Actual source code: mmbaij.c


  2: /*
  3:    Support for the parallel BAIJ matrix vector multiply
  4: */
  5: #include <../src/mat/impls/baij/mpi/mpibaij.h>
  6: #include <petsc/private/isimpl.h>

  8: PetscErrorCode MatSetUpMultiply_MPIBAIJ(Mat mat)
  9: {
 10:   Mat_MPIBAIJ    *baij = (Mat_MPIBAIJ*)mat->data;
 11:   Mat_SeqBAIJ    *B    = (Mat_SeqBAIJ*)(baij->B->data);
 12:   PetscInt       i,j,*aj = B->j,ec = 0,*garray;
 13:   PetscInt       bs = mat->rmap->bs,*stmp;
 14:   IS             from,to;
 15:   Vec            gvec;
 16: #if defined(PETSC_USE_CTABLE)
 17:   PetscTable         gid1_lid1;
 18:   PetscTablePosition tpos;
 19:   PetscInt           gid,lid;
 20: #else
 21:   PetscInt Nbs = baij->Nbs,*indices;
 22: #endif

 24: #if defined(PETSC_USE_CTABLE)
 25:   /* use a table - Mark Adams */
 26:   PetscTableCreate(B->mbs,baij->Nbs+1,&gid1_lid1);
 27:   for (i=0; i<B->mbs; i++) {
 28:     for (j=0; j<B->ilen[i]; j++) {
 29:       PetscInt data,gid1 = aj[B->i[i]+j] + 1;
 30:       PetscTableFind(gid1_lid1,gid1,&data);
 31:       if (!data) {
 32:         /* one based table */
 33:         PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);
 34:       }
 35:     }
 36:   }
 37:   /* form array of columns we need */
 38:   PetscMalloc1(ec,&garray);
 39:   PetscTableGetHeadPosition(gid1_lid1,&tpos);
 40:   while (tpos) {
 41:     PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
 42:     gid--; lid--;
 43:     garray[lid] = gid;
 44:   }
 45:   PetscSortInt(ec,garray);
 46:   PetscTableRemoveAll(gid1_lid1);
 47:   for (i=0; i<ec; i++) {
 48:     PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);
 49:   }
 50:   /* compact out the extra columns in B */
 51:   for (i=0; i<B->mbs; i++) {
 52:     for (j=0; j<B->ilen[i]; j++) {
 53:       PetscInt gid1 = aj[B->i[i] + j] + 1;
 54:       PetscTableFind(gid1_lid1,gid1,&lid);
 55:       lid--;
 56:       aj[B->i[i]+j] = lid;
 57:     }
 58:   }
 59:   B->nbs           = ec;
 60:   PetscLayoutDestroy(&baij->B->cmap);
 61:   PetscLayoutCreateFromSizes(PetscObjectComm((PetscObject)baij->B),ec*mat->rmap->bs,ec*mat->rmap->bs,mat->rmap->bs,&baij->B->cmap);
 62:   PetscTableDestroy(&gid1_lid1);
 63: #else
 64:   /* Make an array as long as the number of columns */
 65:   /* mark those columns that are in baij->B */
 66:   PetscCalloc1(Nbs,&indices);
 67:   for (i=0; i<B->mbs; i++) {
 68:     for (j=0; j<B->ilen[i]; j++) {
 69:       if (!indices[aj[B->i[i] + j]]) ec++;
 70:       indices[aj[B->i[i] + j]] = 1;
 71:     }
 72:   }

 74:   /* form array of columns we need */
 75:   PetscMalloc1(ec,&garray);
 76:   ec   = 0;
 77:   for (i=0; i<Nbs; i++) {
 78:     if (indices[i]) {
 79:       garray[ec++] = i;
 80:     }
 81:   }

 83:   /* make indices now point into garray */
 84:   for (i=0; i<ec; i++) {
 85:     indices[garray[i]] = i;
 86:   }

 88:   /* compact out the extra columns in B */
 89:   for (i=0; i<B->mbs; i++) {
 90:     for (j=0; j<B->ilen[i]; j++) {
 91:       aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
 92:     }
 93:   }
 94:   B->nbs           = ec;
 95:   PetscLayoutDestroy(&baij->B->cmap);
 96:   PetscLayoutCreateFromSizes(PetscObjectComm((PetscObject)baij->B),ec*mat->rmap->bs,ec*mat->rmap->bs,mat->rmap->bs,&baij->B->cmap);
 97:   PetscFree(indices);
 98: #endif

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

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

106:   PetscMalloc1(ec,&stmp);
107:   for (i=0; i<ec; i++) stmp[i] = i;
108:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_OWN_POINTER,&to);

110:   /* create temporary global vector to generate scatter context */
111:   VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);

113:   VecScatterCreate(gvec,from,baij->lvec,to,&baij->Mvctx);
114:   VecScatterViewFromOptions(baij->Mvctx,(PetscObject)mat,"-matmult_vecscatter_view");

116:   PetscLogObjectParent((PetscObject)mat,(PetscObject)baij->Mvctx);
117:   PetscLogObjectParent((PetscObject)mat,(PetscObject)baij->lvec);
118:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
119:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);

121:   baij->garray = garray;

123:   PetscLogObjectMemory((PetscObject)mat,ec*sizeof(PetscInt));
124:   ISDestroy(&from);
125:   ISDestroy(&to);
126:   VecDestroy(&gvec);
127:   return 0;
128: }

130: /*
131:      Takes the local part of an already assembled MPIBAIJ matrix
132:    and disassembles it. This is to allow new nonzeros into the matrix
133:    that require more communication in the matrix vector multiply.
134:    Thus certain data-structures must be rebuilt.

136:    Kind of slow! But that's what application programmers get when
137:    they are sloppy.
138: */
139: PetscErrorCode MatDisAssemble_MPIBAIJ(Mat A)
140: {
141:   Mat_MPIBAIJ    *baij  = (Mat_MPIBAIJ*)A->data;
142:   Mat            B      = baij->B,Bnew;
143:   Mat_SeqBAIJ    *Bbaij = (Mat_SeqBAIJ*)B->data;
144:   PetscInt       i,j,mbs=Bbaij->mbs,n = A->cmap->N,col,*garray=baij->garray;
145:   PetscInt       bs2 = baij->bs2,*nz,ec,m = A->rmap->n;
146:   MatScalar      *a  = Bbaij->a;
147:   MatScalar      *atmp;

149:   /* free stuff related to matrix-vec multiply */
150:   VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
151:   VecDestroy(&baij->lvec); baij->lvec = NULL;
152:   VecScatterDestroy(&baij->Mvctx); baij->Mvctx = NULL;
153:   if (baij->colmap) {
154: #if defined(PETSC_USE_CTABLE)
155:     PetscTableDestroy(&baij->colmap);
156: #else
157:     PetscFree(baij->colmap);
158:     PetscLogObjectMemory((PetscObject)A,-Bbaij->nbs*sizeof(PetscInt));
159: #endif
160:   }

162:   /* make sure that B is assembled so we can access its values */
163:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
164:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

166:   /* invent new B and copy stuff over */
167:   PetscMalloc1(mbs,&nz);
168:   for (i=0; i<mbs; i++) {
169:     nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
170:   }
171:   MatCreate(PetscObjectComm((PetscObject)B),&Bnew);
172:   MatSetSizes(Bnew,m,n,m,n);
173:   MatSetType(Bnew,((PetscObject)B)->type_name);
174:   MatSeqBAIJSetPreallocation(Bnew,B->rmap->bs,0,nz);
175:   if (Bbaij->nonew >= 0) { /* Inherit insertion error options (if positive). */
176:     ((Mat_SeqBAIJ*)Bnew->data)->nonew = Bbaij->nonew;
177:   }

179:   MatSetOption(Bnew,MAT_ROW_ORIENTED,PETSC_FALSE);
180:   /*
181:    Ensure that B's nonzerostate is monotonically increasing.
182:    Or should this follow the MatSetValuesBlocked() loop to preserve B's nonzerstate across a MatDisAssemble() call?
183:    */
184:   Bnew->nonzerostate = B->nonzerostate;

186:   for (i=0; i<mbs; i++) {
187:     for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
188:       col  = garray[Bbaij->j[j]];
189:       atmp = a + j*bs2;
190:       MatSetValuesBlocked_SeqBAIJ(Bnew,1,&i,1,&col,atmp,B->insertmode);
191:     }
192:   }
193:   MatSetOption(Bnew,MAT_ROW_ORIENTED,PETSC_TRUE);

195:   PetscFree(nz);
196:   PetscFree(baij->garray);
197:   PetscLogObjectMemory((PetscObject)A,-ec*sizeof(PetscInt));
198:   MatDestroy(&B);
199:   PetscLogObjectParent((PetscObject)A,(PetscObject)Bnew);

201:   baij->B          = Bnew;
202:   A->was_assembled = PETSC_FALSE;
203:   A->assembled     = PETSC_FALSE;
204:   return 0;
205: }

207: /*      ugly stuff added for Glenn someday we should fix this up */

209: static PetscInt *uglyrmapd = NULL,*uglyrmapo = NULL;  /* mapping from the local ordering to the "diagonal" and "off-diagonal" parts of the local matrix */
210: static Vec      uglydd     = NULL,uglyoo     = NULL;  /* work vectors used to scale the two parts of the local matrix */

212: PetscErrorCode MatMPIBAIJDiagonalScaleLocalSetUp(Mat inA,Vec scale)
213: {
214:   Mat_MPIBAIJ    *ina = (Mat_MPIBAIJ*) inA->data; /*access private part of matrix */
215:   Mat_SeqBAIJ    *B   = (Mat_SeqBAIJ*)ina->B->data;
216:   PetscInt       bs = inA->rmap->bs,i,n,nt,j,cstart,cend,no,*garray = ina->garray,*lindices;
217:   PetscInt       *r_rmapd,*r_rmapo;

219:   MatGetOwnershipRange(inA,&cstart,&cend);
220:   MatGetSize(ina->A,NULL,&n);
221:   PetscCalloc1(inA->rmap->mapping->n+1,&r_rmapd);
222:   nt   = 0;
223:   for (i=0; i<inA->rmap->mapping->n; i++) {
224:     if (inA->rmap->mapping->indices[i]*bs >= cstart && inA->rmap->mapping->indices[i]*bs < cend) {
225:       nt++;
226:       r_rmapd[i] = inA->rmap->mapping->indices[i] + 1;
227:     }
228:   }
230:   PetscMalloc1(n+1,&uglyrmapd);
231:   for (i=0; i<inA->rmap->mapping->n; i++) {
232:     if (r_rmapd[i]) {
233:       for (j=0; j<bs; j++) {
234:         uglyrmapd[(r_rmapd[i]-1)*bs+j-cstart] = i*bs + j;
235:       }
236:     }
237:   }
238:   PetscFree(r_rmapd);
239:   VecCreateSeq(PETSC_COMM_SELF,n,&uglydd);

241:   PetscCalloc1(ina->Nbs+1,&lindices);
242:   for (i=0; i<B->nbs; i++) {
243:     lindices[garray[i]] = i+1;
244:   }
245:   no   = inA->rmap->mapping->n - nt;
246:   PetscCalloc1(inA->rmap->mapping->n+1,&r_rmapo);
247:   nt   = 0;
248:   for (i=0; i<inA->rmap->mapping->n; i++) {
249:     if (lindices[inA->rmap->mapping->indices[i]]) {
250:       nt++;
251:       r_rmapo[i] = lindices[inA->rmap->mapping->indices[i]];
252:     }
253:   }
255:   PetscFree(lindices);
256:   PetscMalloc1(nt*bs+1,&uglyrmapo);
257:   for (i=0; i<inA->rmap->mapping->n; i++) {
258:     if (r_rmapo[i]) {
259:       for (j=0; j<bs; j++) {
260:         uglyrmapo[(r_rmapo[i]-1)*bs+j] = i*bs + j;
261:       }
262:     }
263:   }
264:   PetscFree(r_rmapo);
265:   VecCreateSeq(PETSC_COMM_SELF,nt*bs,&uglyoo);
266:   return 0;
267: }

269: PetscErrorCode  MatMPIBAIJDiagonalScaleLocal(Mat A,Vec scale)
270: {
271:   /* This routine should really be abandoned as it duplicates MatDiagonalScaleLocal */

273:   PetscTryMethod(A,"MatDiagonalScaleLocal_C",(Mat,Vec),(A,scale));
274:   return 0;
275: }

277: PetscErrorCode  MatDiagonalScaleLocal_MPIBAIJ(Mat A,Vec scale)
278: {
279:   Mat_MPIBAIJ       *a = (Mat_MPIBAIJ*) A->data; /*access private part of matrix */
280:   PetscInt          n,i;
281:   PetscScalar       *d,*o;
282:   const PetscScalar *s;

284:   if (!uglyrmapd) {
285:     MatMPIBAIJDiagonalScaleLocalSetUp(A,scale);
286:   }

288:   VecGetArrayRead(scale,&s);

290:   VecGetLocalSize(uglydd,&n);
291:   VecGetArray(uglydd,&d);
292:   for (i=0; i<n; i++) {
293:     d[i] = s[uglyrmapd[i]]; /* copy "diagonal" (true local) portion of scale into dd vector */
294:   }
295:   VecRestoreArray(uglydd,&d);
296:   /* column scale "diagonal" portion of local matrix */
297:   MatDiagonalScale(a->A,NULL,uglydd);

299:   VecGetLocalSize(uglyoo,&n);
300:   VecGetArray(uglyoo,&o);
301:   for (i=0; i<n; i++) {
302:     o[i] = s[uglyrmapo[i]]; /* copy "off-diagonal" portion of scale into oo vector */
303:   }
304:   VecRestoreArrayRead(scale,&s);
305:   VecRestoreArray(uglyoo,&o);
306:   /* column scale "off-diagonal" portion of local matrix */
307:   MatDiagonalScale(a->B,NULL,uglyoo);
308:   return 0;
309: }