Actual source code: sbaijov.c

  1: /*
  2:    Routines to compute overlapping regions of a parallel MPI matrix.
  3:    Used for finding submatrices that were shared across processors.
  4: */
  5: #include <../src/mat/impls/sbaij/mpi/mpisbaij.h>
  6: #include <petscbt.h>

  8: static PetscErrorCode MatIncreaseOverlap_MPISBAIJ_Once(Mat, PetscInt, IS *);
  9: static PetscErrorCode MatIncreaseOverlap_MPISBAIJ_Local(Mat, PetscInt *, PetscInt, PetscInt *, PetscBT *);

 11: PetscErrorCode MatIncreaseOverlap_MPISBAIJ(Mat C, PetscInt is_max, IS is[], PetscInt ov)
 12: {
 13:   PetscInt        i, N = C->cmap->N, bs = C->rmap->bs, M = C->rmap->N, Mbs = M / bs, *nidx, isz, iov;
 14:   IS             *is_new, *is_row;
 15:   Mat            *submats;
 16:   Mat_MPISBAIJ   *c = (Mat_MPISBAIJ *)C->data;
 17:   Mat_SeqSBAIJ   *asub_i;
 18:   PetscBT         table;
 19:   PetscInt       *ai, brow, nz, nis, l, nmax, nstages_local, nstages, max_no, pos;
 20:   const PetscInt *idx;
 21:   PetscBool       flg;

 23:   PetscFunctionBegin;
 24:   PetscCall(PetscMalloc1(is_max, &is_new));
 25:   /* Convert the indices into block format */
 26:   PetscCall(ISCompressIndicesGeneral(N, C->rmap->n, bs, is_max, is, is_new));
 27:   PetscCheck(ov >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Negative overlap specified");

 29:   /*  previous non-scalable implementation  */
 30:   flg = PETSC_FALSE;
 31:   PetscCall(PetscOptionsHasName(NULL, NULL, "-IncreaseOverlap_old", &flg));
 32:   if (flg) { /* previous non-scalable implementation */
 33:     printf("use previous non-scalable implementation...\n");
 34:     for (i = 0; i < ov; ++i) PetscCall(MatIncreaseOverlap_MPISBAIJ_Once(C, is_max, is_new));
 35:   } else { /* implementation using modified BAIJ routines */

 37:     PetscCall(PetscMalloc1(Mbs + 1, &nidx));
 38:     PetscCall(PetscBTCreate(Mbs, &table)); /* for column search */

 40:     /* Create is_row */
 41:     PetscCall(PetscMalloc1(is_max, &is_row));
 42:     PetscCall(ISCreateStride(PETSC_COMM_SELF, Mbs, 0, 1, &is_row[0]));

 44:     for (i = 1; i < is_max; i++) { is_row[i] = is_row[0]; /* reuse is_row[0] */ }

 46:     /* Allocate memory to hold all the submatrices - Modified from MatCreateSubMatrices_MPIBAIJ() */
 47:     PetscCall(PetscMalloc1(is_max + 1, &submats));

 49:     /* Determine the number of stages through which submatrices are done */
 50:     nmax = 20 * 1000000 / (c->Nbs * sizeof(PetscInt));
 51:     if (!nmax) nmax = 1;
 52:     nstages_local = is_max / nmax + ((is_max % nmax) ? 1 : 0);

 54:     /* Make sure every processor loops through the nstages */
 55:     PetscCall(MPIU_Allreduce(&nstages_local, &nstages, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)C)));

 57:     {
 58:       const PetscObject obj = (PetscObject)c->A;
 59:       size_t            new_len, cur_len, max_len;

 61:       PetscCall(PetscStrlen(MATSEQBAIJ, &new_len));
 62:       PetscCall(PetscStrlen(MATSEQSBAIJ, &cur_len));
 63:       max_len = PetscMax(cur_len, new_len) + 1;
 64:       PetscCall(PetscRealloc(max_len * sizeof(*obj->type_name), &obj->type_name));
 65:       /* The resulting submatrices should be BAIJ, not SBAIJ, hence we change this value to
 66:          trigger that */
 67:       for (iov = 0; iov < ov; ++iov) {
 68:         /* 1) Get submats for column search */
 69:         PetscCall(PetscStrncpy(obj->type_name, MATSEQBAIJ, max_len));
 70:         for (i = 0, pos = 0; i < nstages; i++) {
 71:           if (pos + nmax <= is_max) max_no = nmax;
 72:           else if (pos == is_max) max_no = 0;
 73:           else max_no = is_max - pos;
 74:           c->ijonly = PETSC_TRUE; /* only matrix data structures are requested */

 76:           PetscCall(MatCreateSubMatrices_MPIBAIJ_local(C, max_no, is_row + pos, is_new + pos, MAT_INITIAL_MATRIX, submats + pos, PETSC_TRUE));
 77:           pos += max_no;
 78:         }
 79:         PetscCall(PetscStrncpy(obj->type_name, MATSEQSBAIJ, max_len));

 81:         /* 2) Row search */
 82:         PetscCall(MatIncreaseOverlap_MPIBAIJ_Once(C, is_max, is_new));

 84:         /* 3) Column search */
 85:         for (i = 0; i < is_max; i++) {
 86:           asub_i = (Mat_SeqSBAIJ *)submats[i]->data;
 87:           ai     = asub_i->i;

 89:           /* put is_new obtained from MatIncreaseOverlap_MPIBAIJ() to table */
 90:           PetscCall(PetscBTMemzero(Mbs, table));

 92:           PetscCall(ISGetIndices(is_new[i], &idx));
 93:           PetscCall(ISGetLocalSize(is_new[i], &nis));
 94:           for (l = 0; l < nis; l++) {
 95:             PetscCall(PetscBTSet(table, idx[l]));
 96:             nidx[l] = idx[l];
 97:           }
 98:           isz = nis;

100:           /* add column entries to table */
101:           for (brow = 0; brow < Mbs; brow++) {
102:             nz = ai[brow + 1] - ai[brow];
103:             if (nz) {
104:               if (!PetscBTLookupSet(table, brow)) nidx[isz++] = brow;
105:             }
106:           }
107:           PetscCall(ISRestoreIndices(is_new[i], &idx));
108:           PetscCall(ISDestroy(&is_new[i]));

110:           /* create updated is_new */
111:           PetscCall(ISCreateGeneral(PETSC_COMM_SELF, isz, nidx, PETSC_COPY_VALUES, is_new + i));
112:         }

114:         /* Free tmp spaces */
115:         for (i = 0; i < is_max; i++) PetscCall(MatDestroy(&submats[i]));
116:       }

118:       PetscCall(PetscBTDestroy(&table));
119:       PetscCall(PetscFree(submats));
120:       PetscCall(ISDestroy(&is_row[0]));
121:       PetscCall(PetscFree(is_row));
122:       PetscCall(PetscFree(nidx));
123:     }
124:   }
125:   for (i = 0; i < is_max; i++) {
126:     PetscCall(ISDestroy(&is[i]));
127:     PetscCall(ISGetLocalSize(is_new[i], &nis));
128:     PetscCall(ISGetIndices(is_new[i], &idx));
129:     PetscCall(ISCreateBlock(PetscObjectComm((PetscObject)is_new[i]), bs, nis, idx, PETSC_COPY_VALUES, &is[i]));
130:     PetscCall(ISDestroy(&is_new[i]));
131:   }
132:   PetscCall(PetscFree(is_new));
133:   PetscFunctionReturn(PETSC_SUCCESS);
134: }

136: typedef enum {
137:   MINE,
138:   OTHER
139: } WhoseOwner;
140: /*  data1, odata1 and odata2 are packed in the format (for communication):
141:        data[0]          = is_max, no of is
142:        data[1]          = size of is[0]
143:         ...
144:        data[is_max]     = size of is[is_max-1]
145:        data[is_max + 1] = data(is[0])
146:         ...
147:        data[is_max+1+sum(size of is[k]), k=0,...,i-1] = data(is[i])
148:         ...
149:    data2 is packed in the format (for creating output is[]):
150:        data[0]          = is_max, no of is
151:        data[1]          = size of is[0]
152:         ...
153:        data[is_max]     = size of is[is_max-1]
154:        data[is_max + 1] = data(is[0])
155:         ...
156:        data[is_max + 1 + Mbs*i) = data(is[i])
157:         ...
158: */
159: static PetscErrorCode MatIncreaseOverlap_MPISBAIJ_Once(Mat C, PetscInt is_max, IS is[])
160: {
161:   Mat_MPISBAIJ   *c = (Mat_MPISBAIJ *)C->data;
162:   PetscMPIInt     size, rank, tag1, tag2, *len_s, nrqr, nrqs, *id_r1, *len_r1, flag, len, *iwork;
163:   const PetscInt *idx_i;
164:   PetscInt        idx, isz, col, *n, *data1, **data1_start, *data2, *data2_i, *data, *data_i;
165:   PetscInt        Mbs, i, j, k, *odata1, *odata2;
166:   PetscInt        proc_id, **odata2_ptr, *ctable = NULL, *btable, len_max, len_est;
167:   PetscInt        proc_end = 0, len_unused, nodata2;
168:   PetscInt        ois_max; /* max no of is[] in each of processor */
169:   char           *t_p;
170:   MPI_Comm        comm;
171:   MPI_Request    *s_waits1, *s_waits2, r_req;
172:   MPI_Status     *s_status, r_status;
173:   PetscBT        *table; /* mark indices of this processor's is[] */
174:   PetscBT         table_i;
175:   PetscBT         otable; /* mark indices of other processors' is[] */
176:   PetscInt        bs = C->rmap->bs, Bn = c->B->cmap->n, Bnbs = Bn / bs, *Bowners;
177:   IS              garray_local, garray_gl;

179:   PetscFunctionBegin;
180:   PetscCall(PetscObjectGetComm((PetscObject)C, &comm));
181:   size = c->size;
182:   rank = c->rank;
183:   Mbs  = c->Mbs;

185:   PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag1));
186:   PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag2));

188:   /* create tables used in
189:      step 1: table[i] - mark c->garray of proc [i]
190:      step 3: table[i] - mark indices of is[i] when whose=MINE
191:              table[0] - mark incideces of is[] when whose=OTHER */
192:   len = PetscMax(is_max, size);
193:   PetscCall(PetscMalloc2(len, &table, (Mbs / PETSC_BITS_PER_BYTE + 1) * len, &t_p));
194:   for (i = 0; i < len; i++) table[i] = t_p + (Mbs / PETSC_BITS_PER_BYTE + 1) * i;

196:   PetscCall(MPIU_Allreduce(&is_max, &ois_max, 1, MPIU_INT, MPI_MAX, comm));

198:   /* 1. Send this processor's is[] to other processors */
199:   /* allocate spaces */
200:   PetscCall(PetscMalloc1(is_max, &n));
201:   len = 0;
202:   for (i = 0; i < is_max; i++) {
203:     PetscCall(ISGetLocalSize(is[i], &n[i]));
204:     len += n[i];
205:   }
206:   if (!len) {
207:     is_max = 0;
208:   } else {
209:     len += 1 + is_max; /* max length of data1 for one processor */
210:   }

212:   PetscCall(PetscMalloc1(size * len + 1, &data1));
213:   PetscCall(PetscMalloc1(size, &data1_start));
214:   for (i = 0; i < size; i++) data1_start[i] = data1 + i * len;

216:   PetscCall(PetscMalloc4(size, &len_s, size, &btable, size, &iwork, size + 1, &Bowners));

218:   /* gather c->garray from all processors */
219:   PetscCall(ISCreateGeneral(comm, Bnbs, c->garray, PETSC_COPY_VALUES, &garray_local));
220:   PetscCall(ISAllGather(garray_local, &garray_gl));
221:   PetscCall(ISDestroy(&garray_local));
222:   PetscCallMPI(MPI_Allgather(&Bnbs, 1, MPIU_INT, Bowners + 1, 1, MPIU_INT, comm));

224:   Bowners[0] = 0;
225:   for (i = 0; i < size; i++) Bowners[i + 1] += Bowners[i];

227:   if (is_max) {
228:     /* hash table ctable which maps c->row to proc_id) */
229:     PetscCall(PetscMalloc1(Mbs, &ctable));
230:     for (proc_id = 0, j = 0; proc_id < size; proc_id++) {
231:       for (; j < C->rmap->range[proc_id + 1] / bs; j++) ctable[j] = proc_id;
232:     }

234:     /* hash tables marking c->garray */
235:     PetscCall(ISGetIndices(garray_gl, &idx_i));
236:     for (i = 0; i < size; i++) {
237:       table_i = table[i];
238:       PetscCall(PetscBTMemzero(Mbs, table_i));
239:       for (j = Bowners[i]; j < Bowners[i + 1]; j++) { /* go through B cols of proc[i]*/
240:         PetscCall(PetscBTSet(table_i, idx_i[j]));
241:       }
242:     }
243:     PetscCall(ISRestoreIndices(garray_gl, &idx_i));
244:   } /* if (is_max) */
245:   PetscCall(ISDestroy(&garray_gl));

247:   /* evaluate communication - mesg to who, length, and buffer space */
248:   for (i = 0; i < size; i++) len_s[i] = 0;

250:   /* header of data1 */
251:   for (proc_id = 0; proc_id < size; proc_id++) {
252:     iwork[proc_id]        = 0;
253:     *data1_start[proc_id] = is_max;
254:     data1_start[proc_id]++;
255:     for (j = 0; j < is_max; j++) {
256:       if (proc_id == rank) {
257:         *data1_start[proc_id] = n[j];
258:       } else {
259:         *data1_start[proc_id] = 0;
260:       }
261:       data1_start[proc_id]++;
262:     }
263:   }

265:   for (i = 0; i < is_max; i++) {
266:     PetscCall(ISGetIndices(is[i], &idx_i));
267:     for (j = 0; j < n[i]; j++) {
268:       idx                = idx_i[j];
269:       *data1_start[rank] = idx;
270:       data1_start[rank]++; /* for local processing */
271:       proc_end = ctable[idx];
272:       for (proc_id = 0; proc_id <= proc_end; proc_id++) {                        /* for others to process */
273:         if (proc_id == rank) continue;                                           /* done before this loop */
274:         if (proc_id < proc_end && !PetscBTLookup(table[proc_id], idx)) continue; /* no need for sending idx to [proc_id] */
275:         *data1_start[proc_id] = idx;
276:         data1_start[proc_id]++;
277:         len_s[proc_id]++;
278:       }
279:     }
280:     /* update header data */
281:     for (proc_id = 0; proc_id < size; proc_id++) {
282:       if (proc_id == rank) continue;
283:       *(data1 + proc_id * len + 1 + i) = len_s[proc_id] - iwork[proc_id];
284:       iwork[proc_id]                   = len_s[proc_id];
285:     }
286:     PetscCall(ISRestoreIndices(is[i], &idx_i));
287:   }

289:   nrqs = 0;
290:   nrqr = 0;
291:   for (i = 0; i < size; i++) {
292:     data1_start[i] = data1 + i * len;
293:     if (len_s[i]) {
294:       nrqs++;
295:       len_s[i] += 1 + is_max; /* add no. of header msg */
296:     }
297:   }

299:   for (i = 0; i < is_max; i++) PetscCall(ISDestroy(&is[i]));
300:   PetscCall(PetscFree(n));
301:   PetscCall(PetscFree(ctable));

303:   /* Determine the number of messages to expect, their lengths, from from-ids */
304:   PetscCall(PetscGatherNumberOfMessages(comm, NULL, len_s, &nrqr));
305:   PetscCall(PetscGatherMessageLengths(comm, nrqs, nrqr, len_s, &id_r1, &len_r1));

307:   /*  Now  post the sends */
308:   PetscCall(PetscMalloc2(size, &s_waits1, size, &s_waits2));
309:   k = 0;
310:   for (proc_id = 0; proc_id < size; proc_id++) { /* send data1 to processor [proc_id] */
311:     if (len_s[proc_id]) {
312:       PetscCallMPI(MPI_Isend(data1_start[proc_id], len_s[proc_id], MPIU_INT, proc_id, tag1, comm, s_waits1 + k));
313:       k++;
314:     }
315:   }

317:   /* 2. Receive other's is[] and process. Then send back */
318:   len = 0;
319:   for (i = 0; i < nrqr; i++) {
320:     if (len_r1[i] > len) len = len_r1[i];
321:   }
322:   PetscCall(PetscFree(len_r1));
323:   PetscCall(PetscFree(id_r1));

325:   for (proc_id = 0; proc_id < size; proc_id++) len_s[proc_id] = iwork[proc_id] = 0;

327:   PetscCall(PetscMalloc1(len + 1, &odata1));
328:   PetscCall(PetscMalloc1(size, &odata2_ptr));
329:   PetscCall(PetscBTCreate(Mbs, &otable));

331:   len_max = ois_max * (Mbs + 1); /* max space storing all is[] for each receive */
332:   len_est = 2 * len_max;         /* estimated space of storing is[] for all receiving messages */
333:   PetscCall(PetscMalloc1(len_est + 1, &odata2));
334:   nodata2 = 0; /* nodata2+1: num of PetscMalloc(,&odata2_ptr[]) called */

336:   odata2_ptr[nodata2] = odata2;

338:   len_unused = len_est; /* unused space in the array odata2_ptr[nodata2]-- needs to be >= len_max  */

340:   k = 0;
341:   while (k < nrqr) {
342:     /* Receive messages */
343:     PetscCallMPI(MPI_Iprobe(MPI_ANY_SOURCE, tag1, comm, &flag, &r_status));
344:     if (flag) {
345:       PetscCallMPI(MPI_Get_count(&r_status, MPIU_INT, &len));
346:       proc_id = r_status.MPI_SOURCE;
347:       PetscCallMPI(MPI_Irecv(odata1, len, MPIU_INT, proc_id, r_status.MPI_TAG, comm, &r_req));
348:       PetscCallMPI(MPI_Wait(&r_req, &r_status));

350:       /*  Process messages */
351:       /*  make sure there is enough unused space in odata2 array */
352:       if (len_unused < len_max) { /* allocate more space for odata2 */
353:         PetscCall(PetscMalloc1(len_est + 1, &odata2));

355:         odata2_ptr[++nodata2] = odata2;

357:         len_unused = len_est;
358:       }

360:       PetscCall(MatIncreaseOverlap_MPISBAIJ_Local(C, odata1, OTHER, odata2, &otable));
361:       len = 1 + odata2[0];
362:       for (i = 0; i < odata2[0]; i++) len += odata2[1 + i];

364:       /* Send messages back */
365:       PetscCallMPI(MPI_Isend(odata2, len, MPIU_INT, proc_id, tag2, comm, s_waits2 + k));
366:       k++;
367:       odata2 += len;
368:       len_unused -= len;
369:       len_s[proc_id] = len; /* num of messages sending back to [proc_id] by this proc */
370:     }
371:   }
372:   PetscCall(PetscFree(odata1));
373:   PetscCall(PetscBTDestroy(&otable));

375:   /* 3. Do local work on this processor's is[] */
376:   /* make sure there is enough unused space in odata2(=data) array */
377:   len_max = is_max * (Mbs + 1); /* max space storing all is[] for this processor */
378:   if (len_unused < len_max) {   /* allocate more space for odata2 */
379:     PetscCall(PetscMalloc1(len_est + 1, &odata2));

381:     odata2_ptr[++nodata2] = odata2;
382:   }

384:   data = odata2;
385:   PetscCall(MatIncreaseOverlap_MPISBAIJ_Local(C, data1_start[rank], MINE, data, table));
386:   PetscCall(PetscFree(data1_start));

388:   /* 4. Receive work done on other processors, then merge */
389:   /* get max number of messages that this processor expects to recv */
390:   PetscCall(MPIU_Allreduce(len_s, iwork, size, MPI_INT, MPI_MAX, comm));
391:   PetscCall(PetscMalloc1(iwork[rank] + 1, &data2));
392:   PetscCall(PetscFree4(len_s, btable, iwork, Bowners));

394:   k = 0;
395:   while (k < nrqs) {
396:     /* Receive messages */
397:     PetscCallMPI(MPI_Iprobe(MPI_ANY_SOURCE, tag2, comm, &flag, &r_status));
398:     if (flag) {
399:       PetscCallMPI(MPI_Get_count(&r_status, MPIU_INT, &len));

401:       proc_id = r_status.MPI_SOURCE;

403:       PetscCallMPI(MPI_Irecv(data2, len, MPIU_INT, proc_id, r_status.MPI_TAG, comm, &r_req));
404:       PetscCallMPI(MPI_Wait(&r_req, &r_status));
405:       if (len > 1 + is_max) { /* Add data2 into data */
406:         data2_i = data2 + 1 + is_max;
407:         for (i = 0; i < is_max; i++) {
408:           table_i = table[i];
409:           data_i  = data + 1 + is_max + Mbs * i;
410:           isz     = data[1 + i];
411:           for (j = 0; j < data2[1 + i]; j++) {
412:             col = data2_i[j];
413:             if (!PetscBTLookupSet(table_i, col)) data_i[isz++] = col;
414:           }
415:           data[1 + i] = isz;
416:           if (i < is_max - 1) data2_i += data2[1 + i];
417:         }
418:       }
419:       k++;
420:     }
421:   }
422:   PetscCall(PetscFree(data2));
423:   PetscCall(PetscFree2(table, t_p));

425:   /* phase 1 sends are complete */
426:   PetscCall(PetscMalloc1(size, &s_status));
427:   if (nrqs) PetscCallMPI(MPI_Waitall(nrqs, s_waits1, s_status));
428:   PetscCall(PetscFree(data1));

430:   /* phase 2 sends are complete */
431:   if (nrqr) PetscCallMPI(MPI_Waitall(nrqr, s_waits2, s_status));
432:   PetscCall(PetscFree2(s_waits1, s_waits2));
433:   PetscCall(PetscFree(s_status));

435:   /* 5. Create new is[] */
436:   for (i = 0; i < is_max; i++) {
437:     data_i = data + 1 + is_max + Mbs * i;
438:     PetscCall(ISCreateGeneral(PETSC_COMM_SELF, data[1 + i], data_i, PETSC_COPY_VALUES, is + i));
439:   }
440:   for (k = 0; k <= nodata2; k++) PetscCall(PetscFree(odata2_ptr[k]));
441:   PetscCall(PetscFree(odata2_ptr));
442:   PetscFunctionReturn(PETSC_SUCCESS);
443: }

445: /*
446:    MatIncreaseOverlap_MPISBAIJ_Local - Called by MatIncreaseOverlap, to do
447:        the work on the local processor.

449:      Inputs:
450:       C      - MAT_MPISBAIJ;
451:       data   - holds is[]. See MatIncreaseOverlap_MPISBAIJ_Once() for the format.
452:       whose  - whose is[] to be processed,
453:                MINE:  this processor's is[]
454:                OTHER: other processor's is[]
455:      Output:
456:        nidx  - whose = MINE:
457:                      holds input and newly found indices in the same format as data
458:                whose = OTHER:
459:                      only holds the newly found indices
460:        table - table[i]: mark the indices of is[i], i=0,...,is_max. Used only in the case 'whose=MINE'.
461: */
462: /* Would computation be reduced by swapping the loop 'for each is' and 'for each row'? */
463: static PetscErrorCode MatIncreaseOverlap_MPISBAIJ_Local(Mat C, PetscInt *data, PetscInt whose, PetscInt *nidx, PetscBT *table)
464: {
465:   Mat_MPISBAIJ *c = (Mat_MPISBAIJ *)C->data;
466:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ *)c->A->data;
467:   Mat_SeqBAIJ  *b = (Mat_SeqBAIJ *)c->B->data;
468:   PetscInt      row, mbs, Mbs, *nidx_i, col, col_max, isz, isz0, *ai, *aj, *bi, *bj, *garray, rstart, l;
469:   PetscInt      a_start, a_end, b_start, b_end, i, j, k, is_max, *idx_i, n;
470:   PetscBT       table0;  /* mark the indices of input is[] for look up */
471:   PetscBT       table_i; /* points to i-th table. When whose=OTHER, a single table is used for all is[] */

473:   PetscFunctionBegin;
474:   Mbs    = c->Mbs;
475:   mbs    = a->mbs;
476:   ai     = a->i;
477:   aj     = a->j;
478:   bi     = b->i;
479:   bj     = b->j;
480:   garray = c->garray;
481:   rstart = c->rstartbs;
482:   is_max = data[0];

484:   PetscCall(PetscBTCreate(Mbs, &table0));

486:   nidx[0] = is_max;
487:   idx_i   = data + is_max + 1;   /* ptr to input is[0] array */
488:   nidx_i  = nidx + is_max + 1;   /* ptr to output is[0] array */
489:   for (i = 0; i < is_max; i++) { /* for each is */
490:     isz = 0;
491:     n   = data[1 + i]; /* size of input is[i] */

493:     /* initialize and set table_i(mark idx and nidx) and table0(only mark idx) */
494:     if (whose == MINE) { /* process this processor's is[] */
495:       table_i = table[i];
496:       nidx_i  = nidx + 1 + is_max + Mbs * i;
497:     } else { /* process other processor's is[] - only use one temp table */
498:       table_i = table[0];
499:     }
500:     PetscCall(PetscBTMemzero(Mbs, table_i));
501:     PetscCall(PetscBTMemzero(Mbs, table0));
502:     if (n == 0) {
503:       nidx[1 + i] = 0; /* size of new is[i] */
504:       continue;
505:     }

507:     isz0    = 0;
508:     col_max = 0;
509:     for (j = 0; j < n; j++) {
510:       col = idx_i[j];
511:       PetscCheck(col < Mbs, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "index col %" PetscInt_FMT " >= Mbs %" PetscInt_FMT, col, Mbs);
512:       if (!PetscBTLookupSet(table_i, col)) {
513:         PetscCall(PetscBTSet(table0, col));
514:         if (whose == MINE) nidx_i[isz0] = col;
515:         if (col_max < col) col_max = col;
516:         isz0++;
517:       }
518:     }

520:     if (whose == MINE) isz = isz0;
521:     k = 0; /* no. of indices from input is[i] that have been examined */
522:     for (row = 0; row < mbs; row++) {
523:       a_start = ai[row];
524:       a_end   = ai[row + 1];
525:       b_start = bi[row];
526:       b_end   = bi[row + 1];
527:       if (PetscBTLookup(table0, row + rstart)) { /* row is on input is[i]:
528:                                                 do row search: collect all col in this row */
529:         for (l = a_start; l < a_end; l++) {      /* Amat */
530:           col = aj[l] + rstart;
531:           if (!PetscBTLookupSet(table_i, col)) nidx_i[isz++] = col;
532:         }
533:         for (l = b_start; l < b_end; l++) { /* Bmat */
534:           col = garray[bj[l]];
535:           if (!PetscBTLookupSet(table_i, col)) nidx_i[isz++] = col;
536:         }
537:         k++;
538:         if (k >= isz0) break;               /* for (row=0; row<mbs; row++) */
539:       } else {                              /* row is not on input is[i]:
540:                   do col search: add row onto nidx_i if there is a col in nidx_i */
541:         for (l = a_start; l < a_end; l++) { /* Amat */
542:           col = aj[l] + rstart;
543:           if (col > col_max) break;
544:           if (PetscBTLookup(table0, col)) {
545:             if (!PetscBTLookupSet(table_i, row + rstart)) nidx_i[isz++] = row + rstart;
546:             break; /* for l = start; l<end ; l++) */
547:           }
548:         }
549:         for (l = b_start; l < b_end; l++) { /* Bmat */
550:           col = garray[bj[l]];
551:           if (col > col_max) break;
552:           if (PetscBTLookup(table0, col)) {
553:             if (!PetscBTLookupSet(table_i, row + rstart)) nidx_i[isz++] = row + rstart;
554:             break; /* for l = start; l<end ; l++) */
555:           }
556:         }
557:       }
558:     }

560:     if (i < is_max - 1) {
561:       idx_i += n;    /* ptr to input is[i+1] array */
562:       nidx_i += isz; /* ptr to output is[i+1] array */
563:     }
564:     nidx[1 + i] = isz; /* size of new is[i] */
565:   } /* for each is */
566:   PetscCall(PetscBTDestroy(&table0));
567:   PetscFunctionReturn(PETSC_SUCCESS);
568: }