Actual source code: baijov.c
1: /*
2: Routines to compute overlapping regions of a parallel MPI matrix
3: and to find submatrices that were shared across processors.
4: */
5: #include <../src/mat/impls/baij/mpi/mpibaij.h>
6: #include <petscbt.h>
8: static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Local(Mat, PetscInt, char **, PetscInt *, PetscInt **);
9: static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Receive(Mat, PetscInt, PetscInt **, PetscInt **, PetscInt *);
10: extern PetscErrorCode MatGetRow_MPIBAIJ(Mat, PetscInt, PetscInt *, PetscInt **, PetscScalar **);
11: extern PetscErrorCode MatRestoreRow_MPIBAIJ(Mat, PetscInt, PetscInt *, PetscInt **, PetscScalar **);
13: PetscErrorCode MatIncreaseOverlap_MPIBAIJ(Mat C, PetscInt imax, IS is[], PetscInt ov)
14: {
15: PetscInt i, N = C->cmap->N, bs = C->rmap->bs, n;
16: const PetscInt *idx;
17: IS *is_new;
19: PetscFunctionBegin;
20: PetscCall(PetscMalloc1(imax, &is_new));
21: /* Convert the indices into block format */
22: PetscCall(ISCompressIndicesGeneral(N, C->rmap->n, bs, imax, is, is_new));
23: PetscCheck(ov >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Negative overlap specified");
24: for (i = 0; i < ov; ++i) PetscCall(MatIncreaseOverlap_MPIBAIJ_Once(C, imax, is_new));
25: for (i = 0; i < imax; i++) {
26: PetscCall(ISDestroy(&is[i]));
27: PetscCall(ISGetLocalSize(is_new[i], &n));
28: PetscCall(ISGetIndices(is_new[i], &idx));
29: PetscCall(ISCreateBlock(PetscObjectComm((PetscObject)is_new[i]), bs, n, idx, PETSC_COPY_VALUES, &is[i]));
30: PetscCall(ISDestroy(&is_new[i]));
31: }
32: PetscCall(PetscFree(is_new));
33: PetscFunctionReturn(PETSC_SUCCESS);
34: }
36: /*
37: Sample message format:
38: If a processor A wants processor B to process some elements corresponding
39: to index sets is[1], is[5]
40: mesg [0] = 2 (no of index sets in the mesg)
41: -----------
42: mesg [1] = 1 => is[1]
43: mesg [2] = sizeof(is[1]);
44: -----------
45: mesg [5] = 5 => is[5]
46: mesg [6] = sizeof(is[5]);
47: -----------
48: mesg [7]
49: mesg [n] data(is[1])
50: -----------
51: mesg[n+1]
52: mesg[m] data(is[5])
53: -----------
55: Notes:
56: nrqs - no of requests sent (or to be sent out)
57: nrqr - no of requests received (which have to be or which have been processed)
58: */
59: PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Once(Mat C, PetscInt imax, IS is[])
60: {
61: Mat_MPIBAIJ *c = (Mat_MPIBAIJ *)C->data;
62: const PetscInt **idx, *idx_i;
63: PetscInt *n, *w3, *w4, **data, len;
64: PetscMPIInt size, rank, tag1, tag2, *w2, *w1, nrqr;
65: PetscInt Mbs, i, j, k, **rbuf, row, nrqs, msz, **outdat, **ptr;
66: PetscInt *ctr, *pa, *tmp, *isz, *isz1, **xdata, **rbuf2, *d_p;
67: PetscMPIInt *onodes1, *olengths1, *onodes2, *olengths2, proc = -1;
68: PetscBT *table;
69: MPI_Comm comm, *iscomms;
70: MPI_Request *s_waits1, *r_waits1, *s_waits2, *r_waits2;
71: char *t_p;
73: PetscFunctionBegin;
74: PetscCall(PetscObjectGetComm((PetscObject)C, &comm));
75: size = c->size;
76: rank = c->rank;
77: Mbs = c->Mbs;
79: PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag1));
80: PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag2));
82: PetscCall(PetscMalloc2(imax, (PetscInt ***)&idx, imax, &n));
84: for (i = 0; i < imax; i++) {
85: PetscCall(ISGetIndices(is[i], &idx[i]));
86: PetscCall(ISGetLocalSize(is[i], &n[i]));
87: }
89: /* evaluate communication - mesg to who,length of mesg, and buffer space
90: required. Based on this, buffers are allocated, and data copied into them*/
91: PetscCall(PetscCalloc4(size, &w1, size, &w2, size, &w3, size, &w4));
92: for (i = 0; i < imax; i++) {
93: PetscCall(PetscArrayzero(w4, size)); /* initialise work vector*/
94: idx_i = idx[i];
95: len = n[i];
96: for (j = 0; j < len; j++) {
97: row = idx_i[j];
98: PetscCheck(row >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Index set cannot have negative entries");
99: PetscCall(PetscLayoutFindOwner(C->rmap, row * C->rmap->bs, &proc));
100: w4[proc]++;
101: }
102: for (j = 0; j < size; j++) {
103: if (w4[j]) {
104: w1[j] += w4[j];
105: w3[j]++;
106: }
107: }
108: }
110: nrqs = 0; /* no of outgoing messages */
111: msz = 0; /* total mesg length (for all proc */
112: w1[rank] = 0; /* no mesg sent to itself */
113: w3[rank] = 0;
114: for (i = 0; i < size; i++) {
115: if (w1[i]) {
116: w2[i] = 1;
117: nrqs++;
118: } /* there exists a message to proc i */
119: }
120: /* pa - is list of processors to communicate with */
121: PetscCall(PetscMalloc1(nrqs, &pa));
122: for (i = 0, j = 0; i < size; i++) {
123: if (w1[i]) {
124: pa[j] = i;
125: j++;
126: }
127: }
129: /* Each message would have a header = 1 + 2*(no of IS) + data */
130: for (i = 0; i < nrqs; i++) {
131: j = pa[i];
132: w1[j] += w2[j] + 2 * w3[j];
133: msz += w1[j];
134: }
136: /* Determine the number of messages to expect, their lengths, from from-ids */
137: PetscCall(PetscGatherNumberOfMessages(comm, w2, w1, &nrqr));
138: PetscCall(PetscGatherMessageLengths(comm, nrqs, nrqr, w1, &onodes1, &olengths1));
140: /* Now post the Irecvs corresponding to these messages */
141: PetscCall(PetscPostIrecvInt(comm, tag1, nrqr, onodes1, olengths1, &rbuf, &r_waits1));
143: /* Allocate Memory for outgoing messages */
144: PetscCall(PetscMalloc4(size, &outdat, size, &ptr, msz, &tmp, size, &ctr));
145: PetscCall(PetscArrayzero(outdat, size));
146: PetscCall(PetscArrayzero(ptr, size));
147: {
148: PetscInt *iptr = tmp, ict = 0;
149: for (i = 0; i < nrqs; i++) {
150: j = pa[i];
151: iptr += ict;
152: outdat[j] = iptr;
153: ict = w1[j];
154: }
155: }
157: /* Form the outgoing messages */
158: /*plug in the headers*/
159: for (i = 0; i < nrqs; i++) {
160: j = pa[i];
161: outdat[j][0] = 0;
162: PetscCall(PetscArrayzero(outdat[j] + 1, 2 * w3[j]));
163: ptr[j] = outdat[j] + 2 * w3[j] + 1;
164: }
166: /* Memory for doing local proc's work*/
167: {
168: PetscCall(PetscCalloc5(imax, &table, imax, &data, imax, &isz, Mbs * imax, &d_p, (Mbs / PETSC_BITS_PER_BYTE + 1) * imax, &t_p));
170: for (i = 0; i < imax; i++) {
171: table[i] = t_p + (Mbs / PETSC_BITS_PER_BYTE + 1) * i;
172: data[i] = d_p + (Mbs)*i;
173: }
174: }
176: /* Parse the IS and update local tables and the outgoing buf with the data*/
177: {
178: PetscInt n_i, *data_i, isz_i, *outdat_j, ctr_j;
179: PetscBT table_i;
181: for (i = 0; i < imax; i++) {
182: PetscCall(PetscArrayzero(ctr, size));
183: n_i = n[i];
184: table_i = table[i];
185: idx_i = idx[i];
186: data_i = data[i];
187: isz_i = isz[i];
188: for (j = 0; j < n_i; j++) { /* parse the indices of each IS */
189: row = idx_i[j];
190: PetscCall(PetscLayoutFindOwner(C->rmap, row * C->rmap->bs, &proc));
191: if (proc != rank) { /* copy to the outgoing buffer */
192: ctr[proc]++;
193: *ptr[proc] = row;
194: ptr[proc]++;
195: } else { /* Update the local table */
196: if (!PetscBTLookupSet(table_i, row)) data_i[isz_i++] = row;
197: }
198: }
199: /* Update the headers for the current IS */
200: for (j = 0; j < size; j++) { /* Can Optimise this loop by using pa[] */
201: if ((ctr_j = ctr[j])) {
202: outdat_j = outdat[j];
203: k = ++outdat_j[0];
204: outdat_j[2 * k] = ctr_j;
205: outdat_j[2 * k - 1] = i;
206: }
207: }
208: isz[i] = isz_i;
209: }
210: }
212: /* Now post the sends */
213: PetscCall(PetscMalloc1(nrqs, &s_waits1));
214: for (i = 0; i < nrqs; ++i) {
215: j = pa[i];
216: PetscCallMPI(MPI_Isend(outdat[j], w1[j], MPIU_INT, j, tag1, comm, s_waits1 + i));
217: }
219: /* No longer need the original indices*/
220: for (i = 0; i < imax; ++i) PetscCall(ISRestoreIndices(is[i], idx + i));
221: PetscCall(PetscFree2(*(PetscInt ***)&idx, n));
223: PetscCall(PetscMalloc1(imax, &iscomms));
224: for (i = 0; i < imax; ++i) {
225: PetscCall(PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]), &iscomms[i], NULL));
226: PetscCall(ISDestroy(&is[i]));
227: }
229: /* Do Local work*/
230: PetscCall(MatIncreaseOverlap_MPIBAIJ_Local(C, imax, table, isz, data));
232: /* Receive messages*/
233: PetscCallMPI(MPI_Waitall(nrqr, r_waits1, MPI_STATUSES_IGNORE));
234: PetscCallMPI(MPI_Waitall(nrqs, s_waits1, MPI_STATUSES_IGNORE));
236: /* Phase 1 sends are complete - deallocate buffers */
237: PetscCall(PetscFree4(outdat, ptr, tmp, ctr));
238: PetscCall(PetscFree4(w1, w2, w3, w4));
240: PetscCall(PetscMalloc1(nrqr, &xdata));
241: PetscCall(PetscMalloc1(nrqr, &isz1));
242: PetscCall(MatIncreaseOverlap_MPIBAIJ_Receive(C, nrqr, rbuf, xdata, isz1));
243: if (rbuf) {
244: PetscCall(PetscFree(rbuf[0]));
245: PetscCall(PetscFree(rbuf));
246: }
248: /* Send the data back*/
249: /* Do a global reduction to know the buffer space req for incoming messages*/
250: {
251: PetscMPIInt *rw1;
253: PetscCall(PetscCalloc1(size, &rw1));
255: for (i = 0; i < nrqr; ++i) {
256: proc = onodes1[i];
257: rw1[proc] = isz1[i];
258: }
260: /* Determine the number of messages to expect, their lengths, from from-ids */
261: PetscCall(PetscGatherMessageLengths(comm, nrqr, nrqs, rw1, &onodes2, &olengths2));
262: PetscCall(PetscFree(rw1));
263: }
264: /* Now post the Irecvs corresponding to these messages */
265: PetscCall(PetscPostIrecvInt(comm, tag2, nrqs, onodes2, olengths2, &rbuf2, &r_waits2));
267: /* Now post the sends */
268: PetscCall(PetscMalloc1(nrqr, &s_waits2));
269: for (i = 0; i < nrqr; ++i) {
270: j = onodes1[i];
271: PetscCallMPI(MPI_Isend(xdata[i], isz1[i], MPIU_INT, j, tag2, comm, s_waits2 + i));
272: }
274: PetscCall(PetscFree(onodes1));
275: PetscCall(PetscFree(olengths1));
277: /* receive work done on other processors*/
278: {
279: PetscMPIInt idex;
280: PetscInt is_no, ct1, max, *rbuf2_i, isz_i, *data_i, jmax;
281: PetscBT table_i;
283: for (i = 0; i < nrqs; ++i) {
284: PetscCallMPI(MPI_Waitany(nrqs, r_waits2, &idex, MPI_STATUS_IGNORE));
285: /* Process the message*/
286: rbuf2_i = rbuf2[idex];
287: ct1 = 2 * rbuf2_i[0] + 1;
288: jmax = rbuf2[idex][0];
289: for (j = 1; j <= jmax; j++) {
290: max = rbuf2_i[2 * j];
291: is_no = rbuf2_i[2 * j - 1];
292: isz_i = isz[is_no];
293: data_i = data[is_no];
294: table_i = table[is_no];
295: for (k = 0; k < max; k++, ct1++) {
296: row = rbuf2_i[ct1];
297: if (!PetscBTLookupSet(table_i, row)) data_i[isz_i++] = row;
298: }
299: isz[is_no] = isz_i;
300: }
301: }
302: PetscCallMPI(MPI_Waitall(nrqr, s_waits2, MPI_STATUSES_IGNORE));
303: }
305: for (i = 0; i < imax; ++i) {
306: PetscCall(ISCreateGeneral(iscomms[i], isz[i], data[i], PETSC_COPY_VALUES, is + i));
307: PetscCall(PetscCommDestroy(&iscomms[i]));
308: }
310: PetscCall(PetscFree(iscomms));
311: PetscCall(PetscFree(onodes2));
312: PetscCall(PetscFree(olengths2));
314: PetscCall(PetscFree(pa));
315: if (rbuf2) {
316: PetscCall(PetscFree(rbuf2[0]));
317: PetscCall(PetscFree(rbuf2));
318: }
319: PetscCall(PetscFree(s_waits1));
320: PetscCall(PetscFree(r_waits1));
321: PetscCall(PetscFree(s_waits2));
322: PetscCall(PetscFree(r_waits2));
323: PetscCall(PetscFree5(table, data, isz, d_p, t_p));
324: if (xdata) {
325: PetscCall(PetscFree(xdata[0]));
326: PetscCall(PetscFree(xdata));
327: }
328: PetscCall(PetscFree(isz1));
329: PetscFunctionReturn(PETSC_SUCCESS);
330: }
332: /*
333: MatIncreaseOverlap_MPIBAIJ_Local - Called by MatincreaseOverlap, to do
334: the work on the local processor.
336: Inputs:
337: C - MAT_MPIBAIJ;
338: imax - total no of index sets processed at a time;
339: table - an array of char - size = Mbs bits.
341: Output:
342: isz - array containing the count of the solution elements corresponding
343: to each index set;
344: data - pointer to the solutions
345: */
346: static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Local(Mat C, PetscInt imax, PetscBT *table, PetscInt *isz, PetscInt **data)
347: {
348: Mat_MPIBAIJ *c = (Mat_MPIBAIJ *)C->data;
349: Mat A = c->A, B = c->B;
350: Mat_SeqBAIJ *a = (Mat_SeqBAIJ *)A->data, *b = (Mat_SeqBAIJ *)B->data;
351: PetscInt start, end, val, max, rstart, cstart, *ai, *aj;
352: PetscInt *bi, *bj, *garray, i, j, k, row, *data_i, isz_i;
353: PetscBT table_i;
355: PetscFunctionBegin;
356: rstart = c->rstartbs;
357: cstart = c->cstartbs;
358: ai = a->i;
359: aj = a->j;
360: bi = b->i;
361: bj = b->j;
362: garray = c->garray;
364: for (i = 0; i < imax; i++) {
365: data_i = data[i];
366: table_i = table[i];
367: isz_i = isz[i];
368: for (j = 0, max = isz[i]; j < max; j++) {
369: row = data_i[j] - rstart;
370: start = ai[row];
371: end = ai[row + 1];
372: for (k = start; k < end; k++) { /* Amat */
373: val = aj[k] + cstart;
374: if (!PetscBTLookupSet(table_i, val)) data_i[isz_i++] = val;
375: }
376: start = bi[row];
377: end = bi[row + 1];
378: for (k = start; k < end; k++) { /* Bmat */
379: val = garray[bj[k]];
380: if (!PetscBTLookupSet(table_i, val)) data_i[isz_i++] = val;
381: }
382: }
383: isz[i] = isz_i;
384: }
385: PetscFunctionReturn(PETSC_SUCCESS);
386: }
387: /*
388: MatIncreaseOverlap_MPIBAIJ_Receive - Process the received messages,
389: and return the output
391: Input:
392: C - the matrix
393: nrqr - no of messages being processed.
394: rbuf - an array of pointers to the received requests
396: Output:
397: xdata - array of messages to be sent back
398: isz1 - size of each message
400: For better efficiency perhaps we should malloc separately each xdata[i],
401: then if a remalloc is required we need only copy the data for that one row
402: rather than all previous rows as it is now where a single large chunk of
403: memory is used.
405: */
406: static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Receive(Mat C, PetscInt nrqr, PetscInt **rbuf, PetscInt **xdata, PetscInt *isz1)
407: {
408: Mat_MPIBAIJ *c = (Mat_MPIBAIJ *)C->data;
409: Mat A = c->A, B = c->B;
410: Mat_SeqBAIJ *a = (Mat_SeqBAIJ *)A->data, *b = (Mat_SeqBAIJ *)B->data;
411: PetscInt rstart, cstart, *ai, *aj, *bi, *bj, *garray, i, j, k;
412: PetscInt row, total_sz, ct, ct1, ct2, ct3, mem_estimate, oct2, l, start, end;
413: PetscInt val, max1, max2, Mbs, no_malloc = 0, *tmp, new_estimate, ctr;
414: PetscInt *rbuf_i, kmax, rbuf_0;
415: PetscBT xtable;
417: PetscFunctionBegin;
418: Mbs = c->Mbs;
419: rstart = c->rstartbs;
420: cstart = c->cstartbs;
421: ai = a->i;
422: aj = a->j;
423: bi = b->i;
424: bj = b->j;
425: garray = c->garray;
427: for (i = 0, ct = 0, total_sz = 0; i < nrqr; ++i) {
428: rbuf_i = rbuf[i];
429: rbuf_0 = rbuf_i[0];
430: ct += rbuf_0;
431: for (j = 1; j <= rbuf_0; j++) total_sz += rbuf_i[2 * j];
432: }
434: if (c->Mbs) max1 = ct * (a->nz + b->nz) / c->Mbs;
435: else max1 = 1;
436: mem_estimate = 3 * ((total_sz > max1 ? total_sz : max1) + 1);
437: if (nrqr) {
438: PetscCall(PetscMalloc1(mem_estimate, &xdata[0]));
439: ++no_malloc;
440: }
441: PetscCall(PetscBTCreate(Mbs, &xtable));
442: PetscCall(PetscArrayzero(isz1, nrqr));
444: ct3 = 0;
445: for (i = 0; i < nrqr; i++) { /* for easch mesg from proc i */
446: rbuf_i = rbuf[i];
447: rbuf_0 = rbuf_i[0];
448: ct1 = 2 * rbuf_0 + 1;
449: ct2 = ct1;
450: ct3 += ct1;
451: for (j = 1; j <= rbuf_0; j++) { /* for each IS from proc i*/
452: PetscCall(PetscBTMemzero(Mbs, xtable));
453: oct2 = ct2;
454: kmax = rbuf_i[2 * j];
455: for (k = 0; k < kmax; k++, ct1++) {
456: row = rbuf_i[ct1];
457: if (!PetscBTLookupSet(xtable, row)) {
458: if (!(ct3 < mem_estimate)) {
459: new_estimate = (PetscInt)(1.5 * mem_estimate) + 1;
460: PetscCall(PetscMalloc1(new_estimate, &tmp));
461: PetscCall(PetscArraycpy(tmp, xdata[0], mem_estimate));
462: PetscCall(PetscFree(xdata[0]));
463: xdata[0] = tmp;
464: mem_estimate = new_estimate;
465: ++no_malloc;
466: for (ctr = 1; ctr <= i; ctr++) xdata[ctr] = xdata[ctr - 1] + isz1[ctr - 1];
467: }
468: xdata[i][ct2++] = row;
469: ct3++;
470: }
471: }
472: for (k = oct2, max2 = ct2; k < max2; k++) {
473: row = xdata[i][k] - rstart;
474: start = ai[row];
475: end = ai[row + 1];
476: for (l = start; l < end; l++) {
477: val = aj[l] + cstart;
478: if (!PetscBTLookupSet(xtable, val)) {
479: if (!(ct3 < mem_estimate)) {
480: new_estimate = (PetscInt)(1.5 * mem_estimate) + 1;
481: PetscCall(PetscMalloc1(new_estimate, &tmp));
482: PetscCall(PetscArraycpy(tmp, xdata[0], mem_estimate));
483: PetscCall(PetscFree(xdata[0]));
484: xdata[0] = tmp;
485: mem_estimate = new_estimate;
486: ++no_malloc;
487: for (ctr = 1; ctr <= i; ctr++) xdata[ctr] = xdata[ctr - 1] + isz1[ctr - 1];
488: }
489: xdata[i][ct2++] = val;
490: ct3++;
491: }
492: }
493: start = bi[row];
494: end = bi[row + 1];
495: for (l = start; l < end; l++) {
496: val = garray[bj[l]];
497: if (!PetscBTLookupSet(xtable, val)) {
498: if (!(ct3 < mem_estimate)) {
499: new_estimate = (PetscInt)(1.5 * mem_estimate) + 1;
500: PetscCall(PetscMalloc1(new_estimate, &tmp));
501: PetscCall(PetscArraycpy(tmp, xdata[0], mem_estimate));
502: PetscCall(PetscFree(xdata[0]));
503: xdata[0] = tmp;
504: mem_estimate = new_estimate;
505: ++no_malloc;
506: for (ctr = 1; ctr <= i; ctr++) xdata[ctr] = xdata[ctr - 1] + isz1[ctr - 1];
507: }
508: xdata[i][ct2++] = val;
509: ct3++;
510: }
511: }
512: }
513: /* Update the header*/
514: xdata[i][2 * j] = ct2 - oct2; /* Undo the vector isz1 and use only a var*/
515: xdata[i][2 * j - 1] = rbuf_i[2 * j - 1];
516: }
517: xdata[i][0] = rbuf_0;
518: if (i + 1 < nrqr) xdata[i + 1] = xdata[i] + ct2;
519: isz1[i] = ct2; /* size of each message */
520: }
521: PetscCall(PetscBTDestroy(&xtable));
522: PetscCall(PetscInfo(C, "Allocated %" PetscInt_FMT " bytes, required %" PetscInt_FMT ", no of mallocs = %" PetscInt_FMT "\n", mem_estimate, ct3, no_malloc));
523: PetscFunctionReturn(PETSC_SUCCESS);
524: }
526: PetscErrorCode MatCreateSubMatrices_MPIBAIJ(Mat C, PetscInt ismax, const IS isrow[], const IS iscol[], MatReuse scall, Mat *submat[])
527: {
528: IS *isrow_block, *iscol_block;
529: Mat_MPIBAIJ *c = (Mat_MPIBAIJ *)C->data;
530: PetscInt nmax, nstages_local, nstages, i, pos, max_no, N = C->cmap->N, bs = C->rmap->bs;
531: Mat_SeqBAIJ *subc;
532: Mat_SubSppt *smat;
533: PetscBool sym = PETSC_FALSE, flg[2];
535: PetscFunctionBegin;
536: PetscCall(PetscObjectTypeCompare((PetscObject)C, MATMPISBAIJ, flg));
537: if (flg[0]) {
538: if (isrow == iscol) sym = PETSC_TRUE;
539: else {
540: flg[0] = flg[1] = PETSC_TRUE;
541: for (i = 0; i < ismax; i++) {
542: if (isrow[i] != iscol[i]) flg[0] = PETSC_FALSE;
543: PetscCall(ISGetLocalSize(iscol[0], &nmax));
544: if (nmax == C->cmap->N && flg[1]) PetscCall(ISIdentity(iscol[0], flg + 1));
545: }
546: sym = (PetscBool)(flg[0] || flg[1]);
547: }
548: }
549: /* The compression and expansion should be avoided. Doesn't point
550: out errors, might change the indices, hence buggey */
551: PetscCall(PetscMalloc2(ismax, &isrow_block, ismax, &iscol_block));
552: PetscCall(ISCompressIndicesGeneral(C->rmap->N, C->rmap->n, bs, ismax, isrow, isrow_block));
553: if (isrow == iscol) {
554: for (i = 0; i < ismax; i++) {
555: iscol_block[i] = isrow_block[i];
556: PetscCall(PetscObjectReference((PetscObject)iscol_block[i]));
557: }
558: } else PetscCall(ISCompressIndicesGeneral(N, C->cmap->n, bs, ismax, iscol, iscol_block));
560: /* Determine the number of stages through which submatrices are done */
561: if (!C->cmap->N) nmax = 20 * 1000000 / sizeof(PetscInt);
562: else nmax = 20 * 1000000 / (c->Nbs * sizeof(PetscInt));
563: if (!nmax) nmax = 1;
565: if (scall == MAT_INITIAL_MATRIX) {
566: nstages_local = ismax / nmax + ((ismax % nmax) ? 1 : 0); /* local nstages */
568: /* Make sure every processor loops through the nstages */
569: PetscCall(MPIU_Allreduce(&nstages_local, &nstages, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)C)));
571: /* Allocate memory to hold all the submatrices and dummy submatrices */
572: PetscCall(PetscCalloc1(ismax + nstages, submat));
573: } else { /* MAT_REUSE_MATRIX */
574: if (ismax) {
575: subc = (Mat_SeqBAIJ *)((*submat)[0]->data);
576: smat = subc->submatis1;
577: } else { /* (*submat)[0] is a dummy matrix */
578: smat = (Mat_SubSppt *)(*submat)[0]->data;
579: }
580: PetscCheck(smat, PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "MatCreateSubMatrices(...,MAT_REUSE_MATRIX,...) requires submat");
581: nstages = smat->nstages;
582: }
584: for (i = 0, pos = 0; i < nstages; i++) {
585: if (pos + nmax <= ismax) max_no = nmax;
586: else if (pos >= ismax) max_no = 0;
587: else max_no = ismax - pos;
589: PetscCall(MatCreateSubMatrices_MPIBAIJ_local(C, max_no, isrow_block + pos, iscol_block + pos, scall, *submat + pos, sym));
590: if (!max_no) {
591: if (scall == MAT_INITIAL_MATRIX) { /* submat[pos] is a dummy matrix */
592: smat = (Mat_SubSppt *)(*submat)[pos]->data;
593: smat->nstages = nstages;
594: }
595: pos++; /* advance to next dummy matrix if any */
596: } else pos += max_no;
597: }
599: if (scall == MAT_INITIAL_MATRIX && ismax) {
600: /* save nstages for reuse */
601: subc = (Mat_SeqBAIJ *)((*submat)[0]->data);
602: smat = subc->submatis1;
603: smat->nstages = nstages;
604: }
606: for (i = 0; i < ismax; i++) {
607: PetscCall(ISDestroy(&isrow_block[i]));
608: PetscCall(ISDestroy(&iscol_block[i]));
609: }
610: PetscCall(PetscFree2(isrow_block, iscol_block));
611: PetscFunctionReturn(PETSC_SUCCESS);
612: }
614: /* This code is used for BAIJ and SBAIJ matrices (unfortunate dependency) */
615: PetscErrorCode MatCreateSubMatrices_MPIBAIJ_local(Mat C, PetscInt ismax, const IS isrow[], const IS iscol[], MatReuse scall, Mat *submats, PetscBool sym)
616: {
617: Mat_MPIBAIJ *c = (Mat_MPIBAIJ *)C->data;
618: Mat A = c->A;
619: Mat_SeqBAIJ *a = (Mat_SeqBAIJ *)A->data, *b = (Mat_SeqBAIJ *)c->B->data, *subc;
620: const PetscInt **icol, **irow;
621: PetscInt *nrow, *ncol, start;
622: PetscMPIInt rank, size, tag0, tag2, tag3, tag4, *w1, *w2, *w3, *w4, nrqr;
623: PetscInt **sbuf1, **sbuf2, *sbuf2_i, i, j, k, l, ct1, ct2, **rbuf1, row, proc = -1;
624: PetscInt nrqs = 0, msz, **ptr = NULL, *req_size = NULL, *ctr = NULL, *pa, *tmp = NULL, tcol;
625: PetscInt **rbuf3 = NULL, *req_source1 = NULL, *req_source2, **sbuf_aj, **rbuf2 = NULL, max1, max2;
626: PetscInt **lens, is_no, ncols, *cols, mat_i, *mat_j, tmp2, jmax;
627: #if defined(PETSC_USE_CTABLE)
628: PetscHMapI *cmap, cmap_i = NULL, *rmap, rmap_i;
629: #else
630: PetscInt **cmap, *cmap_i = NULL, **rmap, *rmap_i;
631: #endif
632: const PetscInt *irow_i, *icol_i;
633: PetscInt ctr_j, *sbuf1_j, *sbuf_aj_i, *rbuf1_i, kmax, *lens_i;
634: MPI_Request *s_waits1, *r_waits1, *s_waits2, *r_waits2, *r_waits3;
635: MPI_Request *r_waits4, *s_waits3, *s_waits4;
636: MPI_Comm comm;
637: PetscScalar **rbuf4, *rbuf4_i = NULL, **sbuf_aa, *vals, *mat_a = NULL, *imat_a = NULL, *sbuf_aa_i;
638: PetscMPIInt *onodes1, *olengths1, end;
639: PetscInt **row2proc, *row2proc_i, *imat_ilen, *imat_j, *imat_i;
640: Mat_SubSppt *smat_i;
641: PetscBool *issorted, colflag, iscsorted = PETSC_TRUE;
642: PetscInt *sbuf1_i, *rbuf2_i, *rbuf3_i, ilen;
643: PetscInt bs = C->rmap->bs, bs2 = c->bs2, rstart = c->rstartbs;
644: PetscBool ijonly = c->ijonly; /* private flag indicates only matrix data structures are requested */
645: PetscInt nzA, nzB, *a_i = a->i, *b_i = b->i, *a_j = a->j, *b_j = b->j, ctmp, imark, *cworkA, *cworkB;
646: PetscScalar *vworkA = NULL, *vworkB = NULL, *a_a = a->a, *b_a = b->a;
647: PetscInt cstart = c->cstartbs, *bmap = c->garray;
648: PetscBool *allrows, *allcolumns;
650: PetscFunctionBegin;
651: PetscCall(PetscObjectGetComm((PetscObject)C, &comm));
652: size = c->size;
653: rank = c->rank;
655: PetscCall(PetscMalloc5(ismax, &row2proc, ismax, &cmap, ismax, &rmap, ismax + 1, &allcolumns, ismax, &allrows));
656: PetscCall(PetscMalloc5(ismax, (PetscInt ***)&irow, ismax, (PetscInt ***)&icol, ismax, &nrow, ismax, &ncol, ismax, &issorted));
658: for (i = 0; i < ismax; i++) {
659: PetscCall(ISSorted(iscol[i], &issorted[i]));
660: if (!issorted[i]) iscsorted = issorted[i]; /* columns are not sorted! */
661: PetscCall(ISSorted(isrow[i], &issorted[i]));
663: /* Check for special case: allcolumns */
664: PetscCall(ISIdentity(iscol[i], &colflag));
665: PetscCall(ISGetLocalSize(iscol[i], &ncol[i]));
667: if (colflag && ncol[i] == c->Nbs) {
668: allcolumns[i] = PETSC_TRUE;
669: icol[i] = NULL;
670: } else {
671: allcolumns[i] = PETSC_FALSE;
672: PetscCall(ISGetIndices(iscol[i], &icol[i]));
673: }
675: /* Check for special case: allrows */
676: PetscCall(ISIdentity(isrow[i], &colflag));
677: PetscCall(ISGetLocalSize(isrow[i], &nrow[i]));
678: if (colflag && nrow[i] == c->Mbs) {
679: allrows[i] = PETSC_TRUE;
680: irow[i] = NULL;
681: } else {
682: allrows[i] = PETSC_FALSE;
683: PetscCall(ISGetIndices(isrow[i], &irow[i]));
684: }
685: }
687: if (scall == MAT_REUSE_MATRIX) {
688: /* Assumes new rows are same length as the old rows */
689: for (i = 0; i < ismax; i++) {
690: subc = (Mat_SeqBAIJ *)submats[i]->data;
691: PetscCheck(subc->mbs == nrow[i] && subc->nbs == ncol[i], PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Cannot reuse matrix. wrong size");
693: /* Initial matrix as if empty */
694: PetscCall(PetscArrayzero(subc->ilen, subc->mbs));
696: /* Initial matrix as if empty */
697: submats[i]->factortype = C->factortype;
699: smat_i = subc->submatis1;
701: nrqs = smat_i->nrqs;
702: nrqr = smat_i->nrqr;
703: rbuf1 = smat_i->rbuf1;
704: rbuf2 = smat_i->rbuf2;
705: rbuf3 = smat_i->rbuf3;
706: req_source2 = smat_i->req_source2;
708: sbuf1 = smat_i->sbuf1;
709: sbuf2 = smat_i->sbuf2;
710: ptr = smat_i->ptr;
711: tmp = smat_i->tmp;
712: ctr = smat_i->ctr;
714: pa = smat_i->pa;
715: req_size = smat_i->req_size;
716: req_source1 = smat_i->req_source1;
718: allcolumns[i] = smat_i->allcolumns;
719: allrows[i] = smat_i->allrows;
720: row2proc[i] = smat_i->row2proc;
721: rmap[i] = smat_i->rmap;
722: cmap[i] = smat_i->cmap;
723: }
725: if (!ismax) { /* Get dummy submatrices and retrieve struct submatis1 */
726: PetscCheck(submats[0], PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "submats are null, cannot reuse");
727: smat_i = (Mat_SubSppt *)submats[0]->data;
729: nrqs = smat_i->nrqs;
730: nrqr = smat_i->nrqr;
731: rbuf1 = smat_i->rbuf1;
732: rbuf2 = smat_i->rbuf2;
733: rbuf3 = smat_i->rbuf3;
734: req_source2 = smat_i->req_source2;
736: sbuf1 = smat_i->sbuf1;
737: sbuf2 = smat_i->sbuf2;
738: ptr = smat_i->ptr;
739: tmp = smat_i->tmp;
740: ctr = smat_i->ctr;
742: pa = smat_i->pa;
743: req_size = smat_i->req_size;
744: req_source1 = smat_i->req_source1;
746: allcolumns[0] = PETSC_FALSE;
747: }
748: } else { /* scall == MAT_INITIAL_MATRIX */
749: /* Get some new tags to keep the communication clean */
750: PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag2));
751: PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag3));
753: /* evaluate communication - mesg to who, length of mesg, and buffer space
754: required. Based on this, buffers are allocated, and data copied into them*/
755: PetscCall(PetscCalloc4(size, &w1, size, &w2, size, &w3, size, &w4)); /* mesg size, initialize work vectors */
757: for (i = 0; i < ismax; i++) {
758: jmax = nrow[i];
759: irow_i = irow[i];
761: PetscCall(PetscMalloc1(jmax, &row2proc_i));
762: row2proc[i] = row2proc_i;
764: if (issorted[i]) proc = 0;
765: for (j = 0; j < jmax; j++) {
766: if (!issorted[i]) proc = 0;
767: if (allrows[i]) row = j;
768: else row = irow_i[j];
770: while (row >= c->rangebs[proc + 1]) proc++;
771: w4[proc]++;
772: row2proc_i[j] = proc; /* map row index to proc */
773: }
774: for (j = 0; j < size; j++) {
775: if (w4[j]) {
776: w1[j] += w4[j];
777: w3[j]++;
778: w4[j] = 0;
779: }
780: }
781: }
783: nrqs = 0; /* no of outgoing messages */
784: msz = 0; /* total mesg length (for all procs) */
785: w1[rank] = 0; /* no mesg sent to self */
786: w3[rank] = 0;
787: for (i = 0; i < size; i++) {
788: if (w1[i]) {
789: w2[i] = 1;
790: nrqs++;
791: } /* there exists a message to proc i */
792: }
793: PetscCall(PetscMalloc1(nrqs, &pa)); /*(proc -array)*/
794: for (i = 0, j = 0; i < size; i++) {
795: if (w1[i]) {
796: pa[j] = i;
797: j++;
798: }
799: }
801: /* Each message would have a header = 1 + 2*(no of IS) + data */
802: for (i = 0; i < nrqs; i++) {
803: j = pa[i];
804: w1[j] += w2[j] + 2 * w3[j];
805: msz += w1[j];
806: }
807: PetscCall(PetscInfo(0, "Number of outgoing messages %" PetscInt_FMT " Total message length %" PetscInt_FMT "\n", nrqs, msz));
809: /* Determine the number of messages to expect, their lengths, from from-ids */
810: PetscCall(PetscGatherNumberOfMessages(comm, w2, w1, &nrqr));
811: PetscCall(PetscGatherMessageLengths(comm, nrqs, nrqr, w1, &onodes1, &olengths1));
813: /* Now post the Irecvs corresponding to these messages */
814: PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag0));
815: PetscCall(PetscPostIrecvInt(comm, tag0, nrqr, onodes1, olengths1, &rbuf1, &r_waits1));
817: /* Allocate Memory for outgoing messages */
818: PetscCall(PetscMalloc4(size, &sbuf1, size, &ptr, 2 * msz, &tmp, size, &ctr));
819: PetscCall(PetscArrayzero(sbuf1, size));
820: PetscCall(PetscArrayzero(ptr, size));
822: {
823: PetscInt *iptr = tmp;
824: k = 0;
825: for (i = 0; i < nrqs; i++) {
826: j = pa[i];
827: iptr += k;
828: sbuf1[j] = iptr;
829: k = w1[j];
830: }
831: }
833: /* Form the outgoing messages. Initialize the header space */
834: for (i = 0; i < nrqs; i++) {
835: j = pa[i];
836: sbuf1[j][0] = 0;
837: PetscCall(PetscArrayzero(sbuf1[j] + 1, 2 * w3[j]));
838: ptr[j] = sbuf1[j] + 2 * w3[j] + 1;
839: }
841: /* Parse the isrow and copy data into outbuf */
842: for (i = 0; i < ismax; i++) {
843: row2proc_i = row2proc[i];
844: PetscCall(PetscArrayzero(ctr, size));
845: irow_i = irow[i];
846: jmax = nrow[i];
847: for (j = 0; j < jmax; j++) { /* parse the indices of each IS */
848: proc = row2proc_i[j];
849: if (allrows[i]) row = j;
850: else row = irow_i[j];
852: if (proc != rank) { /* copy to the outgoing buf*/
853: ctr[proc]++;
854: *ptr[proc] = row;
855: ptr[proc]++;
856: }
857: }
858: /* Update the headers for the current IS */
859: for (j = 0; j < size; j++) { /* Can Optimise this loop too */
860: if ((ctr_j = ctr[j])) {
861: sbuf1_j = sbuf1[j];
862: k = ++sbuf1_j[0];
863: sbuf1_j[2 * k] = ctr_j;
864: sbuf1_j[2 * k - 1] = i;
865: }
866: }
867: }
869: /* Now post the sends */
870: PetscCall(PetscMalloc1(nrqs, &s_waits1));
871: for (i = 0; i < nrqs; ++i) {
872: j = pa[i];
873: PetscCallMPI(MPI_Isend(sbuf1[j], w1[j], MPIU_INT, j, tag0, comm, s_waits1 + i));
874: }
876: /* Post Receives to capture the buffer size */
877: PetscCall(PetscMalloc1(nrqs, &r_waits2));
878: PetscCall(PetscMalloc3(nrqs, &req_source2, nrqs, &rbuf2, nrqs, &rbuf3));
879: if (nrqs) rbuf2[0] = tmp + msz;
880: for (i = 1; i < nrqs; ++i) rbuf2[i] = rbuf2[i - 1] + w1[pa[i - 1]];
881: for (i = 0; i < nrqs; ++i) {
882: j = pa[i];
883: PetscCallMPI(MPI_Irecv(rbuf2[i], w1[j], MPIU_INT, j, tag2, comm, r_waits2 + i));
884: }
886: /* Send to other procs the buf size they should allocate */
887: /* Receive messages*/
888: PetscCall(PetscMalloc1(nrqr, &s_waits2));
889: PetscCall(PetscMalloc3(nrqr, &sbuf2, nrqr, &req_size, nrqr, &req_source1));
891: PetscCallMPI(MPI_Waitall(nrqr, r_waits1, MPI_STATUSES_IGNORE));
892: for (i = 0; i < nrqr; ++i) {
893: req_size[i] = 0;
894: rbuf1_i = rbuf1[i];
895: start = 2 * rbuf1_i[0] + 1;
896: end = olengths1[i];
897: PetscCall(PetscMalloc1(end, &sbuf2[i]));
898: sbuf2_i = sbuf2[i];
899: for (j = start; j < end; j++) {
900: row = rbuf1_i[j] - rstart;
901: ncols = a_i[row + 1] - a_i[row] + b_i[row + 1] - b_i[row];
902: sbuf2_i[j] = ncols;
903: req_size[i] += ncols;
904: }
905: req_source1[i] = onodes1[i];
906: /* form the header */
907: sbuf2_i[0] = req_size[i];
908: for (j = 1; j < start; j++) sbuf2_i[j] = rbuf1_i[j];
910: PetscCallMPI(MPI_Isend(sbuf2_i, end, MPIU_INT, req_source1[i], tag2, comm, s_waits2 + i));
911: }
913: PetscCall(PetscFree(onodes1));
914: PetscCall(PetscFree(olengths1));
916: PetscCall(PetscFree(r_waits1));
917: PetscCall(PetscFree4(w1, w2, w3, w4));
919: /* Receive messages*/
920: PetscCall(PetscMalloc1(nrqs, &r_waits3));
922: PetscCallMPI(MPI_Waitall(nrqs, r_waits2, MPI_STATUSES_IGNORE));
923: for (i = 0; i < nrqs; ++i) {
924: PetscCall(PetscMalloc1(rbuf2[i][0], &rbuf3[i]));
925: req_source2[i] = pa[i];
926: PetscCallMPI(MPI_Irecv(rbuf3[i], rbuf2[i][0], MPIU_INT, req_source2[i], tag3, comm, r_waits3 + i));
927: }
928: PetscCall(PetscFree(r_waits2));
930: /* Wait on sends1 and sends2 */
931: PetscCallMPI(MPI_Waitall(nrqs, s_waits1, MPI_STATUSES_IGNORE));
932: PetscCallMPI(MPI_Waitall(nrqr, s_waits2, MPI_STATUSES_IGNORE));
933: PetscCall(PetscFree(s_waits1));
934: PetscCall(PetscFree(s_waits2));
936: /* Now allocate sending buffers for a->j, and send them off */
937: PetscCall(PetscMalloc1(nrqr, &sbuf_aj));
938: for (i = 0, j = 0; i < nrqr; i++) j += req_size[i];
939: if (nrqr) PetscCall(PetscMalloc1(j, &sbuf_aj[0]));
940: for (i = 1; i < nrqr; i++) sbuf_aj[i] = sbuf_aj[i - 1] + req_size[i - 1];
942: PetscCall(PetscMalloc1(nrqr, &s_waits3));
943: {
944: for (i = 0; i < nrqr; i++) {
945: rbuf1_i = rbuf1[i];
946: sbuf_aj_i = sbuf_aj[i];
947: ct1 = 2 * rbuf1_i[0] + 1;
948: ct2 = 0;
949: for (j = 1, max1 = rbuf1_i[0]; j <= max1; j++) {
950: kmax = rbuf1[i][2 * j];
951: for (k = 0; k < kmax; k++, ct1++) {
952: row = rbuf1_i[ct1] - rstart;
953: nzA = a_i[row + 1] - a_i[row];
954: nzB = b_i[row + 1] - b_i[row];
955: ncols = nzA + nzB;
956: cworkA = PetscSafePointerPlusOffset(a_j, a_i[row]);
957: cworkB = PetscSafePointerPlusOffset(b_j, b_i[row]);
959: /* load the column indices for this row into cols */
960: cols = sbuf_aj_i + ct2;
961: for (l = 0; l < nzB; l++) {
962: if ((ctmp = bmap[cworkB[l]]) < cstart) cols[l] = ctmp;
963: else break;
964: }
965: imark = l;
966: for (l = 0; l < nzA; l++) cols[imark + l] = cstart + cworkA[l];
967: for (l = imark; l < nzB; l++) cols[nzA + l] = bmap[cworkB[l]];
968: ct2 += ncols;
969: }
970: }
971: PetscCallMPI(MPI_Isend(sbuf_aj_i, req_size[i], MPIU_INT, req_source1[i], tag3, comm, s_waits3 + i));
972: }
973: }
975: /* create col map: global col of C -> local col of submatrices */
976: #if defined(PETSC_USE_CTABLE)
977: for (i = 0; i < ismax; i++) {
978: if (!allcolumns[i]) {
979: PetscCall(PetscHMapICreateWithSize(ncol[i], cmap + i));
981: jmax = ncol[i];
982: icol_i = icol[i];
983: cmap_i = cmap[i];
984: for (j = 0; j < jmax; j++) PetscCall(PetscHMapISet(cmap[i], icol_i[j] + 1, j + 1));
985: } else cmap[i] = NULL;
986: }
987: #else
988: for (i = 0; i < ismax; i++) {
989: if (!allcolumns[i]) {
990: PetscCall(PetscCalloc1(c->Nbs, &cmap[i]));
991: jmax = ncol[i];
992: icol_i = icol[i];
993: cmap_i = cmap[i];
994: for (j = 0; j < jmax; j++) cmap_i[icol_i[j]] = j + 1;
995: } else cmap[i] = NULL;
996: }
997: #endif
999: /* Create lens which is required for MatCreate... */
1000: for (i = 0, j = 0; i < ismax; i++) j += nrow[i];
1001: PetscCall(PetscMalloc1(ismax, &lens));
1003: if (ismax) PetscCall(PetscCalloc1(j, &lens[0]));
1004: for (i = 1; i < ismax; i++) lens[i] = PetscSafePointerPlusOffset(lens[i - 1], nrow[i - 1]);
1006: /* Update lens from local data */
1007: for (i = 0; i < ismax; i++) {
1008: row2proc_i = row2proc[i];
1009: jmax = nrow[i];
1010: if (!allcolumns[i]) cmap_i = cmap[i];
1011: irow_i = irow[i];
1012: lens_i = lens[i];
1013: for (j = 0; j < jmax; j++) {
1014: if (allrows[i]) row = j;
1015: else row = irow_i[j]; /* global blocked row of C */
1017: proc = row2proc_i[j];
1018: if (proc == rank) {
1019: /* Get indices from matA and then from matB */
1020: #if defined(PETSC_USE_CTABLE)
1021: PetscInt tt;
1022: #endif
1023: row = row - rstart;
1024: nzA = a_i[row + 1] - a_i[row];
1025: nzB = b_i[row + 1] - b_i[row];
1026: cworkA = a_j + a_i[row];
1027: cworkB = PetscSafePointerPlusOffset(b_j, b_i[row]);
1029: if (!allcolumns[i]) {
1030: #if defined(PETSC_USE_CTABLE)
1031: for (k = 0; k < nzA; k++) {
1032: PetscCall(PetscHMapIGetWithDefault(cmap_i, cstart + cworkA[k] + 1, 0, &tt));
1033: if (tt) lens_i[j]++;
1034: }
1035: for (k = 0; k < nzB; k++) {
1036: PetscCall(PetscHMapIGetWithDefault(cmap_i, bmap[cworkB[k]] + 1, 0, &tt));
1037: if (tt) lens_i[j]++;
1038: }
1040: #else
1041: for (k = 0; k < nzA; k++) {
1042: if (cmap_i[cstart + cworkA[k]]) lens_i[j]++;
1043: }
1044: for (k = 0; k < nzB; k++) {
1045: if (cmap_i[bmap[cworkB[k]]]) lens_i[j]++;
1046: }
1047: #endif
1048: } else { /* allcolumns */
1049: lens_i[j] = nzA + nzB;
1050: }
1051: }
1052: }
1053: }
1055: /* Create row map: global row of C -> local row of submatrices */
1056: for (i = 0; i < ismax; i++) {
1057: if (!allrows[i]) {
1058: #if defined(PETSC_USE_CTABLE)
1059: PetscCall(PetscHMapICreateWithSize(nrow[i], rmap + i));
1060: irow_i = irow[i];
1061: jmax = nrow[i];
1062: for (j = 0; j < jmax; j++) {
1063: if (allrows[i]) {
1064: PetscCall(PetscHMapISet(rmap[i], j + 1, j + 1));
1065: } else {
1066: PetscCall(PetscHMapISet(rmap[i], irow_i[j] + 1, j + 1));
1067: }
1068: }
1069: #else
1070: PetscCall(PetscCalloc1(c->Mbs, &rmap[i]));
1071: rmap_i = rmap[i];
1072: irow_i = irow[i];
1073: jmax = nrow[i];
1074: for (j = 0; j < jmax; j++) {
1075: if (allrows[i]) rmap_i[j] = j;
1076: else rmap_i[irow_i[j]] = j;
1077: }
1078: #endif
1079: } else rmap[i] = NULL;
1080: }
1082: /* Update lens from offproc data */
1083: {
1084: PetscInt *rbuf2_i, *rbuf3_i, *sbuf1_i;
1086: PetscCallMPI(MPI_Waitall(nrqs, r_waits3, MPI_STATUSES_IGNORE));
1087: for (tmp2 = 0; tmp2 < nrqs; tmp2++) {
1088: sbuf1_i = sbuf1[pa[tmp2]];
1089: jmax = sbuf1_i[0];
1090: ct1 = 2 * jmax + 1;
1091: ct2 = 0;
1092: rbuf2_i = rbuf2[tmp2];
1093: rbuf3_i = rbuf3[tmp2];
1094: for (j = 1; j <= jmax; j++) {
1095: is_no = sbuf1_i[2 * j - 1];
1096: max1 = sbuf1_i[2 * j];
1097: lens_i = lens[is_no];
1098: if (!allcolumns[is_no]) cmap_i = cmap[is_no];
1099: rmap_i = rmap[is_no];
1100: for (k = 0; k < max1; k++, ct1++) {
1101: if (allrows[is_no]) {
1102: row = sbuf1_i[ct1];
1103: } else {
1104: #if defined(PETSC_USE_CTABLE)
1105: PetscCall(PetscHMapIGetWithDefault(rmap_i, sbuf1_i[ct1] + 1, 0, &row));
1106: row--;
1107: PetscCheck(row >= 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "row not found in table");
1108: #else
1109: row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */
1110: #endif
1111: }
1112: max2 = rbuf2_i[ct1];
1113: for (l = 0; l < max2; l++, ct2++) {
1114: if (!allcolumns[is_no]) {
1115: #if defined(PETSC_USE_CTABLE)
1116: PetscCall(PetscHMapIGetWithDefault(cmap_i, rbuf3_i[ct2] + 1, 0, &tcol));
1117: #else
1118: tcol = cmap_i[rbuf3_i[ct2]];
1119: #endif
1120: if (tcol) lens_i[row]++;
1121: } else { /* allcolumns */
1122: lens_i[row]++; /* lens_i[row] += max2 ? */
1123: }
1124: }
1125: }
1126: }
1127: }
1128: }
1129: PetscCall(PetscFree(r_waits3));
1130: PetscCallMPI(MPI_Waitall(nrqr, s_waits3, MPI_STATUSES_IGNORE));
1131: PetscCall(PetscFree(s_waits3));
1133: /* Create the submatrices */
1134: for (i = 0; i < ismax; i++) {
1135: PetscInt bs_tmp;
1136: if (ijonly) bs_tmp = 1;
1137: else bs_tmp = bs;
1139: PetscCall(MatCreate(PETSC_COMM_SELF, submats + i));
1140: PetscCall(MatSetSizes(submats[i], nrow[i] * bs_tmp, ncol[i] * bs_tmp, PETSC_DETERMINE, PETSC_DETERMINE));
1142: PetscCall(MatSetType(submats[i], sym ? ((PetscObject)A)->type_name : MATSEQBAIJ));
1143: PetscCall(MatSeqBAIJSetPreallocation(submats[i], bs_tmp, 0, lens[i]));
1144: PetscCall(MatSeqSBAIJSetPreallocation(submats[i], bs_tmp, 0, lens[i])); /* this subroutine is used by SBAIJ routines */
1146: /* create struct Mat_SubSppt and attached it to submat */
1147: PetscCall(PetscNew(&smat_i));
1148: subc = (Mat_SeqBAIJ *)submats[i]->data;
1149: subc->submatis1 = smat_i;
1151: smat_i->destroy = submats[i]->ops->destroy;
1152: submats[i]->ops->destroy = MatDestroySubMatrix_SeqBAIJ;
1153: submats[i]->factortype = C->factortype;
1155: smat_i->id = i;
1156: smat_i->nrqs = nrqs;
1157: smat_i->nrqr = nrqr;
1158: smat_i->rbuf1 = rbuf1;
1159: smat_i->rbuf2 = rbuf2;
1160: smat_i->rbuf3 = rbuf3;
1161: smat_i->sbuf2 = sbuf2;
1162: smat_i->req_source2 = req_source2;
1164: smat_i->sbuf1 = sbuf1;
1165: smat_i->ptr = ptr;
1166: smat_i->tmp = tmp;
1167: smat_i->ctr = ctr;
1169: smat_i->pa = pa;
1170: smat_i->req_size = req_size;
1171: smat_i->req_source1 = req_source1;
1173: smat_i->allcolumns = allcolumns[i];
1174: smat_i->allrows = allrows[i];
1175: smat_i->singleis = PETSC_FALSE;
1176: smat_i->row2proc = row2proc[i];
1177: smat_i->rmap = rmap[i];
1178: smat_i->cmap = cmap[i];
1179: }
1181: if (!ismax) { /* Create dummy submats[0] for reuse struct subc */
1182: PetscCall(MatCreate(PETSC_COMM_SELF, &submats[0]));
1183: PetscCall(MatSetSizes(submats[0], 0, 0, PETSC_DETERMINE, PETSC_DETERMINE));
1184: PetscCall(MatSetType(submats[0], MATDUMMY));
1186: /* create struct Mat_SubSppt and attached it to submat */
1187: PetscCall(PetscNew(&smat_i));
1188: submats[0]->data = (void *)smat_i;
1190: smat_i->destroy = submats[0]->ops->destroy;
1191: submats[0]->ops->destroy = MatDestroySubMatrix_Dummy;
1192: submats[0]->factortype = C->factortype;
1194: smat_i->id = 0;
1195: smat_i->nrqs = nrqs;
1196: smat_i->nrqr = nrqr;
1197: smat_i->rbuf1 = rbuf1;
1198: smat_i->rbuf2 = rbuf2;
1199: smat_i->rbuf3 = rbuf3;
1200: smat_i->sbuf2 = sbuf2;
1201: smat_i->req_source2 = req_source2;
1203: smat_i->sbuf1 = sbuf1;
1204: smat_i->ptr = ptr;
1205: smat_i->tmp = tmp;
1206: smat_i->ctr = ctr;
1208: smat_i->pa = pa;
1209: smat_i->req_size = req_size;
1210: smat_i->req_source1 = req_source1;
1212: smat_i->allcolumns = PETSC_FALSE;
1213: smat_i->singleis = PETSC_FALSE;
1214: smat_i->row2proc = NULL;
1215: smat_i->rmap = NULL;
1216: smat_i->cmap = NULL;
1217: }
1219: if (ismax) PetscCall(PetscFree(lens[0]));
1220: PetscCall(PetscFree(lens));
1221: if (sbuf_aj) {
1222: PetscCall(PetscFree(sbuf_aj[0]));
1223: PetscCall(PetscFree(sbuf_aj));
1224: }
1226: } /* endof scall == MAT_INITIAL_MATRIX */
1228: /* Post recv matrix values */
1229: if (!ijonly) {
1230: PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag4));
1231: PetscCall(PetscMalloc1(nrqs, &rbuf4));
1232: PetscCall(PetscMalloc1(nrqs, &r_waits4));
1233: for (i = 0; i < nrqs; ++i) {
1234: PetscCall(PetscMalloc1(rbuf2[i][0] * bs2, &rbuf4[i]));
1235: PetscCallMPI(MPI_Irecv(rbuf4[i], rbuf2[i][0] * bs2, MPIU_SCALAR, req_source2[i], tag4, comm, r_waits4 + i));
1236: }
1238: /* Allocate sending buffers for a->a, and send them off */
1239: PetscCall(PetscMalloc1(nrqr, &sbuf_aa));
1240: for (i = 0, j = 0; i < nrqr; i++) j += req_size[i];
1242: if (nrqr) PetscCall(PetscMalloc1(j * bs2, &sbuf_aa[0]));
1243: for (i = 1; i < nrqr; i++) sbuf_aa[i] = sbuf_aa[i - 1] + req_size[i - 1] * bs2;
1245: PetscCall(PetscMalloc1(nrqr, &s_waits4));
1247: for (i = 0; i < nrqr; i++) {
1248: rbuf1_i = rbuf1[i];
1249: sbuf_aa_i = sbuf_aa[i];
1250: ct1 = 2 * rbuf1_i[0] + 1;
1251: ct2 = 0;
1252: for (j = 1, max1 = rbuf1_i[0]; j <= max1; j++) {
1253: kmax = rbuf1_i[2 * j];
1254: for (k = 0; k < kmax; k++, ct1++) {
1255: row = rbuf1_i[ct1] - rstart;
1256: nzA = a_i[row + 1] - a_i[row];
1257: nzB = b_i[row + 1] - b_i[row];
1258: ncols = nzA + nzB;
1259: cworkB = PetscSafePointerPlusOffset(b_j, b_i[row]);
1260: vworkA = PetscSafePointerPlusOffset(a_a, a_i[row] * bs2);
1261: vworkB = PetscSafePointerPlusOffset(b_a, b_i[row] * bs2);
1263: /* load the column values for this row into vals*/
1264: vals = sbuf_aa_i + ct2 * bs2;
1265: for (l = 0; l < nzB; l++) {
1266: if ((bmap[cworkB[l]]) < cstart) {
1267: PetscCall(PetscArraycpy(vals + l * bs2, vworkB + l * bs2, bs2));
1268: } else break;
1269: }
1270: imark = l;
1271: for (l = 0; l < nzA; l++) PetscCall(PetscArraycpy(vals + (imark + l) * bs2, vworkA + l * bs2, bs2));
1272: for (l = imark; l < nzB; l++) PetscCall(PetscArraycpy(vals + (nzA + l) * bs2, vworkB + l * bs2, bs2));
1274: ct2 += ncols;
1275: }
1276: }
1277: PetscCallMPI(MPI_Isend(sbuf_aa_i, req_size[i] * bs2, MPIU_SCALAR, req_source1[i], tag4, comm, s_waits4 + i));
1278: }
1279: }
1281: /* Assemble the matrices */
1282: /* First assemble the local rows */
1283: for (i = 0; i < ismax; i++) {
1284: row2proc_i = row2proc[i];
1285: subc = (Mat_SeqBAIJ *)submats[i]->data;
1286: imat_ilen = subc->ilen;
1287: imat_j = subc->j;
1288: imat_i = subc->i;
1289: imat_a = subc->a;
1291: if (!allcolumns[i]) cmap_i = cmap[i];
1292: rmap_i = rmap[i];
1293: irow_i = irow[i];
1294: jmax = nrow[i];
1295: for (j = 0; j < jmax; j++) {
1296: if (allrows[i]) row = j;
1297: else row = irow_i[j];
1298: proc = row2proc_i[j];
1300: if (proc == rank) {
1301: row = row - rstart;
1302: nzA = a_i[row + 1] - a_i[row];
1303: nzB = b_i[row + 1] - b_i[row];
1304: cworkA = a_j + a_i[row];
1305: cworkB = PetscSafePointerPlusOffset(b_j, b_i[row]);
1306: if (!ijonly) {
1307: vworkA = a_a + a_i[row] * bs2;
1308: vworkB = PetscSafePointerPlusOffset(b_a, b_i[row] * bs2);
1309: }
1311: if (allrows[i]) {
1312: row = row + rstart;
1313: } else {
1314: #if defined(PETSC_USE_CTABLE)
1315: PetscCall(PetscHMapIGetWithDefault(rmap_i, row + rstart + 1, 0, &row));
1316: row--;
1318: PetscCheck(row >= 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "row not found in table");
1319: #else
1320: row = rmap_i[row + rstart];
1321: #endif
1322: }
1323: mat_i = imat_i[row];
1324: if (!ijonly) mat_a = PetscSafePointerPlusOffset(imat_a, mat_i * bs2);
1325: mat_j = PetscSafePointerPlusOffset(imat_j, mat_i);
1326: ilen = imat_ilen[row];
1328: /* load the column indices for this row into cols*/
1329: if (!allcolumns[i]) {
1330: for (l = 0; l < nzB; l++) {
1331: if ((ctmp = bmap[cworkB[l]]) < cstart) {
1332: #if defined(PETSC_USE_CTABLE)
1333: PetscCall(PetscHMapIGetWithDefault(cmap_i, ctmp + 1, 0, &tcol));
1334: if (tcol) {
1335: #else
1336: if ((tcol = cmap_i[ctmp])) {
1337: #endif
1338: *mat_j++ = tcol - 1;
1339: PetscCall(PetscArraycpy(mat_a, vworkB + l * bs2, bs2));
1340: mat_a += bs2;
1341: ilen++;
1342: }
1343: } else break;
1344: }
1345: imark = l;
1346: for (l = 0; l < nzA; l++) {
1347: #if defined(PETSC_USE_CTABLE)
1348: PetscCall(PetscHMapIGetWithDefault(cmap_i, cstart + cworkA[l] + 1, 0, &tcol));
1349: if (tcol) {
1350: #else
1351: if ((tcol = cmap_i[cstart + cworkA[l]])) {
1352: #endif
1353: *mat_j++ = tcol - 1;
1354: if (!ijonly) {
1355: PetscCall(PetscArraycpy(mat_a, vworkA + l * bs2, bs2));
1356: mat_a += bs2;
1357: }
1358: ilen++;
1359: }
1360: }
1361: for (l = imark; l < nzB; l++) {
1362: #if defined(PETSC_USE_CTABLE)
1363: PetscCall(PetscHMapIGetWithDefault(cmap_i, bmap[cworkB[l]] + 1, 0, &tcol));
1364: if (tcol) {
1365: #else
1366: if ((tcol = cmap_i[bmap[cworkB[l]]])) {
1367: #endif
1368: *mat_j++ = tcol - 1;
1369: if (!ijonly) {
1370: PetscCall(PetscArraycpy(mat_a, vworkB + l * bs2, bs2));
1371: mat_a += bs2;
1372: }
1373: ilen++;
1374: }
1375: }
1376: } else { /* allcolumns */
1377: for (l = 0; l < nzB; l++) {
1378: if ((ctmp = bmap[cworkB[l]]) < cstart) {
1379: *mat_j++ = ctmp;
1380: PetscCall(PetscArraycpy(mat_a, vworkB + l * bs2, bs2));
1381: mat_a += bs2;
1382: ilen++;
1383: } else break;
1384: }
1385: imark = l;
1386: for (l = 0; l < nzA; l++) {
1387: *mat_j++ = cstart + cworkA[l];
1388: if (!ijonly) {
1389: PetscCall(PetscArraycpy(mat_a, vworkA + l * bs2, bs2));
1390: mat_a += bs2;
1391: }
1392: ilen++;
1393: }
1394: for (l = imark; l < nzB; l++) {
1395: *mat_j++ = bmap[cworkB[l]];
1396: if (!ijonly) {
1397: PetscCall(PetscArraycpy(mat_a, vworkB + l * bs2, bs2));
1398: mat_a += bs2;
1399: }
1400: ilen++;
1401: }
1402: }
1403: imat_ilen[row] = ilen;
1404: }
1405: }
1406: }
1408: /* Now assemble the off proc rows */
1409: if (!ijonly) PetscCallMPI(MPI_Waitall(nrqs, r_waits4, MPI_STATUSES_IGNORE));
1410: for (tmp2 = 0; tmp2 < nrqs; tmp2++) {
1411: sbuf1_i = sbuf1[pa[tmp2]];
1412: jmax = sbuf1_i[0];
1413: ct1 = 2 * jmax + 1;
1414: ct2 = 0;
1415: rbuf2_i = rbuf2[tmp2];
1416: rbuf3_i = rbuf3[tmp2];
1417: if (!ijonly) rbuf4_i = rbuf4[tmp2];
1418: for (j = 1; j <= jmax; j++) {
1419: is_no = sbuf1_i[2 * j - 1];
1420: rmap_i = rmap[is_no];
1421: if (!allcolumns[is_no]) cmap_i = cmap[is_no];
1422: subc = (Mat_SeqBAIJ *)submats[is_no]->data;
1423: imat_ilen = subc->ilen;
1424: imat_j = subc->j;
1425: imat_i = subc->i;
1426: if (!ijonly) imat_a = subc->a;
1427: max1 = sbuf1_i[2 * j];
1428: for (k = 0; k < max1; k++, ct1++) { /* for each recved block row */
1429: row = sbuf1_i[ct1];
1431: if (allrows[is_no]) {
1432: row = sbuf1_i[ct1];
1433: } else {
1434: #if defined(PETSC_USE_CTABLE)
1435: PetscCall(PetscHMapIGetWithDefault(rmap_i, row + 1, 0, &row));
1436: row--;
1437: PetscCheck(row >= 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "row not found in table");
1438: #else
1439: row = rmap_i[row];
1440: #endif
1441: }
1442: ilen = imat_ilen[row];
1443: mat_i = imat_i[row];
1444: if (!ijonly) mat_a = imat_a + mat_i * bs2;
1445: mat_j = imat_j + mat_i;
1446: max2 = rbuf2_i[ct1];
1447: if (!allcolumns[is_no]) {
1448: for (l = 0; l < max2; l++, ct2++) {
1449: #if defined(PETSC_USE_CTABLE)
1450: PetscCall(PetscHMapIGetWithDefault(cmap_i, rbuf3_i[ct2] + 1, 0, &tcol));
1451: #else
1452: tcol = cmap_i[rbuf3_i[ct2]];
1453: #endif
1454: if (tcol) {
1455: *mat_j++ = tcol - 1;
1456: if (!ijonly) {
1457: PetscCall(PetscArraycpy(mat_a, rbuf4_i + ct2 * bs2, bs2));
1458: mat_a += bs2;
1459: }
1460: ilen++;
1461: }
1462: }
1463: } else { /* allcolumns */
1464: for (l = 0; l < max2; l++, ct2++) {
1465: *mat_j++ = rbuf3_i[ct2]; /* same global column index of C */
1466: if (!ijonly) {
1467: PetscCall(PetscArraycpy(mat_a, rbuf4_i + ct2 * bs2, bs2));
1468: mat_a += bs2;
1469: }
1470: ilen++;
1471: }
1472: }
1473: imat_ilen[row] = ilen;
1474: }
1475: }
1476: }
1478: if (!iscsorted) { /* sort column indices of the rows */
1479: MatScalar *work;
1481: PetscCall(PetscMalloc1(bs2, &work));
1482: for (i = 0; i < ismax; i++) {
1483: subc = (Mat_SeqBAIJ *)submats[i]->data;
1484: imat_ilen = subc->ilen;
1485: imat_j = subc->j;
1486: imat_i = subc->i;
1487: if (!ijonly) imat_a = subc->a;
1488: if (allcolumns[i]) continue;
1490: jmax = nrow[i];
1491: for (j = 0; j < jmax; j++) {
1492: mat_i = imat_i[j];
1493: mat_j = imat_j + mat_i;
1494: ilen = imat_ilen[j];
1495: if (ijonly) {
1496: PetscCall(PetscSortInt(ilen, mat_j));
1497: } else {
1498: mat_a = imat_a + mat_i * bs2;
1499: PetscCall(PetscSortIntWithDataArray(ilen, mat_j, mat_a, bs2 * sizeof(MatScalar), work));
1500: }
1501: }
1502: }
1503: PetscCall(PetscFree(work));
1504: }
1506: if (!ijonly) {
1507: PetscCall(PetscFree(r_waits4));
1508: PetscCallMPI(MPI_Waitall(nrqr, s_waits4, MPI_STATUSES_IGNORE));
1509: PetscCall(PetscFree(s_waits4));
1510: }
1512: /* Restore the indices */
1513: for (i = 0; i < ismax; i++) {
1514: if (!allrows[i]) PetscCall(ISRestoreIndices(isrow[i], irow + i));
1515: if (!allcolumns[i]) PetscCall(ISRestoreIndices(iscol[i], icol + i));
1516: }
1518: for (i = 0; i < ismax; i++) {
1519: PetscCall(MatAssemblyBegin(submats[i], MAT_FINAL_ASSEMBLY));
1520: PetscCall(MatAssemblyEnd(submats[i], MAT_FINAL_ASSEMBLY));
1521: }
1523: PetscCall(PetscFree5(*(PetscInt ***)&irow, *(PetscInt ***)&icol, nrow, ncol, issorted));
1524: PetscCall(PetscFree5(row2proc, cmap, rmap, allcolumns, allrows));
1526: if (!ijonly) {
1527: if (sbuf_aa) {
1528: PetscCall(PetscFree(sbuf_aa[0]));
1529: PetscCall(PetscFree(sbuf_aa));
1530: }
1532: for (i = 0; i < nrqs; ++i) PetscCall(PetscFree(rbuf4[i]));
1533: PetscCall(PetscFree(rbuf4));
1534: }
1535: c->ijonly = PETSC_FALSE; /* set back to the default */
1536: PetscFunctionReturn(PETSC_SUCCESS);
1537: }