Actual source code: ex10.c


  2: static char help[] = "Solve a small system and a large system through preloading\n\
  3:   Input arguments are:\n\
  4:   -permute <natural,rcm,nd,...> : solve system in permuted indexing\n\
  5:   -f0 <small_sys_binary> -f1 <large_sys_binary> \n\n";

  7: /*
  8:   Include "petscksp.h" so that we can use KSP solvers.  Note that this file
  9:   automatically includes:
 10:      petscsys.h       - base PETSc routines   petscvec.h - vectors
 11:      petscmat.h - matrices
 12:      petscis.h     - index sets            petscksp.h - Krylov subspace methods
 13:      petscviewer.h - viewers               petscpc.h  - preconditioners
 14: */
 15: #include <petscksp.h>

 17: typedef enum {
 18:   RHS_FILE,
 19:   RHS_ONE,
 20:   RHS_RANDOM
 21: } RHSType;
 22: const char *const RHSTypes[] = {"FILE", "ONE", "RANDOM", "RHSType", "RHS_", NULL};

 24: PetscErrorCode CheckResult(KSP *ksp, Mat *A, Vec *b, Vec *x, IS *rowperm)
 25: {
 26:   PetscReal norm; /* norm of solution error */
 27:   PetscInt  its;
 28:   PetscFunctionBegin;
 29:   PetscCall(KSPGetTotalIterations(*ksp, &its));
 30:   PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Number of iterations = %" PetscInt_FMT "\n", its));

 32:   PetscCall(KSPGetResidualNorm(*ksp, &norm));
 33:   if (norm < 1.e-12) {
 34:     PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Residual norm < 1.e-12\n"));
 35:   } else {
 36:     PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Residual norm %e\n", (double)norm));
 37:   }

 39:   PetscCall(KSPDestroy(ksp));
 40:   PetscCall(MatDestroy(A));
 41:   PetscCall(VecDestroy(x));
 42:   PetscCall(VecDestroy(b));
 43:   PetscCall(ISDestroy(rowperm));
 44:   PetscFunctionReturn(PETSC_SUCCESS);
 45: }

 47: PetscErrorCode CreateSystem(const char filename[PETSC_MAX_PATH_LEN], RHSType rhstype, MatOrderingType ordering, PetscBool permute, IS *colperm_out, Mat *A_out, Vec *b_out, Vec *x_out)
 48: {
 49:   Vec                x, b, b2;
 50:   Mat                A;      /* linear system matrix */
 51:   PetscViewer        viewer; /* viewer */
 52:   PetscBool          same;
 53:   PetscInt           j, len, start, idx, n1, n2;
 54:   const PetscScalar *val;
 55:   IS                 rowperm = NULL, colperm = NULL;

 57:   PetscFunctionBegin;
 58:   /* open binary file. Note that we use FILE_MODE_READ to indicate reading from this file */
 59:   PetscCall(PetscViewerBinaryOpen(PETSC_COMM_WORLD, filename, FILE_MODE_READ, &viewer));

 61:   /* load the matrix and vector; then destroy the viewer */
 62:   PetscCall(MatCreate(PETSC_COMM_WORLD, &A));
 63:   PetscCall(MatSetFromOptions(A));
 64:   PetscCall(MatLoad(A, viewer));
 65:   switch (rhstype) {
 66:   case RHS_FILE:
 67:     /* Vectors in the file might a different size than the matrix so we need a
 68:      * Vec whose size hasn't been set yet.  It'll get fixed below.  Otherwise we
 69:      * can create the correct size Vec. */
 70:     PetscCall(VecCreate(PETSC_COMM_WORLD, &b));
 71:     PetscCall(VecLoad(b, viewer));
 72:     break;
 73:   case RHS_ONE:
 74:     PetscCall(MatCreateVecs(A, &b, NULL));
 75:     PetscCall(VecSet(b, 1.0));
 76:     break;
 77:   case RHS_RANDOM:
 78:     PetscCall(MatCreateVecs(A, &b, NULL));
 79:     PetscCall(VecSetRandom(b, NULL));
 80:     break;
 81:   }
 82:   PetscCall(PetscViewerDestroy(&viewer));

 84:   /* if the loaded matrix is larger than the vector (due to being padded
 85:      to match the block size of the system), then create a new padded vector
 86:    */
 87:   PetscCall(MatGetLocalSize(A, NULL, &n1));
 88:   PetscCall(VecGetLocalSize(b, &n2));
 89:   same = (n1 == n2) ? PETSC_TRUE : PETSC_FALSE;
 90:   PetscCall(MPIU_Allreduce(MPI_IN_PLACE, &same, 1, MPIU_BOOL, MPI_LAND, PETSC_COMM_WORLD));

 92:   if (!same) { /* create a new vector b by padding the old one */
 93:     PetscCall(VecCreate(PETSC_COMM_WORLD, &b2));
 94:     PetscCall(VecSetSizes(b2, n1, PETSC_DECIDE));
 95:     PetscCall(VecSetFromOptions(b2));
 96:     PetscCall(VecGetOwnershipRange(b, &start, NULL));
 97:     PetscCall(VecGetLocalSize(b, &len));
 98:     PetscCall(VecGetArrayRead(b, &val));
 99:     for (j = 0; j < len; j++) {
100:       idx = start + j;
101:       PetscCall(VecSetValues(b2, 1, &idx, val + j, INSERT_VALUES));
102:     }
103:     PetscCall(VecRestoreArrayRead(b, &val));
104:     PetscCall(VecDestroy(&b));
105:     PetscCall(VecAssemblyBegin(b2));
106:     PetscCall(VecAssemblyEnd(b2));
107:     b = b2;
108:   }
109:   PetscCall(VecDuplicate(b, &x));

111:   if (permute) {
112:     Mat Aperm;
113:     PetscCall(MatGetOrdering(A, ordering, &rowperm, &colperm));
114:     PetscCall(MatPermute(A, rowperm, colperm, &Aperm));
115:     PetscCall(VecPermute(b, rowperm, PETSC_FALSE));
116:     PetscCall(MatDestroy(&A));
117:     A = Aperm; /* Replace original operator with permuted version */
118:     PetscCall(ISDestroy(&rowperm));
119:   }

121:   *b_out       = b;
122:   *x_out       = x;
123:   *A_out       = A;
124:   *colperm_out = colperm;

126:   PetscFunctionReturn(PETSC_SUCCESS);
127: }

129: /* ATTENTION: this is the example used in the Profiling chapter of the PETSc manual,
130:    where we referenced its profiling stages, preloading and output etc.
131:    When you modify it, please make sure it is still consistent with the manual.
132:  */
133: int main(int argc, char **args)
134: {
135:   Vec       x, b;
136:   Mat       A;   /* linear system matrix */
137:   KSP       ksp; /* Krylov subspace method context */
138:   char      file[2][PETSC_MAX_PATH_LEN], ordering[256] = MATORDERINGRCM;
139:   RHSType   rhstype = RHS_FILE;
140:   PetscBool flg, preload = PETSC_FALSE, trans = PETSC_FALSE, permute = PETSC_FALSE;
141:   IS        colperm = NULL;

143:   PetscFunctionBeginUser;
144:   PetscCall(PetscInitialize(&argc, &args, (char *)0, help));

146:   PetscOptionsBegin(PETSC_COMM_WORLD, NULL, "Preloading example options", "");
147:   {
148:     /*
149:        Determine files from which we read the two linear systems
150:        (matrix and right-hand-side vector).
151:     */
152:     PetscCall(PetscOptionsBool("-trans", "Solve transpose system instead", "", trans, &trans, &flg));
153:     PetscCall(PetscOptionsString("-f", "First file to load (small system)", "", file[0], file[0], sizeof(file[0]), &flg));
154:     PetscCall(PetscOptionsFList("-permute", "Permute matrix and vector to solve in new ordering", "", MatOrderingList, ordering, ordering, sizeof(ordering), &permute));

156:     if (flg) {
157:       PetscCall(PetscStrncpy(file[1], file[0], sizeof(file[1])));
158:       preload = PETSC_FALSE;
159:     } else {
160:       PetscCall(PetscOptionsString("-f0", "First file to load (small system)", "", file[0], file[0], sizeof(file[0]), &flg));
161:       PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_USER_INPUT, "Must indicate binary file with the -f0 or -f option");
162:       PetscCall(PetscOptionsString("-f1", "Second file to load (larger system)", "", file[1], file[1], sizeof(file[1]), &flg));
163:       if (!flg) preload = PETSC_FALSE; /* don't bother with second system */
164:     }

166:     PetscCall(PetscOptionsEnum("-rhs", "Right hand side", "", RHSTypes, (PetscEnum)rhstype, (PetscEnum *)&rhstype, NULL));
167:   }
168:   PetscOptionsEnd();

170:   /*
171:     To use preloading, one usually has code like the following:

173:     PetscPreLoadBegin(preload,"first stage);
174:       lines of code
175:     PetscPreLoadStage("second stage");
176:       lines of code
177:     PetscPreLoadEnd();

179:     The two macro PetscPreLoadBegin() and PetscPreLoadEnd() implicitly form a
180:     loop with maximal two iterations, depending whether preloading is turned on or
181:     not. If it is, either through the preload arg of PetscPreLoadBegin or through
182:     -preload command line, the trip count is 2, otherwise it is 1. One can use the
183:     predefined variable PetscPreLoadIt within the loop body to get the current
184:     iteration number, which is 0 or 1. If preload is turned on, the runtime doesn't
185:     do profiling for the first iteration, but it will do profiling for the second
186:     iteration instead.

188:     One can solve a small system in the first iteration and a large system in
189:     the second iteration. This process preloads the instructions with the small
190:     system so that more accurate performance monitoring (via -log_view) can be done
191:     with the large one (that actually is the system of interest).

193:     But in this example, we turned off preloading and duplicated the code for
194:     the large system. In general, it is a bad practice and one should not duplicate
195:     code. We do that because we want to show profiling stages for both the small
196:     system and the large system.
197:   */

199:   /*=========================
200:       solve a small system
201:     =========================*/

203:   PetscPreLoadBegin(preload, "Load System 0");
204:   PetscCall(CreateSystem(file[0], rhstype, ordering, permute, &colperm, &A, &b, &x));

206:   PetscPreLoadStage("KSPSetUp 0");
207:   PetscCall(KSPCreate(PETSC_COMM_WORLD, &ksp));
208:   PetscCall(KSPSetOperators(ksp, A, A));
209:   PetscCall(KSPSetFromOptions(ksp));

211:   /*
212:     Here we explicitly call KSPSetUp() and KSPSetUpOnBlocks() to
213:     enable more precise profiling of setting up the preconditioner.
214:     These calls are optional, since both will be called within
215:     KSPSolve() if they haven't been called already.
216:   */
217:   PetscCall(KSPSetUp(ksp));
218:   PetscCall(KSPSetUpOnBlocks(ksp));

220:   PetscPreLoadStage("KSPSolve 0");
221:   if (trans) PetscCall(KSPSolveTranspose(ksp, b, x));
222:   else PetscCall(KSPSolve(ksp, b, x));

224:   if (permute) PetscCall(VecPermute(x, colperm, PETSC_TRUE));

226:   PetscCall(CheckResult(&ksp, &A, &b, &x, &colperm));

228:   /*=========================
229:     solve a large system
230:     =========================*/

232:   PetscPreLoadStage("Load System 1");

234:   PetscCall(CreateSystem(file[1], rhstype, ordering, permute, &colperm, &A, &b, &x));

236:   PetscPreLoadStage("KSPSetUp 1");
237:   PetscCall(KSPCreate(PETSC_COMM_WORLD, &ksp));
238:   PetscCall(KSPSetOperators(ksp, A, A));
239:   PetscCall(KSPSetFromOptions(ksp));

241:   /*
242:     Here we explicitly call KSPSetUp() and KSPSetUpOnBlocks() to
243:     enable more precise profiling of setting up the preconditioner.
244:     These calls are optional, since both will be called within
245:     KSPSolve() if they haven't been called already.
246:   */
247:   PetscCall(KSPSetUp(ksp));
248:   PetscCall(KSPSetUpOnBlocks(ksp));

250:   PetscPreLoadStage("KSPSolve 1");
251:   if (trans) PetscCall(KSPSolveTranspose(ksp, b, x));
252:   else PetscCall(KSPSolve(ksp, b, x));

254:   if (permute) PetscCall(VecPermute(x, colperm, PETSC_TRUE));

256:   PetscCall(CheckResult(&ksp, &A, &b, &x, &colperm));

258:   PetscPreLoadEnd();
259:   /*
260:      Always call PetscFinalize() before exiting a program.  This routine
261:        - finalizes the PETSc libraries as well as MPI
262:        - provides summary and diagnostic information if certain runtime
263:          options are chosen (e.g., -log_view).
264:   */
265:   PetscCall(PetscFinalize());
266:   return 0;
267: }

269: /*TEST

271:    test:
272:       TODO: Matrix row/column sizes are not compatible with block size
273:       suffix: 1
274:       nsize: 4
275:       output_file: output/ex10_1.out
276:       requires: datafilespath double !complex !defined(PETSC_USE_64BIT_INDICES)
277:       args: -f0 ${DATAFILESPATH}/matrices/medium -f1 ${DATAFILESPATH}/matrices/arco6 -ksp_gmres_classicalgramschmidt -mat_type baij -matload_block_size 3 -pc_type bjacobi

279:    test:
280:       TODO: Matrix row/column sizes are not compatible with block size
281:       suffix: 2
282:       nsize: 4
283:       output_file: output/ex10_2.out
284:       requires: datafilespath double !complex !defined(PETSC_USE_64BIT_INDICES)
285:       args: -f0 ${DATAFILESPATH}/matrices/medium -f1 ${DATAFILESPATH}/matrices/arco6 -ksp_gmres_classicalgramschmidt -mat_type baij -matload_block_size 3 -pc_type bjacobi -trans

287:    test:
288:       suffix: 3
289:       requires: double complex !defined(PETSC_USE_64BIT_INDICES)
290:       args: -f ${wPETSC_DIR}/share/petsc/datafiles/matrices/nh-complex-int32-float64 -ksp_type bicg

292:    test:
293:       suffix: 4
294:       args: -f ${DATAFILESPATH}/matrices/medium -ksp_type bicg -permute rcm
295:       requires: datafilespath double !complex !defined(PETSC_USE_64BIT_INDICES)

297: TEST*/