/[escript]/branches/lapack2681/escript/src/DataConstant.cpp
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Contents of /branches/lapack2681/escript/src/DataConstant.cpp

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Revision 1800 - (show annotations)
Thu Sep 18 05:28:20 2008 UTC (10 years, 10 months ago) by ksteube
Original Path: trunk/escript/src/DataConstant.cpp
File size: 12366 byte(s)
Serialized parallel I/O when writing mesh or data to NetCDF file on multiple MPI processors.
Added domain method getMPIComm() to complement getMPISize() and getMPIRank().

1
2 /* $Id$ */
3
4 /*******************************************************
5 *
6 * Copyright 2003-2007 by ACceSS MNRF
7 * Copyright 2007 by University of Queensland
8 *
9 * http://esscc.uq.edu.au
10 * Primary Business: Queensland, Australia
11 * Licensed under the Open Software License version 3.0
12 * http://www.opensource.org/licenses/osl-3.0.php
13 *
14 *******************************************************/
15
16 #include "DataConstant.h"
17 #include "DataException.h"
18 #include "esysUtils/EsysAssert.h"
19
20 #include <iostream>
21 #include <boost/python/extract.hpp>
22 #ifdef USE_NETCDF
23 #include <netcdfcpp.h>
24 #endif
25
26 #include <boost/python/extract.hpp>
27 #include "DataMaths.h"
28
29 using namespace std;
30 using namespace boost::python;
31
32 namespace escript {
33
34 DataConstant::DataConstant(const boost::python::numeric::array& value,
35 const FunctionSpace& what)
36 : DataAbstract(what,DataTypes::shapeFromNumArray(value))
37 {
38 // // extract the shape of the numarray
39 // DataTypes::ShapeType tempShape;
40 // for (int i=0; i < value.getrank(); i++) {
41 // tempShape.push_back(extract<int>(value.getshape()[i]));
42 // }
43
44 // get the space for the data vector
45 // int len = getNoValues();
46 // DataVector temp_data(len, 0.0, len);
47 // DataArrayView temp_dataView(temp_data, tempShape);
48 // temp_dataView.copy(value);
49
50 m_data.copyFromNumArray(value);
51 //
52
53 // copy the data in the correct format
54 // m_data=temp_data;
55 //
56 // create the view of the data
57 // DataArrayView tempView(m_data,temp_dataView.getShape());
58 // setPointDataView(tempView);
59 }
60
61 // DataConstant::DataConstant(const DataArrayView& value,
62 // const FunctionSpace& what)
63 // : DataAbstract(what)
64 // {
65 // //
66 // // copy the data in the correct format
67 // m_data=value.getData();
68 // //
69 // // create the view of the data
70 // DataArrayView tempView(m_data,value.getShape());
71 // setPointDataView(tempView);
72 // }
73
74 DataConstant::DataConstant(const DataConstant& other)
75 : DataAbstract(other.getFunctionSpace(),other.getShape())
76 { //
77 // copy the data in the correct format
78 m_data=other.m_data;
79 //
80 // // create the view of the data
81 // DataArrayView tempView(m_data,other.getPointDataView().getShape());
82 // setPointDataView(tempView);
83 }
84
85 DataConstant::DataConstant(const DataConstant& other,
86 const DataTypes::RegionType& region)
87 : DataAbstract(other.getFunctionSpace(),DataTypes::getResultSliceShape(region))
88 {
89 //
90 // get the shape of the slice to copy from
91 // DataTypes::ShapeType shape(DataTypes::getResultSliceShape(region));
92 //
93 // allocate space for this new DataConstant's data
94 int len = getNoValues();
95 m_data.resize(len,0.,len);
96 //
97 // create a view of the data with the correct shape
98 // DataArrayView tempView(m_data,shape);
99 DataTypes::RegionLoopRangeType region_loop_range=DataTypes::getSliceRegionLoopRange(region);
100 //
101 // load the view with the data from the slice
102 // tempView.copySlice(other.getPointDataView(),region_loop_range);
103 DataTypes::copySlice(m_data,getShape(),0,other.getVector(),other.getShape(),0,region_loop_range);
104 // setPointDataView(tempView);
105 }
106
107 DataConstant::DataConstant(const FunctionSpace& what,
108 const DataTypes::ShapeType &shape,
109 const DataTypes::ValueType &data)
110 : DataAbstract(what,shape)
111 {
112 //
113 // copy the data in the correct format
114 m_data=data;
115 //
116 // create the view of the data
117 // DataArrayView tempView(m_data,shape);
118 // setPointDataView(tempView);
119 }
120
121 string
122 DataConstant::toString() const
123 {
124 return DataTypes::pointToString(m_data,getShape(),0,"");
125 }
126
127
128 DataAbstract*
129 DataConstant::deepCopy()
130 {
131 return new DataConstant(*this);
132 }
133
134
135 DataTypes::ValueType::size_type
136 DataConstant::getPointOffset(int sampleNo,
137 int dataPointNo) const
138 {
139 EsysAssert((validSamplePointNo(dataPointNo) && validSampleNo(sampleNo)),
140 "Invalid index, sampleNo: " << sampleNo << " dataPointNo: " << dataPointNo);
141 //
142 // Whatever the coord's always return the same value as this is constant data.
143 return 0;
144 }
145
146 DataTypes::ValueType::size_type
147 DataConstant::getLength() const
148 {
149 return m_data.size();
150 }
151
152 // DataArrayView
153 // DataConstant::getDataPoint(int sampleNo,
154 // int dataPointNo)
155 // {
156 // EsysAssert((validSamplePointNo(dataPointNo) && validSampleNo(sampleNo)),
157 // "Invalid index, sampleNo: " << sampleNo << " dataPointNo: " << dataPointNo);
158 // //
159 // // Whatever the coord's always return the same value as this is constant data.
160 // return getPointDataView();
161 // }
162
163 DataAbstract*
164 DataConstant::getSlice(const DataTypes::RegionType& region) const
165 {
166 return new DataConstant(*this,region);
167 }
168
169 void
170 DataConstant::setSlice(const DataAbstract* value,
171 const DataTypes::RegionType& region)
172 {
173 const DataConstant* tempDataConst=dynamic_cast<const DataConstant*>(value);
174 if (tempDataConst==0) {
175 throw DataException("Programming error - casting to DataConstant.");
176 }
177 //
178 DataTypes::ShapeType shape(DataTypes::getResultSliceShape(region));
179 DataTypes::RegionLoopRangeType region_loop_range=DataTypes::getSliceRegionLoopRange(region);
180 //
181 // check shape:
182 if (getRank()!=region.size()) {
183 throw DataException("Error - Invalid slice region.");
184 }
185 if (getRank()>0 && !DataTypes::checkShape(value->getShape(),shape)) {
186 throw DataException (DataTypes::createShapeErrorMessage(
187 "Error - Couldn't copy slice due to shape mismatch.",shape,value->getShape()));
188 }
189 // getPointDataView().copySliceFrom(tempDataConst->getPointDataView(),region_loop_range);
190 DataTypes::copySliceFrom(m_data,getShape(),0,tempDataConst->getVector(), tempDataConst->getShape(),0,region_loop_range);
191 }
192
193
194
195 void
196 DataConstant::symmetric(DataAbstract* ev)
197 {
198 DataConstant* temp_ev=dynamic_cast<DataConstant*>(ev);
199 if (temp_ev==0) {
200 throw DataException("Error - DataConstant::symmetric: casting to DataConstant failed (propably a programming error).");
201 }
202 /* DataArrayView& thisView=getPointDataView();
203 DataArrayView& evView=ev->getPointDataView();*/
204 DataMaths::symmetric(m_data,getShape(),0,temp_ev->getVector(), temp_ev->getShape(),0);
205 }
206
207 void
208 DataConstant::nonsymmetric(DataAbstract* ev)
209 {
210 DataConstant* temp_ev=dynamic_cast<DataConstant*>(ev);
211 if (temp_ev==0) {
212 throw DataException("Error - DataConstant::nonsymmetric: casting to DataConstant failed (propably a programming error).");
213 }
214 /* DataArrayView& thisView=getPointDataView();
215 DataArrayView& evView=ev->getPointDataView();*/
216 DataMaths::nonsymmetric(m_data,getShape(),0,temp_ev->getVector(), temp_ev->getShape(),0);
217 }
218
219 void
220 DataConstant::trace(DataAbstract* ev, int axis_offset)
221 {
222 DataConstant* temp_ev=dynamic_cast<DataConstant*>(ev);
223 if (temp_ev==0) {
224 throw DataException("Error - DataConstant::trace: casting to DataConstant failed (propably a programming error).");
225 }
226 /* DataArrayView& thisView=getPointDataView();
227 DataArrayView& evView=ev->getPointDataView();*/
228 ValueType& evVec=temp_ev->getVector();
229 const ShapeType& evShape=temp_ev->getShape();
230 DataMaths::trace(m_data,getShape(),0,evVec,evShape,0,axis_offset);
231 }
232
233 void
234 DataConstant::swapaxes(DataAbstract* ev, int axis0, int axis1)
235 {
236 DataConstant* temp_ev=dynamic_cast<DataConstant*>(ev);
237 if (temp_ev==0) {
238 throw DataException("Error - DataConstant::swapaxes: casting to DataConstant failed (propably a programming error).");
239 }
240 // DataArrayView& thisView=getPointDataView();
241 // DataArrayView& evView=ev->getPointDataView();
242 DataMaths::swapaxes(m_data,getShape(),0,temp_ev->getVector(), temp_ev->getShape(),0,axis0,axis1);
243 }
244
245 void
246 DataConstant::transpose(DataAbstract* ev, int axis_offset)
247 {
248 DataConstant* temp_ev=dynamic_cast<DataConstant*>(ev);
249 if (temp_ev==0) {
250 throw DataException("Error - DataConstant::transpose: casting to DataConstant failed (propably a programming error).");
251 }
252 /* DataArrayView& thisView=getPointDataView();
253 DataArrayView& evView=ev->getPointDataView();*/
254 DataMaths::transpose(m_data, getShape(),0, temp_ev->getVector(),temp_ev->getShape(),0,axis_offset);
255 }
256
257 void
258 DataConstant::eigenvalues(DataAbstract* ev)
259 {
260 DataConstant* temp_ev=dynamic_cast<DataConstant*>(ev);
261 if (temp_ev==0) {
262 throw DataException("Error - DataConstant::eigenvalues: casting to DataConstant failed (propably a programming error).");
263 }
264 /* DataArrayView& thisView=getPointDataView();
265 DataArrayView& evView=ev->getPointDataView();*/
266 DataMaths::eigenvalues(m_data,getShape(),0,temp_ev->getVector(), temp_ev->getShape(),0);
267 }
268 void
269 DataConstant::eigenvalues_and_eigenvectors(DataAbstract* ev,DataAbstract* V,const double tol)
270 {
271 DataConstant* temp_ev=dynamic_cast<DataConstant*>(ev);
272 if (temp_ev==0) {
273 throw DataException("Error - DataConstant::eigenvalues_and_eigenvectors: casting to DataConstant failed (propably a programming error).");
274 }
275 DataConstant* temp_V=dynamic_cast<DataConstant*>(V);
276 if (temp_V==0) {
277 throw DataException("Error - DataConstant::eigenvalues_and_eigenvectors: casting to DataConstant failed (propably a programming error).");
278 }
279 // DataArrayView thisView=getPointDataView();
280 // DataArrayView evView=ev->getPointDataView();
281 // DataArrayView VView=V->getPointDataView();
282
283 DataMaths::eigenvalues_and_eigenvectors(m_data, getShape(),0,temp_ev->getVector(), temp_ev->getShape(),0,temp_V->getVector(), temp_V->getShape(),0,tol);
284 }
285
286 void
287 DataConstant::setToZero()
288 {
289 DataTypes::ValueType::size_type n=m_data.size();
290 for (int i=0; i<n ;++i) m_data[i]=0.;
291 }
292
293 void
294 DataConstant::dump(const std::string fileName) const
295 {
296 #ifdef PASO_MPI
297 throw DataException("Error - DataConstant:: dump is not implemented for MPI yet.");
298 #endif
299 #ifdef USE_NETCDF
300 const NcDim* ncdims[DataTypes::maxRank];
301 NcVar* var;
302 int rank = getRank();
303 int type= getFunctionSpace().getTypeCode();
304 int ndims =0;
305 long dims[DataTypes::maxRank];
306 const double* d_ptr=&(m_data[0]);
307 DataTypes::ShapeType shape = getShape();
308
309 // netCDF error handler
310 NcError err(NcError::verbose_nonfatal);
311 // Create the file.
312 NcFile dataFile(fileName.c_str(), NcFile::Replace);
313 // check if writing was successful
314 if (!dataFile.is_valid())
315 throw DataException("Error - DataConstant:: opening of netCDF file for output failed.");
316 if (!dataFile.add_att("type_id",0) )
317 throw DataException("Error - DataConstant:: appending data type to netCDF file failed.");
318 if (!dataFile.add_att("rank",rank) )
319 throw DataException("Error - DataConstant:: appending rank attribute to netCDF file failed.");
320 if (!dataFile.add_att("function_space_type",type))
321 throw DataException("Error - DataConstant:: appending function space attribute to netCDF file failed.");
322
323 if (rank == 0) {
324 if( ! (ncdims[0] = dataFile.add_dim("l", 1)) )
325 throw DataException("Error - DataConstant:: appending ncdimension 0 to netCDF file failed.");
326 dims[0]=1,
327 ndims=1;
328 } else {
329 ndims=rank;
330 dims[0]=shape[0];
331 if (! (ncdims[0] = dataFile.add_dim("d0",shape[0])) )
332 throw DataException("Error - DataConstant:: appending ncdimension 0 to netCDF file failed.");
333 if ( rank >1 ) {
334 dims[1]=shape[1];
335 if (! (ncdims[1] = dataFile.add_dim("d1",shape[1])) )
336 throw DataException("Error - DataConstant:: appending ncdimension 1 to netCDF file failed.");
337 }
338 if ( rank >2 ) {
339 dims[2]=shape[2];
340 if (! (ncdims[2] = dataFile.add_dim("d2", shape[2])) )
341 throw DataException("Error - DataConstant:: appending ncdimension 2 to netCDF file failed.");
342 }
343 if ( rank >3 ) {
344 dims[3]=shape[3];
345 if (! (ncdims[3] = dataFile.add_dim("d3", shape[3])) )
346 throw DataException("Error - DataConstant:: appending ncdimension 3 to netCDF file failed.");
347 }
348 }
349
350 if (! ( var = dataFile.add_var("data", ncDouble, ndims, ncdims)) )
351 throw DataException("Error - DataConstant:: appending variable to netCDF file failed.");
352 if (! (var->put(d_ptr,dims)) )
353 throw DataException("Error - DataConstant:: copy data to netCDF buffer failed.");
354 #else
355 throw DataException("Error - DataConstant:: dump is not configured with netCDF. Please contact your installation manager.");
356 #endif
357 }
358
359 } // end of namespace

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