/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by the Board of Trustees of the University of Illinois. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the files COPYING and Copyright.html. COPYING can be found at the root * * of the source code distribution tree; Copyright.html can be found at the * * root level of an installed copy of the electronic HDF5 document set and * * is linked from the top-level documents page. It can also be found at * * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #define H5D_PACKAGE /*suppress error about including H5Dpkg */ #include "H5private.h" /* Generic Functions */ #include "H5Dpkg.h" /* Dataset functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ #include "H5Sprivate.h" /* Dataspace functions */ #include "H5Vprivate.h" /* Vector and array functions */ /*#define H5D_DEBUG*/ /* * The MPIO, MPIPOSIX, & FPHDF5 drivers are needed because there are * file and places where we check for things that aren't handled by these * drivers. */ #include "H5FDfphdf5.h" #include "H5FDmpio.h" #include "H5FDmpiposix.h" #ifdef H5_HAVE_PARALLEL /* Remove this if H5R_DATASET_REGION is no longer used in this file */ # include "H5Rpublic.h" #endif /*H5_HAVE_PARALLEL*/ /* Pablo information */ #define PABLO_MASK H5Dio_mask /* Local typedefs */ /*information for mapping between file space and memory space*/ typedef struct fm_map { H5S_t **fspace; /*file spaces for all chunks*/ H5S_t **mspace; /*memory spaces for all chunks*/ hsize_t elmt_count; /*indicate which element is being processed*/ hsize_t nchunks; /*total number of chunks*/ H5S_sel_iter_t mem_iter; /* Iterator for elements in memory selection */ unsigned m_ndims; /* Number of dimensions for memory dataspace */ hsize_t chunks[H5O_LAYOUT_NDIMS]; /* Number of chunks in each dimension */ hsize_t down_chunks[H5O_LAYOUT_NDIMS]; /* "down" size of number of chunks in each dimension */ hssize_t *chunk_coords; /*coordinates for all chunks*/ H5O_layout_t *layout; /*dataset layout information*/ } fm_map; /* Interface initialization */ static int interface_initialize_g = 0; #define INTERFACE_INIT NULL #ifdef H5_HAVE_PARALLEL /* Global vars whose value can be set from environment variable also */ extern hbool_t H5S_mpi_opt_types_g; #endif /* H5_HAVE_PARALLEL */ /* Local functions */ static herr_t H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, hid_t dset_xfer_plist, void *buf/*out*/); static herr_t H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, hid_t dset_xfer_plist, const void *buf); static herr_t H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t doing_mpio, H5FD_mpio_xfer_t xfer_mode, hid_t src_id, hid_t dst_id, void *buf/*out*/); static herr_t H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t doing_mpio, H5FD_mpio_xfer_t xfer_mode, hid_t src_id, hid_t dst_id, const void *buf); static herr_t H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t doing_mpio, H5FD_mpio_xfer_t xfer_mode, hid_t src_id, hid_t dst_id, void *buf/*out*/); static herr_t H5D_chunk_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t doing_mpio, H5FD_mpio_xfer_t xfer_mode, hid_t src_id, hid_t dst_id, const void *buf); #ifdef H5_HAVE_PARALLEL static herr_t H5D_io_assist_mpio(H5P_genplist_t *dx_plist, hbool_t doing_mpio, H5FD_mpio_xfer_t xfer_mode, hbool_t *xfer_mode_changed); #endif /*H5_HAVE_PARALLEL*/ static herr_t H5D_chunk_mem_file_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_space, const H5S_t *mem_space, fm_map *fm); static herr_t H5D_chunk_coords_assist(hssize_t *coords, size_t ndims, hsize_t chunks[], hsize_t chunk_ptr); static herr_t H5D_chunk_cb(void *elem, hid_t type_id, hsize_t ndims, hssize_t *coords, void *fm); static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id); /* Declare a free list to manage blocks of single datatype element data */ H5FL_BLK_DEFINE(type_elem); /* Declare a free list to manage blocks of type conversion data */ H5FL_BLK_DEFINE(type_conv); /*-------------------------------------------------------------------------- NAME H5Dfill PURPOSE Fill a selection in memory with a value USAGE herr_t H5Dfill(fill, fill_type, space, buf, buf_type) const void *fill; IN: Pointer to fill value to use hid_t fill_type_id; IN: Datatype of the fill value void *buf; IN/OUT: Memory buffer to fill selection within hid_t buf_type_id; IN: Datatype of the elements in buffer hid_t space_id; IN: Dataspace describing memory buffer & containing selection to use. RETURNS Non-negative on success/Negative on failure. DESCRIPTION Use the selection in the dataspace to fill elements in a memory buffer. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS If "fill" parameter is NULL, use all zeros as fill value EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ herr_t H5Dfill(const void *fill, hid_t fill_type_id, void *buf, hid_t buf_type_id, hid_t space_id) { H5S_t *space; /* Dataspace */ H5T_t *fill_type; /* Fill-value datatype */ H5T_t *buf_type; /* Buffer datatype */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dfill, FAIL); H5TRACE5("e","xixii",fill,fill_type_id,buf,buf_type_id,space_id); /* Check args */ if (buf==NULL) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid buffer"); if (NULL == (space=H5I_object_verify(space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a dataspace"); if (NULL == (fill_type=H5I_object_verify(fill_type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype"); if (NULL == (buf_type=H5I_object_verify(buf_type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype"); /* Fill the selection in the memory buffer */ if(H5D_fill(fill,fill_type,buf,buf_type,space, H5AC_dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed"); done: FUNC_LEAVE_API(ret_value); } /* H5Dfill() */ /*-------------------------------------------------------------------------- NAME H5D_fill PURPOSE Fill a selection in memory with a value (internal version) USAGE herr_t H5D_fill(fill, fill_type, buf, buf_type, space) const void *fill; IN: Pointer to fill value to use H5T_t *fill_type; IN: Datatype of the fill value void *buf; IN/OUT: Memory buffer to fill selection within H5T_t *buf_type; IN: Datatype of the elements in buffer H5S_t *space; IN: Dataspace describing memory buffer & containing selection to use. RETURNS Non-negative on success/Negative on failure. DESCRIPTION Use the selection in the dataspace to fill elements in a memory buffer. GLOBAL VARIABLES COMMENTS, BUGS, ASSUMPTIONS If "fill" parameter is NULL, use all zeros as fill value. If "fill_type" parameter is NULL, use "buf_type" for the fill value datatype. EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ static herr_t H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id) { H5T_path_t *tpath = NULL; /* Conversion information*/ uint8_t *tconv_buf = NULL; /* Data type conv buffer */ uint8_t *bkg_buf = NULL; /* Temp conversion buffer */ hid_t src_id = -1, dst_id = -1; /* Temporary type IDs */ size_t src_type_size; /* Size of source type */ size_t dst_type_size; /* Size of destination type*/ size_t buf_size; /* Desired buffer size */ herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_fill); /* Check args */ assert(buf); assert(buf_type); assert(space); /* Check for "default" fill value */ if(fill_type==NULL) fill_type=buf_type; /* Get the memory and file datatype sizes */ src_type_size = H5T_get_size(fill_type); dst_type_size = H5T_get_size(buf_type); /* Get the maximum buffer size needed and allocate it */ buf_size=MAX(src_type_size,dst_type_size); if (NULL==(tconv_buf = H5FL_BLK_MALLOC(type_elem,buf_size)) || NULL==(bkg_buf = H5FL_BLK_CALLOC(type_elem,buf_size))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed"); /* Copy the user's data into the buffer for conversion */ if(fill==NULL) HDmemset(tconv_buf,0,src_type_size); else HDmemcpy(tconv_buf,fill,src_type_size); /* Convert memory buffer into disk buffer */ /* Set up type conversion function */ if (NULL == (tpath = H5T_path_find(fill_type, buf_type, NULL, NULL, dxpl_id))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); } else if (!H5T_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, (hsize_t)1, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed"); /* Fill the selection in the memory buffer */ if(H5S_select_fill(tconv_buf, dst_type_size, space, buf)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed"); done: if (tconv_buf) H5FL_BLK_FREE(type_elem,tconv_buf); if (bkg_buf) H5FL_BLK_FREE(type_elem,bkg_buf); FUNC_LEAVE_NOAPI(ret_value); } /* H5D_fill() */ /*------------------------------------------------------------------------- * Function: H5Dread * * Purpose: Reads (part of) a DSET from the file into application * memory BUF. The part of the dataset to read is defined with * MEM_SPACE_ID and FILE_SPACE_ID. The data points are * converted from their file type to the MEM_TYPE_ID specified. * Additional miscellaneous data transfer properties can be * passed to this function with the PLIST_ID argument. * * The FILE_SPACE_ID can be the constant H5S_ALL which indicates * that the entire file data space is to be referenced. * * The MEM_SPACE_ID can be the constant H5S_ALL in which case * the memory data space is the same as the file data space * defined when the dataset was created. * * The number of elements in the memory data space must match * the number of elements in the file data space. * * The PLIST_ID can be the constant H5P_DEFAULT in which * case the default data transfer properties are used. * * Return: Non-negative on success/Negative on failure * * Errors: * ARGS BADTYPE Not a data space. * ARGS BADTYPE Not a data type. * ARGS BADTYPE Not a dataset. * ARGS BADTYPE Not xfer parms. * ARGS BADVALUE No output buffer. * DATASET READERROR Can't read data. * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t plist_id, void *buf/*out*/) { H5D_t *dset = NULL; const H5T_t *mem_type = NULL; const H5S_t *mem_space = NULL; const H5S_t *file_space = NULL; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dread, FAIL); H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id, plist_id,buf); /* check arguments */ if (NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); if (NULL == dset->ent.file) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); if (NULL == (mem_type = H5I_object_verify(mem_type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); if (H5S_ALL != mem_space_id) { if (NULL == (mem_space = H5I_object_verify(mem_space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); /* Check for valid selection */ if(H5S_select_valid(mem_space)!=TRUE) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); } if (H5S_ALL != file_space_id) { if (NULL == (file_space = H5I_object_verify(file_space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); /* Check for valid selection */ if(H5S_select_valid(file_space)!=TRUE) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); } /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == plist_id) plist_id= H5P_DATASET_XFER_DEFAULT; else if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); if (!buf) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer"); /* read raw data */ if (H5D_read(dset, mem_type, mem_space, file_space, plist_id, buf/*out*/) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data"); done: FUNC_LEAVE_API(ret_value); } /*------------------------------------------------------------------------- * Function: H5Dwrite * * Purpose: Writes (part of) a DSET from application memory BUF to the * file. The part of the dataset to write is defined with the * MEM_SPACE_ID and FILE_SPACE_ID arguments. The data points * are converted from their current type (MEM_TYPE_ID) to their * file data type. Additional miscellaneous data transfer * properties can be passed to this function with the * PLIST_ID argument. * * The FILE_SPACE_ID can be the constant H5S_ALL which indicates * that the entire file data space is to be referenced. * * The MEM_SPACE_ID can be the constant H5S_ALL in which case * the memory data space is the same as the file data space * defined when the dataset was created. * * The number of elements in the memory data space must match * the number of elements in the file data space. * * The PLIST_ID can be the constant H5P_DEFAULT in which * case the default data transfer properties are used. * * Return: Non-negative on success/Negative on failure * * Errors: * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t plist_id, const void *buf) { H5D_t *dset = NULL; const H5T_t *mem_type = NULL; const H5S_t *mem_space = NULL; const H5S_t *file_space = NULL; herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_API(H5Dwrite, FAIL); H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id, plist_id,buf); /* check arguments */ if (NULL == (dset = H5I_object_verify(dset_id, H5I_DATASET))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); if (NULL == dset->ent.file) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset"); if (NULL == (mem_type = H5I_object_verify(mem_type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type"); if (H5S_ALL != mem_space_id) { if (NULL == (mem_space = H5I_object_verify(mem_space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); /* Check for valid selection */ if (H5S_select_valid(mem_space)!=TRUE) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); } if (H5S_ALL != file_space_id) { if (NULL == (file_space = H5I_object_verify(file_space_id, H5I_DATASPACE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space"); /* Check for valid selection */ if (H5S_select_valid(file_space)!=TRUE) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent"); } /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == plist_id) plist_id= H5P_DATASET_XFER_DEFAULT; else if (TRUE!=H5P_isa_class(plist_id,H5P_DATASET_XFER)) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms"); if (!buf) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer"); /* write raw data */ if (H5D_write(dset, mem_type, mem_space, file_space, plist_id, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data"); done: FUNC_LEAVE_API(ret_value); } /*------------------------------------------------------------------------- * Function: H5D_read * * Purpose: Reads (part of) a DATASET into application memory BUF. See * H5Dread() for complete details. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * Robb Matzke, 1998-06-09 * The data space is no longer cached in the dataset struct. * * Robb Matzke, 1998-08-11 * Added timing calls around all the data space I/O functions. * * rky, 1998-09-18 * Added must_convert to do non-optimized read when necessary. * * Quincey Koziol, 1999-07-02 * Changed xfer_parms parameter to xfer plist parameter, so it * could be passed to H5T_convert. * * Albert Cheng, 2000-11-21 * Added the code that when it detects it is not safe to process a * COLLECTIVE read request without hanging, it changes it to * INDEPENDENT calls. * * Albert Cheng, 2000-11-27 * Changed to use the optimized MPIO transfer for Collective calls only. * * Raymond Lu, 2001-10-2 * Changed the way to retrieve property for generic property list. * * Raymond Lu, 2002-2-26 * For the new fill value design, data space can either be allocated * or not allocated at this stage. Fill value or data from space is * returned to outgoing buffer. * * QAK - 2002/04/02 * Removed the must_convert parameter and move preconditions to * H5S__opt_possible() routine * *------------------------------------------------------------------------- */ static herr_t H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, hid_t dxpl_id, void *buf/*out*/) { hssize_t snelmts; /*total number of elmts (signed) */ hsize_t nelmts; /*total number of elmts */ H5T_path_t *tpath = NULL; /*type conversion info */ hid_t src_id = -1, dst_id = -1;/*temporary type atoms */ H5S_conv_t *sconv=NULL; /*space conversion funcs*/ H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; /*xfer_mode for this request */ hbool_t doing_mpio=0; /*This is an MPIO access */ H5P_genplist_t *dx_plist=NULL; /* Data transfer property list */ H5P_genplist_t *dc_plist; /* Dataset creation roperty list */ unsigned sconv_flags=0; /* Flags for the space conversion */ H5S_sel_type fsel_type; /* Selection type on disk */ H5S_sel_type msel_type; /* Selection type in memory */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_read); /* check args */ assert(dataset && dataset->ent.file); assert(mem_type); assert(buf); /* Get the dataset's creation property list */ if (NULL == (dc_plist = H5I_object(dataset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); /* Get the dataset transfer property list */ if (NULL == (dx_plist = H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); if (!file_space) file_space = dataset->space; if (!mem_space) mem_space = file_space; if((snelmts = H5S_get_select_npoints(mem_space))<0) HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection"); nelmts=snelmts; #ifdef H5_HAVE_PARALLEL /* Collect Parallel I/O information for possible later use */ if (H5FD_MPIO==H5P_peek_hid_t(dx_plist,H5D_XFER_VFL_ID_NAME)) { doing_mpio++; xfer_mode=H5P_peek_unsigned(dx_plist, H5D_XFER_IO_XFER_MODE_NAME); } /* end if */ /* Collective access is not permissible without the MPIO or MPIPOSIX driver */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE && !(IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file) || IS_H5FD_FPHDF5(dataset->ent.file))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPIO & MPIPOSIX drivers only"); /* Set the "parallel I/O possible" flag, for H5S_find() */ if (H5S_mpi_opt_types_g && IS_H5FD_MPIO(dataset->ent.file)) { /* Only collective write should call this since it eventually * calls MPI_File_set_view which is a collective call. * See H5S_mpio_spaces_xfer() for details. */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE) sconv_flags |= H5S_CONV_PAR_IO_POSSIBLE; } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* Make certain that the number of elements in each selection is the same */ if (nelmts!=(hsize_t)H5S_get_select_npoints(file_space)) HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); /* Retrieve dataset properties */ /* */ /* If space hasn't been allocated and not using external storage, * return fill value to buffer if fill time is upon allocation, or * do nothing if fill time is never. If the dataset is compact and * fill time is NEVER, there is no way to tell whether part of data * has been overwritten. So just proceed in reading. */ if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) { H5O_fill_t fill; /* Fill value info */ H5D_fill_time_t fill_time; /* When to write the fill values */ H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ /* Retrieve dataset's fill-value properties */ if(H5P_fill_value_defined(dc_plist, &fill_status)<0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined"); if((fill_status==H5D_FILL_VALUE_DEFAULT || fill_status==H5D_FILL_VALUE_USER_DEFINED) && H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill value"); if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill time"); /* Should be impossible, but check anyway... */ if(fill_status == H5D_FILL_VALUE_UNDEFINED && fill_time == H5D_FILL_TIME_ALLOC) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "read failed: dataset doesn't exist, no data can be read"); /* If we're never going to fill this dataset, just leave the junk in the user's buffer */ if(fill_time == H5D_FILL_TIME_NEVER) HGOTO_DONE(SUCCEED); /* Go fill the user's selection with the dataset's fill value */ if(H5D_fill(fill.buf,fill.type,buf,mem_type,mem_space, dxpl_id)<0) { HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "filling buf failed"); } else HGOTO_DONE(SUCCEED); } /* end if */ /* * Locate the type conversion function and data space conversion * functions, and set up the element numbering information. If a data * type conversion is necessary then register data type atoms. Data type * conversion is necessary if the user has set the `need_bkg' to a high * enough value in xfer_parms since turning off data type conversion also * turns off background preservation. */ if (NULL==(tpath=H5T_path_find(dataset->type, mem_type, NULL, NULL, dxpl_id))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); } else if (!H5T_path_noop(tpath)) { if ((src_id=H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0 || (dst_id=H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); } /* end if */ /* Set the storage flags for the space conversion check */ switch(dataset->layout.type) { case H5D_COMPACT: sconv_flags |= H5S_CONV_STORAGE_COMPACT; break; case H5D_CONTIGUOUS: sconv_flags |= H5S_CONV_STORAGE_CONTIGUOUS; break; case H5D_CHUNKED: sconv_flags |= H5S_CONV_STORAGE_CHUNKED; break; default: assert(0 && "Unhandled layout type!"); } /* end switch */ /* Get dataspace functions */ if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from file to memory data space"); /* Get type of selection on disk & in memory */ if((fsel_type=H5S_get_select_type(file_space))<0) HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space"); if((msel_type=H5S_get_select_type(mem_space))<0) HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space"); /* Determine correct I/O routine to invoke */ if((fsel_type==H5S_SEL_POINTS || msel_type==H5S_SEL_POINTS) || dataset->layout.type!=H5D_CHUNKED) { /* Must use "contiguous" code for point selections, * since order of I/O accesses can be different from that of the * other kinds of selections */ if(H5D_contig_read(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, dc_plist, dx_plist, dxpl_id, doing_mpio, xfer_mode, src_id, dst_id, buf)<0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data"); } /* end if */ else { if(H5D_chunk_read(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, dc_plist, dx_plist, dxpl_id, doing_mpio, xfer_mode, src_id, dst_id, buf)<0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data"); } /* end else */ done: if (src_id >= 0) H5I_dec_ref(src_id); if (dst_id >= 0) H5I_dec_ref(dst_id); FUNC_LEAVE_NOAPI(ret_value); } /* end H5D_read() */ /*------------------------------------------------------------------------- * Function: H5D_write * * Purpose: Writes (part of) a DATASET to a file from application memory * BUF. See H5Dwrite() for complete details. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, December 4, 1997 * * Modifications: * Robb Matzke, 9 Jun 1998 * The data space is no longer cached in the dataset struct. * * rky 980918 * Added must_convert to do non-optimized read when necessary. * * Quincey Koziol, 2 July 1999 * Changed xfer_parms parameter to xfer plist parameter, so it could * be passed to H5T_convert * * Albert Cheng, 2000-11-21 * Added the code that when it detects it is not safe to process a * COLLECTIVE write request without hanging, it changes it to * INDEPENDENT calls. * * Albert Cheng, 2000-11-27 * Changed to use the optimized MPIO transfer for Collective calls only. * * Raymond Lu, 2001-10-2 * Changed the way to retrieve property for generic property list. * * Raymond Lu, 2002-2-26 * For the new fill value design, space may not be allocated until * this function is called. Allocate and initialize space if it * hasn't been. * * QAK - 2002/04/02 * Removed the must_convert parameter and move preconditions to * H5S__opt_possible() routine * *------------------------------------------------------------------------- */ static herr_t H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, hid_t dxpl_id, const void *buf) { hssize_t snelmts; /*total number of elmts (signed) */ hsize_t nelmts; /*total number of elmts */ H5T_path_t *tpath = NULL; /*type conversion info */ hid_t src_id = -1, dst_id = -1;/*temporary type atoms */ H5S_conv_t *sconv=NULL; /*space conversion funcs*/ H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; /*xfer_mode for this request */ hbool_t doing_mpio=0; /*This is an MPIO access */ H5P_genplist_t *dx_plist=NULL; /* Data transfer property list */ H5P_genplist_t *dc_plist; /* Dataset creation roperty list */ unsigned sconv_flags=0; /* Flags for the space conversion */ H5S_sel_type fsel_type; /* Selection type on disk */ H5S_sel_type msel_type; /* Selection type in memory */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_write); /* check args */ assert(dataset && dataset->ent.file); assert(mem_type); assert(buf); /* If MPIO, MPIPOSIX, or FPHDF5 is used, no VL datatype support yet. */ /* This is because they use the global heap in the file and we don't */ /* support parallel access of that yet */ if ( (IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file) || IS_H5FD_FPHDF5(dataset->ent.file)) && H5T_get_class(mem_type)==H5T_VLEN) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL datatypes yet"); /* If MPIO, MPIPOSIX, or FPHDF5 is used, no dataset region reference datatype support yet. */ /* This is because they use the global heap in the file and we don't */ /* support parallel access of that yet */ if ((IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file) || IS_H5FD_FPHDF5(dataset->ent.file)) && H5T_get_class(mem_type)==H5T_REFERENCE && H5T_get_ref_type(mem_type)==H5R_DATASET_REGION) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing region reference datatypes yet"); /* Check if we are allowed to write to this file */ if (0==(H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR)) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file"); /* Get the dataset's creation property list */ if (NULL == (dc_plist = H5I_object(dataset->dcpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); /* Get the dataset transfer property list */ if (NULL == (dx_plist = H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); if (!file_space) file_space = dataset->space; if (!mem_space) mem_space = file_space; if((snelmts = H5S_get_select_npoints(mem_space))<0) HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection"); nelmts=snelmts; #ifdef H5_HAVE_PARALLEL /* Collect Parallel I/O information for possible later use */ if (H5FD_MPIO==H5P_peek_hid_t(dx_plist,H5D_XFER_VFL_ID_NAME)) { doing_mpio++; xfer_mode=H5P_peek_unsigned(dx_plist, H5D_XFER_IO_XFER_MODE_NAME); } /* end if */ /* Collective access is not permissible without the MPIO or MPIPOSIX driver */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE && !(IS_H5FD_MPIO(dataset->ent.file) || IS_H5FD_MPIPOSIX(dataset->ent.file) || IS_H5FD_FPHDF5(dataset->ent.file))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPIO driver only"); /* If dataset is compact, collective access is only allowed when file space * selection is H5S_ALL */ if(doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE && dataset->layout.type==H5D_COMPACT) { if(H5S_get_select_type(file_space) != H5S_SEL_ALL) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access to compact dataset doesn't support partial access"); } /* Set the "parallel I/O possible" flag, for H5S_find() */ if (H5S_mpi_opt_types_g && IS_H5FD_MPIO(dataset->ent.file)) { /* Only collective write should call this since it eventually * calls MPI_File_set_view which is a collective call. * See H5S_mpio_spaces_xfer() for details. */ if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE) sconv_flags |= H5S_CONV_PAR_IO_POSSIBLE; } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* Make certain that the number of elements in each selection is the same */ if (nelmts!=(hsize_t)H5S_get_select_npoints(file_space)) HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); /* Retrieve dataset properties */ /* */ /* Allocate data space and initialize it if it hasn't been. */ if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT && dataset->layout.addr==HADDR_UNDEF) { hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */ /* Get the number of elements in file dataset's dataspace */ if((file_nelmts=H5S_get_simple_extent_npoints(file_space))<0) HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset"); /* Allocate storage */ if(H5D_alloc_storage(dataset->ent.file,dxpl_id,dataset,H5D_ALLOC_WRITE, TRUE, (hbool_t)((hsize_t)file_nelmts==nelmts ? TRUE : FALSE))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage"); } /* end if */ /* * Locate the type conversion function and data space conversion * functions, and set up the element numbering information. If a data * type conversion is necessary then register data type atoms. Data type * conversion is necessary if the user has set the `need_bkg' to a high * enough value in xfer_parms since turning off data type conversion also * turns off background preservation. */ if (NULL==(tpath=H5T_path_find(mem_type, dataset->type, NULL, NULL, dxpl_id))) { HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); } else if (!H5T_path_noop(tpath)) { if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0 || (dst_id = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); } /* end if */ /* Set the storage flags for the space conversion check */ switch(dataset->layout.type) { case H5D_COMPACT: sconv_flags |= H5S_CONV_STORAGE_COMPACT; break; case H5D_CONTIGUOUS: sconv_flags |= H5S_CONV_STORAGE_CONTIGUOUS; break; case H5D_CHUNKED: sconv_flags |= H5S_CONV_STORAGE_CHUNKED; break; default: assert(0 && "Unhandled layout type!"); } /* end switch */ /* Get dataspace functions */ if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from memory to file data space"); /* Get type of selection on disk & in memory */ if((fsel_type=H5S_get_select_type(file_space))<0) HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space"); if((msel_type=H5S_get_select_type(mem_space))<0) HGOTO_ERROR (H5E_DATASET, H5E_BADSELECT, FAIL, "unable to convert from file to memory data space"); /* Determine correct I/O routine to invoke */ if((fsel_type==H5S_SEL_POINTS || msel_type==H5S_SEL_POINTS) || dataset->layout.type!=H5D_CHUNKED) { /* Must use "contiguous" code for point selections, * since order of I/O accesses can be different from that of the * other kinds of selections */ if(H5D_contig_write(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, dc_plist, dx_plist, dxpl_id, doing_mpio, xfer_mode, src_id, dst_id, buf)<0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data"); } /* end if */ else { if(H5D_chunk_write(nelmts, dataset, mem_type, mem_space, file_space, tpath, sconv, dc_plist, dx_plist, dxpl_id, doing_mpio, xfer_mode, src_id, dst_id, buf)<0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data"); } /* end else */ /* * Update modification time. We have to do this explicitly because * writing to a dataset doesn't necessarily change the object header. */ if (H5O_touch(&(dataset->ent), FALSE, dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time"); done: if (src_id >= 0) H5I_dec_ref(src_id); if (dst_id >= 0) H5I_dec_ref(dst_id); FUNC_LEAVE_NOAPI(ret_value); } /* end H5D_write() */ /*------------------------------------------------------------------------- * Function: H5D_contig_read * * Purpose: Read from a contiguous dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Raymond Lu * Thursday, April 10, 2003 * * Modifications: * QAK - 2003/04/17 * Hacked on it a lot. :-) * *------------------------------------------------------------------------- */ static herr_t H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t #ifndef H5_HAVE_PARALLEL UNUSED #endif /*H5_HAVE_PARALLEL*/ doing_mpio, H5FD_mpio_xfer_t #ifndef H5_HAVE_PARALLEL UNUSED #endif /*H5_HAVE_PARALLEL*/ xfer_mode, hid_t src_id, hid_t dst_id, void *buf/*out*/) { herr_t status; /*function return status*/ #ifdef H5S_DEBUG H5_timer_t timer; #endif size_t src_type_size; /*size of source type */ size_t dst_type_size; /*size of destination type*/ size_t target_size; /*desired buffer size */ hsize_t request_nelmts; /*requested strip mine */ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */ H5S_sel_iter_t bkg_iter; /*background iteration info*/ hbool_t bkg_iter_init=0; /*background iteration info has been initialized */ H5S_sel_iter_t file_iter; /*file selection iteration info*/ hbool_t file_iter_init=0; /*file selection iteration info has been initialized */ H5T_bkg_t need_bkg; /*type of background buf*/ uint8_t *tconv_buf = NULL; /*data type conv buffer */ uint8_t *bkg_buf = NULL; /*background buffer */ hsize_t smine_start; /*strip mine start loc */ hsize_t n, smine_nelmts; /*elements per strip */ #ifdef H5_HAVE_PARALLEL hbool_t xfer_mode_changed; /* Whether the transfer mode was changed */ #endif /*H5_HAVE_PARALLEL*/ herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOINIT(H5D_contig_read); /* * If there is no type conversion then read directly into the * application's buffer. This saves at least one mem-to-mem copy. */ if (H5T_path_noop(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif /* Sanity check dataset, then read it */ assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); status = (sconv->read)(dataset->ent.file, &(dataset->layout), dc_plist, (H5D_storage_t *)&(dataset->efl), H5T_get_size(dataset->type), file_space, mem_space, dxpl_id, buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].read_timer), &timer); sconv->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->type); sconv->stats[1].read_ncalls++; #endif /* Check return value from optimized read */ if (status<0) { HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed"); } else /* direct xfer accomplished successfully */ HGOTO_DONE(SUCCEED); } /* end if */ /* * This is the general case(type conversion). */ #ifdef H5_HAVE_PARALLEL H5D_io_assist_mpio(dx_plist, doing_mpio, xfer_mode, &xfer_mode_changed); #endif /*H5_HAVE_PARALLEL*/ /* Compute element sizes and other parameters */ src_type_size = H5T_get_size(dataset->type); dst_type_size = H5T_get_size(mem_type); target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME); request_nelmts = target_size / MAX(src_type_size, dst_type_size); /* Figure out the strip mine size. */ if (H5S_select_iter_init(&file_iter, file_space, src_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); file_iter_init=1; /*file selection iteration info has been initialized */ if (H5S_select_iter_init(&mem_iter, mem_space, dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); mem_iter_init=1; /*file selection iteration info has been initialized */ if (H5S_select_iter_init(&bkg_iter, mem_space, dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); bkg_iter_init=1; /*file selection iteration info has been initialized */ /* Sanity check elements in temporary buffer */ if (request_nelmts<=0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); /* * Get a temporary buffer for type conversion unless the app has already * supplied one through the xfer properties. Instead of allocating a * buffer which is the exact size, we allocate the target size. The * malloc() is usually less resource-intensive if we allocate/free the * same size over and over. */ if (H5T_path_bkg(tpath)) { /* Retrieve the bkgr buffer property */ if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); need_bkg = MAX(H5T_path_bkg(tpath), need_bkg); } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { /* Allocate temporary buffer */ if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } /* end if */ if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { /* Allocate background buffer */ H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); if((bkg_buf=H5FL_BLK_MALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); } /* end if */ /* Start strip mining... */ for (smine_start=0; smine_startlayout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), dc_plist, (H5D_storage_t *)&dataset->efl, src_type_size, file_space, &file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].gath_timer), &timer); sconv->stats[1].gath_nbytes += n * src_type_size; sconv->stats[1].gath_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); if (need_bkg) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif n = H5S_select_mgath(buf, dst_type_size, mem_space, &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].bkg_timer), &timer); sconv->stats[1].bkg_nbytes += n * dst_type_size; sconv->stats[1].bkg_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed"); } /* end if */ /* * Perform data type conversion. */ if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); /* * Scatter the data into memory. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = H5S_select_mscat(tconv_buf, dst_type_size, mem_space, &mem_iter, smine_nelmts, dxpl_id, buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].scat_timer), &timer); sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size; sconv->stats[1].scat_ncalls++; #endif if (status<0) HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "scatter failed"); } /* end for */ done: #ifdef H5_HAVE_PARALLEL /* restore xfer_mode due to the kludge */ if (doing_mpio && xfer_mode_changed) { #ifdef H5D_DEBUG if (H5DEBUG(D)) fprintf (H5DEBUG(D), "H5D: dx->xfer_mode was COLLECTIVE, restored to INDEPENDENT\n"); #endif xfer_mode = H5FD_MPIO_COLLECTIVE; if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* Release selection iterators */ if(file_iter_init) H5S_select_iter_release(&file_iter); if(mem_iter_init) H5S_select_iter_release(&mem_iter); if(bkg_iter_init) H5S_select_iter_release(&bkg_iter); assert(dx_plist); if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME)) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) H5FL_BLK_FREE(type_conv,bkg_buf); FUNC_LEAVE_NOAPI(ret_value); } /* end H5D_contig_read() */ /*------------------------------------------------------------------------- * Function: H5D_contig_write * * Purpose: Write to a contiguous dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Raymond Lu * Thursday, April 10, 2003 * * Modifications: * QAK - 2003/04/17 * Hacked on it a lot. :-) * *------------------------------------------------------------------------- */ static herr_t H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t #ifndef H5_HAVE_PARALLEL UNUSED #endif /*H5_HAVE_PARALLEL*/ doing_mpio, H5FD_mpio_xfer_t #ifndef H5_HAVE_PARALLEL UNUSED #endif /*H5_HAVE_PARALLEL*/ xfer_mode, hid_t src_id, hid_t dst_id, const void *buf) { herr_t status; /*function return status*/ #ifdef H5S_DEBUG H5_timer_t timer; #endif size_t src_type_size; /*size of source type */ size_t dst_type_size; /*size of destination type*/ size_t target_size; /*desired buffer size */ hsize_t request_nelmts; /*requested strip mine */ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */ H5S_sel_iter_t bkg_iter; /*background iteration info*/ hbool_t bkg_iter_init=0; /*background iteration info has been initialized */ H5S_sel_iter_t file_iter; /*file selection iteration info*/ hbool_t file_iter_init=0; /*file selection iteration info has been initialized */ H5T_bkg_t need_bkg; /*type of background buf*/ uint8_t *tconv_buf = NULL; /*data type conv buffer */ uint8_t *bkg_buf = NULL; /*background buffer */ hsize_t smine_start; /*strip mine start loc */ hsize_t n, smine_nelmts; /*elements per strip */ #ifdef H5_HAVE_PARALLEL hbool_t xfer_mode_changed; /* Whether the transfer mode was changed */ #endif /*H5_HAVE_PARALLEL*/ herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOINIT(H5D_contig_write); /* * If there is no type conversion then write directly from the * application's buffer. This saves at least one mem-to-mem copy. */ if (H5T_path_noop(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = (sconv->write)(dataset->ent.file, &(dataset->layout), dc_plist, (H5D_storage_t *)&(dataset->efl), H5T_get_size(dataset->type), file_space, mem_space, dxpl_id, buf); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].write_timer), &timer); sconv->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type); sconv->stats[0].write_ncalls++; #endif /* Check return value from optimized write */ if (status<0) { HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed"); } else /* direct xfer accomplished successfully */ HGOTO_DONE(SUCCEED); } /* end if */ /* * This is the general case. */ #ifdef H5_HAVE_PARALLEL H5D_io_assist_mpio(dx_plist, doing_mpio, xfer_mode, &xfer_mode_changed); #endif /*H5_HAVE_PARALLEL*/ /* Compute element sizes and other parameters */ src_type_size = H5T_get_size(mem_type); dst_type_size = H5T_get_size(dataset->type); target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME); request_nelmts = target_size / MAX (src_type_size, dst_type_size); /* Sanity check elements in temporary buffer */ if (request_nelmts<=0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); /* Figure out the strip mine size. */ if (H5S_select_iter_init(&file_iter, file_space, dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); file_iter_init=1; /*file selection iteration info has been initialized */ if (H5S_select_iter_init(&mem_iter, mem_space, src_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); mem_iter_init=1; /*file selection iteration info has been initialized */ if (H5S_select_iter_init(&bkg_iter, file_space, dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); bkg_iter_init=1; /*file selection iteration info has been initialized */ /* * Get a temporary buffer for type conversion unless the app has already * supplied one through the xfer properties. Instead of allocating a * buffer which is the exact size, we allocate the target size. The * malloc() is usually less resource-intensive if we allocate/free the * same size over and over. */ if (H5T_path_bkg(tpath)) { /* Retrieve the bkgr buffer property */ if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); need_bkg = MAX (H5T_path_bkg(tpath), need_bkg); } else if(H5T_detect_class(dataset->type, H5T_VLEN)) { /* Old data is retrieved into background buffer for VL datatype. The * data is used later for freeing heap objects. */ need_bkg = H5T_BKG_YES; } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { /* Allocate temporary buffer */ if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } /* end if */ if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { /* Allocate background buffer */ H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); } /* end if */ /* Start strip mining... */ for (smine_start=0; smine_startstats[0].gath_timer), &timer); sconv->stats[0].gath_nbytes += n * src_type_size; sconv->stats[0].gath_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed"); if (need_bkg) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), dc_plist, (H5D_storage_t *)&(dataset->efl), dst_type_size, file_space, &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].bkg_timer), &timer); sconv->stats[0].bkg_nbytes += n * dst_type_size; sconv->stats[0].bkg_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed"); } /* end if */ /* * Perform data type conversion. */ if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); /* * Scatter the data out to the file. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = H5S_select_fscat(dataset->ent.file, &(dataset->layout), dc_plist, (H5D_storage_t *)&(dataset->efl), dst_type_size, file_space, &file_iter, smine_nelmts, dxpl_id, tconv_buf); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].scat_timer), &timer); sconv->stats[0].scat_nbytes += smine_nelmts * dst_type_size; sconv->stats[0].scat_ncalls++; #endif if (status<0) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed"); } /* end for */ done: #ifdef H5_HAVE_PARALLEL /* restore xfer_mode due to the kludge */ if (doing_mpio && xfer_mode_changed) { #ifdef H5D_DEBUG if (H5DEBUG(D)) fprintf (H5DEBUG(D), "H5D: dx->xfer_mode was COLLECTIVE, restored to INDEPENDENT\n"); #endif xfer_mode = H5FD_MPIO_COLLECTIVE; if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* Release selection iterators */ if(file_iter_init) H5S_select_iter_release(&file_iter); if(mem_iter_init) H5S_select_iter_release(&mem_iter); if(bkg_iter_init) H5S_select_iter_release(&bkg_iter); assert(dx_plist); if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME)) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) H5FL_BLK_FREE(type_conv,bkg_buf); FUNC_LEAVE_NOAPI(ret_value); } /* end H5D_contig_write() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_read * * Purpose: Read from a chunked dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Raymond Lu * Thursday, April 10, 2003 * * Modifications: * QAK - 2003/04/17 * Hacked on it a lot. :-) * *------------------------------------------------------------------------- */ static herr_t H5D_chunk_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, const H5S_t *file_space, H5T_path_t *tpath, H5S_conv_t *sconv, H5P_genplist_t *dc_plist, H5P_genplist_t *dx_plist, hid_t dxpl_id, hbool_t #ifndef H5_HAVE_PARALLEL UNUSED #endif /*H5_HAVE_PARALLEL*/ doing_mpio, H5FD_mpio_xfer_t #ifndef H5_HAVE_PARALLEL UNUSED #endif /*H5_HAVE_PARALLEL*/ xfer_mode, hid_t src_id, hid_t dst_id, void *buf/*out*/) { fm_map fm; /* File<->memory mapping */ herr_t status; /*function return status*/ #ifdef H5S_DEBUG H5_timer_t timer; #endif size_t src_type_size; /*size of source type */ size_t dst_type_size; /*size of destination type*/ size_t target_size; /*desired buffer size */ hsize_t request_nelmts; /*requested strip mine */ hsize_t smine_start; /*strip mine start loc */ hsize_t n, smine_nelmts; /*elements per strip */ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */ H5S_sel_iter_t bkg_iter; /*background iteration info*/ hbool_t bkg_iter_init=0; /*background iteration info has been initialized */ H5S_sel_iter_t file_iter; /*file selection iteration info*/ hbool_t file_iter_init=0; /*file selection iteration info has been initialized */ H5T_bkg_t need_bkg; /*type of background buf*/ uint8_t *tconv_buf = NULL; /*data type conv buffer */ uint8_t *bkg_buf = NULL; /*background buffer */ H5D_storage_t store; /*union of EFL and chunk pointer in file space */ hsize_t h; /* Local index variable */ #ifdef H5_HAVE_PARALLEL hbool_t xfer_mode_changed; /* Whether the transfer mode was changed */ #endif /*H5_HAVE_PARALLEL*/ herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOINIT(H5D_chunk_read); /* Initialize fm_map*/ HDmemset(&fm, 0, sizeof(fm_map)); fm.layout = &(dataset->layout); /* Map elements between file and memory for each chunk*/ H5D_chunk_mem_file_map(dataset, mem_type, file_space, mem_space, &fm); /* * If there is no type conversion then read directly into the * application's buffer. This saves at least one mem-to-mem copy. */ if (H5T_path_noop(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif /* Sanity check dataset, then read it */ assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); /*loop through each chunk, read data*/ for(h=0; h 0) { /*pass in chunk's coordinates in a union. LAYOUT puts datatype size as an extra dimension, * have to take it out.*/ store.chunk_coords = fm.chunk_coords + h*dataset->layout.ndims; status = (sconv->read)(dataset->ent.file, &(dataset->layout), dc_plist, &store, H5T_get_size(dataset->type), fm.fspace[h], fm.mspace[h], dxpl_id, buf/*out*/); /* Check return value from optimized read */ if (status<0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed"); } /* end if */ } /* end for */ #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].read_timer), &timer); sconv->stats[1].read_nbytes += nelmts * H5T_get_size(dataset->type); sconv->stats[1].read_ncalls++; #endif /* direct xfer accomplished successfully */ HGOTO_DONE(SUCCEED); } /* end if */ /* * This is the general case(type conversion). */ #ifdef H5_HAVE_PARALLEL H5D_io_assist_mpio(dx_plist, doing_mpio, xfer_mode, &xfer_mode_changed); #endif /*H5_HAVE_PARALLEL*/ /* Compute element sizes and other parameters */ src_type_size = H5T_get_size(dataset->type); dst_type_size = H5T_get_size(mem_type); target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME); request_nelmts = target_size / MAX(src_type_size, dst_type_size); /* Sanity check elements in temporary buffer */ if (request_nelmts<=0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); /* * Get a temporary buffer for type conversion unless the app has already * supplied one through the xfer properties. Instead of allocating a * buffer which is the exact size, we allocate the target size. The * malloc() is usually less resource-intensive if we allocate/free the * same size over and over. */ if (H5T_path_bkg(tpath)) { /* Retrieve the bkgr buffer property */ if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); need_bkg = MAX(H5T_path_bkg(tpath), need_bkg); } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { /* Allocate temporary buffer */ if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } /* end if */ if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { /* Allocate background buffer */ H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); if((bkg_buf=H5FL_BLK_MALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); } /* end if */ /* Loop over all the chunks, performing I/O on each */ for(h=0; h 0) { /* initialize selection iterator */ if (H5S_select_iter_init(&file_iter, fm.fspace[h], src_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); file_iter_init=1; /*file selection iteration info has been initialized */ if (H5S_select_iter_init(&mem_iter, fm.mspace[h], dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); mem_iter_init=1; /*file selection iteration info has been initialized */ if (H5S_select_iter_init(&bkg_iter, fm.mspace[h], dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); bkg_iter_init=1; /*file selection iteration info has been initialized */ /*pass in chunk's coordinates in a union*/ store.chunk_coords = fm.chunk_coords + h*dataset->layout.ndims; for (smine_start=0; smine_startlayout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), dc_plist, &store, src_type_size, fm.fspace[h], &file_iter, smine_nelmts, dxpl_id, tconv_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].gath_timer), &timer); sconv->stats[1].gath_nbytes += n * src_type_size; sconv->stats[1].gath_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); if (need_bkg) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif n = H5S_select_mgath(buf, dst_type_size, fm.mspace[h], &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].bkg_timer), &timer); sconv->stats[1].bkg_nbytes += n * dst_type_size; sconv->stats[1].bkg_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed"); } /* end if */ /* * Perform data type conversion. */ if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); /* * Scatter the data into memory. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = H5S_select_mscat(tconv_buf, dst_type_size, fm.mspace[h], &mem_iter, smine_nelmts, dxpl_id, buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[1].scat_timer), &timer); sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size; sconv->stats[1].scat_ncalls++; #endif if (status<0) HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "scatter failed"); } /* end for */ /* Release selection iterators */ if(file_iter_init) { H5S_select_iter_release(&file_iter); file_iter_init=0; } /* end if */ if(mem_iter_init) { H5S_select_iter_release(&mem_iter); mem_iter_init=0; } /* end if */ if(bkg_iter_init) { H5S_select_iter_release(&bkg_iter); bkg_iter_init=0; } /* end if */ } /* end if */ } /* end for */ done: #ifdef H5_HAVE_PARALLEL /* restore xfer_mode due to the kludge */ if (doing_mpio && xfer_mode_changed) { #ifdef H5D_DEBUG if (H5DEBUG(D)) fprintf (H5DEBUG(D), "H5D: dx->xfer_mode was COLLECTIVE, restored to INDEPENDENT\n"); #endif xfer_mode = H5FD_MPIO_COLLECTIVE; if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); } /* end if */ #endif /*H5_HAVE_PARALLEL*/ assert(dx_plist); if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME)) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) H5FL_BLK_FREE(type_conv,bkg_buf); /* Release selection iterators, if necessary */ if(file_iter_init) H5S_select_iter_release(&file_iter); if(mem_iter_init) H5S_select_iter_release(&mem_iter); if(bkg_iter_init) H5S_select_iter_release(&bkg_iter); /* Close file space and memory space for each chunk*/ for(h=0; hmemory mapping */ herr_t status; /*function return status*/ #ifdef H5S_DEBUG H5_timer_t timer; #endif size_t src_type_size; /*size of source type */ size_t dst_type_size; /*size of destination type*/ size_t target_size; /*desired buffer size */ hsize_t request_nelmts; /*requested strip mine */ hsize_t smine_start; /*strip mine start loc */ hsize_t n, smine_nelmts; /*elements per strip */ H5S_sel_iter_t mem_iter; /*memory selection iteration info*/ hbool_t mem_iter_init=0; /*memory selection iteration info has been initialized */ H5S_sel_iter_t bkg_iter; /*background iteration info*/ hbool_t bkg_iter_init=0; /*background iteration info has been initialized */ H5S_sel_iter_t file_iter; /*file selection iteration info*/ hbool_t file_iter_init=0; /*file selection iteration info has been initialized */ H5T_bkg_t need_bkg; /*type of background buf*/ uint8_t *tconv_buf = NULL; /*data type conv buffer */ uint8_t *bkg_buf = NULL; /*background buffer */ H5D_storage_t store; /*union of EFL and chunk pointer in file space */ hsize_t h; /* Local index variable */ #ifdef H5_HAVE_PARALLEL hbool_t xfer_mode_changed; /* Whether the transfer mode was changed */ #endif /*H5_HAVE_PARALLEL*/ herr_t ret_value = SUCCEED; /*return value */ FUNC_ENTER_NOINIT(H5D_chunk_write); /* Initialize fm_map*/ HDmemset(&fm, 0, sizeof(fm_map)); fm.layout = &(dataset->layout); /* Map elements between file and memory for each chunk*/ H5D_chunk_mem_file_map(dataset, mem_type, file_space, mem_space, &fm); /* * If there is no type conversion then write directly from the * application's buffer. This saves at least one mem-to-mem copy. */ if (H5T_path_noop(tpath)) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif /*loop through each chunk, write data*/ for(h=0; h 0) { /*pass in chunk's coordinates in a union. LAYOUT puts datatype size as an extra dimension, * have to take it out.*/ store.chunk_coords = fm.chunk_coords + h*dataset->layout.ndims; status = (sconv->write)(dataset->ent.file, &(dataset->layout), dc_plist, &store, H5T_get_size(dataset->type), fm.fspace[h], fm.mspace[h], dxpl_id, buf); /* Check return value from optimized write */ if (status<0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed"); } } #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].write_timer), &timer); sconv->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type); sconv->stats[0].write_ncalls++; #endif /* direct xfer accomplished successfully */ HGOTO_DONE(SUCCEED); } /* end if */ /* * This is the general case(type conversion). */ #ifdef H5_HAVE_PARALLEL H5D_io_assist_mpio(dx_plist, doing_mpio, xfer_mode, &xfer_mode_changed); #endif /*H5_HAVE_PARALLEL*/ /* Compute element sizes and other parameters */ src_type_size = H5T_get_size(mem_type); dst_type_size = H5T_get_size(dataset->type); target_size = H5P_peek_size_t(dx_plist,H5D_XFER_MAX_TEMP_BUF_NAME); request_nelmts = target_size / MAX (src_type_size, dst_type_size); /* Sanity check elements in temporary buffer */ if (request_nelmts<=0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); /* * Get a temporary buffer for type conversion unless the app has already * supplied one through the xfer properties. Instead of allocating a * buffer which is the exact size, we allocate the target size. The * malloc() is usually less resource-intensive if we allocate/free the * same size over and over. */ if (H5T_path_bkg(tpath)) { /* Retrieve the bkgr buffer property */ if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); need_bkg = MAX (H5T_path_bkg(tpath), need_bkg); } else if(H5T_detect_class(dataset->type, H5T_VLEN)) { /* Old data is retrieved into background buffer for VL datatype. The * data is used later for freeing heap objects. */ need_bkg = H5T_BKG_YES; } else { need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { /* Allocate temporary buffer */ if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); } /* end if */ if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { /* Allocate background buffer */ H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); } /* end if */ /* Loop over all the chunks, performing I/O on each */ for(h=0; h 0) { /* initialize selection iterator */ if (H5S_select_iter_init(&file_iter, fm.fspace[h], dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize file selection information"); file_iter_init=1; /*file selection iteration info has been initialized */ if (H5S_select_iter_init(&mem_iter, fm.mspace[h], src_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information"); mem_iter_init=1; /*file selection iteration info has been initialized */ if (H5S_select_iter_init(&bkg_iter, fm.fspace[h], dst_type_size)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); bkg_iter_init=1; /*file selection iteration info has been initialized */ /*pass in chunk's coordinates in a union*/ store.chunk_coords = fm.chunk_coords + h*dataset->layout.ndims; for (smine_start=0; smine_startstats[1].gath_timer), &timer); sconv->stats[1].gath_nbytes += n * src_type_size; sconv->stats[1].gath_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed"); if (need_bkg) { #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), dc_plist, &store, dst_type_size, fm.fspace[h], &bkg_iter, smine_nelmts, dxpl_id, bkg_buf/*out*/); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].bkg_timer), &timer); sconv->stats[0].bkg_nbytes += n * dst_type_size; sconv->stats[0].bkg_ncalls++; #endif if (n!=smine_nelmts) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed"); } /* end if */ /* * Perform data type conversion. */ if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed"); /* * Scatter the data out to the file. */ #ifdef H5S_DEBUG H5_timer_begin(&timer); #endif status = H5S_select_fscat(dataset->ent.file, &(dataset->layout), dc_plist, &store, dst_type_size, fm.fspace[h], &file_iter, smine_nelmts, dxpl_id, tconv_buf); #ifdef H5S_DEBUG H5_timer_end(&(sconv->stats[0].scat_timer), &timer); sconv->stats[0].scat_nbytes += n * dst_type_size; sconv->stats[0].scat_ncalls++; #endif if (status<0) HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "scatter failed"); } /* end for */ /* Release selection iterators */ if(file_iter_init) { H5S_select_iter_release(&file_iter); file_iter_init=0; } /* end if */ if(mem_iter_init) { H5S_select_iter_release(&mem_iter); mem_iter_init=0; } /* end if */ if(bkg_iter_init) { H5S_select_iter_release(&bkg_iter); bkg_iter_init=0; } /* end if */ } /* end if */ } /* end for */ done: #ifdef H5_HAVE_PARALLEL /* restore xfer_mode due to the kludge */ if (doing_mpio && xfer_mode_changed) { #ifdef H5D_DEBUG if (H5DEBUG(D)) fprintf (H5DEBUG(D), "H5D: dx->xfer_mode was COLLECTIVE, restored to INDEPENDENT\n"); #endif xfer_mode = H5FD_MPIO_COLLECTIVE; if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); } /* end if */ #endif /*H5_HAVE_PARALLEL*/ assert(dx_plist); if (tconv_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME)) H5FL_BLK_FREE(type_conv,tconv_buf); if (bkg_buf && NULL==H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME)) H5FL_BLK_FREE(type_conv,bkg_buf); /* Release selection iterators, if necessary */ if(file_iter_init) H5S_select_iter_release(&file_iter); if(mem_iter_init) H5S_select_iter_release(&mem_iter); if(bkg_iter_init) H5S_select_iter_release(&bkg_iter); /* Close file space and memory space for each chunk*/ for(h=0; hlayout.ndims-1),dataset->layout.dim,NULL))) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace"); /*make a copy of mem_space*/ if((tmp_mspace = H5S_copy(mem_space))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space"); /*de-select the file space and mem space copies*/ if(H5S_select_none(tmp_fspace)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select file space"); if(H5S_select_none(tmp_mspace)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to de-select memory space"); /* Get dim number and dimensionality for each dataspace */ f_ndims=dataset->layout.ndims-1; if((sm_ndims = H5S_get_simple_extent_ndims(tmp_mspace))<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimension number"); fm->m_ndims=m_ndims=sm_ndims; if(H5S_get_simple_extent_dims(file_space, f_dims, NULL)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality"); /* Decide the number of chunks in each dimension*/ fm->nchunks = 1; for(u=0; uchunks[u] = ((f_dims[u]+dataset->layout.dim[u])-1) / dataset->layout.dim[u]; fm->nchunks *= fm->chunks[u]; } /* Compute the "down" size of 'chunks' information */ if(H5V_array_down(f_ndims,fm->chunks,fm->down_chunks)<0) HGOTO_ERROR (H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes"); /* Allocate arrays to hold each chunk's dataspace & selection, for both the * file and memory */ H5_CHECK_OVERFLOW((sizeof(H5S_t*)*fm->nchunks),hsize_t,size_t); fm->fspace = (H5S_t**)H5MM_malloc((size_t)(sizeof(H5S_t*)*fm->nchunks)); fm->mspace = (H5S_t**)H5MM_malloc((size_t)(sizeof(H5S_t*)*fm->nchunks)); fm->elmt_count = 0; /* Allocate array to hold coordinates of each chunk in file's dataspace */ H5_CHECK_OVERFLOW((sizeof(hsize_t)*fm->nchunks*(f_ndims+1)),hsize_t,size_t); fm->chunk_coords = (hssize_t*)H5MM_malloc((size_t)(sizeof(hsize_t)*fm->nchunks*(f_ndims+1))); /* Make per-chunk copies of memory and chunk dataspaces * (with each one's selection set to "none" */ for(j=0; jnchunks; j++) { if((fm->mspace[j] = H5S_copy(tmp_mspace))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy memory space"); if((fm->fspace[j] = H5S_copy(tmp_fspace))==NULL) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTCOPY, FAIL, "unable to copy file space"); /* Initialize chunk_coords for each chunk. each stride is the number of * file space dimensions, with fast-growing dimension at the last */ H5D_chunk_coords_assist(fm->chunk_coords+j*(f_ndims+1), f_ndims, fm->chunks, j); } /* Create temporary datatypes for selection iteration */ if((f_tid = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0) HGOTO_ERROR (H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register file datatype"); /* Create selection iterator for memory selection */ if((elmt_size=H5T_get_size(mem_type))==0) HGOTO_ERROR(H5E_DATATYPE, H5E_BADSIZE, FAIL, "datatype size invalid"); if (H5S_select_iter_init(&(fm->mem_iter), mem_space, elmt_size)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); iter_init=1; /* Selection iteration info has been initialized */ /* Build the file & memory selection for each chunk */ if(H5S_select_iterate(&bogus, f_tid, file_space, H5D_chunk_cb, fm)<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to iterate file space"); /* Clean hyperslab span "scratch" information */ for(j=0; jnchunks; j++) { if(H5S_hyper_reset_scratch(fm->fspace[j])<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info"); if(H5S_hyper_reset_scratch(fm->mspace[j])<0) HGOTO_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset span scratch info"); } /* end for */ done: if(iter_init) { if (H5S_select_iter_release(&(fm->mem_iter))<0) HDONE_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); } if(tmp_fspace) H5S_close(tmp_fspace); if(tmp_mspace) H5S_close(tmp_mspace); if(f_tid!=(-1)) H5Tclose(f_tid); FUNC_LEAVE_NOAPI(ret_value); } /* end H5D_chunk_mem_file_map() */ /*------------------------------------------------------------------------- * Function: H5D_chunk_cb * * Purpose: Callback routine for file selection iterator. Used when * creating selections in memory and each chunk for each chunk. * * Return: Non-negative on success/Negative on failure * * Programmer: Raymond Lu * Thursday, April 10, 2003 * * Modifications: * QAK - 2003/04/17 * Hacked on it a lot. :-) * *------------------------------------------------------------------------- */ static herr_t H5D_chunk_cb(void UNUSED *elem, hid_t UNUSED type_id, hsize_t ndims, hssize_t *coords, void *_fm) { fm_map *fm = (fm_map*)_fm; /* File<->memory chunk mapping info */ hssize_t coords_in_chunk[H5O_LAYOUT_NDIMS]; /* Coordinates of element in chunk */ hssize_t coords_in_mem[H5O_LAYOUT_NDIMS]; /* Coordinates of element in memory */ hsize_t chunk_idx; /* Chunk index */ hsize_t u; /* Local index variables */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_chunk_cb); #ifdef QAK { unsigned u; HDfprintf(stderr,"%s: coords={",FUNC); for(u=0; ulayout->dim,fm->chunks,fm->down_chunks,&chunk_idx)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index"); #ifdef QAK HDfprintf(stderr,"%s: chunk_idx=%Hu\n",FUNC,chunk_idx); #endif /* QAK */ /*convert coords from relative to whole file space to relative to its chunk space, *pass into H5S_select_hyperslab.*/ for(u=0; ulayout->dim[u]; #ifdef QAK { unsigned u; HDfprintf(stderr,"%s: coords_in_chunk={",FUNC); for(u=0; ufspace[chunk_idx], (unsigned)ndims, coords_in_chunk)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element"); /* Get coordinates of selection iterator for memory */ if(H5S_select_iter_coords(&fm->mem_iter,coords_in_mem)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get iterator coordinates"); #ifdef QAK { unsigned u; HDfprintf(stderr,"%s: coords_in_mem={",FUNC); for(u=0; um_ndims; u++) HDfprintf(stderr,"%Hd%s",coords_in_mem[u],(u<(fm->m_ndims-1)?", ":"}\n")); } #endif /* QAK */ /* Add point to memory selection for chunk */ if(H5S_hyper_add_span_element(fm->mspace[chunk_idx], fm->m_ndims, coords_in_mem)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTSELECT, FAIL, "unable to select element"); /* Move memory selection iterator to next element in selection */ if(H5S_select_iter_next(&fm->mem_iter,1)<0) HGOTO_ERROR (H5E_DATASPACE, H5E_CANTNEXT, FAIL, "unable to move to next iterator location"); done: FUNC_LEAVE_NOAPI(ret_value); } /* end H5D_chunk_cb() */