/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 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://support.hdfgroup.org/ftp/HDF5/releases. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /****************/ /* Module Setup */ /****************/ #define H5D_PACKAGE /*suppress error about including H5Dpkg */ /***********/ /* Headers */ /***********/ #include "H5private.h" /* Generic Functions */ #include "H5Dpkg.h" /* Datasets */ #include "H5Eprivate.h" /* Error handling */ #include "H5HLprivate.h" /* Local heaps */ /****************/ /* Local Macros */ /****************/ /******************/ /* Local Typedefs */ /******************/ /********************/ /* Local Prototypes */ /********************/ /*********************/ /* Package Variables */ /*********************/ /*****************************/ /* Library Private Variables */ /*****************************/ /*******************/ /* Local Variables */ /*******************/ /*------------------------------------------------------------------------- * Function: H5D__layout_set_io_ops * * Purpose: Set the I/O operation function pointers for a dataset, * according to the dataset's layout * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, March 20, 2008 * *------------------------------------------------------------------------- */ herr_t H5D__layout_set_io_ops(const H5D_t *dataset) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* check args */ HDassert(dataset); /* Set the I/O functions for each layout type */ switch (dataset->shared->layout.type) { case H5D_CONTIGUOUS: if (dataset->shared->dcpl_cache.efl.nused > 0) dataset->shared->layout.ops = H5D_LOPS_EFL; else dataset->shared->layout.ops = H5D_LOPS_CONTIG; break; case H5D_CHUNKED: dataset->shared->layout.ops = H5D_LOPS_CHUNK; /* Set the chunk operations */ /* (Only "B-tree" indexing type currently supported) */ dataset->shared->layout.storage.u.chunk.ops = H5D_COPS_BTREE; break; case H5D_COMPACT: dataset->shared->layout.ops = H5D_LOPS_COMPACT; break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unknown storage method") } /* end switch */ /*lint !e788 All appropriate cases are covered */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__layout_set_io_ops() */ /*------------------------------------------------------------------------- * Function: H5D__layout_meta_size * * Purpose: Returns the size of the raw message in bytes except raw data * part for compact dataset. This function doesn't take into * account message alignment. * * Return: Success: Message data size in bytes * Failure: 0 * * Programmer: Raymond Lu * August 14, 2002 * *------------------------------------------------------------------------- */ size_t H5D__layout_meta_size(const H5F_t *f, const H5O_layout_t *layout, hbool_t include_compact_data) { size_t ret_value = 0; /* Return value */ FUNC_ENTER_PACKAGE /* check args */ HDassert(f); HDassert(layout); ret_value = 1 + /* Version number */ 1; /* layout class type */ switch (layout->type) { case H5D_COMPACT: /* This information only present in older versions of message */ /* Size of raw data */ ret_value += 2; if (include_compact_data) ret_value += layout->storage.u.compact.size; /* data for compact dataset */ break; case H5D_CONTIGUOUS: /* This information only present in older versions of message */ ret_value += H5F_SIZEOF_ADDR(f); /* Address of data */ ret_value += H5F_SIZEOF_SIZE(f); /* Length of data */ break; case H5D_CHUNKED: /* Number of dimensions (1 byte) */ HDassert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS); ret_value++; /* Dimension sizes */ ret_value += layout->u.chunk.ndims * 4; /* B-tree address */ ret_value += H5F_SIZEOF_ADDR(f); /* Address of data */ break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: default: HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, 0, "Invalid layout class") } /* end switch */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__layout_meta_size() */ /*------------------------------------------------------------------------- * Function: H5D__layout_oh_create * * Purpose: Create layout/pline/efl information for dataset * * Return: Success: SUCCEED * Failure: FAIL * * Programmer: Quincey Koziol * Monday, July 27, 2009 * *------------------------------------------------------------------------- */ herr_t H5D__layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset, hid_t dapl_id) { H5O_layout_t * layout; /* Dataset's layout information */ const H5O_fill_t *fill_prop; /* Pointer to dataset's fill value information */ hbool_t layout_init = FALSE; /* Flag to indicate that chunk information was initialized */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity checking */ HDassert(file); HDassert(oh); HDassert(dset); /* Set some local variables, for convenience */ layout = &dset->shared->layout; fill_prop = &dset->shared->dcpl_cache.fill; /* Update the filters message, if this is a chunked dataset */ if (layout->type == H5D_CHUNKED) { H5O_pline_t *pline; /* Dataset's I/O pipeline information */ pline = &dset->shared->dcpl_cache.pline; if (pline->nused > 0 && H5O_msg_append_oh(file, dxpl_id, oh, H5O_PLINE_ID, H5O_MSG_FLAG_CONSTANT, 0, pline) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message") } /* end if */ /* Initialize the layout information for the new dataset */ if (dset->shared->layout.ops->init && (dset->shared->layout.ops->init)(file, dxpl_id, dset, dapl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize layout information") /* Indicate that the layout information was initialized */ layout_init = TRUE; /* * Allocate storage if space allocate time is early; otherwise delay * allocation until later. */ if (fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY) if (H5D__alloc_storage(dset, dxpl_id, H5D_ALLOC_CREATE, FALSE, NULL) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage") /* Update external storage message, if it's used */ if (dset->shared->dcpl_cache.efl.nused > 0) { H5O_efl_t *efl = &dset->shared->dcpl_cache.efl; /* Dataset's external file list */ H5HL_t * heap; /* Pointer to local heap for EFL file names */ size_t heap_size = H5HL_ALIGN(1); size_t u; /* Determine size of heap needed to stored the file names */ for (u = 0; u < efl->nused; ++u) heap_size += H5HL_ALIGN(HDstrlen(efl->slot[u].name) + 1); /* Create the heap for the EFL file names */ if (H5HL_create(file, dxpl_id, heap_size, &efl->heap_addr /*out*/) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create EFL file name heap") /* Pin the heap down in memory */ if (NULL == (heap = H5HL_protect(file, dxpl_id, efl->heap_addr, H5AC_WRITE))) HGOTO_ERROR(H5E_DATASET, H5E_CANTPROTECT, FAIL, "unable to protect EFL file name heap") /* Insert "empty" name first */ if ((size_t)(-1) == H5HL_insert(file, dxpl_id, heap, (size_t)1, "")) { H5HL_unprotect(heap); HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap") } /* end if */ for (u = 0; u < efl->nused; ++u) { size_t offset; /* Offset of file name in heap */ /* Insert file name into heap */ if ((size_t)(-1) == (offset = H5HL_insert(file, dxpl_id, heap, HDstrlen(efl->slot[u].name) + 1, efl->slot[u].name))) { H5HL_unprotect(heap); HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap") } /* end if */ /* Store EFL file name offset */ HDassert(0 == efl->slot[u].name_offset); efl->slot[u].name_offset = offset; } /* end for */ /* Release the heap */ if (H5HL_unprotect(heap) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTUNPROTECT, FAIL, "unable to unprotect EFL file name heap") heap = NULL; /* Insert EFL message into dataset object header */ if (H5O_msg_append_oh(file, dxpl_id, oh, H5O_EFL_ID, H5O_MSG_FLAG_CONSTANT, 0, efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update external file list message") } /* end if */ /* Create layout message */ /* (Don't make layout message constant unless allocation time is early, since space may not be allocated) */ /* (Note: this is relying on H5D__alloc_storage not calling H5O_msg_write during dataset creation) */ if (H5O_msg_append_oh(file, dxpl_id, oh, H5O_LAYOUT_ID, ((fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY && H5D_COMPACT != layout->type) ? H5O_MSG_FLAG_CONSTANT : 0), 0, layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout") done: /* Error cleanup */ if (ret_value < 0) { if (dset->shared->layout.type == H5D_CHUNKED && layout_init) { if (H5D__chunk_dest(file, dxpl_id, dset) < 0) HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy chunk cache") } /* end if */ } /* end if */ FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__layout_oh_create() */ /*------------------------------------------------------------------------- * Function: H5D__layout_oh_read * * Purpose: Read layout/pline/efl information for dataset * * Return: Success: SUCCEED * Failure: FAIL * * Programmer: Quincey Koziol * Monday, July 27, 2009 * *------------------------------------------------------------------------- */ herr_t H5D__layout_oh_read(H5D_t *dataset, hid_t dxpl_id, hid_t dapl_id, H5P_genplist_t *plist) { htri_t msg_exists; /* Whether a particular type of message exists */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity checking */ HDassert(dataset); HDassert(plist); /* Get the optional filters message */ if ((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_PLINE_ID, dxpl_id)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists") if (msg_exists) { /* Retrieve the I/O pipeline message */ if (NULL == H5O_msg_read(&(dataset->oloc), H5O_PLINE_ID, &dataset->shared->dcpl_cache.pline, dxpl_id)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message") /* Set the I/O pipeline info in the property list */ if (H5P_set(plist, H5O_CRT_PIPELINE_NAME, &dataset->shared->dcpl_cache.pline) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set pipeline") } /* end if */ /* * Get the raw data layout info. It's actually stored in two locations: * the storage message of the dataset (dataset->storage) and certain * values are copied to the dataset create plist so the user can query * them. */ if (NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout), dxpl_id)) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message") /* Check for external file list message (which might not exist) */ if ((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_EFL_ID, dxpl_id)) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists") if (msg_exists) { /* Retrieve the EFL message */ if (NULL == H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl, dxpl_id)) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message") /* Set the EFL info in the property list */ if (H5P_set(plist, H5D_CRT_EXT_FILE_LIST_NAME, &dataset->shared->dcpl_cache.efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set external file list") /* Set the dataset's I/O operations */ dataset->shared->layout.ops = H5D_LOPS_EFL; } /* end if */ /* Sanity check that the layout operations are set up */ HDassert(dataset->shared->layout.ops); /* Adjust chunk dimensions to omit datatype size (in last dimension) for creation property */ if (H5D_CHUNKED == dataset->shared->layout.type) dataset->shared->layout.u.chunk.ndims--; /* Copy layout to the DCPL */ if (H5P_set(plist, H5D_CRT_LAYOUT_NAME, &dataset->shared->layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout") /* Adjust chunk dimensions back again (*sigh*) */ if (H5D_CHUNKED == dataset->shared->layout.type) dataset->shared->layout.u.chunk.ndims++; switch (dataset->shared->layout.type) { case H5D_CONTIGUOUS: { hsize_t tmp_size; /* Temporary holder for raw data size */ size_t tmp_sieve_buf_size; /* Temporary holder for sieve buffer size */ /* 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 (dataset->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(dataset->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(dataset->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 */ dataset->shared->layout.storage.u.contig.size = tmp_size; } else tmp_size = dataset->shared->layout.storage.u.contig.size; /* Get the sieve buffer size for the file */ tmp_sieve_buf_size = H5F_SIEVE_BUF_SIZE(dataset->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) dataset->shared->cache.contig.sieve_buf_size = tmp_size; else dataset->shared->cache.contig.sieve_buf_size = tmp_sieve_buf_size; } break; case H5D_CHUNKED: /* Initialize the chunk cache for the dataset */ if (H5D__chunk_init(dataset->oloc.file, dxpl_id, dataset, dapl_id) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize chunk cache") break; case H5D_COMPACT: break; case H5D_LAYOUT_ERROR: case H5D_NLAYOUTS: default: HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unknown storage method") } /* end switch */ /*lint !e788 All appropriate cases are covered */ done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__layout_oh_read() */ /*------------------------------------------------------------------------- * Function: H5D__layout_oh_write * * Purpose: Write layout information for dataset * * Return: Success: SUCCEED * Failure: FAIL * * Programmer: Quincey Koziol * Monday, July 27, 2009 * *------------------------------------------------------------------------- */ herr_t H5D__layout_oh_write(H5D_t *dataset, hid_t dxpl_id, H5O_t *oh, unsigned update_flags) { herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_PACKAGE /* Sanity checking */ HDassert(dataset); HDassert(oh); /* Write the layout message to the dataset's header */ if (H5O_msg_write_oh(dataset->oloc.file, dxpl_id, oh, H5O_LAYOUT_ID, H5O_MSG_FLAG_CONSTANT, update_flags, &dataset->shared->layout) < 0) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout message") done: FUNC_LEAVE_NOAPI(ret_value) } /* end H5D__layout_oh_write() */