/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /****************/ /* 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 "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ #include "H5Sprivate.h" /* Dataspace */ #include "H5VLnative_private.h" /* Native VOL connector */ /****************/ /* Local Macros */ /****************/ /******************/ /* Local Typedefs */ /******************/ /********************/ /* Local Prototypes */ /********************/ /* Setup/teardown routines */ static herr_t H5D__ioinfo_init(H5D_t *dset, const H5D_type_info_t *type_info, H5D_storage_t *store, H5D_io_info_t *io_info); static herr_t H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write, H5D_type_info_t *type_info); #ifdef H5_HAVE_PARALLEL static herr_t H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, const H5S_t *file_space, const H5S_t *mem_space, const H5D_type_info_t *type_info); #endif /* H5_HAVE_PARALLEL */ static herr_t H5D__typeinfo_term(const H5D_type_info_t *type_info); /*********************/ /* Package Variables */ /*********************/ /*******************/ /* Local Variables */ /*******************/ /* Declare a free list to manage blocks of type conversion data */ H5FL_BLK_DEFINE(type_conv); /* Declare a free list to manage the H5D_chunk_map_t struct */ H5FL_DEFINE(H5D_chunk_map_t); /*------------------------------------------------------------------------- * Function: H5D__read * * Purpose: Reads (part of) a DATASET into application memory BUF. See * H5Dread() for complete details. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, December 4, 1997 * *------------------------------------------------------------------------- */ herr_t H5D__read(H5D_t *dataset, hid_t mem_type_id, H5S_t *mem_space, H5S_t *file_space, void *buf /*out*/) { H5D_chunk_map_t *fm = NULL; /* Chunk file<->memory mapping */ H5D_io_info_t io_info; /* Dataset I/O info */ H5D_type_info_t type_info; /* Datatype info for operation */ hbool_t type_info_init = FALSE; /* Whether the datatype info has been initialized */ H5S_t * projected_mem_space = NULL; /* If not NULL, ptr to dataspace containing a */ /* projection of the supplied mem_space to a new */ /* dataspace with rank equal to that of */ /* file_space. */ /* */ /* This field is only used if */ /* H5S_select_shape_same() returns TRUE when */ /* comparing the mem_space and the data_space, */ /* and the mem_space have different rank. */ /* */ /* Note that if this variable is used, the */ /* projected mem space must be discarded at the */ /* end of the function to avoid a memory leak. */ H5D_storage_t store; /* union of EFL and chunk pointer in file space */ hsize_t nelmts; /* total number of elmts */ hbool_t io_op_init = FALSE; /* Whether the I/O op has been initialized */ char fake_char; /* Temporary variable for NULL buffer pointers */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dataset->oloc.addr) /* check args */ HDassert(dataset && dataset->oloc.file); HDassert(file_space); HDassert(mem_space); /* Set up datatype info for operation */ if (H5D__typeinfo_init(dataset, mem_type_id, FALSE, &type_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info") type_info_init = TRUE; #ifdef H5_HAVE_PARALLEL /* Check for non-MPI-based VFD */ if (!(H5F_HAS_FEATURE(dataset->oloc.file, H5FD_FEAT_HAS_MPI))) { H5FD_mpio_xfer_t io_xfer_mode; /* MPI I/O transfer mode */ /* Get I/O transfer mode */ if (H5CX_get_io_xfer_mode(&io_xfer_mode) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode") /* Collective access is not permissible without a MPI based VFD */ if (io_xfer_mode == H5FD_MPIO_COLLECTIVE) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based drivers only") } /* end if */ #endif /*H5_HAVE_PARALLEL*/ /* Make certain that the number of elements in each selection is the same */ nelmts = H5S_GET_SELECT_NPOINTS(mem_space); if (nelmts != H5S_GET_SELECT_NPOINTS(file_space)) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest dataspaces have different number of elements selected") /* Check for a NULL buffer */ if (NULL == buf) { /* Check for any elements selected (which is invalid) */ if (nelmts > 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer") /* If the buffer is nil, and 0 element is selected, make a fake buffer. * This is for some MPI package like ChaMPIon on NCSA's tungsten which * doesn't support this feature. */ buf = &fake_char; } /* end if */ /* Make sure that both selections have their extents set */ if (!(H5S_has_extent(file_space))) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file dataspace does not have extent set") if (!(H5S_has_extent(mem_space))) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "memory dataspace does not have extent set") /* H5S_select_shape_same() has been modified to accept topologically identical * selections with different rank as having the same shape (if the most * rapidly changing coordinates match up), but the I/O code still has * difficulties with the notion. * * To solve this, we check to see if H5S_select_shape_same() returns true, * and if the ranks of the mem and file spaces are different. If they are, * construct a new mem space that is equivalent to the old mem space, and * use that instead. * * Note that in general, this requires us to touch up the memory buffer as * well. */ if (nelmts > 0 && TRUE == H5S_SELECT_SHAPE_SAME(mem_space, file_space) && H5S_GET_EXTENT_NDIMS(mem_space) != H5S_GET_EXTENT_NDIMS(file_space)) { const void *adj_buf = NULL; /* Pointer to the location in buf corresponding */ /* to the beginning of the projected mem space. */ /* Attempt to construct projected dataspace for memory dataspace */ if (H5S_select_construct_projection(mem_space, &projected_mem_space, (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, &adj_buf, type_info.dst_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to construct projected memory dataspace") HDassert(projected_mem_space); HDassert(adj_buf); /* Switch to using projected memory dataspace & adjusted buffer */ mem_space = projected_mem_space; buf = (void *)adj_buf; /* Casting away 'const' OK -QAK */ } /* end if */ /* Retrieve dataset properties */ /* */ /* If space hasn't been allocated and not using external storage, * return fill value to buffer if fill time is upon allocation, or * do nothing if fill time is never. If the dataset is compact and * fill time is NEVER, there is no way to tell whether part of data * has been overwritten. So just proceed in reading. */ if (nelmts > 0 && dataset->shared->dcpl_cache.efl.nused == 0 && !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) && !(dataset->shared->layout.ops->is_data_cached && (*dataset->shared->layout.ops->is_data_cached)(dataset->shared))) { H5D_fill_value_t fill_status; /* Whether/How the fill value is defined */ /* Retrieve dataset's fill-value properties */ if (H5P_is_fill_value_defined(&dataset->shared->dcpl_cache.fill, &fill_status) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't tell if fill value defined") /* Should be impossible, but check anyway... */ if (fill_status == H5D_FILL_VALUE_UNDEFINED && (dataset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_ALLOC || dataset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_IFSET)) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "read failed: dataset doesn't exist, no data can be read") /* If we're never going to fill this dataset, just leave the junk in the user's buffer */ if (dataset->shared->dcpl_cache.fill.fill_time == H5D_FILL_TIME_NEVER) HGOTO_DONE(SUCCEED) /* Go fill the user's selection with the dataset's fill value */ if (H5D__fill(dataset->shared->dcpl_cache.fill.buf, dataset->shared->type, buf, type_info.mem_type, mem_space) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "filling buf failed") else HGOTO_DONE(SUCCEED) } /* end if */ /* Set up I/O operation */ io_info.op_type = H5D_IO_OP_READ; io_info.u.rbuf = buf; if (H5D__ioinfo_init(dataset, &type_info, &store, &io_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to set up I/O operation") /* Sanity check that space is allocated, if there are elements */ if (nelmts > 0) HDassert((*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) || (dataset->shared->layout.ops->is_data_cached && (*dataset->shared->layout.ops->is_data_cached)(dataset->shared)) || dataset->shared->dcpl_cache.efl.nused > 0 || dataset->shared->layout.type == H5D_COMPACT); /* Allocate the chunk map */ if (NULL == (fm = H5FL_CALLOC(H5D_chunk_map_t))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk map") /* Call storage method's I/O initialization routine */ if (io_info.layout_ops.io_init && (*io_info.layout_ops.io_init)(&io_info, &type_info, nelmts, file_space, mem_space, fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize I/O info") io_op_init = TRUE; #ifdef H5_HAVE_PARALLEL /* Adjust I/O info for any parallel I/O */ if (H5D__ioinfo_adjust(&io_info, dataset, file_space, mem_space, &type_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to adjust I/O info for parallel I/O") #endif /*H5_HAVE_PARALLEL*/ /* Invoke correct "high level" I/O routine */ if ((*io_info.io_ops.multi_read)(&io_info, &type_info, nelmts, file_space, mem_space, fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data") done: /* Shut down the I/O op information */ if (io_op_init && io_info.layout_ops.io_term && (*io_info.layout_ops.io_term)(fm) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down I/O op info") if (fm) fm = H5FL_FREE(H5D_chunk_map_t, fm); /* Shut down datatype info for operation */ if (type_info_init && H5D__typeinfo_term(&type_info) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down type info") /* discard projected mem space if it was created */ if (NULL != projected_mem_space) if (H5S_close(projected_mem_space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down projected memory dataspace") FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__read() */ /*------------------------------------------------------------------------- * Function: H5D__write * * Purpose: Writes (part of) a DATASET to a file from application memory * BUF. See H5Dwrite() for complete details. * * Return: Non-negative on success/Negative on failure * * Programmer: Robb Matzke * Thursday, December 4, 1997 * *------------------------------------------------------------------------- */ herr_t H5D__write(H5D_t *dataset, hid_t mem_type_id, H5S_t *mem_space, H5S_t *file_space, const void *buf) { H5D_chunk_map_t *fm = NULL; /* Chunk file<->memory mapping */ H5D_io_info_t io_info; /* Dataset I/O info */ H5D_type_info_t type_info; /* Datatype info for operation */ hbool_t type_info_init = FALSE; /* Whether the datatype info has been initialized */ hbool_t should_alloc_space = FALSE; /* Whether or not to initialize dataset's storage */ H5S_t * projected_mem_space = NULL; /* If not NULL, ptr to dataspace containing a */ /* projection of the supplied mem_space to a new */ /* dataspace with rank equal to that of */ /* file_space. */ /* */ /* This field is only used if */ /* H5S_select_shape_same() returns TRUE when */ /* comparing the mem_space and the data_space, */ /* and the mem_space have different rank. */ /* */ /* Note that if this variable is used, the */ /* projected mem space must be discarded at the */ /* end of the function to avoid a memory leak. */ H5D_storage_t store; /* union of EFL and chunk pointer in file space */ hsize_t nelmts; /* total number of elmts */ hbool_t io_op_init = FALSE; /* Whether the I/O op has been initialized */ char fake_char; /* Temporary variable for NULL buffer pointers */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE_TAG(dataset->oloc.addr) /* check args */ HDassert(dataset && dataset->oloc.file); HDassert(file_space); HDassert(mem_space); /* All filters in the DCPL must have encoding enabled. */ if (!dataset->shared->checked_filters) { if (H5Z_can_apply(dataset->shared->dcpl_id, dataset->shared->type_id) < 0) HGOTO_ERROR(H5E_PLINE, H5E_CANAPPLY, FAIL, "can't apply filters") dataset->shared->checked_filters = TRUE; } /* end if */ /* Check if we are allowed to write to this file */ if (0 == (H5F_INTENT(dataset->oloc.file) & H5F_ACC_RDWR)) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file") /* Set up datatype info for operation */ if (H5D__typeinfo_init(dataset, mem_type_id, TRUE, &type_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info") type_info_init = TRUE; /* Various MPI based checks */ #ifdef H5_HAVE_PARALLEL if (H5F_HAS_FEATURE(dataset->oloc.file, H5FD_FEAT_HAS_MPI)) { /* If MPI based VFD is used, no VL or region reference datatype support yet. */ /* This is because they use the global heap in the file and we don't */ /* support parallel access of that yet */ if (H5T_is_vl_storage(type_info.mem_type) > 0) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "Parallel IO does not support writing VL or region reference datatypes yet") } /* end if */ else { H5FD_mpio_xfer_t io_xfer_mode; /* MPI I/O transfer mode */ /* Get I/O transfer mode */ if (H5CX_get_io_xfer_mode(&io_xfer_mode) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode") /* Collective access is not permissible without a MPI based VFD */ if (io_xfer_mode == H5FD_MPIO_COLLECTIVE) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "collective access for MPI-based driver only") } /* end else */ #endif /*H5_HAVE_PARALLEL*/ /* Make certain that the number of elements in each selection is the same */ nelmts = H5S_GET_SELECT_NPOINTS(mem_space); if (nelmts != H5S_GET_SELECT_NPOINTS(file_space)) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest dataspaces have different number of elements selected") /* Check for a NULL buffer */ if (NULL == buf) { /* Check for any elements selected (which is invalid) */ if (nelmts > 0) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer") /* If the buffer is nil, and 0 element is selected, make a fake buffer. * This is for some MPI package like ChaMPIon on NCSA's tungsten which * doesn't support this feature. */ buf = &fake_char; } /* end if */ /* Make sure that both selections have their extents set */ if (!(H5S_has_extent(file_space))) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file dataspace does not have extent set") if (!(H5S_has_extent(mem_space))) HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "memory dataspace does not have extent set") /* H5S_select_shape_same() has been modified to accept topologically * identical selections with different rank as having the same shape * (if the most rapidly changing coordinates match up), but the I/O * code still has difficulties with the notion. * * To solve this, we check to see if H5S_select_shape_same() returns * true, and if the ranks of the mem and file spaces are different. * If the are, construct a new mem space that is equivalent to the * old mem space, and use that instead. * * Note that in general, this requires us to touch up the memory buffer * as well. */ if (nelmts > 0 && TRUE == H5S_SELECT_SHAPE_SAME(mem_space, file_space) && H5S_GET_EXTENT_NDIMS(mem_space) != H5S_GET_EXTENT_NDIMS(file_space)) { const void *adj_buf = NULL; /* Pointer to the location in buf corresponding */ /* to the beginning of the projected mem space. */ /* Attempt to construct projected dataspace for memory dataspace */ if (H5S_select_construct_projection(mem_space, &projected_mem_space, (unsigned)H5S_GET_EXTENT_NDIMS(file_space), buf, &adj_buf, type_info.src_type_size) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to construct projected memory dataspace") HDassert(projected_mem_space); HDassert(adj_buf); /* Switch to using projected memory dataspace & adjusted buffer */ mem_space = projected_mem_space; buf = adj_buf; } /* end if */ /* Retrieve dataset properties */ /* */ /* Set up I/O operation */ io_info.op_type = H5D_IO_OP_WRITE; io_info.u.wbuf = buf; if (H5D__ioinfo_init(dataset, &type_info, &store, &io_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up I/O operation") /* Allocate dataspace and initialize it if it hasn't been. */ should_alloc_space = dataset->shared->dcpl_cache.efl.nused == 0 && !(*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage); /* * If not using an MPI-based VFD, we only need to allocate * and initialize storage if there's a selection in the * dataset's dataspace. Otherwise, we always need to participate * in the storage allocation since this may use collective * operations and we will hang if we don't participate. */ if (!H5F_HAS_FEATURE(dataset->oloc.file, H5FD_FEAT_HAS_MPI)) should_alloc_space = should_alloc_space && (nelmts > 0); if (should_alloc_space) { hssize_t file_nelmts; /* Number of elements in file dataset's dataspace */ hbool_t full_overwrite; /* Whether we are over-writing all the elements */ /* Get the number of elements in file dataset's dataspace */ if ((file_nelmts = H5S_GET_EXTENT_NPOINTS(file_space)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "can't retrieve number of elements in file dataset") /* Always allow fill values to be written if the dataset has a VL datatype */ if (H5T_detect_class(dataset->shared->type, H5T_VLEN, FALSE)) full_overwrite = FALSE; else full_overwrite = (hbool_t)((hsize_t)file_nelmts == nelmts ? TRUE : FALSE); /* Allocate storage */ if (H5D__alloc_storage(&io_info, H5D_ALLOC_WRITE, full_overwrite, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") } /* end if */ /* Allocate the chunk map */ if (NULL == (fm = H5FL_CALLOC(H5D_chunk_map_t))) HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk map") /* Call storage method's I/O initialization routine */ if (io_info.layout_ops.io_init && (*io_info.layout_ops.io_init)(&io_info, &type_info, nelmts, file_space, mem_space, fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize I/O info") io_op_init = TRUE; #ifdef H5_HAVE_PARALLEL /* Adjust I/O info for any parallel I/O */ if (H5D__ioinfo_adjust(&io_info, dataset, file_space, mem_space, &type_info) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to adjust I/O info for parallel I/O") #endif /*H5_HAVE_PARALLEL*/ /* Invoke correct "high level" I/O routine */ if ((*io_info.io_ops.multi_write)(&io_info, &type_info, nelmts, file_space, mem_space, fm) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data") #ifdef OLD_WAY /* * This was taken out because it can be called in a parallel program with * independent access, causing the metadata cache to get corrupted. Its been * disabled for all types of access (serial as well as parallel) to make the * modification time consistent for all programs. -QAK * * We should set a value in the dataset's shared information instead and flush * it to the file when the dataset is being closed. -QAK */ /* * Update modification time. We have to do this explicitly because * writing to a dataset doesn't necessarily change the object header. */ if (H5O_touch(&(dataset->oloc), FALSE) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update modification time") #endif /* OLD_WAY */ done: /* Shut down the I/O op information */ if (io_op_init && io_info.layout_ops.io_term && (*io_info.layout_ops.io_term)(fm) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down I/O op info") if (fm) fm = H5FL_FREE(H5D_chunk_map_t, fm); /* Shut down datatype info for operation */ if (type_info_init && H5D__typeinfo_term(&type_info) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down type info") /* discard projected mem space if it was created */ if (NULL != projected_mem_space) if (H5S_close(projected_mem_space) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTCLOSEOBJ, FAIL, "unable to shut down projected memory dataspace") FUNC_LEAVE_NOAPI_TAG(ret_value) } /* end H5D__write() */ /*------------------------------------------------------------------------- * Function: H5D__ioinfo_init * * Purpose: Routine for determining correct I/O operations for * each I/O action. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, September 30, 2004 * *------------------------------------------------------------------------- */ static herr_t H5D__ioinfo_init(H5D_t *dset, const H5D_type_info_t *type_info, H5D_storage_t *store, H5D_io_info_t *io_info) { FUNC_ENTER_STATIC_NOERR /* check args */ HDassert(dset); HDassert(dset->oloc.file); HDassert(type_info); HDassert(type_info->tpath); HDassert(io_info); /* Set up "normal" I/O fields */ io_info->dset = dset; io_info->f_sh = H5F_SHARED(dset->oloc.file); io_info->store = store; /* Set I/O operations to initial values */ io_info->layout_ops = *dset->shared->layout.ops; /* Set the "high-level" I/O operations for the dataset */ io_info->io_ops.multi_read = dset->shared->layout.ops->ser_read; io_info->io_ops.multi_write = dset->shared->layout.ops->ser_write; /* Set the I/O operations for reading/writing single blocks on disk */ if (type_info->is_xform_noop && type_info->is_conv_noop) { /* * If there is no data transform or type conversion then read directly into * the application's buffer. This saves at least one mem-to-mem copy. */ io_info->io_ops.single_read = H5D__select_read; io_info->io_ops.single_write = H5D__select_write; } /* end if */ else { /* * This is the general case (type conversion, usually). */ io_info->io_ops.single_read = H5D__scatgath_read; io_info->io_ops.single_write = H5D__scatgath_write; } /* end else */ #ifdef H5_HAVE_PARALLEL /* Determine if the file was opened with an MPI VFD */ io_info->using_mpi_vfd = H5F_HAS_FEATURE(dset->oloc.file, H5FD_FEAT_HAS_MPI); #endif /* H5_HAVE_PARALLEL */ FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D__ioinfo_init() */ /*------------------------------------------------------------------------- * Function: H5D__typeinfo_init * * Purpose: Routine for determining correct datatype information for * each I/O action. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Tuesday, March 4, 2008 * *------------------------------------------------------------------------- */ static herr_t H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write, H5D_type_info_t *type_info) { const H5T_t * src_type; /* Source datatype */ const H5T_t * dst_type; /* Destination datatype */ H5Z_data_xform_t *data_transform; /* Data transform info */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* check args */ HDassert(type_info); HDassert(dset); /* Patch the top level file pointer for dt->shared->u.vlen.f if needed */ if (H5T_patch_vlen_file(dset->shared->type, H5F_VOL_OBJ(dset->oloc.file)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't patch VL datatype file pointer") /* Initialize type info safely */ HDmemset(type_info, 0, sizeof(*type_info)); /* Get the memory & dataset datatypes */ if (NULL == (type_info->mem_type = (const H5T_t *)H5I_object_verify(mem_type_id, H5I_DATATYPE))) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype") type_info->dset_type = dset->shared->type; if (do_write) { src_type = type_info->mem_type; dst_type = dset->shared->type; type_info->src_type_id = mem_type_id; type_info->dst_type_id = dset->shared->type_id; } /* end if */ else { src_type = dset->shared->type; dst_type = type_info->mem_type; type_info->src_type_id = dset->shared->type_id; type_info->dst_type_id = mem_type_id; } /* end else */ /* Locate the type conversion function and dataspace conversion * functions, and set up the element numbering information. If a data * type conversion is necessary then register datatype IDs. Data type * conversion is necessary if the user has set the `need_bkg' to a high * enough value in xfer_parms since turning off datatype conversion also * turns off background preservation. */ if (NULL == (type_info->tpath = H5T_path_find(src_type, dst_type))) HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest datatype") /* Retrieve info from API context */ if (H5CX_get_data_transform(&data_transform) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data transform info") /* Precompute some useful information */ type_info->src_type_size = H5T_get_size(src_type); type_info->dst_type_size = H5T_get_size(dst_type); type_info->max_type_size = MAX(type_info->src_type_size, type_info->dst_type_size); type_info->is_conv_noop = H5T_path_noop(type_info->tpath); type_info->is_xform_noop = H5Z_xform_noop(data_transform); if (type_info->is_xform_noop && type_info->is_conv_noop) { type_info->cmpd_subset = NULL; type_info->need_bkg = H5T_BKG_NO; } /* end if */ else { void * tconv_buf; /* Temporary conversion buffer pointer */ void * bkgr_buf; /* Background conversion buffer pointer */ size_t max_temp_buf; /* Maximum temporary buffer size */ H5T_bkg_t bkgr_buf_type; /* Background buffer type */ size_t target_size; /* Desired buffer size */ /* Get info from API context */ if (H5CX_get_max_temp_buf(&max_temp_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve max. temp. buf size") if (H5CX_get_tconv_buf(&tconv_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve temp. conversion buffer pointer") if (H5CX_get_bkgr_buf(&bkgr_buf) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve background conversion buffer pointer") if (H5CX_get_bkgr_buf_type(&bkgr_buf_type) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve background buffer type") /* Check if the datatypes are compound subsets of one another */ type_info->cmpd_subset = H5T_path_compound_subset(type_info->tpath); /* Check if we need a background buffer */ if (do_write && H5T_detect_class(dset->shared->type, H5T_VLEN, FALSE)) type_info->need_bkg = H5T_BKG_YES; else { H5T_bkg_t path_bkg; /* Type conversion's background info */ if ((path_bkg = H5T_path_bkg(type_info->tpath))) { /* Retrieve the bkgr buffer property */ type_info->need_bkg = bkgr_buf_type; type_info->need_bkg = MAX(path_bkg, type_info->need_bkg); } /* end if */ else type_info->need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/ } /* end else */ /* Set up datatype conversion/background buffers */ target_size = max_temp_buf; /* If the buffer is too small to hold even one element, try to make it bigger */ if (target_size < type_info->max_type_size) { hbool_t default_buffer_info; /* Whether the buffer information are the defaults */ /* Detect if we have all default settings for buffers */ default_buffer_info = (hbool_t)((H5D_TEMP_BUF_SIZE == max_temp_buf) && (NULL == tconv_buf) && (NULL == bkgr_buf)); /* Check if we are using the default buffer info */ if (default_buffer_info) /* OK to get bigger for library default settings */ target_size = type_info->max_type_size; else /* Don't get bigger than the application has requested */ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small") } /* end if */ /* Compute the number of elements that will fit into buffer */ type_info->request_nelmts = target_size / type_info->max_type_size; /* Sanity check elements in temporary buffer */ if (type_info->request_nelmts == 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "temporary buffer max size is too small") /* Get a temporary buffer for type conversion unless the app has already * supplied one through the xfer properties. Instead of allocating a * buffer which is the exact size, we allocate the target size. */ if (NULL == (type_info->tconv_buf = (uint8_t *)tconv_buf)) { /* Allocate temporary buffer */ if (NULL == (type_info->tconv_buf = H5FL_BLK_CALLOC(type_conv, target_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for type conversion") type_info->tconv_buf_allocated = TRUE; } /* end if */ if (type_info->need_bkg && NULL == (type_info->bkg_buf = (uint8_t *)bkgr_buf)) { size_t bkg_size; /* Desired background buffer size */ /* Compute the background buffer size */ /* (don't try to use buffers smaller than the default size) */ bkg_size = type_info->request_nelmts * type_info->dst_type_size; if (bkg_size < max_temp_buf) bkg_size = max_temp_buf; /* Allocate background buffer */ /* (Need calloc()-like call since memory needs to be initialized) */ if (NULL == (type_info->bkg_buf = H5FL_BLK_CALLOC(type_conv, bkg_size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for background conversion") type_info->bkg_buf_allocated = TRUE; } /* end if */ } /* end else */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__typeinfo_init() */ #ifdef H5_HAVE_PARALLEL /*------------------------------------------------------------------------- * Function: H5D__ioinfo_adjust * * Purpose: Adjust operation's I/O info for any parallel I/O * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, March 27, 2008 * *------------------------------------------------------------------------- */ static herr_t H5D__ioinfo_adjust(H5D_io_info_t *io_info, const H5D_t *dset, const H5S_t *file_space, const H5S_t *mem_space, const H5D_type_info_t *type_info) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_STATIC /* check args */ HDassert(dset); HDassert(dset->oloc.file); HDassert(mem_space); HDassert(file_space); HDassert(type_info); HDassert(type_info->tpath); HDassert(io_info); /* Reset the actual io mode properties to the default values in case * the DXPL (if it's non-default) was previously used in a collective * I/O operation. */ if (!H5CX_is_def_dxpl()) { H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_NO_CHUNK_OPTIMIZATION); H5CX_set_mpio_actual_io_mode(H5D_MPIO_NO_COLLECTIVE); } /* end if */ /* Make any parallel I/O adjustments */ if (io_info->using_mpi_vfd) { H5FD_mpio_xfer_t xfer_mode; /* Parallel transfer for this request */ htri_t opt; /* Flag whether a selection is optimizable */ /* Get the original state of parallel I/O transfer mode */ if (H5CX_get_io_xfer_mode(&xfer_mode) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode") /* Get MPI communicator */ if (MPI_COMM_NULL == (io_info->comm = H5F_mpi_get_comm(dset->oloc.file))) HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve MPI communicator") /* Check if we can set direct MPI-IO read/write functions */ if ((opt = H5D__mpio_opt_possible(io_info, file_space, mem_space, type_info)) < 0) HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "invalid check for direct IO dataspace ") /* Check if we can use the optimized parallel I/O routines */ if (opt == TRUE) { /* Override the I/O op pointers to the MPI-specific routines */ io_info->io_ops.multi_read = dset->shared->layout.ops->par_read; io_info->io_ops.multi_write = dset->shared->layout.ops->par_write; io_info->io_ops.single_read = H5D__mpio_select_read; io_info->io_ops.single_write = H5D__mpio_select_write; } /* end if */ else { /* Check if there are any filters in the pipeline. If there are, * we cannot break to independent I/O if this is a write operation * with multiple ranks involved; otherwise, there will be metadata * inconsistencies in the file. */ if (io_info->op_type == H5D_IO_OP_WRITE && io_info->dset->shared->dcpl_cache.pline.nused > 0) { int comm_size = 0; /* Retrieve size of MPI communicator used for file */ if ((comm_size = H5F_shared_mpi_get_size(io_info->f_sh)) < 0) HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "can't get MPI communicator size") if (comm_size > 1) { char local_no_coll_cause_string[512]; char global_no_coll_cause_string[512]; if (H5D__mpio_get_no_coll_cause_strings(local_no_coll_cause_string, 512, global_no_coll_cause_string, 512) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get reasons for breaking collective I/O") HGOTO_ERROR(H5E_IO, H5E_NO_INDEPENDENT, FAIL, "Can't perform independent write with filters in pipeline.\n" " The following caused a break from collective I/O:\n" " Local causes: %s\n" " Global causes: %s", local_no_coll_cause_string, global_no_coll_cause_string); } } /* If we won't be doing collective I/O, but the user asked for * collective I/O, change the request to use independent I/O */ if (xfer_mode == H5FD_MPIO_COLLECTIVE) { /* Change the xfer_mode to independent for handling the I/O */ if (H5CX_set_io_xfer_mode(H5FD_MPIO_INDEPENDENT) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O transfer mode") } /* end if */ } /* end else */ } /* end if */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__ioinfo_adjust() */ #endif /* H5_HAVE_PARALLEL */ /*------------------------------------------------------------------------- * Function: H5D__typeinfo_term * * Purpose: Common logic for terminating a type info object * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, March 6, 2008 * *------------------------------------------------------------------------- */ static herr_t H5D__typeinfo_term(const H5D_type_info_t *type_info) { FUNC_ENTER_STATIC_NOERR /* Check for releasing datatype conversion & background buffers */ if (type_info->tconv_buf_allocated) { HDassert(type_info->tconv_buf); (void)H5FL_BLK_FREE(type_conv, type_info->tconv_buf); } /* end if */ if (type_info->bkg_buf_allocated) { HDassert(type_info->bkg_buf); (void)H5FL_BLK_FREE(type_conv, type_info->bkg_buf); } /* end if */ FUNC_LEAVE_NOAPI(SUCCEED) } /* end H5D__typeinfo_term() */