Actual source code: matstash.c
1: #define PETSCMAT_DLL
3: #include private/matimpl.h
5: #define DEFAULT_STASH_SIZE 10000
7: /*
8: MatStashCreate_Private - Creates a stash,currently used for all the parallel
9: matrix implementations. The stash is where elements of a matrix destined
10: to be stored on other processors are kept until matrix assembly is done.
12: This is a simple minded stash. Simply adds entries to end of stash.
14: Input Parameters:
15: comm - communicator, required for scatters.
16: bs - stash block size. used when stashing blocks of values
18: Output Parameters:
19: stash - the newly created stash
20: */
23: PetscErrorCode MatStashCreate_Private(MPI_Comm comm,PetscInt bs,MatStash *stash)
24: {
26: PetscInt max,*opt,nopt;
27: PetscTruth flg;
30: /* Require 2 tags,get the second using PetscCommGetNewTag() */
31: stash->comm = comm;
32: PetscCommGetNewTag(stash->comm,&stash->tag1);
33: PetscCommGetNewTag(stash->comm,&stash->tag2);
34: MPI_Comm_size(stash->comm,&stash->size);
35: MPI_Comm_rank(stash->comm,&stash->rank);
37: nopt = stash->size;
38: PetscMalloc(nopt*sizeof(PetscInt),&opt);
39: PetscOptionsGetIntArray(PETSC_NULL,"-matstash_initial_size",opt,&nopt,&flg);
40: if (flg) {
41: if (nopt == 1) max = opt[0];
42: else if (nopt == stash->size) max = opt[stash->rank];
43: else if (stash->rank < nopt) max = opt[stash->rank];
44: else max = 0; /* Use default */
45: stash->umax = max;
46: } else {
47: stash->umax = 0;
48: }
49: PetscFree(opt);
50: if (bs <= 0) bs = 1;
52: stash->bs = bs;
53: stash->nmax = 0;
54: stash->oldnmax = 0;
55: stash->n = 0;
56: stash->reallocs = -1;
57: stash->space_head = 0;
58: stash->space = 0;
60: stash->send_waits = 0;
61: stash->recv_waits = 0;
62: stash->send_status = 0;
63: stash->nsends = 0;
64: stash->nrecvs = 0;
65: stash->svalues = 0;
66: stash->rvalues = 0;
67: stash->rindices = 0;
68: stash->nprocs = 0;
69: stash->nprocessed = 0;
70: return(0);
71: }
73: /*
74: MatStashDestroy_Private - Destroy the stash
75: */
78: PetscErrorCode MatStashDestroy_Private(MatStash *stash)
79: {
83: if (stash->space_head){
84: PetscMatStashSpaceDestroy(stash->space_head);
85: stash->space_head = 0;
86: stash->space = 0;
87: }
88: return(0);
89: }
91: /*
92: MatStashScatterEnd_Private - This is called as the fial stage of
93: scatter. The final stages of messagepassing is done here, and
94: all the memory used for messagepassing is cleanedu up. This
95: routine also resets the stash, and deallocates the memory used
96: for the stash. It also keeps track of the current memory usage
97: so that the same value can be used the next time through.
98: */
101: PetscErrorCode MatStashScatterEnd_Private(MatStash *stash)
102: {
104: PetscInt nsends=stash->nsends,bs2,oldnmax;
105: MPI_Status *send_status;
108: /* wait on sends */
109: if (nsends) {
110: PetscMalloc(2*nsends*sizeof(MPI_Status),&send_status);
111: MPI_Waitall(2*nsends,stash->send_waits,send_status);
112: PetscFree(send_status);
113: }
115: /* Now update nmaxold to be app 10% more than max n used, this way the
116: wastage of space is reduced the next time this stash is used.
117: Also update the oldmax, only if it increases */
118: if (stash->n) {
119: bs2 = stash->bs*stash->bs;
120: oldnmax = ((int)(stash->n * 1.1) + 5)*bs2;
121: if (oldnmax > stash->oldnmax) stash->oldnmax = oldnmax;
122: }
124: stash->nmax = 0;
125: stash->n = 0;
126: stash->reallocs = -1;
127: stash->nprocessed = 0;
128: if (stash->space_head){
129: PetscMatStashSpaceDestroy(stash->space_head);
130: stash->space_head = 0;
131: stash->space = 0;
132: }
133: PetscFree(stash->send_waits);
134: stash->send_waits = 0;
135: PetscFree(stash->recv_waits);
136: stash->recv_waits = 0;
137: PetscFree(stash->svalues);
138: stash->svalues = 0;
139: PetscFree(stash->rvalues);
140: stash->rvalues = 0;
141: PetscFree(stash->rindices);
142: stash->rindices = 0;
143: PetscFree(stash->nprocs);
144: stash->nprocs = 0;
145: return(0);
146: }
148: /*
149: MatStashGetInfo_Private - Gets the relavant statistics of the stash
151: Input Parameters:
152: stash - the stash
153: nstash - the size of the stash. Indicates the number of values stored.
154: reallocs - the number of additional mallocs incurred.
155:
156: */
159: PetscErrorCode MatStashGetInfo_Private(MatStash *stash,PetscInt *nstash,PetscInt *reallocs)
160: {
161: PetscInt bs2 = stash->bs*stash->bs;
164: if (nstash) *nstash = stash->n*bs2;
165: if (reallocs) {
166: if (stash->reallocs < 0) *reallocs = 0;
167: else *reallocs = stash->reallocs;
168: }
169: return(0);
170: }
172: /*
173: MatStashSetInitialSize_Private - Sets the initial size of the stash
175: Input Parameters:
176: stash - the stash
177: max - the value that is used as the max size of the stash.
178: this value is used while allocating memory.
179: */
182: PetscErrorCode MatStashSetInitialSize_Private(MatStash *stash,PetscInt max)
183: {
185: stash->umax = max;
186: return(0);
187: }
189: /* MatStashExpand_Private - Expand the stash. This function is called
190: when the space in the stash is not sufficient to add the new values
191: being inserted into the stash.
192:
193: Input Parameters:
194: stash - the stash
195: incr - the minimum increase requested
196:
197: Notes:
198: This routine doubles the currently used memory.
199: */
202: static PetscErrorCode MatStashExpand_Private(MatStash *stash,PetscInt incr)
203: {
205: PetscInt newnmax,bs2= stash->bs*stash->bs;
208: /* allocate a larger stash */
209: if (!stash->oldnmax && !stash->nmax) { /* new stash */
210: if (stash->umax) newnmax = stash->umax/bs2;
211: else newnmax = DEFAULT_STASH_SIZE/bs2;
212: } else if (!stash->nmax) { /* resuing stash */
213: if (stash->umax > stash->oldnmax) newnmax = stash->umax/bs2;
214: else newnmax = stash->oldnmax/bs2;
215: } else newnmax = stash->nmax*2;
216: if (newnmax < (stash->nmax + incr)) newnmax += 2*incr;
218: /* Get a MatStashSpace and attach it to stash */
219: PetscMatStashSpaceGet(bs2,newnmax,&stash->space);
220: if (!stash->space_head) { /* new stash or resuing stash->oldnmax */
221: stash->space_head = stash->space;
222: }
224: stash->reallocs++;
225: stash->nmax = newnmax;
226: return(0);
227: }
228: /*
229: MatStashValuesRow_Private - inserts values into the stash. This function
230: expects the values to be roworiented. Multiple columns belong to the same row
231: can be inserted with a single call to this function.
233: Input Parameters:
234: stash - the stash
235: row - the global row correspoiding to the values
236: n - the number of elements inserted. All elements belong to the above row.
237: idxn - the global column indices corresponding to each of the values.
238: values - the values inserted
239: */
242: PetscErrorCode MatStashValuesRow_Private(MatStash *stash,PetscInt row,PetscInt n,const PetscInt idxn[],const PetscScalar values[],PetscTruth ignorezeroentries)
243: {
244: PetscErrorCode ierr;
245: PetscInt i,k,cnt = 0;
246: PetscMatStashSpace space=stash->space;
249: /* Check and see if we have sufficient memory */
250: if (!space || space->local_remaining < n){
251: MatStashExpand_Private(stash,n);
252: }
253: space = stash->space;
254: k = space->local_used;
255: for (i=0; i<n; i++) {
256: if (ignorezeroentries && (values[i] == 0.0)) continue;
257: space->idx[k] = row;
258: space->idy[k] = idxn[i];
259: space->val[k] = values[i];
260: k++;
261: cnt++;
262: }
263: stash->n += cnt;
264: space->local_used += cnt;
265: space->local_remaining -= cnt;
266: return(0);
267: }
269: /*
270: MatStashValuesCol_Private - inserts values into the stash. This function
271: expects the values to be columnoriented. Multiple columns belong to the same row
272: can be inserted with a single call to this function.
274: Input Parameters:
275: stash - the stash
276: row - the global row correspoiding to the values
277: n - the number of elements inserted. All elements belong to the above row.
278: idxn - the global column indices corresponding to each of the values.
279: values - the values inserted
280: stepval - the consecutive values are sepated by a distance of stepval.
281: this happens because the input is columnoriented.
282: */
285: PetscErrorCode MatStashValuesCol_Private(MatStash *stash,PetscInt row,PetscInt n,const PetscInt idxn[],const PetscScalar values[],PetscInt stepval,PetscTruth ignorezeroentries)
286: {
287: PetscErrorCode ierr;
288: PetscInt i,k,cnt = 0;
289: PetscMatStashSpace space=stash->space;
292: /* Check and see if we have sufficient memory */
293: if (!space || space->local_remaining < n){
294: MatStashExpand_Private(stash,n);
295: }
296: space = stash->space;
297: k = space->local_used;
298: for (i=0; i<n; i++) {
299: if (ignorezeroentries && (values[i*stepval] == 0.0)) continue;
300: space->idx[k] = row;
301: space->idy[k] = idxn[i];
302: space->val[k] = values[i*stepval];
303: k++;
304: cnt++;
305: }
306: stash->n += cnt;
307: space->local_used += cnt;
308: space->local_remaining -= cnt;
309: return(0);
310: }
312: /*
313: MatStashValuesRowBlocked_Private - inserts blocks of values into the stash.
314: This function expects the values to be roworiented. Multiple columns belong
315: to the same block-row can be inserted with a single call to this function.
316: This function extracts the sub-block of values based on the dimensions of
317: the original input block, and the row,col values corresponding to the blocks.
319: Input Parameters:
320: stash - the stash
321: row - the global block-row correspoiding to the values
322: n - the number of elements inserted. All elements belong to the above row.
323: idxn - the global block-column indices corresponding to each of the blocks of
324: values. Each block is of size bs*bs.
325: values - the values inserted
326: rmax - the number of block-rows in the original block.
327: cmax - the number of block-columsn on the original block.
328: idx - the index of the current block-row in the original block.
329: */
332: PetscErrorCode MatStashValuesRowBlocked_Private(MatStash *stash,PetscInt row,PetscInt n,const PetscInt idxn[],const PetscScalar values[],PetscInt rmax,PetscInt cmax,PetscInt idx)
333: {
334: PetscErrorCode ierr;
335: PetscInt i,j,k,bs2,bs=stash->bs,l;
336: const PetscScalar *vals;
337: PetscScalar *array;
338: PetscMatStashSpace space=stash->space;
341: if (!space || space->local_remaining < n){
342: MatStashExpand_Private(stash,n);
343: }
344: space = stash->space;
345: l = space->local_used;
346: bs2 = bs*bs;
347: for (i=0; i<n; i++) {
348: space->idx[l] = row;
349: space->idy[l] = idxn[i];
350: /* Now copy over the block of values. Store the values column oriented.
351: This enables inserting multiple blocks belonging to a row with a single
352: funtion call */
353: array = space->val + bs2*l;
354: vals = values + idx*bs2*n + bs*i;
355: for (j=0; j<bs; j++) {
356: for (k=0; k<bs; k++) array[k*bs] = vals[k];
357: array++;
358: vals += cmax*bs;
359: }
360: l++;
361: }
362: stash->n += n;
363: space->local_used += n;
364: space->local_remaining -= n;
365: return(0);
366: }
368: /*
369: MatStashValuesColBlocked_Private - inserts blocks of values into the stash.
370: This function expects the values to be roworiented. Multiple columns belong
371: to the same block-row can be inserted with a single call to this function.
372: This function extracts the sub-block of values based on the dimensions of
373: the original input block, and the row,col values corresponding to the blocks.
375: Input Parameters:
376: stash - the stash
377: row - the global block-row correspoiding to the values
378: n - the number of elements inserted. All elements belong to the above row.
379: idxn - the global block-column indices corresponding to each of the blocks of
380: values. Each block is of size bs*bs.
381: values - the values inserted
382: rmax - the number of block-rows in the original block.
383: cmax - the number of block-columsn on the original block.
384: idx - the index of the current block-row in the original block.
385: */
388: PetscErrorCode MatStashValuesColBlocked_Private(MatStash *stash,PetscInt row,PetscInt n,const PetscInt idxn[],const PetscScalar values[],PetscInt rmax,PetscInt cmax,PetscInt idx)
389: {
390: PetscErrorCode ierr;
391: PetscInt i,j,k,bs2,bs=stash->bs,l;
392: const PetscScalar *vals;
393: PetscScalar *array;
394: PetscMatStashSpace space=stash->space;
397: if (!space || space->local_remaining < n){
398: MatStashExpand_Private(stash,n);
399: }
400: space = stash->space;
401: l = space->local_used;
402: bs2 = bs*bs;
403: for (i=0; i<n; i++) {
404: space->idx[l] = row;
405: space->idy[l] = idxn[i];
406: /* Now copy over the block of values. Store the values column oriented.
407: This enables inserting multiple blocks belonging to a row with a single
408: funtion call */
409: array = space->val + bs2*l;
410: vals = values + idx*bs2*n + bs*i;
411: for (j=0; j<bs; j++) {
412: for (k=0; k<bs; k++) {array[k] = vals[k];}
413: array += bs;
414: vals += rmax*bs;
415: }
416: l++;
417: }
418: stash->n += n;
419: space->local_used += n;
420: space->local_remaining -= n;
421: return(0);
422: }
423: /*
424: MatStashScatterBegin_Private - Initiates the transfer of values to the
425: correct owners. This function goes through the stash, and check the
426: owners of each stashed value, and sends the values off to the owner
427: processors.
429: Input Parameters:
430: stash - the stash
431: owners - an array of size 'no-of-procs' which gives the ownership range
432: for each node.
434: Notes: The 'owners' array in the cased of the blocked-stash has the
435: ranges specified blocked global indices, and for the regular stash in
436: the proper global indices.
437: */
440: PetscErrorCode MatStashScatterBegin_Private(Mat mat,MatStash *stash,PetscInt *owners)
441: {
442: PetscInt *owner,*startv,*starti,tag1=stash->tag1,tag2=stash->tag2,bs2;
443: PetscInt size=stash->size,nsends;
444: PetscErrorCode ierr;
445: PetscInt count,*sindices,**rindices,i,j,idx,lastidx,l;
446: PetscScalar **rvalues,*svalues;
447: MPI_Comm comm = stash->comm;
448: MPI_Request *send_waits,*recv_waits,*recv_waits1,*recv_waits2;
449: PetscMPIInt *nprocs,*nlengths,nreceives;
450: PetscInt *sp_idx,*sp_idy;
451: PetscScalar *sp_val;
452: PetscMatStashSpace space,space_next;
455: bs2 = stash->bs*stash->bs;
456:
457: /* first count number of contributors to each processor */
458: PetscMalloc(2*size*sizeof(PetscMPIInt),&nprocs);
459: PetscMemzero(nprocs,2*size*sizeof(PetscMPIInt));
460: PetscMalloc((stash->n+1)*sizeof(PetscInt),&owner);
462: nlengths = nprocs+size;
463: i = j = 0;
464: lastidx = -1;
465: space = stash->space_head;
466: while (space != PETSC_NULL){
467: space_next = space->next;
468: sp_idx = space->idx;
469: for (l=0; l<space->local_used; l++){
470: /* if indices are NOT locally sorted, need to start search at the beginning */
471: if (lastidx > (idx = sp_idx[l])) j = 0;
472: lastidx = idx;
473: for (; j<size; j++) {
474: if (idx >= owners[j] && idx < owners[j+1]) {
475: nlengths[j]++; owner[i] = j; break;
476: }
477: }
478: i++;
479: }
480: space = space_next;
481: }
482: /* Now check what procs get messages - and compute nsends. */
483: for (i=0, nsends=0 ; i<size; i++) {
484: if (nlengths[i]) { nprocs[i] = 1; nsends ++;}
485: }
487: {PetscMPIInt *onodes,*olengths;
488: /* Determine the number of messages to expect, their lengths, from from-ids */
489: PetscGatherNumberOfMessages(comm,nprocs,nlengths,&nreceives);
490: PetscGatherMessageLengths(comm,nsends,nreceives,nlengths,&onodes,&olengths);
491: /* since clubbing row,col - lengths are multiplied by 2 */
492: for (i=0; i<nreceives; i++) olengths[i] *=2;
493: PetscPostIrecvInt(comm,tag1,nreceives,onodes,olengths,&rindices,&recv_waits1);
494: /* values are size 'bs2' lengths (and remove earlier factor 2 */
495: for (i=0; i<nreceives; i++) olengths[i] = olengths[i]*bs2/2;
496: PetscPostIrecvScalar(comm,tag2,nreceives,onodes,olengths,&rvalues,&recv_waits2);
497: PetscFree(onodes);
498: PetscFree(olengths);
499: }
501: /* do sends:
502: 1) starts[i] gives the starting index in svalues for stuff going to
503: the ith processor
504: */
505: PetscMalloc((stash->n+1)*(bs2*sizeof(PetscScalar)+2*sizeof(PetscInt)),&svalues);
506: sindices = (PetscInt*)(svalues + bs2*stash->n);
507: PetscMalloc(2*(nsends+1)*sizeof(MPI_Request),&send_waits);
508: PetscMalloc(2*size*sizeof(PetscInt),&startv);
509: starti = startv + size;
510: /* use 2 sends the first with all_a, the next with all_i and all_j */
511: startv[0] = 0; starti[0] = 0;
512: for (i=1; i<size; i++) {
513: startv[i] = startv[i-1] + nlengths[i-1];
514: starti[i] = starti[i-1] + nlengths[i-1]*2;
515: }
516:
517: i = 0;
518: space = stash->space_head;
519: while (space != PETSC_NULL){
520: space_next = space->next;
521: sp_idx = space->idx;
522: sp_idy = space->idy;
523: sp_val = space->val;
524: for (l=0; l<space->local_used; l++){
525: j = owner[i];
526: if (bs2 == 1) {
527: svalues[startv[j]] = sp_val[l];
528: } else {
529: PetscInt k;
530: PetscScalar *buf1,*buf2;
531: buf1 = svalues+bs2*startv[j];
532: buf2 = space->val + bs2*l;
533: for (k=0; k<bs2; k++){ buf1[k] = buf2[k]; }
534: }
535: sindices[starti[j]] = sp_idx[l];
536: sindices[starti[j]+nlengths[j]] = sp_idy[l];
537: startv[j]++;
538: starti[j]++;
539: i++;
540: }
541: space = space_next;
542: }
543: startv[0] = 0;
544: for (i=1; i<size; i++) { startv[i] = startv[i-1] + nlengths[i-1];}
546: for (i=0,count=0; i<size; i++) {
547: if (nprocs[i]) {
548: MPI_Isend(sindices+2*startv[i],2*nlengths[i],MPIU_INT,i,tag1,comm,send_waits+count++);
549: MPI_Isend(svalues+bs2*startv[i],bs2*nlengths[i],MPIU_SCALAR,i,tag2,comm,send_waits+count++);
550: }
551: }
552: #if defined(PETSC_USE_INFO)
553: PetscInfo1(mat,"No of messages: %d \n",nsends);
554: for (i=0; i<size; i++) {
555: if (nprocs[i]) {
556: PetscInfo2(mat,"Mesg_to: %d: size: %d \n",i,nlengths[i]*bs2*sizeof(PetscScalar)+2*sizeof(PetscInt));
557: }
558: }
559: #endif
560: PetscFree(owner);
561: PetscFree(startv);
562: /* This memory is reused in scatter end for a different purpose*/
563: for (i=0; i<2*size; i++) nprocs[i] = -1;
564: stash->nprocs = nprocs;
565:
566: /* recv_waits need to be contiguous for MatStashScatterGetMesg_Private() */
567: PetscMalloc((nreceives+1)*2*sizeof(MPI_Request),&recv_waits);
569: for (i=0; i<nreceives; i++) {
570: recv_waits[2*i] = recv_waits1[i];
571: recv_waits[2*i+1] = recv_waits2[i];
572: }
573: stash->recv_waits = recv_waits;
574: PetscFree(recv_waits1);
575: PetscFree(recv_waits2);
577: stash->svalues = svalues; stash->rvalues = rvalues;
578: stash->rindices = rindices; stash->send_waits = send_waits;
579: stash->nsends = nsends; stash->nrecvs = nreceives;
580: return(0);
581: }
583: /*
584: MatStashScatterGetMesg_Private - This function waits on the receives posted
585: in the function MatStashScatterBegin_Private() and returns one message at
586: a time to the calling function. If no messages are left, it indicates this
587: by setting flg = 0, else it sets flg = 1.
589: Input Parameters:
590: stash - the stash
592: Output Parameters:
593: nvals - the number of entries in the current message.
594: rows - an array of row indices (or blocked indices) corresponding to the values
595: cols - an array of columnindices (or blocked indices) corresponding to the values
596: vals - the values
597: flg - 0 indicates no more message left, and the current call has no values associated.
598: 1 indicates that the current call successfully received a message, and the
599: other output parameters nvals,rows,cols,vals are set appropriately.
600: */
603: PetscErrorCode MatStashScatterGetMesg_Private(MatStash *stash,PetscMPIInt *nvals,PetscInt **rows,PetscInt** cols,PetscScalar **vals,PetscInt *flg)
604: {
606: PetscMPIInt i,*flg_v,i1,i2;
607: PetscInt bs2;
608: MPI_Status recv_status;
609: PetscTruth match_found = PETSC_FALSE;
613: *flg = 0; /* When a message is discovered this is reset to 1 */
614: /* Return if no more messages to process */
615: if (stash->nprocessed == stash->nrecvs) { return(0); }
617: flg_v = stash->nprocs;
618: bs2 = stash->bs*stash->bs;
619: /* If a matching pair of receieves are found, process them, and return the data to
620: the calling function. Until then keep receiving messages */
621: while (!match_found) {
622: MPI_Waitany(2*stash->nrecvs,stash->recv_waits,&i,&recv_status);
623: /* Now pack the received message into a structure which is useable by others */
624: if (i % 2) {
625: MPI_Get_count(&recv_status,MPIU_SCALAR,nvals);
626: flg_v[2*recv_status.MPI_SOURCE] = i/2;
627: *nvals = *nvals/bs2;
628: } else {
629: MPI_Get_count(&recv_status,MPIU_INT,nvals);
630: flg_v[2*recv_status.MPI_SOURCE+1] = i/2;
631: *nvals = *nvals/2; /* This message has both row indices and col indices */
632: }
633:
634: /* Check if we have both messages from this proc */
635: i1 = flg_v[2*recv_status.MPI_SOURCE];
636: i2 = flg_v[2*recv_status.MPI_SOURCE+1];
637: if (i1 != -1 && i2 != -1) {
638: *rows = stash->rindices[i2];
639: *cols = *rows + *nvals;
640: *vals = stash->rvalues[i1];
641: *flg = 1;
642: stash->nprocessed ++;
643: match_found = PETSC_TRUE;
644: }
645: }
646: return(0);
647: }