Actual source code: vecstash.c

petsc-3.7.1 2016-05-15
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  2: #include <petsc/private/vecimpl.h>

  4: #define DEFAULT_STASH_SIZE   100

  6: /*
  7:   VecStashCreate_Private - Creates a stash,currently used for all the parallel
  8:   matrix implementations. The stash is where elements of a matrix destined
  9:   to be stored on other processors are kept until matrix assembly is done.

 11:   This is a simple minded stash. Simply adds entries to end of stash.

 13:   Input Parameters:
 14:   comm - communicator, required for scatters.
 15:   bs   - stash block size. used when stashing blocks of values

 17:   Output Parameters:
 18:   stash    - the newly created stash
 19: */
 22: PetscErrorCode VecStashCreate_Private(MPI_Comm comm,PetscInt bs,VecStash *stash)
 23: {
 25:   PetscInt       max,*opt,nopt;
 26:   PetscBool      flg;

 29:   /* Require 2 tags, get the second using PetscCommGetNewTag() */
 30:   stash->comm = comm;
 31:   PetscCommGetNewTag(stash->comm,&stash->tag1);
 32:   PetscCommGetNewTag(stash->comm,&stash->tag2);
 33:   MPI_Comm_size(stash->comm,&stash->size);
 34:   MPI_Comm_rank(stash->comm,&stash->rank);

 36:   nopt = stash->size;
 37:   PetscMalloc1(nopt,&opt);
 38:   PetscOptionsGetIntArray(NULL,NULL,"-vecstash_initial_size",opt,&nopt,&flg);
 39:   if (flg) {
 40:     if (nopt == 1)                max = opt[0];
 41:     else if (nopt == stash->size) max = opt[stash->rank];
 42:     else if (stash->rank < nopt)  max = opt[stash->rank];
 43:     else                          max = 0; /* use default */
 44:     stash->umax = max;
 45:   } else {
 46:     stash->umax = 0;
 47:   }
 48:   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->idx      = 0;
 58:   stash->array    = 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->rmax         = 0;
 68:   stash->nprocs       = 0;
 69:   stash->nprocessed   = 0;
 70:   stash->donotstash   = PETSC_FALSE;
 71:   stash->ignorenegidx = PETSC_FALSE;
 72:   return(0);
 73: }

 75: /*
 76:    VecStashDestroy_Private - Destroy the stash
 77: */
 80: PetscErrorCode VecStashDestroy_Private(VecStash *stash)
 81: {

 85:   PetscFree2(stash->array,stash->idx);
 86:   PetscFree(stash->bowners);
 87:   return(0);
 88: }

 90: /*
 91:    VecStashScatterEnd_Private - This is called as the fial stage of
 92:    scatter. The final stages of message passing is done here, and
 93:    all the memory used for message passing is cleanedu up. This
 94:    routine also resets the stash, and deallocates the memory used
 95:    for the stash. It also keeps track of the current memory usage
 96:    so that the same value can be used the next time through.
 97: */
100: PetscErrorCode VecStashScatterEnd_Private(VecStash *stash)
101: {
103:   PetscInt       nsends=stash->nsends,oldnmax;
104:   MPI_Status     *send_status;

107:   /* wait on sends */
108:   if (nsends) {
109:     PetscMalloc1(2*nsends,&send_status);
110:     MPI_Waitall(2*nsends,stash->send_waits,send_status);
111:     PetscFree(send_status);
112:   }

114:   /* Now update nmaxold to be app 10% more than max n, this way the
115:      wastage of space is reduced the next time this stash is used.
116:      Also update the oldmax, only if it increases */
117:   if (stash->n) {
118:     oldnmax = ((PetscInt)(stash->n * 1.1) + 5)*stash->bs;
119:     if (oldnmax > stash->oldnmax) stash->oldnmax = oldnmax;
120:   }

122:   stash->nmax       = 0;
123:   stash->n          = 0;
124:   stash->reallocs   = -1;
125:   stash->rmax       = 0;
126:   stash->nprocessed = 0;

128:   PetscFree2(stash->array,stash->idx);
129:   stash->array = 0;
130:   stash->idx   = 0;
131:   PetscFree(stash->send_waits);
132:   PetscFree(stash->recv_waits);
133:   PetscFree2(stash->svalues,stash->sindices);
134:   PetscFree2(stash->rvalues,stash->rindices);
135:   PetscFree(stash->nprocs);
136:   return(0);
137: }

139: /*
140:    VecStashGetInfo_Private - Gets the relavant statistics of the stash

142:    Input Parameters:
143:    stash    - the stash
144:    nstash   - the size of the stash
145:    reallocs - the number of additional mallocs incurred.

147: */
150: PetscErrorCode VecStashGetInfo_Private(VecStash *stash,PetscInt *nstash,PetscInt *reallocs)
151: {
153:   if (nstash) *nstash = stash->n*stash->bs;
154:   if (reallocs) {
155:     if (stash->reallocs < 0) *reallocs = 0;
156:     else                     *reallocs = stash->reallocs;
157:   }
158:   return(0);
159: }


162: /*
163:    VecStashSetInitialSize_Private - Sets the initial size of the stash

165:    Input Parameters:
166:    stash  - the stash
167:    max    - the value that is used as the max size of the stash.
168:             this value is used while allocating memory. It specifies
169:             the number of vals stored, even with the block-stash
170: */
173: PetscErrorCode VecStashSetInitialSize_Private(VecStash *stash,PetscInt max)
174: {
176:   stash->umax = max;
177:   return(0);
178: }

180: /* VecStashExpand_Private - Expand the stash. This function is called
181:    when the space in the stash is not sufficient to add the new values
182:    being inserted into the stash.

184:    Input Parameters:
185:    stash - the stash
186:    incr  - the minimum increase requested

188:    Notes:
189:    This routine doubles the currently used memory.
190: */
193: PetscErrorCode VecStashExpand_Private(VecStash *stash,PetscInt incr)
194: {
196:   PetscInt       *n_idx,newnmax,bs=stash->bs;
197:   PetscScalar    *n_array;

200:   /* allocate a larger stash. */
201:   if (!stash->oldnmax && !stash->nmax) { /* new stash */
202:     if (stash->umax)                  newnmax = stash->umax/bs;
203:     else                              newnmax = DEFAULT_STASH_SIZE/bs;
204:   } else if (!stash->nmax) { /* resuing stash */
205:     if (stash->umax > stash->oldnmax) newnmax = stash->umax/bs;
206:     else                              newnmax = stash->oldnmax/bs;
207:   } else                              newnmax = stash->nmax*2;

209:   if (newnmax  < (stash->nmax + incr)) newnmax += 2*incr;

211:   PetscMalloc2(bs*newnmax,&n_array,newnmax,&n_idx);
212:   PetscMemcpy(n_array,stash->array,bs*stash->nmax*sizeof(PetscScalar));
213:   PetscMemcpy(n_idx,stash->idx,stash->nmax*sizeof(PetscInt));
214:   PetscFree2(stash->array,stash->idx);

216:   stash->array = n_array;
217:   stash->idx   = n_idx;
218:   stash->nmax  = newnmax;
219:   stash->reallocs++;
220:   return(0);
221: }
222: /*
223:   VecStashScatterBegin_Private - Initiates the transfer of values to the
224:   correct owners. This function goes through the stash, and check the
225:   owners of each stashed value, and sends the values off to the owner
226:   processors.

228:   Input Parameters:
229:   stash  - the stash
230:   owners - an array of size 'no-of-procs' which gives the ownership range
231:            for each node.

233:   Notes: The 'owners' array in the cased of the blocked-stash has the
234:   ranges specified blocked global indices, and for the regular stash in
235:   the proper global indices.
236: */
239: PetscErrorCode VecStashScatterBegin_Private(VecStash *stash,PetscInt *owners)
240: {
242:   PetscMPIInt    size = stash->size,tag1=stash->tag1,tag2=stash->tag2;
243:   PetscInt       *owner,*start,*nprocs,nsends,nreceives;
244:   PetscInt       nmax,count,*sindices,*rindices,i,j,idx,bs=stash->bs,lastidx;
245:   PetscScalar    *rvalues,*svalues;
246:   MPI_Comm       comm = stash->comm;
247:   MPI_Request    *send_waits,*recv_waits;

250:   /*  first count number of contributors to each processor */
251:   PetscCalloc1(2*size,&nprocs);
252:   PetscMalloc1(stash->n,&owner);

254:   j       = 0;
255:   lastidx = -1;
256:   for (i=0; i<stash->n; i++) {
257:     /* if indices are NOT locally sorted, need to start search at the beginning */
258:     if (lastidx > (idx = stash->idx[i])) j = 0;
259:     lastidx = idx;
260:     for (; j<size; j++) {
261:       if (idx >= owners[j] && idx < owners[j+1]) {
262:         nprocs[2*j]++; nprocs[2*j+1] = 1; owner[i] = j; break;
263:       }
264:     }
265:   }
266:   nsends = 0;
267:   for (i=0; i<size; i++) nsends += nprocs[2*i+1];

269:   /* inform other processors of number of messages and max length*/
270:   PetscMaxSum(comm,nprocs,&nmax,&nreceives);

272:   /* post receives:
273:      since we don't know how long each individual message is we
274:      allocate the largest needed buffer for each receive. Potentially
275:      this is a lot of wasted space.
276:   */
277:   PetscMalloc2(nreceives*nmax*bs,&rvalues,nreceives*nmax,&rindices);
278:   PetscMalloc1(2*nreceives,&recv_waits);
279:   for (i=0,count=0; i<nreceives; i++) {
280:     MPI_Irecv(rvalues+bs*nmax*i,bs*nmax,MPIU_SCALAR,MPI_ANY_SOURCE,tag1,comm,recv_waits+count++);
281:     MPI_Irecv(rindices+nmax*i,nmax,MPIU_INT,MPI_ANY_SOURCE,tag2,comm,recv_waits+count++);
282:   }

284:   /* do sends:
285:       1) starts[i] gives the starting index in svalues for stuff going to
286:          the ith processor
287:   */
288:   PetscMalloc2(stash->n*bs,&svalues,stash->n,&sindices);
289:   PetscMalloc1(2*nsends,&send_waits);
290:   PetscMalloc1(size,&start);
291:   /* use 2 sends the first with all_v, the next with all_i */
292:   start[0] = 0;
293:   for (i=1; i<size; i++) start[i] = start[i-1] + nprocs[2*i-2];

295:   for (i=0; i<stash->n; i++) {
296:     j = owner[i];
297:     if (bs == 1) svalues[start[j]] = stash->array[i];
298:     else {
299:       PetscMemcpy(svalues+bs*start[j],stash->array+bs*i,bs*sizeof(PetscScalar));
300:     }
301:     sindices[start[j]] = stash->idx[i];
302:     start[j]++;
303:   }
304:   start[0] = 0;
305:   for (i=1; i<size; i++) start[i] = start[i-1] + nprocs[2*i-2];

307:   for (i=0,count=0; i<size; i++) {
308:     if (nprocs[2*i+1]) {
309:       MPI_Isend(svalues+bs*start[i],bs*nprocs[2*i],MPIU_SCALAR,i,tag1,comm,send_waits+count++);
310:       MPI_Isend(sindices+start[i],nprocs[2*i],MPIU_INT,i,tag2,comm,send_waits+count++);
311:     }
312:   }
313:   PetscFree(owner);
314:   PetscFree(start);
315:   /* This memory is reused in scatter end  for a different purpose*/
316:   for (i=0; i<2*size; i++) nprocs[i] = -1;

318:   stash->nprocs     = nprocs;
319:   stash->svalues    = svalues;
320:   stash->sindices   = sindices;
321:   stash->rvalues    = rvalues;
322:   stash->rindices   = rindices;
323:   stash->nsends     = nsends;
324:   stash->nrecvs     = nreceives;
325:   stash->send_waits = send_waits;
326:   stash->recv_waits = recv_waits;
327:   stash->rmax       = nmax;
328:   return(0);
329: }

331: /*
332:    VecStashScatterGetMesg_Private - This function waits on the receives posted
333:    in the function VecStashScatterBegin_Private() and returns one message at
334:    a time to the calling function. If no messages are left, it indicates this
335:    by setting flg = 0, else it sets flg = 1.

337:    Input Parameters:
338:    stash - the stash

340:    Output Parameters:
341:    nvals - the number of entries in the current message.
342:    rows  - an array of row indices (or blocked indices) corresponding to the values
343:    cols  - an array of columnindices (or blocked indices) corresponding to the values
344:    vals  - the values
345:    flg   - 0 indicates no more message left, and the current call has no values associated.
346:            1 indicates that the current call successfully received a message, and the
347:              other output parameters nvals,rows,cols,vals are set appropriately.
348: */
351: PetscErrorCode VecStashScatterGetMesg_Private(VecStash *stash,PetscMPIInt *nvals,PetscInt **rows,PetscScalar **vals,PetscInt *flg)
352: {
354:   PetscMPIInt    i = 0; /* dummy value so MPI-Uni doesn't think it is not set */
355:   PetscInt       *flg_v;
356:   PetscInt       i1,i2,bs=stash->bs;
357:   MPI_Status     recv_status;
358:   PetscBool      match_found = PETSC_FALSE;

361:   *flg = 0; /* When a message is discovered this is reset to 1 */
362:   /* Return if no more messages to process */
363:   if (stash->nprocessed == stash->nrecvs) return(0);

365:   flg_v = stash->nprocs;
366:   /* If a matching pair of receives are found, process them, and return the data to
367:      the calling function. Until then keep receiving messages */
368:   while (!match_found) {
369:     MPI_Waitany(2*stash->nrecvs,stash->recv_waits,&i,&recv_status);
370:     /* Now pack the received message into a structure which is useable by others */
371:     if (i % 2) {
372:       MPI_Get_count(&recv_status,MPIU_INT,nvals);
373:       flg_v[2*recv_status.MPI_SOURCE+1] = i/2;
374:     } else {
375:       MPI_Get_count(&recv_status,MPIU_SCALAR,nvals);
376:       flg_v[2*recv_status.MPI_SOURCE] = i/2;
377:       *nvals = *nvals/bs;
378:     }

380:     /* Check if we have both the messages from this proc */
381:     i1 = flg_v[2*recv_status.MPI_SOURCE];
382:     i2 = flg_v[2*recv_status.MPI_SOURCE+1];
383:     if (i1 != -1 && i2 != -1) {
384:       *rows = stash->rindices + i2*stash->rmax;
385:       *vals = stash->rvalues + i1*bs*stash->rmax;
386:       *flg  = 1;
387:       stash->nprocessed++;
388:       match_found = PETSC_TRUE;
389:     }
390:   }
391:   return(0);
392: }

396: /*
397:  * Sort the stash, removing duplicates (combining as appropriate).
398:  */
399: PetscErrorCode VecStashSortCompress_Private(VecStash *stash)
400: {
402:   PetscInt i,j,bs = stash->bs;

405:   if (!stash->n) return(0);
406:   if (bs == 1) {
407:     PetscSortIntWithScalarArray(stash->n,stash->idx,stash->array);
408:     for (i=1,j=0; i<stash->n; i++) {
409:       if (stash->idx[i] == stash->idx[j]) {
410:         switch (stash->insertmode) {
411:         case ADD_VALUES:
412:           stash->array[j] += stash->array[i];
413:           break;
414:         case INSERT_VALUES:
415:           stash->array[j] = stash->array[i];
416:           break;
417:         default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Insert mode not supported 0x%x",stash->insertmode);
418:         }
419:       } else {
420:         j++;
421:         stash->idx[j]   = stash->idx[i];
422:         stash->array[j] = stash->array[i];
423:       }
424:     }
425:     stash->n = j + 1;
426:   } else {                      /* block stash */
427:     PetscInt *perm = NULL;
428:     PetscScalar *arr;
429:     PetscMalloc2(stash->n,&perm,stash->n*bs,&arr);
430:     for (i=0; i<stash->n; i++) perm[i] = i;
431:     PetscSortIntWithArray(stash->n,stash->idx,perm);

433:     /* Out-of-place copy of arr */
434:     PetscMemcpy(arr,stash->array,bs*sizeof(PetscScalar));
435:     for (i=1,j=0; i<stash->n; i++) {
436:       PetscInt k;
437:       if (stash->idx[i] == stash->idx[j]) {
438:         switch (stash->insertmode) {
439:         case ADD_VALUES:
440:           for (k=0; k<bs; k++) arr[j*bs+k] += stash->array[perm[i]*bs+k];
441:           break;
442:         case INSERT_VALUES:
443:           for (k=0; k<bs; k++) arr[j*bs+k] = stash->array[perm[i]*bs+k];
444:           break;
445:         default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Insert mode not supported 0x%x",stash->insertmode);
446:         }
447:       } else {
448:         j++;
449:         stash->idx[j] = stash->idx[i];
450:         for (k=0; k<bs; k++) arr[j*bs+k] = stash->array[perm[i]*bs+k];
451:       }
452:     }
453:     stash->n = j + 1;
454:     PetscMemcpy(stash->array,arr,stash->n*bs*sizeof(PetscScalar));
455:     PetscFree2(perm,arr);
456:   }
457:   return(0);
458: }

462: PetscErrorCode VecStashGetOwnerList_Private(VecStash *stash,PetscLayout map,PetscMPIInt *nowners,PetscMPIInt **owners)
463: {
465:   PetscInt i,bs = stash->bs,r;
466:   PetscSegBuffer seg;

469:   if (bs != 1 && bs != map->bs) SETERRQ2(map->comm,PETSC_ERR_PLIB,"Stash block size %D does not match layout block size %D",bs,map->bs);
470:   PetscSegBufferCreate(sizeof(PetscMPIInt),50,&seg);
471:   *nowners = 0;
472:   for (i=0,r=-1; i<stash->n; i++) {
473:     if (stash->idx[i]*bs >= map->range[r+1]) {
474:       PetscMPIInt *rank;
475:       PetscSegBufferGet(seg,1,&rank);
476:       PetscLayoutFindOwner(map,stash->idx[i]*bs,&r);
477:       *rank = r;
478:       (*nowners)++;
479:     }
480:   }
481:   PetscSegBufferExtractAlloc(seg,owners);
482:   PetscSegBufferDestroy(&seg);
483:   return(0);
484: }