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Diffstat (limited to 'src/H5Farray.c')
| -rw-r--r-- | src/H5Farray.c | 511 |
1 files changed, 0 insertions, 511 deletions
diff --git a/src/H5Farray.c b/src/H5Farray.c deleted file mode 100644 index 1965a59..0000000 --- a/src/H5Farray.c +++ /dev/null @@ -1,511 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * 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. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/* - * Programmer: Robb Matzke <matzke@llnl.gov> - * Thursday, January 15, 1998 - * - * Purpose: Provides I/O facilities for multi-dimensional arrays of bytes - * stored with various layout policies. If the caller is - * interested in arrays of elements >1 byte then add an extra - * dimension. For example, a 10x20 array of int would - * translate to a 10x20x4 array of bytes at this level. - */ - -#define H5F_PACKAGE /*suppress error about including H5Fpkg */ - -#include "H5private.h" -#include "H5Dprivate.h" -#include "H5Eprivate.h" -#include "H5Fpkg.h" -#include "H5FDprivate.h" /*file driver */ -#include "H5Iprivate.h" -#include "H5MMprivate.h" /*memory management */ -#include "H5Oprivate.h" -#include "H5Pprivate.h" -#include "H5Vprivate.h" - -/* MPIO driver functions are needed for some special checks */ -#include "H5FDmpio.h" - -/* Interface initialization */ -#define PABLO_MASK H5Farray_mask -#define INTERFACE_INIT NULL -static int interface_initialize_g = 0; - - - -/*------------------------------------------------------------------------- - * Function: H5F_arr_read - * - * Purpose: Reads a hyperslab of a file byte array into a hyperslab of - * a byte array in memory. The data is read from file F and the - * array's size and storage information is in LAYOUT. External - * files are described according to the external file list, EFL. - * The hyperslab offset is FILE_OFFSET[] in the file and - * MEM_OFFSET[] in memory (offsets are relative to the origin of - * the array) and the size of the hyperslab is HSLAB_SIZE[]. The - * total size of the file array is implied in the LAYOUT - * argument and the total size of the memory array is - * MEM_SIZE[]. The dimensionality of these vectors is implied by - * the LAYOUT argument. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Friday, January 16, 1998 - * - * Modifications: - * Albert Cheng, 1998-06-02 - * Added xfer_mode argument - * - * Robb Matzke, 1998-09-28 - * Added the `xfer' argument and removed the `xfer_mode' - * argument since it's a field of `xfer'. - * - * Robb Matzke, 1999-08-02 - * Data transfer properties are passed by ID since that's how - * the virtual file layer wants them. - *------------------------------------------------------------------------- - */ -herr_t -H5F_arr_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, - H5P_genplist_t *dc_plist, const hsize_t _hslab_size[], - const hsize_t mem_size[], const hssize_t mem_offset[], - const hssize_t file_offset[], void *_buf/*out*/) -{ - uint8_t *buf = (uint8_t*)_buf; /*cast for arithmetic */ - hssize_t file_stride[H5O_LAYOUT_NDIMS]; /*strides through file */ - hssize_t mem_stride[H5O_LAYOUT_NDIMS]; /*strides through memory*/ - hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /*hyperslab size */ - hsize_t idx[H5O_LAYOUT_NDIMS]; /*multi-dim counter */ - size_t mem_start; /*byte offset to start */ - hsize_t file_start; /*byte offset to start */ - hsize_t max_data = 0; /*bytes in dataset */ - hsize_t elmt_size = 1; /*bytes per element */ - hsize_t nelmts, z; /*number of elements */ - unsigned ndims; /*stride dimensionality */ - haddr_t addr; /*address in file */ - int j; /*counters */ - unsigned u; /*counters */ - hbool_t carray; /*carry for subtraction */ - struct H5O_efl_t efl; /* External File List info */ -#ifdef H5_HAVE_PARALLEL - H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; -#endif /* H5_HAVE_PARALLEL */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(H5F_arr_read, FAIL); - - /* Check args */ - assert(f); - assert(layout); - assert(_hslab_size); - assert(file_offset); - assert(mem_offset); - assert(mem_size); - assert(buf); - /* Make certain we have the correct type of property list */ - assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); - - /* Make a local copy of size so we can modify it */ - H5V_vector_cpy(layout->ndims, hslab_size, _hslab_size); - -#ifdef H5_HAVE_PARALLEL - /* Get the transfer mode for MPIO transfers */ - if(IS_H5FD_MPIO(f)) { - hid_t driver_id; /* VFL driver ID */ - H5P_genplist_t *plist; /* Property list */ - - /* Get the plist structure */ - if(NULL == (plist = H5I_object(dxpl_id))) - HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID"); - - /* Get the driver ID */ - if(H5P_get(plist, H5D_XFER_VFL_ID_NAME, &driver_id)<0) - HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver ID"); - - /* Check if we are using the MPIO driver (for the DXPL) */ - if(H5FD_MPIO==driver_id) { - /* Get the transfer mode */ - xfer_mode=H5P_peek_unsigned(plist, H5D_XFER_IO_XFER_MODE_NAME); - } /* end if */ - } /* end if */ - - /* Collective MPIO access is unsupported for non-contiguous datasets */ - if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) - HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "collective access on non-contiguous datasets not supported yet"); -#endif /* H5_HAVE_PARALLEL */ - - /* Get necessary properties from property list */ - if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get EFL value"); - - switch (layout->type) { - case H5D_CONTIGUOUS: - ndims = layout->ndims; - /* - * Offsets must not be negative for this type of storage. - */ - for (u=0; u<ndims; u++) { - if (mem_offset[u]<0 || file_offset[u]<0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "negative offsets are not valid"); - } - - /* - * Calculate the strides needed to walk through the array on disk - * and memory. Optimize the strides to result in the fewest number of - * I/O requests. - */ - H5_ASSIGN_OVERFLOW(mem_start,H5V_hyper_stride(ndims, hslab_size, mem_size, mem_offset, mem_stride/*out*/),hsize_t,size_t); - file_start = H5V_hyper_stride(ndims, hslab_size, layout->dim, - file_offset, file_stride/*out*/); - H5V_stride_optimize2(&ndims, &elmt_size, hslab_size, - mem_stride, file_stride); - - /* - * Initialize loop variables. The loop is a multi-dimensional loop - * that counts from SIZE down to zero and IDX is the counter. Each - * element of IDX is treated as a digit with IDX[0] being the least - * significant digit. - */ - H5V_vector_cpy(ndims, idx, hslab_size); - nelmts = H5V_vector_reduce_product(ndims, hslab_size); - if (efl.nused>0) { - addr = 0; - } else { - addr = layout->addr; - - /* Compute the size of the dataset in bytes */ - for(u=0, max_data=1; u<layout->ndims; u++) - max_data *= layout->dim[u]; - - /* Adjust the maximum size of the data by the offset into it */ - max_data -= file_start; - } - addr += file_start; - buf += mem_start; - - /* - * Now begin to walk through the array, copying data from disk to - * memory. - */ -#ifdef H5_HAVE_PARALLEL - if (H5FD_MPIO_COLLECTIVE==xfer_mode) { - /* - * Currently supports same number of collective access. Need to - * be changed LATER to combine all reads into one collective MPIO - * call. - */ - unsigned long max, min, temp; - - H5_ASSIGN_OVERFLOW(temp,nelmts,hsize_t,unsigned long); - MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX, - H5FD_mpio_communicator(f->shared->lf)); - MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN, - H5FD_mpio_communicator(f->shared->lf)); -#ifdef AKC - printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max); -#endif - if (max != min) - HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "collective access with unequal number of blocks not supported yet"); - } -#endif /* H5_HAVE_PARALLEL */ - - for (z=0; z<nelmts; z++) { - /* Read directly from file if the dataset is in an external file */ - /* Note: We can't use data sieve buffers for datasets in external files - * because the 'addr' of all external files is set to 0 (above) and - * all datasets in external files would alias to the same set of - * file offsets, totally mixing up the data sieve buffer information. -QAK - */ - if (efl.nused>0) { - H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t); - if (H5O_efl_read(f, &efl, addr, (size_t)elmt_size, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "external data read failed"); - } else { - H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t); - if (H5F_contig_read(f, max_data, H5FD_MEM_DRAW, addr, (size_t)elmt_size, dxpl_id, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "block read failed"); - } /* end else */ - - /* Decrement indices and advance pointers */ - for (j=ndims-1, carray=TRUE; j>=0 && carray; --j) { - addr += file_stride[j]; - buf += mem_stride[j]; - - /* Adjust the maximum size of the data by the offset into it */ - max_data -= file_stride[j]; - - if (--idx[j]) - carray = FALSE; - else - idx[j] = hslab_size[j]; - } - } - break; - - case H5D_CHUNKED: - /* - * This method is unable to access external raw data files - */ - if (efl.nused>0) - HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "chunking and external files are mutually exclusive"); - - /* Go get the data from the chunks */ - if (H5F_istore_read(f, dxpl_id, layout, dc_plist, mem_size, - mem_offset, file_offset, hslab_size, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); - break; - - default: - assert("not implemented yet" && 0); - HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout"); - } - -done: - FUNC_LEAVE_NOAPI(ret_value); -} - - -/*------------------------------------------------------------------------- - * Function: H5F_arr_write - * - * Purpose: Copies a hyperslab of a memory array to a hyperslab of a - * file array. The data is written to file F and the file - * array's size and storage information is implied by LAYOUT. - * The data is stored in external files according to the - * external file list, EFL. The hyperslab offset is - * FILE_OFFSET[] in the file and MEM_OFFSET[] in memory (offsets - * are relative to the origin of the array) and the size of the - * hyperslab is HSLAB_SIZE[]. The total size of the file array - * is implied by the LAYOUT argument and the total size of the - * memory array is MEM_SIZE[]. The dimensionality of these - * vectors is implied by the LAYOUT argument. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Robb Matzke - * Friday, January 16, 1998 - * - * Modifications: - * Albert Cheng, 1998-06-02 - * Added xfer_mode argument - * - * Robb Matzke, 1998-09-28 - * Added `xfer' argument, removed `xfer_mode' argument since it - * is a member of H5D_xfer_t. - * - * Robb Matzke, 1999-08-02 - * Data transfer properties are passed by ID since that's how - * the virtual file layer wants them. - *------------------------------------------------------------------------- - */ -herr_t -H5F_arr_write(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout, - H5P_genplist_t *dc_plist, - const hsize_t _hslab_size[], const hsize_t mem_size[], - const hssize_t mem_offset[], const hssize_t file_offset[], - const void *_buf) -{ - const uint8_t *buf = (const uint8_t *)_buf; /*cast for arithmetic */ - hssize_t file_stride[H5O_LAYOUT_NDIMS]; /*strides through file */ - hssize_t mem_stride[H5O_LAYOUT_NDIMS]; /*strides through memory*/ - hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /*hyperslab size */ - hsize_t idx[H5O_LAYOUT_NDIMS]; /*multi-dim counter */ - hsize_t mem_start; /*byte offset to start */ - hsize_t file_start; /*byte offset to start */ - hsize_t max_data = 0; /*bytes in dataset */ - hsize_t elmt_size = 1; /*bytes per element */ - hsize_t nelmts, z; /*number of elements */ - unsigned ndims; /*dimensionality */ - haddr_t addr; /*address in file */ - int j; /*counters */ - unsigned u; /*counters */ - hbool_t carray; /*carry for subtraction */ - struct H5O_efl_t efl; /* External File List info */ -#ifdef H5_HAVE_PARALLEL - H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; -#endif /* H5_HAVE_PARALLEL */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(H5F_arr_write, FAIL); - - /* Check args */ - assert(f); - assert(layout); - assert(_hslab_size); - assert(file_offset); - assert(mem_offset); - assert(mem_size); - assert(buf); - /* Make certain we have the correct type of property list */ - assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); - - /* Make a local copy of _size so we can modify it */ - H5V_vector_cpy(layout->ndims, hslab_size, _hslab_size); - -#ifdef H5_HAVE_PARALLEL - /* Get the transfer mode for MPIO transfers */ - if(IS_H5FD_MPIO(f)) { - hid_t driver_id; /* VFL driver ID */ - H5P_genplist_t *plist; /* Property list */ - - /* Get the plist structure */ - if(NULL == (plist = H5I_object(dxpl_id))) - HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID"); - - /* Get the driver ID */ - if(H5P_get(plist, H5D_XFER_VFL_ID_NAME, &driver_id)<0) - HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver ID"); - - /* Check if we are using the MPIO driver (for the DXPL) */ - if(H5FD_MPIO==driver_id) { - /* Get the transfer mode */ - xfer_mode=H5P_peek_unsigned(plist, H5D_XFER_IO_XFER_MODE_NAME); - } /* end if */ - } /* end if */ - - if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) - HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "collective access on non-contiguous datasets not supported yet"); -#endif /* H5_HAVE_PARALLEL */ - - /* Get necessary properties from property list */ - if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get EFL value"); - - switch (layout->type) { - case H5D_CONTIGUOUS: - ndims = layout->ndims; - /* - * Offsets must not be negative for this type of storage. - */ - for (u=0; u<ndims; u++) { - if (mem_offset[u]<0 || file_offset[u]<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "negative offsets are not valid"); - } - - /* - * Calculate the strides needed to walk through the array on disk. - * Optimize the strides to result in the fewest number of I/O - * requests. - */ - mem_start = H5V_hyper_stride(ndims, hslab_size, mem_size, - mem_offset, mem_stride/*out*/); - file_start = H5V_hyper_stride(ndims, hslab_size, layout->dim, - file_offset, file_stride/*out*/); - H5V_stride_optimize2(&ndims, &elmt_size, hslab_size, - mem_stride, file_stride); - - /* - * Initialize loop variables. The loop is a multi-dimensional loop - * that counts from SIZE down to zero and IDX is the counter. Each - * element of IDX is treated as a digit with IDX[0] being the least - * significant digit. - */ - H5V_vector_cpy(ndims, idx, hslab_size); - nelmts = H5V_vector_reduce_product(ndims, hslab_size); - - if (efl.nused>0) { - addr = 0; - } else { - addr = layout->addr; - - /* Compute the size of the dataset in bytes */ - for(u=0, max_data=1; u<layout->ndims; u++) - max_data *= layout->dim[u]; - - /* Adjust the maximum size of the data by the offset into it */ - max_data -= file_start; - } - addr += file_start; - buf += mem_start; - - /* - * Now begin to walk through the array, copying data from memory to - * disk. - */ -#ifdef H5_HAVE_PARALLEL - if (H5FD_MPIO_COLLECTIVE==xfer_mode){ - /* - * Currently supports same number of collective access. Need to - * be changed LATER to combine all writes into one collective - * MPIO call. - */ - unsigned long max, min, temp; - - H5_ASSIGN_OVERFLOW(temp,nelmts,hsize_t,unsigned long); - MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX, - H5FD_mpio_communicator(f->shared->lf)); - MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN, - H5FD_mpio_communicator(f->shared->lf)); -#ifdef AKC - printf("nelmts=%lu, min=%lu, max=%lu\n", temp, min, max); -#endif - if (max != min) - HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "collective access with unequal number of blocks not supported yet"); - } -#endif /* H5_HAVE_PARALLEL */ - - for (z=0; z<nelmts; z++) { - - /* Write to file */ - if (efl.nused>0) { - H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t); - if (H5O_efl_write(f, &efl, addr, (size_t)elmt_size, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "external data write failed"); - } else { - H5_CHECK_OVERFLOW(elmt_size,hsize_t,size_t); - if (H5F_contig_write(f, max_data, H5FD_MEM_DRAW, addr, (size_t)elmt_size, dxpl_id, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed"); - } /* end else */ - - /* Decrement indices and advance pointers */ - for (j=ndims-1, carray=TRUE; j>=0 && carray; --j) { - addr += file_stride[j]; - buf += mem_stride[j]; - - /* Adjust the maximum size of the data by the offset into it */ - max_data -= file_stride[j]; - - if (--idx[j]) - carray = FALSE; - else - idx[j] = hslab_size[j]; - } - - } - break; - - case H5D_CHUNKED: - /* - * This method is unable to access external raw data files - */ - if (efl.nused>0) - HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "chunking and external files are mutually exclusive"); - - /* Write the read to the chunks */ - if (H5F_istore_write(f, dxpl_id, layout, dc_plist, mem_size, - mem_offset, file_offset, hslab_size, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); - break; - - default: - assert("not implemented yet" && 0); - HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout"); - } - -done: - FUNC_LEAVE_NOAPI(ret_value); -} |