diff options
Diffstat (limited to 'src/H5D.c')
| -rw-r--r-- | src/H5D.c | 1215 |
1 files changed, 7 insertions, 1208 deletions
@@ -12,24 +12,19 @@ * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ -#define H5S_PACKAGE /*suppress error about including H5Spkg */ +#define H5D_PACKAGE /*suppress error about including H5Dpkg */ #include "H5private.h" /* Generic Functions */ -#include "H5Dprivate.h" /* Dataset functions */ +#include "H5Dpkg.h" /* Dataset functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5FDprivate.h" /* File drivers */ #include "H5FLprivate.h" /* Free Lists */ #include "H5FOprivate.h" /* File objects */ -#include "H5Gprivate.h" /* Group headers */ #include "H5HLprivate.h" /* Name heap */ #include "H5Iprivate.h" /* IDs */ -#include "H5MFprivate.h" /* File space management */ #include "H5MMprivate.h" /* Memory management */ -#include "H5Oprivate.h" /* Object headers */ -#include "H5Pprivate.h" /* Property lists */ -#include "H5Spkg.h" /* Dataspace functions */ +#include "H5Sprivate.h" /* Dataspace functions */ #include "H5Vprivate.h" /* Vector and array functions */ -#include "H5Zprivate.h" /* Data filters */ /*#define H5D_DEBUG*/ @@ -42,45 +37,20 @@ #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 H5D_mask -/* Local typedefs */ - -/* Enumerated type for allocating dataset's storage */ -typedef enum { - H5D_ALLOC_CREATE, /* Dataset is being created */ - H5D_ALLOC_OPEN, /* Dataset is being opened */ - H5D_ALLOC_EXTEND, /* Dataset's dataspace is being extended */ - H5D_ALLOC_WRITE /* Dataset is being extended */ -} H5D_time_alloc_t; - /* Interface initialization */ static int interface_initialize_g = 0; #define INTERFACE_INIT H5D_init_interface /* Local functions */ static herr_t H5D_init_interface(void); -static herr_t H5D_alloc_storage (H5F_t *f, hid_t dxpl_id, H5D_t *dset,H5D_time_alloc_t time_alloc, - hbool_t update_time, hbool_t full_overwrite); static herr_t H5D_init_storage(H5D_t *dataset, hbool_t full_overwrite, hid_t dxpl_id); static H5D_t * H5D_new(hid_t dcpl_id, hbool_t creating); static H5D_t * H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space, hid_t dcpl_id, hid_t dxpl_id); static H5D_t * H5D_open_oid(H5G_entry_t *ent, hid_t dxpl_id); -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_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_get_space_status(H5D_t *dset, H5D_space_status_t *allocation, hid_t dxpl_id); static hsize_t H5D_get_storage_size(H5D_t *dset, hid_t dxpl_id); static haddr_t H5D_get_offset(H5D_t *dset); @@ -91,12 +61,6 @@ static herr_t H5D_close(H5D_t *dataset); /* Declare a free list to manage the H5D_t struct */ H5FL_DEFINE_STATIC(H5D_t); -/* Declare a free list to manage blocks of type conversion data */ -H5FL_BLK_DEFINE(type_conv); - -/* 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 VL data */ H5FL_BLK_DEFINE_STATIC(vlen_vl_buf); @@ -1192,193 +1156,6 @@ done: /*------------------------------------------------------------------------- - * 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((*mem_space->select.is_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((*file_space->select.is_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 ((*mem_space->select.is_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 ((*file_space->select.is_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: H5Dextend * * Purpose: This function makes sure that the dataset is at least of size @@ -2434,837 +2211,6 @@ done: /*------------------------------------------------------------------------- - * Function: H5D_read - * - * Purpose: Reads (part of) a DATASET into application memory BUF. See - * H5Dread() for complete details. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Thursday, December 4, 1997 - * - * Modifications: - * Robb Matzke, 1998-06-09 - * The data space is no longer cached in the dataset struct. - * - * Robb Matzke, 1998-08-11 - * Added timing calls around all the data space I/O functions. - * - * rky, 1998-09-18 - * Added must_convert to do non-optimized read when necessary. - * - * Quincey Koziol, 1999-07-02 - * Changed xfer_parms parameter to xfer plist parameter, so it - * could be passed to H5T_convert. - * - * Albert Cheng, 2000-11-21 - * Added the code that when it detects it is not safe to process a - * COLLECTIVE read request without hanging, it changes it to - * INDEPENDENT calls. - * - * Albert Cheng, 2000-11-27 - * Changed to use the optimized MPIO transfer for Collective calls only. - * - * Raymond Lu, 2001-10-2 - * Changed the way to retrieve property for generic property list. - * - * Raymond Lu, 2002-2-26 - * For the new fill value design, data space can either be allocated - * or not allocated at this stage. Fill value or data from space is - * returned to outgoing buffer. - * - * QAK - 2002/04/02 - * Removed the must_convert parameter and move preconditions to - * H5S_<foo>_opt_possible() routine - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, - const H5S_t *file_space, hid_t dxpl_id, void *buf/*out*/) -{ - hsize_t nelmts; /*total number of elmts */ - hsize_t smine_start; /*strip mine start loc */ - hsize_t n, smine_nelmts; /*elements per strip */ - uint8_t *tconv_buf = NULL; /*data type conv buffer */ - uint8_t *bkg_buf = NULL; /*background buffer */ - 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*/ - 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 */ - herr_t ret_value = SUCCEED; /*return value */ - herr_t status; /*function return status*/ - 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 */ - H5T_bkg_t need_bkg; /*type of background buf*/ -#ifdef H5_HAVE_PARALLEL - H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; /*xfer_mode for this request */ - hbool_t xfer_mode_changed=0; /*xfer_mode needs restore */ - hbool_t doing_mpio=0; /*This is an MPIO access */ -#endif /*H5_HAVE_PARALLEL*/ -#ifdef H5S_DEBUG - H5_timer_t timer; -#endif - 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 */ - - FUNC_ENTER_NOAPI(H5D_read, FAIL); - - /* 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; - nelmts = (*mem_space->select.get_npoints)(mem_space); - -#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!=(*file_space->select.get_npoints) (file_space)) - HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); - - /* Retrieve dataset properties */ - /* <none needed in the general case> */ - - /* If space hasn't been allocated and not using external storage, - * return fill value to buffer if fill time is upon allocation, or - * do nothing if fill time is never. If the dataset is compact and - * fill time is NEVER, there is no way to tell whether part of data - * has been overwritten. So just proceed in reading. - */ - if(nelmts > 0 && dataset->efl.nused==0 && dataset->layout.type!=H5D_COMPACT - && dataset->layout.addr==HADDR_UNDEF) { - H5O_fill_t fill; /* Fill value info */ - H5D_fill_time_t fill_time; /* When to write the fill values */ - H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ - - /* Retrieve dataset's fill-value properties */ - if(H5P_fill_value_defined(dc_plist, &fill_status)<0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined"); - if((fill_status==H5D_FILL_VALUE_DEFAULT || fill_status==H5D_FILL_VALUE_USER_DEFINED) - && H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill value"); - if(H5P_get(dc_plist, H5D_CRT_FILL_TIME_NAME, &fill_time) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,"can't retrieve fill time"); - - /* Should be impossible, but check anyway... */ - if(fill_status == H5D_FILL_VALUE_UNDEFINED && fill_time == H5D_FILL_TIME_ALLOC) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "read failed: dataset doesn't exist, no data can be read"); - - /* If we're never going to fill this dataset, just leave the junk in the user's buffer */ - if(fill_time == H5D_FILL_TIME_NEVER) - HGOTO_DONE(SUCCEED); - - /* Go fill the user's selection with the dataset's fill value */ - if(H5D_fill(fill.buf,fill.type,buf,mem_type,mem_space, dxpl_id)<0) { - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "filling buf failed"); - } else - HGOTO_DONE(SUCCEED); - } /* end if */ - - /* - * Locate the type conversion function and data space conversion - * functions, and set up the element numbering information. If a data - * type conversion is necessary then register data type atoms. Data type - * conversion is necessary if the user has set the `need_bkg' to a high - * enough value in xfer_parms since turning off data type conversion also - * turns off background preservation. - */ - if (NULL==(tpath=H5T_path_find(dataset->type, mem_type, NULL, NULL, dxpl_id))) { - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); - } else if (!H5T_IS_NOOP(tpath)) { - if ((src_id=H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0 || - (dst_id=H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); - } /* end if */ - - /* Set the storage flags for the space conversion check */ - switch(dataset->layout.type) { - case H5D_COMPACT: - sconv_flags |= H5S_CONV_STORAGE_COMPACT; - break; - - case H5D_CONTIGUOUS: - sconv_flags |= H5S_CONV_STORAGE_CONTIGUOUS; - break; - - case H5D_CHUNKED: - sconv_flags |= H5S_CONV_STORAGE_CHUNKED; - break; - - default: - assert(0 && "Unhandled layout type!"); - } /* end switch */ - - /* Get dataspace functions */ - if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags))) - HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from file to memory data space"); - - /* - * If there is no type conversion then read directly into the - * application's buffer. This saves at least one mem-to-mem copy. - */ - if (H5T_IS_NOOP(tpath)) { -#ifdef H5S_DEBUG - H5_timer_begin(&timer); -#endif - /* Sanity check dataset, then read it */ - assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); - status = (sconv->read)(dataset->ent.file, &(dataset->layout), - dc_plist, &(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 */ - -#ifdef H5_HAVE_PARALLEL - /* The following may not handle a collective call correctly - * since it does not ensure all processes can handle the read - * request according to the MPI collective specification. - * Do the collective request via independent mode. - */ - if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE) { - /* Kludge: change the xfer_mode to independent, handle the request, - * then xfer_mode before return. - * Better way is to get a temporary data_xfer property with - * INDEPENDENT xfer_mode and pass it downwards. - */ - xfer_mode = H5FD_MPIO_INDEPENDENT; - if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); - xfer_mode_changed++; /* restore it before return */ -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - fprintf(H5DEBUG(D), - "H5D: Cannot handle this COLLECTIVE read request. Do it via INDEPENDENT calls\n"); -#endif - } /* end if */ -#endif /*H5_HAVE_PARALLEL*/ - /* - * This is the general case. - */ - - /* 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 ((*file_space->select.iter_init)(file_space, src_type_size, &file_iter)<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 ((*mem_space->select.iter_init)(mem_space, dst_type_size, &mem_iter)<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 ((*mem_space->select.iter_init)(mem_space, dst_type_size, &bkg_iter)<0) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); - bkg_iter_init=1; /*file selection iteration info has been initialized */ - - /* Sanity check elements in temporary buffer */ - if (request_nelmts<=0) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small"); - - /* - * Get a temporary buffer for type conversion unless the app has already - * supplied one through the xfer properties. Instead of allocating a - * buffer which is the exact size, we allocate the target size. The - * malloc() is usually less resource-intensive if we allocate/free the - * same size over and over. - */ - if (tpath->cdata.need_bkg) { - /* Retrieve the bkgr buffer property */ - if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) - HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); - need_bkg = MAX(tpath->cdata.need_bkg, need_bkg); - } else { - need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ - } /* end else */ - if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { - /* Allocate temporary buffer */ - if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); - } /* end if */ - if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { - /* Allocate background buffer */ - H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); - if((bkg_buf=H5FL_BLK_MALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); - } /* end if */ - - /* Start strip mining... */ - for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) { - /* Go figure out how many elements to read from the file */ - assert((*file_space->select.iter_nelmts)(&file_iter)==(nelmts-smine_start)); - smine_nelmts = MIN(request_nelmts, (nelmts-smine_start)); - - /* - * Gather the data from disk into the data type conversion - * buffer. Also gather data from application to background buffer - * if necessary. - */ -#ifdef H5S_DEBUG - H5_timer_begin(&timer); -#endif - /* Sanity check that space is allocated, then read data from it */ - assert(dataset->layout.addr!=HADDR_UNDEF || dataset->efl.nused>0 || dataset->layout.type==H5D_COMPACT); - n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), - dc_plist, &(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) - (*file_space->select.iter_release)(&file_iter); - if(mem_iter_init) - (*mem_space->select.iter_release)(&mem_iter); - if(bkg_iter_init) - (*mem_space->select.iter_release)(&bkg_iter); - - if (src_id >= 0) - H5I_dec_ref(src_id); - if (dst_id >= 0) - H5I_dec_ref(dst_id); - 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_read() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_write - * - * Purpose: Writes (part of) a DATASET to a file from application memory - * BUF. See H5Dwrite() for complete details. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Thursday, December 4, 1997 - * - * Modifications: - * Robb Matzke, 9 Jun 1998 - * The data space is no longer cached in the dataset struct. - * - * rky 980918 - * Added must_convert to do non-optimized read when necessary. - * - * Quincey Koziol, 2 July 1999 - * Changed xfer_parms parameter to xfer plist parameter, so it could - * be passed to H5T_convert - * - * Albert Cheng, 2000-11-21 - * Added the code that when it detects it is not safe to process a - * COLLECTIVE write request without hanging, it changes it to - * INDEPENDENT calls. - * - * Albert Cheng, 2000-11-27 - * Changed to use the optimized MPIO transfer for Collective calls only. - * - * Raymond Lu, 2001-10-2 - * Changed the way to retrieve property for generic property list. - * - * Raymond Lu, 2002-2-26 - * For the new fill value design, space may not be allocated until - * this function is called. Allocate and initialize space if it - * hasn't been. - * - * QAK - 2002/04/02 - * Removed the must_convert parameter and move preconditions to - * H5S_<foo>_opt_possible() routine - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space, - const H5S_t *file_space, hid_t dxpl_id, const void *buf) -{ - hsize_t nelmts; /*total number of elmts */ - hsize_t smine_start; /*strip mine start loc */ - hsize_t n, smine_nelmts; /*elements per strip */ - uint8_t *tconv_buf = NULL; /*data type conv buffer */ - uint8_t *bkg_buf = NULL; /*background buffer */ - 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*/ - 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 */ - herr_t ret_value = SUCCEED; /*return value */ - herr_t status; /*function return status*/ - 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 */ - H5T_bkg_t need_bkg; /*type of background buf*/ -#ifdef H5_HAVE_PARALLEL - H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; /*xfer_mode for this request */ - hbool_t xfer_mode_changed=0; /*xfer_mode needs restore */ - hbool_t doing_mpio=0; /*This is an MPIO access */ -#endif /*H5_HAVE_PARALLEL*/ -#ifdef H5S_DEBUG - H5_timer_t timer; -#endif - 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 */ - - FUNC_ENTER_NOAPI(H5D_write, FAIL); - - /* check args */ - assert(dataset && dataset->ent.file); - assert(mem_type); - assert(H5I_GENPROP_LST==H5I_get_type(dxpl_id)); - 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; - nelmts = (*mem_space->select.get_npoints)(mem_space); - - /* 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"); - - if (0==(H5F_get_intent(dataset->ent.file) & H5F_ACC_RDWR)) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file"); - -#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(file_space->select.type != 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!=(*file_space->select.get_npoints) (file_space)) - HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest data spaces have different sizes"); - - /* Retrieve dataset properties */ - /* <none needed currently> */ - - /* Allocate data space and initialize it if it hasn't been. */ - if(nelmts > 0 && dataset->layout.type!=H5D_COMPACT && - dataset->layout.addr==HADDR_UNDEF) { - hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */ - - /* Get the number of elements in file dataset's dataspace */ - if((file_nelmts=H5S_get_simple_extent_npoints(file_space))<0) - HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset"); - - /* Allocate storage */ - if(H5D_alloc_storage(dataset->ent.file,dxpl_id,dataset,H5D_ALLOC_WRITE, TRUE, (hbool_t)((hsize_t)file_nelmts==nelmts ? TRUE : FALSE))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage"); - } /* end if */ - - /* - * Locate the type conversion function and data space conversion - * functions, and set up the element numbering information. If a data - * type conversion is necessary then register data type atoms. Data type - * conversion is necessary if the user has set the `need_bkg' to a high - * enough value in xfer_parms since turning off data type conversion also - * turns off background preservation. - */ - if (NULL==(tpath=H5T_path_find(mem_type, dataset->type, NULL, NULL, dxpl_id))) { - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); - } else if (!H5T_IS_NOOP(tpath)) { - if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(mem_type, H5T_COPY_ALL)))<0 || - (dst_id = H5I_register(H5I_DATATYPE, H5T_copy(dataset->type, H5T_COPY_ALL)))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); - } /* end if */ - - /* Set the storage flags for the space conversion check */ - switch(dataset->layout.type) { - case H5D_COMPACT: - sconv_flags |= H5S_CONV_STORAGE_COMPACT; - break; - - case H5D_CONTIGUOUS: - sconv_flags |= H5S_CONV_STORAGE_CONTIGUOUS; - break; - - case H5D_CHUNKED: - sconv_flags |= H5S_CONV_STORAGE_CHUNKED; - break; - - default: - assert(0 && "Unhandled layout type!"); - } /* end switch */ - - /* Get dataspace functions */ - if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags))) - HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from memory to file data space"); - - /* - * If there is no type conversion then write directly from the - * application's buffer. This saves at least one mem-to-mem copy. - */ - if (H5T_IS_NOOP(tpath)) { -#ifdef H5S_DEBUG - H5_timer_begin(&timer); -#endif - status = (sconv->write)(dataset->ent.file, &(dataset->layout), - dc_plist, &(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 */ - -#ifdef H5_HAVE_PARALLEL - /* The following may not handle a collective call correctly - * since it does not ensure all processes can handle the write - * request according to the MPI collective specification. - * Do the collective request via independent mode. - */ - if (doing_mpio && xfer_mode==H5FD_MPIO_COLLECTIVE) { - /* Kludge: change the xfer_mode to independent, handle the request, - * then xfer_mode before return. - * Better way is to get a temporary data_xfer property with - * INDEPENDENT xfer_mode and pass it downwards. - */ - xfer_mode = H5FD_MPIO_INDEPENDENT; - if(H5P_set (dx_plist, H5D_XFER_IO_XFER_MODE_NAME, &xfer_mode) < 0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set transfer mode"); - xfer_mode_changed++; /* restore it before return */ -#ifdef H5D_DEBUG - if (H5DEBUG(D)) - fprintf(H5DEBUG(D), "H5D: Cannot handle this COLLECTIVE write request. Do it via INDEPENDENT calls\n"); -#endif - } /* end if */ -#endif /*H5_HAVE_PARALLEL*/ - /* - * This is the general case. - */ - - /* 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 ((*file_space->select.iter_init)(file_space, dst_type_size, &file_iter)<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 ((*mem_space->select.iter_init)(mem_space, src_type_size, &mem_iter)<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 ((*file_space->select.iter_init)(file_space, dst_type_size, &bkg_iter)<0) - HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize background selection information"); - bkg_iter_init=1; /*file selection iteration info has been initialized */ - - /* - * Get a temporary buffer for type conversion unless the app has already - * supplied one through the xfer properties. Instead of allocating a - * buffer which is the exact size, we allocate the target size. The - * malloc() is usually less resource-intensive if we allocate/free the - * same size over and over. - */ - if (tpath->cdata.need_bkg) { - /* Retrieve the bkgr buffer property */ - if(H5P_get(dx_plist, H5D_XFER_BKGR_BUF_TYPE_NAME, &need_bkg)<0) - HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve background buffer type"); - need_bkg = MAX (tpath->cdata.need_bkg, need_bkg); - } else if(H5T_detect_class(dataset->type, H5T_VLEN)) { - /* Old data is retrieved into background buffer for VL datatype. The - * data is used later for freeing heap objects. */ - need_bkg = H5T_BKG_YES; - } else { - need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ - } /* end else */ - if (NULL==(tconv_buf=H5P_peek_voidp(dx_plist,H5D_XFER_TCONV_BUF_NAME))) { - /* Allocate temporary buffer */ - if((tconv_buf=H5FL_BLK_MALLOC(type_conv,target_size))==NULL) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion"); - } /* end if */ - if (need_bkg && NULL==(bkg_buf=H5P_peek_voidp(dx_plist,H5D_XFER_BKGR_BUF_NAME))) { - /* Allocate background buffer */ - H5_CHECK_OVERFLOW((request_nelmts*dst_type_size),hsize_t,size_t); - if((bkg_buf=H5FL_BLK_CALLOC(type_conv,(size_t)(request_nelmts*dst_type_size)))==NULL) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion"); - } /* end if */ - - /* Start strip mining... */ - for (smine_start=0; smine_start<nelmts; smine_start+=smine_nelmts) { - /* Go figure out how many elements to read from the file */ - assert((*file_space->select.iter_nelmts)(&file_iter)==(nelmts-smine_start)); - smine_nelmts = MIN(request_nelmts, (nelmts-smine_start)); - - /* - * Gather data from application buffer into the data type conversion - * buffer. Also gather data from the file into the background buffer - * if necessary. - */ -#ifdef H5S_DEBUG - H5_timer_begin(&timer); -#endif - n = H5S_select_mgath(buf, src_type_size, mem_space, &mem_iter, - smine_nelmts, dxpl_id, tconv_buf/*out*/); -#ifdef H5S_DEBUG - H5_timer_end(&(sconv->stats[0].gath_timer), &timer); - sconv->stats[0].gath_nbytes += n * src_type_size; - sconv->stats[0].gath_ncalls++; -#endif - if (n!=smine_nelmts) - HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed"); - - if (need_bkg) { -#ifdef H5S_DEBUG - H5_timer_begin(&timer); -#endif - n = H5S_select_fgath(dataset->ent.file, &(dataset->layout), - dc_plist, &(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, &(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 */ - - /* - * 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: -#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) - (*file_space->select.iter_release)(&file_iter); - if(mem_iter_init) - (*mem_space->select.iter_release)(&mem_iter); - if(bkg_iter_init) - (*file_space->select.iter_release)(&bkg_iter); - - if (src_id >= 0) - H5I_dec_ref(src_id); - if (dst_id >= 0) - H5I_dec_ref(dst_id); - 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_write() */ - - -/*------------------------------------------------------------------------- * Function: H5D_extend * * Purpose: Increases the size of a dataset. @@ -3426,14 +2372,12 @@ H5D_get_file (const H5D_t *dset) * *------------------------------------------------------------------------- */ -static herr_t +herr_t H5D_alloc_storage (H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_alloc_t time_alloc, hbool_t update_time, hbool_t full_overwrite) { struct H5O_layout_t *layout; /* The dataset's layout information */ - hsize_t nbytes; /* The number of bytes in the dataset */ unsigned space_allocated=0; /* Flag to indicate that space was allocated */ - unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_alloc_storage); @@ -3454,11 +2398,8 @@ H5D_alloc_storage (H5F_t *f, hid_t dxpl_id, H5D_t *dset/*in,out*/, H5D_time_allo case H5D_CONTIGUOUS: if(layout->addr==HADDR_UNDEF) { /* Reserve space in the file for the entire array */ - for (u=0, nbytes=1; u<layout->ndims; u++) - nbytes *= layout->dim[u]; - assert (nbytes>0); - if (HADDR_UNDEF==(layout->addr=H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, nbytes))) - HGOTO_ERROR (H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space"); + if (H5F_contig_create (f, dxpl_id, layout/*out*/)<0) + HGOTO_ERROR (H5E_IO, H5E_CANTINIT, FAIL, "unable to initialize contiguous storage"); /* Indicate that we allocated space */ space_allocated=1; @@ -3587,7 +2528,7 @@ H5D_init_storage(H5D_t *dset, hbool_t full_overwrite, hid_t dxpl_id) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); if (H5F_contig_fill(dset->ent.file, dxpl_id, &(dset->layout), - plist, &(dset->efl), space, &dset->fill, H5T_get_size(dset->type))<0) + plist, space, &dset->fill, H5T_get_size(dset->type))<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset"); } /* end if */ break; @@ -4148,148 +3089,6 @@ done: } /* end H5Dvlen_get_buf_size() */ -/*-------------------------------------------------------------------------- - NAME - H5D_fill - PURPOSE - Fill a selection in memory with a value (internal version) - USAGE - herr_t H5Dfill(fill, fill_type, buf, buf_type, space) - const void *fill; IN: Pointer to fill value to use - H5T_t *fill_type; IN: Datatype of the fill value - void *buf; IN/OUT: Memory buffer to fill selection within - H5T_t *buf_type; IN: Datatype of the elements in buffer - H5S_t *space; IN: Dataspace describing memory buffer & - containing selection to use. - RETURNS - Non-negative on success/Negative on failure. - DESCRIPTION - Use the selection in the dataspace to fill elements in a memory buffer. - GLOBAL VARIABLES - COMMENTS, BUGS, ASSUMPTIONS - If "fill" parameter is NULL, use all zeros as fill value. If "fill_type" - parameter is NULL, use "buf_type" for the fill value datatype. - EXAMPLES - REVISION LOG ---------------------------------------------------------------------------*/ -static herr_t -H5D_fill(const void *fill, const H5T_t *fill_type, void *buf, const H5T_t *buf_type, const H5S_t *space, hid_t dxpl_id) -{ - H5T_path_t *tpath = NULL; /* Conversion information*/ - uint8_t *tconv_buf = NULL; /* Data type conv buffer */ - uint8_t *bkg_buf = NULL; /* Temp conversion buffer */ - hid_t src_id = -1, dst_id = -1; /* Temporary type IDs */ - size_t src_type_size; /* Size of source type */ - size_t dst_type_size; /* Size of destination type*/ - size_t buf_size; /* Desired buffer size */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOINIT(H5D_fill); - - /* Check args */ - assert(buf); - assert(buf_type); - assert(space); - - /* Check for "default" fill value */ - if(fill_type==NULL) - fill_type=buf_type; - - /* Get the memory and file datatype sizes */ - src_type_size = H5T_get_size(fill_type); - dst_type_size = H5T_get_size(buf_type); - - /* Get the maximum buffer size needed and allocate it */ - buf_size=MAX(src_type_size,dst_type_size); - if (NULL==(tconv_buf = H5FL_BLK_MALLOC(type_elem,buf_size)) || NULL==(bkg_buf = H5FL_BLK_CALLOC(type_elem,buf_size))) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed"); - - /* Copy the user's data into the buffer for conversion */ - if(fill==NULL) - HDmemset(tconv_buf,0,src_type_size); - else - HDmemcpy(tconv_buf,fill,src_type_size); - - /* Convert memory buffer into disk buffer */ - /* Set up type conversion function */ - if (NULL == (tpath = H5T_path_find(fill_type, buf_type, NULL, NULL, dxpl_id))) { - HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest data types"); - } else if (!H5T_IS_NOOP(tpath)) { - if ((src_id = H5I_register(H5I_DATATYPE, H5T_copy(fill_type, H5T_COPY_ALL)))<0 || - (dst_id = H5I_register(H5I_DATATYPE, H5T_copy(buf_type, H5T_COPY_ALL)))<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register types for conversion"); - } - - /* Perform data type conversion */ - if (H5T_convert(tpath, src_id, dst_id, (hsize_t)1, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed"); - - /* Fill the selection in the memory buffer */ - if(H5S_select_fill(tconv_buf, dst_type_size, space, buf)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed"); - -done: - if (tconv_buf) - H5FL_BLK_FREE(type_elem,tconv_buf); - if (bkg_buf) - H5FL_BLK_FREE(type_elem,bkg_buf); - FUNC_LEAVE_NOAPI(ret_value); -} /* H5D_fill() */ - - -/*-------------------------------------------------------------------------- - 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() */ - - /*------------------------------------------------------------------------- * Function: H5Dset_extent * |