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hdf5/src/H5D.c

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/****************************************************************************
* NCSA HDF *
* Software Development Group *
* National Center for Supercomputing Applications *
* University of Illinois at Urbana-Champaign *
* 605 E. Springfield, Champaign IL 61820 *
* *
* For conditions of distribution and use, see the accompanying *
* hdf/COPYING file. *
* *
****************************************************************************/
#ifdef RCSID
static char RcsId[] = "@(#)$Revision$";
#endif
/* $Id$ */
#include <H5private.h> /* Generic Functions */
#include <H5Iprivate.h> /* IDs */
#include <H5Dprivate.h> /* Dataset functions */
#include <H5Eprivate.h> /* Error handling */
#include <H5FLprivate.h> /*Free Lists */
#include <H5Gprivate.h> /* Group headers */
#include <H5HLprivate.h> /* Name heap */
#include <H5MMprivate.h> /* Memory management */
#include <H5Oprivate.h> /* Object headers */
#include <H5Pprivate.h> /* Property lists */
#include <H5Sprivate.h> /* Dataspace functions rky 980813 */
#include <H5Vprivate.h> /* Vector and array functions */
#include <H5Zprivate.h> /* Data filters */
/*
* The MPIO driver is needed because there are kludges in this file and
* places where we check for things that aren't handled by this driver.
*/
#include <H5FDmpio.h>
#ifdef H5_HAVE_PARALLEL
/* Remove this if H5R_DATASET_REGION is no longer used in this file */
#include <H5Rpublic.h>
#endif
#define PABLO_MASK H5D_mask
/*
* A dataset is the following struct.
*/
struct H5D_t {
H5G_entry_t ent; /*cached object header stuff */
H5T_t *type; /*datatype of this dataset */
H5D_create_t *create_parms; /*creation parameters */
H5O_layout_t layout; /*data layout */
};
/* Default dataset creation property list */
const H5D_create_t H5D_create_dflt = {
H5D_CONTIGUOUS, /* Layout */
1, /* Chunk dimensions */
{1, 1, 1, 1, 1, 1, 1, 1, /* Chunk size. These default values....*/
1, 1, 1, 1, 1, 1, 1, 1, /*...are quite useless. Larger chunks..*/
1, 1, 1, 1, 1, 1, 1, 1, /*...produce fewer, but larger I/O......*/
1, 1, 1, 1, 1, 1, 1, 1}, /*...requests. */
/* Fill value */
{NULL, 0, NULL}, /* No fill value */
/* External file list */
{HADDR_UNDEF, /* External file list heap address */
0, /*...slots allocated */
0, /*...slots used */
NULL}, /*...slot array */
/* Filters */
{0, 0, NULL} /* No filters in pipeline */
};
/* Interface initialization? */
static intn interface_initialize_g = 0;
#define INTERFACE_INIT H5D_init_interface
static herr_t H5D_init_interface(void);
static herr_t H5D_init_storage(H5D_t *dataset, const H5S_t *space);
H5D_t * H5D_new(const H5D_create_t *create_parms);
/* Declare a free list to manage the H5D_t struct */
H5FL_DEFINE_STATIC(H5D_t);
/* Declare a free list to manage blocks of type conversion data */
H5FL_BLK_DEFINE_STATIC(type_conv);
/* Declare a free list to manage blocks of background conversion data */
H5FL_BLK_DEFINE_STATIC(bkgr_conv);
/* Declare a free list to manage blocks of fill conversion data */
H5FL_BLK_DEFINE_STATIC(fill_conv);
/* Declare a free list to manage blocks of VL data */
H5FL_BLK_DEFINE_STATIC(vlen_vl_buf);
/* Declare a free list to manage other blocks of VL data */
H5FL_BLK_DEFINE_STATIC(vlen_fl_buf);
/*-------------------------------------------------------------------------
* Function: H5D_init
*
* Purpose: Initialize the interface from some other layer.
*
* Return: Success: non-negative
*
* Failure: negative
*
* Programmer: Quincey Koziol
* Saturday, March 4, 2000
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_init(void)
{
FUNC_ENTER(H5D_init, FAIL);
/* FUNC_ENTER() does all the work */
FUNC_LEAVE(SUCCEED);
}
/*--------------------------------------------------------------------------
NAME
H5D_init_interface -- Initialize interface-specific information
USAGE
herr_t H5D_init_interface()
RETURNS
Non-negative on success/Negative on failure
DESCRIPTION
Initializes any interface-specific data or routines.
--------------------------------------------------------------------------*/
static herr_t
H5D_init_interface(void)
{
FUNC_ENTER(H5D_init_interface, FAIL);
/* Initialize the atom group for the dataset IDs */
if (H5I_init_group(H5I_DATASET, H5I_DATASETID_HASHSIZE, H5D_RESERVED_ATOMS,
(H5I_free_t)H5D_close)<0) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize interface");
}
/* Register the default dataset creation & data xfer properties */
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5D_term_interface
*
* Purpose: Terminate this interface.
*
* Return: Success: Positive if anything was done that might
* affect other interfaces; zero otherwise.
*
* Failure: Negative.
*
* Programmer: Robb Matzke
* Friday, November 20, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
intn
H5D_term_interface(void)
{
int n=0;
if (interface_initialize_g) {
if ((n=H5I_nmembers(H5I_DATASET))) {
H5I_clear_group(H5I_DATASET, FALSE);
} else {
H5I_destroy_group(H5I_DATASET);
interface_initialize_g = 0;
n = 1; /*H5I*/
}
}
return n;
}
/*-------------------------------------------------------------------------
* Function: H5Dcreate
*
* Purpose: Creates a new dataset named NAME at LOC_ID, opens the
* dataset for access, and associates with that dataset constant
* and initial persistent properties including the type of each
* datapoint as stored in the file (TYPE_ID), the size of the
* dataset (SPACE_ID), and other initial miscellaneous
* properties (PLIST_ID).
*
* All arguments are copied into the dataset, so the caller is
* allowed to derive new types, data spaces, and creation
* parameters from the old ones and reuse them in calls to
* create other datasets.
*
* Return: Success: The object ID of the new dataset. At this
* point, the dataset is ready to receive its
* raw data. Attempting to read raw data from
* the dataset will probably return the fill
* value. The dataset should be closed when
* the caller is no longer interested in it.
*
* Failure: FAIL
*
* Errors:
* ARGS BADTYPE Not a data space.
* ARGS BADTYPE Not a dataset creation plist.
* ARGS BADTYPE Not a file.
* ARGS BADTYPE Not a type.
* ARGS BADVALUE No name.
* DATASET CANTINIT Can't create dataset.
* DATASET CANTREGISTER Can't register dataset.
*
* Programmer: Robb Matzke
* Wednesday, December 3, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
hid_t
H5Dcreate(hid_t loc_id, const char *name, hid_t type_id, hid_t space_id,
hid_t plist_id)
{
H5G_entry_t *loc = NULL;
H5T_t *type = NULL;
H5S_t *space = NULL;
H5D_t *new_dset = NULL;
hid_t ret_value = FAIL;
const H5D_create_t *create_parms = NULL;
FUNC_ENTER(H5Dcreate, FAIL);
H5TRACE5("i","isiii",loc_id,name,type_id,space_id,plist_id);
/* Check arguments */
if (NULL == (loc = H5G_loc(loc_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location");
}
if (!name || !*name) {
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name");
}
if (H5I_DATATYPE != H5I_get_type(type_id) ||
NULL == (type = H5I_object(type_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a type");
}
if (H5I_DATASPACE != H5I_get_type(space_id) ||
NULL == (space = H5I_object(space_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
}
if (H5P_DEFAULT==plist_id) {
create_parms = &H5D_create_dflt;
} else if (H5P_DATASET_CREATE != H5P_get_class(plist_id) ||
NULL == (create_parms = H5I_object(plist_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL,
"not a dataset creation property list");
}
/* build and open the new dataset */
if (NULL == (new_dset = H5D_create(loc, name, type, space,
create_parms))) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to create dataset");
}
/* Register the new dataset to get an ID for it */
if ((ret_value = H5I_register(H5I_DATASET, new_dset)) < 0) {
H5D_close(new_dset);
HRETURN_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
"unable to register dataset");
}
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5Dopen
*
* Purpose: Finds a dataset named NAME at LOC_ID, opens it, and returns
* its ID. The dataset should be close when the caller is no
* longer interested in it.
*
* Return: Success: A new dataset ID
*
* Failure: FAIL
*
* Errors:
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
hid_t
H5Dopen(hid_t loc_id, const char *name)
{
H5G_entry_t *loc = NULL; /*location holding the dataset */
H5D_t *dataset = NULL; /*the dataset */
hid_t ret_value = FAIL;
FUNC_ENTER(H5Dopen, FAIL);
H5TRACE2("i","is",loc_id,name);
/* Check args */
if (NULL == (loc = H5G_loc(loc_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location");
}
if (!name || !*name) {
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name");
}
/* Find the dataset */
if (NULL == (dataset = H5D_open(loc, name))) {
HRETURN_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "dataset not found");
}
/* Create an atom for the dataset */
if ((ret_value = H5I_register(H5I_DATASET, dataset)) < 0) {
H5D_close(dataset);
HRETURN_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
"can't register dataset");
}
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5Dclose
*
* Purpose: Closes access to a dataset (DATASET_ID) and releases
* resources used by it. It is illegal to subsequently use that
* same dataset ID in calls to other dataset functions.
*
* Return: Non-negative on success/Negative on failure
*
* Errors:
* ARGS BADTYPE Not a dataset.
* DATASET CANTINIT Can't free.
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dclose(hid_t dset_id)
{
H5D_t *dset = NULL; /* dataset object to release */
FUNC_ENTER(H5Dclose, FAIL);
H5TRACE1("e","i",dset_id);
/* Check args */
if (H5I_DATASET != H5I_get_type(dset_id) ||
NULL == (dset = H5I_object(dset_id)) ||
NULL == dset->ent.file) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
/*
* Decrement the counter on the dataset. It will be freed if the count
* reaches zero.
*/
if (H5I_dec_ref(dset_id) < 0) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't free");
}
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5Dget_space
*
* Purpose: Returns a copy of the file data space for a dataset.
*
* Return: Success: ID for a copy of the data space. The data
* space should be released by calling
* H5Sclose().
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Wednesday, January 28, 1998
*
* Modifications:
* Robb Matzke, 9 Jun 1998
* The data space is not constant and is no longer cached by the dataset
* struct.
*-------------------------------------------------------------------------
*/
hid_t
H5Dget_space(hid_t dset_id)
{
H5D_t *dset = NULL;
H5S_t *space = NULL;
hid_t ret_value = FAIL;
FUNC_ENTER (H5Dget_space, FAIL);
H5TRACE1("i","i",dset_id);
/* Check args */
if (H5I_DATASET!=H5I_get_type (dset_id) ||
NULL==(dset=H5I_object (dset_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
/* Read the data space message and return a data space object */
if (NULL==(space=H5D_get_space (dset))) {
HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to get data space");
}
/* Create an atom */
if ((ret_value=H5I_register (H5I_DATASPACE, space))<0) {
H5S_close(space);
HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL,
"unable to register data space");
}
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5D_get_space
*
* Purpose: Returns the data space associated with the dataset.
*
* Return: Success: Ptr to a copy of the data space.
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Tuesday, August 25, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
H5S_t *
H5D_get_space(H5D_t *dset)
{
H5S_t *space = NULL;
FUNC_ENTER(H5D_get_space, NULL);
assert(dset);
if (NULL==(space=H5S_read(&(dset->ent)))) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to load space info from dataset header");
}
FUNC_LEAVE(space);
}
/*-------------------------------------------------------------------------
* Function: H5Dget_type
*
* Purpose: Returns a copy of the file data type for a dataset.
*
* Return: Success: ID for a copy of the data type. The data
* type should be released by calling
* H5Tclose().
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Tuesday, February 3, 1998
*
* Modifications:
*
* Robb Matzke, 1 Jun 1998
* If the dataset has a named data type then a handle to the opened data
* type is returned. Otherwise the returned data type is read-only. If
* atomization of the data type fails then the data type is closed.
*
*-------------------------------------------------------------------------
*/
hid_t
H5Dget_type(hid_t dset_id)
{
H5D_t *dset = NULL;
H5T_t *copied_type = NULL;
hid_t ret_value = FAIL;
FUNC_ENTER (H5Dget_type, FAIL);
H5TRACE1("i","i",dset_id);
/* Check args */
if (H5I_DATASET!=H5I_get_type (dset_id) ||
NULL==(dset=H5I_object (dset_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
/* Copy the data type and mark it read-only */
if (NULL==(copied_type=H5T_copy (dset->type, H5T_COPY_REOPEN))) {
HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to copy the data type");
}
/* Mark any VL datatypes as being in memory now */
if (H5T_vlen_mark(copied_type, NULL, H5T_VLEN_MEMORY)<0) {
HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "invalid VL location");
}
if (H5T_lock (copied_type, FALSE)<0) {
H5T_close (copied_type);
HRETURN_ERROR (H5E_DATATYPE, H5E_CANTINIT, FAIL,
"unable to lock transient data type");
}
/* Create an atom */
if ((ret_value=H5I_register (H5I_DATATYPE, copied_type))<0) {
H5T_close (copied_type);
HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL,
"unable to register data type");
}
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5Dget_create_plist
*
* Purpose: Returns a copy of the dataset creation property list.
*
* Return: Success: ID for a copy of the dataset creation
* property list. The template should be
* released by calling H5Pclose().
*
* Failure: FAIL
*
* Programmer: Robb Matzke
* Tuesday, February 3, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
hid_t
H5Dget_create_plist(hid_t dset_id)
{
H5D_t *dset = NULL;
H5D_create_t *copied_parms = NULL;
hid_t ret_value = FAIL;
FUNC_ENTER (H5Dget_create_plist, FAIL);
H5TRACE1("i","i",dset_id);
/* Check args */
if (H5I_DATASET!=H5I_get_type (dset_id) ||
NULL==(dset=H5I_object (dset_id))) {
HRETURN_ERROR (H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
/* Copy the creation property list */
if (NULL==(copied_parms=H5P_copy (H5P_DATASET_CREATE,
dset->create_parms))) {
HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to copy the creation property list");
}
/* Copy the dataset type into the fill value message */
if (!copied_parms->fill.type &&
NULL==(copied_parms->fill.type=H5T_copy(dset->type,
H5T_COPY_TRANSIENT))) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to copy dataset data type for fill value");
}
/* Create an atom */
if ((ret_value=H5I_register ((H5I_type_t)(H5I_TEMPLATE_0+
H5P_DATASET_CREATE),
copied_parms))<0) {
HRETURN_ERROR (H5E_ATOM, H5E_CANTREGISTER, FAIL,
"unable to register creation property list");
}
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* 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 data space is to be referenced.
*
* The MEM_SPACE_ID can be the constant H5S_ALL in which case
* the memory data space is the same as the file data space
* defined when the dataset was created.
*
* The number of elements in the memory data space must match
* the number of elements in the file data space.
*
* 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
*
* Errors:
* ARGS BADTYPE Not a data space.
* ARGS BADTYPE Not a data type.
* ARGS BADTYPE Not a dataset.
* ARGS BADTYPE Not xfer parms.
* ARGS BADVALUE No output buffer.
* DATASET READERROR Can't read data.
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t plist_id, void *buf/*out*/)
{
H5D_t *dset = NULL;
const H5T_t *mem_type = NULL;
const H5S_t *mem_space = NULL;
const H5S_t *file_space = NULL;
FUNC_ENTER(H5Dread, FAIL);
H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id,
plist_id,buf);
/* check arguments */
if (H5I_DATASET != H5I_get_type(dset_id) ||
NULL == (dset = H5I_object(dset_id)) ||
NULL == dset->ent.file) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
if (H5I_DATATYPE != H5I_get_type(mem_type_id) ||
NULL == (mem_type = H5I_object(mem_type_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
}
if (H5S_ALL != mem_space_id) {
if (H5I_DATASPACE != H5I_get_type(mem_space_id) ||
NULL == (mem_space = H5I_object(mem_space_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
}
/* Check for valid selection */
if(H5S_select_valid(mem_space)!=TRUE) {
HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL,
"selection+offset not within extent");
}
}
if (H5S_ALL != file_space_id) {
if (H5I_DATASPACE != H5I_get_type(file_space_id) ||
NULL == (file_space = H5I_object(file_space_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
}
/* Check for valid selection */
if(H5S_select_valid(file_space)!=TRUE) {
HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL,
"selection+offset not within extent");
}
}
if (H5P_DEFAULT != plist_id && H5P_DATA_XFER != H5P_get_class(plist_id)) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
}
if (!buf) {
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer");
}
/* read raw data */
if (H5D_read(dset, mem_type, mem_space, file_space, plist_id,
buf/*out*/) < 0) {
HRETURN_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data");
}
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* 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 data type. 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 data space is to be referenced.
*
* The MEM_SPACE_ID can be the constant H5S_ALL in which case
* the memory data space is the same as the file data space
* defined when the dataset was created.
*
* The number of elements in the memory data space must match
* the number of elements in the file data space.
*
* 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
*
* Errors:
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t plist_id, const void *buf)
{
H5D_t *dset = NULL;
const H5T_t *mem_type = NULL;
const H5S_t *mem_space = NULL;
const H5S_t *file_space = NULL;
FUNC_ENTER(H5Dwrite, FAIL);
H5TRACE6("e","iiiiix",dset_id,mem_type_id,mem_space_id,file_space_id,
plist_id,buf);
/* check arguments */
if (H5I_DATASET != H5I_get_type(dset_id) ||
NULL == (dset = H5I_object(dset_id)) ||
NULL == dset->ent.file) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
if (H5I_DATATYPE != H5I_get_type(mem_type_id) ||
NULL == (mem_type = H5I_object(mem_type_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
}
if (H5S_ALL != mem_space_id) {
if (H5I_DATASPACE != H5I_get_type(mem_space_id) ||
NULL == (mem_space = H5I_object(mem_space_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
}
/* Check for valid selection */
if (H5S_select_valid(mem_space)!=TRUE) {
HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL,
"selection+offset not within extent");
}
}
if (H5S_ALL != file_space_id) {
if (H5I_DATASPACE != H5I_get_type(file_space_id) ||
NULL == (file_space = H5I_object(file_space_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
}
/* Check for valid selection */
if (H5S_select_valid(file_space)!=TRUE) {
HRETURN_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL,
"selection+offset not within extent");
}
}
if (H5P_DEFAULT != plist_id && H5P_DATA_XFER != H5P_get_class(plist_id)) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
}
if (!buf) {
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no output buffer");
}
/* write raw data */
if (H5D_write(dset, mem_type, mem_space, file_space, plist_id,
buf) < 0) {
HRETURN_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data");
}
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5Dextend
*
* Purpose: This function makes sure that the dataset is at least of size
* SIZE. The dimensionality of SIZE is the same as the data
* space of the dataset being changed.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Friday, January 30, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dextend(hid_t dset_id, const hsize_t *size)
{
H5D_t *dset = NULL;
FUNC_ENTER (H5Dextend, FAIL);
H5TRACE2("e","i*h",dset_id,size);
/* Check args */
if (H5I_DATASET!=H5I_get_type(dset_id) ||
NULL==(dset=H5I_object(dset_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
if (!size) {
HRETURN_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL, "no size specified");
}
/* Increase size */
if (H5D_extend (dset, size)<0) {
HRETURN_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to extend dataset");
}
FUNC_LEAVE (SUCCEED);
}
/*-------------------------------------------------------------------------
* Function: H5D_new
*
* Purpose: Creates a new, empty dataset structure
*
* Return: Success: Pointer to a new dataset descriptor.
*
* Failure: NULL
*
* Errors:
*
* Programmer: Quincey Koziol
* Monday, October 12, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
H5D_t *
H5D_new(const H5D_create_t *create_parms)
{
H5D_t *ret_value = NULL; /*return value */
FUNC_ENTER(H5D_new, NULL);
/* check args */
/* Nothing to check */
if (NULL==(ret_value = H5FL_ALLOC(H5D_t,1))) {
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL,
"memory allocation failed");
}
if(create_parms!=NULL) {
ret_value->create_parms = H5P_copy (H5P_DATASET_CREATE, create_parms);
} else {
ret_value->create_parms = H5P_copy (H5P_DATASET_CREATE,
&H5D_create_dflt);
}
ret_value->ent.header = HADDR_UNDEF;
/* Success */
done:
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5D_create
*
* Purpose: Creates a new dataset with name NAME in file F and associates
* with it a datatype TYPE for each element as stored in the
* file, dimensionality information or dataspace SPACE, and
* other miscellaneous properties CREATE_PARMS. All arguments
* are deep-copied before being associated with the new dataset,
* so the caller is free to subsequently modify them without
* affecting the dataset.
*
* Return: Success: Pointer to a new dataset
*
* Failure: NULL
*
* Errors:
* DATASET CANTINIT Can't update dataset header.
* DATASET CANTINIT Problem with the dataset name.
* DATASET CANTINIT Fail in file space allocation for
* chunks
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
* Robb Matzke, 9 Jun 1998
* The data space message is no longer cached in the dataset struct.
*
* Robb Matzke, 27 Jul 1998
* Added the MTIME message to the dataset object header.
*
* Robb Matzke, 1999-10-14
* The names for the external file list are entered into the heap hear
* instead of when the efl message is encoded, preventing a possible
* infinite recursion situation.
*-------------------------------------------------------------------------
*/
H5D_t *
H5D_create(H5G_entry_t *loc, const char *name, const H5T_t *type,
const H5S_t *space, const H5D_create_t *create_parms)
{
H5D_t *new_dset = NULL;
H5D_t *ret_value = NULL;
intn i, ndims;
hsize_t max_dim[H5O_LAYOUT_NDIMS]={0};
H5O_efl_t *efl = NULL;
H5F_t *f = NULL;
FUNC_ENTER(H5D_create, NULL);
/* check args */
assert (loc);
assert (name && *name);
assert (type);
assert (space);
assert (create_parms);
if (create_parms->pline.nfilters>0 &&
H5D_CHUNKED!=create_parms->layout) {
HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL,
"filters can only be used with chunked layout");
}
/* What file is the dataset being added to? */
if (NULL==(f=H5G_insertion_file(loc, name))) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to locate insertion point");
}
#ifdef H5_HAVE_PARALLEL
/* If MPIO is used, no filter support yet. */
if (IS_H5FD_MPIO(f) &&
create_parms->pline.nfilters>0) {
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL,
"Parallel IO does not support filters yet");
}
#endif
/* Initialize the dataset object */
if (NULL==(new_dset = H5D_new(create_parms))) {
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL,
"memory allocation failed");
}
/* Copy datatype for dataset */
new_dset->type = H5T_copy(type, H5T_COPY_ALL);
/* Mark any VL datatypes as being on disk now */
if (H5T_vlen_mark(new_dset->type, f, H5T_VLEN_DISK)<0) {
HRETURN_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "invalid VL location");
}
efl = &(new_dset->create_parms->efl);
/* Total raw data size */
new_dset->layout.type = new_dset->create_parms->layout;
new_dset->layout.ndims = H5S_get_simple_extent_ndims(space) + 1;
assert((unsigned)(new_dset->layout.ndims) <= NELMTS(new_dset->layout.dim));
new_dset->layout.dim[new_dset->layout.ndims-1] = H5T_get_size(new_dset->type);
switch (new_dset->create_parms->layout) {
case H5D_CONTIGUOUS:
/*
* The maximum size of the dataset cannot exceed the storage size.
* Also, only the slowest varying dimension of a simple data space
* can be extendible.
*/
if ((ndims=H5S_get_simple_extent_dims(space, new_dset->layout.dim,
max_dim))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to initialize contiguous storage");
}
for (i=1; i<ndims; i++) {
if (max_dim[i]>new_dset->layout.dim[i]) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"only the first dimension can be extendible");
}
}
if (efl->nused>0) {
hsize_t max_points = H5S_get_npoints_max (space);
hsize_t max_storage = H5O_efl_total_size (efl);
if (H5S_UNLIMITED==max_points) {
if (H5O_EFL_UNLIMITED!=max_storage) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"unlimited data space but finite storage");
}
} else if (max_points * H5T_get_size (type) < max_points) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"data space * type size overflowed");
} else if (max_points * H5T_get_size (type) > max_storage) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"data space size exceeds external storage size");
}
} else if (ndims>0 && max_dim[0]>new_dset->layout.dim[0]) {
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL,
"extendible contiguous non-external dataset");
}
break;
case H5D_CHUNKED:
/*
* Chunked storage allows any type of data space extension, so we
* don't even bother checking.
*/
if (new_dset->create_parms->chunk_ndims !=
H5S_get_simple_extent_ndims(space)) {
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL,
"dimensionality of chunks doesn't match the data space");
}
if (efl->nused>0) {
HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL,
"external storage not supported with chunked layout");
}
for (i=0; i<new_dset->layout.ndims-1; i++) {
new_dset->layout.dim[i] = new_dset->create_parms->chunk_size[i];
}
break;
default:
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL, "not implemented yet");
}
/* Create (open for write access) an object header */
if (H5O_create(f, 256, &(new_dset->ent)) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to create dataset object header");
}
/* Convert the fill value to the dataset type and write the message */
if (H5O_fill_convert(&(new_dset->create_parms->fill), new_dset->type)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to convert fill value to dataset type");
}
if (new_dset->create_parms->fill.buf &&
H5O_modify(&(new_dset->ent), H5O_FILL, 0, H5O_FLAG_CONSTANT,
&(new_dset->create_parms->fill))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update fill value header message");
}
/* Update the type and space header messages */
if (H5O_modify(&(new_dset->ent), H5O_DTYPE, 0,
H5O_FLAG_CONSTANT|H5O_FLAG_SHARED, new_dset->type)<0 ||
H5S_modify(&(new_dset->ent), space) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update type or space header messages");
}
/* Update the filters message */
if (new_dset->create_parms->pline.nfilters>0 &&
H5O_modify (&(new_dset->ent), H5O_PLINE, 0, H5O_FLAG_CONSTANT,
&(new_dset->create_parms->pline))<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update filter header message");
}
/*
* Add a modification time message.
*/
if (H5O_touch(&(new_dset->ent), TRUE)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update modification time message");
}
#ifdef QAK
printf("%s: check 0.5\n",FUNC);
#endif /* QAK */
/* Give the dataset a name */
if (H5G_insert(loc, name, &(new_dset->ent)) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to name dataset");
}
/*
* Initialize storage. We assume that external storage is already
* initialized by the caller, or at least will be before I/O is
* performed.
*/
#ifdef QAK
printf("%s: check 1.0\n",FUNC);
#endif /* QAK */
if (0==efl->nused) {
if (H5F_arr_create(f, &(new_dset->layout)) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to initialize storage");
}
} else {
new_dset->layout.addr = HADDR_UNDEF;
}
#ifdef QAK
printf("%s: check 2.0\n",FUNC);
#endif /* QAK */
/* Update layout message */
if (H5O_modify (&(new_dset->ent), H5O_LAYOUT, 0, H5O_FLAG_CONSTANT,
&(new_dset->layout)) < 0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update layout message");
}
#ifdef QAK
printf("%s: check 3.0\n",FUNC);
#endif /* QAK */
/* Update external storage message */
if (efl->nused>0) {
size_t heap_size = H5HL_ALIGN (1);
for (i=0; i<efl->nused; i++) {
heap_size += H5HL_ALIGN (HDstrlen (efl->slot[i].name)+1);
}
if (H5HL_create (f, heap_size, &(efl->heap_addr)/*out*/)<0 ||
(size_t)(-1)==H5HL_insert(f, efl->heap_addr, 1, "")) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"unable to create external file list name heap");
}
for (i=0; i<efl->nused; i++) {
size_t offset = H5HL_insert(f, efl->heap_addr,
HDstrlen(efl->slot[i].name)+1,
efl->slot[i].name);
assert(0==efl->slot[i].name_offset);
if ((size_t)(-1)==offset) {
HGOTO_ERROR(H5E_EFL, H5E_CANTINIT, NULL,
"unable to insert URL into name heap");
}
efl->slot[i].name_offset = offset;
}
if (H5O_modify (&(new_dset->ent), H5O_EFL, 0, H5O_FLAG_CONSTANT,
efl)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"unable to update external file list message");
}
}
#ifdef QAK
printf("%s: check 4.0\n",FUNC);
#endif /* QAK */
/* Initialize the raw data */
if (H5D_init_storage(new_dset, space)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to initialize storage");
}
#ifdef QAK
printf("%s: check 6.0\n",FUNC);
#endif /* QAK */
/* Success */
ret_value = new_dset;
done:
if (!ret_value && new_dset) {
if (new_dset->type) H5T_close(new_dset->type);
if (new_dset->create_parms) {
H5P_close (new_dset->create_parms);
new_dset->create_parms = NULL;
}
if (H5F_addr_defined(new_dset->ent.header)) {
H5O_close(&(new_dset->ent));
}
new_dset->ent.file = NULL;
H5FL_FREE(H5D_t,new_dset);
}
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5D_isa
*
* Purpose: Determines if an object has the requisite messages for being
* a dataset.
*
* Return: Success: TRUE if the required dataset messages are
* present; FALSE otherwise.
*
* Failure: FAIL if the existence of certain messages
* cannot be determined.
*
* Programmer: Robb Matzke
* Monday, November 2, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
htri_t
H5D_isa(H5G_entry_t *ent)
{
htri_t exists;
FUNC_ENTER(H5D_isa, FAIL);
assert(ent);
/* Data type */
if ((exists=H5O_exists(ent, H5O_DTYPE, 0))<0) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to read object header");
} else if (!exists) {
HRETURN(FALSE);
}
/* Layout */
if ((exists=H5O_exists(ent, H5O_LAYOUT, 0))<0) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to read object header");
} else if (!exists) {
HRETURN(FALSE);
}
FUNC_LEAVE(TRUE);
}
/*
*-------------------------------------------------------------------------
* Function: H5D_open
*
* Purpose: Finds a dataset named NAME in file F and builds a descriptor
* for it, opening it for access.
*
* Return: Success: Pointer to a new dataset descriptor.
*
* Failure: NULL
*
* Errors:
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
* Robb Matzke, 9 Jun 1998
* The data space message is no longer cached in the dataset struct.
*
* Quincey Koziol, 12 Oct 1998
* Moved guts of function into H5D_open_oid
*
*-------------------------------------------------------------------------
*/
H5D_t *
H5D_open(H5G_entry_t *loc, const char *name)
{
H5D_t *dataset = NULL; /*the dataset which was found */
H5D_t *ret_value = NULL; /*return value */
H5G_entry_t ent; /*dataset symbol table entry */
FUNC_ENTER(H5D_open, NULL);
/* check args */
assert (loc);
assert (name && *name);
/* Find the dataset object */
if (H5G_find(loc, name, NULL, &ent) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found");
}
/* Open the dataset object */
if ((dataset=H5D_open_oid(&ent)) ==NULL) {
HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, NULL, "not found");
}
/* Success */
ret_value = dataset;
done:
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5D_open_oid
*
* Purpose: Opens a dataset for access.
*
* Return: Dataset pointer on success, NULL on failure
*
* Errors:
*
* Programmer: Quincey Koziol
* Monday, October 12, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
H5D_t *
H5D_open_oid(H5G_entry_t *ent)
{
H5D_t *dataset = NULL; /*new dataset struct */
H5D_t *ret_value = NULL; /*return value */
H5S_t *space = NULL; /*data space */
intn i;
FUNC_ENTER(H5D_open_oid, NULL);
/* check args */
assert (ent);
/* Allocate the dataset structure */
if (NULL==(dataset = H5D_new(NULL))) {
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL,
"memory allocation failed");
}
/* Copy over the symbol table information if it's provided */
HDmemcpy(&(dataset->ent),ent,sizeof(H5G_entry_t));
/* Find the dataset object */
if (H5O_open(&(dataset->ent)) < 0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, NULL, "unable to open");
}
/* Get the type and space */
if (NULL==(dataset->type=H5O_read(&(dataset->ent), H5O_DTYPE, 0, NULL))) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to load type info from dataset header");
}
if (NULL==(space=H5S_read (&(dataset->ent)))) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"unable to read data space info from dataset header");
}
/* Get the optional fill value message */
if (NULL==H5O_read(&(dataset->ent), H5O_FILL, 0,
&(dataset->create_parms->fill))) {
H5E_clear();
HDmemset(&(dataset->create_parms->fill), 0,
sizeof(dataset->create_parms->fill));
}
/* Get the optional filters message */
if (NULL==H5O_read (&(dataset->ent), H5O_PLINE, 0,
&(dataset->create_parms->pline))) {
H5E_clear ();
HDmemset (&(dataset->create_parms->pline), 0,
sizeof(dataset->create_parms->pline));
}
#ifdef H5_HAVE_PARALLEL
/* If MPIO is used, no filter support yet. */
if (IS_H5FD_MPIO(dataset->ent.file) &&
dataset->create_parms->pline.nfilters>0){
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, NULL,
"Parallel IO does not support filters yet");
}
#endif
/*
* 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_read(&(dataset->ent), H5O_LAYOUT, 0, &(dataset->layout))) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to read data layout message");
}
switch (dataset->layout.type) {
case H5D_CONTIGUOUS:
dataset->create_parms->layout = H5D_CONTIGUOUS;
break;
case H5D_CHUNKED:
/*
* Chunked storage. The creation plist's dimension is one less than
* the chunk dimension because the chunk includes a dimension for the
* individual bytes of the data type.
*/
dataset->create_parms->layout = H5D_CHUNKED;
dataset->create_parms->chunk_ndims = dataset->layout.ndims - 1;
for (i = 0; i < dataset->layout.ndims - 1; i++) {
dataset->create_parms->chunk_size[i] = dataset->layout.dim[i];
}
break;
default:
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, NULL,
"not implemented yet");
}
/* Get the external file list message, which might not exist */
if (NULL==H5O_read (&(dataset->ent), H5O_EFL, 0,
&(dataset->create_parms->efl)) &&
!H5F_addr_defined (dataset->layout.addr)) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, NULL,
"storage address is undefined an no external file list");
}
/*
* Make sure all storage is properly initialized for chunked datasets.
* This is especially important for parallel I/O where the B-tree must
* be fully populated before I/O can happen.
*/
if ((dataset->ent.file->intent & H5F_ACC_RDWR) &&
H5D_CHUNKED==dataset->layout.type) {
if (H5D_init_storage(dataset, space)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL,
"unable to initialize file storage");
}
}
/* Success */
ret_value = dataset;
done:
if (space) H5S_close(space);
if (ret_value==NULL && dataset) {
if (H5F_addr_defined(dataset->ent.header)) {
H5O_close(&(dataset->ent));
}
if (dataset->type) {
H5T_close(dataset->type);
}
if (dataset->create_parms) {
H5P_close (dataset->create_parms);
}
dataset->ent.file = NULL;
H5FL_FREE(H5D_t,dataset);
}
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5D_close
*
* Purpose: Insures that all data has been saved to the file, closes the
* dataset object header, and frees all resources used by the
* descriptor.
*
* Return: Non-negative on success/Negative on failure
*
* Errors:
* DATASET CANTINIT Couldn't free the type or space,
* but the dataset was freed anyway.
*
* Programmer: Robb Matzke
* Thursday, December 4, 1997
*
* Modifications:
* Robb Matzke, 9 Jun 1998
* The data space message is no longer cached in the dataset struct.
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_close(H5D_t *dataset)
{
uintn free_failed;
FUNC_ENTER(H5D_close, FAIL);
/* check args */
assert(dataset && dataset->ent.file);
/*
* Release data type and creation property list -- there isn't much we
* can do if one of these fails, so we just continue.
*/
free_failed = (H5T_close(dataset->type) < 0 ||
H5P_close(dataset->create_parms));
/* Close the dataset object */
H5O_close(&(dataset->ent));
/*
* Free memory. Before freeing the memory set the file pointer to NULL.
* We always check for a null file pointer in other H5D functions to be
* sure we're not accessing an already freed dataset (see the assert()
* above).
*/
dataset->ent.file = NULL;
H5FL_FREE(H5D_t,dataset);
if (free_failed) {
HRETURN_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"couldn't free the type or creation property list, "
"but the dataset was freed anyway.");
}
FUNC_LEAVE(SUCCEED);
}
/*-------------------------------------------------------------------------
* 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
*
* Modifications:
* Robb Matzke, 1998-06-09
* The data space is no longer cached in the dataset struct.
*
* Robb Matzke, 1998-08-11
* Added timing calls around all the data space I/O functions.
*
* rky, 1998-09-18
* Added must_convert to do non-optimized read when necessary.
*
* Quincey Koziol, 1999-07-02
* Changed xfer_parms parameter to xfer plist parameter, so it
* could be passed to H5T_convert.
*-------------------------------------------------------------------------
*/
herr_t
H5D_read(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, hid_t dxpl_id, void *buf/*out*/)
{
const H5F_xfer_t *xfer_parms = NULL;
hssize_t nelmts; /*number of elements */
size_t smine_start; /*strip mine start loc */
size_t n, smine_nelmts; /*elements per strip */
uint8_t *tconv_buf = NULL; /*data type conv buffer */
uint8_t *bkg_buf = NULL; /*background buffer */
H5T_path_t *tpath = NULL; /*type conversion info */
hid_t src_id = -1, dst_id = -1;/*temporary type atoms */
H5S_conv_t *sconv=NULL; /*space conversion funcs*/
H5S_sel_iter_t mem_iter; /*mem selection iteration info*/
H5S_sel_iter_t bkg_iter; /*background iteration info*/
H5S_sel_iter_t file_iter; /*file selection iter info*/
herr_t ret_value = FAIL; /*return value */
herr_t status; /*function return status*/
size_t src_type_size; /*size of source type */
size_t dst_type_size; /*size of destination type*/
size_t target_size; /*desired buffer size */
size_t request_nelmts; /*requested strip mine */
size_t min_elem_out=1;/*Minimum # of elements to output*/
H5T_bkg_t need_bkg; /*type of background buf*/
H5S_t *free_this_space=NULL; /*data space to free */
hbool_t must_convert; /*have to xfer the slow way*/
#ifdef H5S_DEBUG
H5_timer_t timer;
#endif
FUNC_ENTER(H5D_read, FAIL);
/* check args */
assert(dataset && dataset->ent.file);
assert(mem_type);
assert(buf);
/* Initialize these before any errors can occur */
HDmemset(&mem_iter,0,sizeof(H5S_sel_iter_t));
HDmemset(&bkg_iter,0,sizeof(H5S_sel_iter_t));
HDmemset(&file_iter,0,sizeof(H5S_sel_iter_t));
/* Get the dataset transfer property list */
if (H5P_DEFAULT == dxpl_id) {
xfer_parms = &H5F_xfer_dflt;
} else if (H5P_DATA_XFER != H5P_get_class(dxpl_id) ||
NULL == (xfer_parms = H5I_object(dxpl_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
}
if (!file_space) {
if (NULL==(free_this_space=H5S_read (&(dataset->ent)))) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to read data space from dataset header");
}
file_space = free_this_space;
}
if (!mem_space) mem_space = file_space;
nelmts = H5S_get_select_npoints(mem_space);
#ifdef H5_HAVE_PARALLEL
{
/* Collective access is not permissible without the MPIO driver */
H5FD_mpio_dxpl_t *dx;
if (H5FD_MPIO==xfer_parms->driver_id &&
(dx=xfer_parms->driver_info) &&
H5FD_MPIO_COLLECTIVE==dx->xfer_mode) {
if (!(IS_H5FD_MPIO(dataset->ent.file)))
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"collective access for MPIO driver only");
}
}
#endif
/*
* Locate the type conversion function and data space conversion
* functions, and set up the element numbering information. If a data
* type conversion is necessary then register data type 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 data type conversion also
* turns off background preservation.
*/
if (nelmts!=H5S_get_select_npoints (file_space)) {
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,
"src and dest data spaces have different sizes");
}
if (NULL==(tpath=H5T_path_find(dataset->type, mem_type, NULL, NULL))) {
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to convert between src and dest data types");
} else if (!H5T_IS_NOOP(tpath)) {
if ((src_id=H5I_register(H5I_DATATYPE,
H5T_copy(dataset->type, H5T_COPY_ALL)))<0 ||
(dst_id=H5I_register(H5I_DATATYPE,
H5T_copy(mem_type, H5T_COPY_ALL)))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
"unable to register types for conversion");
}
}
if (NULL==(sconv=H5S_find(mem_space, file_space))) {
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to convert from file to memory data space");
}
#ifdef H5_HAVE_PARALLEL
/* rky 980813 This is a temporary KLUGE.
* The sconv functions should be set by H5S_find,
* or we should use a different way to call the MPI-IO
* mem-and-file-dataspace-xfer functions
* (the latter in case the arguments to sconv_funcs
* turn out to be inappropriate for MPI-IO). */
if (H5_mpi_opt_types_g &&
IS_H5FD_MPIO(dataset->ent.file)) {
sconv->read = H5S_mpio_spaces_read;
}
#endif /*HAVE_PARALLEL*/
/*
* If there is no type conversion then try reading directly into the
* application's buffer. This saves at least one mem-to-mem copy.
*/
if (H5T_IS_NOOP(tpath) && sconv->read) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = (sconv->read)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->pline),
&(dataset->create_parms->efl),
H5T_get_size (dataset->type), file_space,
mem_space, dxpl_id, buf/*out*/,
&must_convert);
if (status<0) {
/* Supports only no conversion, type or space, for now. */
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL,
"optimized read failed");
}
if (must_convert) {
/* sconv->read cannot do a direct transfer;
* fall through and xfer the data in the more roundabout way */
} else {
/* direct xfer accomplished successfully */
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].read_timer), &timer);
sconv->stats[1].read_nbytes += nelmts *
H5T_get_size(dataset->type);
sconv->stats[1].read_ncalls++;
#endif
goto succeed;
}
#ifdef H5D_DEBUG
if (H5DEBUG(D)) {
fprintf (H5DEBUG(D), "H5D: data space conversion could not be "
"optimized for this case (using general method "
"instead)\n");
}
#endif
H5E_clear ();
}
/*
* This is the general case. Figure out the strip mine size.
*/
if ((sconv->f->init)(&(dataset->layout), file_space, &file_iter, &min_elem_out)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize file selection information");
}
if ((sconv->m->init)(&(dataset->layout), mem_space, &mem_iter, &min_elem_out)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize memory selection information");
}
if ((sconv->m->init)(&(dataset->layout), mem_space, &bkg_iter, &min_elem_out)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize background selection information");
}
src_type_size = H5T_get_size(dataset->type);
dst_type_size = H5T_get_size(mem_type);
target_size = xfer_parms->buf_size;
#ifdef QAK
printf("%s: check 2.0, src_type_size=%d, dst_type_size=%d, target_size=%d, min_elem_out=%d\n",FUNC,(int)src_type_size,(int)dst_type_size,(int)target_size,(int)min_elem_out);
#endif /* QAK */
request_nelmts = target_size / MAX(src_type_size, dst_type_size);
/* Adjust to the min. # of elements to output */
request_nelmts = (request_nelmts/min_elem_out)*min_elem_out;
#ifdef QAK
printf("%s: check 3.0, request_nelmts=%d\n",FUNC,(int)request_nelmts);
#endif
if (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. The
* malloc() is usually less resource-intensive if we allocate/free the
* same size over and over.
*/
if (tpath->cdata.need_bkg) {
need_bkg = MAX(tpath->cdata.need_bkg, xfer_parms->need_bkg);
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
}
if (NULL==(tconv_buf=xfer_parms->tconv_buf)) {
/* Allocate temporary buffer */
if((tconv_buf=H5FL_BLK_ALLOC(type_conv,target_size,0))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed for type conversion");
}
if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) {
/* Allocate temporary buffer */
if((bkg_buf=H5FL_BLK_ALLOC(bkgr_conv,request_nelmts*dst_type_size,0))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed for background conversion");
}
#ifdef QAK
printf("%s: check 4.0, nelmts=%d, need_bkg=%d\n",
FUNC,(int)nelmts,(int)need_bkg);
#endif
/* Start strip mining... */
assert(nelmts==(hssize_t)(size_t)nelmts); /*check for overflow*/
for (smine_start=0;
smine_start<(size_t)nelmts;
smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
smine_nelmts = (sconv->f->avail)(file_space,&file_iter,
MIN(request_nelmts,
(nelmts-smine_start)));
#ifdef QAK
printf("%s: check 5.0, nelmts=%d, smine_start=%d, smine_nelmts=%d\n",
FUNC,(int)nelmts,(int)smine_start,(int)smine_nelmts);
#endif
/*
* Gather the data from disk into the data type conversion
* buffer. Also gather data from application to background buffer
* if necessary.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = (sconv->f->gath)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->pline),
&(dataset->create_parms->fill),
&(dataset->create_parms->efl), src_type_size,
file_space, &file_iter, smine_nelmts,
dxpl_id, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].gath_timer), &timer);
sconv->stats[1].gath_nbytes += n * src_type_size;
sconv->stats[1].gath_ncalls++;
#endif
if (n!=smine_nelmts) {
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file gather failed");
}
#ifdef QAK
printf("%s: check 6.0\n",FUNC);
{
int i;
int *b;
/* if(qak_debug) { */
b=tconv_buf;
printf("\ntconv_buf:");
for (i=0; i<smine_nelmts; i++,b++) {
printf("(%d)%d ",i,(int)*b);
}
printf("\n");
/* } */
}
#endif
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = (sconv->m->gath)(buf, dst_type_size, mem_space, &bkg_iter,
smine_nelmts, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].bkg_timer), &timer);
sconv->stats[1].bkg_nbytes += n * dst_type_size;
sconv->stats[1].bkg_ncalls++;
#endif
if (n!=smine_nelmts) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "mem gather failed");
}
} else if (need_bkg) {
HDmemset(bkg_buf, 0, request_nelmts*dst_type_size);
}
#ifdef QAK
printf("%s: check 7.0\n",FUNC);
#endif
/*
* Perform data type conversion.
*/
if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf,
bkg_buf, dxpl_id)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"data type conversion failed");
}
#ifdef QAK
printf("%s: check 8.0\n",FUNC);
#endif
/*
* Scatter the data into memory.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = (sconv->m->scat)(tconv_buf, dst_type_size, mem_space,
&mem_iter, smine_nelmts, buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[1].scat_timer), &timer);
sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size;
sconv->stats[1].scat_ncalls++;
#endif
if (status<0) {
HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "scatter failed");
}
#ifdef QAK
printf("%s: check 9.0\n",FUNC);
#endif /* QAK */
}
succeed:
ret_value = SUCCEED;
done:
/* Release selection iterators */
H5S_sel_iter_release(file_space,&file_iter);
H5S_sel_iter_release(mem_space,&mem_iter);
H5S_sel_iter_release(mem_space,&bkg_iter);
if (src_id >= 0) H5I_dec_ref(src_id);
if (dst_id >= 0) H5I_dec_ref(dst_id);
if (tconv_buf && NULL==xfer_parms->tconv_buf)
H5FL_BLK_FREE(type_conv,tconv_buf);
if (bkg_buf && NULL==xfer_parms->bkg_buf)
H5FL_BLK_FREE(bkgr_conv,bkg_buf);
if (free_this_space) H5S_close(free_this_space);
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* 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
*
* Modifications:
* Robb Matzke, 9 Jun 1998
* The data space is no longer cached in the dataset struct.
*
* rky 980918
* Added must_convert to do non-optimized read when necessary.
*
* Quincey Koziol, 2 July 1999
* Changed xfer_parms parameter to xfer plist parameter, so it could be passed
* to H5T_convert
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
const H5S_t *file_space, hid_t dxpl_id, const void *buf)
{
const H5F_xfer_t *xfer_parms = NULL;
hssize_t nelmts; /*total number of elmts */
size_t smine_start; /*strip mine start loc */
size_t n, smine_nelmts; /*elements per strip */
uint8_t *tconv_buf = NULL; /*data type conv buffer */
uint8_t *bkg_buf = NULL; /*background buffer */
H5T_path_t *tpath = NULL; /*type conversion info */
hid_t src_id = -1, dst_id = -1;/*temporary type atoms */
H5S_conv_t *sconv=NULL; /*space conversion funcs*/
H5S_sel_iter_t mem_iter; /*memory selection iteration info*/
H5S_sel_iter_t bkg_iter; /*background iteration info*/
H5S_sel_iter_t file_iter; /*file selection iteration info*/
herr_t ret_value = FAIL; /*return value */
herr_t status; /*function return status*/
size_t src_type_size; /*size of source type */
size_t dst_type_size; /*size of destination type*/
size_t target_size; /*desired buffer size */
size_t request_nelmts; /*requested strip mine */
size_t min_elem_out=1;/*Minimum # of elements to output*/
H5T_bkg_t need_bkg; /*type of background buf*/
H5S_t *free_this_space=NULL; /*data space to free */
hbool_t must_convert; /*have to xfer the slow way*/
#ifdef H5S_DEBUG
H5_timer_t timer;
#endif
FUNC_ENTER(H5D_write, FAIL);
/* check args */
assert(dataset && dataset->ent.file);
assert(mem_type);
assert(buf);
#ifdef H5_HAVE_PARALLEL
/* If MPIO is used, no VL 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 (IS_H5FD_MPIO(dataset->ent.file) &&
H5T_get_class(mem_type)==H5T_VLEN) {
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"Parallel IO does not support writing VL datatypes yet");
}
#endif
#ifdef H5_HAVE_PARALLEL
/* If MPIO is used, no dataset region reference support yet. */
/* This is because they use the global heap in the file and we don't */
/* support parallel access of that yet */
if (IS_H5FD_MPIO(dataset->ent.file) &&
H5T_get_class(mem_type)==H5T_REFERENCE &&
H5T_get_ref_type(mem_type)==H5R_DATASET_REGION) {
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"Parallel IO does not support writing VL datatypes yet");
}
#endif
/* Initialize these before any errors can occur */
HDmemset(&mem_iter,0,sizeof(H5S_sel_iter_t));
HDmemset(&bkg_iter,0,sizeof(H5S_sel_iter_t));
HDmemset(&file_iter,0,sizeof(H5S_sel_iter_t));
#ifdef QAK
printf("%s: check 0.3, buf=%p\n", FUNC,buf);
#endif /* QAK */
/* Get the dataset transfer property list */
if (H5P_DEFAULT == dxpl_id) {
xfer_parms = &H5F_xfer_dflt;
} else if (H5P_DATA_XFER != H5P_get_class(dxpl_id) ||
NULL == (xfer_parms = H5I_object(dxpl_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
}
if (0==(dataset->ent.file->intent & H5F_ACC_RDWR)) {
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"no write intent on file");
}
if (!file_space) {
if (NULL==(free_this_space=H5S_read (&(dataset->ent)))) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to read data space from dataset header");
}
file_space = free_this_space;
}
if (!mem_space) mem_space = file_space;
nelmts = H5S_get_select_npoints(mem_space);
#ifdef H5_HAVE_PARALLEL
{
/* Collective access is not permissible without the MPIO driver */
H5FD_mpio_dxpl_t *dx;
if (H5FD_MPIO==xfer_parms->driver_id &&
(dx=xfer_parms->driver_info) &&
H5FD_MPIO_COLLECTIVE==dx->xfer_mode) {
if (!(IS_H5FD_MPIO(dataset->ent.file)))
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"collective access for MPIO driver only");
}
}
#endif
/*
* Locate the type conversion function and data space conversion
* functions, and set up the element numbering information. If a data
* type conversion is necessary then register data type 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 data type conversion also
* turns off background preservation.
*/
#ifdef QAK
printf("%s: check 0.5, nelmts=%d, mem_space->rank=%d\n", FUNC,
(int)nelmts, mem_space->extent.u.simple.rank);
#endif /* QAK */
if (nelmts!=H5S_get_select_npoints (file_space)) {
HGOTO_ERROR (H5E_ARGS, H5E_BADVALUE, FAIL,
"src and dest data spaces have different sizes");
}
if (NULL==(tpath=H5T_path_find(mem_type, dataset->type, NULL, NULL))) {
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to convert between src and dest data types");
} else if (!H5T_IS_NOOP(tpath)) {
if ((src_id = H5I_register(H5I_DATATYPE,
H5T_copy(mem_type, H5T_COPY_ALL)))<0 ||
(dst_id = H5I_register(H5I_DATATYPE,
H5T_copy(dataset->type, H5T_COPY_ALL)))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL,
"unable to register types for conversion");
}
}
#ifdef QAK
printf("%s: after H5T_find, tpath=%p, tpath->name=%s\n",FUNC,tpath,tpath->name);
#endif /* QAK */
if (NULL==(sconv=H5S_find(mem_space, file_space))) {
HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to convert from memory to file data space");
}
#ifdef H5_HAVE_PARALLEL
/* rky 980813 This is a temporary KLUGE.
* The sconv functions should be set by H5S_find,
* or we should use a different way to call the MPI-IO
* mem-and-file-dataspace-xfer functions
* (the latter in case the arguments to sconv_funcs
* turn out to be inappropriate for MPI-IO). */
if (H5_mpi_opt_types_g &&
IS_H5FD_MPIO(dataset->ent.file)) {
sconv->write = H5S_mpio_spaces_write;
}
#endif /*HAVE_PARALLEL*/
/*
* If there is no type conversion then try writing directly from
* application buffer to file.
*/
if (H5T_IS_NOOP(tpath) && sconv->write) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = (sconv->write)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->pline),
&(dataset->create_parms->efl),
H5T_get_size (dataset->type), file_space,
mem_space, dxpl_id, buf, &must_convert/*out*/);
if (status<0) {
/* Supports only no conversion, type or space, for now. */
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL,
"optimized write failed");
}
if (must_convert) {
/* sconv->write cannot do a direct transfer;
* fall through and xfer the data in the more roundabout way */
} else {
/* direct xfer accomplished successfully */
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].write_timer), &timer);
sconv->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type);
sconv->stats[0].write_ncalls++;
#endif
goto succeed;
}
#ifdef H5D_DEBUG
if (H5DEBUG(D)) {
fprintf (H5DEBUG(D), "H5D: data space conversion could not be "
"optimized for this case (using general method "
"instead)\n");
}
#endif
H5E_clear ();
}
/*
* This is the general case. Figure out the strip mine size.
*/
if ((sconv->f->init)(&(dataset->layout), file_space, &file_iter, &min_elem_out)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize file selection information");
}
if ((sconv->m->init)(&(dataset->layout), mem_space, &mem_iter, &min_elem_out)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize memory selection information");
}
if ((sconv->f->init)(&(dataset->layout), file_space, &bkg_iter, &min_elem_out)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize memory selection information");
}
src_type_size = H5T_get_size(mem_type);
dst_type_size = H5T_get_size(dataset->type);
target_size = xfer_parms->buf_size;
request_nelmts = target_size / MAX (src_type_size, dst_type_size);
/* Adjust to the min. # of elements to output */
request_nelmts = (request_nelmts/min_elem_out)*min_elem_out;
if (request_nelmts<=0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"temporary buffer max size is too small");
}
#ifdef QAK
printf("%s: check 3.0, request_nelmts=%d\n",FUNC,(int)request_nelmts);
#endif
/*
* 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. The
* malloc() is usually less resource-intensive if we allocate/free the
* same size over and over.
*/
if (tpath->cdata.need_bkg) {
need_bkg = MAX (tpath->cdata.need_bkg, xfer_parms->need_bkg);
} else {
need_bkg = H5T_BKG_NO; /*never needed even if app says yes*/
}
if (NULL==(tconv_buf=xfer_parms->tconv_buf)) {
/* Allocate temporary buffer */
if((tconv_buf=H5FL_BLK_ALLOC(type_conv,target_size,0))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed for type conversion");
}
if (need_bkg && NULL==(bkg_buf=xfer_parms->bkg_buf)) {
/* Allocate temporary buffer */
if((bkg_buf=H5FL_BLK_ALLOC(bkgr_conv,request_nelmts*dst_type_size,0))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed for background conversion");
}
#ifdef QAK
printf("%s: check 4.0, nelmts=%d, request_nelmts=%d, need_bkg=%d\n",
FUNC,(int)nelmts,(int)request_nelmts,(int)need_bkg);
#endif
/* Start strip mining... */
assert(nelmts==(hssize_t)(size_t)nelmts); /*check for overflow*/
for (smine_start=0;
smine_start<(size_t)nelmts;
smine_start+=smine_nelmts) {
/* Go figure out how many elements to read from the file */
smine_nelmts = (sconv->f->avail)(file_space,&file_iter,
MIN(request_nelmts,
(nelmts-smine_start)));
#ifdef QAK
printf("%s: check 5.0, nelmts=%d, smine_start=%d, smine_nelmts=%d\n",
FUNC,(int)nelmts,(int)smine_start,(int)smine_nelmts);
#endif
/*
* Gather data from application buffer into the data type conversion
* buffer. Also gather data from the file into the background buffer
* if necessary.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = (sconv->m->gath)(buf, src_type_size, mem_space, &mem_iter,
smine_nelmts, tconv_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].gath_timer), &timer);
sconv->stats[0].gath_nbytes += n * src_type_size;
sconv->stats[0].gath_ncalls++;
#endif
if (n!=smine_nelmts) {
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "mem gather failed");
}
#ifdef QAK
{
int i;
uint16_t *b;
if(qak_debug) {
b=tconv_buf;
printf("\ntconv_buf:");
for (i=0; i<smine_nelmts; i++,b++) {
printf("(%d)%d ",i,(int)*b);
}
printf("\n");
}
}
printf("%s: check 6.0, tconv_buf=%p, *tconv_buf=%p\n",FUNC,tconv_buf,*(char **)tconv_buf);
#endif
if (H5T_BKG_YES==need_bkg) {
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
n = (sconv->f->gath)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->pline),
&(dataset->create_parms->fill),
&(dataset->create_parms->efl), dst_type_size,
file_space, &bkg_iter, smine_nelmts,
dxpl_id, bkg_buf/*out*/);
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].bkg_timer), &timer);
sconv->stats[0].bkg_nbytes += n * dst_type_size;
sconv->stats[0].bkg_ncalls++;
#endif
if (n!=smine_nelmts) {
HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL,
"file gather failed");
}
} else if (need_bkg) {
HDmemset(bkg_buf, 0, request_nelmts*dst_type_size);
}
/*
* Perform data type conversion.
*/
if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf,
bkg_buf, dxpl_id)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"data type conversion failed");
}
#ifdef QAK
printf("%s: check 6.3\n",FUNC);
#endif
/*
* Scatter the data out to the file.
*/
#ifdef H5S_DEBUG
H5_timer_begin(&timer);
#endif
status = (sconv->f->scat)(dataset->ent.file, &(dataset->layout),
&(dataset->create_parms->pline),
&(dataset->create_parms->fill),
&(dataset->create_parms->efl), dst_type_size,
file_space, &file_iter, smine_nelmts,
dxpl_id, tconv_buf);
#ifdef QAK
printf("%s: check 6.35\n",FUNC);
#endif
#ifdef H5S_DEBUG
H5_timer_end(&(sconv->stats[0].scat_timer), &timer);
sconv->stats[0].scat_nbytes += smine_nelmts * dst_type_size;
sconv->stats[0].scat_ncalls++;
#endif
if (status<0) {
HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "scatter failed");
}
}
#ifdef QAK
printf("%s: check 6.4\n",FUNC);
#endif
/*
* 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->ent), FALSE)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to update modification time");
}
succeed:
ret_value = SUCCEED;
done:
/* Release selection iterators */
H5S_sel_iter_release(file_space,&file_iter);
H5S_sel_iter_release(mem_space,&mem_iter);
H5S_sel_iter_release(file_space,&bkg_iter);
if (src_id >= 0) H5I_dec_ref(src_id);
if (dst_id >= 0) H5I_dec_ref(dst_id);
if (tconv_buf && NULL==xfer_parms->tconv_buf)
H5FL_BLK_FREE(type_conv,tconv_buf);
if (bkg_buf && NULL==xfer_parms->bkg_buf)
H5FL_BLK_FREE(bkgr_conv,bkg_buf);
if (free_this_space) H5S_close(free_this_space);
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5D_extend
*
* Purpose: Increases the size of a dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Friday, January 30, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_extend (H5D_t *dataset, const hsize_t *size)
{
herr_t changed, ret_value=FAIL;
H5S_t *space = NULL;
FUNC_ENTER (H5D_extend, FAIL);
/* Check args */
assert (dataset);
assert (size);
/*
* NOTE: Restrictions on extensions were checked when the dataset was
* created. All extensions are allowed here since none should be
* able to muck things up.
*/
/* Increase the size of the data space */
if (NULL==(space=H5S_read (&(dataset->ent)))) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to read data space info from dataset header");
}
if ((changed=H5S_extend (space, size))<0) {
HGOTO_ERROR (H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to increase size of data space");
}
if (changed>0){
/* Save the new dataspace in the file if necessary */
if (H5S_modify (&(dataset->ent), space)<0) {
HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL,
"unable to update file with new dataspace");
}
/* Initialize the new parts of the dataset */
#ifdef LATER
if (H5S_select_all(space)<0 ||
H5S_select_hyperslab(space, H5S_SELECT_DIFF, zero, NULL,
old_dims, NULL)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to select new extents for fill value");
}
#else
/*
* We don't have the H5S_SELECT_DIFF operator yet. We really only
* need it for contiguous datasets because the chunked datasets will
* either fill on demand during I/O or attempt a fill of all chunks.
*/
if (H5D_CONTIGUOUS==dataset->layout.type &&
dataset->create_parms->fill.buf) {
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to select fill value region");
}
#endif
if (H5D_init_storage(dataset, space)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize dataset with fill value");
}
}
ret_value = SUCCEED;
done:
H5S_close(space);
FUNC_LEAVE (ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5D_entof
*
* Purpose: Returns a pointer to the entry for a dataset.
*
* Return: Success: Ptr to entry
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Friday, April 24, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
H5G_entry_t *
H5D_entof (H5D_t *dataset)
{
return dataset ? &(dataset->ent) : NULL;
}
/*-------------------------------------------------------------------------
* Function: H5D_typeof
*
* Purpose: Returns a pointer to the dataset's data type. The data type
* is not copied.
*
* Return: Success: Ptr to the dataset's data type, uncopied.
*
* Failure: NULL
*
* Programmer: Robb Matzke
* Thursday, June 4, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
H5T_t *
H5D_typeof (H5D_t *dset)
{
FUNC_ENTER (H5D_typeof, NULL);
assert (dset);
assert (dset->type);
FUNC_LEAVE (dset->type);
}
/*-------------------------------------------------------------------------
* Function: H5D_get_file
*
* Purpose: Returns the dataset's file pointer.
*
* Return: Success: Ptr to the dataset's file pointer.
*
* Failure: NULL
*
* Programmer: Quincey Koziol
* Thursday, October 22, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
H5F_t *
H5D_get_file (const H5D_t *dset)
{
FUNC_ENTER (H5D_get_file, NULL);
assert (dset);
assert (dset->ent.file);
FUNC_LEAVE (dset->ent.file);
}
/*-------------------------------------------------------------------------
* Function: H5D_init_storage
*
* Purpose: Initialize the data for a new dataset. If a selection is
* defined for SPACE then initialize only that part of the
* dataset.
*
* Return: Non-negative on success/Negative on failure
*
* Programmer: Robb Matzke
* Monday, October 5, 1998
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D_init_storage(H5D_t *dset, const H5S_t *space)
{
hssize_t npoints, ptsperbuf;
size_t size, bufsize=8*1024;
haddr_t addr;
herr_t ret_value = FAIL;
void *buf = NULL;
FUNC_ENTER(H5D_init_storage, FAIL);
assert(dset);
assert(space);
switch (dset->layout.type) {
case H5D_CONTIGUOUS:
/*
* If the fill value is set then write it to the specified selection
* even if it is all zero. This allows the application to force
* filling when the underlying storage isn't initialized to zero.
*/
npoints = H5S_get_simple_extent_npoints(space);
if (dset->create_parms->fill.buf &&
npoints==H5S_get_select_npoints(space)) {
/*
* Fill the entire current extent with the fill value. We can do
* this quite efficiently by making sure we copy the fill value
* in relatively large pieces.
*/
ptsperbuf = (hssize_t)MAX(1,
bufsize/dset->create_parms->fill.size);
bufsize = ptsperbuf * dset->create_parms->fill.size;
/* Allocate temporary buffer */
if ((buf=H5FL_BLK_ALLOC(fill_conv,bufsize,0))==NULL)
HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed for fill buffer");
H5V_array_fill(buf, dset->create_parms->fill.buf,
dset->create_parms->fill.size, ptsperbuf);
if (dset->create_parms->efl.nused) {
addr = 0;
} else {
addr = dset->layout.addr;
}
while (npoints>0) {
size = MIN(ptsperbuf, npoints) * dset->create_parms->fill.size;
if (dset->create_parms->efl.nused) {
if (H5O_efl_write(dset->ent.file,
&(dset->create_parms->efl),
addr, size, buf)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to write fill value to dataset");
}
} else {
if (H5F_block_write(dset->ent.file, H5FD_MEM_DRAW, addr, size,
H5P_DEFAULT, buf)<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to write fill value to dataset");
}
}
npoints -= MIN(ptsperbuf, npoints);
addr += size;
}
} else if (dset->create_parms->fill.buf) {
/*
* Fill the specified selection with the fill value.
*/
HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL,
"unable to initialize dataset with fill value");
}
break;
case H5D_CHUNKED:
#ifdef H5_HAVE_PARALLEL
/*
* If the dataset is accessed via parallel I/O, allocate file space
* for all chunks now and initialize each chunk with the fill value.
*/
if (IS_H5FD_MPIO(dset->ent.file)) {
/* We only handle simple data spaces so far */
intn ndims;
hsize_t dim[H5O_LAYOUT_NDIMS];
if ((ndims=H5S_get_simple_extent_dims(space, dim, NULL))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to get simple data space info");
}
dim[ndims] = dset->layout.dim[ndims];
ndims++;
if (H5F_istore_allocate(dset->ent.file, H5P_DEFAULT,
&(dset->layout), dim,
&(dset->create_parms->pline),
&(dset->create_parms->fill))<0) {
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to allocate all chunks of dataset");
}
}
#endif /*H5_HAVE_PARALLEL*/
break;
}
ret_value = SUCCEED;
done:
if (buf)
H5FL_BLK_FREE(fill_conv,buf);
FUNC_LEAVE(ret_value);
}
/*-------------------------------------------------------------------------
* Function: H5Dget_storage_size
*
* Purpose: Returns the amount of storage that is required for the
* dataset. For chunked datasets this is the number of allocated
* chunks times the chunk size.
*
* Return: Success: The amount of storage space allocated for the
* dataset, not counting meta data. The return
* value may be zero if no data has been stored.
*
* Failure: Zero
*
* Programmer: Robb Matzke
* Wednesday, April 21, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
hsize_t
H5Dget_storage_size(hid_t dset_id)
{
H5D_t *dset=NULL;
hsize_t size;
FUNC_ENTER(H5Dget_storage_size, 0);
H5TRACE1("h","i",dset_id);
/* Check args */
if (H5I_DATASET!=H5I_get_type(dset_id) ||
NULL==(dset=H5I_object(dset_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
size = H5D_get_storage_size(dset);
FUNC_LEAVE(size);
}
/*-------------------------------------------------------------------------
* Function: H5D_get_storage_size
*
* Purpose: Determines how much space has been reserved to store the raw
* data of a dataset.
*
* Return: Success: Number of bytes reserved to hold raw data.
*
* Failure: 0
*
* Programmer: Robb Matzke
* Wednesday, April 21, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
hsize_t
H5D_get_storage_size(H5D_t *dset)
{
hsize_t size;
int i;
FUNC_ENTER(H5D_get_storage_size, 0);
if (H5D_CHUNKED==dset->layout.type) {
size = H5F_istore_allocated(dset->ent.file, dset->layout.ndims,
dset->layout.addr);
} else {
for (i=0, size=1; i<dset->layout.ndims; i++) {
size *= dset->layout.dim[i];
}
}
FUNC_LEAVE(size);
}
/*-------------------------------------------------------------------------
* Function: H5Diterate
*
* Purpose: This routine iterates over all the elements selected in a memory
* buffer. The callback function is called once for each element selected
* in the dataspace. The selection in the dataspace is modified so
* that any elements already iterated over are removed from the selection
* if the iteration is interrupted (by the H5D_operator_t function
* returning non-zero) in the "middle" of the iteration and may be
* re-started by the user where it left off.
*
* NOTE: Until "subtracting" elements from a selection is implemented,
* the selection is not modified.
*
* Parameters:
* void *buf; IN/OUT: Pointer to the buffer in memory containing
* the elements to iterate over.
* hid_t type_id; IN: Datatype ID for the elements stored in BUF.
* hid_t space_id; IN: Dataspace ID for BUF, also contains the
* selection to iterate over.
* H5D_operator_t op; IN: Function pointer to the routine to be
* called for each element in BUF iterated over.
* void *operator_data; IN/OUT: Pointer to any user-defined data
* associated with the operation.
*
* Operation information:
* H5D_operator_t is defined as:
* typedef herr_t (*H5D_operator_t)(void *elem, hid_t type_id,
* hsize_t ndim, hssize_t *point, void *operator_data);
*
* H5D_operator_t parameters:
* void *elem; IN/OUT: Pointer to the element in memory containing
* the current point.
* hid_t type_id; IN: Datatype ID for the elements stored in ELEM.
* hsize_t ndim; IN: Number of dimensions for POINT array
* hssize_t *point; IN: Array containing the location of the element
* within the original dataspace.
* void *operator_data; IN/OUT: Pointer to any user-defined data
* associated with the operation.
*
* The return values from an operator are:
* Zero causes the iterator to continue, returning zero when all
* elements have been processed.
* Positive causes the iterator to immediately return that positive
* value, indicating short-circuit success. The iterator can be
* restarted at the next element.
* Negative causes the iterator to immediately return that value,
* indicating failure. The iterator can be restarted at the next
* element.
*
* Return: Returns the return value of the last operator if it was non-zero,
* or zero if all elements were processed. Otherwise returns a
* negative value.
*
* Programmer: Quincey Koziol
* Friday, June 11, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Diterate(void *buf, hid_t type_id, hid_t space_id, H5D_operator_t op,
void *operator_data)
{
H5S_t *space = NULL;
herr_t ret_value=FAIL;
FUNC_ENTER(H5Diterate, FAIL);
H5TRACE5("e","xiixx",buf,type_id,space_id,op,operator_data);
/* Check args */
if (NULL==op)
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid operator");
if (buf==NULL)
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid buffer");
if (H5I_DATATYPE != H5I_get_type(type_id))
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid datatype");
if (H5I_DATASPACE != H5I_get_type(space_id) ||
NULL == (space = H5I_object(space_id)))
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataspace");
ret_value=H5S_select_iterate(buf,type_id,space,op,operator_data);
FUNC_LEAVE(ret_value);
} /* end H5Diterate() */
/*-------------------------------------------------------------------------
* Function: H5Dvlen_reclaim
*
* Purpose: Frees the buffers allocated for storing variable-length data
* in memory. Only frees the VL data in the selection defined in the
* dataspace. The dataset transfer property list is required to find the
* correct allocation/free methods for the VL data in the buffer.
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Quincey Koziol
* Thursday, June 10, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf)
{
H5F_xfer_t tmp_xfer_parms; /* Temporary copy of the default xfer parms */
H5F_xfer_t *xfer_parms = NULL; /* xfer parms as iterator op_data */
herr_t ret_value=FAIL;
FUNC_ENTER(H5Dvlen_reclaim, FAIL);
H5TRACE4("e","iiix",type_id,space_id,plist_id,buf);
/* Check args */
if (H5I_DATATYPE!=H5I_get_type(type_id) ||
H5I_DATASPACE!=H5I_get_type(space_id) ||
buf==NULL) {
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument");
}
/* Retrieve dataset transfer property list */
if (H5P_DEFAULT == plist_id) {
HDmemcpy(&tmp_xfer_parms,&H5F_xfer_dflt,sizeof(H5F_xfer_t));
xfer_parms = &tmp_xfer_parms;
} else if (H5P_DATA_XFER != H5P_get_class(plist_id) ||
NULL == (xfer_parms = H5I_object(plist_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms");
}
/* Call H5Diterate with args, etc. */
ret_value=H5Diterate(buf,type_id,space_id,H5T_vlen_reclaim,xfer_parms);
FUNC_LEAVE(ret_value);
} /* end H5Dvlen_reclaim() */
/*-------------------------------------------------------------------------
* Function: H5D_vlen_get_buf_size_alloc
*
* Purpose: This routine makes certain there is enough space in the temporary
* buffer for the new data to read in. All the VL data read in is actually
* placed in this buffer, overwriting the previous data. Needless to say,
* this data is not actually usable.
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, August 17, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
void *H5D_vlen_get_buf_size_alloc(size_t size, void *info)
{
H5T_vlen_bufsize_t *vlen_bufsize=(H5T_vlen_bufsize_t *)info;
FUNC_ENTER(H5D_vlen_get_buf_size_alloc, NULL);
/* Get a temporary pointer to space for the VL data */
if ((vlen_bufsize->vl_tbuf=H5FL_BLK_REALLOC(vlen_vl_buf,vlen_bufsize->vl_tbuf,size))!=NULL)
vlen_bufsize->size+=size;
FUNC_LEAVE(vlen_bufsize->vl_tbuf);
} /* end H5D_vlen_get_buf_size_alloc() */
/*-------------------------------------------------------------------------
* Function: H5D_vlen_get_buf_size
*
* Purpose: This routine checks the number of bytes required to store a single
* element from a dataset in memory, creating a selection with just the
* single element selected to read in the element and using a custom memory
* allocator for any VL data encountered.
* The *size value is modified according to how many bytes are
* required to store the element in memory.
*
* Implementation: This routine actually performs the read with a custom
* memory manager which basically just counts the bytes requested and
* uses a temporary memory buffer (through the H5FL API) to make certain
* enough space is available to perform the read. Then the temporary
* buffer is released and the number of bytes allocated is returned.
* Kinda kludgy, but easier than the other method of trying to figure out
* the sizes without actually reading the data in... - QAK
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Quincey Koziol
* Tuesday, August 17, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5D_vlen_get_buf_size(void UNUSED *elem, hid_t type_id, hsize_t UNUSED ndim, hssize_t *point, void *op_data)
{
H5T_vlen_bufsize_t *vlen_bufsize=(H5T_vlen_bufsize_t *)op_data;
H5T_t *dt = NULL;
herr_t ret_value=FAIL;
FUNC_ENTER(H5D_vlen_get_buf_size, FAIL);
assert(op_data);
assert(H5I_DATATYPE == H5I_get_type(type_id));
/* Check args */
if (NULL==(dt=H5I_object(type_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data type");
/* Make certain there is enough fixed-length buffer available */
if ((vlen_bufsize->fl_tbuf=H5FL_BLK_REALLOC(vlen_fl_buf,vlen_bufsize->fl_tbuf,H5T_get_size(dt)))==NULL)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't resize tbuf");
/* Select point to read in */
if (H5Sselect_elements(vlen_bufsize->fspace_id,H5S_SELECT_SET,1,(const hssize_t **)point)<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCREATE, FAIL, "can't select point");
/* Read in the point (with the custom VL memory allocator) */
if(H5Dread(vlen_bufsize->dataset_id,type_id,vlen_bufsize->mspace_id,vlen_bufsize->fspace_id,vlen_bufsize->xfer_pid,vlen_bufsize->fl_tbuf)<0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read point");
/* Set the correct return value, if we get this far */
ret_value=0;
done:
FUNC_LEAVE(ret_value);
} /* end H5D_vlen_get_buf_size() */
/*-------------------------------------------------------------------------
* Function: H5Dvlen_get_buf_size
*
* Purpose: This routine checks the number of bytes required to store the VL
* data from the dataset, using the space_id for the selection in the
* dataset on disk and the type_id for the memory representation of the
* VL data, in memory. The *size value is modified according to how many
* bytes are required to store the VL data in memory.
*
* Implementation: This routine actually performs the read with a custom
* memory manager which basically just counts the bytes requested and
* uses a temporary memory buffer (through the H5FL API) to make certain
* enough space is available to perform the read. Then the temporary
* buffer is released and the number of bytes allocated is returned.
* Kinda kludgy, but easier than the other method of trying to figure out
* the sizes without actually reading the data in... - QAK
*
* Return: Non-negative on success, negative on failure
*
* Programmer: Quincey Koziol
* Wednesday, August 11, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Dvlen_get_buf_size(hid_t dataset_id, hid_t type_id, hid_t space_id,
hsize_t *size)
{
H5T_vlen_bufsize_t vlen_bufsize = {0, 0, 0, 0, 0, 0, 0};
char bogus; /* bogus value to pass to H5Diterate() */
herr_t ret_value=FAIL;
FUNC_ENTER(H5Dvlen_get_buf_size, FAIL);
H5TRACE4("e","iii*h",dataset_id,type_id,space_id,size);
/* Check args */
if (H5I_DATASET!=H5I_get_type(dataset_id) ||
H5I_DATATYPE!=H5I_get_type(type_id) ||
H5I_DATASPACE!=H5I_get_type(space_id) || size==NULL) {
HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument");
}
/* Save the dataset ID */
vlen_bufsize.dataset_id=dataset_id;
/* Get a copy of the dataspace ID */
if((vlen_bufsize.fspace_id=H5Dget_space(dataset_id))<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "can't copy dataspace");
/* Create a scalar for the memory dataspace */
if((vlen_bufsize.mspace_id=H5Screate(H5S_SCALAR))<0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTCOPY, FAIL, "can't create dataspace");
/* Grab the temporary buffers required */
if((vlen_bufsize.fl_tbuf=H5FL_BLK_ALLOC(vlen_fl_buf,1,0))==NULL)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available");
if((vlen_bufsize.vl_tbuf=H5FL_BLK_ALLOC(vlen_vl_buf,1,0))==NULL)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "no temporary buffers available");
/* Change to the custom memory allocation routines for reading VL data */
if((vlen_bufsize.xfer_pid=H5Pcreate(H5P_DATA_XFER))<0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTCREATE, FAIL, "no dataset xfer plists available");
if(H5Pset_vlen_mem_manager(vlen_bufsize.xfer_pid,H5D_vlen_get_buf_size_alloc,&vlen_bufsize,NULL,NULL)<0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "can't set VL data allocation routine");
/* Set the initial number of bytes required */
vlen_bufsize.size=0;
/* Call H5Diterate with args, etc. */
ret_value=H5Diterate(&bogus,type_id,space_id,H5D_vlen_get_buf_size,
&vlen_bufsize);
/* Get the size if we succeeded */
if(ret_value>=0)
*size=vlen_bufsize.size;
done:
if(vlen_bufsize.fspace_id>0)
H5Sclose(vlen_bufsize.fspace_id);
if(vlen_bufsize.mspace_id>0)
H5Sclose(vlen_bufsize.mspace_id);
if(vlen_bufsize.fl_tbuf!=NULL)
H5FL_BLK_FREE(vlen_fl_buf,vlen_bufsize.fl_tbuf);
if(vlen_bufsize.vl_tbuf!=NULL)
H5FL_BLK_FREE(vlen_vl_buf,vlen_bufsize.vl_tbuf);
if(vlen_bufsize.xfer_pid>0)
H5Pclose(vlen_bufsize.xfer_pid);
FUNC_LEAVE(ret_value);
} /* end H5Dvlen_get_buf_size() */
/*-------------------------------------------------------------------------
* Function: H5Ddebug
*
* Purpose: Prints various information about a dataset. This function is
* not to be documented in the API at this time.
*
* Return: Success: Non-negative
*
* Failure: Negative
*
* Programmer: Robb Matzke
* Wednesday, April 28, 1999
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t
H5Ddebug(hid_t dset_id, unsigned UNUSED flags)
{
H5D_t *dset=NULL;
FUNC_ENTER(H5Ddebug, FAIL);
H5TRACE2("e","iIu",dset_id,flags);
/* Check args */
if (H5I_DATASET!=H5I_get_type(dset_id) ||
NULL==(dset=H5I_object(dset_id))) {
HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset");
}
/* Print B-tree information */
if (H5D_CHUNKED==dset->layout.type) {
H5F_istore_dump_btree(dset->ent.file, stdout, dset->layout.ndims,
dset->layout.addr);
} else if (H5D_CONTIGUOUS==dset->layout.type) {
HDfprintf(stdout, " %-10s %a\n", "Address:",
dset->layout.addr);
}
FUNC_LEAVE(SUCCEED);
}
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