Actual source code: mmsbaij.c

  2: /*
  3:    Support for the parallel SBAIJ matrix vector multiply
  4: */
  5: #include <../src/mat/impls/sbaij/mpi/mpisbaij.h>



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

 26:   VecScatterDestroy(&sbaij->sMvctx);
 27: 
 28:   /* For the first stab we make an array as long as the number of columns */
 29:   /* mark those columns that are in sbaij->B */
 30:   PetscMalloc(Nbs*sizeof(PetscInt),&indices);
 31:   PetscMemzero(indices,Nbs*sizeof(PetscInt));
 32:   for (i=0; i<mbs; i++) {
 33:     for (j=0; j<B->ilen[i]; j++) {
 34:       if (!indices[aj[B->i[i] + j]]) ec++;
 35:       indices[aj[B->i[i] + j] ] = 1;
 36:     }
 37:   }

 39:   /* form arrays of columns we need */
 40:   PetscMalloc(ec*sizeof(PetscInt),&garray);
 41:   PetscMalloc2(2*ec,PetscInt,&sgarray,ec,PetscInt,&ec_owner);
 42: 
 43:   ec = 0;
 44:   for (j=0; j<size; j++){
 45:     for (i=owners[j]; i<owners[j+1]; i++){
 46:       if (indices[i]) {
 47:         garray[ec]   = i;
 48:         ec_owner[ec] = j;
 49:         ec++;
 50:       }
 51:     }
 52:   }

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

 57:   /* compact out the extra columns in B */
 58:   for (i=0; i<mbs; i++) {
 59:     for (j=0; j<B->ilen[i]; j++) aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
 60:   }
 61:   B->nbs      = ec;
 62:   sbaij->B->cmap->n = sbaij->B->cmap->N = ec*mat->rmap->bs;
 63:   PetscLayoutSetUp((sbaij->B->cmap));
 64:   PetscFree(indices);

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

 69:   /* create two temporary index sets for building scatter-gather */
 70:   PetscMalloc(2*ec*sizeof(PetscInt),&stmp);
 71:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,PETSC_COPY_VALUES,&from);
 72:   for (i=0; i<ec; i++) { stmp[i] = i; }
 73:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_COPY_VALUES,&to);

 75:   /* generate the scatter context 
 76:      -- Mvctx and lvec are not used by MatMult_MPISBAIJ(), but usefule for some applications */
 77:   VecCreateMPIWithArray(((PetscObject)mat)->comm,mat->cmap->n,mat->cmap->N,PETSC_NULL,&gvec);
 78:   VecScatterCreate(gvec,from,sbaij->lvec,to,&sbaij->Mvctx);
 79:   VecDestroy(&gvec);

 81:   sbaij->garray = garray;
 82:   PetscLogObjectParent(mat,sbaij->Mvctx);
 83:   PetscLogObjectParent(mat,sbaij->lvec);
 84:   PetscLogObjectParent(mat,from);
 85:   PetscLogObjectParent(mat,to);

 87:   ISDestroy(&from);
 88:   ISDestroy(&to);

 90:   /* create parallel vector that is used by SBAIJ matrix to scatter from/into */
 91:   lsize = (mbs + ec)*bs;
 92:   VecCreateMPI(((PetscObject)mat)->comm,lsize,PETSC_DETERMINE,&sbaij->slvec0);
 93:   VecDuplicate(sbaij->slvec0,&sbaij->slvec1);
 94:   VecGetSize(sbaij->slvec0,&vec_size);

 96:   sowners = sbaij->slvec0->map->range;
 97: 
 98:   /* x index in the IS sfrom */
 99:   for (i=0; i<ec; i++) {
100:     j = ec_owner[i];
101:     sgarray[i]  = garray[i] + (sowners[j]/bs - owners[j]);
102:   }
103:   /* b index in the IS sfrom */
104:   k = sowners[rank]/bs + mbs;
105:   for (i=ec,j=0; i< 2*ec; i++,j++) sgarray[i] = k + j;
106:   ISCreateBlock(PETSC_COMM_SELF,bs,2*ec,sgarray,PETSC_COPY_VALUES,&from);
107: 
108:   /* x index in the IS sto */
109:   k = sowners[rank]/bs + mbs;
110:   for (i=0; i<ec; i++) stmp[i] = (k + i);
111:   /* b index in the IS sto */
112:   for (i=ec; i<2*ec; i++) stmp[i] = sgarray[i-ec];

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

116:   VecScatterCreate(sbaij->slvec0,from,sbaij->slvec1,to,&sbaij->sMvctx);
117: 
118:   VecGetLocalSize(sbaij->slvec1,&nt);
119:   VecGetArray(sbaij->slvec1,&ptr);
120:   VecCreateSeqWithArray(PETSC_COMM_SELF,bs*mbs,ptr,&sbaij->slvec1a);
121:   VecCreateSeqWithArray(PETSC_COMM_SELF,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec1b);
122:   VecRestoreArray(sbaij->slvec1,&ptr);

124:   VecGetArray(sbaij->slvec0,&ptr);
125:   VecCreateSeqWithArray(PETSC_COMM_SELF,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec0b);
126:   VecRestoreArray(sbaij->slvec0,&ptr);

128:   PetscFree(stmp);
129:   MPI_Barrier(((PetscObject)mat)->comm);
130: 
131:   PetscLogObjectParent(mat,sbaij->sMvctx);
132:   PetscLogObjectParent(mat,sbaij->slvec0);
133:   PetscLogObjectParent(mat,sbaij->slvec1);
134:   PetscLogObjectParent(mat,sbaij->slvec0b);
135:   PetscLogObjectParent(mat,sbaij->slvec1a);
136:   PetscLogObjectParent(mat,sbaij->slvec1b);
137:   PetscLogObjectParent(mat,from);
138:   PetscLogObjectParent(mat,to);
139: 
140:   PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
141:   ISDestroy(&from);
142:   ISDestroy(&to);
143:   PetscFree2(sgarray,ec_owner);
144:   return(0);
145: }

149: PetscErrorCode MatSetUpMultiply_MPISBAIJ_2comm(Mat mat)
150: {
151:   Mat_MPISBAIJ       *baij = (Mat_MPISBAIJ*)mat->data;
152:   Mat_SeqBAIJ        *B = (Mat_SeqBAIJ*)(baij->B->data);
153:   PetscErrorCode     ierr;
154:   PetscInt           i,j,*aj = B->j,ec = 0,*garray;
155:   PetscInt           bs = mat->rmap->bs,*stmp;
156:   IS                 from,to;
157:   Vec                gvec;
158: #if defined (PETSC_USE_CTABLE)
159:   PetscTable         gid1_lid1;
160:   PetscTablePosition tpos;
161:   PetscInt           gid,lid;
162: #else
163:   PetscInt           Nbs = baij->Nbs,*indices;
164: #endif  

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

218:   /* form array of columns we need */
219:   PetscMalloc(ec*sizeof(PetscInt),&garray);
220:   ec = 0;
221:   for (i=0; i<Nbs; i++) {
222:     if (indices[i]) {
223:       garray[ec++] = i;
224:     }
225:   }

227:   /* make indices now point into garray */
228:   for (i=0; i<ec; i++) {
229:     indices[garray[i]] = i;
230:   }

232:   /* compact out the extra columns in B */
233:   for (i=0; i<B->mbs; i++) {
234:     for (j=0; j<B->ilen[i]; j++) {
235:       aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
236:     }
237:   }
238:   B->nbs       = ec;
239:   baij->B->cmap->n   = ec*mat->rmap->bs;
240:   PetscFree(indices);
241: #endif  
242: 
243:   /* create local vector that is used to scatter into */
244:   VecCreateSeq(PETSC_COMM_SELF,ec*bs,&baij->lvec);

246:   /* create two temporary index sets for building scatter-gather */
247:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,PETSC_COPY_VALUES,&from);

249:   PetscMalloc(ec*sizeof(PetscInt),&stmp);
250:   for (i=0; i<ec; i++) { stmp[i] = i; }
251:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_OWN_POINTER,&to);

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

258:   PetscLogObjectParent(mat,baij->Mvctx);
259:   PetscLogObjectParent(mat,baij->lvec);
260:   PetscLogObjectParent(mat,from);
261:   PetscLogObjectParent(mat,to);
262:   baij->garray = garray;
263:   PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
264:   ISDestroy(&from);
265:   ISDestroy(&to);
266:   return(0);
267: }

269: /*
270:      Takes the local part of an already assembled MPISBAIJ matrix
271:    and disassembles it. This is to allow new nonzeros into the matrix
272:    that require more communication in the matrix vector multiply. 
273:    Thus certain data-structures must be rebuilt.

275:    Kind of slow! But that's what application programmers get when 
276:    they are sloppy.
277: */
280: PetscErrorCode DisAssemble_MPISBAIJ(Mat A)
281: {
282:   Mat_MPISBAIJ   *baij = (Mat_MPISBAIJ*)A->data;
283:   Mat            B = baij->B,Bnew;
284:   Mat_SeqBAIJ    *Bbaij = (Mat_SeqBAIJ*)B->data;
286:   PetscInt       i,j,mbs=Bbaij->mbs,n = A->cmap->N,col,*garray=baij->garray;
287:   PetscInt       k,bs=A->rmap->bs,bs2=baij->bs2,*rvals,*nz,ec,m=A->rmap->n;
288:   MatScalar      *a = Bbaij->a;
289:   PetscScalar    *atmp;
290: #if defined(PETSC_USE_REAL_MAT_SINGLE)
291:   PetscInt       l;
292: #endif

295: #if defined(PETSC_USE_REAL_MAT_SINGLE)
296:   PetscMalloc(A->rmap->bs*sizeof(PetscScalar),&atmp);
297: #endif
298:   /* free stuff related to matrix-vec multiply */
299:   VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
300:   VecDestroy(&baij->lvec);
301:   VecScatterDestroy(&baij->Mvctx);

303:   VecDestroy(&baij->slvec0);
304:   VecDestroy(&baij->slvec0b);
305:   VecDestroy(&baij->slvec1);
306:   VecDestroy(&baij->slvec1a);
307:   VecDestroy(&baij->slvec1b);

309:   if (baij->colmap) {
310: #if defined (PETSC_USE_CTABLE)
311:     PetscTableDestroy(&baij->colmap);
312: #else
313:     PetscFree(baij->colmap);
314:     PetscLogObjectMemory(A,-Bbaij->nbs*sizeof(PetscInt));
315: #endif
316:   }

318:   /* make sure that B is assembled so we can access its values */
319:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
320:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

322:   /* invent new B and copy stuff over */
323:   PetscMalloc(mbs*sizeof(PetscInt),&nz);
324:   for (i=0; i<mbs; i++) {
325:     nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
326:   }
327:   MatCreate(PETSC_COMM_SELF,&Bnew);
328:   MatSetSizes(Bnew,m,n,m,n);
329:   MatSetType(Bnew,((PetscObject)B)->type_name);
330:   MatSeqBAIJSetPreallocation(Bnew,B->rmap->bs,0,nz);
331:   PetscFree(nz);
332: 
333:   PetscMalloc(bs*sizeof(PetscInt),&rvals);
334:   for (i=0; i<mbs; i++) {
335:     rvals[0] = bs*i;
336:     for (j=1; j<bs; j++) { rvals[j] = rvals[j-1] + 1; }
337:     for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
338:       col = garray[Bbaij->j[j]]*bs;
339:       for (k=0; k<bs; k++) {
340: #if defined(PETSC_USE_REAL_MAT_SINGLE)
341:         for (l=0; l<bs; l++) atmp[l] = a[j*bs2+l];
342: #else
343:         atmp = a+j*bs2 + k*bs;
344: #endif
345:         MatSetValues_SeqSBAIJ(Bnew,bs,rvals,1,&col,atmp,B->insertmode);
346:         col++;
347:       }
348:     }
349:   }
350: #if defined(PETSC_USE_REAL_MAT_SINGLE)
351:   PetscFree(atmp);
352: #endif
353:   PetscFree(baij->garray);
354:   baij->garray = 0;
355:   PetscFree(rvals);
356:   PetscLogObjectMemory(A,-ec*sizeof(PetscInt));
357:   MatDestroy(&B);
358:   PetscLogObjectParent(A,Bnew);
359:   baij->B = Bnew;
360:   A->was_assembled = PETSC_FALSE;
361:   return(0);
362: }