/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* 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. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/****************/
/* 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 */
#ifdef H5_HAVE_PARALLEL
/* Remove this if H5R_DATASET_REGION is no longer used in this file */
#include "H5Rpublic.h"
#endif /*H5_HAVE_PARALLEL*/
/****************/
/* Local Macros */
/****************/
/******************/
/* Local Typedefs */
/******************/
/********************/
/* Local Prototypes */
/********************/
/* Setup/teardown routines */
static herr_t H5D__get_offset_copy(const H5D_t *dset, const hsize_t *offset, hsize_t *offset_copy /*out*/);
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__get_offset_copy
*
* Purpose: Gets a copy of the user's offset array that is guaraneteed
* to be suitable for use by the library.
*
* Return: SUCCEED/FAIL
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__get_offset_copy(const H5D_t *dset, const hsize_t *offset, hsize_t *offset_copy)
{
unsigned u;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_NOAPI(FAIL)
HDassert(dset);
HDassert(offset);
HDassert(offset_copy);
/* The library's chunking code requires the offset to terminate with a zero.
* So transfer the offset array to an internal offset array that we
* can properly terminate (handled via the calloc call).
*/
HDmemset(offset_copy, 0, H5O_LAYOUT_NDIMS * sizeof(hsize_t));
for (u = 0; u < dset->shared->ndims; u++) {
/* Make sure the offset doesn't exceed the dataset's dimensions */
if (offset[u] > dset->shared->curr_dims[u])
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset")
/* Make sure the offset fall right on a chunk's boundary */
if (offset[u] % dset->shared->layout.u.chunk.dim[u])
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
offset_copy[u] = offset[u];
}
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__get_offset_copy() */
/*-------------------------------------------------------------------------
* Function: H5Dread
*
* Purpose: Reads (part of) a DSET from the file into application
* memory BUF. The part of the dataset to read is defined with
* MEM_SPACE_ID and FILE_SPACE_ID. The data points are
* converted from their file type to the MEM_TYPE_ID specified.
* Additional miscellaneous data transfer properties can be
* passed to this function with the PLIST_ID argument.
*
* The FILE_SPACE_ID can be the constant H5S_ALL which indicates
* that the entire file dataspace is to be referenced.
*
* The MEM_SPACE_ID can be the constant H5S_ALL in which case
* the memory dataspace is the same as the file dataspace
* defined when the dataset was created.
*
* The number of elements in the memory dataspace must match
* the number of elements in the file dataspace.
*
* The PLIST_ID can be the constant H5P_DEFAULT in which
* case the default data transfer properties are used.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t dxpl_id,
void *buf /*out*/)
{
H5D_t *dset = NULL;
H5S_t *mem_space = NULL;
H5S_t *file_space = NULL;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE6("e", "iiiiix", dset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf);
/* Get dataset pointer */
if (NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dset_id is not a dataset ID")
if (NULL == dset->oloc.file)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
/* Get validated dataspace pointers */
if (H5S_get_validated_dataspace(mem_space_id, &mem_space) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "could not get a validated dataspace from mem_space_id")
if (H5S_get_validated_dataspace(file_space_id, &file_space) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "could not get a validated dataspace from file_space_id")
/* Get the default dataset transfer property list if the user didn't provide one */
if (H5P_DEFAULT == dxpl_id)
dxpl_id = H5P_DATASET_XFER_DEFAULT;
else if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
/* Set DXPL for operation */
H5CX_set_dxpl(dxpl_id);
/* Read the data */
if (H5D__read(dset, mem_type_id, mem_space, file_space, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dread() */
/*-------------------------------------------------------------------------
* Function: H5Dread_chunk
*
* Purpose: Reads an entire chunk from the file directly.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Matthew Strong (GE Healthcare)
* 14 February 2016
*
*---------------------------------------------------------------------------
*/
herr_t
H5Dread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters, void *buf)
{
H5D_t *dset = NULL;
hsize_t offset_copy[H5O_LAYOUT_NDIMS]; /* Internal copy of chunk offset */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE5("e", "ii*h*Iu*x", dset_id, dxpl_id, offset, filters, buf);
/* Check arguments */
if (NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dset_id is not a dataset ID")
if (NULL == dset->oloc.file)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
if (H5D_CHUNKED != dset->shared->layout.type)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
if (!buf)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "buf cannot be NULL")
if (!offset)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "offset cannot be NULL")
if (!filters)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "filters cannot be NULL")
/* Get the default dataset transfer property list if the user didn't provide one */
if (H5P_DEFAULT == dxpl_id)
dxpl_id = H5P_DATASET_XFER_DEFAULT;
else if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dxpl_id is not a dataset transfer property list ID")
/* Set DXPL for operation */
H5CX_set_dxpl(dxpl_id);
/* Copy the user's offset array so we can be sure it's terminated properly.
* (we don't want to mess with the user's buffer).
*/
if (H5D__get_offset_copy(dset, offset, offset_copy) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "failure to copy offset array")
/* Read the raw chunk */
if (H5D__chunk_direct_read(dset, offset_copy, filters, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read unprocessed chunk data")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dread_chunk() */
/*-------------------------------------------------------------------------
* Function: H5Dwrite
*
* Purpose: Writes (part of) a DSET from application memory BUF to the
* file. The part of the dataset to write is defined with the
* MEM_SPACE_ID and FILE_SPACE_ID arguments. The data points
* are converted from their current type (MEM_TYPE_ID) to their
* file datatype. Additional miscellaneous data transfer
* properties can be passed to this function with the
* PLIST_ID argument.
*
* The FILE_SPACE_ID can be the constant H5S_ALL which indicates
* that the entire file dataspace is to be referenced.
*
* The MEM_SPACE_ID can be the constant H5S_ALL in which case
* the memory dataspace is the same as the file dataspace
* defined when the dataset was created.
*
* The number of elements in the memory dataspace must match
* the number of elements in the file dataspace.
*
* The PLIST_ID can be the constant H5P_DEFAULT in which
* case the default data transfer properties are used.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id, hid_t file_space_id, hid_t dxpl_id,
const void *buf)
{
H5D_t *dset = NULL;
H5S_t *mem_space = NULL;
H5S_t *file_space = NULL;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE6("e", "iiiii*x", dset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buf);
/* Get dataset pointer and ensure it's associated with a file */
if (NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dset_id is not a dataset ID")
if (NULL == dset->oloc.file)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
/* Get validated dataspace pointers */
if (H5S_get_validated_dataspace(mem_space_id, &mem_space) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "could not get a validated dataspace from mem_space_id")
if (H5S_get_validated_dataspace(file_space_id, &file_space) < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "could not get a validated dataspace from file_space_id")
/* Get the default dataset transfer property list if the user didn't provide one */
if (H5P_DEFAULT == dxpl_id)
dxpl_id = H5P_DATASET_XFER_DEFAULT;
else if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
/* Set DXPL for operation */
H5CX_set_dxpl(dxpl_id);
/* Write the data */
if (H5D__write(dset, mem_type_id, mem_space, file_space, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dwrite() */
/*-------------------------------------------------------------------------
* Function: H5Dwrite_chunk
*
* Purpose: Writes an entire chunk to the file directly.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Raymond Lu
* 30 July 2012
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, size_t data_size,
const void *buf)
{
H5D_t *dset = NULL;
hsize_t offset_copy[H5O_LAYOUT_NDIMS]; /* Internal copy of chunk offset */
uint32_t data_size_32; /* Chunk data size (limited to 32-bits currently) */
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE6("e", "iiIu*hz*x", dset_id, dxpl_id, filters, offset, data_size, buf);
/* Check arguments */
if (NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset ID")
if (NULL == dset->oloc.file)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
if (H5D_CHUNKED != dset->shared->layout.type)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
if (!buf)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "buf cannot be NULL")
if (!offset)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "offset cannot be NULL")
if (0 == data_size)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "data_size cannot be zero")
/* Make sure data size is less than 4 GiB */
data_size_32 = (uint32_t)data_size;
if (data_size != (size_t)data_size_32)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid data_size - chunks cannot be > 4 GiB")
/* Get the default dataset transfer property list if the user didn't provide one */
if (H5P_DEFAULT == dxpl_id)
dxpl_id = H5P_DATASET_XFER_DEFAULT;
else if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dxpl_id is not a dataset transfer property list ID")
/* Set DXPL for operation */
H5CX_set_dxpl(dxpl_id);
/* Copy the user's offset array so we can be sure it's terminated properly.
* (we don't want to mess with the user's buffer).
*/
if (H5D__get_offset_copy(dset, offset, offset_copy) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "failure to copy offset array")
/* Write chunk */
if (H5D__chunk_direct_write(dset, filters, offset_copy, data_size_32, buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write unprocessed chunk data")
done:
FUNC_LEAVE_API(ret_value)
} /* end H5Dwrite_chunk() */
/*-------------------------------------------------------------------------
* 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 */
H5D_layout_t layout_type; /* Dataset's layout type (contig, chunked, compact, etc.) */
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);
if (!file_space)
file_space = dataset->shared->space;
if (!mem_space)
mem_space = file_space;
nelmts = H5S_GET_SELECT_NPOINTS(mem_space);
layout_type = dataset->shared->layout.type;
/* 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 */
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, after the H5S_ALL dataspace selection has been handled */
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 (TRUE == H5S_SELECT_SHAPE_SAME(mem_space, file_space) &&
H5S_GET_EXTENT_NDIMS(mem_space) != H5S_GET_EXTENT_NDIMS(file_space)) {
ptrdiff_t buf_adj = 0;
/* 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),
type_info.dst_type_size, &buf_adj) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to construct projected memory dataspace")
HDassert(projected_mem_space);
/* Adjust the buffer by the given amount */
buf = (void *)(((uint8_t *)buf) + buf_adj);
/* Switch to using projected memory dataspace & adjusted buffer */
mem_space = projected_mem_space;
} /* end if */
/* Retrieve dataset properties */
/* <none needed in the general case> */
/* 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 || layout_type == H5D_COMPACT);
/* Allocate the chunk map */
if (H5D_CONTIGUOUS != layout_type && H5D_COMPACT != layout_type) {
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 */
H5D_layout_t layout_type; /* Dataset's layout type (contig, chunked, compact, etc.) */
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);
layout_type = dataset->shared->layout.type;
/* 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*/
/* Initialize dataspace information */
if (!file_space)
file_space = dataset->shared->space;
if (!mem_space)
mem_space = file_space;
nelmts = H5S_GET_SELECT_NPOINTS(mem_space);
/* Make certain that the number of elements in each selection is the same */
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, after the H5S_ALL dataspace selection has been handled */
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 (TRUE == H5S_SELECT_SHAPE_SAME(mem_space, file_space) &&
H5S_GET_EXTENT_NDIMS(mem_space) != H5S_GET_EXTENT_NDIMS(file_space)) {
ptrdiff_t buf_adj = 0;
/* 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),
type_info.src_type_size, &buf_adj) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to construct projected memory dataspace")
HDassert(projected_mem_space);
/* Adjust the buffer by the given amount */
buf = (const void *)(((const uint8_t *)buf) + buf_adj);
/* Switch to using projected memory dataspace & adjusted buffer */
mem_space = projected_mem_space;
} /* end if */
/* Retrieve dataset properties */
/* <none needed currently> */
/* 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 (H5D_CONTIGUOUS != layout_type && H5D_COMPACT != layout_type) {
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->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, 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 atoms. 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_mpi_get_size(io_info->dset->oloc.file)) < 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() */