/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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 * 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; udim, 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; undims; 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; z0) { 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; udim, 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; undims; 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; z0) { 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); }