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:   PetscMapSetUp((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:   VecCreateMPIWithArray(((PetscObject)mat)->comm,mat->cmap->n,mat->cmap->N,PETSC_NULL,&gvec);
 86:   VecScatterCreate(gvec,from,sbaij->lvec,to,&sbaij->Mvctx);
 87:   VecDestroy(gvec);

 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(((PetscObject)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:   VecScatterCreate(sbaij->slvec0,from,sbaij->slvec1,to,&sbaij->sMvctx);
127: 
128:   VecGetLocalSize(sbaij->slvec1,&nt);
129:   VecGetArray(sbaij->slvec1,&ptr);
130:   VecCreateSeqWithArray(PETSC_COMM_SELF,bs*mbs,ptr,&sbaij->slvec1a);
131:   VecCreateSeqWithArray(PETSC_COMM_SELF,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec1b);
132:   VecRestoreArray(sbaij->slvec1,&ptr);

134:   VecGetArray(sbaij->slvec0,&ptr);
135:   VecCreateSeqWithArray(PETSC_COMM_SELF,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec0b);
136:   VecRestoreArray(sbaij->slvec0,&ptr);

138:   PetscFree(stmp);
139:   MPI_Barrier(((PetscObject)mat)->comm);
140: 
141:   PetscLogObjectParent(mat,sbaij->sMvctx);
142:   PetscLogObjectParent(mat,sbaij->slvec0);
143:   PetscLogObjectParent(mat,sbaij->slvec1);
144:   PetscLogObjectParent(mat,sbaij->slvec0b);
145:   PetscLogObjectParent(mat,sbaij->slvec1a);
146:   PetscLogObjectParent(mat,sbaij->slvec1b);
147:   PetscLogObjectParent(mat,from);
148:   PetscLogObjectParent(mat,to);
149: 
150:   PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
151:   ISDestroy(from);
152:   ISDestroy(to);
153:   PetscFree(sgarray);
154:   return(0);
155: }

159: PetscErrorCode MatSetUpMultiply_MPISBAIJ_2comm(Mat mat)
160: {
161:   Mat_MPISBAIJ       *baij = (Mat_MPISBAIJ*)mat->data;
162:   Mat_SeqBAIJ        *B = (Mat_SeqBAIJ*)(baij->B->data);
163:   PetscErrorCode     ierr;
164:   PetscInt           i,j,*aj = B->j,ec = 0,*garray;
165:   PetscInt           bs = mat->rmap->bs,*stmp;
166:   IS                 from,to;
167:   Vec                gvec;
168: #if defined (PETSC_USE_CTABLE)
169:   PetscTable         gid1_lid1;
170:   PetscTablePosition tpos;
171:   PetscInt           gid,lid;
172: #else
173:   PetscInt           Nbs = baij->Nbs,*indices;
174: #endif  

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

229:   /* form array of columns we need */
230:   PetscMalloc((ec+1)*sizeof(PetscInt),&garray);
231:   ec = 0;
232:   for (i=0; i<Nbs; i++) {
233:     if (indices[i]) {
234:       garray[ec++] = i;
235:     }
236:   }

238:   /* make indices now point into garray */
239:   for (i=0; i<ec; i++) {
240:     indices[garray[i]] = i;
241:   }

243:   /* compact out the extra columns in B */
244:   for (i=0; i<B->mbs; i++) {
245:     for (j=0; j<B->ilen[i]; j++) {
246:       aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
247:     }
248:   }
249:   B->nbs       = ec;
250:   baij->B->cmap->n   = ec*mat->rmap->bs;
251:   PetscFree(indices);
252: #endif  
253: 
254:   /* create local vector that is used to scatter into */
255:   VecCreateSeq(PETSC_COMM_SELF,ec*bs,&baij->lvec);

257:   /* create two temporary index sets for building scatter-gather */
258:   for (i=0; i<ec; i++) {
259:     garray[i] = bs*garray[i];
260:   }
261:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,&from);
262:   for (i=0; i<ec; i++) {
263:     garray[i] = garray[i]/bs;
264:   }

266:   PetscMalloc((ec+1)*sizeof(PetscInt),&stmp);
267:   for (i=0; i<ec; i++) { stmp[i] = bs*i; }
268:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,&to);
269:   PetscFree(stmp);

271:   /* create temporary global vector to generate scatter context */
272:   VecCreateMPIWithArray(((PetscObject)mat)->comm,mat->cmap->n,mat->cmap->N,PETSC_NULL,&gvec);
273:   VecScatterCreate(gvec,from,baij->lvec,to,&baij->Mvctx);
274:   VecDestroy(gvec);

276:   PetscLogObjectParent(mat,baij->Mvctx);
277:   PetscLogObjectParent(mat,baij->lvec);
278:   PetscLogObjectParent(mat,from);
279:   PetscLogObjectParent(mat,to);
280:   baij->garray = garray;
281:   PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
282:   ISDestroy(from);
283:   ISDestroy(to);
284:   return(0);
285: }

287: /*
288:      Takes the local part of an already assembled MPISBAIJ matrix
289:    and disassembles it. This is to allow new nonzeros into the matrix
290:    that require more communication in the matrix vector multiply. 
291:    Thus certain data-structures must be rebuilt.

293:    Kind of slow! But that's what application programmers get when 
294:    they are sloppy.
295: */
298: PetscErrorCode DisAssemble_MPISBAIJ(Mat A)
299: {
300:   Mat_MPISBAIJ   *baij = (Mat_MPISBAIJ*)A->data;
301:   Mat            B = baij->B,Bnew;
302:   Mat_SeqBAIJ    *Bbaij = (Mat_SeqBAIJ*)B->data;
304:   PetscInt       i,j,mbs=Bbaij->mbs,n = A->cmap->N,col,*garray=baij->garray;
305:   PetscInt       k,bs=A->rmap->bs,bs2=baij->bs2,*rvals,*nz,ec,m=A->rmap->n;
306:   MatScalar      *a = Bbaij->a;
307:   PetscScalar    *atmp;
308: #if defined(PETSC_USE_MAT_SINGLE)
309:   PetscInt       l;
310: #endif

313: #if defined(PETSC_USE_MAT_SINGLE)
314:   PetscMalloc(A->rmap->bs*sizeof(PetscScalar),&atmp);
315: #endif
316:   /* free stuff related to matrix-vec multiply */
317:   VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
318:   VecDestroy(baij->lvec);
319:   baij->lvec = 0;
320:   VecScatterDestroy(baij->Mvctx);
321:   baij->Mvctx = 0;

323:   VecDestroy(baij->slvec0);
324:   VecDestroy(baij->slvec0b);
325:   baij->slvec0 = 0;
326:   VecDestroy(baij->slvec1);
327:   VecDestroy(baij->slvec1a);
328:   VecDestroy(baij->slvec1b);
329:   baij->slvec1 = 0;

331:   if (baij->colmap) {
332: #if defined (PETSC_USE_CTABLE)
333:     PetscTableDestroy(baij->colmap); baij->colmap = 0;
334: #else
335:     PetscFree(baij->colmap);
336:     baij->colmap = 0;
337:     PetscLogObjectMemory(A,-Bbaij->nbs*sizeof(PetscInt));
338: #endif
339:   }

341:   /* make sure that B is assembled so we can access its values */
342:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
343:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

345:   /* invent new B and copy stuff over */
346:   PetscMalloc(mbs*sizeof(PetscInt),&nz);
347:   for (i=0; i<mbs; i++) {
348:     nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
349:   }
350:   MatCreate(PETSC_COMM_SELF,&Bnew);
351:   MatSetSizes(Bnew,m,n,m,n);
352:   MatSetType(Bnew,((PetscObject)B)->type_name);
353:   MatSeqBAIJSetPreallocation(Bnew,B->rmap->bs,0,nz);
354:   PetscFree(nz);
355: 
356:   PetscMalloc(bs*sizeof(PetscInt),&rvals);
357:   for (i=0; i<mbs; i++) {
358:     rvals[0] = bs*i;
359:     for (j=1; j<bs; j++) { rvals[j] = rvals[j-1] + 1; }
360:     for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
361:       col = garray[Bbaij->j[j]]*bs;
362:       for (k=0; k<bs; k++) {
363: #if defined(PETSC_USE_MAT_SINGLE)
364:         for (l=0; l<bs; l++) atmp[l] = a[j*bs2+l];
365: #else
366:         atmp = a+j*bs2 + k*bs;
367: #endif
368:         MatSetValues_SeqSBAIJ(Bnew,bs,rvals,1,&col,atmp,B->insertmode);
369:         col++;
370:       }
371:     }
372:   }
373: #if defined(PETSC_USE_MAT_SINGLE)
374:   PetscFree(atmp);
375: #endif
376:   PetscFree(baij->garray);
377:   baij->garray = 0;
378:   PetscFree(rvals);
379:   PetscLogObjectMemory(A,-ec*sizeof(PetscInt));
380:   MatDestroy(B);
381:   PetscLogObjectParent(A,Bnew);
382:   baij->B = Bnew;
383:   A->was_assembled = PETSC_FALSE;
384:   return(0);
385: }