/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * 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 COPYING file, which can be found at the root of the source code * * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * Programmer: Quincey Koziol * Thursday, September 28, 2000 * * Purpose: * Contiguous dataset I/O functions. These routines are similar to * the H5D_chunk_* routines and really only an abstract way of dealing * with the data sieve buffer from H5F_seq_read/write. */ /****************/ /* Module Setup */ /****************/ #include "H5Dmodule.h" /* This source code file is part of the H5D module */ /***********/ /* Headers */ /***********/ #include "H5private.h" /* Generic Functions */ #include "H5CXprivate.h" /* API Contexts */ #include "H5Dpkg.h" /* Dataset functions */ #include "H5Eprivate.h" /* Error handling */ #include "H5Fprivate.h" /* Files */ #include "H5FDprivate.h" /* File drivers */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ #include "H5MFprivate.h" /* File memory management */ #include "H5MMprivate.h" /* Memory management */ #include "H5FOprivate.h" /* File objects */ #include "H5Oprivate.h" /* Object headers */ #include "H5Pprivate.h" /* Property lists */ #include "H5PBprivate.h" /* Page Buffer */ #include "H5VMprivate.h" /* Vector and array functions */ /****************/ /* Local Macros */ /****************/ /******************/ /* Local Typedefs */ /******************/ /* Callback info for sieve buffer readvv operation */ typedef struct H5D_contig_readvv_sieve_ud_t { H5F_shared_t * f_sh; /* Shared file for dataset */ H5D_rdcdc_t * dset_contig; /* Cached information about contiguous data */ const H5D_contig_storage_t *store_contig; /* Contiguous storage info for this I/O operation */ unsigned char * rbuf; /* Pointer to buffer to fill */ } H5D_contig_readvv_sieve_ud_t; /* Callback info for [plain] readvv operation */ typedef struct H5D_contig_readvv_ud_t { H5F_shared_t * f_sh; /* Shared file for dataset */ haddr_t dset_addr; /* Address of dataset */ unsigned char *rbuf; /* Pointer to buffer to fill */ } H5D_contig_readvv_ud_t; /* Callback info for sieve buffer writevv operation */ typedef struct H5D_contig_writevv_sieve_ud_t { H5F_shared_t * f_sh; /* Shared file for dataset */ H5D_rdcdc_t * dset_contig; /* Cached information about contiguous data */ const H5D_contig_storage_t *store_contig; /* Contiguous storage info for this I/O operation */ const unsigned char * wbuf; /* Pointer to buffer to write */ } H5D_contig_writevv_sieve_ud_t; /* Callback info for [plain] writevv operation */ typedef struct H5D_contig_writevv_ud_t { H5F_shared_t * f_sh; /* Shared file for dataset */ haddr_t dset_addr; /* Address of dataset */ const unsigned char *wbuf; /* Pointer to buffer to write */ } H5D_contig_writevv_ud_t; /********************/ /* Local Prototypes */ /********************/ /* Layout operation callbacks */ static herr_t H5D__contig_construct(H5F_t *f, H5D_t *dset); static herr_t H5D__contig_init(H5F_t *f, const H5D_t *dset, hid_t dapl_id); static herr_t H5D__contig_io_init(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t *cm); static ssize_t H5D__contig_readvv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]); static ssize_t H5D__contig_writevv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]); static herr_t H5D__contig_flush(H5D_t *dset); /* Helper routines */ static herr_t H5D__contig_write_one(H5D_io_info_t *io_info, hsize_t offset, size_t size); static htri_t H5D__contig_may_use_select_io(const H5D_io_info_t *io_info, H5D_io_op_type_t op_type); /*********************/ /* Package Variables */ /*********************/ /* Contiguous storage layout I/O ops */ const H5D_layout_ops_t H5D_LOPS_CONTIG[1] = { {H5D__contig_construct, H5D__contig_init, H5D__contig_is_space_alloc, H5D__contig_is_data_cached, H5D__contig_io_init, H5D__contig_read, H5D__contig_write, #ifdef H5_HAVE_PARALLEL H5D__contig_collective_read, H5D__contig_collective_write, #endif /* H5_HAVE_PARALLEL */ H5D__contig_readvv, H5D__contig_writevv, H5D__contig_flush, NULL, NULL}}; /*******************/ /* Local Variables */ /*******************/ /* Declare a PQ free list to manage the sieve buffer information */ H5FL_BLK_DEFINE(sieve_buf); /* Declare extern the free list to manage blocks of type conversion data */ H5FL_BLK_EXTERN(type_conv); /*------------------------------------------------------------------------- * Function: H5D__contig_alloc * * Purpose: Allocate file space for a contiguously stored dataset * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * April 19, 2003 * *------------------------------------------------------------------------- */ herr_t H5D__contig_alloc(H5F_t *f, H5O_storage_contig_t *storage /*out */) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* check args */ HDassert(f); HDassert(storage); /* Allocate space for the contiguous data */ if (HADDR_UNDEF == (storage->addr = H5MF_alloc(f, H5FD_MEM_DRAW, storage->size))) HGOTO_ERROR(H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_alloc */ /*------------------------------------------------------------------------- * Function: H5D__contig_fill * * Purpose: Write fill values to a contiguously stored dataset. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * August 22, 2002 * *------------------------------------------------------------------------- */ herr_t H5D__contig_fill(const H5D_io_info_t *io_info) { const H5D_t * dset = io_info->dset; /* the dataset pointer */ H5D_io_info_t ioinfo; /* Dataset I/O info */ H5D_storage_t store; /* Union of storage info for dataset */ hssize_t snpoints; /* Number of points in space (for error checking) */ size_t npoints; /* Number of points in space */ hsize_t offset; /* Offset of dataset */ size_t max_temp_buf; /* Maximum size of temporary buffer */ #ifdef H5_HAVE_PARALLEL MPI_Comm mpi_comm = MPI_COMM_NULL; /* MPI communicator for file */ int mpi_rank = (-1); /* This process's rank */ int mpi_code; /* MPI return code */ hbool_t blocks_written = FALSE; /* Flag to indicate that chunk was actually written */ hbool_t using_mpi = FALSE; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */ #endif /* H5_HAVE_PARALLEL */ H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */ hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ HDassert(dset && H5D_CONTIGUOUS == dset->shared->layout.type); HDassert(H5F_addr_defined(dset->shared->layout.storage.u.contig.addr)); HDassert(dset->shared->layout.storage.u.contig.size > 0); HDassert(dset->shared->space); HDassert(dset->shared->type); #ifdef H5_HAVE_PARALLEL /* Retrieve MPI parameters */ if (H5F_HAS_FEATURE(dset->oloc.file, H5FD_FEAT_HAS_MPI)) { /* Get the MPI communicator */ if (MPI_COMM_NULL == (mpi_comm = H5F_mpi_get_comm(dset->oloc.file))) HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator") /* Get the MPI rank */ if ((mpi_rank = H5F_mpi_get_rank(dset->oloc.file)) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank") /* Set the MPI-capable file driver flag */ using_mpi = TRUE; } /* end if */ #endif /* H5_HAVE_PARALLEL */ /* Initialize storage info for this dataset */ store.contig.dset_addr = dset->shared->layout.storage.u.contig.addr; store.contig.dset_size = dset->shared->layout.storage.u.contig.size; /* Get the number of elements in the dataset's dataspace */ if ((snpoints = H5S_GET_EXTENT_NPOINTS(dset->shared->space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "dataset has negative number of elements") H5_CHECKED_ASSIGN(npoints, size_t, snpoints, hssize_t); /* Get the maximum size of temporary buffers */ if (H5CX_get_max_temp_buf(&max_temp_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve max. temp. buf size") /* Initialize the fill value buffer */ if (H5D__fill_init(&fb_info, NULL, NULL, NULL, NULL, NULL, &dset->shared->dcpl_cache.fill, dset->shared->type, dset->shared->type_id, npoints, max_temp_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info") fb_info_init = TRUE; /* Start at the beginning of the dataset */ offset = 0; /* Simple setup for dataset I/O info struct */ H5D_BUILD_IO_INFO_WRT(&ioinfo, dset, &store, fb_info.fill_buf); /* * Fill the entire current extent with the fill value. We can do * this quite efficiently by making sure we copy the fill value * in relatively large pieces. */ /* Loop through writing the fill value to the dataset */ while (npoints > 0) { size_t curr_points; /* Number of elements to write on this iteration of the loop */ size_t size; /* Size of buffer to write */ /* Compute # of elements and buffer size to write for this iteration */ curr_points = MIN(fb_info.elmts_per_buf, npoints); size = curr_points * fb_info.file_elmt_size; /* Check for VL datatype & non-default fill value */ if (fb_info.has_vlen_fill_type) /* Re-fill the buffer to use for this I/O operation */ if (H5D__fill_refill_vl(&fb_info, curr_points) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer") #ifdef H5_HAVE_PARALLEL /* Check if this file is accessed with an MPI-capable file driver */ if (using_mpi) { /* Write the chunks out from only one process */ /* !! Use the internal "independent" DXPL!! -QAK */ if (H5_PAR_META_WRITE == mpi_rank) if (H5D__contig_write_one(&ioinfo, offset, size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset") /* Indicate that blocks are being written */ blocks_written = TRUE; } /* end if */ else { #endif /* H5_HAVE_PARALLEL */ H5_CHECK_OVERFLOW(size, size_t, hsize_t); if (H5D__contig_write_one(&ioinfo, offset, size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset") #ifdef H5_HAVE_PARALLEL } /* end else */ #endif /* H5_HAVE_PARALLEL */ npoints -= curr_points; offset += size; } /* end while */ #ifdef H5_HAVE_PARALLEL /* Only need to block at the barrier if we actually wrote fill values */ /* And if we are using an MPI-capable file driver */ if (using_mpi && blocks_written) { /* Wait at barrier to avoid race conditions where some processes are * still writing out fill values and other processes race ahead to data * in, getting bogus data. */ if (MPI_SUCCESS != (mpi_code = MPI_Barrier(mpi_comm))) HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code) } /* end if */ #endif /* H5_HAVE_PARALLEL */ done: /* Release the fill buffer info, if it's been initialized */ if (fb_info_init && H5D__fill_term(&fb_info) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release fill buffer info") FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_fill() */ /*------------------------------------------------------------------------- * Function: H5D__contig_delete * * Purpose: Delete the file space for a contiguously stored dataset * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * March 20, 2003 * *------------------------------------------------------------------------- */ herr_t H5D__contig_delete(H5F_t *f, const H5O_storage_t *storage) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* check args */ HDassert(f); HDassert(storage); /* Free the file space for the chunk */ if (H5MF_xfree(f, H5FD_MEM_DRAW, storage->u.contig.addr, storage->u.contig.size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to free contiguous storage space") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_delete */ /*------------------------------------------------------------------------- * Function: H5D__contig_construct * * Purpose: Constructs new contiguous layout information for dataset * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, May 22, 2008 * *------------------------------------------------------------------------- */ static herr_t H5D__contig_construct(H5F_t *f, H5D_t *dset) { hssize_t snelmts; /* Temporary holder for number of elements in dataspace */ hsize_t nelmts; /* Number of elements in dataspace */ size_t dt_size; /* Size of datatype */ hsize_t tmp_size; /* Temporary holder for raw data size */ size_t tmp_sieve_buf_size; /* Temporary holder for sieve buffer size */ unsigned u; /* Local index variable */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity checks */ HDassert(f); HDassert(dset); /* * The maximum size of the dataset cannot exceed the storage size. * Also, only the slowest varying dimension of a simple dataspace * can be extendible (currently only for external data storage). */ /* Check for invalid dataset dimensions */ for (u = 0; u < dset->shared->ndims; u++) if (dset->shared->max_dims[u] > dset->shared->curr_dims[u]) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "extendible contiguous non-external dataset not allowed") /* Retrieve the number of elements in the dataspace */ if ((snelmts = H5S_GET_EXTENT_NPOINTS(dset->shared->space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve number of elements in dataspace") nelmts = (hsize_t)snelmts; /* Get the datatype's size */ if (0 == (dt_size = H5T_GET_SIZE(dset->shared->type))) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve size of datatype") /* Compute the size of the dataset's contiguous storage */ tmp_size = nelmts * dt_size; /* Check for overflow during multiplication */ if (nelmts != (tmp_size / dt_size)) HGOTO_ERROR(H5E_DATASET, H5E_OVERFLOW, FAIL, "size of dataset's storage overflowed") /* Assign the dataset's contiguous storage size */ dset->shared->layout.storage.u.contig.size = tmp_size; /* Get the sieve buffer size for the file */ tmp_sieve_buf_size = H5F_SIEVE_BUF_SIZE(f); /* Adjust the sieve buffer size to the smaller one between the dataset size and the buffer size * from the file access property. (SLU - 2012/3/30) */ if (tmp_size < tmp_sieve_buf_size) dset->shared->cache.contig.sieve_buf_size = tmp_size; else dset->shared->cache.contig.sieve_buf_size = tmp_sieve_buf_size; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_construct() */ /*------------------------------------------------------------------------- * Function: H5D__contig_init * * Purpose: Initialize the contiguous info for a dataset. This is * called when the dataset is initialized. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Friday, August 28, 2015 * *------------------------------------------------------------------------- */ static herr_t H5D__contig_init(H5F_t H5_ATTR_UNUSED *f, const H5D_t *dset, hid_t H5_ATTR_UNUSED dapl_id) { hsize_t tmp_size; /* Temporary holder for raw data size */ size_t tmp_sieve_buf_size; /* Temporary holder for sieve buffer size */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(f); HDassert(dset); /* Compute the size of the contiguous storage for versions of the * layout message less than version 3 because versions 1 & 2 would * truncate the dimension sizes to 32-bits of information. - QAK 5/26/04 */ if (dset->shared->layout.version < 3) { hssize_t snelmts; /* Temporary holder for number of elements in dataspace */ hsize_t nelmts; /* Number of elements in dataspace */ size_t dt_size; /* Size of datatype */ /* Retrieve the number of elements in the dataspace */ if ((snelmts = H5S_GET_EXTENT_NPOINTS(dset->shared->space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve number of elements in dataspace") nelmts = (hsize_t)snelmts; /* Get the datatype's size */ if (0 == (dt_size = H5T_GET_SIZE(dset->shared->type))) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve size of datatype") /* Compute the size of the dataset's contiguous storage */ tmp_size = nelmts * dt_size; /* Check for overflow during multiplication */ if (nelmts != (tmp_size / dt_size)) HGOTO_ERROR(H5E_DATASET, H5E_OVERFLOW, FAIL, "size of dataset's storage overflowed") /* Assign the dataset's contiguous storage size */ dset->shared->layout.storage.u.contig.size = tmp_size; } /* end if */ else tmp_size = dset->shared->layout.storage.u.contig.size; /* Get the sieve buffer size for the file */ tmp_sieve_buf_size = H5F_SIEVE_BUF_SIZE(dset->oloc.file); /* Adjust the sieve buffer size to the smaller one between the dataset size and the buffer size * from the file access property. (SLU - 2012/3/30) */ if (tmp_size < tmp_sieve_buf_size) dset->shared->cache.contig.sieve_buf_size = tmp_size; else dset->shared->cache.contig.sieve_buf_size = tmp_sieve_buf_size; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_init() */ /*------------------------------------------------------------------------- * Function: H5D__contig_is_space_alloc * * Purpose: Query if space is allocated for layout * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, January 15, 2009 * *------------------------------------------------------------------------- */ hbool_t H5D__contig_is_space_alloc(const H5O_storage_t *storage) { hbool_t ret_value = FALSE; /* Return value */ FUNC_ENTER_PACKAGE_NOERR /* Sanity checks */ HDassert(storage); /* Set return value */ ret_value = (hbool_t)H5F_addr_defined(storage->u.contig.addr); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_is_space_alloc() */ /*------------------------------------------------------------------------- * Function: H5D__contig_is_data_cached * * Purpose: Query if raw data is cached for dataset * * Return: Non-negative on success/Negative on failure * * Programmer: Neil Fortner * Wednessday, March 6, 2016 * *------------------------------------------------------------------------- */ hbool_t H5D__contig_is_data_cached(const H5D_shared_t *shared_dset) { FUNC_ENTER_PACKAGE_NOERR /* Sanity checks */ HDassert(shared_dset); FUNC_LEAVE_NOAPI(shared_dset->cache.contig.sieve_size > 0) } /* end H5D__contig_is_data_cached() */ /*------------------------------------------------------------------------- * Function: H5D__contig_io_init * * Purpose: Performs initialization before any sort of I/O on the raw data * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, March 20, 2008 * *------------------------------------------------------------------------- */ static herr_t H5D__contig_io_init(H5D_io_info_t *io_info, const H5D_type_info_t H5_ATTR_UNUSED *type_info, hsize_t H5_ATTR_UNUSED nelmts, const H5S_t H5_ATTR_UNUSED *file_space, const H5S_t H5_ATTR_UNUSED *mem_space, H5D_chunk_map_t H5_ATTR_UNUSED *cm) { htri_t use_selection_io = FALSE; /* Whether to use selection I/O */ htri_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC io_info->store->contig.dset_addr = io_info->dset->shared->layout.storage.u.contig.addr; io_info->store->contig.dset_size = io_info->dset->shared->layout.storage.u.contig.size; /* Check if we're performing selection I/O */ if ((use_selection_io = H5D__contig_may_use_select_io(io_info, H5D_IO_OP_READ)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if selection I/O is possible") io_info->use_select_io = (hbool_t)use_selection_io; done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_io_init() */ /*------------------------------------------------------------------------- * Function: H5D__contig_may_use_select_io * * Purpose: A small internal function to if it may be possible to use * selection I/O. * * Return: TRUE or FALSE * * Programmer: Neil Fortner * 3 August 2021 * *------------------------------------------------------------------------- */ static htri_t H5D__contig_may_use_select_io(const H5D_io_info_t *io_info, H5D_io_op_type_t op_type) { const H5D_t *dataset = io_info->dset; /* Local pointer to dataset info */ htri_t ret_value = FAIL; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(io_info); HDassert(dataset); HDassert(op_type == H5D_IO_OP_READ || op_type == H5D_IO_OP_WRITE); /* Don't use selection I/O if it's globally disabled, if there is a type * conversion, or if it's not a contiguous dataset, or if the sieve buffer * exists (write) or is dirty (read) */ if (!H5_use_selection_io_g || io_info->io_ops.single_read != H5D__select_read || io_info->layout_ops.readvv != H5D__contig_readvv || (op_type == H5D_IO_OP_READ && io_info->dset->shared->cache.contig.sieve_dirty) || (op_type == H5D_IO_OP_WRITE && io_info->dset->shared->cache.contig.sieve_buf)) ret_value = FALSE; else { htri_t page_buf_enabled; HDassert(io_info->io_ops.single_write == H5D__select_write); HDassert(io_info->layout_ops.writevv == H5D__contig_writevv); /* Check if the page buffer is enabled */ if ((page_buf_enabled = H5PB_enabled(io_info->f_sh, H5FD_MEM_DRAW)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if page buffer is enabled") if (page_buf_enabled) ret_value = FALSE; else ret_value = TRUE; } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_may_use_select_io() */ /*------------------------------------------------------------------------- * 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 * *------------------------------------------------------------------------- */ herr_t H5D__contig_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t H5_ATTR_UNUSED *fm) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity check */ HDassert(io_info); HDassert(io_info->u.rbuf); HDassert(type_info); HDassert(mem_space); HDassert(file_space); if (io_info->use_select_io) { size_t dst_type_size = type_info->dst_type_size; /* Issue selection I/O call (we can skip the page buffer because we've * already verified it won't be used, and the metadata accumulator * because this is raw data) */ if (H5F_shared_select_read(H5F_SHARED(io_info->dset->oloc.file), H5FD_MEM_DRAW, nelmts > 0 ? 1 : 0, &mem_space, &file_space, &(io_info->store->contig.dset_addr), &dst_type_size, &(io_info->u.rbuf)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "contiguous selection read failed") } /* end if */ else /* Read data through legacy (non-selection I/O) pathway */ if ((io_info->io_ops.single_read)(io_info, type_info, nelmts, file_space, mem_space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "contiguous read failed") done: 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 * *------------------------------------------------------------------------- */ herr_t H5D__contig_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, hsize_t nelmts, const H5S_t *file_space, const H5S_t *mem_space, H5D_chunk_map_t H5_ATTR_UNUSED *fm) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity check */ HDassert(io_info); HDassert(io_info->u.wbuf); HDassert(type_info); HDassert(mem_space); HDassert(file_space); if (io_info->use_select_io) { size_t dst_type_size = type_info->dst_type_size; /* Issue selection I/O call (we can skip the page buffer because we've * already verified it won't be used, and the metadata accumulator * because this is raw data) */ if (H5F_shared_select_write(H5F_SHARED(io_info->dset->oloc.file), H5FD_MEM_DRAW, nelmts > 0 ? 1 : 0, &mem_space, &file_space, &(io_info->store->contig.dset_addr), &dst_type_size, &(io_info->u.wbuf)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "contiguous selection write failed") } /* end if */ else /* Write data through legacy (non-selection I/O) pathway */ if ((io_info->io_ops.single_write)(io_info, type_info, nelmts, file_space, mem_space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "contiguous write failed") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_write() */ /*------------------------------------------------------------------------- * Function: H5D__contig_write_one * * Purpose: Writes some data from a dataset into a buffer. * The data is contiguous. The address is relative to the base * address for the file. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, September 28, 2000 * *------------------------------------------------------------------------- */ static herr_t H5D__contig_write_one(H5D_io_info_t *io_info, hsize_t offset, size_t size) { hsize_t dset_off = offset; /* Offset in dataset */ size_t dset_len = size; /* Length in dataset */ size_t dset_curr_seq = 0; /* "Current sequence" in dataset */ hsize_t mem_off = 0; /* Offset in memory */ size_t mem_len = size; /* Length in memory */ size_t mem_curr_seq = 0; /* "Current sequence" in memory */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC HDassert(io_info); if (H5D__contig_writevv(io_info, (size_t)1, &dset_curr_seq, &dset_len, &dset_off, (size_t)1, &mem_curr_seq, &mem_len, &mem_off) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vector write failed") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_write_one() */ /*------------------------------------------------------------------------- * Function: H5D__contig_readvv_sieve_cb * * Purpose: Callback operator for H5D__contig_readvv() with sieve buffer. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, Sept 30, 2010 * *------------------------------------------------------------------------- */ static herr_t H5D__contig_readvv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len, void *_udata) { H5D_contig_readvv_sieve_ud_t *udata = (H5D_contig_readvv_sieve_ud_t *)_udata; /* User data for H5VM_opvv() operator */ H5F_shared_t *f_sh = udata->f_sh; /* Shared file for dataset */ H5D_rdcdc_t * dset_contig = udata->dset_contig; /* Cached information about contiguous data */ const H5D_contig_storage_t *store_contig = udata->store_contig; /* Contiguous storage info for this I/O operation */ unsigned char *buf; /* Pointer to buffer to fill */ haddr_t addr; /* Actual address to read */ haddr_t sieve_start = HADDR_UNDEF, sieve_end = HADDR_UNDEF; /* Start & end locations of sieve buffer */ haddr_t contig_end; /* End locations of block to write */ size_t sieve_size = (size_t)-1; /* Size of sieve buffer */ haddr_t rel_eoa; /* Relative end of file address */ hsize_t max_data; /* Actual maximum size of data to cache */ hsize_t min; /* temporary minimum value (avoids some ugly macro nesting) */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Stash local copies of these value */ if (dset_contig->sieve_buf != NULL) { sieve_start = dset_contig->sieve_loc; sieve_size = dset_contig->sieve_size; sieve_end = sieve_start + sieve_size; } /* end if */ /* Compute offset on disk */ addr = store_contig->dset_addr + dst_off; /* Compute offset in memory */ buf = udata->rbuf + src_off; /* Check if the sieve buffer is allocated yet */ if (NULL == dset_contig->sieve_buf) { /* Check if we can actually hold the I/O request in the sieve buffer */ if (len > dset_contig->sieve_buf_size) { if (H5F_shared_block_read(f_sh, H5FD_MEM_DRAW, addr, len, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "block read failed") } /* end if */ else { /* Allocate room for the data sieve buffer */ if (NULL == (dset_contig->sieve_buf = H5FL_BLK_CALLOC(sieve_buf, dset_contig->sieve_buf_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "memory allocation failed") /* Determine the new sieve buffer size & location */ dset_contig->sieve_loc = addr; /* Make certain we don't read off the end of the file */ if (HADDR_UNDEF == (rel_eoa = H5F_shared_get_eoa(f_sh, H5FD_MEM_DRAW))) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to determine file size") /* Set up the buffer parameters */ max_data = store_contig->dset_size - dst_off; /* Compute the size of the sieve buffer */ min = MIN3(rel_eoa - dset_contig->sieve_loc, max_data, dset_contig->sieve_buf_size); H5_CHECKED_ASSIGN(dset_contig->sieve_size, size_t, min, hsize_t); /* Read the new sieve buffer */ if (H5F_shared_block_read(f_sh, H5FD_MEM_DRAW, dset_contig->sieve_loc, dset_contig->sieve_size, dset_contig->sieve_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "block read failed") /* Grab the data out of the buffer (must be first piece of data in buffer ) */ H5MM_memcpy(buf, dset_contig->sieve_buf, len); /* Reset sieve buffer dirty flag */ dset_contig->sieve_dirty = FALSE; } /* end else */ } /* end if */ else { /* Compute end of sequence to retrieve */ contig_end = addr + len - 1; /* If entire read is within the sieve buffer, read it from the buffer */ if (addr >= sieve_start && contig_end < sieve_end) { unsigned char *base_sieve_buf = dset_contig->sieve_buf + (addr - sieve_start); /* Grab the data out of the buffer */ H5MM_memcpy(buf, base_sieve_buf, len); } /* end if */ /* Entire request is not within this data sieve buffer */ else { /* Check if we can actually hold the I/O request in the sieve buffer */ if (len > dset_contig->sieve_buf_size) { /* Check for any overlap with the current sieve buffer */ if ((sieve_start >= addr && sieve_start < (contig_end + 1)) || ((sieve_end - 1) >= addr && (sieve_end - 1) < (contig_end + 1))) { /* Flush the sieve buffer, if it's dirty */ if (dset_contig->sieve_dirty) { /* Write to file */ if (H5F_shared_block_write(f_sh, H5FD_MEM_DRAW, sieve_start, sieve_size, dset_contig->sieve_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "block write failed") /* Reset sieve buffer dirty flag */ dset_contig->sieve_dirty = FALSE; } /* end if */ } /* end if */ /* Read directly into the user's buffer */ if (H5F_shared_block_read(f_sh, H5FD_MEM_DRAW, addr, len, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "block read failed") } /* end if */ /* Element size fits within the buffer size */ else { /* Flush the sieve buffer if it's dirty */ if (dset_contig->sieve_dirty) { /* Write to file */ if (H5F_shared_block_write(f_sh, H5FD_MEM_DRAW, sieve_start, sieve_size, dset_contig->sieve_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "block write failed") /* Reset sieve buffer dirty flag */ dset_contig->sieve_dirty = FALSE; } /* end if */ /* Determine the new sieve buffer size & location */ dset_contig->sieve_loc = addr; /* Make certain we don't read off the end of the file */ if (HADDR_UNDEF == (rel_eoa = H5F_shared_get_eoa(f_sh, H5FD_MEM_DRAW))) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to determine file size") /* Only need this when resizing sieve buffer */ max_data = store_contig->dset_size - dst_off; /* Compute the size of the sieve buffer. * Don't read off the end of the file, don't read past * the end of the data element, and don't read more than * the buffer size. */ min = MIN3(rel_eoa - dset_contig->sieve_loc, max_data, dset_contig->sieve_buf_size); H5_CHECKED_ASSIGN(dset_contig->sieve_size, size_t, min, hsize_t); /* Read the new sieve buffer */ if (H5F_shared_block_read(f_sh, H5FD_MEM_DRAW, dset_contig->sieve_loc, dset_contig->sieve_size, dset_contig->sieve_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "block read failed") /* Grab the data out of the buffer (must be first piece of data in buffer ) */ H5MM_memcpy(buf, dset_contig->sieve_buf, len); /* Reset sieve buffer dirty flag */ dset_contig->sieve_dirty = FALSE; } /* end else */ } /* end else */ } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_readvv_sieve_cb() */ /*------------------------------------------------------------------------- * Function: H5D__contig_readvv_cb * * Purpose: Callback operator for H5D__contig_readvv() without sieve buffer. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, Sept 30, 2010 * *------------------------------------------------------------------------- */ static herr_t H5D__contig_readvv_cb(hsize_t dst_off, hsize_t src_off, size_t len, void *_udata) { H5D_contig_readvv_ud_t *udata = (H5D_contig_readvv_ud_t *)_udata; /* User data for H5VM_opvv() operator */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Write data */ if (H5F_shared_block_read(udata->f_sh, H5FD_MEM_DRAW, (udata->dset_addr + dst_off), len, (udata->rbuf + src_off)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "block write failed") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_readvv_cb() */ /*------------------------------------------------------------------------- * Function: H5D__contig_readvv * * Purpose: Reads some data vectors from a dataset into a buffer. * The data is contiguous. The address is the start of the dataset, * relative to the base address for the file and the offsets and * sequence lengths are in bytes. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Friday, May 3, 2001 * * Notes: * Offsets in the sequences must be monotonically increasing * *------------------------------------------------------------------------- */ static ssize_t H5D__contig_readvv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_off_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_off_arr[]) { ssize_t ret_value = -1; /* Return value */ FUNC_ENTER_STATIC /* Check args */ HDassert(io_info); HDassert(dset_curr_seq); HDassert(dset_len_arr); HDassert(dset_off_arr); HDassert(mem_curr_seq); HDassert(mem_len_arr); HDassert(mem_off_arr); /* Check if data sieving is enabled */ if (H5F_SHARED_HAS_FEATURE(io_info->f_sh, H5FD_FEAT_DATA_SIEVE)) { H5D_contig_readvv_sieve_ud_t udata; /* User data for H5VM_opvv() operator */ /* Set up user data for H5VM_opvv() */ udata.f_sh = io_info->f_sh; udata.dset_contig = &(io_info->dset->shared->cache.contig); udata.store_contig = &(io_info->store->contig); udata.rbuf = (unsigned char *)io_info->u.rbuf; /* Call generic sequence operation routine */ if ((ret_value = H5VM_opvv(dset_max_nseq, dset_curr_seq, dset_len_arr, dset_off_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_off_arr, H5D__contig_readvv_sieve_cb, &udata)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPERATE, FAIL, "can't perform vectorized sieve buffer read") } /* end if */ else { H5D_contig_readvv_ud_t udata; /* User data for H5VM_opvv() operator */ /* Set up user data for H5VM_opvv() */ udata.f_sh = io_info->f_sh; udata.dset_addr = io_info->store->contig.dset_addr; udata.rbuf = (unsigned char *)io_info->u.rbuf; /* Call generic sequence operation routine */ if ((ret_value = H5VM_opvv(dset_max_nseq, dset_curr_seq, dset_len_arr, dset_off_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_off_arr, H5D__contig_readvv_cb, &udata)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPERATE, FAIL, "can't perform vectorized read") } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_readvv() */ /*------------------------------------------------------------------------- * Function: H5D__contig_writevv_sieve_cb * * Purpose: Callback operator for H5D__contig_writevv() with sieve buffer. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, Sept 30, 2010 * *------------------------------------------------------------------------- */ static herr_t H5D__contig_writevv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len, void *_udata) { H5D_contig_writevv_sieve_ud_t *udata = (H5D_contig_writevv_sieve_ud_t *)_udata; /* User data for H5VM_opvv() operator */ H5F_shared_t *f_sh = udata->f_sh; /* Shared file for dataset */ H5D_rdcdc_t * dset_contig = udata->dset_contig; /* Cached information about contiguous data */ const H5D_contig_storage_t *store_contig = udata->store_contig; /* Contiguous storage info for this I/O operation */ const unsigned char *buf; /* Pointer to buffer to fill */ haddr_t addr; /* Actual address to read */ haddr_t sieve_start = HADDR_UNDEF, sieve_end = HADDR_UNDEF; /* Start & end locations of sieve buffer */ haddr_t contig_end; /* End locations of block to write */ size_t sieve_size = (size_t)-1; /* size of sieve buffer */ haddr_t rel_eoa; /* Relative end of file address */ hsize_t max_data; /* Actual maximum size of data to cache */ hsize_t min; /* temporary minimum value (avoids some ugly macro nesting) */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Stash local copies of these values */ if (dset_contig->sieve_buf != NULL) { sieve_start = dset_contig->sieve_loc; sieve_size = dset_contig->sieve_size; sieve_end = sieve_start + sieve_size; } /* end if */ /* Compute offset on disk */ addr = store_contig->dset_addr + dst_off; /* Compute offset in memory */ buf = udata->wbuf + src_off; /* No data sieve buffer yet, go allocate one */ if (NULL == dset_contig->sieve_buf) { /* Check if we can actually hold the I/O request in the sieve buffer */ if (len > dset_contig->sieve_buf_size) { if (H5F_shared_block_write(f_sh, H5FD_MEM_DRAW, addr, len, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "block write failed") } /* end if */ else { /* Allocate room for the data sieve buffer */ if (NULL == (dset_contig->sieve_buf = H5FL_BLK_CALLOC(sieve_buf, dset_contig->sieve_buf_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "memory allocation failed") /* Clear memory */ if (dset_contig->sieve_size > len) HDmemset(dset_contig->sieve_buf + len, 0, (dset_contig->sieve_size - len)); /* Determine the new sieve buffer size & location */ dset_contig->sieve_loc = addr; /* Make certain we don't read off the end of the file */ if (HADDR_UNDEF == (rel_eoa = H5F_shared_get_eoa(f_sh, H5FD_MEM_DRAW))) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to determine file size") /* Set up the buffer parameters */ max_data = store_contig->dset_size - dst_off; /* Compute the size of the sieve buffer */ min = MIN3(rel_eoa - dset_contig->sieve_loc, max_data, dset_contig->sieve_buf_size); H5_CHECKED_ASSIGN(dset_contig->sieve_size, size_t, min, hsize_t); /* Check if there is any point in reading the data from the file */ if (dset_contig->sieve_size > len) { /* Read the new sieve buffer */ if (H5F_shared_block_read(f_sh, H5FD_MEM_DRAW, dset_contig->sieve_loc, dset_contig->sieve_size, dset_contig->sieve_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "block read failed") } /* end if */ /* Grab the data out of the buffer (must be first piece of data in buffer ) */ H5MM_memcpy(dset_contig->sieve_buf, buf, len); /* Set sieve buffer dirty flag */ dset_contig->sieve_dirty = TRUE; /* Stash local copies of these values */ sieve_start = dset_contig->sieve_loc; sieve_size = dset_contig->sieve_size; sieve_end = sieve_start + sieve_size; } /* end else */ } /* end if */ else { /* Compute end of sequence to retrieve */ contig_end = addr + len - 1; /* If entire write is within the sieve buffer, write it to the buffer */ if (addr >= sieve_start && contig_end < sieve_end) { unsigned char *base_sieve_buf = dset_contig->sieve_buf + (addr - sieve_start); /* Put the data into the sieve buffer */ H5MM_memcpy(base_sieve_buf, buf, len); /* Set sieve buffer dirty flag */ dset_contig->sieve_dirty = TRUE; } /* end if */ /* Entire request is not within this data sieve buffer */ else { /* Check if we can actually hold the I/O request in the sieve buffer */ if (len > dset_contig->sieve_buf_size) { /* Check for any overlap with the current sieve buffer */ if ((sieve_start >= addr && sieve_start < (contig_end + 1)) || ((sieve_end - 1) >= addr && (sieve_end - 1) < (contig_end + 1))) { /* Flush the sieve buffer, if it's dirty */ if (dset_contig->sieve_dirty) { /* Write to file */ if (H5F_shared_block_write(f_sh, H5FD_MEM_DRAW, sieve_start, sieve_size, dset_contig->sieve_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "block write failed") /* Reset sieve buffer dirty flag */ dset_contig->sieve_dirty = FALSE; } /* end if */ /* Force the sieve buffer to be re-read the next time */ dset_contig->sieve_loc = HADDR_UNDEF; dset_contig->sieve_size = 0; } /* end if */ /* Write directly from the user's buffer */ if (H5F_shared_block_write(f_sh, H5FD_MEM_DRAW, addr, len, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "block write failed") } /* end if */ /* Element size fits within the buffer size */ else { /* Check if it is possible to (exactly) prepend or append to existing (dirty) sieve buffer */ if (((addr + len) == sieve_start || addr == sieve_end) && (len + sieve_size) <= dset_contig->sieve_buf_size && dset_contig->sieve_dirty) { /* Prepend to existing sieve buffer */ if ((addr + len) == sieve_start) { /* Move existing sieve information to correct location */ HDmemmove(dset_contig->sieve_buf + len, dset_contig->sieve_buf, dset_contig->sieve_size); /* Copy in new information (must be first in sieve buffer) */ H5MM_memcpy(dset_contig->sieve_buf, buf, len); /* Adjust sieve location */ dset_contig->sieve_loc = addr; } /* end if */ /* Append to existing sieve buffer */ else { /* Copy in new information */ H5MM_memcpy(dset_contig->sieve_buf + sieve_size, buf, len); } /* end else */ /* Adjust sieve size */ dset_contig->sieve_size += len; } /* end if */ /* Can't add the new data onto the existing sieve buffer */ else { /* Flush the sieve buffer if it's dirty */ if (dset_contig->sieve_dirty) { /* Write to file */ if (H5F_shared_block_write(f_sh, H5FD_MEM_DRAW, sieve_start, sieve_size, dset_contig->sieve_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "block write failed") /* Reset sieve buffer dirty flag */ dset_contig->sieve_dirty = FALSE; } /* end if */ /* Determine the new sieve buffer size & location */ dset_contig->sieve_loc = addr; /* Make certain we don't read off the end of the file */ if (HADDR_UNDEF == (rel_eoa = H5F_shared_get_eoa(f_sh, H5FD_MEM_DRAW))) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to determine file size") /* Only need this when resizing sieve buffer */ max_data = store_contig->dset_size - dst_off; /* Compute the size of the sieve buffer. * Don't read off the end of the file, don't read past * the end of the data element, and don't read more than * the buffer size. */ min = MIN3(rel_eoa - dset_contig->sieve_loc, max_data, dset_contig->sieve_buf_size); H5_CHECKED_ASSIGN(dset_contig->sieve_size, size_t, min, hsize_t); /* Check if there is any point in reading the data from the file */ if (dset_contig->sieve_size > len) { /* Read the new sieve buffer */ if (H5F_shared_block_read(f_sh, H5FD_MEM_DRAW, dset_contig->sieve_loc, dset_contig->sieve_size, dset_contig->sieve_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "block read failed") } /* end if */ /* Grab the data out of the buffer (must be first piece of data in buffer ) */ H5MM_memcpy(dset_contig->sieve_buf, buf, len); /* Set sieve buffer dirty flag */ dset_contig->sieve_dirty = TRUE; } /* end else */ } /* end else */ } /* end else */ } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_writevv_sieve_cb() */ /*------------------------------------------------------------------------- * Function: H5D__contig_writevv_cb * * Purpose: Callback operator for H5D__contig_writevv(). * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, Sept 30, 2010 * *------------------------------------------------------------------------- */ static herr_t H5D__contig_writevv_cb(hsize_t dst_off, hsize_t src_off, size_t len, void *_udata) { H5D_contig_writevv_ud_t *udata = (H5D_contig_writevv_ud_t *)_udata; /* User data for H5VM_opvv() operator */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Write data */ if (H5F_shared_block_write(udata->f_sh, H5FD_MEM_DRAW, (udata->dset_addr + dst_off), len, (udata->wbuf + src_off)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "block write failed") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_writevv_cb() */ /*------------------------------------------------------------------------- * Function: H5D__contig_writevv * * Purpose: Writes some data vectors into a dataset from vectors into a * buffer. The address is the start of the dataset, * relative to the base address for the file and the offsets and * sequence lengths are in bytes. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Friday, May 2, 2003 * * Notes: * Offsets in the sequences must be monotonically increasing * *------------------------------------------------------------------------- */ static ssize_t H5D__contig_writevv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_off_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_off_arr[]) { ssize_t ret_value = -1; /* Return value (Size of sequence in bytes) */ FUNC_ENTER_STATIC /* Check args */ HDassert(io_info); HDassert(dset_curr_seq); HDassert(dset_len_arr); HDassert(dset_off_arr); HDassert(mem_curr_seq); HDassert(mem_len_arr); HDassert(mem_off_arr); /* Check if data sieving is enabled */ if (H5F_SHARED_HAS_FEATURE(io_info->f_sh, H5FD_FEAT_DATA_SIEVE)) { H5D_contig_writevv_sieve_ud_t udata; /* User data for H5VM_opvv() operator */ /* Set up user data for H5VM_opvv() */ udata.f_sh = io_info->f_sh; udata.dset_contig = &(io_info->dset->shared->cache.contig); udata.store_contig = &(io_info->store->contig); udata.wbuf = (const unsigned char *)io_info->u.wbuf; /* Call generic sequence operation routine */ if ((ret_value = H5VM_opvv(dset_max_nseq, dset_curr_seq, dset_len_arr, dset_off_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_off_arr, H5D__contig_writevv_sieve_cb, &udata)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPERATE, FAIL, "can't perform vectorized sieve buffer write") } /* end if */ else { H5D_contig_writevv_ud_t udata; /* User data for H5VM_opvv() operator */ /* Set up user data for H5VM_opvv() */ udata.f_sh = io_info->f_sh; udata.dset_addr = io_info->store->contig.dset_addr; udata.wbuf = (const unsigned char *)io_info->u.wbuf; /* Call generic sequence operation routine */ if ((ret_value = H5VM_opvv(dset_max_nseq, dset_curr_seq, dset_len_arr, dset_off_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_off_arr, H5D__contig_writevv_cb, &udata)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPERATE, FAIL, "can't perform vectorized read") } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_writevv() */ /*------------------------------------------------------------------------- * Function: H5D__contig_flush * * Purpose: Writes all dirty data to disk. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Monday, July 27, 2009 * *------------------------------------------------------------------------- */ static herr_t H5D__contig_flush(H5D_t *dset) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* Sanity check */ HDassert(dset); /* Flush any data in sieve buffer */ if (H5D__flush_sieve_buf(dset) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to flush sieve buffer") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_flush() */ /*------------------------------------------------------------------------- * Function: H5D__contig_copy * * Purpose: Copy contiguous storage raw data from SRC file to DST file. * * Return: Non-negative on success, negative on failure. * * Programmer: Quincey Koziol * Monday, November 21, 2005 * *------------------------------------------------------------------------- */ herr_t H5D__contig_copy(H5F_t *f_src, const H5O_storage_contig_t *storage_src, H5F_t *f_dst, H5O_storage_contig_t *storage_dst, H5T_t *dt_src, H5O_copy_t *cpy_info) { haddr_t addr_src; /* File offset in source dataset */ haddr_t addr_dst; /* File offset in destination dataset */ H5T_path_t * tpath_src_mem = NULL, *tpath_mem_dst = NULL; /* Datatype conversion paths */ H5T_t * dt_dst = NULL; /* Destination datatype */ H5T_t * dt_mem = NULL; /* Memory datatype */ hid_t tid_src = -1; /* Datatype ID for source datatype */ hid_t tid_dst = -1; /* Datatype ID for destination datatype */ hid_t tid_mem = -1; /* Datatype ID for memory datatype */ size_t src_dt_size = 0; /* Source datatype size */ size_t mem_dt_size = 0; /* Memory datatype size */ size_t dst_dt_size = 0; /* Destination datatype size */ size_t max_dt_size; /* Max. datatype size */ size_t nelmts = 0; /* Number of elements in buffer */ size_t src_nbytes; /* Number of bytes to read from source */ size_t mem_nbytes; /* Number of bytes to convert in memory */ size_t dst_nbytes; /* Number of bytes to write to destination */ hsize_t total_src_nbytes; /* Total number of bytes to copy */ size_t buf_size; /* Size of copy buffer */ void * buf = NULL; /* Buffer for copying data */ void * bkg = NULL; /* Temporary buffer for copying data */ void * reclaim_buf = NULL; /* Buffer for reclaiming data */ H5S_t * buf_space = NULL; /* Dataspace describing buffer */ hid_t buf_sid = -1; /* ID for buffer dataspace */ hsize_t buf_dim[1] = {0}; /* Dimension for buffer */ hbool_t is_vlen = FALSE; /* Flag to indicate that VL type conversion should occur */ hbool_t fix_ref = FALSE; /* Flag to indicate that ref values should be fixed */ H5D_shared_t *shared_fo = (H5D_shared_t *)cpy_info->shared_fo; /* Pointer to the shared struct for dataset object */ hbool_t try_sieve = FALSE; /* Try to get data from the sieve buffer */ haddr_t sieve_start = HADDR_UNDEF; /* Start location of sieve buffer */ haddr_t sieve_end = HADDR_UNDEF; /* End locations of sieve buffer */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ HDassert(f_src); HDassert(storage_src); HDassert(f_dst); HDassert(storage_dst); HDassert(dt_src); /* Allocate space for destination raw data */ if (H5D__contig_alloc(f_dst, storage_dst) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "unable to allocate contiguous storage") /* Set up number of bytes to copy, and initial buffer size */ /* (actually use the destination size, which has been fixed up, if necessary) */ total_src_nbytes = storage_dst->size; H5_CHECK_OVERFLOW(total_src_nbytes, hsize_t, size_t); buf_size = MIN(H5D_TEMP_BUF_SIZE, (size_t)total_src_nbytes); /* Create datatype ID for src datatype. We may or may not use this ID, * but this ensures that the src datatype will be freed. */ if ((tid_src = H5I_register(H5I_DATATYPE, dt_src, FALSE)) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "unable to register source file datatype") /* If there's a VLEN source datatype, set up type conversion information */ if (H5T_detect_class(dt_src, H5T_VLEN, FALSE) > 0) { /* create a memory copy of the variable-length datatype */ if (NULL == (dt_mem = H5T_copy(dt_src, H5T_COPY_TRANSIENT))) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to copy") if ((tid_mem = H5I_register(H5I_DATATYPE, dt_mem, FALSE)) < 0) { (void)H5T_close_real(dt_mem); HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register memory datatype") } /* end if */ /* create variable-length datatype at the destinaton file */ if (NULL == (dt_dst = H5T_copy(dt_src, H5T_COPY_TRANSIENT))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to copy") if (H5T_set_loc(dt_dst, H5F_VOL_OBJ(f_dst), H5T_LOC_DISK) < 0) { (void)H5T_close_real(dt_dst); HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "cannot mark datatype on disk") } /* end if */ if ((tid_dst = H5I_register(H5I_DATATYPE, dt_dst, FALSE)) < 0) { (void)H5T_close_real(dt_dst); HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "unable to register destination file datatype") } /* end if */ /* Set up the conversion functions */ if (NULL == (tpath_src_mem = H5T_path_find(dt_src, dt_mem))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert between src and mem datatypes") if (NULL == (tpath_mem_dst = H5T_path_find(dt_mem, dt_dst))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to convert between mem and dst datatypes") /* Determine largest datatype size */ if (0 == (src_dt_size = H5T_get_size(dt_src))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to determine datatype size") if (0 == (mem_dt_size = H5T_get_size(dt_mem))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to determine datatype size") max_dt_size = MAX(src_dt_size, mem_dt_size); if (0 == (dst_dt_size = H5T_get_size(dt_dst))) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to determine datatype size") max_dt_size = MAX(max_dt_size, dst_dt_size); /* Set maximum number of whole elements that fit in buffer */ if (0 == (nelmts = buf_size / max_dt_size)) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "element size too large") /* Set the number of bytes to transfer */ src_nbytes = nelmts * src_dt_size; dst_nbytes = nelmts * dst_dt_size; mem_nbytes = nelmts * mem_dt_size; /* Adjust buffer size to be multiple of elements */ buf_size = nelmts * max_dt_size; /* Create dataspace for number of elements in buffer */ buf_dim[0] = nelmts; /* Create the space and set the initial extent */ if (NULL == (buf_space = H5S_create_simple((unsigned)1, buf_dim, NULL))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't create simple dataspace") /* Register */ if ((buf_sid = H5I_register(H5I_DATASPACE, buf_space, FALSE)) < 0) { H5S_close(buf_space); HGOTO_ERROR(H5E_ID, H5E_CANTREGISTER, FAIL, "unable to register dataspace ID") } /* end if */ /* Set flag to do type conversion */ is_vlen = TRUE; } /* end if */ else { /* Check for reference datatype */ if (H5T_get_class(dt_src, FALSE) == H5T_REFERENCE) { /* Need to fix values of references when copying across files */ if (f_src != f_dst) fix_ref = TRUE; } /* end if */ /* Set the number of bytes to read & write to the buffer size */ src_nbytes = dst_nbytes = mem_nbytes = buf_size; } /* end else */ /* Allocate space for copy buffer */ HDassert(buf_size); if (NULL == (buf = H5FL_BLK_MALLOC(type_conv, buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for copy buffer") /* Need extra buffer for datatype conversions, to prevent stranding/leaking memory */ if (is_vlen || fix_ref) { if (NULL == (reclaim_buf = H5FL_BLK_MALLOC(type_conv, buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for copy buffer") /* allocate temporary bkg buff for data conversion */ if (NULL == (bkg = H5FL_BLK_MALLOC(type_conv, buf_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for copy buffer") } /* end if */ /* Loop over copying data */ addr_src = storage_src->addr; addr_dst = storage_dst->addr; /* If data sieving is enabled and the dataset is open in the file, set up to copy data out of the sieve buffer if deemed possible later */ if (H5F_HAS_FEATURE(f_src, H5FD_FEAT_DATA_SIEVE) && shared_fo && shared_fo->cache.contig.sieve_buf) { try_sieve = TRUE; sieve_start = shared_fo->cache.contig.sieve_loc; sieve_end = sieve_start + shared_fo->cache.contig.sieve_size; } while (total_src_nbytes > 0) { /* Check if we should reduce the number of bytes to transfer */ if (total_src_nbytes < src_nbytes) { /* Adjust bytes to transfer */ src_nbytes = (size_t)total_src_nbytes; /* Adjust dataspace describing buffer */ if (is_vlen) { /* Adjust destination & memory bytes to transfer */ nelmts = src_nbytes / src_dt_size; dst_nbytes = nelmts * dst_dt_size; mem_nbytes = nelmts * mem_dt_size; /* Adjust size of buffer's dataspace dimension */ buf_dim[0] = nelmts; /* Adjust size of buffer's dataspace */ if (H5S_set_extent_real(buf_space, buf_dim) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSET, FAIL, "unable to change buffer dataspace size") } /* end if */ else /* Adjust destination & memory bytes to transfer */ dst_nbytes = mem_nbytes = src_nbytes; } /* end if */ /* If the entire copy is within the sieve buffer, copy data from the sieve buffer */ if (try_sieve && (addr_src >= sieve_start) && ((addr_src + src_nbytes - 1) < sieve_end)) { unsigned char *base_sieve_buf = shared_fo->cache.contig.sieve_buf + (addr_src - sieve_start); H5MM_memcpy(buf, base_sieve_buf, src_nbytes); } else /* Read raw data from source file */ if (H5F_block_read(f_src, H5FD_MEM_DRAW, addr_src, src_nbytes, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "unable to read raw data") /* Perform datatype conversion, if necessary */ if (is_vlen) { /* Convert from source file to memory */ if (H5T_convert(tpath_src_mem, tid_src, tid_mem, nelmts, (size_t)0, (size_t)0, buf, bkg) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed") /* Copy into another buffer, to reclaim memory later */ H5MM_memcpy(reclaim_buf, buf, mem_nbytes); /* Set background buffer to all zeros */ HDmemset(bkg, 0, buf_size); /* Convert from memory to destination file */ if (H5T_convert(tpath_mem_dst, tid_mem, tid_dst, nelmts, (size_t)0, (size_t)0, buf, bkg) < 0) HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "datatype conversion failed") /* Reclaim space from variable length data */ if (H5T_reclaim(tid_mem, buf_space, reclaim_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADITER, FAIL, "unable to reclaim variable-length data") } /* end if */ else if (fix_ref) { /* Check for expanding references */ if (cpy_info->expand_ref) { /* Copy the reference elements */ if (H5O_copy_expand_ref(f_src, tid_src, dt_src, buf, buf_size, f_dst, bkg, cpy_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "unable to copy reference attribute") /* After fix ref, copy the new reference elements to the buffer to write out */ H5MM_memcpy(buf, bkg, buf_size); } /* end if */ else /* Reset value to zero */ HDmemset(buf, 0, src_nbytes); } /* end if */ /* Write raw data to destination file */ if (H5F_block_write(f_dst, H5FD_MEM_DRAW, addr_dst, dst_nbytes, buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to write raw data") /* Adjust loop variables */ addr_src += src_nbytes; addr_dst += dst_nbytes; total_src_nbytes -= src_nbytes; } /* end while */ done: if (buf_sid > 0 && H5I_dec_ref(buf_sid) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't decrement temporary dataspace ID") if (tid_src > 0 && H5I_dec_ref(tid_src) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if (tid_dst > 0 && H5I_dec_ref(tid_dst) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if (tid_mem > 0 && H5I_dec_ref(tid_mem) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "Can't decrement temporary datatype ID") if (buf) buf = H5FL_BLK_FREE(type_conv, buf); if (reclaim_buf) reclaim_buf = H5FL_BLK_FREE(type_conv, reclaim_buf); if (bkg) bkg = H5FL_BLK_FREE(type_conv, bkg); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__contig_copy() */