Actual source code: aomapping.c
petsc-3.9.4 2018-09-11
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: .keywords: AO, index
143: .seealso: AOMappingHasPetscIndex(), AOCreateMapping()
144: @*/
145: PetscErrorCode AOMappingHasApplicationIndex(AO ao, PetscInt idex, PetscBool *hasIndex)
146: {
147: AO_Mapping *aomap;
148: PetscInt *app;
149: PetscInt low, high, mid;
154: aomap = (AO_Mapping*) ao->data;
155: app = aomap->app;
156: /* Use bisection since the array is sorted */
157: low = 0;
158: high = aomap->N - 1;
159: while (low <= high) {
160: mid = (low + high)/2;
161: if (idex == app[mid]) break;
162: else if (idex < app[mid]) high = mid - 1;
163: else low = mid + 1;
164: }
165: if (low > high) *hasIndex = PETSC_FALSE;
166: else *hasIndex = PETSC_TRUE;
167: return(0);
168: }
170: /*@
171: AOMappingHasPetscIndex - Searches for the supplied petsc index.
173: Input Parameters:
174: + ao - The AOMapping
175: - index - The petsc index
177: Output Parameter:
178: . hasIndex - Flag is PETSC_TRUE if the index exists
180: Level: intermediate
182: .keywords: AO, index
183: .seealso: AOMappingHasApplicationIndex(), AOCreateMapping()
184: @*/
185: PetscErrorCode AOMappingHasPetscIndex(AO ao, PetscInt idex, PetscBool *hasIndex)
186: {
187: AO_Mapping *aomap;
188: PetscInt *petsc;
189: PetscInt low, high, mid;
194: aomap = (AO_Mapping*) ao->data;
195: petsc = aomap->petsc;
196: /* Use bisection since the array is sorted */
197: low = 0;
198: high = aomap->N - 1;
199: while (low <= high) {
200: mid = (low + high)/2;
201: if (idex == petsc[mid]) break;
202: else if (idex < petsc[mid]) high = mid - 1;
203: else low = mid + 1;
204: }
205: if (low > high) *hasIndex = PETSC_FALSE;
206: else *hasIndex = PETSC_TRUE;
207: return(0);
208: }
210: /*@C
211: AOCreateMapping - Creates a basic application mapping using two integer arrays.
213: Input Parameters:
214: + comm - MPI communicator that is to share AO
215: . napp - size of integer arrays
216: . myapp - integer array that defines an ordering
217: - mypetsc - integer array that defines another ordering (may be NULL to indicate the identity ordering)
219: Output Parameter:
220: . aoout - the new application mapping
222: Options Database Key:
223: . -ao_view : call AOView() at the conclusion of AOCreateMapping()
225: Level: beginner
227: Notes: 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.
228: Use AOCreateBasic() or AOCreateBasicIS() if they do not have holes for better performance.
230: .keywords: AO, create
231: .seealso: AOCreateBasic(), AOCreateBasic(), AOCreateMappingIS(), AODestroy()
232: @*/
233: PetscErrorCode AOCreateMapping(MPI_Comm comm,PetscInt napp,const PetscInt myapp[],const PetscInt mypetsc[],AO *aoout)
234: {
235: AO ao;
236: AO_Mapping *aomap;
237: PetscInt *allpetsc, *allapp;
238: PetscInt *petscPerm, *appPerm;
239: PetscInt *petsc;
240: PetscMPIInt size, rank,*lens, *disp,nnapp;
241: PetscInt N, start;
242: PetscInt i;
247: *aoout = 0;
248: AOInitializePackage();
250: PetscHeaderCreate(ao, AO_CLASSID, "AO", "Application Ordering", "AO", comm, AODestroy, AOView);
251: PetscNewLog(ao,&aomap);
252: PetscMemcpy(ao->ops, &AOps, sizeof(AOps));
253: ao->data = (void*) aomap;
255: /* transmit all lengths to all processors */
256: MPI_Comm_size(comm, &size);
257: MPI_Comm_rank(comm, &rank);
258: PetscMalloc2(size, &lens,size,&disp);
259: nnapp = napp;
260: MPI_Allgather(&nnapp, 1, MPI_INT, lens, 1, MPI_INT, comm);
261: N = 0;
262: for (i = 0; i < size; i++) {
263: disp[i] = N;
264: N += lens[i];
265: }
266: aomap->N = N;
267: ao->N = N;
268: ao->n = N;
270: /* If mypetsc is 0 then use "natural" numbering */
271: if (!mypetsc) {
272: start = disp[rank];
273: PetscMalloc1(napp+1, &petsc);
274: for (i = 0; i < napp; i++) petsc[i] = start + i;
275: } else {
276: petsc = (PetscInt*)mypetsc;
277: }
279: /* get all indices on all processors */
280: PetscMalloc4(N, &allapp,N,&appPerm,N,&allpetsc,N,&petscPerm);
281: MPI_Allgatherv((void*)myapp, napp, MPIU_INT, allapp, lens, disp, MPIU_INT, comm);
282: MPI_Allgatherv((void*)petsc, napp, MPIU_INT, allpetsc, lens, disp, MPIU_INT, comm);
283: PetscFree2(lens,disp);
285: /* generate a list of application and PETSc node numbers */
286: PetscMalloc4(N, &aomap->app,N,&aomap->appPerm,N,&aomap->petsc,N,&aomap->petscPerm);
287: PetscLogObjectMemory((PetscObject)ao, 4*N * sizeof(PetscInt));
288: for (i = 0; i < N; i++) {
289: appPerm[i] = i;
290: petscPerm[i] = i;
291: }
292: PetscSortIntWithPermutation(N, allpetsc, petscPerm);
293: PetscSortIntWithPermutation(N, allapp, appPerm);
294: /* Form sorted arrays of indices */
295: for (i = 0; i < N; i++) {
296: aomap->app[i] = allapp[appPerm[i]];
297: aomap->petsc[i] = allpetsc[petscPerm[i]];
298: }
299: /* Invert petscPerm[] into aomap->petscPerm[] */
300: for (i = 0; i < N; i++) aomap->petscPerm[petscPerm[i]] = i;
302: /* Form map between aomap->app[] and aomap->petsc[] */
303: for (i = 0; i < N; i++) aomap->appPerm[i] = aomap->petscPerm[appPerm[i]];
305: /* Invert appPerm[] into allapp[] */
306: for (i = 0; i < N; i++) allapp[appPerm[i]] = i;
308: /* Form map between aomap->petsc[] and aomap->app[] */
309: for (i = 0; i < N; i++) aomap->petscPerm[i] = allapp[petscPerm[i]];
311: #if defined(PETSC_USE_DEBUG)
312: /* Check that the permutations are complementary */
313: for (i = 0; i < N; i++) {
314: if (i != aomap->appPerm[aomap->petscPerm[i]]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Invalid ordering");
315: }
316: #endif
317: /* Cleanup */
318: if (!mypetsc) {
319: PetscFree(petsc);
320: }
321: PetscFree4(allapp,appPerm,allpetsc,petscPerm);
323: AOViewFromOptions(ao,NULL,"-ao_view");
325: *aoout = ao;
326: return(0);
327: }
329: /*@C
330: AOCreateMappingIS - Creates a basic application ordering using two index sets.
332: Input Parameters:
333: + comm - MPI communicator that is to share AO
334: . isapp - index set that defines an ordering
335: - ispetsc - index set that defines another ordering, maybe NULL for identity IS
337: Output Parameter:
338: . aoout - the new application ordering
340: Options Database Key:
341: . -ao_view : call AOView() at the conclusion of AOCreateMappingIS()
343: Level: beginner
345: Notes: 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.
346: Use AOCreateBasic() or AOCreateBasicIS() if they do not have holes for better performance.
348: .keywords: AO, create
349: .seealso: AOCreateBasic(), AOCreateMapping(), AODestroy()
350: @*/
351: PetscErrorCode AOCreateMappingIS(IS isapp, IS ispetsc, AO *aoout)
352: {
353: MPI_Comm comm;
354: const PetscInt *mypetsc, *myapp;
355: PetscInt napp, npetsc;
359: PetscObjectGetComm((PetscObject) isapp, &comm);
360: ISGetLocalSize(isapp, &napp);
361: if (ispetsc) {
362: ISGetLocalSize(ispetsc, &npetsc);
363: if (napp != npetsc) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ, "Local IS lengths must match");
364: ISGetIndices(ispetsc, &mypetsc);
365: } else {
366: mypetsc = NULL;
367: }
368: ISGetIndices(isapp, &myapp);
370: AOCreateMapping(comm, napp, myapp, mypetsc, aoout);
372: ISRestoreIndices(isapp, &myapp);
373: if (ispetsc) {
374: ISRestoreIndices(ispetsc, &mypetsc);
375: }
376: return(0);
377: }