ typedef struct H5D_chunk_info_t { hsize_t index; /* "Index" of chunk in dataset */ size_t chunk_points; /* Number of elements selected in chunk */ H5S_t *fspace; /* Dataspace describing chunk & selection in it */ hsize_t coords[H5O_LAYOUT_NDIMS]; /* Coordinates of chunk in file dataset's dataspace */ H5S_t *mspace; /* Dataspace describing selection in memory corresponding to this chunk */ unsigned mspace_shared; /* Indicate that the memory space for a chunk is shared and shouldn't be freed */ } H5D_chunk_info_t; /* Main structure holding the mapping between file chunks and memory */ typedef struct fm_map { H5SL_t *fsel; /* Skip list containing file dataspaces for all chunks */ hsize_t last_index; /* Index of last chunk operated on */ H5D_chunk_info_t *last_chunk_info; /* Pointer to last chunk's info */ const H5S_t *file_space; /* Pointer to the file dataspace */ const H5S_t *mem_space; /* Pointer to the memory dataspace */ unsigned mem_space_copy; /* Flag to indicate that the memory dataspace must be copied */ hsize_t f_dims[H5O_LAYOUT_NDIMS]; /* File dataspace dimensions */ H5S_t *mchunk_tmpl; /* Dataspace template for new memory chunks */ unsigned f_ndims; /* Number of dimensions for file dataspace */ 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 chunk_dim[H5O_LAYOUT_NDIMS]; /* Size of chunk in each dimension */ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */ H5O_layout_t *layout; /* Dataset layout information*/ H5S_sel_type msel_type; /* Selection type in memory */ } fm_map; /* Local functions */ 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); static herr_t H5D_read(H5D_t *dataset, hid_t mem_type_id, 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, hid_t mem_type_id, const H5S_t *mem_space, const H5S_t *file_space, hid_t dset_xfer_plist, const void *buf); static herr_t H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, hid_t src_id, hid_t dst_id, void *buf/*out*/); static herr_t H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, hid_t src_id, hid_t dst_id, const void *buf); static herr_t H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, hid_t src_id, hid_t dst_id, void *buf/*out*/); static herr_t H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, hid_t src_id, hid_t dst_id, const void *buf); #ifdef H5_HAVE_PARALLEL static herr_t H5D_io_assist_mpio(hid_t dxpl_id, H5D_dxpl_cache_t *dxpl_cache, hbool_t *xfer_mode_changed); static herr_t H5D_io_restore_mpio(hid_t dxpl_id); static htri_t H5D_get_collective_io_consensus(const H5F_t *file, const htri_t local_opinion, const unsigned flags); #endif /* H5_HAVE_PARALLEL */ /* I/O info operations */ static herr_t H5D_ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, const H5S_t *mem_space, const H5S_t *file_space, unsigned flags, hbool_t *use_par_opt_io, H5D_io_info_t *io_info); /* Chunk operations */ static herr_t H5D_create_chunk_map(const H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_space, const H5S_t *mem_space, fm_map *fm); static herr_t H5D_destroy_chunk_map(const fm_map *fm); static herr_t H5D_free_chunk_info(void *item, void *key, void *opdata); static herr_t H5D_create_chunk_file_map_hyper(const fm_map *fm); static herr_t H5D_create_chunk_mem_map_hyper(const fm_map *fm); static herr_t H5D_chunk_file_cb(void *elem, hid_t type_id, unsigned ndims, const hsize_t *coords, void *fm); static herr_t H5D_chunk_mem_cb(void *elem, hid_t type_id, unsigned ndims, const hsize_t *coords, void *fm); /* 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); /* Declare a free list to manage the H5D_chunk_info_t struct */ H5FL_DEFINE_STATIC(H5D_chunk_info_t); /*-------------------------------------------------------------------------- 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_NOAPI_NOINIT(H5D_fill) /* Check args */ assert(fill_type); assert(buf); assert(buf_type); assert(space); /* Make sure the dataspace has an extent set (or is NULL) */ if( !(H5S_has_extent(space)) ) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dataspace extent has not been set") /* 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") /* Check for actual fill value to replicate */ if(fill==NULL) /* If there's no fill value, just use zeros */ HDmemset(tconv_buf,0,dst_type_size); else { /* Copy the user's data into the buffer for conversion */ HDmemcpy(tconv_buf,fill,src_type_size); /* 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") /* Convert memory buffer into disk buffer */ if (!H5T_path_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, 1, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed") } /* end if */ } /* end if */ /* 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() */ /*-------------------------------------------------------------------------- NAME H5D_get_dxpl_cache_real PURPOSE Get all the values for the DXPL cache. USAGE herr_t H5D_get_dxpl_cache_real(dxpl_id, cache) hid_t dxpl_id; IN: DXPL to query H5D_dxpl_cache_t *cache;IN/OUT: DXPL cache to fill with values RETURNS Non-negative on success/Negative on failure. DESCRIPTION Query all the values from a DXPL that are needed by internal routines within the library. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ herr_t H5D_get_dxpl_cache_real(hid_t dxpl_id, H5D_dxpl_cache_t *cache) { H5P_genplist_t *dx_plist; /* Data transfer property list */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_get_dxpl_cache_real,FAIL) /* Check args */ assert(cache); /* Get the dataset transfer property list */ if (NULL == (dx_plist = H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list") /* Get maximum temporary buffer size */ if(H5P_get(dx_plist, H5D_XFER_MAX_TEMP_BUF_NAME, &cache->max_temp_buf)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve maximum temporary buffer size") /* Get temporary buffer pointer */ if(H5P_get(dx_plist, H5D_XFER_TCONV_BUF_NAME, &cache->tconv_buf)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve temporary buffer pointer") /* Get background buffer pointer */ if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_NAME, &cache->bkgr_buf)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer pointer") /* Get background buffer type */ if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &cache->bkgr_buf_type)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type") /* Get B-tree split ratios */ if(H5P_get(dx_plist, H5D_XFER_BTREE_SPLIT_RATIO_NAME, &cache->btree_split_ratio)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve B-tree split ratios") /* Get I/O vector size */ if(H5P_get(dx_plist, H5D_XFER_HYPER_VECTOR_SIZE_NAME, &cache->vec_size)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve I/O vector size") #ifdef H5_HAVE_PARALLEL /* Collect Parallel I/O information for possible later use */ if(H5P_get(dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &cache->xfer_mode)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve parallel transfer method") #endif /*H5_HAVE_PARALLEL*/ /* Get error detection properties */ if(H5P_get(dx_plist, H5D_XFER_EDC_NAME, &cache->err_detect)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve error detection info") /* Get filter callback function */ if(H5P_get(dx_plist, H5D_XFER_FILTER_CB_NAME, &cache->filter_cb)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve filter callback function") /* Get the data transform property */ if(H5P_get(dx_plist, H5D_XFER_XFORM_NAME, &cache->data_xform_prop)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve data transform info") done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_get_dxpl_cache_real() */ /*-------------------------------------------------------------------------- NAME H5D_get_dxpl_cache PURPOSE Get all the values for the DXPL cache. USAGE herr_t H5D_get_dxpl_cache(dxpl_id, cache) hid_t dxpl_id; IN: DXPL to query H5D_dxpl_cache_t *cache;IN/OUT: DXPL cache to fill with values RETURNS Non-negative on success/Negative on failure. DESCRIPTION Query all the values from a DXPL that are needed by internal routines within the library. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS The CACHE pointer should point at already allocated memory to place non-default property list info. If a default property list is used, the CACHE pointer will be changed to point at the default information. EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ herr_t H5D_get_dxpl_cache(hid_t dxpl_id, H5D_dxpl_cache_t **cache) { herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5D_get_dxpl_cache,FAIL) /* Check args */ assert(cache); /* Check for the default DXPL */ if(dxpl_id==H5P_DATASET_XFER_DEFAULT) *cache=&H5D_def_dxpl_cache; else if(H5D_get_dxpl_cache_real(dxpl_id,*cache)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTGET, FAIL, "Can't retrieve DXPL values") done: FUNC_LEAVE_NOAPI(ret_value) } /* H5D_get_dxpl_cache() */ /*------------------------------------------------------------------------- * 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 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 (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 && H5S_GET_SELECT_NPOINTS(file_space)!=0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer") /* read raw data */ if (H5D_read(dset, mem_type_id, 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 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 (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, "memory 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, "file 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 && H5S_GET_SELECT_NPOINTS(file_space)!=0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer") /* write raw data */ if (H5D_write(dset, mem_type_id, 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__opt_possible() routine * *------------------------------------------------------------------------- */ static herr_t H5D_read(H5D_t *dataset, hid_t mem_type_id, 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 */ const H5T_t *mem_type = NULL; /* Memory datatype */ H5D_io_info_t io_info; /* Dataset I/O info */ hbool_t use_par_opt_io=FALSE; /* Whether the 'optimized' I/O routines with be parallel */ #ifdef H5_HAVE_PARALLEL hbool_t xfer_mode_changed=FALSE; /* Whether the transfer mode was changed */ #ifdef H5_HAVE_INSTRUMENTED_LIBRARY int prop_value,new_value; htri_t check_prop; #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ #endif /*H5_HAVE_PARALLEL*/ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */ unsigned sconv_flags=0; /* Flags for the space conversion */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_read) /* check args */ assert(dataset && dataset->ent.file); /* Get memory datatype */ if (NULL == (mem_type = H5I_object_verify(mem_type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type") if (!file_space) file_space = dataset->shared->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") H5_ASSIGN_OVERFLOW(nelmts,snelmts,hssize_t,hsize_t); /* Fill the DXPL cache values for later use */ if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") #ifdef H5_HAVE_PARALLEL /* Collective access is not permissible without a MPI based VFD */ if (dxpl_cache->xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPI(dataset->ent.file)) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based drivers only") /* Set the "parallel I/O possible" flag, for H5S_find(), if we are doing collective I/O */ /* (Don't set the parallel I/O possible flag for the MPI-posix driver, since it doesn't do real collective I/O) */ if (H5S_mpi_opt_types_g && dxpl_cache->xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPIPOSIX(dataset->ent.file)) sconv_flags |= H5S_CONV_PAR_IO_POSSIBLE; #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") /* Make sure that both selections have their extents set */ if( !(H5S_has_extent(file_space)) ) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file dataspace does not have extent set") if( !(H5S_has_extent(mem_space)) ) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "memory dataspace does not have extent set") /* Retrieve dataset properties */ /* */ /* 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->shared->efl.nused==0 && ((dataset->shared->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr)) || (dataset->shared->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))) { H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ /* Retrieve dataset's fill-value properties */ if(H5P_is_fill_value_defined(&dataset->shared->dcpl_cache.fill, &fill_status)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") /* Should be impossible, but check anyway... */ if(fill_status == H5D_FILL_VALUE_UNDEFINED && (dataset->shared->dcpl_cache.fill_time == H5D_FILL_TIME_ALLOC || dataset->shared->dcpl_cache.fill_time == H5D_FILL_TIME_IFSET)) 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(dataset->shared->dcpl_cache.fill_time == H5D_FILL_TIME_NEVER) HGOTO_DONE(SUCCEED) /* Go fill the user's selection with the dataset's fill value */ if(H5D_fill(dataset->shared->dcpl_cache.fill.buf,dataset->shared->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->shared->type, mem_type, NULL, NULL, dxpl_id))) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types") /* Set the storage flags for the space conversion check */ switch(dataset->shared->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 */ /* Set up I/O operation */ if(H5D_ioinfo_init(dataset,dxpl_cache,dxpl_id,mem_space,file_space,sconv_flags,&use_par_opt_io,&io_info)<0) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to set up I/O operation") #ifdef H5_HAVE_PARALLEL #ifdef H5_HAVE_INSTRUMENTED_LIBRARY /**** Test for collective chunk IO notice the following code should be removed after a more general collective chunk IO algorithm is applied. */ if(dataset->shared->layout.type == H5D_CHUNKED) { /*only check for chunking storage */ check_prop = H5Pexist(dxpl_id,H5D_XFER_COLL_CHUNK_NAME); if(check_prop < 0) HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to check property list"); if(check_prop > 0) { if(H5Pget(dxpl_id,H5D_XFER_COLL_CHUNK_NAME,&prop_value)<0) HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to get property value"); if(!use_par_opt_io) { new_value = 0; if(H5Pset(dxpl_id,H5D_XFER_COLL_CHUNK_NAME,&new_value)<0) HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to set property value"); } } } /* end Test for collective chunk IO */ #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ /* Don't reset the transfer mode if we can't or won't use it */ if(!use_par_opt_io || !H5T_path_noop(tpath)) H5D_io_assist_mpio(dxpl_id, dxpl_cache, &xfer_mode_changed); #endif /*H5_HAVE_PARALLEL*/ /* Determine correct I/O routine to invoke */ if(dataset->shared->layout.type!=H5D_CHUNKED) { if(H5D_contig_read(&io_info, nelmts, mem_type, mem_space, file_space, tpath, dataset->shared->type_id, mem_type_id, buf)<0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data") } /* end if */ else { if(H5D_chunk_read(&io_info, nelmts, mem_type, mem_space, file_space, tpath, dataset->shared->type_id, mem_type_id, buf)<0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data") } /* end else */ done: #ifdef H5_HAVE_PARALLEL /* Restore xfer_mode due to the kludge */ if (xfer_mode_changed) H5D_io_restore_mpio(dxpl_id); #endif /*H5_HAVE_PARALLEL*/ 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__opt_possible() routine * * Nat Furrer and James Laird, 2004/6/7 * Added check for filter encode capability *------------------------------------------------------------------------- */ static herr_t H5D_write(H5D_t *dataset, hid_t mem_type_id, 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 */ const H5T_t *mem_type = NULL; /* Memory datatype */ H5D_io_info_t io_info; /* Dataset I/O info */ hbool_t use_par_opt_io=FALSE; /* Whether the 'optimized' I/O routines with be parallel */ #ifdef H5_HAVE_PARALLEL hbool_t xfer_mode_changed=FALSE; /* Whether the transfer mode was changed */ #ifdef H5_HAVE_INSTRUMENTED_LIBRARY int prop_value,new_value; htri_t check_prop; #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ #endif /*H5_HAVE_PARALLEL*/ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */ unsigned sconv_flags=0; /* Flags for the space conversion */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_write) /* check args */ assert(dataset && dataset->ent.file); /* Get the memory datatype */ if (NULL == (mem_type = H5I_object_verify(mem_type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type") /* All filters in the DCPL must have encoding enabled. */ if(! dataset->shared->checked_filters) { if(H5Z_can_apply(dataset->shared->dcpl_id, dataset->shared->type_id) <0) HGOTO_ERROR(H5E_PLINE, H5E_CANAPPLY, FAIL, "can't apply filters") dataset->shared->checked_filters = TRUE; } /* If MPI based VFD 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_MPI(dataset->ent.file) && H5T_detect_class(mem_type, H5T_VLEN)>0) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL datatypes yet") /* If MPI based VFD 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 */ /* We should really use H5T_detect_class() here, but it will be difficult * to detect the type of the reference if it is nested... -QAK */ if (IS_H5FD_MPI(dataset->ent.file) && H5T_get_class(mem_type, TRUE)==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") /* Fill the DXPL cache values for later use */ if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache") if (!file_space) file_space = dataset->shared->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") H5_ASSIGN_OVERFLOW(nelmts,snelmts,hssize_t,hsize_t); #ifdef H5_HAVE_PARALLEL /* Collective access is not permissible without a MPI based VFD */ if (dxpl_cache->xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPI(dataset->ent.file)) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based driver only") /* Set the "parallel I/O possible" flag, for H5S_find(), if we are doing collective I/O */ /* (Don't set the parallel I/O possible flag for the MPI-posix driver, since it doesn't do real collective I/O) */ if (H5S_mpi_opt_types_g && dxpl_cache->xfer_mode==H5FD_MPIO_COLLECTIVE && !IS_H5FD_MPIPOSIX(dataset->ent.file)) sconv_flags |= H5S_CONV_PAR_IO_POSSIBLE; #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") /* Make sure that both selections have their extents set */ if( !(H5S_has_extent(file_space)) ) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file dataspace does not have extent set") if( !(H5S_has_extent(mem_space)) ) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "memory dataspace does not have extent set") /* Retrieve dataset properties */ /* */ /* Allocate data space and initialize it if it hasn't been. */ if(nelmts > 0 && dataset->shared->efl.nused==0 && ((dataset->shared->layout.type==H5D_CONTIGUOUS && !H5F_addr_defined(dataset->shared->layout.u.contig.addr)) || (dataset->shared->layout.type==H5D_CHUNKED && !H5F_addr_defined(dataset->shared->layout.u.chunk.addr)))) { hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */ hbool_t full_overwrite; /* Whether we are over-writing all the elements */ /* Get the number of elements in file dataset's dataspace */ if((file_nelmts=H5S_GET_EXTENT_NPOINTS(file_space))<0) HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset") /* Always allow fill values to be written if the dataset has a VL datatype */ if(H5T_detect_class(dataset->shared->type, H5T_VLEN)) full_overwrite=FALSE; else full_overwrite=(hsize_t)file_nelmts==nelmts ? TRUE : FALSE; /* Allocate storage */ if(H5D_alloc_storage(dataset->ent.file,dxpl_id,dataset,H5D_ALLOC_WRITE, TRUE, full_overwrite)<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->shared->type, NULL, NULL, dxpl_id))) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types") /* Set the storage flags for the space conversion check */ switch(dataset->shared->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 */ /* Set up I/O operation */ if(H5D_ioinfo_init(dataset,dxpl_cache,dxpl_id,mem_space,file_space,sconv_flags,&use_par_opt_io,&io_info)<0) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to set up I/O operation") #ifdef H5_HAVE_PARALLEL #ifdef H5_HAVE_INSTRUMENTED_LIBRARY /**** Test for collective chunk IO notice the following code should be removed after a more general collective chunk IO algorithm is applied. */ if(dataset->shared->layout.type == H5D_CHUNKED) { /*only check for chunking storage */ check_prop = H5Pexist(dxpl_id,H5D_XFER_COLL_CHUNK_NAME); if(check_prop < 0) HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to check property list"); if(check_prop > 0) { if(H5Pget(dxpl_id,H5D_XFER_COLL_CHUNK_NAME,&prop_value)<0) HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to get property value"); if(!use_par_opt_io) { new_value = 0; if(H5Pset(dxpl_id,H5D_XFER_COLL_CHUNK_NAME,&new_value)<0) HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to set property value"); } } } #endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ /* Don't reset the transfer mode if we can't or won't use it */ if(!use_par_opt_io || !H5T_path_noop(tpath)) H5D_io_assist_mpio(dxpl_id, dxpl_cache, &xfer_mode_changed); #endif /*H5_HAVE_PARALLEL*/ /* Determine correct I/O routine to invoke */ if(dataset->shared->layout.type!=H5D_CHUNKED) { if(H5D_contig_write(&io_info, nelmts, mem_type, mem_space, file_space, tpath, mem_type_id, dataset->shared->type_id, buf)<0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") } /* end if */ else { if(H5D_chunk_write(&io_info, nelmts, mem_type, mem_space, file_space, tpath, mem_type_id, dataset->shared->type_id, buf)<0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") } /* end else */ #ifdef OLD_WAY /* * This was taken out because it can be called in a parallel program with * independent access, causing the metadata cache to get corrupted. Its been * disabled for all types of access (serial as well as parallel) to make the * modification time consistent for all programs. -QAK */ /* * 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") #endif /* OLD_WAY */ done: #ifdef H5_HAVE_PARALLEL /* Restore xfer_mode due to the kludge */ if (xfer_mode_changed) H5D_io_restore_mpio(dxpl_id); #endif /*H5_HAVE_PARALLEL*/ 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. :-) * Leon Arber: 4/20/04 * Added support for data transforms. * *------------------------------------------------------------------------- */ static herr_t H5D_contig_read(H5D_io_info_t *io_info, hsize_t nelmts, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, hid_t src_id, hid_t dst_id, void *buf/*out*/) { H5D_t *dataset=io_info->dset; /* Local pointer to dataset info */ const H5D_dxpl_cache_t *dxpl_cache=io_info->dxpl_cache; /* Local pointer to dataset transfer info */ 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 max_type_size; /* Size of largest source/destination type */ size_t target_size; /*desired buffer size */ size_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 */ size_t n, smine_nelmts; /*elements per strip */ H5D_storage_t store; /*union of storage info for dataset */ herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_contig_read) /* Initialize storage info for this dataset */ if (dataset->shared->efl.nused>0) HDmemcpy(&store.efl,&(dataset->shared->efl),sizeof(H5O_efl_t)); else { store.contig.dset_addr=dataset->shared->layout.u.contig.addr; store.contig.dset_size=dataset->shared->layout.u.contig.size; } /* end if */ /* Set dataset storage for I/O info */ io_info->store=&store; /* * If there is no type conversion then read directly into the * application's buffer. This saves at least one mem-to-mem copy. */ if ( H5Z_xform_noop(dxpl_cache->data_xform_prop) && H5T_path_noop(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif /* Sanity check dataset, then read it */ assert(((dataset->shared->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr)) || (dataset->shared->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) || dataset->shared->efl.nused>0 || 0 == nelmts || dataset->shared->layout.type==H5D_COMPACT); H5_CHECK_OVERFLOW(nelmts,hsize_t,size_t); status = (io_info->ops.read)(io_info, (size_t)nelmts, H5T_get_size(dataset->shared->type), file_space, mem_space, buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[1].read_timer), &timer); io_info->stats->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->shared->type); io_info->stats->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, usually). */ if(nelmts==0) HGOTO_DONE(SUCCEED) /* Compute element sizes and other parameters */ src_type_size = H5T_get_size(dataset->shared->type); dst_type_size = H5T_get_size(mem_type); max_type_size = MAX(src_type_size, dst_type_size); target_size = dxpl_cache->max_temp_buf; /* XXX: This could cause a problem if the user sets their buffer size * to the same size as the default, and then the dataset elements are * too large for the buffer... - QAK */ if(target_size==H5D_XFER_MAX_TEMP_BUF_DEF) { /* If the buffer is too small to hold even one element, make it bigger */ if(target_size(nelmts*max_type_size)) target_size=(size_t)(nelmts*max_type_size); } /* end if */ request_nelmts = target_size / max_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, 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 */ /* * 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 (H5T_path_bkg(tpath)) { H5T_bkg_t path_bkg; /* Type conversion's background info */ /* Retrieve the bkgr buffer property */ need_bkg=dxpl_cache->bkgr_buf_type; path_bkg = H5T_path_bkg(tpath); need_bkg = MAX(path_bkg, need_bkg); } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ if (NULL==(tconv_buf=dxpl_cache->tconv_buf)) { /* 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=dxpl_cache->bkgr_buf)) { /* Allocate background buffer */ /* (Need calloc()-like call since memory needs to be initialized) */ if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(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_startshared->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr)) || (dataset->shared->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) || dataset->shared->efl.nused>0 || dataset->shared->layout.type==H5D_COMPACT); n = H5D_select_fgath(io_info, file_space, &file_iter, smine_nelmts, tconv_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[1].gath_timer), &timer); io_info->stats->stats[1].gath_nbytes += n * src_type_size; io_info->stats->stats[1].gath_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed") if (H5T_BKG_YES==need_bkg) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif n = H5D_select_mgath(buf, mem_space, &bkg_iter, smine_nelmts, dxpl_cache, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[1].bkg_timer), &timer); io_info->stats->stats[1].bkg_nbytes += n * dst_type_size; io_info->stats->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, io_info->dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed") /* Do the data transform after the conversion (since we're using type mem_type) */ if(!H5Z_xform_noop(dxpl_cache->data_xform_prop)) if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, mem_type) < 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform") /* * Scatter the data into memory. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = H5D_select_mscat(tconv_buf, mem_space, &mem_iter, smine_nelmts, dxpl_cache, buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[1].scat_timer), &timer); io_info->stats->stats[1].scat_nbytes += smine_nelmts * dst_type_size; io_info->stats->stats[1].scat_ncalls++; #endif if (status<0) HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "scatter failed") } /* end for */ done: /* Release selection iterators */ if(file_iter_init) { if(H5S_SELECT_ITER_RELEASE(&file_iter)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") } /* end if */ if(mem_iter_init) { if(H5S_SELECT_ITER_RELEASE(&mem_iter)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") } /* end if */ if(bkg_iter_init) { if(H5S_SELECT_ITER_RELEASE(&bkg_iter)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") } /* end if */ if (tconv_buf && NULL==dxpl_cache->tconv_buf) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==dxpl_cache->bkgr_buf) 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. :-) * Leon Arber: 4/20/04 * Added support for data transforms. * *------------------------------------------------------------------------- */ static herr_t H5D_contig_write(H5D_io_info_t *io_info, hsize_t nelmts, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, hid_t src_id, hid_t dst_id, const void *buf) { H5D_t *dataset=io_info->dset; /* Local pointer to dataset info */ const H5D_dxpl_cache_t *dxpl_cache=io_info->dxpl_cache; /* Local pointer to dataset transfer info */ 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 max_type_size; /* Size of largest source/destination type */ size_t target_size; /*desired buffer size */ size_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 */ size_t n, smine_nelmts; /*elements per strip */ H5D_storage_t store; /*union of storage info for dataset */ herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_contig_write) /* Initialize storage info for this dataset */ if (dataset->shared->efl.nused>0) HDmemcpy(&store.efl,&(dataset->shared->efl),sizeof(H5O_efl_t)); else { store.contig.dset_addr=dataset->shared->layout.u.contig.addr; store.contig.dset_size=dataset->shared->layout.u.contig.size; } /* end if */ /* Set dataset storage for I/O info */ io_info->store=&store; /* * If there is no type conversion then write directly from the * application's buffer. This saves at least one mem-to-mem copy. */ if ( H5Z_xform_noop(dxpl_cache->data_xform_prop) && H5T_path_noop(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif H5_CHECK_OVERFLOW(nelmts,hsize_t,size_t); status = (io_info->ops.write)(io_info, (size_t)nelmts, H5T_get_size(dataset->shared->type), file_space, mem_space, buf); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[0].write_timer), &timer); io_info->stats->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type); io_info->stats->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. */ if(nelmts==0) HGOTO_DONE(SUCCEED) /* Compute element sizes and other parameters */ src_type_size = H5T_get_size(mem_type); dst_type_size = H5T_get_size(dataset->shared->type); max_type_size = MAX(src_type_size, dst_type_size); target_size = dxpl_cache->max_temp_buf; /* XXX: This could cause a problem if the user sets their buffer size * to the same size as the default, and then the dataset elements are * too large for the buffer... - QAK */ if(target_size==H5D_XFER_MAX_TEMP_BUF_DEF) { /* If the buffer is too small to hold even one element, make it bigger */ if(target_size(nelmts*max_type_size)) target_size=(size_t)(nelmts*max_type_size); } /* end if */ request_nelmts = target_size / max_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(H5T_detect_class(dataset->shared->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 if (H5T_path_bkg(tpath)) { H5T_bkg_t path_bkg; /* Type conversion's background info */ /* Retrieve the bkgr buffer property */ need_bkg=dxpl_cache->bkgr_buf_type; path_bkg = H5T_path_bkg(tpath); need_bkg = MAX (path_bkg, need_bkg); } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ if (NULL==(tconv_buf=dxpl_cache->tconv_buf)) { /* 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=dxpl_cache->bkgr_buf)) { /* Allocate background buffer */ /* (Don't need calloc()-like call since file data is already initialized) */ if((bkg_buf=H5FL_BLK_MALLOC(type_conv,(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_startstats->stats[0].gath_timer), &timer); io_info->stats->stats[0].gath_nbytes += n * src_type_size; io_info->stats->stats[0].gath_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed") if (H5T_BKG_YES==need_bkg) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif n = H5D_select_fgath(io_info, file_space, &bkg_iter, smine_nelmts, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[0].bkg_timer), &timer); io_info->stats->stats[0].bkg_nbytes += n * dst_type_size; io_info->stats->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, io_info->dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed") /* Do the data transform after the type conversion (since we're using dataset->shared->type). */ if(!H5Z_xform_noop(dxpl_cache->data_xform_prop)) if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, dataset->shared->type) < 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform") /* * Scatter the data out to the file. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = H5D_select_fscat(io_info, file_space, &file_iter, smine_nelmts, tconv_buf); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[0].scat_timer), &timer); io_info->stats->stats[0].scat_nbytes += smine_nelmts * dst_type_size; io_info->stats->stats[0].scat_ncalls++; #endif if (status<0) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed") } /* end for */ done: /* Release selection iterators */ if(file_iter_init) { if(H5S_SELECT_ITER_RELEASE(&file_iter)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") } /* end if */ if(mem_iter_init) { if(H5S_SELECT_ITER_RELEASE(&mem_iter)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") } /* end if */ if(bkg_iter_init) { if(H5S_SELECT_ITER_RELEASE(&bkg_iter)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") } /* end if */ if (tconv_buf && NULL==dxpl_cache->tconv_buf) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==dxpl_cache->bkgr_buf) 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. :-) * Leon Arber: 4/20/04 * Added support for data transforms. * *------------------------------------------------------------------------- */ static herr_t H5D_chunk_read(H5D_io_info_t *io_info, hsize_t nelmts, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, hid_t src_id, hid_t dst_id, void *buf/*out*/) { H5D_t *dataset=io_info->dset; /* Local pointer to dataset info */ const H5D_dxpl_cache_t *dxpl_cache=io_info->dxpl_cache; /* Local pointer to dataset transfer info */ fm_map fm; /* File<->memory mapping */ H5SL_node_t *chunk_node; /* Current node in chunk skip list */ 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 max_type_size; /* Size of largest source/destination type */ size_t target_size; /*desired buffer size */ size_t request_nelmts; /*requested strip mine */ hsize_t smine_start; /*strip mine start loc */ size_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 */ herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_read) /* Map elements between file and memory for each chunk*/ if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping") /* Set dataset storage for I/O info */ io_info->store=&store; /* * If there is no type conversion then read directly into the * application's buffer. This saves at least one mem-to-mem copy. */ if ( H5Z_xform_noop(dxpl_cache->data_xform_prop) && H5T_path_noop(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif /* Sanity check dataset, then read it */ assert(((dataset->shared->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr)) || (dataset->shared->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) || dataset->shared->efl.nused>0 || 0 == nelmts || dataset->shared->layout.type==H5D_COMPACT); /* Get first node in chunk skip list */ chunk_node=H5SL_first(fm.fsel); /* Iterate through chunks to be operated on */ while(chunk_node) { H5D_chunk_info_t *chunk_info; /* chunk information */ /* Get the actual chunk information from the skip list node */ chunk_info=H5SL_item(chunk_node); /* Pass in chunk's coordinates in a union. */ store.chunk.offset = chunk_info->coords; store.chunk.index = chunk_info->index; /* Perform the actual read operation */ status = (io_info->ops.read)(io_info, chunk_info->chunk_points, H5T_get_size(dataset->shared->type), chunk_info->fspace, chunk_info->mspace, buf); /* Check return value from optimized read */ if (status<0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed") /* Get the next chunk node in the skip list */ chunk_node=H5SL_next(chunk_node); } /* end while */ #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[1].read_timer), &timer); io_info->stats->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->shared->type); io_info->stats->stats[1].read_ncalls++; #endif /* direct xfer accomplished successfully */ HGOTO_DONE(SUCCEED) } /* end if */ /* * This is the general case (type conversion, usually). */ if(nelmts==0) HGOTO_DONE(SUCCEED) /* Compute element sizes and other parameters */ src_type_size = H5T_get_size(dataset->shared->type); dst_type_size = H5T_get_size(mem_type); max_type_size = MAX(src_type_size, dst_type_size); target_size = dxpl_cache->max_temp_buf; /* XXX: This could cause a problem if the user sets their buffer size * to the same size as the default, and then the dataset elements are * too large for the buffer... - QAK */ if(target_size==H5D_XFER_MAX_TEMP_BUF_DEF) { /* If the buffer is too small to hold even one element, make it bigger */ if(target_size(nelmts*max_type_size)) target_size=(size_t)(nelmts*max_type_size); } /* end if */ request_nelmts = target_size / max_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 (H5T_path_bkg(tpath)) { H5T_bkg_t path_bkg; /* Type conversion's background info */ /* Retrieve the bkgr buffer property */ need_bkg=dxpl_cache->bkgr_buf_type; path_bkg = H5T_path_bkg(tpath); need_bkg = MAX(path_bkg, need_bkg); } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ if (NULL==(tconv_buf=dxpl_cache->tconv_buf)) { /* 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=dxpl_cache->bkgr_buf)) { /* Allocate background buffer */ /* (Need calloc()-like call since memory needs to be initialized) */ if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(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 */ /* Get first node in chunk skip list */ chunk_node=H5SL_first(fm.fsel); /* Iterate through chunks to be operated on */ while(chunk_node) { H5D_chunk_info_t *chunk_info; /* chunk information */ /* Get the actual chunk information from the skip list nodes */ chunk_info=H5SL_item(chunk_node); /* initialize selection iterator */ if (H5S_select_iter_init(&file_iter, chunk_info->fspace, 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, chunk_info->mspace, 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, chunk_info->mspace, 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.offset = chunk_info->coords; store.chunk.index = chunk_info->index; for (smine_start=0; smine_startchunk_points; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ assert(H5S_SELECT_ITER_NELMTS(&file_iter)==(chunk_info->chunk_points-smine_start)); smine_nelmts = (size_t)MIN(request_nelmts, (chunk_info->chunk_points-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->shared->layout.type==H5D_CONTIGUOUS && H5F_addr_defined(dataset->shared->layout.u.contig.addr)) || (dataset->shared->layout.type==H5D_CHUNKED && H5F_addr_defined(dataset->shared->layout.u.chunk.addr))) || dataset->shared->efl.nused>0 || dataset->shared->layout.type==H5D_COMPACT); n = H5D_select_fgath(io_info, chunk_info->fspace, &file_iter, smine_nelmts, tconv_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[1].gath_timer), &timer); io_info->stats->stats[1].gath_nbytes += n * src_type_size; io_info->stats->stats[1].gath_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed") if (H5T_BKG_YES==need_bkg) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif n = H5D_select_mgath(buf, chunk_info->mspace, &bkg_iter, smine_nelmts, dxpl_cache, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[1].bkg_timer), &timer); io_info->stats->stats[1].bkg_nbytes += n * dst_type_size; io_info->stats->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, io_info->dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed") /* Do the data transform after the conversion (since we're using type mem_type) */ if(!H5Z_xform_noop(dxpl_cache->data_xform_prop)) if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, mem_type) < 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform") /* * Scatter the data into memory. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = H5D_select_mscat(tconv_buf, chunk_info->mspace, &mem_iter, smine_nelmts, dxpl_cache, buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[1].scat_timer), &timer); io_info->stats->stats[1].scat_nbytes += smine_nelmts * dst_type_size; io_info->stats->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) { if(H5S_SELECT_ITER_RELEASE(&file_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") file_iter_init=0; } /* end if */ if(mem_iter_init) { if(H5S_SELECT_ITER_RELEASE(&mem_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") mem_iter_init=0; } /* end if */ if(bkg_iter_init) { if(H5S_SELECT_ITER_RELEASE(&bkg_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") bkg_iter_init=0; } /* end if */ /* Get the next chunk node in the skip list */ chunk_node=H5SL_next(chunk_node); } /* end while */ done: /* Release selection iterators, if necessary */ if(file_iter_init) { if(H5S_SELECT_ITER_RELEASE(&file_iter)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") } /* end if */ if(mem_iter_init) { if(H5S_SELECT_ITER_RELEASE(&mem_iter)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") } /* end if */ if(bkg_iter_init) { if(H5S_SELECT_ITER_RELEASE(&bkg_iter)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") } /* end if */ if (tconv_buf && NULL==dxpl_cache->tconv_buf) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==dxpl_cache->bkgr_buf) H5FL_BLK_FREE(type_conv,bkg_buf); /* Release chunk mapping information */ if(H5D_destroy_chunk_map(&fm) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release chunk mapping") 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. :-) * Leon Arber: 4/20/04 * Added support for data transforms. * *------------------------------------------------------------------------- */ static herr_t H5D_chunk_write(H5D_io_info_t *io_info, hsize_t nelmts, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, hid_t src_id, hid_t dst_id, const void *buf) { H5D_t *dataset=io_info->dset; /* Local pointer to dataset info */ const H5D_dxpl_cache_t *dxpl_cache=io_info->dxpl_cache; /* Local pointer to dataset transfer info */ fm_map fm; /* File<->memory mapping */ H5SL_node_t *chunk_node; /* Current node in chunk skip list */ 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 max_type_size; /* Size of largest source/destination type */ size_t target_size; /*desired buffer size */ size_t request_nelmts; /*requested strip mine */ hsize_t smine_start; /*strip mine start loc */ size_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 */ herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_write) /* Map elements between file and memory for each chunk*/ if(H5D_create_chunk_map(dataset, mem_type, file_space, mem_space, &fm)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't build chunk mapping") /* Set dataset storage for I/O info */ io_info->store=&store; /* * If there is no type conversion then write directly from the * application's buffer. This saves at least one mem-to-mem copy. */ if ( H5Z_xform_noop(dxpl_cache->data_xform_prop) && H5T_path_noop(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif /* Get first node in chunk skip list */ chunk_node=H5SL_first(fm.fsel); /* Iterate through chunks to be operated on */ while(chunk_node) { H5D_chunk_info_t *chunk_info; /* chunk information */ /* Get the actual chunk information from the skip list node */ chunk_info=H5SL_item(chunk_node); /* Pass in chunk's coordinates in a union. */ store.chunk.offset = chunk_info->coords; store.chunk.index = chunk_info->index; /* Perform the actual write operation */ status = (io_info->ops.write)(io_info, chunk_info->chunk_points, H5T_get_size(dataset->shared->type), chunk_info->fspace, chunk_info->mspace, buf); /* Check return value from optimized write */ if (status<0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed") /* Get the next chunk node in the skip list */ chunk_node=H5SL_next(chunk_node); } /* end while */ #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[0].write_timer), &timer); io_info->stats->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type); io_info->stats->stats[0].write_ncalls++; #endif /* direct xfer accomplished successfully */ HGOTO_DONE(SUCCEED) } /* end if */ /* * This is the general case (type conversion, usually). */ if(nelmts==0) HGOTO_DONE(SUCCEED) /* Compute element sizes and other parameters */ src_type_size = H5T_get_size(mem_type); dst_type_size = H5T_get_size(dataset->shared->type); max_type_size = MAX(src_type_size, dst_type_size); target_size = dxpl_cache->max_temp_buf; /* XXX: This could cause a problem if the user sets their buffer size * to the same size as the default, and then the dataset elements are * too large for the buffer... - QAK */ if(target_size==H5D_XFER_MAX_TEMP_BUF_DEF) { /* If the buffer is too small to hold even one element, make it bigger */ if(target_size(nelmts*max_type_size)) target_size=(size_t)(nelmts*max_type_size); } /* end if */ request_nelmts = target_size / max_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(H5T_detect_class(dataset->shared->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 if (H5T_path_bkg(tpath)) { H5T_bkg_t path_bkg; /* Type conversion's background info */ /* Retrieve the bkgr buffer property */ need_bkg=dxpl_cache->bkgr_buf_type; path_bkg = H5T_path_bkg(tpath); need_bkg = MAX (path_bkg, need_bkg); } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ if (NULL==(tconv_buf=dxpl_cache->tconv_buf)) { /* 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=dxpl_cache->bkgr_buf)) { /* Allocate background buffer */ /* (Don't need calloc()-like call since file data is already initialized) */ if((bkg_buf=H5FL_BLK_MALLOC(type_conv,(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 */ /* Get first node in chunk skip list */ chunk_node=H5SL_first(fm.fsel); /* Iterate through chunks to be operated on */ while(chunk_node) { H5D_chunk_info_t *chunk_info; /* chunk information */ /* Get the actual chunk information from the skip list node */ chunk_info=H5SL_item(chunk_node); /* initialize selection iterator */ if (H5S_select_iter_init(&file_iter, chunk_info->fspace, 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, chunk_info->mspace, 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, chunk_info->fspace, 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.offset = chunk_info->coords; store.chunk.index = chunk_info->index; for (smine_start=0; smine_startchunk_points; smine_start+=smine_nelmts) { /* Go figure out how many elements to read from the file */ assert(H5S_SELECT_ITER_NELMTS(&file_iter)==(chunk_info->chunk_points-smine_start)); smine_nelmts = (size_t)MIN(request_nelmts, (chunk_info->chunk_points-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 = H5D_select_mgath(buf, chunk_info->mspace, &mem_iter, smine_nelmts, dxpl_cache, tconv_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[1].gath_timer), &timer); io_info->stats->stats[1].gath_nbytes += n * src_type_size; io_info->stats->stats[1].gath_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed") if (H5T_BKG_YES==need_bkg) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif n = H5D_select_fgath(io_info, chunk_info->fspace, &bkg_iter, smine_nelmts, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[0].bkg_timer), &timer); io_info->stats->stats[0].bkg_nbytes += n * dst_type_size; io_info->stats->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, io_info->dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed") /* Do the data transform after the type conversion (since we're using dataset->shared->type) */ if(!H5Z_xform_noop(dxpl_cache->data_xform_prop)) if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, dataset->shared->type) < 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform") /* * Scatter the data out to the file. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = H5D_select_fscat(io_info, chunk_info->fspace, &file_iter, smine_nelmts, tconv_buf); #ifdef H5S_DEBUG H5_timer_end(&(io_info->stats->stats[0].scat_timer), &timer); io_info->stats->stats[0].scat_nbytes += n * dst_type_size; io_info->stats->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) { if(H5S_SELECT_ITER_RELEASE(&file_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") file_iter_init=0; } /* end if */ if(mem_iter_init) { if(H5S_SELECT_ITER_RELEASE(&mem_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") mem_iter_init=0; } /* end if */ if(bkg_iter_init) { if(H5S_SELECT_ITER_RELEASE(&bkg_iter)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") bkg_iter_init=0; } /* end if */ /* Get the next chunk node in the skip list */ chunk_node=H5SL_next(chunk_node); } /* end while */ done: /* Release selection iterators, if necessary */ if(file_iter_init) { if(H5S_SELECT_ITER_RELEASE(&file_iter)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") } /* end if */ if(mem_iter_init) { if(H5S_SELECT_ITER_RELEASE(&mem_iter)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") } /* end if */ if(bkg_iter_init) { if(H5S_SELECT_ITER_RELEASE(&bkg_iter)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator") } /* end if */ if (tconv_buf && NULL==dxpl_cache->tconv_buf) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==dxpl_cache->bkgr_buf) H5FL_BLK_FREE(type_conv,bkg_buf); /* Release chunk mapping information */ if(H5D_destroy_chunk_map(&fm) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "can't release chunk mapping") 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(hid_t dxpl_id, H5D_dxpl_cache_t *dxpl_cache, hbool_t *xfer_mode_changed) { herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOAPI_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 (dxpl_cache->xfer_mode==H5FD_MPIO_COLLECTIVE) { H5P_genplist_t *dx_plist; /* Data transer 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") /* 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. */ dxpl_cache->xfer_mode = H5FD_MPIO_INDEPENDENT; if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &dxpl_cache->xfer_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode") *xfer_mode_changed=TRUE; /* restore it before return */ } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_io_assist_mpio() */ /*------------------------------------------------------------------------- * Function: H5D_io_restore_mpio * * Purpose: Common logic for restoring MPI transfer mode * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Friday, February 6, 2004 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5D_io_restore_mpio(hid_t dxpl_id) { H5P_genplist_t *dx_plist; /* Data transer property list */ H5FD_mpio_xfer_t xfer_mode; /*xfer_mode for this request */ herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_io_restore_mpio) /* 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") /* 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_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") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_io_restore_mpio() */ #endif /*H5_HAVE_PARALLEL*/ /*------------------------------------------------------------------------- * Function: H5D_create_chunk_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_create_chunk_map(const H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_space, const H5S_t *mem_space, fm_map *fm) { H5S_t *tmp_mspace=NULL; /* Temporary memory dataspace */ H5S_t *equiv_mspace=NULL; /* Equivalent memory dataspace */ hbool_t equiv_mspace_init=0;/* Equivalent memory dataspace was created */ hid_t f_tid=(-1); /* Temporary copy of file datatype for iteration */ 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) */ H5SL_node_t *curr_node; /* Current node in skip list */ H5S_sel_type fsel_type; /* Selection type on disk */ char bogus; /* "bogus" buffer to pass to selection iterator */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_map) /* Get layout for dataset */ fm->layout = &(dataset->shared->layout); /* Check if the memory space is scalar & make equivalent memory space */ if((sm_ndims = H5S_GET_EXTENT_NDIMS(mem_space))<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number") if(sm_ndims==0) { hsize_t dims[H5O_LAYOUT_NDIMS]; /* Temporary dimension information */ /* Set up "equivalent" n-dimensional dataspace with size '1' in each dimension */ for(u=0; ushared->layout.u.chunk.ndims-1; u++) dims[u]=1; if((equiv_mspace = H5S_create_simple(dataset->shared->layout.u.chunk.ndims-1,dims,NULL))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create equivalent dataspace for scalar space") /* Indicate that this space needs to be released */ equiv_mspace_init=1; /* Set the number of dimensions for the memory dataspace */ fm->m_ndims=dataset->shared->layout.u.chunk.ndims-1; } /* end else */ else { equiv_mspace=(H5S_t *)mem_space; /* Casting away 'const' OK... */ /* Set the number of dimensions for the memory dataspace */ H5_ASSIGN_OVERFLOW(fm->m_ndims,sm_ndims,int,unsigned); } /* end else */ /* Get dim number and dimensionality for each dataspace */ fm->f_ndims=f_ndims=dataset->shared->layout.u.chunk.ndims-1; if(H5S_get_simple_extent_dims(file_space, fm->f_dims, NULL)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality") /* Decide the number of chunks in each dimension*/ for(u=0; uchunk_dim[u]=fm->layout->u.chunk.dim[u]; /* Round up to the next integer # of chunks, to accomodate partial chunks */ fm->chunks[u] = ((fm->f_dims[u]+dataset->shared->layout.u.chunk.dim[u])-1) / dataset->shared->layout.u.chunk.dim[u]; } /* end for */ /* 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") /* Initialize skip list for chunk selections */ if((fm->fsel=H5SL_create(H5SL_TYPE_HSIZE,0.5,H5D_DEFAULT_SKIPLIST_HEIGHT))==NULL) HGOTO_ERROR(H5E_DATASET,H5E_CANTCREATE,FAIL,"can't create skip list for chunk selections") /* Initialize "last chunk" information */ fm->last_index=(hsize_t)-1; fm->last_chunk_info=NULL; /* Point at the dataspaces */ fm->file_space=file_space; fm->mem_space=equiv_mspace; fm->mem_space_copy=equiv_mspace_init; /* Make certain to copy memory dataspace if necessary */ /* Get type of selection on disk & in memory */ if((fsel_type=H5S_GET_SELECT_TYPE(file_space))msel_type=H5S_GET_SELECT_TYPE(equiv_mspace))shared->type, H5T_COPY_ALL)))<0) HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype") /* Spaces aren't the same shape, iterate over the memory selection directly */ if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_file_cb, fm)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") /* Reset "last chunk" info */ fm->last_index=(hsize_t)-1; fm->last_chunk_info=NULL; } /* end if */ else { /* Build the file selection for each chunk */ if(H5D_create_chunk_file_map_hyper(fm)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create file chunk selections") /* Clean file chunks' hyperslab span "scratch" information */ curr_node=H5SL_first(fm->fsel); while(curr_node) { H5D_chunk_info_t *chunk_info; /* Pointer chunk information */ /* Get pointer to chunk's information */ chunk_info=H5SL_item(curr_node); assert(chunk_info); /* Clean hyperslab span's "scratch" information */ if(H5S_hyper_reset_scratch(chunk_info->fspace)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info") /* Get the next chunk node in the skip list */ curr_node=H5SL_next(curr_node); } /* end while */ } /* end else */ /* Build the memory selection for each chunk */ if(fsel_type!=H5S_SEL_POINTS && H5S_select_shape_same(file_space,equiv_mspace)==TRUE) { /* Reset chunk template information */ fm->mchunk_tmpl=NULL; /* If the selections are the same shape, use the file chunk information * to generate the memory chunk information quickly. */ if(H5D_create_chunk_mem_map_hyper(fm)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections") } /* end if */ else { size_t elmt_size; /* Memory datatype size */ /* Make a copy of equivalent memory space */ if((tmp_mspace = H5S_copy(equiv_mspace,TRUE))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space") /* De-select the mem space copy */ if(H5S_select_none(tmp_mspace)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select memory space") /* Save chunk template information */ fm->mchunk_tmpl=tmp_mspace; /* Create temporary datatypes for selection iteration */ if(f_tid<0) { if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->shared->type, H5T_COPY_ALL)))<0) HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype") } /* end if */ /* 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), equiv_mspace, elmt_size)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator") iter_init=1; /* Selection iteration info has been initialized */ /* Spaces aren't the same shape, iterate over the memory selection directly */ if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_mem_cb, fm)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create memory chunk selections") /* Clean up hyperslab stuff, if necessary */ if(fm->msel_type!=H5S_SEL_POINTS) { /* Clean memory chunks' hyperslab span "scratch" information */ curr_node=H5SL_first(fm->fsel); while(curr_node) { H5D_chunk_info_t *chunk_info; /* Pointer chunk information */ /* Get pointer to chunk's information */ chunk_info=H5SL_item(curr_node); assert(chunk_info); /* Clean hyperslab span's "scratch" information */ if(H5S_hyper_reset_scratch(chunk_info->mspace)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info") /* Get the next chunk node in the skip list */ curr_node=H5SL_next(curr_node); } /* end while */ } /* end if */ } /* end else */ done: /* Release the [potentially partially built] chunk mapping information if an error occurs */ if(ret_value<0) { if(tmp_mspace && !fm->mchunk_tmpl) { if(H5S_close(tmp_mspace)<0) HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template") } /* end if */ if (H5D_destroy_chunk_map(fm)<0) HDONE_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release chunk mapping") } /* end if */ /* Reset the global dataspace info */ fm->file_space=NULL; fm->mem_space=NULL; if(equiv_mspace_init && equiv_mspace) { if(H5S_close(equiv_mspace)<0) HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template") } /* end if */ 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(f_tid!=(-1)) { if(H5I_dec_ref(f_tid)<0) HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_create_chunk_map() */ /*-------------------------------------------------------------------------- NAME H5D_free_chunk_info PURPOSE Internal routine to destroy a chunk info node USAGE void H5D_free_chunk_info(chunk_info) void *chunk_info; IN: Pointer to chunk info to destroy RETURNS No return value DESCRIPTION Releases all the memory for a chunk info node. Called by H5SL_iterate GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ static herr_t H5D_free_chunk_info(void *item, void UNUSED *key, void UNUSED *opdata) { H5D_chunk_info_t *chunk_info=(H5D_chunk_info_t *)item; FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_free_chunk_info) assert(chunk_info); /* Close the chunk's file dataspace */ (void)H5S_close(chunk_info->fspace); /* Close the chunk's memory dataspace, if it's not shared */ if(!chunk_info->mspace_shared) (void)H5S_close(chunk_info->mspace); /* Free the actual chunk info */ H5FL_FREE(H5D_chunk_info_t,chunk_info); FUNC_LEAVE_NOAPI(0); } /* H5D_free_chunk_info() */ /*------------------------------------------------------------------------- * Function: H5D_destroy_chunk_map * * Purpose: Destroy chunk mapping information. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Saturday, May 17, 2003 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5D_destroy_chunk_map(const fm_map *fm) { herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_destroy_chunk_map) /* Free the chunk info skip list */ if(fm->fsel) { if(H5SL_count(fm->fsel)>0) if(H5SL_iterate(fm->fsel,H5D_free_chunk_info,NULL)<0) HGOTO_ERROR(H5E_PLIST,H5E_CANTNEXT,FAIL,"can't iterate over chunks") H5SL_close(fm->fsel); } /* end if */ /* Free the memory chunk dataspace template */ if(fm->mchunk_tmpl) if(H5S_close(fm->mchunk_tmpl)<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "can't release memory chunk dataspace template") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_destroy_chunk_map() */ /*------------------------------------------------------------------------- * Function: H5D_create_chunk_file_map_hyper * * Purpose: Create all chunk selections in file. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, May 29, 2003 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5D_create_chunk_file_map_hyper(const fm_map *fm) { hssize_t ssel_points; /* Number of elements in file selection */ hsize_t sel_points; /* Number of elements in file selection */ hsize_t sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ hsize_t sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ hsize_t start_coords[H5O_LAYOUT_NDIMS]; /* Starting coordinates of selection */ hsize_t coords[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */ hsize_t end[H5O_LAYOUT_NDIMS]; /* Current coordinates of chunk */ hsize_t chunk_index; /* Index of chunk */ int curr_dim; /* Current dimension to increment */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_file_map_hyper) /* Sanity check */ assert(fm->f_ndims>0); /* Get number of elements selected in file */ if((ssel_points=H5S_GET_SELECT_NPOINTS(fm->file_space))<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements") H5_ASSIGN_OVERFLOW(sel_points,ssel_points,hssize_t,hsize_t); /* Get bounding box for selection (to reduce the number of chunks to iterate over) */ if(H5S_SELECT_BOUNDS(fm->file_space, sel_start, sel_end)<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info") /* Set initial chunk location & hyperslab size */ for(u=0; uf_ndims; u++) { start_coords[u]=(sel_start[u]/fm->layout->u.chunk.dim[u])*fm->layout->u.chunk.dim[u]; coords[u]=start_coords[u]; end[u]=(coords[u]+fm->chunk_dim[u])-1; } /* end for */ /* Calculate the index of this chunk */ if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Iterate through each chunk in the dataset */ while(sel_points) { /* Check for intersection of temporary chunk and file selection */ /* (Casting away const OK - QAK) */ if(H5S_hyper_intersect_block((H5S_t *)fm->file_space,coords,end)==TRUE) { H5S_t *tmp_fchunk; /* Temporary file dataspace */ H5D_chunk_info_t *new_chunk_info; /* chunk information to insert into skip list */ hssize_t schunk_points; /* Number of elements in chunk selection */ /* Create "temporary" chunk for selection operations (copy file space) */ if((tmp_fchunk = H5S_copy(fm->file_space,TRUE))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space") /* Make certain selections are stored in span tree form (not "optimized hyperslab" or "all") */ if(H5S_hyper_convert(tmp_fchunk)<0) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to convert selection to span trees") } /* end if */ /* Normalize hyperslab selections by adjusting them by the offset */ if(H5S_hyper_normalize_offset(tmp_fchunk)<0) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to normalize dataspace by offset") } /* end if */ /* "AND" temporary chunk and current chunk */ if(H5S_select_hyperslab(tmp_fchunk,H5S_SELECT_AND,coords,NULL,fm->chunk_dim,NULL)<0) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't create chunk selection") } /* end if */ /* Resize chunk's dataspace dimensions to size of chunk */ if(H5S_set_extent_real(tmp_fchunk,fm->chunk_dim)<0) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk dimensions") } /* end if */ /* Move selection back to have correct offset in chunk */ if(H5S_hyper_adjust_u(tmp_fchunk,coords)<0) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection") } /* end if */ /* Add temporary chunk to the list of chunks */ /* Allocate the file & memory chunk information */ if (NULL==(new_chunk_info = H5FL_MALLOC (H5D_chunk_info_t))) { (void)H5S_close(tmp_fchunk); HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") } /* end if */ /* Initialize the chunk information */ /* Set the chunk index */ new_chunk_info->index=chunk_index; /* Set the file chunk dataspace */ new_chunk_info->fspace=tmp_fchunk; /* Set the memory chunk dataspace */ new_chunk_info->mspace=NULL; new_chunk_info->mspace_shared=0; /* Copy the chunk's coordinates */ for(u=0; uf_ndims; u++) new_chunk_info->coords[u]=coords[u]; new_chunk_info->coords[fm->f_ndims]=0; /* Insert the new chunk into the skip list */ if(H5SL_insert(fm->fsel,new_chunk_info,&new_chunk_info->index)<0) { H5D_free_chunk_info(new_chunk_info,NULL,NULL); HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into skip list") } /* end if */ /* Get number of elements selected in chunk */ if((schunk_points=H5S_GET_SELECT_NPOINTS(tmp_fchunk))<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection # of elements") H5_ASSIGN_OVERFLOW(new_chunk_info->chunk_points,schunk_points,hssize_t,size_t); /* Decrement # of points left in file selection */ sel_points-=(hsize_t)schunk_points; /* Leave if we are done */ if(sel_points==0) HGOTO_DONE(SUCCEED) assert(sel_points>0); } /* end if */ /* Increment chunk index */ chunk_index++; /* Set current increment dimension */ curr_dim=(int)fm->f_ndims-1; /* Increment chunk location in fastest changing dimension */ H5_CHECK_OVERFLOW(fm->chunk_dim[curr_dim],hsize_t,hssize_t); coords[curr_dim]+=fm->chunk_dim[curr_dim]; end[curr_dim]+=fm->chunk_dim[curr_dim]; /* Bring chunk location back into bounds, if necessary */ if(coords[curr_dim]>sel_end[curr_dim]) { do { /* Reset current dimension's location to 0 */ coords[curr_dim]=start_coords[curr_dim]; /*lint !e771 The start_coords will always be initialized */ end[curr_dim]=(coords[curr_dim]+(hssize_t)fm->chunk_dim[curr_dim])-1; /* Decrement current dimension */ curr_dim--; /* Increment chunk location in current dimension */ coords[curr_dim]+=fm->chunk_dim[curr_dim]; end[curr_dim]=(coords[curr_dim]+fm->chunk_dim[curr_dim])-1; } while(coords[curr_dim]>sel_end[curr_dim]); /* Re-Calculate the index of this chunk */ if(H5V_chunk_index(fm->f_ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") } /* end if */ } /* end while */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_create_chunk_file_map_hyper() */ /*------------------------------------------------------------------------- * Function: H5D_create_chunk_mem_map_hyper * * Purpose: Create all chunk selections in memory by copying the file * chunk selections and adjusting their offsets to be correct * for the memory. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, May 29, 2003 * * Assumptions: That the file and memory selections are the same shape. * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5D_create_chunk_mem_map_hyper(const fm_map *fm) { H5SL_node_t *curr_node; /* Current node in skip list */ hsize_t file_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ hsize_t file_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ hsize_t mem_sel_start[H5O_LAYOUT_NDIMS]; /* Offset of low bound of file selection */ hsize_t mem_sel_end[H5O_LAYOUT_NDIMS]; /* Offset of high bound of file selection */ hssize_t adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to all file chunks */ hssize_t chunk_adjust[H5O_LAYOUT_NDIMS]; /* Adjustment to make to a particular chunk */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_create_chunk_mem_map_hyper) /* Sanity check */ assert(fm->f_ndims>0); /* Check for all I/O going to a single chunk */ if(H5SL_count(fm->fsel)==1) { H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */ /* Get the node */ curr_node=H5SL_first(fm->fsel); /* Get pointer to chunk's information */ chunk_info=H5SL_item(curr_node); assert(chunk_info); /* Check if it's OK to share dataspace */ if(fm->mem_space_copy) { /* Copy the memory dataspace & selection to be the chunk's dataspace & selection */ if((chunk_info->mspace = H5S_copy(fm->mem_space,FALSE))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space") } /* end if */ else { /* Just point at the memory dataspace & selection */ /* (Casting away const OK -QAK) */ chunk_info->mspace=(H5S_t *)fm->mem_space; /* Indicate that the chunk's memory space is shared */ chunk_info->mspace_shared=1; } /* end else */ } /* end if */ else { /* Get bounding box for file selection */ if(H5S_SELECT_BOUNDS(fm->file_space, file_sel_start, file_sel_end)<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info") /* Get bounding box for memory selection */ if(H5S_SELECT_BOUNDS(fm->mem_space, mem_sel_start, mem_sel_end)<0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't get file selection bound info") /* Calculate the adjustment for memory selection from file selection */ assert(fm->m_ndims==fm->f_ndims); for(u=0; uf_ndims; u++) { H5_CHECK_OVERFLOW(file_sel_start[u],hsize_t,hssize_t); H5_CHECK_OVERFLOW(mem_sel_start[u],hsize_t,hssize_t); adjust[u]=(hssize_t)file_sel_start[u]-(hssize_t)mem_sel_start[u]; } /* end for */ /* Iterate over each chunk in the chunk list */ curr_node=H5SL_first(fm->fsel); while(curr_node) { H5D_chunk_info_t *chunk_info; /* Pointer to chunk information */ /* Get pointer to chunk's information */ chunk_info=H5SL_item(curr_node); assert(chunk_info); /* Copy the information */ /* Copy the memory dataspace */ if((chunk_info->mspace = H5S_copy(fm->mem_space,TRUE))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space") /* Release the current selection */ if(H5S_SELECT_RELEASE(chunk_info->mspace)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection") /* Copy the file chunk's selection */ if(H5S_select_copy(chunk_info->mspace,chunk_info->fspace,FALSE)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy selection") /* Compensate for the chunk offset */ for(u=0; uf_ndims; u++) { H5_CHECK_OVERFLOW(chunk_info->coords[u],hsize_t,hssize_t); chunk_adjust[u]=adjust[u]-(hssize_t)chunk_info->coords[u]; /*lint !e771 The adjust array will always be initialized */ } /* end for */ /* Adjust the selection */ if(H5S_hyper_adjust_s(chunk_info->mspace,chunk_adjust)<0) /*lint !e772 The chunk_adjust array will always be initialized */ HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSELECT, FAIL, "can't adjust chunk selection") /* Get the next chunk node in the skip list */ curr_node=H5SL_next(curr_node); } /* end while */ } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_create_chunk_mem_map_hyper() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_file_cb * * Purpose: Callback routine for file selection iterator. Used when * creating selections in file for each point selected. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Wednesday, July 23, 2003 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5D_chunk_file_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_fm) { fm_map *fm = (fm_map*)_fm; /* File<->memory chunk mapping info */ H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */ hsize_t coords_in_chunk[H5O_LAYOUT_NDIMS]; /* Coordinates of element in chunk */ hsize_t chunk_index; /* Chunk index */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_file_cb) /* Calculate the index of this chunk */ if(H5V_chunk_index(ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Find correct chunk in file & memory skip list */ if(chunk_index==fm->last_index) { /* If the chunk index is the same as the last chunk index we used, * get the cached info to operate on. */ chunk_info=fm->last_chunk_info; } /* end if */ else { /* If the chunk index is not the same as the last chunk index we used, * find the chunk in the skip list. */ /* Get the chunk node from the skip list */ if((chunk_info=H5SL_search(fm->fsel,&chunk_index))==NULL) { H5S_t *fspace; /* Memory chunk's dataspace */ /* Allocate the file & memory chunk information */ if (NULL==(chunk_info = H5FL_MALLOC (H5D_chunk_info_t))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate chunk info") /* Initialize the chunk information */ /* Set the chunk index */ chunk_info->index=chunk_index; /* Create a dataspace for the chunk */ if((fspace = H5S_create_simple(fm->f_ndims,fm->chunk_dim,NULL))==NULL) { H5FL_FREE(H5D_chunk_info_t,chunk_info); HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "unable to create dataspace for chunk") } /* end if */ /* De-select the chunk space */ if(H5S_select_none(fspace)<0) { (void)H5S_close(fspace); H5FL_FREE(H5D_chunk_info_t,chunk_info); HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select dataspace") } /* end if */ /* Set the file chunk dataspace */ chunk_info->fspace=fspace; /* Set the memory chunk dataspace */ chunk_info->mspace=NULL; chunk_info->mspace_shared=0; /* Set the number of selected elements in chunk to zero */ chunk_info->chunk_points=0; /* Compute the chunk's coordinates */ for(u=0; uf_ndims; u++) { H5_CHECK_OVERFLOW(fm->layout->u.chunk.dim[u],hsize_t,hssize_t); chunk_info->coords[u]=(coords[u]/(hssize_t)fm->layout->u.chunk.dim[u])*(hssize_t)fm->layout->u.chunk.dim[u]; } /* end for */ chunk_info->coords[fm->f_ndims]=0; /* Insert the new chunk into the skip list */ if(H5SL_insert(fm->fsel,chunk_info,&chunk_info->index)<0) { H5D_free_chunk_info(chunk_info,NULL,NULL); HGOTO_ERROR(H5E_DATASPACE,H5E_CANTINSERT,FAIL,"can't insert chunk into skip list") } /* end if */ } /* end if */ /* Update the "last chunk seen" information */ fm->last_index=chunk_index; fm->last_chunk_info=chunk_info; } /* end else */ /* Get the coordinates of the element in the chunk */ for(u=0; uf_ndims; u++) coords_in_chunk[u]=coords[u]%fm->layout->u.chunk.dim[u]; /* Add point to file selection for chunk */ if(H5S_select_elements(chunk_info->fspace,H5S_SELECT_APPEND,1,(const hsize_t **)coords_in_chunk)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element") /* Increment the number of elemented selected in chunk */ chunk_info->chunk_points++; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_chunk_file_cb() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_mem_cb * * Purpose: Callback routine for file selection iterator. Used when * creating selections in memory 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. :-) * *------------------------------------------------------------------------- */ /* ARGSUSED */ static herr_t H5D_chunk_mem_cb(void UNUSED *elem, hid_t UNUSED type_id, unsigned ndims, const hsize_t *coords, void *_fm) { fm_map *fm = (fm_map*)_fm; /* File<->memory chunk mapping info */ H5D_chunk_info_t *chunk_info; /* Chunk information for current chunk */ hsize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */ hsize_t chunk_index; /* Chunk index */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_mem_cb) /* Calculate the index of this chunk */ if(H5V_chunk_index(ndims,coords,fm->layout->u.chunk.dim,fm->down_chunks,&chunk_index)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index") /* Find correct chunk in file & memory skip list */ if(chunk_index==fm->last_index) { /* If the chunk index is the same as the last chunk index we used, * get the cached spaces to operate on. */ chunk_info=fm->last_chunk_info; } /* end if */ else { /* If the chunk index is not the same as the last chunk index we used, * find the chunk in the skip list. */ /* Get the chunk node from the skip list */ if((chunk_info=H5SL_search(fm->fsel,&chunk_index))==NULL) HGOTO_ERROR(H5E_DATASPACE,H5E_NOTFOUND,FAIL,"can't locate chunk in skip list") /* Check if the chunk already has a memory space */ if(chunk_info->mspace==NULL) { /* Copy the template memory chunk dataspace */ if((chunk_info->mspace = H5S_copy(fm->mchunk_tmpl,FALSE))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space") } /* end else */ /* Update the "last chunk seen" information */ fm->last_index=chunk_index; fm->last_chunk_info=chunk_info; } /* end else */ /* 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") /* Add point to memory selection for chunk */ if(fm->msel_type==H5S_SEL_POINTS) { if(H5S_select_elements(chunk_info->mspace,H5S_SELECT_APPEND,1,(const hsize_t **)coords_in_mem)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element") } /* end if */ else { if(H5S_hyper_add_span_element(chunk_info->mspace, fm->m_ndims, coords_in_mem)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element") } /* end else */ /* 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_mem_cb() */ /*------------------------------------------------------------------------- * Function: H5D_get_collective_io_consensus * * Purpose: Compare notes with all other processes involved in this I/O * and see if all are go for collective I/O. * * If all are, return TRUE. * * If any process can't manage collective I/O, then collective * I/O is impossible, and we return FALSE. * * If the flags indicate that collective I/O is impossible, * skip the interprocess communication and just return FALSE. * * In any error is detected, return FAIL. * * Return: Success: TRUE or FALSE * * Failure: FAIL * * Programmer: JRM -- 8/30/04 * * Modifications: * * None. * *------------------------------------------------------------------------- */ #ifdef H5_HAVE_PARALLEL static htri_t H5D_get_collective_io_consensus(const H5F_t *file, const htri_t local_opinion, const unsigned flags) { htri_t ret_value = FAIL; /* will update if successful */ MPI_Comm comm; int int_local_opinion; int consensus; int mpi_result; FUNC_ENTER_NOAPI_NOINIT(H5D_get_collective_io_consensus); HDassert ( ( local_opinion == TRUE ) || ( local_opinion == FALSE ) ); /* Don't do the interprocess communication unless the Parallel I/O * conversion flag is set -- there may not be other processes to * talk to. */ if ( ! ( flags & flags&H5S_CONV_PAR_IO_POSSIBLE ) ) { HGOTO_DONE(FALSE); } comm = H5F_mpi_get_comm(file); if ( comm == MPI_COMM_NULL ) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, \ "can't retrieve MPI communicator") if ( local_opinion == TRUE ) { int_local_opinion = 1; } else { int_local_opinion = 0; } mpi_result = MPI_Allreduce((void *)(&int_local_opinion), (void *)(&consensus), 1, MPI_INT, MPI_LAND, comm); if ( mpi_result != MPI_SUCCESS ) HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_result) if ( consensus ) { ret_value = TRUE; } else { ret_value = FALSE; } done: FUNC_LEAVE_NOAPI(ret_value); } /* H5D_get_collective_io_consensus() */ #endif /* H5_HAVE_PARALLEL */ /*------------------------------------------------------------------------- * Function: H5D_ioinfo_init * * Purpose: Routine for determining correct I/O operations for * each I/O action. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, September 30, 2004 * * Modifications: * *------------------------------------------------------------------------- */ static herr_t H5D_ioinfo_init(H5D_t *dset, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, const H5S_t #if !(defined H5_HAVE_PARALLEL || defined H5S_DEBUG) UNUSED #endif /* H5_HAVE_PARALLEL */ *mem_space, const H5S_t #if !(defined H5_HAVE_PARALLEL || defined H5S_DEBUG) UNUSED #endif /* H5_HAVE_PARALLEL */ *file_space, unsigned #ifndef H5_HAVE_PARALLEL UNUSED #endif /* H5_HAVE_PARALLEL */ flags, hbool_t #ifndef H5_HAVE_PARALLEL UNUSED #endif /* H5_HAVE_PARALLEL */ *use_par_opt_io, H5D_io_info_t *io_info) { #ifdef H5_HAVE_PARALLEL htri_t opt; /* Flag whether a selection is optimizable */ #endif /* H5_HAVE_PARALLEL */ herr_t ret_value = SUCCEED; /* Return value */ #if defined H5_HAVE_PARALLEL || defined H5S_DEBUG FUNC_ENTER_NOAPI_NOINIT(H5D_ioinfo_init) #else /* defined H5_HAVE_PARALLEL || defined H5S_DEBUG */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_ioinfo_init) #endif /* defined H5_HAVE_PARALLEL || defined H5S_DEBUG */ /* check args */ HDassert(dset); HDassert(dset->ent.file); HDassert(mem_space); HDassert(file_space); HDassert(use_par_opt_io); HDassert(io_info); /* Set up "normal" I/O fields */ io_info->dset=dset; io_info->dxpl_cache=dxpl_cache; io_info->dxpl_id=dxpl_id; io_info->store=NULL; /* Set later in I/O routine? */ /* Set I/O operations to initial values */ io_info->ops=dset->shared->io_ops; #ifdef H5_HAVE_PARALLEL /* * Check if we can set direct MPI-IO read/write functions */ opt=H5D_mpio_opt_possible(dset,mem_space,file_space,flags); if(opt==FAIL) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "invalid check for direct IO dataspace "); opt = H5D_get_collective_io_consensus(dset->ent.file, opt, flags); if ( opt == FAIL ) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, \ "check for collective I/O consensus failed."); /* Check if we can use the optimized parallel I/O routines */ if(opt==TRUE) { /* Set the pointers to the MPI-specific routines */ if((H5S_SELECT_IS_REGULAR(file_space) == TRUE) && (H5S_SELECT_IS_REGULAR(mem_space) == TRUE)){ io_info->ops.read = H5D_mpio_spaces_read; io_info->ops.write = H5D_mpio_spaces_write; } #ifdef H5_MPI_COMPLEX_DERIVED_DATATYPE_WORKS else { io_info->ops.read = H5D_mpio_spaces_span_read; io_info->ops.write = H5D_mpio_spaces_span_write; } #endif /* Indicate that the I/O will be parallel */ *use_par_opt_io=TRUE; } /* end if */ else { /* Indicate that the I/O will _NOT_ be parallel */ *use_par_opt_io=FALSE; io_info->ops.read = H5D_select_read; io_info->ops.write = H5D_select_write; } /* end else */ #else io_info->ops.read = H5D_select_read; io_info->ops.write = H5D_select_write; #endif /* H5_HAVE_PARALLEL */ #ifdef H5S_DEBUG /* Get the information for the I/O statistics */ if((io_info->stats=H5S_find(mem_space,file_space))==NULL) HGOTO_ERROR(H5E_DATASET, H5E_BADSELECT, FAIL, "can't set up selection statistics"); #endif /* H5S_DEBUG */ #if defined H5_HAVE_PARALLEL || defined H5S_DEBUG done: #endif /* H5_HAVE_PARALLEL || H5S_DEBUG */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_ioinfo_init() */