Actual source code: aomapping.c

petsc-master 2019-09-15
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  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;

 24:   PetscFree4(aomap->app,aomap->appPerm,aomap->petsc,aomap->petscPerm);
 25:   PetscFree(aomap);
 26:   return(0);
 27: }

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

 38:   MPI_Comm_rank(PetscObjectComm((PetscObject)ao), &rank);
 39:   if (rank) return(0);
 40:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
 41:   if (iascii) {
 42:     PetscViewerASCIIPrintf(viewer, "Number of elements in ordering %D\n", aomap->N);
 43:     PetscViewerASCIIPrintf(viewer, "   App.   PETSc\n");
 44:     for (i = 0; i < aomap->N; i++) {
 45:       PetscViewerASCIIPrintf(viewer, "%D   %D    %D\n", i, aomap->app[i], aomap->petsc[aomap->appPerm[i]]);
 46:     }
 47:   }
 48:   return(0);
 49: }

 51: PetscErrorCode AOPetscToApplication_Mapping(AO ao, PetscInt n, PetscInt *ia)
 52: {
 53:   AO_Mapping *aomap = (AO_Mapping*) ao->data;
 54:   PetscInt   *app   = aomap->app;
 55:   PetscInt   *petsc = aomap->petsc;
 56:   PetscInt   *perm  = aomap->petscPerm;
 57:   PetscInt   N      = aomap->N;
 58:   PetscInt   low, high, mid=0;
 59:   PetscInt   idex;
 60:   PetscInt   i;

 62:   /* It would be possible to use a single bisection search, which
 63:      recursively divided the indices to be converted, and searched
 64:      partitions which contained an index. This would result in
 65:      better running times if indices are clustered.
 66:   */
 68:   for (i = 0; i < n; i++) {
 69:     idex = ia[i];
 70:     if (idex < 0) continue;
 71:     /* Use bisection since the array is sorted */
 72:     low  = 0;
 73:     high = N - 1;
 74:     while (low <= high) {
 75:       mid = (low + high)/2;
 76:       if (idex == petsc[mid]) break;
 77:       else if (idex < petsc[mid]) high = mid - 1;
 78:       else low = mid + 1;
 79:     }
 80:     if (low > high) ia[i] = -1;
 81:     else            ia[i] = app[perm[mid]];
 82:   }
 83:   return(0);
 84: }

 86: PetscErrorCode AOApplicationToPetsc_Mapping(AO ao, PetscInt n, PetscInt *ia)
 87: {
 88:   AO_Mapping *aomap = (AO_Mapping*) ao->data;
 89:   PetscInt   *app   = aomap->app;
 90:   PetscInt   *petsc = aomap->petsc;
 91:   PetscInt   *perm  = aomap->appPerm;
 92:   PetscInt   N      = aomap->N;
 93:   PetscInt   low, high, mid=0;
 94:   PetscInt   idex;
 95:   PetscInt   i;

 97:   /* It would be possible to use a single bisection search, which
 98:      recursively divided the indices to be converted, and searched
 99:      partitions which contained an index. This would result in
100:      better running times if indices are clustered.
101:   */
103:   for (i = 0; i < n; i++) {
104:     idex = ia[i];
105:     if (idex < 0) continue;
106:     /* Use bisection since the array is sorted */
107:     low  = 0;
108:     high = N - 1;
109:     while (low <= high) {
110:       mid = (low + high)/2;
111:       if (idex == app[mid]) break;
112:       else if (idex < app[mid]) high = mid - 1;
113:       else low = mid + 1;
114:     }
115:     if (low > high) ia[i] = -1;
116:     else            ia[i] = petsc[perm[mid]];
117:   }
118:   return(0);
119: }

121: static struct _AOOps AOps = {AOView_Mapping,
122:                              AODestroy_Mapping,
123:                              AOPetscToApplication_Mapping,
124:                              AOApplicationToPetsc_Mapping,
125:                              NULL,
126:                              NULL,
127:                              NULL,
128:                              NULL};

130: /*@C
131:   AOMappingHasApplicationIndex - Searches for the supplied application index.

133:   Input Parameters:
134: + ao       - The AOMapping
135: - index    - The application index

137:   Output Parameter:
138: . hasIndex - Flag is PETSC_TRUE if the index exists

140:   Level: intermediate

142: .seealso: AOMappingHasPetscIndex(), AOCreateMapping()
143: @*/
144: PetscErrorCode  AOMappingHasApplicationIndex(AO ao, PetscInt idex, PetscBool  *hasIndex)
145: {
146:   AO_Mapping *aomap;
147:   PetscInt   *app;
148:   PetscInt   low, high, mid;

153:   aomap = (AO_Mapping*) ao->data;
154:   app   = aomap->app;
155:   /* Use bisection since the array is sorted */
156:   low  = 0;
157:   high = aomap->N - 1;
158:   while (low <= high) {
159:     mid = (low + high)/2;
160:     if (idex == app[mid]) break;
161:     else if (idex < app[mid]) high = mid - 1;
162:     else low = mid + 1;
163:   }
164:   if (low > high) *hasIndex = PETSC_FALSE;
165:   else *hasIndex = PETSC_TRUE;
166:   return(0);
167: }

169: /*@
170:   AOMappingHasPetscIndex - Searches for the supplied petsc index.

172:   Input Parameters:
173: + ao       - The AOMapping
174: - index    - The petsc index

176:   Output Parameter:
177: . hasIndex - Flag is PETSC_TRUE if the index exists

179:   Level: intermediate

181: .seealso: AOMappingHasApplicationIndex(), AOCreateMapping()
182: @*/
183: PetscErrorCode  AOMappingHasPetscIndex(AO ao, PetscInt idex, PetscBool  *hasIndex)
184: {
185:   AO_Mapping *aomap;
186:   PetscInt   *petsc;
187:   PetscInt   low, high, mid;

192:   aomap = (AO_Mapping*) ao->data;
193:   petsc = aomap->petsc;
194:   /* Use bisection since the array is sorted */
195:   low  = 0;
196:   high = aomap->N - 1;
197:   while (low <= high) {
198:     mid = (low + high)/2;
199:     if (idex == petsc[mid]) break;
200:     else if (idex < petsc[mid]) high = mid - 1;
201:     else low = mid + 1;
202:   }
203:   if (low > high) *hasIndex = PETSC_FALSE;
204:   else *hasIndex = PETSC_TRUE;
205:   return(0);
206: }

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

211:   Input Parameters:
212: + comm    - MPI communicator that is to share AO
213: . napp    - size of integer arrays
214: . myapp   - integer array that defines an ordering
215: - mypetsc - integer array that defines another ordering (may be NULL to indicate the identity ordering)

217:   Output Parameter:
218: . aoout   - the new application mapping

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

223:   Level: beginner

225:     Notes:
226:     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.
227:        Use AOCreateBasic() or AOCreateBasicIS() if they do not have holes for better performance.

229: .seealso: AOCreateBasic(), AOCreateBasic(), AOCreateMappingIS(), AODestroy()
230: @*/
231: PetscErrorCode  AOCreateMapping(MPI_Comm comm,PetscInt napp,const PetscInt myapp[],const PetscInt mypetsc[],AO *aoout)
232: {
233:   AO             ao;
234:   AO_Mapping     *aomap;
235:   PetscInt       *allpetsc,  *allapp;
236:   PetscInt       *petscPerm, *appPerm;
237:   PetscInt       *petsc;
238:   PetscMPIInt    size, rank,*lens, *disp,nnapp;
239:   PetscInt       N, start;
240:   PetscInt       i;

245:   *aoout = 0;
246:   AOInitializePackage();

248:   PetscHeaderCreate(ao, AO_CLASSID, "AO", "Application Ordering", "AO", comm, AODestroy, AOView);
249:   PetscNewLog(ao,&aomap);
250:   PetscMemcpy(ao->ops, &AOps, sizeof(AOps));
251:   ao->data = (void*) aomap;

253:   /* transmit all lengths to all processors */
254:   MPI_Comm_size(comm, &size);
255:   MPI_Comm_rank(comm, &rank);
256:   PetscMalloc2(size, &lens,size,&disp);
257:   nnapp = napp;
258:   MPI_Allgather(&nnapp, 1, MPI_INT, lens, 1, MPI_INT, comm);
259:   N     = 0;
260:   for (i = 0; i < size; i++) {
261:     disp[i] = N;
262:     N      += lens[i];
263:   }
264:   aomap->N = N;
265:   ao->N    = N;
266:   ao->n    = N;

268:   /* If mypetsc is 0 then use "natural" numbering */
269:   if (!mypetsc) {
270:     start = disp[rank];
271:     PetscMalloc1(napp+1, &petsc);
272:     for (i = 0; i < napp; i++) petsc[i] = start + i;
273:   } else {
274:     petsc = (PetscInt*)mypetsc;
275:   }

277:   /* get all indices on all processors */
278:   PetscMalloc4(N, &allapp,N,&appPerm,N,&allpetsc,N,&petscPerm);
279:   MPI_Allgatherv((void*)myapp, napp, MPIU_INT, allapp,   lens, disp, MPIU_INT, comm);
280:   MPI_Allgatherv((void*)petsc, napp, MPIU_INT, allpetsc, lens, disp, MPIU_INT, comm);
281:   PetscFree2(lens,disp);

283:   /* generate a list of application and PETSc node numbers */
284:   PetscMalloc4(N, &aomap->app,N,&aomap->appPerm,N,&aomap->petsc,N,&aomap->petscPerm);
285:   PetscLogObjectMemory((PetscObject)ao, 4*N * sizeof(PetscInt));
286:   for (i = 0; i < N; i++) {
287:     appPerm[i]   = i;
288:     petscPerm[i] = i;
289:   }
290:   PetscSortIntWithPermutation(N, allpetsc, petscPerm);
291:   PetscSortIntWithPermutation(N, allapp,   appPerm);
292:   /* Form sorted arrays of indices */
293:   for (i = 0; i < N; i++) {
294:     aomap->app[i]   = allapp[appPerm[i]];
295:     aomap->petsc[i] = allpetsc[petscPerm[i]];
296:   }
297:   /* Invert petscPerm[] into aomap->petscPerm[] */
298:   for (i = 0; i < N; i++) aomap->petscPerm[petscPerm[i]] = i;

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

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

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

309: #if defined(PETSC_USE_DEBUG)
310:   /* Check that the permutations are complementary */
311:   for (i = 0; i < N; i++) {
312:     if (i != aomap->appPerm[aomap->petscPerm[i]]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid ordering");
313:   }
314: #endif
315:   /* Cleanup */
316:   if (!mypetsc) {
317:     PetscFree(petsc);
318:   }
319:   PetscFree4(allapp,appPerm,allpetsc,petscPerm);

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

323:   *aoout = ao;
324:   return(0);
325: }

327: /*@
328:   AOCreateMappingIS - Creates a basic application ordering using two index sets.

330:   Input Parameters:
331: + comm    - MPI communicator that is to share AO
332: . isapp   - index set that defines an ordering
333: - ispetsc - index set that defines another ordering, maybe NULL for identity IS

335:   Output Parameter:
336: . aoout   - the new application ordering

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

341:   Level: beginner

343:     Notes:
344:     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.
345:        Use AOCreateBasic() or AOCreateBasicIS() if they do not have holes for better performance.

347: .seealso: AOCreateBasic(), AOCreateMapping(), AODestroy()
348: @*/
349: PetscErrorCode  AOCreateMappingIS(IS isapp, IS ispetsc, AO *aoout)
350: {
351:   MPI_Comm       comm;
352:   const PetscInt *mypetsc, *myapp;
353:   PetscInt       napp, npetsc;

357:   PetscObjectGetComm((PetscObject) isapp, &comm);
358:   ISGetLocalSize(isapp, &napp);
359:   if (ispetsc) {
360:     ISGetLocalSize(ispetsc, &npetsc);
361:     if (napp != npetsc) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ, "Local IS lengths must match");
362:     ISGetIndices(ispetsc, &mypetsc);
363:   } else {
364:     mypetsc = NULL;
365:   }
366:   ISGetIndices(isapp, &myapp);

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

370:   ISRestoreIndices(isapp, &myapp);
371:   if (ispetsc) {
372:     ISRestoreIndices(ispetsc, &mypetsc);
373:   }
374:   return(0);
375: }