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Copy pathHdf5ArrayDataWriter.cpp
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400 lines (336 loc) · 11.3 KB
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/* \file
* $Id$
* \author Caton Little
* \brief
*
* \section LICENSE
*
* Version: MPL 1.1/GPL 2.0/LGPL 2.1
*
* The contents of this file are subject to the Mozilla Public License
* Version 1.1 (the "License"); you may not use this file except in
* compliance with the License. You may obtain a copy of the License at
* http://www.mozilla.org/MPL/
*
* Software distributed under the License is distributed on an "AS IS"
* basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
* License for the specific language governing rights and limitations
* under the License.
*
* The Original Code is FieldML
*
* The Initial Developer of the Original Code is Auckland Uniservices Ltd,
* Auckland, New Zealand. Portions created by the Initial Developer are
* Copyright (C) 2010 the Initial Developer. All Rights Reserved.
*
* Contributor(s):
*
* Alternatively, the contents of this file may be used under the terms of
* either the GNU General Public License Version 2 or later (the "GPL"), or
* the GNU Lesser General Public License Version 2.1 or later (the "LGPL"),
* in which case the provisions of the GPL or the LGPL are applicable instead
* of those above. If you wish to allow use of your version of this file only
* under the terms of either the GPL or the LGPL, and not to allow others to
* use your version of this file under the terms of the MPL, indicate your
* decision by deleting the provisions above and replace them with the notice
* and other provisions required by the GPL or the LGPL. If you do not delete
* the provisions above, a recipient may use your version of this file under
* the terms of any one of the MPL, the GPL or the LGPL.
*
*/
#include "StringUtil.h"
#include "FieldmlIoApi.h"
#include "ArrayDataWriter.h"
#include "Hdf5ArrayDataWriter.h"
using namespace std;
#if defined FIELDML_HDF5_ARRAY || defined FIELDML_PHDF5_ARRAY
Hdf5ArrayDataWriter *Hdf5ArrayDataWriter::create( FieldmlIoContext *context, const string root, FmlObjectHandle source, FieldmlHandleType handleType, bool append, int *sizes, int rank )
{
Hdf5ArrayDataWriter *writer = NULL;
FmlObjectHandle resource = Fieldml_GetDataSourceResource( context->getSession(), source );
char *temp_string = Fieldml_GetDataResourceFormat( context->getSession(), resource );
string format;
if( !StringUtil::safeString( temp_string, format ) )
{
context->setError( FML_IOERR_CORE_ERROR );
}
else if( format == StringUtil::HDF5_NAME )
{
#ifdef FIELDML_HDF5_ARRAY
Hdf5ArrayDataWriter *hdf5writer = new Hdf5ArrayDataWriter( context, root, source, handleType, append, sizes, rank, H5P_DEFAULT );
if( !hdf5writer->ok )
{
delete hdf5writer;
}
else
{
writer = hdf5writer;
}
#endif //FIELDML_HDF5_ARRAY
}
else if( format == StringUtil::PHDF5_NAME )
{
#ifdef FIELDML_PHDF5_ARRAY
hid_t accessProperties = H5Pcreate( H5P_FILE_ACCESS );
if( H5Pset_fapl_mpio( accessProperties, MPI_COMM_WORLD, MPI_INFO_NULL ) >= 0 )
{
Hdf5ArrayDataWriter *hdf5writer = new Hdf5ArrayDataWriter( context, root, source, handleType, append, sizes, rank, accessProperties );
if( !hdf5writer->ok )
{
delete hdf5writer;
}
else
{
writer = hdf5writer;
}
}
H5Pclose( accessProperties );
#endif //FIELDML_PHDF5_ARRAY
}
Fieldml_FreeString(temp_string);
return writer;
}
Hdf5ArrayDataWriter::Hdf5ArrayDataWriter( FieldmlIoContext *_context, const string root, FmlObjectHandle source, FieldmlHandleType handleType, bool append, int *sizes, int _rank, hid_t accessProperties ) :
ArrayDataWriter( _context )
{
rank = _rank;
file = -1;
dataset = -1;
dataspace = -1;
hStrides = NULL;
hSizes = NULL;
hOffsets = NULL;
ok = false;
closed = true;
FmlObjectHandle resource = Fieldml_GetDataSourceResource( context->getSession(), source );
while( true )
{
string description;
char *temp_href = Fieldml_GetDataResourceHref( context->getSession(), resource );
if( !StringUtil::safeString( Fieldml_GetDataResourceHref( context->getSession(), resource ), description ) )
{
break;
}
Fieldml_FreeString(temp_href);
string location;
char *temp_string = Fieldml_GetArrayDataSourceLocation( context->getSession(), source );
if( !StringUtil::safeString( temp_string, location ) )
{
break;
}
Fieldml_FreeString(temp_string);
const string filename = StringUtil::makeFilename( root, description );
//TODO Add an API-level enum to allow the user to append data, nuke any existing file, or fail if the file already exists.
if( !append )
{
file = H5Fcreate( filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, accessProperties );
}
else
{
file = H5Fopen( filename.c_str(), H5F_ACC_RDWR, accessProperties );
if( file < 0 )
{
file = H5Fcreate( filename.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, accessProperties );
}
}
if( file < 0 )
{
break;
}
hOffsets = new hsize_t[rank];
hSizes = new hsize_t[rank];
hStrides = new hsize_t[rank];
for( int i = 0; i < rank; i++ )
{
hStrides[i] = 1;
}
//Temporarily disable errors.
H5E_auto1_t func;
void *client_data;
H5Eget_auto1( &func, &client_data );
H5Eset_auto1( NULL, NULL );
//It's fine if this call fails.
dataset = H5Dopen( file, location.c_str(), H5P_DEFAULT );
H5Eset_auto1( func, client_data );
if( dataset < 0 )
{
if( !initializeWithNewDataset( location, sizes, handleType ) )
{
break;
}
}
else
{
if( !initializeWithExistingDataset( sizes ) )
{
break;
}
}
datatype = H5Dget_type( dataset );
if( datatype < 0 )
{
break;
}
hid_t nativeType = H5Tget_native_type( datatype, H5T_DIR_DESCEND );
if( H5Tequal( nativeType, H5T_NATIVE_INT ) || H5Tequal( nativeType, H5T_NATIVE_SHORT ) )
{
datatype = H5T_NATIVE_INT;
}
else if( H5Tequal( nativeType, H5T_NATIVE_DOUBLE ) || H5Tequal( nativeType, H5T_NATIVE_FLOAT ) )
{
datatype = H5T_NATIVE_DOUBLE;
}
else if( H5Tequal( nativeType, H5T_NATIVE_INT8 ) )
{
datatype = H5T_NATIVE_INT8;
}
ok = true;
closed = false;
break;
}
}
bool Hdf5ArrayDataWriter::initializeWithNewDataset( const string location, int *sizes, FieldmlHandleType handleType )
{
for( int i = 0; i < rank; i++ )
{
hSizes[i] = sizes[i];
}
dataspace = H5Screate_simple( rank, hSizes, NULL );
if( dataspace < 0 )
{
return false;
}
if( handleType == FHT_CONTINUOUS_TYPE )
{
datatype = H5T_NATIVE_DOUBLE;
}
else if( handleType == FHT_ENSEMBLE_TYPE )
{
datatype = H5T_NATIVE_INT;
}
else if( handleType == FHT_BOOLEAN_TYPE )
{
//HDF5 has no boolean type.
//TODO Bit-packing for booleans.
datatype = H5T_NATIVE_INT8;
}
else
{
return false;
}
dataset = H5Dcreate( file, location.c_str(), datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
if( dataset < 0 )
{
return false;
}
return true;
}
bool Hdf5ArrayDataWriter::initializeWithExistingDataset( int *sizes )
{
//The dataset already exists. Make sure its dataspace is compatible with the one requested.
dataspace = H5Dget_space( dataset );
if( dataspace < 0 )
{
return false;
}
int existingRank = H5Sget_simple_extent_ndims( dataspace );
if( ( existingRank < 0 ) || ( existingRank != rank ) )
{
return false;
}
existingRank = H5Sget_simple_extent_dims( dataspace, NULL, hSizes );
if( existingRank != rank )
{
return false;
}
for( int i = 0; i < rank; i++ )
{
if( ( hSizes[i] != H5S_UNLIMITED ) && ( hSizes[i] < sizes[i] ) )
{
existingRank = -1;
}
}
if( existingRank < 0 )
{
return false;
}
//The dataset already exists. Make sure its datatype is compatible with the one requested.
return true;
}
FmlIoErrorNumber Hdf5ArrayDataWriter::writeSlab( const int *offsets, const int *sizes, hid_t requiredDatatype, const void *valueBuffer )
{
if( datatype != requiredDatatype )
{
context->setError( FML_IOERR_UNSUPPORTED );
return -1;
}
for( int i = 0; i < rank; i++ )
{
hOffsets[i] = offsets[i];
hSizes[i] = sizes[i];
}
hid_t bufferSpace = H5Screate_simple( rank, hSizes, NULL );
herr_t status;
status = H5Sselect_hyperslab( dataspace, H5S_SELECT_SET, hOffsets, NULL, hSizes, NULL );
hid_t transferProperties = H5P_DEFAULT;
// if( collective )
// {
// transferProperties = H5Pcreate (H5P_DATASET_XFER);
// H5Pset_dxpl_mpio(transferProperties, H5FD_MPIO_COLLECTIVE);
// }
status = H5Dwrite( dataset, requiredDatatype, bufferSpace, dataspace, transferProperties, valueBuffer );
// H5Pclose( transferProperties );
H5Sclose( bufferSpace );
if( status >= 0 )
{
return FML_IOERR_NO_ERROR;
}
return context->setError( FML_IOERR_WRITE_ERROR );
}
FmlIoErrorNumber Hdf5ArrayDataWriter::writeIntSlab( const int *offsets, const int *sizes, const int *valueBuffer )
{
if( closed )
{
return FML_IOERR_RESOURCE_CLOSED;
}
return writeSlab( offsets, sizes, H5T_NATIVE_INT, valueBuffer );
}
FmlIoErrorNumber Hdf5ArrayDataWriter::writeDoubleSlab( const int *offsets, const int *sizes, const double *valueBuffer )
{
if( closed )
{
return FML_IOERR_RESOURCE_CLOSED;
}
return writeSlab( offsets, sizes, H5T_NATIVE_DOUBLE, valueBuffer );
}
FmlIoErrorNumber Hdf5ArrayDataWriter::writeBooleanSlab( const int *offsets, const int *sizes, const FmlBoolean *valueBuffer )
{
if( closed )
{
return FML_IOERR_RESOURCE_CLOSED;
}
return writeSlab( offsets, sizes, H5T_NATIVE_INT8, valueBuffer );
}
FmlIoErrorNumber Hdf5ArrayDataWriter::close()
{
if( closed )
{
return FML_IOERR_NO_ERROR;
}
closed = true;
H5Sclose( dataspace );
H5Dclose( dataset );
H5Fclose( file );
return FML_IOERR_NO_ERROR;
}
Hdf5ArrayDataWriter::~Hdf5ArrayDataWriter()
{
if( !closed )
{
close();
}
delete[] hStrides;
delete[] hSizes;
delete[] hOffsets;
}
#endif //FIELDML_HDF5_ARRAY
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