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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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 files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdfgroup.org/HDF5/doc/Copyright.html. 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;
FUNC_ENTER_PACKAGE
/* check args */
HDassert(f);
HDassert(layout);
ret_value = 1 + /* Version number */
1; /* layout class type */
switch(layout->type) {
case H5D_COMPACT:
/* 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:
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_TAG(dxpl_id, dset->oloc.addr, FAIL)
/* 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__NO_FLAGS_SET)))
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_TAG(ret_value, FAIL)
} /* 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/pline/efl 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() */
|
