Actual source code: sbaijov.c


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

111:           /* create updated is_new */
112:           PetscCall(ISCreateGeneral(PETSC_COMM_SELF, isz, nidx, PETSC_COPY_VALUES, is_new + i));
113:         }

115:         /* Free tmp spaces */
116:         for (i = 0; i < is_max; i++) PetscCall(MatDestroy(&submats[i]));
117:       }

119:       PetscCall(PetscBTDestroy(&table));
120:       PetscCall(PetscFree(submats));
121:       PetscCall(ISDestroy(&is_row[0]));
122:       PetscCall(PetscFree(is_row));
123:       PetscCall(PetscFree(nidx));
124:     }
125:   }
126:   for (i = 0; i < is_max; i++) {
127:     PetscCall(ISDestroy(&is[i]));
128:     PetscCall(ISGetLocalSize(is_new[i], &nis));
129:     PetscCall(ISGetIndices(is_new[i], &idx));
130:     PetscCall(ISCreateBlock(PetscObjectComm((PetscObject)is_new[i]), bs, nis, idx, PETSC_COPY_VALUES, &is[i]));
131:     PetscCall(ISDestroy(&is_new[i]));
132:   }
133:   PetscCall(PetscFree(is_new));
134:   PetscFunctionReturn(PETSC_SUCCESS);
135: }

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

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

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

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

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

199:   /* 1. Send this processor's is[] to other processors */
200:   /* allocate spaces */
201:   PetscCall(PetscMalloc1(is_max, &n));
202:   len = 0;
203:   for (i = 0; i < is_max; i++) {
204:     PetscCall(ISGetLocalSize(is[i], &n[i]));
205:     len += n[i];
206:   }
207:   if (!len) {
208:     is_max = 0;
209:   } else {
210:     len += 1 + is_max; /* max length of data1 for one processor */
211:   }

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

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

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

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

228:   if (is_max) {
229:     /* hash table ctable which maps c->row to proc_id) */
230:     PetscCall(PetscMalloc1(Mbs, &ctable));
231:     for (proc_id = 0, j = 0; proc_id < size; proc_id++) {
232:       for (; j < C->rmap->range[proc_id + 1] / bs; j++) ctable[j] = proc_id;
233:     }

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

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

251:   /* header of data1 */
252:   for (proc_id = 0; proc_id < size; proc_id++) {
253:     iwork[proc_id]        = 0;
254:     *data1_start[proc_id] = is_max;
255:     data1_start[proc_id]++;
256:     for (j = 0; j < is_max; j++) {
257:       if (proc_id == rank) {
258:         *data1_start[proc_id] = n[j];
259:       } else {
260:         *data1_start[proc_id] = 0;
261:       }
262:       data1_start[proc_id]++;
263:     }
264:   }

266:   for (i = 0; i < is_max; i++) {
267:     PetscCall(ISGetIndices(is[i], &idx_i));
268:     for (j = 0; j < n[i]; j++) {
269:       idx                = idx_i[j];
270:       *data1_start[rank] = idx;
271:       data1_start[rank]++; /* for local processing */
272:       proc_end = ctable[idx];
273:       for (proc_id = 0; proc_id <= proc_end; proc_id++) {                        /* for others to process */
274:         if (proc_id == rank) continue;                                           /* done before this loop */
275:         if (proc_id < proc_end && !PetscBTLookup(table[proc_id], idx)) continue; /* no need for sending idx to [proc_id] */
276:         *data1_start[proc_id] = idx;
277:         data1_start[proc_id]++;
278:         len_s[proc_id]++;
279:       }
280:     }
281:     /* update header data */
282:     for (proc_id = 0; proc_id < size; proc_id++) {
283:       if (proc_id == rank) continue;
284:       *(data1 + proc_id * len + 1 + i) = len_s[proc_id] - iwork[proc_id];
285:       iwork[proc_id]                   = len_s[proc_id];
286:     }
287:     PetscCall(ISRestoreIndices(is[i], &idx_i));
288:   }

290:   nrqs = 0;
291:   nrqr = 0;
292:   for (i = 0; i < size; i++) {
293:     data1_start[i] = data1 + i * len;
294:     if (len_s[i]) {
295:       nrqs++;
296:       len_s[i] += 1 + is_max; /* add no. of header msg */
297:     }
298:   }

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

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

308:   /*  Now  post the sends */
309:   PetscCall(PetscMalloc2(size, &s_waits1, size, &s_waits2));
310:   k = 0;
311:   for (proc_id = 0; proc_id < size; proc_id++) { /* send data1 to processor [proc_id] */
312:     if (len_s[proc_id]) {
313:       PetscCallMPI(MPI_Isend(data1_start[proc_id], len_s[proc_id], MPIU_INT, proc_id, tag1, comm, s_waits1 + k));
314:       k++;
315:     }
316:   }

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

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

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

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

337:   odata2_ptr[nodata2] = odata2;

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

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

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

356:         odata2_ptr[++nodata2] = odata2;

358:         len_unused = len_est;
359:       }

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

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

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

382:     odata2_ptr[++nodata2] = odata2;
383:   }

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

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

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

402:       proc_id = r_status.MPI_SOURCE;

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

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

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

436:   /* 5. Create new is[] */
437:   for (i = 0; i < is_max; i++) {
438:     data_i = data + 1 + is_max + Mbs * i;
439:     PetscCall(ISCreateGeneral(PETSC_COMM_SELF, data[1 + i], data_i, PETSC_COPY_VALUES, is + i));
440:   }
441:   for (k = 0; k <= nodata2; k++) PetscCall(PetscFree(odata2_ptr[k]));
442:   PetscCall(PetscFree(odata2_ptr));
443:   PetscFunctionReturn(PETSC_SUCCESS);
444: }

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

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

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

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

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

494:     /* initialize and set table_i(mark idx and nidx) and table0(only mark idx) */
495:     if (whose == MINE) { /* process this processor's is[] */
496:       table_i = table[i];
497:       nidx_i  = nidx + 1 + is_max + Mbs * i;
498:     } else { /* process other processor's is[] - only use one temp table */
499:       table_i = table[0];
500:     }
501:     PetscCall(PetscBTMemzero(Mbs, table_i));
502:     PetscCall(PetscBTMemzero(Mbs, table0));
503:     if (n == 0) {
504:       nidx[1 + i] = 0; /* size of new is[i] */
505:       continue;
506:     }

508:     isz0    = 0;
509:     col_max = 0;
510:     for (j = 0; j < n; j++) {
511:       col = idx_i[j];
512:       PetscCheck(col < Mbs, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "index col %" PetscInt_FMT " >= Mbs %" PetscInt_FMT, col, Mbs);
513:       if (!PetscBTLookupSet(table_i, col)) {
514:         PetscCall(PetscBTSet(table0, col));
515:         if (whose == MINE) nidx_i[isz0] = col;
516:         if (col_max < col) col_max = col;
517:         isz0++;
518:       }
519:     }

521:     if (whose == MINE) isz = isz0;
522:     k = 0; /* no. of indices from input is[i] that have been examined */
523:     for (row = 0; row < mbs; row++) {
524:       a_start = ai[row];
525:       a_end   = ai[row + 1];
526:       b_start = bi[row];
527:       b_end   = bi[row + 1];
528:       if (PetscBTLookup(table0, row + rstart)) { /* row is on input is[i]:
529:                                                 do row search: collect all col in this row */
530:         for (l = a_start; l < a_end; l++) {      /* Amat */
531:           col = aj[l] + rstart;
532:           if (!PetscBTLookupSet(table_i, col)) nidx_i[isz++] = col;
533:         }
534:         for (l = b_start; l < b_end; l++) { /* Bmat */
535:           col = garray[bj[l]];
536:           if (!PetscBTLookupSet(table_i, col)) nidx_i[isz++] = col;
537:         }
538:         k++;
539:         if (k >= isz0) break;               /* for (row=0; row<mbs; row++) */
540:       } else {                              /* row is not on input is[i]:
541:                   do col search: add row onto nidx_i if there is a col in nidx_i */
542:         for (l = a_start; l < a_end; l++) { /* Amat */
543:           col = aj[l] + rstart;
544:           if (col > col_max) break;
545:           if (PetscBTLookup(table0, col)) {
546:             if (!PetscBTLookupSet(table_i, row + rstart)) nidx_i[isz++] = row + rstart;
547:             break; /* for l = start; l<end ; l++) */
548:           }
549:         }
550:         for (l = b_start; l < b_end; l++) { /* Bmat */
551:           col = garray[bj[l]];
552:           if (col > col_max) break;
553:           if (PetscBTLookup(table0, col)) {
554:             if (!PetscBTLookupSet(table_i, row + rstart)) nidx_i[isz++] = row + rstart;
555:             break; /* for l = start; l<end ; l++) */
556:           }
557:         }
558:       }
559:     }

561:     if (i < is_max - 1) {
562:       idx_i += n;    /* ptr to input is[i+1] array */
563:       nidx_i += isz; /* ptr to output is[i+1] array */
564:     }
565:     nidx[1 + i] = isz; /* size of new is[i] */
566:   }                    /* for each is */
567:   PetscCall(PetscBTDestroy(&table0));
568:   PetscFunctionReturn(PETSC_SUCCESS);
569: }