Actual source code: mpiov.c
1: /*$Id: mpiov.c,v 1.26.1.76.2.22 2001/09/07 20:09:38 bsmith Exp $*/
2: /*
3: Routines to compute overlapping regions of a parallel MPI matrix
4: and to find submatrices that were shared across processors.
5: */
6: #include src/mat/impls/aij/mpi/mpiaij.h
7: #include petscbt.h
9: static int MatIncreaseOverlap_MPIAIJ_Once(Mat,int,IS *);
10: static int MatIncreaseOverlap_MPIAIJ_Local(Mat,int,char **,int*,int**);
11: static int MatIncreaseOverlap_MPIAIJ_Receive(Mat,int,int **,int**,int*);
12: EXTERN int MatGetRow_MPIAIJ(Mat,int,int*,int**,PetscScalar**);
13: EXTERN int MatRestoreRow_MPIAIJ(Mat,int,int*,int**,PetscScalar**);
17: int MatIncreaseOverlap_MPIAIJ(Mat C,int imax,IS is[],int ov)
18: {
19: int i,ierr;
22: if (ov < 0) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Negative overlap specified");
23: for (i=0; i<ov; ++i) {
24: MatIncreaseOverlap_MPIAIJ_Once(C,imax,is);
25: }
26: return(0);
27: }
29: /*
30: Sample message format:
31: If a processor A wants processor B to process some elements corresponding
32: to index sets is[1],is[5]
33: mesg [0] = 2 (no of index sets in the mesg)
34: -----------
35: mesg [1] = 1 => is[1]
36: mesg [2] = sizeof(is[1]);
37: -----------
38: mesg [3] = 5 => is[5]
39: mesg [4] = sizeof(is[5]);
40: -----------
41: mesg [5]
42: mesg [n] datas[1]
43: -----------
44: mesg[n+1]
45: mesg[m] data(is[5])
46: -----------
47:
48: Notes:
49: nrqs - no of requests sent (or to be sent out)
50: nrqr - no of requests recieved (which have to be or which have been processed
51: */
54: static int MatIncreaseOverlap_MPIAIJ_Once(Mat C,int imax,IS is[])
55: {
56: Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data;
57: int **idx,*n,*w1,*w2,*w3,*w4,*rtable,**data,len,*idx_i;
58: int size,rank,m,i,j,k,ierr,**rbuf,row,proc,nrqs,msz,**outdat,**ptr;
59: int *ctr,*pa,*tmp,nrqr,*isz,*isz1,**xdata,**rbuf2;
60: int *onodes1,*olengths1,tag1,tag2,*onodes2,*olengths2;
61: PetscBT *table;
62: MPI_Comm comm;
63: MPI_Request *s_waits1,*r_waits1,*s_waits2,*r_waits2;
64: MPI_Status *s_status,*recv_status;
67: comm = C->comm;
68: size = c->size;
69: rank = c->rank;
70: m = C->M;
72: PetscObjectGetNewTag((PetscObject)C,&tag1);
73: PetscObjectGetNewTag((PetscObject)C,&tag2);
74:
75: len = (imax+1)*sizeof(int*)+ (imax + m)*sizeof(int);
76: PetscMalloc(len,&idx);
77: n = (int*)(idx + imax);
78: rtable = n + imax;
79:
80: for (i=0; i<imax; i++) {
81: ISGetIndices(is[i],&idx[i]);
82: ISGetLocalSize(is[i],&n[i]);
83: }
84:
85: /* Create hash table for the mapping :row -> proc*/
86: for (i=0,j=0; i<size; i++) {
87: len = c->rowners[i+1];
88: for (; j<len; j++) {
89: rtable[j] = i;
90: }
91: }
93: /* evaluate communication - mesg to who,length of mesg, and buffer space
94: required. Based on this, buffers are allocated, and data copied into them*/
95: PetscMalloc(size*4*sizeof(int),&w1);/* mesg size */
96: w2 = w1 + size; /* if w2[i] marked, then a message to proc i*/
97: w3 = w2 + size; /* no of IS that needs to be sent to proc i */
98: w4 = w3 + size; /* temp work space used in determining w1, w2, w3 */
99: PetscMemzero(w1,size*3*sizeof(int)); /* initialise work vector*/
100: for (i=0; i<imax; i++) {
101: PetscMemzero(w4,size*sizeof(int)); /* initialise work vector*/
102: idx_i = idx[i];
103: len = n[i];
104: for (j=0; j<len; j++) {
105: row = idx_i[j];
106: if (row < 0) {
107: SETERRQ(1,"Index set cannot have negative entries");
108: }
109: proc = rtable[row];
110: w4[proc]++;
111: }
112: for (j=0; j<size; j++){
113: if (w4[j]) { w1[j] += w4[j]; w3[j]++;}
114: }
115: }
117: nrqs = 0; /* no of outgoing messages */
118: msz = 0; /* total mesg length (for all proc */
119: w1[rank] = 0; /* no mesg sent to intself */
120: w3[rank] = 0;
121: for (i=0; i<size; i++) {
122: if (w1[i]) {w2[i] = 1; nrqs++;} /* there exists a message to proc i */
123: }
124: /* pa - is list of processors to communicate with */
125: PetscMalloc((nrqs+1)*sizeof(int),&pa);
126: for (i=0,j=0; i<size; i++) {
127: if (w1[i]) {pa[j] = i; j++;}
128: }
130: /* Each message would have a header = 1 + 2*(no of IS) + data */
131: for (i=0; i<nrqs; i++) {
132: j = pa[i];
133: w1[j] += w2[j] + 2*w3[j];
134: msz += w1[j];
135: }
137: /* Determine the number of messages to expect, their lengths, from from-ids */
138: PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);
139: PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);
141: /* Now post the Irecvs corresponding to these messages */
142: PetscPostIrecvInt(comm,tag1,nrqr,onodes1,olengths1,&rbuf,&r_waits1);
144: /* Allocate Memory for outgoing messages */
145: len = 2*size*sizeof(int*) + (size+msz)*sizeof(int);
146: PetscMalloc(len,&outdat);
147: ptr = outdat + size; /* Pointers to the data in outgoing buffers */
148: PetscMemzero(outdat,2*size*sizeof(int*));
149: tmp = (int*)(outdat + 2*size);
150: ctr = tmp + msz;
152: {
153: int *iptr = tmp,ict = 0;
154: for (i=0; i<nrqs; i++) {
155: j = pa[i];
156: iptr += ict;
157: outdat[j] = iptr;
158: ict = w1[j];
159: }
160: }
162: /* Form the outgoing messages */
163: /*plug in the headers*/
164: for (i=0; i<nrqs; i++) {
165: j = pa[i];
166: outdat[j][0] = 0;
167: PetscMemzero(outdat[j]+1,2*w3[j]*sizeof(int));
168: ptr[j] = outdat[j] + 2*w3[j] + 1;
169: }
170:
171: /* Memory for doing local proc's work*/
172: {
173: int *d_p;
174: char *t_p;
176: len = (imax)*(sizeof(PetscBT) + sizeof(int*)+ sizeof(int)) +
177: (m)*imax*sizeof(int) + (m/PETSC_BITS_PER_BYTE+1)*imax*sizeof(char) + 1;
178: PetscMalloc(len,&table);
179: PetscMemzero(table,len);
180: data = (int **)(table + imax);
181: isz = (int *)(data + imax);
182: d_p = (int *)(isz + imax);
183: t_p = (char *)(d_p + m*imax);
184: for (i=0; i<imax; i++) {
185: table[i] = t_p + (m/PETSC_BITS_PER_BYTE+1)*i;
186: data[i] = d_p + (m)*i;
187: }
188: }
190: /* Parse the IS and update local tables and the outgoing buf with the data*/
191: {
192: int n_i,*data_i,isz_i,*outdat_j,ctr_j;
193: PetscBT table_i;
195: for (i=0; i<imax; i++) {
196: PetscMemzero(ctr,size*sizeof(int));
197: n_i = n[i];
198: table_i = table[i];
199: idx_i = idx[i];
200: data_i = data[i];
201: isz_i = isz[i];
202: for (j=0; j<n_i; j++) { /* parse the indices of each IS */
203: row = idx_i[j];
204: proc = rtable[row];
205: if (proc != rank) { /* copy to the outgoing buffer */
206: ctr[proc]++;
207: *ptr[proc] = row;
208: ptr[proc]++;
209: } else { /* Update the local table */
210: if (!PetscBTLookupSet(table_i,row)) { data_i[isz_i++] = row;}
211: }
212: }
213: /* Update the headers for the current IS */
214: for (j=0; j<size; j++) { /* Can Optimise this loop by using pa[] */
215: if ((ctr_j = ctr[j])) {
216: outdat_j = outdat[j];
217: k = ++outdat_j[0];
218: outdat_j[2*k] = ctr_j;
219: outdat_j[2*k-1] = i;
220: }
221: }
222: isz[i] = isz_i;
223: }
224: }
225:
228: /* Now post the sends */
229: PetscMalloc((nrqs+1)*sizeof(MPI_Request),&s_waits1);
230: for (i=0; i<nrqs; ++i) {
231: j = pa[i];
232: MPI_Isend(outdat[j],w1[j],MPI_INT,j,tag1,comm,s_waits1+i);
233: }
234:
235: /* No longer need the original indices*/
236: for (i=0; i<imax; ++i) {
237: ISRestoreIndices(is[i],idx+i);
238: }
239: PetscFree(idx);
241: for (i=0; i<imax; ++i) {
242: ISDestroy(is[i]);
243: }
244:
245: /* Do Local work*/
246: MatIncreaseOverlap_MPIAIJ_Local(C,imax,table,isz,data);
248: /* Receive messages*/
249: PetscMalloc((nrqr+1)*sizeof(MPI_Status),&recv_status);
250: MPI_Waitall(nrqr,r_waits1,recv_status);
251:
252: PetscMalloc((nrqs+1)*sizeof(MPI_Status),&s_status);
253: MPI_Waitall(nrqs,s_waits1,s_status);
255: /* Phase 1 sends are complete - deallocate buffers */
256: PetscFree(outdat);
257: PetscFree(w1);
259: PetscMalloc((nrqr+1)*sizeof(int *),&xdata);
260: PetscMalloc((nrqr+1)*sizeof(int),&isz1);
261: MatIncreaseOverlap_MPIAIJ_Receive(C,nrqr,rbuf,xdata,isz1);
262: PetscFree(rbuf);
264:
265: /* Send the data back*/
266: /* Do a global reduction to know the buffer space req for incoming messages*/
267: {
268: int *rw1;
269:
270: PetscMalloc(size*sizeof(int),&rw1);
271: PetscMemzero(rw1,size*sizeof(int));
273: for (i=0; i<nrqr; ++i) {
274: proc = recv_status[i].MPI_SOURCE;
275: if (proc != onodes1[i]) SETERRQ(1,"MPI_SOURCE mismatch");
276: rw1[proc] = isz1[i];
277: }
278: PetscFree(onodes1);
279: PetscFree(olengths1);
281: /* Determine the number of messages to expect, their lengths, from from-ids */
282: PetscGatherMessageLengths(comm,nrqr,nrqs,rw1,&onodes2,&olengths2);
283: PetscFree(rw1);
284: }
285: /* Now post the Irecvs corresponding to these messages */
286: PetscPostIrecvInt(comm,tag2,nrqs,onodes2,olengths2,&rbuf2,&r_waits2);
288: /* Now post the sends */
289: PetscMalloc((nrqr+1)*sizeof(MPI_Request),&s_waits2);
290: for (i=0; i<nrqr; ++i) {
291: j = recv_status[i].MPI_SOURCE;
292: MPI_Isend(xdata[i],isz1[i],MPI_INT,j,tag2,comm,s_waits2+i);
293: }
295: /* receive work done on other processors*/
296: {
297: int idex,is_no,ct1,max,*rbuf2_i,isz_i,*data_i,jmax;
298: PetscBT table_i;
299: MPI_Status *status2;
300:
301: PetscMalloc((PetscMax(nrqr,nrqs)+1)*sizeof(MPI_Status),&status2);
302: for (i=0; i<nrqs; ++i) {
303: MPI_Waitany(nrqs,r_waits2,&idex,status2+i);
304: /* Process the message*/
305: rbuf2_i = rbuf2[idex];
306: ct1 = 2*rbuf2_i[0]+1;
307: jmax = rbuf2[idex][0];
308: for (j=1; j<=jmax; j++) {
309: max = rbuf2_i[2*j];
310: is_no = rbuf2_i[2*j-1];
311: isz_i = isz[is_no];
312: data_i = data[is_no];
313: table_i = table[is_no];
314: for (k=0; k<max; k++,ct1++) {
315: row = rbuf2_i[ct1];
316: if (!PetscBTLookupSet(table_i,row)) { data_i[isz_i++] = row;}
317: }
318: isz[is_no] = isz_i;
319: }
320: }
322: MPI_Waitall(nrqr,s_waits2,status2);
323: PetscFree(status2);
324: }
325:
326: for (i=0; i<imax; ++i) {
327: ISCreateGeneral(PETSC_COMM_SELF,isz[i],data[i],is+i);
328: }
329:
330: PetscFree(onodes2);
331: PetscFree(olengths2);
333: PetscFree(pa);
334: PetscFree(rbuf2);
335: PetscFree(s_waits1);
336: PetscFree(r_waits1);
337: PetscFree(s_waits2);
338: PetscFree(r_waits2);
339: PetscFree(table);
340: PetscFree(s_status);
341: PetscFree(recv_status);
342: PetscFree(xdata[0]);
343: PetscFree(xdata);
344: PetscFree(isz1);
345: return(0);
346: }
350: /*
351: MatIncreaseOverlap_MPIAIJ_Local - Called by MatincreaseOverlap, to do
352: the work on the local processor.
354: Inputs:
355: C - MAT_MPIAIJ;
356: imax - total no of index sets processed at a time;
357: table - an array of char - size = m bits.
358:
359: Output:
360: isz - array containing the count of the solution elements correspondign
361: to each index set;
362: data - pointer to the solutions
363: */
364: static int MatIncreaseOverlap_MPIAIJ_Local(Mat C,int imax,PetscBT *table,int *isz,int **data)
365: {
366: Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data;
367: Mat A = c->A,B = c->B;
368: Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data;
369: int start,end,val,max,rstart,cstart,*ai,*aj;
370: int *bi,*bj,*garray,i,j,k,row,*data_i,isz_i;
371: PetscBT table_i;
374: rstart = c->rstart;
375: cstart = c->cstart;
376: ai = a->i;
377: aj = a->j;
378: bi = b->i;
379: bj = b->j;
380: garray = c->garray;
382:
383: for (i=0; i<imax; i++) {
384: data_i = data[i];
385: table_i = table[i];
386: isz_i = isz[i];
387: for (j=0,max=isz[i]; j<max; j++) {
388: row = data_i[j] - rstart;
389: start = ai[row];
390: end = ai[row+1];
391: for (k=start; k<end; k++) { /* Amat */
392: val = aj[k] + cstart;
393: if (!PetscBTLookupSet(table_i,val)) { data_i[isz_i++] = val;}
394: }
395: start = bi[row];
396: end = bi[row+1];
397: for (k=start; k<end; k++) { /* Bmat */
398: val = garray[bj[k]];
399: if (!PetscBTLookupSet(table_i,val)) { data_i[isz_i++] = val;}
400: }
401: }
402: isz[i] = isz_i;
403: }
404: return(0);
405: }
409: /*
410: MatIncreaseOverlap_MPIAIJ_Receive - Process the recieved messages,
411: and return the output
413: Input:
414: C - the matrix
415: nrqr - no of messages being processed.
416: rbuf - an array of pointers to the recieved requests
417:
418: Output:
419: xdata - array of messages to be sent back
420: isz1 - size of each message
422: For better efficiency perhaps we should malloc seperately each xdata[i],
423: then if a remalloc is required we need only copy the data for that one row
424: rather then all previous rows as it is now where a single large chunck of
425: memory is used.
427: */
428: static int MatIncreaseOverlap_MPIAIJ_Receive(Mat C,int nrqr,int **rbuf,int **xdata,int * isz1)
429: {
430: Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data;
431: Mat A = c->A,B = c->B;
432: Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)B->data;
433: int rstart,cstart,*ai,*aj,*bi,*bj,*garray,i,j,k;
434: int row,total_sz,ct,ct1,ct2,ct3,mem_estimate,oct2,l,start,end;
435: int val,max1,max2,rank,m,no_malloc =0,*tmp,new_estimate,ctr;
436: int *rbuf_i,kmax,rbuf_0,ierr;
437: PetscBT xtable;
440: rank = c->rank;
441: m = C->M;
442: rstart = c->rstart;
443: cstart = c->cstart;
444: ai = a->i;
445: aj = a->j;
446: bi = b->i;
447: bj = b->j;
448: garray = c->garray;
449:
450:
451: for (i=0,ct=0,total_sz=0; i<nrqr; ++i) {
452: rbuf_i = rbuf[i];
453: rbuf_0 = rbuf_i[0];
454: ct += rbuf_0;
455: for (j=1; j<=rbuf_0; j++) { total_sz += rbuf_i[2*j]; }
456: }
457:
458: if (C->m) max1 = ct*(a->nz + b->nz)/C->m;
459: else max1 = 1;
460: mem_estimate = 3*((total_sz > max1 ? total_sz : max1)+1);
461: PetscMalloc(mem_estimate*sizeof(int),&xdata[0]);
462: ++no_malloc;
463: PetscBTCreate(m,xtable);
464: PetscMemzero(isz1,nrqr*sizeof(int));
465:
466: ct3 = 0;
467: for (i=0; i<nrqr; i++) { /* for easch mesg from proc i */
468: rbuf_i = rbuf[i];
469: rbuf_0 = rbuf_i[0];
470: ct1 = 2*rbuf_0+1;
471: ct2 = ct1;
472: ct3 += ct1;
473: for (j=1; j<=rbuf_0; j++) { /* for each IS from proc i*/
474: PetscBTMemzero(m,xtable);
475: oct2 = ct2;
476: kmax = rbuf_i[2*j];
477: for (k=0; k<kmax; k++,ct1++) {
478: row = rbuf_i[ct1];
479: if (!PetscBTLookupSet(xtable,row)) {
480: if (!(ct3 < mem_estimate)) {
481: new_estimate = (int)(1.5*mem_estimate)+1;
482: PetscMalloc(new_estimate*sizeof(int),&tmp);
483: PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(int));
484: PetscFree(xdata[0]);
485: xdata[0] = tmp;
486: mem_estimate = new_estimate; ++no_malloc;
487: for (ctr=1; ctr<=i; ctr++) { xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];}
488: }
489: xdata[i][ct2++] = row;
490: ct3++;
491: }
492: }
493: for (k=oct2,max2=ct2; k<max2; k++) {
494: row = xdata[i][k] - rstart;
495: start = ai[row];
496: end = ai[row+1];
497: for (l=start; l<end; l++) {
498: val = aj[l] + cstart;
499: if (!PetscBTLookupSet(xtable,val)) {
500: if (!(ct3 < mem_estimate)) {
501: new_estimate = (int)(1.5*mem_estimate)+1;
502: PetscMalloc(new_estimate*sizeof(int),&tmp);
503: PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(int));
504: PetscFree(xdata[0]);
505: xdata[0] = tmp;
506: mem_estimate = new_estimate; ++no_malloc;
507: for (ctr=1; ctr<=i; ctr++) { xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];}
508: }
509: xdata[i][ct2++] = val;
510: ct3++;
511: }
512: }
513: start = bi[row];
514: end = bi[row+1];
515: for (l=start; l<end; l++) {
516: val = garray[bj[l]];
517: if (!PetscBTLookupSet(xtable,val)) {
518: if (!(ct3 < mem_estimate)) {
519: new_estimate = (int)(1.5*mem_estimate)+1;
520: PetscMalloc(new_estimate*sizeof(int),&tmp);
521: PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(int));
522: PetscFree(xdata[0]);
523: xdata[0] = tmp;
524: mem_estimate = new_estimate; ++no_malloc;
525: for (ctr =1; ctr <=i; ctr++) { xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];}
526: }
527: xdata[i][ct2++] = val;
528: ct3++;
529: }
530: }
531: }
532: /* Update the header*/
533: xdata[i][2*j] = ct2 - oct2; /* Undo the vector isz1 and use only a var*/
534: xdata[i][2*j-1] = rbuf_i[2*j-1];
535: }
536: xdata[i][0] = rbuf_0;
537: xdata[i+1] = xdata[i] + ct2;
538: isz1[i] = ct2; /* size of each message */
539: }
540: PetscBTDestroy(xtable);
541: PetscLogInfo(0,"MatIncreaseOverlap_MPIAIJ:[%d] Allocated %d bytes, required %d bytes, no of mallocs = %d\n",rank,mem_estimate, ct3,no_malloc);
542: return(0);
543: }
544: /* -------------------------------------------------------------------------*/
545: EXTERN int MatGetSubMatrices_MPIAIJ_Local(Mat,int,const IS[],const IS[],MatReuse,Mat*);
546: EXTERN int MatAssemblyEnd_SeqAIJ(Mat,MatAssemblyType);
547: /*
548: Every processor gets the entire matrix
549: */
552: int MatGetSubMatrix_MPIAIJ_All(Mat A,MatReuse scall,Mat *Bin[])
553: {
554: Mat B;
555: Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data;
556: Mat_SeqAIJ *b,*ad = (Mat_SeqAIJ*)a->A->data,*bd = (Mat_SeqAIJ*)a->B->data;
557: int ierr,sendcount,*recvcounts = 0,*displs = 0,size,i,*rstarts = a->rowners,rank,n,cnt,j;
558: int m,*b_sendj,*garray = a->garray,*lens,*jsendbuf,*a_jsendbuf,*b_jsendbuf;
559: PetscScalar *sendbuf,*recvbuf,*a_sendbuf,*b_sendbuf;
562: MPI_Comm_size(A->comm,&size);
563: MPI_Comm_rank(A->comm,&rank);
565: if (scall == MAT_INITIAL_MATRIX) {
566: /* ----------------------------------------------------------------
567: Tell every processor the number of nonzeros per row
568: */
569: PetscMalloc(A->M*sizeof(int),&lens);
570: for (i=a->rstart; i<a->rend; i++) {
571: lens[i] = ad->i[i-a->rstart+1] - ad->i[i-a->rstart] + bd->i[i-a->rstart+1] - bd->i[i-a->rstart];
572: }
573: sendcount = a->rend - a->rstart;
574: PetscMalloc(2*size*sizeof(int),&recvcounts);
575: displs = recvcounts + size;
576: for (i=0; i<size; i++) {
577: recvcounts[i] = a->rowners[i+1] - a->rowners[i];
578: displs[i] = a->rowners[i];
579: }
580: MPI_Allgatherv(lens+a->rstart,sendcount,MPI_INT,lens,recvcounts,displs,MPI_INT,A->comm);
582: /* ---------------------------------------------------------------
583: Create the sequential matrix
584: */
585: MatCreateSeqAIJ(PETSC_COMM_SELF,A->M,A->N,0,lens,&B);
586: PetscMalloc(sizeof(Mat),Bin);
587: **Bin = B;
588: b = (Mat_SeqAIJ *)B->data;
590: /*--------------------------------------------------------------------
591: Copy my part of matrix column indices over
592: */
593: sendcount = ad->nz + bd->nz;
594: jsendbuf = b->j + b->i[rstarts[rank]];
595: a_jsendbuf = ad->j;
596: b_jsendbuf = bd->j;
597: n = a->rend - a->rstart;
598: cnt = 0;
599: for (i=0; i<n; i++) {
601: /* put in lower diagonal portion */
602: m = bd->i[i+1] - bd->i[i];
603: while (m > 0) {
604: /* is it above diagonal (in bd (compressed) numbering) */
605: if (garray[*b_jsendbuf] > a->rstart + i) break;
606: jsendbuf[cnt++] = garray[*b_jsendbuf++];
607: m--;
608: }
610: /* put in diagonal portion */
611: for (j=ad->i[i]; j<ad->i[i+1]; j++) {
612: jsendbuf[cnt++] = a->rstart + *a_jsendbuf++;
613: }
615: /* put in upper diagonal portion */
616: while (m-- > 0) {
617: jsendbuf[cnt++] = garray[*b_jsendbuf++];
618: }
619: }
620: if (cnt != sendcount) SETERRQ2(1,"Corrupted PETSc matrix: nz given %d actual nz %d",sendcount,cnt);
622: /*--------------------------------------------------------------------
623: Gather all column indices to all processors
624: */
625: for (i=0; i<size; i++) {
626: recvcounts[i] = 0;
627: for (j=a->rowners[i]; j<a->rowners[i+1]; j++) {
628: recvcounts[i] += lens[j];
629: }
630: }
631: displs[0] = 0;
632: for (i=1; i<size; i++) {
633: displs[i] = displs[i-1] + recvcounts[i-1];
634: }
635: MPI_Allgatherv(jsendbuf,sendcount,MPI_INT,b->j,recvcounts,displs,MPI_INT,A->comm);
637: /*--------------------------------------------------------------------
638: Assemble the matrix into useable form (note numerical values not yet set)
639: */
640: /* set the b->ilen (length of each row) values */
641: PetscMemcpy(b->ilen,lens,A->M*sizeof(int));
642: /* set the b->i indices */
643: b->i[0] = 0;
644: for (i=1; i<=A->M; i++) {
645: b->i[i] = b->i[i-1] + lens[i-1];
646: }
647: PetscFree(lens);
648: MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
649: MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
650: } else {
651: B = **Bin;
652: b = (Mat_SeqAIJ *)B->data;
653: }
655: /*--------------------------------------------------------------------
656: Copy my part of matrix numerical values into the values location
657: */
658: sendcount = ad->nz + bd->nz;
659: sendbuf = b->a + b->i[rstarts[rank]];
660: a_sendbuf = ad->a;
661: b_sendbuf = bd->a;
662: b_sendj = bd->j;
663: n = a->rend - a->rstart;
664: cnt = 0;
665: for (i=0; i<n; i++) {
667: /* put in lower diagonal portion */
668: m = bd->i[i+1] - bd->i[i];
669: while (m > 0) {
670: /* is it above diagonal (in bd (compressed) numbering) */
671: if (garray[*b_sendj] > a->rstart + i) break;
672: sendbuf[cnt++] = *b_sendbuf++;
673: m--;
674: b_sendj++;
675: }
677: /* put in diagonal portion */
678: for (j=ad->i[i]; j<ad->i[i+1]; j++) {
679: sendbuf[cnt++] = *a_sendbuf++;
680: }
682: /* put in upper diagonal portion */
683: while (m-- > 0) {
684: sendbuf[cnt++] = *b_sendbuf++;
685: b_sendj++;
686: }
687: }
688: if (cnt != sendcount) SETERRQ2(1,"Corrupted PETSc matrix: nz given %d actual nz %d",sendcount,cnt);
689:
690: /* -----------------------------------------------------------------
691: Gather all numerical values to all processors
692: */
693: if (!recvcounts) {
694: PetscMalloc(2*size*sizeof(int),&recvcounts);
695: displs = recvcounts + size;
696: }
697: for (i=0; i<size; i++) {
698: recvcounts[i] = b->i[rstarts[i+1]] - b->i[rstarts[i]];
699: }
700: displs[0] = 0;
701: for (i=1; i<size; i++) {
702: displs[i] = displs[i-1] + recvcounts[i-1];
703: }
704: recvbuf = b->a;
705: MPI_Allgatherv(sendbuf,sendcount,MPIU_SCALAR,recvbuf,recvcounts,displs,MPIU_SCALAR,A->comm);
706: PetscFree(recvcounts);
708: return(0);
709: }
713: int MatGetSubMatrices_MPIAIJ(Mat C,int ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
714: {
715: int nmax,nstages_local,nstages,i,pos,max_no,ierr,nrow,ncol;
716: PetscTruth rowflag,colflag,wantallmatrix = PETSC_FALSE,twantallmatrix;
719: /*
720: Check for special case each processor gets entire matrix
721: */
722: if (ismax == 1 && C->M == C->N) {
723: ISIdentity(*isrow,&rowflag);
724: ISIdentity(*iscol,&colflag);
725: ISGetLocalSize(*isrow,&nrow);
726: ISGetLocalSize(*iscol,&ncol);
727: if (rowflag && colflag && nrow == C->M && ncol == C->N) {
728: wantallmatrix = PETSC_TRUE;
729: PetscOptionsGetLogical(C->prefix,"-use_fast_submatrix",&wantallmatrix,PETSC_NULL);
730: }
731: }
732: MPI_Allreduce(&wantallmatrix,&twantallmatrix,1,MPI_INT,MPI_MIN,C->comm);
733: if (twantallmatrix) {
734: MatGetSubMatrix_MPIAIJ_All(C,scall,submat);
735: return(0);
736: }
738: /* Allocate memory to hold all the submatrices */
739: if (scall != MAT_REUSE_MATRIX) {
740: PetscMalloc((ismax+1)*sizeof(Mat),submat);
741: }
742: /* Determine the number of stages through which submatrices are done */
743: nmax = 20*1000000 / (C->N * sizeof(int));
744: if (!nmax) nmax = 1;
745: nstages_local = ismax/nmax + ((ismax % nmax)?1:0);
747: /* Make sure every processor loops through the nstages */
748: MPI_Allreduce(&nstages_local,&nstages,1,MPI_INT,MPI_MAX,C->comm);
750: for (i=0,pos=0; i<nstages; i++) {
751: if (pos+nmax <= ismax) max_no = nmax;
752: else if (pos == ismax) max_no = 0;
753: else max_no = ismax-pos;
754: MatGetSubMatrices_MPIAIJ_Local(C,max_no,isrow+pos,iscol+pos,scall,*submat+pos);
755: pos += max_no;
756: }
757: return(0);
758: }
759: /* -------------------------------------------------------------------------*/
762: int MatGetSubMatrices_MPIAIJ_Local(Mat C,int ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submats)
763: {
764: Mat_MPIAIJ *c = (Mat_MPIAIJ*)C->data;
765: Mat A = c->A;
766: Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*b = (Mat_SeqAIJ*)c->B->data,*mat;
767: int **irow,**icol,*nrow,*ncol,*w1,*w2,*w3,*w4,*rtable,start,end,size;
768: int **sbuf1,**sbuf2,rank,m,i,j,k,l,ct1,ct2,ierr,**rbuf1,row,proc;
769: int nrqs,msz,**ptr,idex,*req_size,*ctr,*pa,*tmp,tcol,nrqr;
770: int **rbuf3,*req_source,**sbuf_aj,**rbuf2,max1,max2,**rmap;
771: int **cmap,**lens,is_no,ncols,*cols,mat_i,*mat_j,tmp2,jmax,*irow_i;
772: int len,ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*cmap_i,*lens_i;
773: int *rmap_i,tag0,tag1,tag2,tag3;
774: MPI_Request *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3;
775: MPI_Request *r_waits4,*s_waits3,*s_waits4;
776: MPI_Status *r_status1,*r_status2,*s_status1,*s_status3,*s_status2;
777: MPI_Status *r_status3,*r_status4,*s_status4;
778: MPI_Comm comm;
779: PetscScalar **rbuf4,**sbuf_aa,*vals,*mat_a,*sbuf_aa_i;
780: PetscTruth sorted;
781: int *onodes1,*olengths1;
784: comm = C->comm;
785: tag0 = C->tag;
786: size = c->size;
787: rank = c->rank;
788: m = C->M;
789:
790: /* Get some new tags to keep the communication clean */
791: PetscObjectGetNewTag((PetscObject)C,&tag1);
792: PetscObjectGetNewTag((PetscObject)C,&tag2);
793: PetscObjectGetNewTag((PetscObject)C,&tag3);
795: /* Check if the col indices are sorted */
796: for (i=0; i<ismax; i++) {
797: ISSorted(isrow[i],&sorted);
798: if (!sorted) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"ISrow is not sorted");
799: ISSorted(iscol[i],&sorted);
800: /* if (!sorted) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"IScol is not sorted"); */
801: }
803: len = (2*ismax+1)*(sizeof(int*)+ sizeof(int)) + (m+1)*sizeof(int);
804: PetscMalloc(len,&irow);
805: icol = irow + ismax;
806: nrow = (int*)(icol + ismax);
807: ncol = nrow + ismax;
808: rtable = ncol + ismax;
810: for (i=0; i<ismax; i++) {
811: ISGetIndices(isrow[i],&irow[i]);
812: ISGetIndices(iscol[i],&icol[i]);
813: ISGetLocalSize(isrow[i],&nrow[i]);
814: ISGetLocalSize(iscol[i],&ncol[i]);
815: }
817: /* Create hash table for the mapping :row -> proc*/
818: for (i=0,j=0; i<size; i++) {
819: jmax = c->rowners[i+1];
820: for (; j<jmax; j++) {
821: rtable[j] = i;
822: }
823: }
825: /* evaluate communication - mesg to who, length of mesg, and buffer space
826: required. Based on this, buffers are allocated, and data copied into them*/
827: PetscMalloc(size*4*sizeof(int),&w1); /* mesg size */
828: w2 = w1 + size; /* if w2[i] marked, then a message to proc i*/
829: w3 = w2 + size; /* no of IS that needs to be sent to proc i */
830: w4 = w3 + size; /* temp work space used in determining w1, w2, w3 */
831: PetscMemzero(w1,size*3*sizeof(int)); /* initialize work vector*/
832: for (i=0; i<ismax; i++) {
833: PetscMemzero(w4,size*sizeof(int)); /* initialize work vector*/
834: jmax = nrow[i];
835: irow_i = irow[i];
836: for (j=0; j<jmax; j++) {
837: row = irow_i[j];
838: proc = rtable[row];
839: w4[proc]++;
840: }
841: for (j=0; j<size; j++) {
842: if (w4[j]) { w1[j] += w4[j]; w3[j]++;}
843: }
844: }
845:
846: nrqs = 0; /* no of outgoing messages */
847: msz = 0; /* total mesg length (for all procs) */
848: w1[rank] = 0; /* no mesg sent to self */
849: w3[rank] = 0;
850: for (i=0; i<size; i++) {
851: if (w1[i]) { w2[i] = 1; nrqs++;} /* there exists a message to proc i */
852: }
853: PetscMalloc((nrqs+1)*sizeof(int),&pa); /*(proc -array)*/
854: for (i=0,j=0; i<size; i++) {
855: if (w1[i]) { pa[j] = i; j++; }
856: }
858: /* Each message would have a header = 1 + 2*(no of IS) + data */
859: for (i=0; i<nrqs; i++) {
860: j = pa[i];
861: w1[j] += w2[j] + 2* w3[j];
862: msz += w1[j];
863: }
865: /* Determine the number of messages to expect, their lengths, from from-ids */
866: PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);
867: PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);
869: /* Now post the Irecvs corresponding to these messages */
870: PetscPostIrecvInt(comm,tag0,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);
871:
872: PetscFree(onodes1);
873: PetscFree(olengths1);
874:
875: /* Allocate Memory for outgoing messages */
876: len = 2*size*sizeof(int*) + 2*msz*sizeof(int) + size*sizeof(int);
877: PetscMalloc(len,&sbuf1);
878: ptr = sbuf1 + size; /* Pointers to the data in outgoing buffers */
879: PetscMemzero(sbuf1,2*size*sizeof(int*));
880: /* allocate memory for outgoing data + buf to receive the first reply */
881: tmp = (int*)(ptr + size);
882: ctr = tmp + 2*msz;
884: {
885: int *iptr = tmp,ict = 0;
886: for (i=0; i<nrqs; i++) {
887: j = pa[i];
888: iptr += ict;
889: sbuf1[j] = iptr;
890: ict = w1[j];
891: }
892: }
894: /* Form the outgoing messages */
895: /* Initialize the header space */
896: for (i=0; i<nrqs; i++) {
897: j = pa[i];
898: sbuf1[j][0] = 0;
899: PetscMemzero(sbuf1[j]+1,2*w3[j]*sizeof(int));
900: ptr[j] = sbuf1[j] + 2*w3[j] + 1;
901: }
902:
903: /* Parse the isrow and copy data into outbuf */
904: for (i=0; i<ismax; i++) {
905: PetscMemzero(ctr,size*sizeof(int));
906: irow_i = irow[i];
907: jmax = nrow[i];
908: for (j=0; j<jmax; j++) { /* parse the indices of each IS */
909: row = irow_i[j];
910: proc = rtable[row];
911: if (proc != rank) { /* copy to the outgoing buf*/
912: ctr[proc]++;
913: *ptr[proc] = row;
914: ptr[proc]++;
915: }
916: }
917: /* Update the headers for the current IS */
918: for (j=0; j<size; j++) { /* Can Optimise this loop too */
919: if ((ctr_j = ctr[j])) {
920: sbuf1_j = sbuf1[j];
921: k = ++sbuf1_j[0];
922: sbuf1_j[2*k] = ctr_j;
923: sbuf1_j[2*k-1] = i;
924: }
925: }
926: }
928: /* Now post the sends */
929: PetscMalloc((nrqs+1)*sizeof(MPI_Request),&s_waits1);
930: for (i=0; i<nrqs; ++i) {
931: j = pa[i];
932: MPI_Isend(sbuf1[j],w1[j],MPI_INT,j,tag0,comm,s_waits1+i);
933: }
935: /* Post Receives to capture the buffer size */
936: PetscMalloc((nrqs+1)*sizeof(MPI_Request),&r_waits2);
937: PetscMalloc((nrqs+1)*sizeof(int *),&rbuf2);
938: rbuf2[0] = tmp + msz;
939: for (i=1; i<nrqs; ++i) {
940: rbuf2[i] = rbuf2[i-1]+w1[pa[i-1]];
941: }
942: for (i=0; i<nrqs; ++i) {
943: j = pa[i];
944: MPI_Irecv(rbuf2[i],w1[j],MPI_INT,j,tag1,comm,r_waits2+i);
945: }
947: /* Send to other procs the buf size they should allocate */
948:
950: /* Receive messages*/
951: PetscMalloc((nrqr+1)*sizeof(MPI_Request),&s_waits2);
952: PetscMalloc((nrqr+1)*sizeof(MPI_Status),&r_status1);
953: len = 2*nrqr*sizeof(int) + (nrqr+1)*sizeof(int*);
954: PetscMalloc(len,&sbuf2);
955: req_size = (int*)(sbuf2 + nrqr);
956: req_source = req_size + nrqr;
957:
958: {
959: Mat_SeqAIJ *sA = (Mat_SeqAIJ*)c->A->data,*sB = (Mat_SeqAIJ*)c->B->data;
960: int *sAi = sA->i,*sBi = sB->i,id,rstart = c->rstart;
961: int *sbuf2_i;
963: for (i=0; i<nrqr; ++i) {
964: MPI_Waitany(nrqr,r_waits1,&idex,r_status1+i);
965: req_size[idex] = 0;
966: rbuf1_i = rbuf1[idex];
967: start = 2*rbuf1_i[0] + 1;
968: MPI_Get_count(r_status1+i,MPI_INT,&end);
969: PetscMalloc((end+1)*sizeof(int),&sbuf2[idex]);
970: sbuf2_i = sbuf2[idex];
971: for (j=start; j<end; j++) {
972: id = rbuf1_i[j] - rstart;
973: ncols = sAi[id+1] - sAi[id] + sBi[id+1] - sBi[id];
974: sbuf2_i[j] = ncols;
975: req_size[idex] += ncols;
976: }
977: req_source[idex] = r_status1[i].MPI_SOURCE;
978: /* form the header */
979: sbuf2_i[0] = req_size[idex];
980: for (j=1; j<start; j++) { sbuf2_i[j] = rbuf1_i[j]; }
981: MPI_Isend(sbuf2_i,end,MPI_INT,req_source[idex],tag1,comm,s_waits2+i);
982: }
983: }
984: PetscFree(r_status1);
985: PetscFree(r_waits1);
987: /* recv buffer sizes */
988: /* Receive messages*/
989:
990: PetscMalloc((nrqs+1)*sizeof(int*),&rbuf3);
991: PetscMalloc((nrqs+1)*sizeof(PetscScalar*),&rbuf4);
992: PetscMalloc((nrqs+1)*sizeof(MPI_Request),&r_waits3);
993: PetscMalloc((nrqs+1)*sizeof(MPI_Request),&r_waits4);
994: PetscMalloc((nrqs+1)*sizeof(MPI_Status),&r_status2);
996: for (i=0; i<nrqs; ++i) {
997: MPI_Waitany(nrqs,r_waits2,&idex,r_status2+i);
998: PetscMalloc((rbuf2[idex][0]+1)*sizeof(int),&rbuf3[idex]);
999: PetscMalloc((rbuf2[idex][0]+1)*sizeof(PetscScalar),&rbuf4[idex]);
1000: MPI_Irecv(rbuf3[idex],rbuf2[idex][0],MPI_INT,r_status2[i].MPI_SOURCE,tag2,comm,r_waits3+idex);
1001: MPI_Irecv(rbuf4[idex],rbuf2[idex][0],MPIU_SCALAR,r_status2[i].MPI_SOURCE,tag3,comm,r_waits4+idex);
1002: }
1003: PetscFree(r_status2);
1004: PetscFree(r_waits2);
1005:
1006: /* Wait on sends1 and sends2 */
1007: PetscMalloc((nrqs+1)*sizeof(MPI_Status),&s_status1);
1008: PetscMalloc((nrqr+1)*sizeof(MPI_Status),&s_status2);
1010: MPI_Waitall(nrqs,s_waits1,s_status1);
1011: MPI_Waitall(nrqr,s_waits2,s_status2);
1012: PetscFree(s_status1);
1013: PetscFree(s_status2);
1014: PetscFree(s_waits1);
1015: PetscFree(s_waits2);
1017: /* Now allocate buffers for a->j, and send them off */
1018: PetscMalloc((nrqr+1)*sizeof(int*),&sbuf_aj);
1019: for (i=0,j=0; i<nrqr; i++) j += req_size[i];
1020: PetscMalloc((j+1)*sizeof(int),&sbuf_aj[0]);
1021: for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1];
1022:
1023: PetscMalloc((nrqr+1)*sizeof(MPI_Request),&s_waits3);
1024: {
1025: int nzA,nzB,*a_i = a->i,*b_i = b->i,imark;
1026: int *cworkA,*cworkB,cstart = c->cstart,rstart = c->rstart,*bmap = c->garray;
1027: int *a_j = a->j,*b_j = b->j,ctmp;
1029: for (i=0; i<nrqr; i++) {
1030: rbuf1_i = rbuf1[i];
1031: sbuf_aj_i = sbuf_aj[i];
1032: ct1 = 2*rbuf1_i[0] + 1;
1033: ct2 = 0;
1034: for (j=1,max1=rbuf1_i[0]; j<=max1; j++) {
1035: kmax = rbuf1[i][2*j];
1036: for (k=0; k<kmax; k++,ct1++) {
1037: row = rbuf1_i[ct1] - rstart;
1038: nzA = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row];
1039: ncols = nzA + nzB;
1040: cworkA = a_j + a_i[row]; cworkB = b_j + b_i[row];
1042: /* load the column indices for this row into cols*/
1043: cols = sbuf_aj_i + ct2;
1044:
1045: for (l=0; l<nzB; l++) {
1046: if ((ctmp = bmap[cworkB[l]]) < cstart) cols[l] = ctmp;
1047: else break;
1048: }
1049: imark = l;
1050: for (l=0; l<nzA; l++) cols[imark+l] = cstart + cworkA[l];
1051: for (l=imark; l<nzB; l++) cols[nzA+l] = bmap[cworkB[l]];
1053: ct2 += ncols;
1054: }
1055: }
1056: MPI_Isend(sbuf_aj_i,req_size[i],MPI_INT,req_source[i],tag2,comm,s_waits3+i);
1057: }
1058: }
1059: PetscMalloc((nrqs+1)*sizeof(MPI_Status),&r_status3);
1060: PetscMalloc((nrqr+1)*sizeof(MPI_Status),&s_status3);
1062: /* Allocate buffers for a->a, and send them off */
1063: PetscMalloc((nrqr+1)*sizeof(PetscScalar*),&sbuf_aa);
1064: for (i=0,j=0; i<nrqr; i++) j += req_size[i];
1065: PetscMalloc((j+1)*sizeof(PetscScalar),&sbuf_aa[0]);
1066: for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1];
1067:
1068: PetscMalloc((nrqr+1)*sizeof(MPI_Request),&s_waits4);
1069: {
1070: int nzA,nzB,*a_i = a->i,*b_i = b->i, *cworkB,imark;
1071: int cstart = c->cstart,rstart = c->rstart,*bmap = c->garray;
1072: int *b_j = b->j;
1073: PetscScalar *vworkA,*vworkB,*a_a = a->a,*b_a = b->a;
1074:
1075: for (i=0; i<nrqr; i++) {
1076: rbuf1_i = rbuf1[i];
1077: sbuf_aa_i = sbuf_aa[i];
1078: ct1 = 2*rbuf1_i[0]+1;
1079: ct2 = 0;
1080: for (j=1,max1=rbuf1_i[0]; j<=max1; j++) {
1081: kmax = rbuf1_i[2*j];
1082: for (k=0; k<kmax; k++,ct1++) {
1083: row = rbuf1_i[ct1] - rstart;
1084: nzA = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row];
1085: ncols = nzA + nzB;
1086: cworkB = b_j + b_i[row];
1087: vworkA = a_a + a_i[row];
1088: vworkB = b_a + b_i[row];
1090: /* load the column values for this row into vals*/
1091: vals = sbuf_aa_i+ct2;
1092:
1093: for (l=0; l<nzB; l++) {
1094: if ((bmap[cworkB[l]]) < cstart) vals[l] = vworkB[l];
1095: else break;
1096: }
1097: imark = l;
1098: for (l=0; l<nzA; l++) vals[imark+l] = vworkA[l];
1099: for (l=imark; l<nzB; l++) vals[nzA+l] = vworkB[l];
1100:
1101: ct2 += ncols;
1102: }
1103: }
1104: MPI_Isend(sbuf_aa_i,req_size[i],MPIU_SCALAR,req_source[i],tag3,comm,s_waits4+i);
1105: }
1106: }
1107: PetscMalloc((nrqs+1)*sizeof(MPI_Status),&r_status4);
1108: PetscMalloc((nrqr+1)*sizeof(MPI_Status),&s_status4);
1109: PetscFree(rbuf1);
1111: /* Form the matrix */
1112: /* create col map */
1113: {
1114: int *icol_i;
1115:
1116: len = (1+ismax)*sizeof(int*)+ ismax*C->N*sizeof(int);
1117: PetscMalloc(len,&cmap);
1118: cmap[0] = (int *)(cmap + ismax);
1119: PetscMemzero(cmap[0],(1+ismax*C->N)*sizeof(int));
1120: for (i=1; i<ismax; i++) { cmap[i] = cmap[i-1] + C->N; }
1121: for (i=0; i<ismax; i++) {
1122: jmax = ncol[i];
1123: icol_i = icol[i];
1124: cmap_i = cmap[i];
1125: for (j=0; j<jmax; j++) {
1126: cmap_i[icol_i[j]] = j+1;
1127: }
1128: }
1129: }
1131: /* Create lens which is required for MatCreate... */
1132: for (i=0,j=0; i<ismax; i++) { j += nrow[i]; }
1133: len = (1+ismax)*sizeof(int*)+ j*sizeof(int);
1134: PetscMalloc(len,&lens);
1135: lens[0] = (int *)(lens + ismax);
1136: PetscMemzero(lens[0],j*sizeof(int));
1137: for (i=1; i<ismax; i++) { lens[i] = lens[i-1] + nrow[i-1]; }
1138:
1139: /* Update lens from local data */
1140: for (i=0; i<ismax; i++) {
1141: jmax = nrow[i];
1142: cmap_i = cmap[i];
1143: irow_i = irow[i];
1144: lens_i = lens[i];
1145: for (j=0; j<jmax; j++) {
1146: row = irow_i[j];
1147: proc = rtable[row];
1148: if (proc == rank) {
1149: MatGetRow_MPIAIJ(C,row,&ncols,&cols,0);
1150: for (k=0; k<ncols; k++) {
1151: if (cmap_i[cols[k]]) { lens_i[j]++;}
1152: }
1153: MatRestoreRow_MPIAIJ(C,row,&ncols,&cols,0);
1154: }
1155: }
1156: }
1157:
1158: /* Create row map*/
1159: len = (1+ismax)*sizeof(int*)+ ismax*C->M*sizeof(int);
1160: PetscMalloc(len,&rmap);
1161: rmap[0] = (int *)(rmap + ismax);
1162: PetscMemzero(rmap[0],ismax*C->M*sizeof(int));
1163: for (i=1; i<ismax; i++) { rmap[i] = rmap[i-1] + C->M;}
1164: for (i=0; i<ismax; i++) {
1165: rmap_i = rmap[i];
1166: irow_i = irow[i];
1167: jmax = nrow[i];
1168: for (j=0; j<jmax; j++) {
1169: rmap_i[irow_i[j]] = j;
1170: }
1171: }
1172:
1173: /* Update lens from offproc data */
1174: {
1175: int *rbuf2_i,*rbuf3_i,*sbuf1_i;
1177: for (tmp2=0; tmp2<nrqs; tmp2++) {
1178: MPI_Waitany(nrqs,r_waits3,&i,r_status3+tmp2);
1179: idex = pa[i];
1180: sbuf1_i = sbuf1[idex];
1181: jmax = sbuf1_i[0];
1182: ct1 = 2*jmax+1;
1183: ct2 = 0;
1184: rbuf2_i = rbuf2[i];
1185: rbuf3_i = rbuf3[i];
1186: for (j=1; j<=jmax; j++) {
1187: is_no = sbuf1_i[2*j-1];
1188: max1 = sbuf1_i[2*j];
1189: lens_i = lens[is_no];
1190: cmap_i = cmap[is_no];
1191: rmap_i = rmap[is_no];
1192: for (k=0; k<max1; k++,ct1++) {
1193: row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */
1194: max2 = rbuf2_i[ct1];
1195: for (l=0; l<max2; l++,ct2++) {
1196: if (cmap_i[rbuf3_i[ct2]]) {
1197: lens_i[row]++;
1198: }
1199: }
1200: }
1201: }
1202: }
1203: }
1204: PetscFree(r_status3);
1205: PetscFree(r_waits3);
1206: MPI_Waitall(nrqr,s_waits3,s_status3);
1207: PetscFree(s_status3);
1208: PetscFree(s_waits3);
1210: /* Create the submatrices */
1211: if (scall == MAT_REUSE_MATRIX) {
1212: PetscTruth flag;
1214: /*
1215: Assumes new rows are same length as the old rows,hence bug!
1216: */
1217: for (i=0; i<ismax; i++) {
1218: mat = (Mat_SeqAIJ *)(submats[i]->data);
1219: if ((submats[i]->m != nrow[i]) || (submats[i]->n != ncol[i])) {
1220: SETERRQ(PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size");
1221: }
1222: PetscMemcmp(mat->ilen,lens[i],submats[i]->m*sizeof(int),&flag);
1223: if (flag == PETSC_FALSE) {
1224: SETERRQ(PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong no of nonzeros");
1225: }
1226: /* Initial matrix as if empty */
1227: PetscMemzero(mat->ilen,submats[i]->m*sizeof(int));
1228: submats[i]->factor = C->factor;
1229: }
1230: } else {
1231: for (i=0; i<ismax; i++) {
1232: MatCreateSeqAIJ(PETSC_COMM_SELF,nrow[i],ncol[i],0,lens[i],submats+i);
1233: }
1234: }
1236: /* Assemble the matrices */
1237: /* First assemble the local rows */
1238: {
1239: int ilen_row,*imat_ilen,*imat_j,*imat_i,old_row;
1240: PetscScalar *imat_a;
1241:
1242: for (i=0; i<ismax; i++) {
1243: mat = (Mat_SeqAIJ*)submats[i]->data;
1244: imat_ilen = mat->ilen;
1245: imat_j = mat->j;
1246: imat_i = mat->i;
1247: imat_a = mat->a;
1248: cmap_i = cmap[i];
1249: rmap_i = rmap[i];
1250: irow_i = irow[i];
1251: jmax = nrow[i];
1252: for (j=0; j<jmax; j++) {
1253: row = irow_i[j];
1254: proc = rtable[row];
1255: if (proc == rank) {
1256: old_row = row;
1257: row = rmap_i[row];
1258: ilen_row = imat_ilen[row];
1259: MatGetRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);
1260: mat_i = imat_i[row] ;
1261: mat_a = imat_a + mat_i;
1262: mat_j = imat_j + mat_i;
1263: for (k=0; k<ncols; k++) {
1264: if ((tcol = cmap_i[cols[k]])) {
1265: *mat_j++ = tcol - 1;
1266: *mat_a++ = vals[k];
1267: ilen_row++;
1268: }
1269: }
1270: MatRestoreRow_MPIAIJ(C,old_row,&ncols,&cols,&vals);
1271: imat_ilen[row] = ilen_row;
1272: }
1273: }
1274: }
1275: }
1277: /* Now assemble the off proc rows*/
1278: {
1279: int *sbuf1_i,*rbuf2_i,*rbuf3_i,*imat_ilen,ilen;
1280: int *imat_j,*imat_i;
1281: PetscScalar *imat_a,*rbuf4_i;
1283: for (tmp2=0; tmp2<nrqs; tmp2++) {
1284: MPI_Waitany(nrqs,r_waits4,&i,r_status4+tmp2);
1285: idex = pa[i];
1286: sbuf1_i = sbuf1[idex];
1287: jmax = sbuf1_i[0];
1288: ct1 = 2*jmax + 1;
1289: ct2 = 0;
1290: rbuf2_i = rbuf2[i];
1291: rbuf3_i = rbuf3[i];
1292: rbuf4_i = rbuf4[i];
1293: for (j=1; j<=jmax; j++) {
1294: is_no = sbuf1_i[2*j-1];
1295: rmap_i = rmap[is_no];
1296: cmap_i = cmap[is_no];
1297: mat = (Mat_SeqAIJ*)submats[is_no]->data;
1298: imat_ilen = mat->ilen;
1299: imat_j = mat->j;
1300: imat_i = mat->i;
1301: imat_a = mat->a;
1302: max1 = sbuf1_i[2*j];
1303: for (k=0; k<max1; k++,ct1++) {
1304: row = sbuf1_i[ct1];
1305: row = rmap_i[row];
1306: ilen = imat_ilen[row];
1307: mat_i = imat_i[row] ;
1308: mat_a = imat_a + mat_i;
1309: mat_j = imat_j + mat_i;
1310: max2 = rbuf2_i[ct1];
1311: for (l=0; l<max2; l++,ct2++) {
1312: if ((tcol = cmap_i[rbuf3_i[ct2]])) {
1313: *mat_j++ = tcol - 1;
1314: *mat_a++ = rbuf4_i[ct2];
1315: ilen++;
1316: }
1317: }
1318: imat_ilen[row] = ilen;
1319: }
1320: }
1321: }
1322: }
1323: PetscFree(r_status4);
1324: PetscFree(r_waits4);
1325: MPI_Waitall(nrqr,s_waits4,s_status4);
1326: PetscFree(s_waits4);
1327: PetscFree(s_status4);
1329: /* Restore the indices */
1330: for (i=0; i<ismax; i++) {
1331: ISRestoreIndices(isrow[i],irow+i);
1332: ISRestoreIndices(iscol[i],icol+i);
1333: }
1335: /* Destroy allocated memory */
1336: PetscFree(irow);
1337: PetscFree(w1);
1338: PetscFree(pa);
1340: PetscFree(sbuf1);
1341: PetscFree(rbuf2);
1342: for (i=0; i<nrqr; ++i) {
1343: PetscFree(sbuf2[i]);
1344: }
1345: for (i=0; i<nrqs; ++i) {
1346: PetscFree(rbuf3[i]);
1347: PetscFree(rbuf4[i]);
1348: }
1350: PetscFree(sbuf2);
1351: PetscFree(rbuf3);
1352: PetscFree(rbuf4);
1353: PetscFree(sbuf_aj[0]);
1354: PetscFree(sbuf_aj);
1355: PetscFree(sbuf_aa[0]);
1356: PetscFree(sbuf_aa);
1357:
1358: PetscFree(cmap);
1359: PetscFree(rmap);
1360: PetscFree(lens);
1362: for (i=0; i<ismax; i++) {
1363: MatAssemblyBegin(submats[i],MAT_FINAL_ASSEMBLY);
1364: MatAssemblyEnd(submats[i],MAT_FINAL_ASSEMBLY);
1365: }
1366: return(0);
1367: }