Actual source code: mmsbaij.c

  1: #define PETSCMAT_DLL

  3: /*
  4:    Support for the parallel SBAIJ matrix vector multiply
  5: */
 6:  #include src/mat/impls/sbaij/mpi/mpisbaij.h

  8: EXTERN PetscErrorCode MatSetValues_SeqSBAIJ(Mat,PetscInt,const PetscInt [],PetscInt,const PetscInt [],const PetscScalar [],InsertMode);


 13: PetscErrorCode MatSetUpMultiply_MPISBAIJ(Mat mat)
 14: {
 15:   Mat_MPISBAIJ   *sbaij = (Mat_MPISBAIJ*)mat->data;
 16:   Mat_SeqBAIJ    *B = (Mat_SeqBAIJ*)(sbaij->B->data);
 18:   PetscInt       Nbs = sbaij->Nbs,i,j,*indices,*aj = B->j,ec = 0,*garray,*sgarray;
 19:   PetscInt       bs = mat->rmap.bs,*stmp,mbs=sbaij->mbs, vec_size,nt;
 20:   IS             from,to;
 21:   Vec            gvec;
 22:   PetscMPIInt    rank=sbaij->rank,lsize,size=sbaij->size;
 23:   PetscInt       *owners=sbaij->rangebs,*sowners,*ec_owner,k;
 24:   PetscScalar    *ptr;

 27:   if (sbaij->sMvctx) {
 28:     /* This two lines should be in DisAssemble_MPISBAIJ(). Don't know why it causes crash there? */
 29:     VecScatterDestroy(sbaij->sMvctx);
 30:     sbaij->sMvctx = 0;
 31:   }
 32: 
 33:   /* For the first stab we make an array as long as the number of columns */
 34:   /* mark those columns that are in sbaij->B */
 35:   PetscMalloc((Nbs+1)*sizeof(PetscInt),&indices);
 36:   PetscMemzero(indices,Nbs*sizeof(PetscInt));
 37:   for (i=0; i<mbs; i++) {
 38:     for (j=0; j<B->ilen[i]; j++) {
 39:       if (!indices[aj[B->i[i] + j]]) ec++;
 40:       indices[aj[B->i[i] + j] ] = 1;
 41:     }
 42:   }

 44:   /* form arrays of columns we need */
 45:   PetscMalloc((ec+1)*sizeof(PetscInt),&garray);
 46:   PetscMalloc((3*ec+1)*sizeof(PetscInt),&sgarray);
 47:   ec_owner = sgarray + 2*ec;
 48: 
 49:   ec = 0;
 50:   for (j=0; j<size; j++){
 51:     for (i=owners[j]; i<owners[j+1]; i++){
 52:       if (indices[i]) {
 53:         garray[ec]   = i;
 54:         ec_owner[ec] = j;
 55:         ec++;
 56:       }
 57:     }
 58:   }

 60:   /* make indices now point into garray */
 61:   for (i=0; i<ec; i++) indices[garray[i]] = i;

 63:   /* compact out the extra columns in B */
 64:   for (i=0; i<mbs; i++) {
 65:     for (j=0; j<B->ilen[i]; j++) aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
 66:   }
 67:   B->nbs      = ec;
 68:   sbaij->B->cmap.n = sbaij->B->cmap.N = ec*mat->rmap.bs;
 69:   PetscMapInitialize(sbaij->B->comm,&(sbaij->B->cmap));
 70:   PetscFree(indices);

 72:   /* create local vector that is used to scatter into */
 73:   VecCreateSeq(PETSC_COMM_SELF,ec*bs,&sbaij->lvec);

 75:   /* create two temporary index sets for building scatter-gather */
 76:   PetscMalloc((2*ec+1)*sizeof(PetscInt),&stmp);
 77:   for (i=0; i<ec; i++) stmp[i] = bs*garray[i];
 78:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,&from);
 79: 
 80:   for (i=0; i<ec; i++) { stmp[i] = bs*i; }
 81:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,&to);

 83:   /* generate the scatter context 
 84:      -- Mvctx and lvec are not used by MatMult_MPISBAIJ(), but usefule for some applications */
 85:   VecCreateMPI(mat->comm,mat->cmap.n,mat->cmap.N,&gvec);
 86:   VecScatterCreate(gvec,from,sbaij->lvec,to,&sbaij->Mvctx);
 87:   VecScatterPostRecvs(gvec,sbaij->lvec,INSERT_VALUES,SCATTER_FORWARD,sbaij->Mvctx);

 89:   sbaij->garray = garray;
 90:   PetscLogObjectParent(mat,sbaij->Mvctx);
 91:   PetscLogObjectParent(mat,sbaij->lvec);
 92:   PetscLogObjectParent(mat,from);
 93:   PetscLogObjectParent(mat,to);

 95:   ISDestroy(from);
 96:   ISDestroy(to);

 98:   /* create parallel vector that is used by SBAIJ matrix to scatter from/into */
 99:   lsize = (mbs + ec)*bs;
100:   VecCreateMPI(mat->comm,lsize,PETSC_DETERMINE,&sbaij->slvec0);
101:   VecDuplicate(sbaij->slvec0,&sbaij->slvec1);
102:   VecGetSize(sbaij->slvec0,&vec_size);

104:   sowners = sbaij->slvec0->map.range;
105: 
106:   /* x index in the IS sfrom */
107:   for (i=0; i<ec; i++) {
108:     j = ec_owner[i];
109:     sgarray[i]  = garray[i] + (sowners[j]/bs - owners[j]);
110:   }
111:   /* b index in the IS sfrom */
112:   k = sowners[rank]/bs + mbs;
113:   for (i=ec,j=0; i< 2*ec; i++,j++) sgarray[i] = k + j;
114: 
115:   for (i=0; i<2*ec; i++) stmp[i] = bs*sgarray[i];
116:   ISCreateBlock(PETSC_COMM_SELF,bs,2*ec,stmp,&from);
117: 
118:   /* x index in the IS sto */
119:   k = sowners[rank]/bs + mbs;
120:   for (i=0; i<ec; i++) stmp[i] = bs*(k + i);
121:   /* b index in the IS sto */
122:   for (i=ec; i<2*ec; i++) stmp[i] = bs*sgarray[i-ec];

124:   ISCreateBlock(PETSC_COMM_SELF,bs,2*ec,stmp,&to);

126:   /* gnerate the SBAIJ scatter context */
127:   VecScatterCreate(sbaij->slvec0,from,sbaij->slvec1,to,&sbaij->sMvctx);
128: 
129:    /*
130:       Post the receives for the first matrix vector product. We sync-chronize after
131:     this on the chance that the user immediately calls MatMult() after assemblying 
132:     the matrix.
133:   */
134:   VecScatterPostRecvs(sbaij->slvec0,sbaij->slvec1,INSERT_VALUES,SCATTER_FORWARD,sbaij->sMvctx);

136:   VecGetLocalSize(sbaij->slvec1,&nt);
137:   VecGetArray(sbaij->slvec1,&ptr);
138:   VecCreateSeqWithArray(PETSC_COMM_SELF,bs*mbs,ptr,&sbaij->slvec1a);
139:   VecCreateSeqWithArray(PETSC_COMM_SELF,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec1b);
140:   VecRestoreArray(sbaij->slvec1,&ptr);

142:   VecGetArray(sbaij->slvec0,&ptr);
143:   VecCreateSeqWithArray(PETSC_COMM_SELF,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec0b);
144:   VecRestoreArray(sbaij->slvec0,&ptr);

146:   PetscFree(stmp);
147:   MPI_Barrier(mat->comm);
148: 
149:   PetscLogObjectParent(mat,sbaij->sMvctx);
150:   PetscLogObjectParent(mat,sbaij->slvec0);
151:   PetscLogObjectParent(mat,sbaij->slvec1);
152:   PetscLogObjectParent(mat,sbaij->slvec0b);
153:   PetscLogObjectParent(mat,sbaij->slvec1a);
154:   PetscLogObjectParent(mat,sbaij->slvec1b);
155:   PetscLogObjectParent(mat,from);
156:   PetscLogObjectParent(mat,to);
157: 
158:   PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
159:   ISDestroy(from);
160:   ISDestroy(to);
161:   VecDestroy(gvec);
162:   PetscFree(sgarray);
163:   return(0);
164: }

168: PetscErrorCode MatSetUpMultiply_MPISBAIJ_2comm(Mat mat)
169: {
170:   Mat_MPISBAIJ       *baij = (Mat_MPISBAIJ*)mat->data;
171:   Mat_SeqBAIJ        *B = (Mat_SeqBAIJ*)(baij->B->data);
172:   PetscErrorCode     ierr;
173:   PetscInt           i,j,*aj = B->j,ec = 0,*garray;
174:   PetscInt           bs = mat->rmap.bs,*stmp;
175:   IS                 from,to;
176:   Vec                gvec;
177: #if defined (PETSC_USE_CTABLE)
178:   PetscTable         gid1_lid1;
179:   PetscTablePosition tpos;
180:   PetscInt           gid,lid;
181: #else
182:   PetscInt           Nbs = baij->Nbs,*indices;
183: #endif  

186: #if defined (PETSC_USE_CTABLE)
187:   /* use a table - Mark Adams */
188:   PetscTableCreate(B->mbs,&gid1_lid1);
189:   for (i=0; i<B->mbs; i++) {
190:     for (j=0; j<B->ilen[i]; j++) {
191:       PetscInt data,gid1 = aj[B->i[i]+j] + 1;
192:       PetscTableFind(gid1_lid1,gid1,&data);
193:       if (!data) {
194:         /* one based table */
195:         PetscTableAdd(gid1_lid1,gid1,++ec);
196:       }
197:     }
198:   }
199:   /* form array of columns we need */
200:   PetscMalloc((ec+1)*sizeof(PetscInt),&garray);
201:   PetscTableGetHeadPosition(gid1_lid1,&tpos);
202:   while (tpos) {
203:     PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
204:     gid--; lid--;
205:     garray[lid] = gid;
206:   }
207:   PetscSortInt(ec,garray);
208:   PetscTableRemoveAll(gid1_lid1);
209:   for (i=0; i<ec; i++) {
210:     PetscTableAdd(gid1_lid1,garray[i]+1,i+1);
211:   }
212:   /* compact out the extra columns in B */
213:   for (i=0; i<B->mbs; i++) {
214:     for (j=0; j<B->ilen[i]; j++) {
215:       PetscInt gid1 = aj[B->i[i] + j] + 1;
216:       PetscTableFind(gid1_lid1,gid1,&lid);
217:       lid --;
218:       aj[B->i[i]+j] = lid;
219:     }
220:   }
221:   B->nbs     = ec;
222:   baij->B->cmap.n = baij->B->cmap.N = ec*mat->rmap.bs;
223:   PetscMapInitialize(baij->B->comm,&(baij->B->cmap));
224:   PetscTableDelete(gid1_lid1);
225:   /* Mark Adams */
226: #else
227:   /* For the first stab we make an array as long as the number of columns */
228:   /* mark those columns that are in baij->B */
229:   PetscMalloc((Nbs+1)*sizeof(PetscInt),&indices);
230:   PetscMemzero(indices,Nbs*sizeof(PetscInt));
231:   for (i=0; i<B->mbs; i++) {
232:     for (j=0; j<B->ilen[i]; j++) {
233:       if (!indices[aj[B->i[i] + j]]) ec++;
234:       indices[aj[B->i[i] + j] ] = 1;
235:     }
236:   }

238:   /* form array of columns we need */
239:   PetscMalloc((ec+1)*sizeof(PetscInt),&garray);
240:   ec = 0;
241:   for (i=0; i<Nbs; i++) {
242:     if (indices[i]) {
243:       garray[ec++] = i;
244:     }
245:   }

247:   /* make indices now point into garray */
248:   for (i=0; i<ec; i++) {
249:     indices[garray[i]] = i;
250:   }

252:   /* compact out the extra columns in B */
253:   for (i=0; i<B->mbs; i++) {
254:     for (j=0; j<B->ilen[i]; j++) {
255:       aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
256:     }
257:   }
258:   B->nbs       = ec;
259:   baij->B->cmap.n   = ec*mat->rmap.bs;
260:   PetscFree(indices);
261: #endif  
262: 
263:   /* create local vector that is used to scatter into */
264:   VecCreateSeq(PETSC_COMM_SELF,ec*bs,&baij->lvec);

266:   /* create two temporary index sets for building scatter-gather */
267:   for (i=0; i<ec; i++) {
268:     garray[i] = bs*garray[i];
269:   }
270:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,&from);
271:   for (i=0; i<ec; i++) {
272:     garray[i] = garray[i]/bs;
273:   }

275:   PetscMalloc((ec+1)*sizeof(PetscInt),&stmp);
276:   for (i=0; i<ec; i++) { stmp[i] = bs*i; }
277:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,&to);
278:   PetscFree(stmp);

280:   /* create temporary global vector to generate scatter context */
281:   /* this is inefficient, but otherwise we must do either 
282:      1) save garray until the first actual scatter when the vector is known or
283:      2) have another way of generating a scatter context without a vector.*/
284:   VecCreateMPI(mat->comm,mat->cmap.n,mat->cmap.N,&gvec);

286:   /* gnerate the scatter context */
287:   VecScatterCreate(gvec,from,baij->lvec,to,&baij->Mvctx);

289:   /*
290:       Post the receives for the first matrix vector product. We sync-chronize after
291:     this on the chance that the user immediately calls MatMult() after assemblying 
292:     the matrix.
293:   */
294:   VecScatterPostRecvs(gvec,baij->lvec,INSERT_VALUES,SCATTER_FORWARD,baij->Mvctx);
295:   MPI_Barrier(mat->comm);

297:   PetscLogObjectParent(mat,baij->Mvctx);
298:   PetscLogObjectParent(mat,baij->lvec);
299:   PetscLogObjectParent(mat,from);
300:   PetscLogObjectParent(mat,to);
301:   baij->garray = garray;
302:   PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
303:   ISDestroy(from);
304:   ISDestroy(to);
305:   VecDestroy(gvec);
306:   return(0);
307: }

309: /*
310:      Takes the local part of an already assembled MPISBAIJ matrix
311:    and disassembles it. This is to allow new nonzeros into the matrix
312:    that require more communication in the matrix vector multiply. 
313:    Thus certain data-structures must be rebuilt.

315:    Kind of slow! But that's what application programmers get when 
316:    they are sloppy.
317: */
320: PetscErrorCode DisAssemble_MPISBAIJ(Mat A)
321: {
322:   Mat_MPISBAIJ   *baij = (Mat_MPISBAIJ*)A->data;
323:   Mat            B = baij->B,Bnew;
324:   Mat_SeqBAIJ    *Bbaij = (Mat_SeqBAIJ*)B->data;
326:   PetscInt       i,j,mbs=Bbaij->mbs,n = A->cmap.n,col,*garray=baij->garray;
327:   PetscInt       k,bs=A->rmap.bs,bs2=baij->bs2,*rvals,*nz,ec,m=A->rmap.n;
328:   MatScalar      *a = Bbaij->a;
329:   PetscScalar    *atmp;
330: #if defined(PETSC_USE_MAT_SINGLE)
331:   PetscInt       l;
332: #endif

335: #if defined(PETSC_USE_MAT_SINGLE)
336:   PetscMalloc(A->rmap.bs*sizeof(PetscScalar),&atmp);
337: #endif
338:   /* free stuff related to matrix-vec multiply */
339:   VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
340:   VecDestroy(baij->lvec);
341:   baij->lvec = 0;
342:   VecScatterDestroy(baij->Mvctx);
343:   baij->Mvctx = 0;

345:   VecDestroy(baij->slvec0);
346:   VecDestroy(baij->slvec0b);
347:   baij->slvec0 = 0;
348:   VecDestroy(baij->slvec1);
349:   VecDestroy(baij->slvec1a);
350:   VecDestroy(baij->slvec1b);
351:   baij->slvec1 = 0;

353:   if (baij->colmap) {
354: #if defined (PETSC_USE_CTABLE)
355:     PetscTableDelete(baij->colmap); baij->colmap = 0;
356: #else
357:     PetscFree(baij->colmap);
358:     baij->colmap = 0;
359:     PetscLogObjectMemory(A,-Bbaij->nbs*sizeof(PetscInt));
360: #endif
361:   }

363:   /* make sure that B is assembled so we can access its values */
364:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
365:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

367:   /* invent new B and copy stuff over */
368:   PetscMalloc(mbs*sizeof(PetscInt),&nz);
369:   for (i=0; i<mbs; i++) {
370:     nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
371:   }
372:   MatCreate(PETSC_COMM_SELF,&Bnew);
373:   MatSetSizes(Bnew,m,n,m,n);
374:   MatSetType(Bnew,B->type_name);
375:   MatSeqBAIJSetPreallocation(Bnew,B->rmap.bs,0,nz);
376:   PetscFree(nz);
377: 
378:   PetscMalloc(bs*sizeof(PetscInt),&rvals);
379:   for (i=0; i<mbs; i++) {
380:     rvals[0] = bs*i;
381:     for (j=1; j<bs; j++) { rvals[j] = rvals[j-1] + 1; }
382:     for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
383:       col = garray[Bbaij->j[j]]*bs;
384:       for (k=0; k<bs; k++) {
385: #if defined(PETSC_USE_MAT_SINGLE)
386:         for (l=0; l<bs; l++) atmp[l] = a[j*bs2+l];
387: #else
388:         atmp = a+j*bs2 + k*bs;
389: #endif
390:         MatSetValues_SeqSBAIJ(Bnew,bs,rvals,1,&col,atmp,B->insertmode);
391:         col++;
392:       }
393:     }
394:   }
395: #if defined(PETSC_USE_MAT_SINGLE)
396:   PetscFree(atmp);
397: #endif
398:   PetscFree(baij->garray);
399:   baij->garray = 0;
400:   PetscFree(rvals);
401:   PetscLogObjectMemory(A,-ec*sizeof(PetscInt));
402:   MatDestroy(B);
403:   PetscLogObjectParent(A,Bnew);
404:   baij->B = Bnew;
405:   A->was_assembled = PETSC_FALSE;
406:   return(0);
407: }