Actual source code: aomapping.c


  2: /*
  3:   These AO application ordering routines do not require that the input
  4:   be a permutation, but merely a 1-1 mapping. This implementation still
  5:   keeps the entire ordering on each processor.
  6: */

  8: #include <../src/vec/is/ao/aoimpl.h>

 10: typedef struct {
 11:   PetscInt  N;
 12:   PetscInt *app; /* app[i] is the partner for petsc[appPerm[i]] */
 13:   PetscInt *appPerm;
 14:   PetscInt *petsc; /* petsc[j] is the partner for app[petscPerm[j]] */
 15:   PetscInt *petscPerm;
 16: } AO_Mapping;

 18: PetscErrorCode AODestroy_Mapping(AO ao)
 19: {
 20:   AO_Mapping *aomap = (AO_Mapping *)ao->data;

 22:   PetscFree4(aomap->app, aomap->appPerm, aomap->petsc, aomap->petscPerm);
 23:   PetscFree(aomap);
 24:   return 0;
 25: }

 27: PetscErrorCode AOView_Mapping(AO ao, PetscViewer viewer)
 28: {
 29:   AO_Mapping *aomap = (AO_Mapping *)ao->data;
 30:   PetscMPIInt rank;
 31:   PetscInt    i;
 32:   PetscBool   iascii;

 34:   MPI_Comm_rank(PetscObjectComm((PetscObject)ao), &rank);
 35:   if (rank) return 0;
 36:   PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &iascii);
 37:   if (iascii) {
 38:     PetscViewerASCIIPrintf(viewer, "Number of elements in ordering %" PetscInt_FMT "\n", aomap->N);
 39:     PetscViewerASCIIPrintf(viewer, "   App.   PETSc\n");
 40:     for (i = 0; i < aomap->N; i++) PetscViewerASCIIPrintf(viewer, "%" PetscInt_FMT "   %" PetscInt_FMT "    %" PetscInt_FMT "\n", i, aomap->app[i], aomap->petsc[aomap->appPerm[i]]);
 41:   }
 42:   return 0;
 43: }

 45: PetscErrorCode AOPetscToApplication_Mapping(AO ao, PetscInt n, PetscInt *ia)
 46: {
 47:   AO_Mapping *aomap = (AO_Mapping *)ao->data;
 48:   PetscInt   *app   = aomap->app;
 49:   PetscInt   *petsc = aomap->petsc;
 50:   PetscInt   *perm  = aomap->petscPerm;
 51:   PetscInt    N     = aomap->N;
 52:   PetscInt    low, high, mid = 0;
 53:   PetscInt    idex;
 54:   PetscInt    i;

 56:   /* It would be possible to use a single bisection search, which
 57:      recursively divided the indices to be converted, and searched
 58:      partitions which contained an index. This would result in
 59:      better running times if indices are clustered.
 60:   */
 61:   for (i = 0; i < n; i++) {
 62:     idex = ia[i];
 63:     if (idex < 0) continue;
 64:     /* Use bisection since the array is sorted */
 65:     low  = 0;
 66:     high = N - 1;
 67:     while (low <= high) {
 68:       mid = (low + high) / 2;
 69:       if (idex == petsc[mid]) break;
 70:       else if (idex < petsc[mid]) high = mid - 1;
 71:       else low = mid + 1;
 72:     }
 73:     if (low > high) ia[i] = -1;
 74:     else ia[i] = app[perm[mid]];
 75:   }
 76:   return 0;
 77: }

 79: PetscErrorCode AOApplicationToPetsc_Mapping(AO ao, PetscInt n, PetscInt *ia)
 80: {
 81:   AO_Mapping *aomap = (AO_Mapping *)ao->data;
 82:   PetscInt   *app   = aomap->app;
 83:   PetscInt   *petsc = aomap->petsc;
 84:   PetscInt   *perm  = aomap->appPerm;
 85:   PetscInt    N     = aomap->N;
 86:   PetscInt    low, high, mid = 0;
 87:   PetscInt    idex;
 88:   PetscInt    i;

 90:   /* It would be possible to use a single bisection search, which
 91:      recursively divided the indices to be converted, and searched
 92:      partitions which contained an index. This would result in
 93:      better running times if indices are clustered.
 94:   */
 95:   for (i = 0; i < n; i++) {
 96:     idex = ia[i];
 97:     if (idex < 0) continue;
 98:     /* Use bisection since the array is sorted */
 99:     low  = 0;
100:     high = N - 1;
101:     while (low <= high) {
102:       mid = (low + high) / 2;
103:       if (idex == app[mid]) break;
104:       else if (idex < app[mid]) high = mid - 1;
105:       else low = mid + 1;
106:     }
107:     if (low > high) ia[i] = -1;
108:     else ia[i] = petsc[perm[mid]];
109:   }
110:   return 0;
111: }

113: static struct _AOOps AOps = {
114:   PetscDesignatedInitializer(view, AOView_Mapping),
115:   PetscDesignatedInitializer(destroy, AODestroy_Mapping),
116:   PetscDesignatedInitializer(petsctoapplication, AOPetscToApplication_Mapping),
117:   PetscDesignatedInitializer(applicationtopetsc, AOApplicationToPetsc_Mapping),
118: };

120: /*@C
121:   AOMappingHasApplicationIndex - Searches for the supplied application index.

123:   Input Parameters:
124: + ao       - The AOMapping
125: - index    - The application index

127:   Output Parameter:
128: . hasIndex - Flag is PETSC_TRUE if the index exists

130:   Level: intermediate

132: .seealso: `AOMappingHasPetscIndex()`, `AOCreateMapping()`
133: @*/
134: PetscErrorCode AOMappingHasApplicationIndex(AO ao, PetscInt idex, PetscBool *hasIndex)
135: {
136:   AO_Mapping *aomap;
137:   PetscInt   *app;
138:   PetscInt    low, high, mid;

142:   aomap = (AO_Mapping *)ao->data;
143:   app   = aomap->app;
144:   /* Use bisection since the array is sorted */
145:   low  = 0;
146:   high = aomap->N - 1;
147:   while (low <= high) {
148:     mid = (low + high) / 2;
149:     if (idex == app[mid]) break;
150:     else if (idex < app[mid]) high = mid - 1;
151:     else low = mid + 1;
152:   }
153:   if (low > high) *hasIndex = PETSC_FALSE;
154:   else *hasIndex = PETSC_TRUE;
155:   return 0;
156: }

158: /*@
159:   AOMappingHasPetscIndex - Searches for the supplied petsc index.

161:   Input Parameters:
162: + ao       - The AOMapping
163: - index    - The petsc index

165:   Output Parameter:
166: . hasIndex - Flag is PETSC_TRUE if the index exists

168:   Level: intermediate

170: .seealso: `AOMappingHasApplicationIndex()`, `AOCreateMapping()`
171: @*/
172: PetscErrorCode AOMappingHasPetscIndex(AO ao, PetscInt idex, PetscBool *hasIndex)
173: {
174:   AO_Mapping *aomap;
175:   PetscInt   *petsc;
176:   PetscInt    low, high, mid;

180:   aomap = (AO_Mapping *)ao->data;
181:   petsc = aomap->petsc;
182:   /* Use bisection since the array is sorted */
183:   low  = 0;
184:   high = aomap->N - 1;
185:   while (low <= high) {
186:     mid = (low + high) / 2;
187:     if (idex == petsc[mid]) break;
188:     else if (idex < petsc[mid]) high = mid - 1;
189:     else low = mid + 1;
190:   }
191:   if (low > high) *hasIndex = PETSC_FALSE;
192:   else *hasIndex = PETSC_TRUE;
193:   return 0;
194: }

196: /*@C
197:   AOCreateMapping - Creates a basic application mapping using two integer arrays.

199:   Input Parameters:
200: + comm    - MPI communicator that is to share AO
201: . napp    - size of integer arrays
202: . myapp   - integer array that defines an ordering
203: - mypetsc - integer array that defines another ordering (may be NULL to indicate the identity ordering)

205:   Output Parameter:
206: . aoout   - the new application mapping

208:   Options Database Key:
209: . -ao_view - call AOView() at the conclusion of AOCreateMapping()

211:   Level: beginner

213:     Notes:
214:     the arrays myapp and mypetsc need NOT contain the all the integers 0 to napp-1, that is there CAN be "holes"  in the indices.
215:        Use AOCreateBasic() or AOCreateBasicIS() if they do not have holes for better performance.

217: .seealso: `AOCreateBasic()`, `AOCreateBasic()`, `AOCreateMappingIS()`, `AODestroy()`
218: @*/
219: PetscErrorCode AOCreateMapping(MPI_Comm comm, PetscInt napp, const PetscInt myapp[], const PetscInt mypetsc[], AO *aoout)
220: {
221:   AO          ao;
222:   AO_Mapping *aomap;
223:   PetscInt   *allpetsc, *allapp;
224:   PetscInt   *petscPerm, *appPerm;
225:   PetscInt   *petsc;
226:   PetscMPIInt size, rank, *lens, *disp, nnapp;
227:   PetscInt    N, start;
228:   PetscInt    i;

231:   *aoout = NULL;
232:   AOInitializePackage();

234:   PetscHeaderCreate(ao, AO_CLASSID, "AO", "Application Ordering", "AO", comm, AODestroy, AOView);
235:   PetscNew(&aomap);
236:   PetscMemcpy(ao->ops, &AOps, sizeof(AOps));
237:   ao->data = (void *)aomap;

239:   /* transmit all lengths to all processors */
240:   MPI_Comm_size(comm, &size);
241:   MPI_Comm_rank(comm, &rank);
242:   PetscMalloc2(size, &lens, size, &disp);
243:   nnapp = napp;
244:   MPI_Allgather(&nnapp, 1, MPI_INT, lens, 1, MPI_INT, comm);
245:   N = 0;
246:   for (i = 0; i < size; i++) {
247:     disp[i] = N;
248:     N += lens[i];
249:   }
250:   aomap->N = N;
251:   ao->N    = N;
252:   ao->n    = N;

254:   /* If mypetsc is 0 then use "natural" numbering */
255:   if (!mypetsc) {
256:     start = disp[rank];
257:     PetscMalloc1(napp + 1, &petsc);
258:     for (i = 0; i < napp; i++) petsc[i] = start + i;
259:   } else {
260:     petsc = (PetscInt *)mypetsc;
261:   }

263:   /* get all indices on all processors */
264:   PetscMalloc4(N, &allapp, N, &appPerm, N, &allpetsc, N, &petscPerm);
265:   MPI_Allgatherv((void *)myapp, napp, MPIU_INT, allapp, lens, disp, MPIU_INT, comm);
266:   MPI_Allgatherv((void *)petsc, napp, MPIU_INT, allpetsc, lens, disp, MPIU_INT, comm);
267:   PetscFree2(lens, disp);

269:   /* generate a list of application and PETSc node numbers */
270:   PetscMalloc4(N, &aomap->app, N, &aomap->appPerm, N, &aomap->petsc, N, &aomap->petscPerm);
271:   for (i = 0; i < N; i++) {
272:     appPerm[i]   = i;
273:     petscPerm[i] = i;
274:   }
275:   PetscSortIntWithPermutation(N, allpetsc, petscPerm);
276:   PetscSortIntWithPermutation(N, allapp, appPerm);
277:   /* Form sorted arrays of indices */
278:   for (i = 0; i < N; i++) {
279:     aomap->app[i]   = allapp[appPerm[i]];
280:     aomap->petsc[i] = allpetsc[petscPerm[i]];
281:   }
282:   /* Invert petscPerm[] into aomap->petscPerm[] */
283:   for (i = 0; i < N; i++) aomap->petscPerm[petscPerm[i]] = i;

285:   /* Form map between aomap->app[] and aomap->petsc[] */
286:   for (i = 0; i < N; i++) aomap->appPerm[i] = aomap->petscPerm[appPerm[i]];

288:   /* Invert appPerm[] into allapp[] */
289:   for (i = 0; i < N; i++) allapp[appPerm[i]] = i;

291:   /* Form map between aomap->petsc[] and aomap->app[] */
292:   for (i = 0; i < N; i++) aomap->petscPerm[i] = allapp[petscPerm[i]];

294:   if (PetscDefined(USE_DEBUG)) {
295:     /* Check that the permutations are complementary */
297:   }
298:   /* Cleanup */
299:   if (!mypetsc) PetscFree(petsc);
300:   PetscFree4(allapp, appPerm, allpetsc, petscPerm);

302:   AOViewFromOptions(ao, NULL, "-ao_view");

304:   *aoout = ao;
305:   return 0;
306: }

308: /*@
309:   AOCreateMappingIS - Creates a basic application ordering using two index sets.

311:   Input Parameters:
312: + comm    - MPI communicator that is to share AO
313: . isapp   - index set that defines an ordering
314: - ispetsc - index set that defines another ordering, maybe NULL for identity IS

316:   Output Parameter:
317: . aoout   - the new application ordering

319:   Options Database Key:
320: . -ao_view - call AOView() at the conclusion of AOCreateMappingIS()

322:   Level: beginner

324:     Notes:
325:     the index sets isapp and ispetsc need NOT contain the all the integers 0 to N-1, that is there CAN be "holes"  in the indices.
326:        Use AOCreateBasic() or AOCreateBasicIS() if they do not have holes for better performance.

328: .seealso: `AOCreateBasic()`, `AOCreateMapping()`, `AODestroy()`
329: @*/
330: PetscErrorCode AOCreateMappingIS(IS isapp, IS ispetsc, AO *aoout)
331: {
332:   MPI_Comm        comm;
333:   const PetscInt *mypetsc, *myapp;
334:   PetscInt        napp, npetsc;

336:   PetscObjectGetComm((PetscObject)isapp, &comm);
337:   ISGetLocalSize(isapp, &napp);
338:   if (ispetsc) {
339:     ISGetLocalSize(ispetsc, &npetsc);
341:     ISGetIndices(ispetsc, &mypetsc);
342:   } else {
343:     mypetsc = NULL;
344:   }
345:   ISGetIndices(isapp, &myapp);

347:   AOCreateMapping(comm, napp, myapp, mypetsc, aoout);

349:   ISRestoreIndices(isapp, &myapp);
350:   if (ispetsc) ISRestoreIndices(ispetsc, &mypetsc);
351:   return 0;
352: }