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Revision 751 - (show annotations)
Mon Jun 26 01:46:34 2006 UTC (12 years, 11 months ago) by bcumming
Original Path: trunk/finley/src/Assemble_PDE.c
File MIME type: text/plain
File size: 17136 byte(s)
Changes relating to the MPI version of escript
The standard OpenMP version of escript is unchanged

- updated data types (Finley_Mesh, Finley_NodeFile, etc) to store meshes
  over multiple MPI processes.
- added CommBuffer code in Paso for communication of Data associated
  with distributed meshes
- updates in Finley and Escript to support distributed data and operations
  on distributed data (such as interpolation).
- construction of RHS in MPI, so that simple explicit schemes (such as
  /docs/examples/wave.py without IO and the Locator) can run in MPI.
- updated mesh generation for first order line, rectangle and brick
  meshes and second order line meshes in MPI.        
- small changes to trunk/SConstruct and trunk/scons/ess_options.py to
  build the MPI version, these changes are turned off by default.

1 /*
2 ************************************************************
3 * Copyright 2006 by ACcESS MNRF *
4 * *
5 * http://www.access.edu.au *
6 * Primary Business: Queensland, Australia *
7 * Licensed under the Open Software License version 3.0 *
8 * http://www.opensource.org/licenses/osl-3.0.php *
9 * *
10 ************************************************************
11 */
12
13
14 /**************************************************************/
15
16 /* assembles the system of numEq PDEs into the stiffness matrix S and right hand side F */
17
18 /* -div(A*grad u)-div(B*u)+C*grad u + D*u= -div X + Y */
19
20 /* -(A_{k,i,m,j} u_m,j)_i-(B_{k,i,m} u_m)_i+C_{k,m,j} u_m,j-D_{k,m} u_m = -(X_{k,i})_i + Y_k */
21
22 /* u has numComp components. */
23
24 /* Shape of the coefficients: */
25
26 /* A = numEqu x numDim x numComp x numDim */
27 /* B = numDim x numEqu x numComp */
28 /* C = numEqu x numDim x numComp */
29 /* D = numEqu x numComp */
30 /* X = numEqu x numDim */
31 /* Y = numEqu */
32
33 /* The coefficients A,B,C,D,X and Y have to be defined on the integartion points or not present (=NULL). */
34
35 /* S and F have to be initialized before the routine is called. S or F can be NULL. In this case the left or */
36 /* the right hand side of the PDE is not processed. */
37
38 /* The routine does not consider any boundary conditions. */
39
40 /**************************************************************/
41
42 /* Author: gross@access.edu.au */
43 /* Version: $Id$ */
44
45 /**************************************************************/
46
47 #include "Assemble.h"
48 #include "Util.h"
49 #ifdef _OPENMP
50 #include <omp.h>
51 #endif
52
53
54 /**************************************************************/
55
56 void Finley_Assemble_PDE(Finley_NodeFile* nodes,Finley_ElementFile* elements,Paso_SystemMatrix* S, escriptDataC* F,
57 escriptDataC* A, escriptDataC* B, escriptDataC* C, escriptDataC* D, escriptDataC* X, escriptDataC* Y ) {
58
59 char error_msg[LenErrorMsg_MAX];
60 double *EM_S=NULL,*EM_F=NULL,*V=NULL,*dVdv=NULL,*dSdV=NULL,*Vol=NULL,*dvdV=NULL;
61 double time0;
62 dim_t dimensions[ESCRIPT_MAX_DATA_RANK],e,q;
63 Assemble_Parameters p;
64 index_t *index_row=NULL,*index_col=NULL,color;
65 Finley_resetError();
66
67 if (nodes==NULL || elements==NULL) return;
68 if (S==NULL && isEmpty(F)) return;
69
70 /* set all parameters in p*/
71 Assemble_getAssembleParameters(nodes,elements,S,F,&p);
72 if (! Finley_noError()) return;
73
74 /* this function assumes NS=NN */
75 if (p.NN!=p.NS) {
76 Finley_setError(SYSTEM_ERROR,"Finley_Assemble_PDE: for Finley_Assemble_PDE numNodes and numShapes have to be identical.");
77 return;
78 }
79 if (p.numDim!=p.numElementDim) {
80 Finley_setError(SYSTEM_ERROR,"Finley_Assemble_PDE: Finley_Assemble_PDE accepts volume elements only.");
81 return;
82 }
83 /* get a functionspace */
84 type_t funcspace=UNKNOWN;
85 updateFunctionSpaceType(funcspace,A);
86 updateFunctionSpaceType(funcspace,B);
87 updateFunctionSpaceType(funcspace,C);
88 updateFunctionSpaceType(funcspace,D);
89 updateFunctionSpaceType(funcspace,X);
90 updateFunctionSpaceType(funcspace,Y);
91 if (funcspace==UNKNOWN) return; /* all data are empty */
92
93 /* check if all function spaces are the same */
94
95 if (! functionSpaceTypeEqual(funcspace,A) ) {
96 Finley_setError(TYPE_ERROR,"Finley_Assemble_PDE: unexpected function space type for coefficient A");
97 }
98 if (! functionSpaceTypeEqual(funcspace,B) ) {
99 Finley_setError(TYPE_ERROR,"Finley_Assemble_PDE: unexpected function space type for coefficient B");
100 }
101 if (! functionSpaceTypeEqual(funcspace,C) ) {
102 Finley_setError(TYPE_ERROR,"Finley_Assemble_PDE: unexpected function space type for coefficient C");
103 }
104 if (! functionSpaceTypeEqual(funcspace,D) ) {
105 Finley_setError(TYPE_ERROR,"Finley_Assemble_PDE: unexpected function space type for coefficient D");
106 }
107 if (! functionSpaceTypeEqual(funcspace,X) ) {
108 Finley_setError(TYPE_ERROR,"Finley_Assemble_PDE: unexpected function space type for coefficient X");
109 }
110 if (! functionSpaceTypeEqual(funcspace,Y) ) {
111 Finley_setError(TYPE_ERROR,"Finley_Assemble_PDE: unexpected function space type for coefficient Y");
112 }
113
114 /* check if all function spaces are the same */
115
116 if (! numSamplesEqual(A,p.numQuad,elements->numElements) ) {
117 sprintf(error_msg,"Finley_Assemble_PDE: sample points of coefficient A don't match (%d,%d)",p.numQuad,elements->numElements);
118 Finley_setError(TYPE_ERROR,error_msg);
119 }
120
121 if (! numSamplesEqual(B,p.numQuad,elements->numElements) ) {
122 sprintf(error_msg,"Finley_Assemble_PDE: sample points of coefficient B don't match (%d,%d)",p.numQuad,elements->numElements);
123 Finley_setError(TYPE_ERROR,error_msg);
124 }
125
126 if (! numSamplesEqual(C,p.numQuad,elements->numElements) ) {
127 sprintf(error_msg,"Finley_Assemble_PDE: sample points of coefficient C don't match (%d,%d)",p.numQuad,elements->numElements);
128 Finley_setError(TYPE_ERROR,error_msg);
129 }
130
131 if (! numSamplesEqual(D,p.numQuad,elements->numElements) ) {
132 sprintf(error_msg,"Finley_Assemble_PDE: sample points of coefficient D don't match (%d,%d)",p.numQuad,elements->numElements);
133 Finley_setError(TYPE_ERROR,error_msg);
134 }
135
136 if (! numSamplesEqual(X,p.numQuad,elements->numElements) ) {
137 sprintf(error_msg,"Finley_Assemble_PDE: sample points of coefficient X don't match (%d,%d)",p.numQuad,elements->numElements);
138 Finley_setError(TYPE_ERROR,error_msg);
139 }
140
141 if (! numSamplesEqual(Y,p.numQuad,elements->numElements) ) {
142 sprintf(error_msg,"Finley_Assemble_PDE: sample points of coefficient Y don't match (%d,%d)",p.numQuad,elements->numElements);
143 Finley_setError(TYPE_ERROR,error_msg);
144 }
145
146 /* check the dimensions: */
147
148 if (p.numEqu==1 && p.numComp==1) {
149 if (!isEmpty(A)) {
150 dimensions[0]=p.numDim;
151 dimensions[1]=p.numDim;
152 if (!isDataPointShapeEqual(A,2,dimensions)) {
153 sprintf(error_msg,"Finley_Assemble_PDE: coefficient A: illegal shape, expected shape (%d,%d)",dimensions[0],dimensions[1]);
154 Finley_setError(TYPE_ERROR,error_msg);
155 }
156 }
157 if (!isEmpty(B)) {
158 dimensions[0]=p.numDim;
159 if (!isDataPointShapeEqual(B,1,dimensions)) {
160 sprintf(error_msg,"Finley_Assemble_PDE: coefficient B: illegal shape (%d,)",dimensions[0]);
161 Finley_setError(TYPE_ERROR,error_msg);
162 }
163 }
164 if (!isEmpty(C)) {
165 dimensions[0]=p.numDim;
166 if (!isDataPointShapeEqual(C,1,dimensions)) {
167 sprintf(error_msg,"Finley_Assemble_PDE: coefficient C, expected shape (%d,)",dimensions[0]);
168 Finley_setError(TYPE_ERROR,error_msg);
169 }
170 }
171 if (!isEmpty(D)) {
172 if (!isDataPointShapeEqual(D,0,dimensions)) {
173 Finley_setError(TYPE_ERROR,"Finley_Assemble_PDE: coefficient D, rank 0 expected.");
174 }
175 }
176 if (!isEmpty(X)) {
177 dimensions[0]=p.numDim;
178 if (!isDataPointShapeEqual(X,1,dimensions)) {
179 sprintf(error_msg,"Finley_Assemble_PDE: coefficient X, expected shape (%d,",dimensions[0]);
180 Finley_setError(TYPE_ERROR,error_msg);
181 }
182 }
183 if (!isEmpty(Y)) {
184 if (!isDataPointShapeEqual(Y,0,dimensions)) {
185 Finley_setError(TYPE_ERROR,"Finley_Assemble_PDE: coefficient Y, rank 0 expected.");
186 }
187 }
188 } else {
189 if (!isEmpty(A)) {
190 dimensions[0]=p.numEqu;
191 dimensions[1]=p.numDim;
192 dimensions[2]=p.numComp;
193 dimensions[3]=p.numDim;
194 if (!isDataPointShapeEqual(A,4,dimensions)) {
195 sprintf(error_msg,"Finley_Assemble_PDE: coefficient A, expected shape (%d,%d,%d,%d)",dimensions[0],dimensions[1],dimensions[2],dimensions[3]);
196 Finley_setError(TYPE_ERROR,error_msg);
197 }
198 }
199 if (!isEmpty(B)) {
200 dimensions[0]=p.numEqu;
201 dimensions[1]=p.numDim;
202 dimensions[2]=p.numComp;
203 if (!isDataPointShapeEqual(B,3,dimensions)) {
204 sprintf(error_msg,"Finley_Assemble_PDE: coefficient B, expected shape (%d,%d,%d)",dimensions[0],dimensions[1],dimensions[2]);
205 Finley_setError(TYPE_ERROR,error_msg);
206 }
207 }
208 if (!isEmpty(C)) {
209 dimensions[0]=p.numEqu;
210 dimensions[1]=p.numComp;
211 dimensions[2]=p.numDim;
212 if (!isDataPointShapeEqual(C,3,dimensions)) {
213 sprintf(error_msg,"Finley_Assemble_PDE: coefficient C, expected shape (%d,%d,%d)",dimensions[0],dimensions[1],dimensions[2]);
214 Finley_setError(TYPE_ERROR,error_msg);
215 }
216 }
217 if (!isEmpty(D)) {
218 dimensions[0]=p.numEqu;
219 dimensions[1]=p.numComp;
220 if (!isDataPointShapeEqual(D,2,dimensions)) {
221 sprintf(error_msg,"Finley_Assemble_PDE: coefficient D, expected shape (%d,%d)",dimensions[0],dimensions[1]);
222 Finley_setError(TYPE_ERROR,error_msg);
223 }
224 }
225 if (!isEmpty(X)) {
226 dimensions[0]=p.numEqu;
227 dimensions[1]=p.numDim;
228 if (!isDataPointShapeEqual(X,2,dimensions)) {
229 sprintf(error_msg,"Finley_Assemble_PDE: coefficient X, expected shape (%d,%d)",dimensions[0],dimensions[1]);
230 Finley_setError(TYPE_ERROR,error_msg);
231 }
232 }
233 if (!isEmpty(Y)) {
234 dimensions[0]=p.numEqu;
235 if (!isDataPointShapeEqual(Y,1,dimensions)) {
236 sprintf(error_msg,"Finley_Assemble_PDE: coefficient Y, expected shape (%d,)",dimensions[0]);
237 Finley_setError(TYPE_ERROR,error_msg);
238 }
239 }
240 }
241
242 if (Finley_noError()) {
243 time0=Finley_timer();
244 #pragma omp parallel private(index_col,index_row,EM_S,EM_F,V,dVdv,dSdV,Vol,dvdV,color,q) \
245 firstprivate(elements,nodes,S,F,A,B,C,D,X,Y)
246 {
247 EM_S=EM_F=V=dVdv=dSdV=Vol=dvdV=NULL;
248 index_row=index_col=NULL;
249
250 /* allocate work arrays: */
251
252 EM_S=(double*) THREAD_MEMALLOC(p.NN_row*p.NN_col*p.numEqu*p.numComp,double);
253 EM_F=(double*) THREAD_MEMALLOC(p.NN_row*p.numEqu,double);
254 V=(double*) THREAD_MEMALLOC(p.NN*p.numDim,double);
255 dVdv=(double*) THREAD_MEMALLOC(p.numDim*p.numDim*p.numQuad,double);
256 dvdV=(double*) THREAD_MEMALLOC(p.numDim*p.numDim*p.numQuad,double);
257 dSdV=(double*) THREAD_MEMALLOC(p.NS_row*p.numQuad*p.numDim,double);
258 Vol=(double*) THREAD_MEMALLOC(p.numQuad,double);
259 index_col=(index_t*) THREAD_MEMALLOC(p.NN_col,index_t);
260 index_row=(index_t*) THREAD_MEMALLOC(p.NN_row,index_t);
261
262 if (! (Finley_checkPtr(EM_S) || Finley_checkPtr(EM_F) || Finley_checkPtr(V) || Finley_checkPtr(index_col) ||
263 Finley_checkPtr(index_row) || Finley_checkPtr(dVdv) || Finley_checkPtr(dSdV) || Finley_checkPtr(Vol) )) {
264
265 /* open loop over all colors: */
266 #ifndef PASO_MPI
267 for (color=elements->minColor;color<=elements->maxColor;color++) {
268 /* open loop over all elements: */
269 #pragma omp for private(e) schedule(static)
270 for(e=0;e<elements->numElements;e++){
271 if (elements->Color[e]==color) {
272 #else
273 for(e=0;e<elements->numElements;e++){
274 #endif
275 //============================
276 for (q=0;q<p.NN_row;q++) index_row[q]=p.label_row[elements->Nodes[INDEX2(p.row_node[q],e,p.NN)]];
277 /* gather V-coordinates of nodes into V: */
278 Finley_Util_Gather_double(p.NN,&(elements->Nodes[INDEX2(0,e,p.NN)]),p.numDim,nodes->Coordinates,V);
279 /* calculate dVdv(i,j,q)=V(i,k)*DSDv(k,j,q) */
280 Finley_Util_SmallMatMult(p.numDim,p.numDim*p.numQuad,dVdv,p.NS,V,p.referenceElement->dSdv);
281 /* dvdV=invert(dVdv) inplace */
282 Finley_Util_InvertSmallMat(p.numQuad,p.numDim,dVdv,dvdV,Vol);
283 /* calculate dSdV=DSDv*DvDV */
284 Finley_Util_SmallMatSetMult(p.numQuad,p.NS_row,p.numDim,dSdV,p.numDim,p.referenceElement_row->dSdv,dvdV);
285 /* scale volume: */
286 for (q=0;q<p.numQuad;q++) Vol[q]=ABS(Vol[q]*p.referenceElement->QuadWeights[q]);
287 //============================
288
289 /* integration for the stiffness matrix: */
290 /* in order to optimze the number of operations the case of constants coefficience needs a bit more work */
291 /* to make use of some symmetry. */
292
293 if (S!=NULL) {
294 for (q=0;q<p.NN_row*p.NN_col*p.numEqu*p.numComp;q++) EM_S[q]=0;
295 if (p.numEqu==1 && p.numComp==1) {
296 Finley_Assemble_PDEMatrix_Single2(p.NS_row,p.numDim,p.numQuad,
297 p.referenceElement_row->S,dSdV,Vol,p.NN_row,EM_S,
298 getSampleData(A,e),isExpanded(A),
299 getSampleData(B,e),isExpanded(B),
300 getSampleData(C,e),isExpanded(C),
301 getSampleData(D,e),isExpanded(D));
302 } else {
303 Finley_Assemble_PDEMatrix_System2(p.NS_row,p.numDim,p.numQuad,p.numEqu,p.numComp,
304 p.referenceElement_row->S,dSdV,Vol,p.NN_row,EM_S,
305 getSampleData(A,e),isExpanded(A),
306 getSampleData(B,e),isExpanded(B),
307 getSampleData(C,e),isExpanded(C),
308 getSampleData(D,e),isExpanded(D));
309 }
310 for (q=0;q<p.NN_col;q++) index_col[q]=p.label_col[elements->Nodes[INDEX2(p.col_node[q],e,p.NN)]];
311 Finley_Assemble_addToSystemMatrix(S,p.NN_row,index_row,p.numEqu,p.NN_col,index_col,p.numComp,EM_S);
312 }
313 if (!isEmpty(F)) {
314 for (q=0;q<p.NN_row*p.numEqu;q++) EM_F[q]=0;
315 if (p.numEqu==1) {
316 Finley_Assemble_RHSMatrix_Single(p.NS_row,p.numDim,p.numQuad,
317 p.referenceElement_row->S,dSdV,Vol,p.NN_row,EM_F,
318 getSampleData(X,e),isExpanded(X),
319 getSampleData(Y,e),isExpanded(Y));
320 } else {
321 Finley_Assemble_RHSMatrix_System(p.NS_row,p.numDim,p.numQuad,
322 p.numEqu,p.referenceElement_row->S,dSdV,Vol,p.NN_row,EM_F,
323 getSampleData(X,e),isExpanded(X),
324 getSampleData(Y,e),isExpanded(Y));
325 }
326 /* add */
327 #ifndef PASO_MPI
328 Finley_Util_AddScatter(p.NN_row,index_row,p.numEqu,EM_F,getSampleData(F,0));
329 #else
330 Finley_Util_AddScatter_upperBound(p.NN_row,index_row,p.numEqu,EM_F,getSampleData(F,0),p.degreeOfFreedomUpperBound);
331 #endif
332 }
333 }
334 }
335 #ifndef PASO_MPI
336 }
337 }
338 #endif
339 /* clean up */
340 THREAD_MEMFREE(EM_S);
341 THREAD_MEMFREE(EM_F);
342 THREAD_MEMFREE(V);
343 THREAD_MEMFREE(dVdv);
344 THREAD_MEMFREE(dvdV);
345 THREAD_MEMFREE(dSdV);
346 THREAD_MEMFREE(Vol);
347 THREAD_MEMFREE(index_col);
348 THREAD_MEMFREE(index_row);
349 }
350 #ifdef Finley_TRACE
351 printf("timing: assemblage PDE: %.4e sec\n",Finley_timer()-time0);
352 #endif
353 }
354 }
355 /*
356 * $Log$
357 * Revision 1.8 2005/09/15 03:44:21 jgs
358 * Merge of development branch dev-02 back to main trunk on 2005-09-15
359 *
360 * Revision 1.7 2005/09/01 03:31:35 jgs
361 * Merge of development branch dev-02 back to main trunk on 2005-09-01
362 *
363 * Revision 1.6 2005/08/12 01:45:42 jgs
364 * erge of development branch dev-02 back to main trunk on 2005-08-12
365 *
366 * Revision 1.5.2.3 2005/09/07 06:26:17 gross
367 * the solver from finley are put into the standalone package paso now
368 *
369 * Revision 1.5.2.2 2005/08/24 02:02:18 gross
370 * timing output switched off. solver output can be swiched through getSolution(verbose=True) now.
371 *
372 * Revision 1.5.2.1 2005/08/03 08:54:27 gross
373 * contact element assemblage was called with wrong element table pointer
374 *
375 * Revision 1.5 2005/07/08 04:07:46 jgs
376 * Merge of development branch back to main trunk on 2005-07-08
377 *
378 * Revision 1.4 2004/12/15 07:08:32 jgs
379 * *** empty log message ***
380 * Revision 1.1.1.1.2.2 2005/06/29 02:34:47 gross
381 * some changes towards 64 integers in finley
382 *
383 * Revision 1.1.1.1.2.1 2004/11/24 01:37:12 gross
384 * some changes dealing with the integer overflow in memory allocation. Finley solves 4M unknowns now
385 *
386 *
387 *
388 */

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