/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * 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. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /* * Purpose: Dataspace I/O functions. */ /****************/ /* 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" /* Datasets */ #include "H5Eprivate.h" /* Error handling */ #include "H5FLprivate.h" /* Free Lists */ #include "H5VMprivate.h" /* Vector Functions */ /****************/ /* Local Macros */ /****************/ /******************/ /* Local Typedefs */ /******************/ /********************/ /* Local Prototypes */ /********************/ static herr_t H5D__select_io(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info, size_t elmt_size); /*********************/ /* Package Variables */ /*********************/ /*******************/ /* Local Variables */ /*******************/ /* Declare a free list to manage sequences of size_t */ H5FL_SEQ_DEFINE(size_t); /* Declare a free list to manage sequences of hsize_t */ H5FL_SEQ_DEFINE(hsize_t); /* Declare extern free list to manage the H5S_sel_iter_t struct */ H5FL_EXTERN(H5S_sel_iter_t); /*------------------------------------------------------------------------- * Function: H5D__select_io * * Purpose: Perform I/O directly from application memory and a file * * Return: Non-negative on success/Negative on failure * *------------------------------------------------------------------------- */ static herr_t H5D__select_io(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info, size_t elmt_size) { H5S_sel_iter_t *mem_iter = NULL; /* Memory selection iteration info */ bool mem_iter_init = false; /* Memory selection iteration info has been initialized */ H5S_sel_iter_t *file_iter = NULL; /* File selection iteration info */ bool file_iter_init = false; /* File selection iteration info has been initialized */ hsize_t *mem_off = NULL; /* Pointer to sequence offsets in memory */ hsize_t *file_off = NULL; /* Pointer to sequence offsets in the file */ size_t *mem_len = NULL; /* Pointer to sequence lengths in memory */ size_t *file_len = NULL; /* Pointer to sequence lengths in the file */ size_t curr_mem_seq; /* Current memory sequence to operate on */ size_t curr_file_seq; /* Current file sequence to operate on */ size_t mem_nseq; /* Number of sequences generated in the file */ size_t file_nseq; /* Number of sequences generated in memory */ size_t dxpl_vec_size; /* Vector length from API context's DXPL */ size_t vec_size; /* Vector length */ ssize_t tmp_file_len; /* Temporary number of bytes in file sequence */ size_t nelmts; /* Number of elements to process */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Check args */ assert(io_info); assert(dset_info->dset); assert(dset_info->store); assert(dset_info->buf.vp); if (elmt_size == 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "invalid elmt_size of 0"); /* Initialize nelmts */ nelmts = dset_info->nelmts; /* Check for only one element in selection */ if (nelmts == 1) { hsize_t single_mem_off; /* Offset in memory */ hsize_t single_file_off; /* Offset in the file */ size_t single_mem_len; /* Length in memory */ size_t single_file_len; /* Length in the file */ /* Get offset of first element in selections */ if (H5S_SELECT_OFFSET(dset_info->file_space, &single_file_off) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "can't retrieve file selection offset"); if (H5S_SELECT_OFFSET(dset_info->mem_space, &single_mem_off) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "can't retrieve memory selection offset"); /* Set up necessary information for I/O operation */ file_nseq = mem_nseq = 1; curr_mem_seq = curr_file_seq = 0; single_file_off *= elmt_size; single_mem_off *= elmt_size; single_file_len = single_mem_len = elmt_size; /* Perform I/O on memory and file sequences */ if (io_info->op_type == H5D_IO_OP_READ) { if ((tmp_file_len = (*dset_info->layout_ops.readvv)( io_info, dset_info, file_nseq, &curr_file_seq, &single_file_len, &single_file_off, mem_nseq, &curr_mem_seq, &single_mem_len, &single_mem_off)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error"); } /* end if */ else { assert(io_info->op_type == H5D_IO_OP_WRITE); if ((tmp_file_len = (*dset_info->layout_ops.writevv)( io_info, dset_info, file_nseq, &curr_file_seq, &single_file_len, &single_file_off, mem_nseq, &curr_mem_seq, &single_mem_len, &single_mem_off)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); } /* end else */ /* Decrement number of elements left to process */ assert(((size_t)tmp_file_len % elmt_size) == 0); } /* end if */ else { size_t mem_nelem; /* Number of elements used in memory sequences */ size_t file_nelem; /* Number of elements used in file sequences */ /* Get info from API context */ if (H5CX_get_vec_size(&dxpl_vec_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve I/O vector size"); /* Allocate the vector I/O arrays */ if (dxpl_vec_size > H5D_IO_VECTOR_SIZE) vec_size = dxpl_vec_size; else vec_size = H5D_IO_VECTOR_SIZE; if (NULL == (mem_len = H5FL_SEQ_MALLOC(size_t, vec_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array"); if (NULL == (mem_off = H5FL_SEQ_MALLOC(hsize_t, vec_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array"); if (NULL == (file_len = H5FL_SEQ_MALLOC(size_t, vec_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array"); if (NULL == (file_off = H5FL_SEQ_MALLOC(hsize_t, vec_size))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array"); /* Allocate the iterators */ if (NULL == (mem_iter = H5FL_MALLOC(H5S_sel_iter_t))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate memory iterator"); if (NULL == (file_iter = H5FL_MALLOC(H5S_sel_iter_t))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate file iterator"); /* Initialize file iterator */ if (H5S_select_iter_init(file_iter, dset_info->file_space, elmt_size, H5S_SEL_ITER_GET_SEQ_LIST_SORTED) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); file_iter_init = 1; /* File selection iteration info has been initialized */ /* Initialize memory iterator */ if (H5S_select_iter_init(mem_iter, dset_info->mem_space, elmt_size, 0) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); mem_iter_init = 1; /* Memory selection iteration info has been initialized */ /* Initialize sequence counts */ curr_mem_seq = curr_file_seq = 0; mem_nseq = file_nseq = 0; /* Loop, until all bytes are processed */ while (nelmts > 0) { /* Check if more file sequences are needed */ if (curr_file_seq >= file_nseq) { /* Get sequences for file selection */ if (H5S_SELECT_ITER_GET_SEQ_LIST(file_iter, vec_size, nelmts, &file_nseq, &file_nelem, file_off, file_len) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); /* Start at the beginning of the sequences again */ curr_file_seq = 0; } /* end if */ /* Check if more memory sequences are needed */ if (curr_mem_seq >= mem_nseq) { /* Get sequences for memory selection */ if (H5S_SELECT_ITER_GET_SEQ_LIST(mem_iter, vec_size, nelmts, &mem_nseq, &mem_nelem, mem_off, mem_len) < 0) HGOTO_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL, "sequence length generation failed"); /* Start at the beginning of the sequences again */ curr_mem_seq = 0; } /* end if */ /* Perform I/O on memory and file sequences */ if (io_info->op_type == H5D_IO_OP_READ) { if ((tmp_file_len = (*dset_info->layout_ops.readvv)( io_info, dset_info, file_nseq, &curr_file_seq, file_len, file_off, mem_nseq, &curr_mem_seq, mem_len, mem_off)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error"); } /* end if */ else { assert(io_info->op_type == H5D_IO_OP_WRITE); if ((tmp_file_len = (*dset_info->layout_ops.writevv)( io_info, dset_info, file_nseq, &curr_file_seq, file_len, file_off, mem_nseq, &curr_mem_seq, mem_len, mem_off)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); } /* end else */ /* Decrement number of elements left to process */ assert(((size_t)tmp_file_len % elmt_size) == 0); nelmts -= ((size_t)tmp_file_len / elmt_size); } /* end while */ } /* end else */ done: /* Release selection iterators */ if (file_iter_init && H5S_SELECT_ITER_RELEASE(file_iter) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); if (file_iter) file_iter = H5FL_FREE(H5S_sel_iter_t, file_iter); if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); if (mem_iter) mem_iter = H5FL_FREE(H5S_sel_iter_t, mem_iter); /* Release vector arrays, if allocated */ if (file_len) file_len = H5FL_SEQ_FREE(size_t, file_len); if (file_off) file_off = H5FL_SEQ_FREE(hsize_t, file_off); if (mem_len) mem_len = H5FL_SEQ_FREE(size_t, mem_len); if (mem_off) mem_off = H5FL_SEQ_FREE(hsize_t, mem_off); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__select_io() */ /*------------------------------------------------------------------------- * Function: H5D_select_io_mem * * Purpose: Perform memory copies directly between two memory buffers * according to the selections in the `dst_space` and * `src_space` dataspaces. * * Note: This routine is [basically] the same as H5D__select_io, * with the only difference being that the readvv/writevv * calls are exchanged for H5VM_memcpyvv calls. Changes should * be made to both routines. * * Return: Non-negative on success/Negative on failure * *------------------------------------------------------------------------- */ herr_t H5D_select_io_mem(void *dst_buf, H5S_t *dst_space, const void *src_buf, H5S_t *src_space, size_t elmt_size, size_t nelmts) { H5S_sel_iter_t *dst_sel_iter = NULL; /* Destination dataspace iteration info */ H5S_sel_iter_t *src_sel_iter = NULL; /* Source dataspace iteration info */ bool dst_sel_iter_init = false; /* Destination dataspace selection iterator initialized? */ bool src_sel_iter_init = false; /* Source dataspace selection iterator initialized? */ hsize_t *dst_off = NULL; /* Pointer to sequence offsets in destination buffer */ hsize_t *src_off = NULL; /* Pointer to sequence offsets in source buffer */ size_t *dst_len = NULL; /* Pointer to sequence lengths in destination buffer */ size_t *src_len = NULL; /* Pointer to sequence lengths in source buffer */ size_t curr_dst_seq; /* Current destination buffer sequence to operate on */ size_t curr_src_seq; /* Current source buffer sequence to operate on */ size_t dst_nseq; /* Number of sequences generated for destination buffer */ size_t src_nseq; /* Number of sequences generated for source buffer */ size_t dxpl_vec_size; /* Vector length from API context's DXPL */ size_t vec_size; /* Vector length */ ssize_t bytes_copied; herr_t ret_value = SUCCEED; FUNC_ENTER_NOAPI(FAIL) assert(dst_buf); assert(dst_space); assert(src_buf); assert(src_space); if (elmt_size == 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADVALUE, FAIL, "invalid elmt_size of 0"); /* Check for only one element in selection */ if (nelmts == 1) { hsize_t single_dst_off; /* Offset in dst_space */ hsize_t single_src_off; /* Offset in src_space */ size_t single_dst_len; /* Length in dst_space */ size_t single_src_len; /* Length in src_space */ /* Get offset of first element in selections */ if (H5S_SELECT_OFFSET(dst_space, &single_dst_off) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve destination selection offset"); if (H5S_SELECT_OFFSET(src_space, &single_src_off) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve source selection offset"); /* Set up necessary information for I/O operation */ dst_nseq = src_nseq = 1; curr_dst_seq = curr_src_seq = 0; single_dst_off *= elmt_size; single_src_off *= elmt_size; single_dst_len = single_src_len = elmt_size; /* Perform vectorized memcpy from src_buf to dst_buf */ if ((bytes_copied = H5VM_memcpyvv(dst_buf, dst_nseq, &curr_dst_seq, &single_dst_len, &single_dst_off, src_buf, src_nseq, &curr_src_seq, &single_src_len, &single_src_off)) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed"); assert(((size_t)bytes_copied % elmt_size) == 0); } else { unsigned sel_iter_flags = H5S_SEL_ITER_GET_SEQ_LIST_SORTED | H5S_SEL_ITER_SHARE_WITH_DATASPACE; size_t dst_nelem; /* Number of elements used in destination buffer sequences */ size_t src_nelem; /* Number of elements used in source buffer sequences */ /* Get info from API context */ if (H5CX_get_vec_size(&dxpl_vec_size) < 0) HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "can't retrieve I/O vector size"); /* Allocate the vector I/O arrays */ if (dxpl_vec_size > H5D_IO_VECTOR_SIZE) vec_size = dxpl_vec_size; else vec_size = H5D_IO_VECTOR_SIZE; if (NULL == (dst_len = H5FL_SEQ_MALLOC(size_t, vec_size))) HGOTO_ERROR(H5E_IO, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array"); if (NULL == (dst_off = H5FL_SEQ_MALLOC(hsize_t, vec_size))) HGOTO_ERROR(H5E_IO, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array"); if (NULL == (src_len = H5FL_SEQ_MALLOC(size_t, vec_size))) HGOTO_ERROR(H5E_IO, H5E_CANTALLOC, FAIL, "can't allocate I/O length vector array"); if (NULL == (src_off = H5FL_SEQ_MALLOC(hsize_t, vec_size))) HGOTO_ERROR(H5E_IO, H5E_CANTALLOC, FAIL, "can't allocate I/O offset vector array"); /* Allocate the dataspace selection iterators */ if (NULL == (dst_sel_iter = H5FL_MALLOC(H5S_sel_iter_t))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate destination selection iterator"); if (NULL == (src_sel_iter = H5FL_MALLOC(H5S_sel_iter_t))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTALLOC, FAIL, "can't allocate source selection iterator"); /* Initialize destination selection iterator */ if (H5S_select_iter_init(dst_sel_iter, dst_space, elmt_size, sel_iter_flags) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); dst_sel_iter_init = true; /* Destination selection iteration info has been initialized */ /* Initialize source selection iterator */ if (H5S_select_iter_init(src_sel_iter, src_space, elmt_size, H5S_SEL_ITER_SHARE_WITH_DATASPACE) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); src_sel_iter_init = true; /* Source selection iteration info has been initialized */ /* Initialize sequence counts */ curr_dst_seq = curr_src_seq = 0; dst_nseq = src_nseq = 0; /* Loop, until all bytes are processed */ while (nelmts > 0) { /* Check if more destination buffer sequences are needed */ if (curr_dst_seq >= dst_nseq) { /* Get sequences for destination selection */ if (H5S_SELECT_ITER_GET_SEQ_LIST(dst_sel_iter, vec_size, nelmts, &dst_nseq, &dst_nelem, dst_off, dst_len) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "sequence length generation failed"); /* Start at the beginning of the sequences again */ curr_dst_seq = 0; } /* Check if more source buffer sequences are needed */ if (curr_src_seq >= src_nseq) { /* Get sequences for source selection */ if (H5S_SELECT_ITER_GET_SEQ_LIST(src_sel_iter, vec_size, nelmts, &src_nseq, &src_nelem, src_off, src_len) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "sequence length generation failed"); /* Start at the beginning of the sequences again */ curr_src_seq = 0; } /* end if */ /* Perform vectorized memcpy from src_buf to dst_buf */ if ((bytes_copied = H5VM_memcpyvv(dst_buf, dst_nseq, &curr_dst_seq, dst_len, dst_off, src_buf, src_nseq, &curr_src_seq, src_len, src_off)) < 0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed"); /* Decrement number of elements left to process */ assert(((size_t)bytes_copied % elmt_size) == 0); nelmts -= ((size_t)bytes_copied / elmt_size); } } done: /* Release selection iterators */ if (src_sel_iter) { if (src_sel_iter_init && H5S_SELECT_ITER_RELEASE(src_sel_iter) < 0) HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); src_sel_iter = H5FL_FREE(H5S_sel_iter_t, src_sel_iter); } if (dst_sel_iter) { if (dst_sel_iter_init && H5S_SELECT_ITER_RELEASE(dst_sel_iter) < 0) HDONE_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); dst_sel_iter = H5FL_FREE(H5S_sel_iter_t, dst_sel_iter); } /* Release vector arrays, if allocated */ if (src_off) src_off = H5FL_SEQ_FREE(hsize_t, src_off); if (src_len) src_len = H5FL_SEQ_FREE(size_t, src_len); if (dst_off) dst_off = H5FL_SEQ_FREE(hsize_t, dst_off); if (dst_len) dst_len = H5FL_SEQ_FREE(size_t, dst_len); FUNC_LEAVE_NOAPI(ret_value) } /* end H5D_select_io_mem() */ /*------------------------------------------------------------------------- * Function: H5D__select_read * * Purpose: Reads directly from file into application memory. * * Return: Non-negative on success/Negative on failure * *------------------------------------------------------------------------- */ herr_t H5D__select_read(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Call generic selection operation */ if (H5D__select_io(io_info, dset_info, dset_info->type_info.src_type_size) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error"); done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__select_read() */ /*------------------------------------------------------------------------- * Function: H5D__select_write * * Purpose: Writes directly from application memory into a file * * Return: Non-negative on success/Negative on failure * *------------------------------------------------------------------------- */ herr_t H5D__select_write(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Call generic selection operation */ if (H5D__select_io(io_info, dset_info, dset_info->type_info.dst_type_size) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__select_write() */