Actual source code: ex10.c

  2: static char help[] = "Reads a PETSc matrix and vector from a file and solves a linear system.\n\
  3: This version first preloads and solves a small system, then loads \n\
  4: another (larger) system and solves it as well.  This example illustrates\n\
  5: preloading of instructions with the smaller system so that more accurate\n\
  6: performance monitoring can be done with the larger one (that actually\n\
  7: is the system of interest).  See the 'Performance Hints' chapter of the\n\
  8: users manual for a discussion of preloading.  Input parameters include\n\
  9:   -f0 <input_file> : first file to load (small system)\n\
 10:   -f1 <input_file> : second file to load (larger system)\n\n\
 11:   -trans  : solve transpose system instead\n\n";
 12: /*
 13:   This code can be used to test PETSc interface to other packages.\n\
 14:   Examples of command line options:       \n\
 15:    ex10 -f0 <datafile> -ksp_type preonly  \n\
 16:         -help -ksp_view                  \n\
 17:         -num_numfac <num_numfac> -num_rhs <num_rhs> \n\
 18:         -ksp_type preonly -pc_type lu -mat_type aijspooles/superlu/superlu_dist/aijmumps \n\
 19:         -ksp_type preonly -pc_type cholesky -mat_type sbaijspooles/dscpack/sbaijmumps \n\
 20:         -f0 <A> -fB <B> -mat_type sbaijmumps -ksp_type preonly -pc_type cholesky -test_inertia -mat_sigma <sigma> \n\
 21:    mpirun -np <np> ex10 -f0 <datafile> -ksp_type cg -pc_type asm -pc_asm_type basic -sub_pc_type icc -mat_type sbaij
 22:  \n\n";
 23: */
 24: /*T
 25:    Concepts: KSP^solving a linear system
 26:    Processors: n
 27: T*/

 29: /* 
 30:   Include "petscksp.h" so that we can use KSP solvers.  Note that this file
 31:   automatically includes:
 32:      petsc.h       - base PETSc routines   petscvec.h - vectors
 33:      petscsys.h    - system routines       petscmat.h - matrices
 34:      petscis.h     - index sets            petscksp.h - Krylov subspace methods
 35:      petscviewer.h - viewers               petscpc.h  - preconditioners
 36: */
 37:  #include petscksp.h

 41: int main(int argc,char **args)
 42: {
 43:   KSP            ksp;             /* linear solver context */
 44:   Mat            A,B;            /* matrix */
 45:   Vec            x,b,u;          /* approx solution, RHS, exact solution */
 46:   PetscViewer    fd;               /* viewer */
 47:   char           file[3][PETSC_MAX_PATH_LEN];     /* input file name */
 48:   PetscTruth     table,flg,flgB=PETSC_FALSE,trans=PETSC_FALSE,partition=PETSC_FALSE;
 50:   PetscInt       its,num_numfac;
 51:   PetscReal      norm;
 52:   PetscLogDouble tsetup,tsetup1,tsetup2,tsolve,tsolve1,tsolve2;
 53:   PetscTruth     preload=PETSC_TRUE,diagonalscale,isSymmetric,cknorm=PETSC_FALSE,Test_MatDuplicate=PETSC_FALSE;
 54:   PetscMPIInt    rank;
 55:   PetscScalar    sigma;

 57:   PetscInitialize(&argc,&args,(char *)0,help);
 58:   MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
 59:   PetscOptionsHasName(PETSC_NULL,"-table",&table);
 60:   PetscOptionsHasName(PETSC_NULL,"-trans",&trans);
 61:   PetscOptionsHasName(PETSC_NULL,"-partition",&partition);

 63:   /* 
 64:      Determine files from which we read the two linear systems
 65:      (matrix and right-hand-side vector).
 66:   */
 67:   PetscOptionsGetString(PETSC_NULL,"-f",file[0],PETSC_MAX_PATH_LEN-1,&flg);
 68:   if (flg) {
 69:     PetscStrcpy(file[1],file[0]);
 70:     preload = PETSC_FALSE;
 71:   } else {
 72:     PetscOptionsGetString(PETSC_NULL,"-f0",file[0],PETSC_MAX_PATH_LEN-1,&flg);
 73:     if (!flg) SETERRQ(1,"Must indicate binary file with the -f0 or -f option");
 74:     PetscOptionsGetString(PETSC_NULL,"-f1",file[1],PETSC_MAX_PATH_LEN-1,&flg);
 75:     if (!flg) {preload = PETSC_FALSE;} /* don't bother with second system */
 76:   }

 78:   /* -----------------------------------------------------------
 79:                   Beginning of linear solver loop
 80:      ----------------------------------------------------------- */
 81:   /* 
 82:      Loop through the linear solve 2 times.  
 83:       - The intention here is to preload and solve a small system;
 84:         then load another (larger) system and solve it as well.
 85:         This process preloads the instructions with the smaller
 86:         system so that more accurate performance monitoring (via
 87:         -log_summary) can be done with the larger one (that actually
 88:         is the system of interest). 
 89:   */
 90:   PreLoadBegin(preload,"Load system");

 92:     /* - - - - - - - - - - - New Stage - - - - - - - - - - - - -
 93:                            Load system
 94:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

 96:     /* 
 97:        Open binary file.  Note that we use FILE_MODE_READ to indicate
 98:        reading from this file.
 99:     */
100:     PetscViewerBinaryOpen(PETSC_COMM_WORLD,file[PreLoadIt],FILE_MODE_READ,&fd);
101: 
102:     /*
103:        Load the matrix and vector; then destroy the viewer.
104:     */
105:     MatLoad(fd,MATAIJ,&A);
106: 
107:     if (!preload){
108:       flg = PETSC_FALSE;
109:       PetscOptionsGetString(PETSC_NULL,"-rhs",file[2],PETSC_MAX_PATH_LEN-1,&flg);
110:       if (flg){ /* rhs is stored in a separate file */
111:         PetscViewerDestroy(fd);
112:         PetscViewerBinaryOpen(PETSC_COMM_WORLD,file[2],FILE_MODE_READ,&fd);
113:       }
114:     }
115:     if (rank){
116:         PetscExceptionTry1(VecLoad(fd,PETSC_NULL,&b),PETSC_ERR_FILE_UNEXPECTED);
117:     } else {
118:       PetscExceptionTry1(VecLoad(fd,PETSC_NULL,&b),PETSC_ERR_FILE_READ);
119:     }
120:     if (PetscExceptionCaught(ierr,PETSC_ERR_FILE_UNEXPECTED) || PetscExceptionCaught(ierr,PETSC_ERR_FILE_READ)) { /* if file contains no RHS, then use a vector of all ones */
121:       PetscInt    m;
122:       PetscScalar one = 1.0;
123:       PetscInfo(0,"Using vector of ones for RHS\n");
124:       MatGetLocalSize(A,&m,PETSC_NULL);
125:       VecCreate(PETSC_COMM_WORLD,&b);
126:       VecSetSizes(b,m,PETSC_DECIDE);
127:       VecSetFromOptions(b);
128:       VecSet(b,one);
129:     } else
130:     PetscViewerDestroy(fd);

132:     /* Test MatDuplicate() */
133:     if (Test_MatDuplicate){
134:       MatDuplicate(A,MAT_COPY_VALUES,&B);
135:       MatEqual(A,B,&flg);
136:       if (!flg){
137:         PetscPrintf(PETSC_COMM_WORLD,"  A != B \n");
138:       }
139:       MatDestroy(B);
140:     }

142:     /* Add a shift to A */
143:     PetscOptionsGetScalar(PETSC_NULL,"-mat_sigma",&sigma,&flg);
144:     if(flg) {
145:       PetscOptionsGetString(PETSC_NULL,"-fB",file[2],PETSC_MAX_PATH_LEN-1,&flgB);
146:       if (flgB){
147:         /* load B to get A = A + sigma*B */
148:         PetscViewerBinaryOpen(PETSC_COMM_WORLD,file[2],FILE_MODE_READ,&fd);
149:         MatLoad(fd,MATAIJ,&B);
150:         PetscViewerDestroy(fd);
151:         MatAXPY(A,sigma,B,DIFFERENT_NONZERO_PATTERN); /* A <- sigma*B + A */
152:       } else {
153:         MatShift(A,sigma);
154:       }
155:     }

157:     /* Make A singular for testing zero-pivot of ilu factorization        */
158:     /* Example: ./ex10 -f0 <datafile> -test_zeropivot -set_row_zero -pc_factor_shift_nonzero */
159:     PetscOptionsHasName(PETSC_NULL, "-test_zeropivot", &flg);
160:     if (flg) {
161:       PetscInt          row,ncols;
162:       const PetscInt    *cols;
163:       const PetscScalar *vals;
164:       PetscTruth        flg1=PETSC_FALSE;
165:       PetscScalar       *zeros;
166:       row = 0;
167:       MatGetRow(A,row,&ncols,&cols,&vals);
168:       PetscMalloc(sizeof(PetscScalar)*(ncols+1),&zeros);
169:       PetscMemzero(zeros,(ncols+1)*sizeof(PetscScalar));
170:       PetscOptionsHasName(PETSC_NULL, "-set_row_zero", &flg1);
171:       if (flg1){ /* set entire row as zero */
172:         MatSetValues(A,1,&row,ncols,cols,zeros,INSERT_VALUES);
173:       } else { /* only set (row,row) entry as zero */
174:         MatSetValues(A,1,&row,1,&row,zeros,INSERT_VALUES);
175:       }
176:       MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
177:       MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
178:     }

180:     /* Check whether A is symmetric */
181:     PetscOptionsHasName(PETSC_NULL, "-check_symmetry", &flg);
182:     if (flg) {
183:       Mat Atrans;
184:       MatTranspose(A, &Atrans);
185:       MatEqual(A, Atrans, &isSymmetric);
186:       if (isSymmetric) {
187:         PetscPrintf(PETSC_COMM_WORLD,"A is symmetric \n");
188:       } else {
189:         PetscPrintf(PETSC_COMM_WORLD,"A is non-symmetric \n");
190:       }
191:       MatDestroy(Atrans);
192:     }

194:     /* 
195:        If the loaded matrix is larger than the vector (due to being padded 
196:        to match the block size of the system), then create a new padded vector.
197:     */
198:     {
199:       PetscInt    m,n,j,mvec,start,end,indx;
200:       Vec         tmp;
201:       PetscScalar *bold;

203:       /* Create a new vector b by padding the old one */
204:       MatGetLocalSize(A,&m,&n);
205:       if (m != n) {
206:         SETERRQ2(PETSC_ERR_ARG_SIZ, "This example is not intended for rectangular matrices (%d, %d)", m, n);
207:       }
208:       VecCreate(PETSC_COMM_WORLD,&tmp);
209:       VecSetSizes(tmp,m,PETSC_DECIDE);
210:       VecSetFromOptions(tmp);
211:       VecGetOwnershipRange(b,&start,&end);
212:       VecGetLocalSize(b,&mvec);
213:       VecGetArray(b,&bold);
214:       for (j=0; j<mvec; j++) {
215:         indx = start+j;
216:         VecSetValues(tmp,1,&indx,bold+j,INSERT_VALUES);
217:       }
218:       VecRestoreArray(b,&bold);
219:       VecDestroy(b);
220:       VecAssemblyBegin(tmp);
221:       VecAssemblyEnd(tmp);
222:       b = tmp;
223:     }
224:     VecDuplicate(b,&x);
225:     VecDuplicate(b,&u);
226:     VecSet(x,0.0);

228:     /* - - - - - - - - - - - New Stage - - - - - - - - - - - - -
229:                       Setup solve for system
230:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */


233:     if (partition) {
234:       MatPartitioning mpart;
235:       IS              mis,nis,isn,is;
236:       PetscInt        *count;
237:       PetscMPIInt     size;
238:       Mat             BB;
239:       MPI_Comm_size(PETSC_COMM_WORLD,&size);
240:       MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
241:       PetscMalloc(size*sizeof(PetscInt),&count);
242:       MatPartitioningCreate(PETSC_COMM_WORLD, &mpart);
243:       MatPartitioningSetAdjacency(mpart, A);
244:       /* MatPartitioningSetVertexWeights(mpart, weight); */
245:       MatPartitioningSetFromOptions(mpart);
246:       MatPartitioningApply(mpart, &mis);
247:       MatPartitioningDestroy(mpart);
248:       ISPartitioningToNumbering(mis,&nis);
249:       ISPartitioningCount(mis,count);
250:       ISDestroy(mis);
251:       ISInvertPermutation(nis, count[rank], &is);
252:       PetscFree(count);
253:       ISDestroy(nis);
254:       ISSort(is);
255:       ISAllGather(is,&isn);
256:       MatGetSubMatrix(A,is,isn,PETSC_DECIDE,MAT_INITIAL_MATRIX,&BB);

258:       /* need to move the vector also */
259:       ISDestroy(is);
260:       ISDestroy(isn);
261:       MatDestroy(A);
262:       A    = BB;
263:     }
264: 
265:     /*
266:        Conclude profiling last stage; begin profiling next stage.
267:     */
268:     PreLoadStage("KSPSetUp");

270:     /*
271:        We also explicitly time this stage via PetscGetTime()
272:     */
273:     PetscGetTime(&tsetup1);

275:     /*
276:        Create linear solver; set operators; set runtime options.
277:     */
278:     KSPCreate(PETSC_COMM_WORLD,&ksp);

280:     num_numfac = 1;
281:     PetscOptionsGetInt(PETSC_NULL,"-num_numfac",&num_numfac,PETSC_NULL);
282:     while ( num_numfac-- ){
283:       /* KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN); */
284:     KSPSetOperators(ksp,A,A,SAME_NONZERO_PATTERN);
285:     KSPSetFromOptions(ksp);

287:     /* 
288:        Here we explicitly call KSPSetUp() and KSPSetUpOnBlocks() to
289:        enable more precise profiling of setting up the preconditioner.
290:        These calls are optional, since both will be called within
291:        KSPSolve() if they haven't been called already.
292:     */
293:     KSPSetUp(ksp);
294:     KSPSetUpOnBlocks(ksp);
295:     PetscGetTime(&tsetup2);
296:     tsetup = tsetup2 - tsetup1;

298:     /*
299:       Test MatGetInertia()
300:       Usage:
301:       ex10 -f0 <mat_binaryfile> -ksp_type preonly -pc_type cholesky -mat_type seqsbaij -test_inertia -mat_sigma <sigma>
302:      */
303:     PetscOptionsHasName(PETSC_NULL,"-test_inertia",&flg);
304:     if (flg){
305:       PC        pc;
306:       PetscInt  nneg, nzero, npos;
307:       Mat       F;
308: 
309:       KSPGetPC(ksp,&pc);
310:       PCGetFactoredMatrix(pc,&F);
311:       MatGetInertia(F,&nneg,&nzero,&npos);
312:       PetscPrintf(PETSC_COMM_SELF," MatInertia: nneg: %D, nzero: %D, npos: %D\n",nneg,nzero,npos);
313:     }

315:     /*
316:        Tests "diagonal-scaling of preconditioned residual norm" as used 
317:        by many ODE integrator codes including SUNDIALS. Note this is different
318:        than diagonally scaling the matrix before computing the preconditioner
319:     */
320:     PetscOptionsHasName(PETSC_NULL,"-diagonal_scale",&diagonalscale);
321:     if (diagonalscale) {
322:       PC       pc;
323:       PetscInt j,start,end,n;
324:       Vec      scale;
325: 
326:       KSPGetPC(ksp,&pc);
327:       VecGetSize(x,&n);
328:       VecDuplicate(x,&scale);
329:       VecGetOwnershipRange(scale,&start,&end);
330:       for (j=start; j<end; j++) {
331:         VecSetValue(scale,j,((PetscReal)(j+1))/((PetscReal)n),INSERT_VALUES);
332:       }
333:       VecAssemblyBegin(scale);
334:       VecAssemblyEnd(scale);
335:       PCDiagonalScaleSet(pc,scale);
336:       VecDestroy(scale);

338:     }

340:     /* - - - - - - - - - - - New Stage - - - - - - - - - - - - -
341:                            Solve system
342:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

344:     /*
345:        Begin profiling next stage
346:     */
347:     PreLoadStage("KSPSolve");

349:     /*
350:        Solve linear system; we also explicitly time this stage.
351:     */
352:     PetscGetTime(&tsolve1);
353:     if (trans) {
354:       KSPSolveTranspose(ksp,b,x);
355:       KSPGetIterationNumber(ksp,&its);
356:     } else {
357:       PetscInt  num_rhs=1;
358:       PetscOptionsGetInt(PETSC_NULL,"-num_rhs",&num_rhs,PETSC_NULL);
359:       PetscOptionsHasName(PETSC_NULL,"-cknorm",&cknorm);
360:       while ( num_rhs-- ) {
361:         KSPSolve(ksp,b,x);
362:       }
363:       KSPGetIterationNumber(ksp,&its);
364:       if (cknorm){   /* Check error for each rhs */
365:         if (trans) {
366:           MatMultTranspose(A,x,u);
367:         } else {
368:           MatMult(A,x,u);
369:         }
370:         VecAXPY(u,-1.0,b);
371:         VecNorm(u,NORM_2,&norm);
372:         PetscPrintf(PETSC_COMM_WORLD,"  Number of iterations = %3D\n",its);
373:         PetscPrintf(PETSC_COMM_WORLD,"  Residual norm %A\n",norm);
374:       }
375:     } /* while ( num_rhs-- ) */
376:     PetscGetTime(&tsolve2);
377:     tsolve = tsolve2 - tsolve1;

379:    /* 
380:        Conclude profiling this stage
381:     */
382:     PreLoadStage("Cleanup");

384:     /* - - - - - - - - - - - New Stage - - - - - - - - - - - - -
385:             Check error, print output, free data structures.
386:      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

388:     /* 
389:        Check error
390:     */
391:     if (trans) {
392:       MatMultTranspose(A,x,u);
393:     } else {
394:       MatMult(A,x,u);
395:     }
396:     VecAXPY(u,-1.0,b);
397:     VecNorm(u,NORM_2,&norm);

399:     /*
400:        Write output (optinally using table for solver details).
401:         - PetscPrintf() handles output for multiprocessor jobs 
402:           by printing from only one processor in the communicator.
403:         - KSPView() prints information about the linear solver.
404:     */
405:     if (table) {
406:       char        *matrixname,kspinfo[120];
407:       PetscViewer viewer;

409:       /*
410:          Open a string viewer; then write info to it.
411:       */
412:       PetscViewerStringOpen(PETSC_COMM_WORLD,kspinfo,120,&viewer);
413:       KSPView(ksp,viewer);
414:       PetscStrrchr(file[PreLoadIt],'/',&matrixname);
415:       PetscPrintf(PETSC_COMM_WORLD,"%-8.8s %3D %2.0e %2.1e %2.1e %2.1e %s \n",
416:                 matrixname,its,norm,tsetup+tsolve,tsetup,tsolve,kspinfo);

418:       /*
419:          Destroy the viewer
420:       */
421:       PetscViewerDestroy(viewer);
422:     } else {
423:       PetscPrintf(PETSC_COMM_WORLD,"Number of iterations = %3D\n",its);
424:       PetscPrintf(PETSC_COMM_WORLD,"Residual norm %A\n",norm);
425:     }

427:     PetscOptionsHasName(PETSC_NULL, "-ksp_reason", &flg);
428:     if (flg){
429:       KSPConvergedReason reason;
430:       KSPGetConvergedReason(ksp,&reason);
431:       PetscPrintf(PETSC_COMM_WORLD,"KSPConvergedReason: %D\n", reason);
432:     }
433: 
434:     } /* while ( num_numfac-- ) */

436:     /* 
437:        Free work space.  All PETSc objects should be destroyed when they
438:        are no longer needed.
439:     */
440:     MatDestroy(A); VecDestroy(b);
441:     VecDestroy(u); VecDestroy(x);
442:     KSPDestroy(ksp);
443:     if (flgB) { MatDestroy(B); }
444:   PreLoadEnd();
445:   /* -----------------------------------------------------------
446:                       End of linear solver loop
447:      ----------------------------------------------------------- */

449:   PetscFinalize();
450:   return 0;
451: }