Actual source code: mmaij.c

petsc-3.8.4 2018-03-24
Report Typos and Errors

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

  8: PetscErrorCode MatSetUpMultiply_MPIAIJ(Mat mat)
  9: {
 10:   Mat_MPIAIJ     *aij = (Mat_MPIAIJ*)mat->data;
 11:   Mat_SeqAIJ     *B   = (Mat_SeqAIJ*)(aij->B->data);
 13:   PetscInt       i,j,*aj = B->j,ec = 0,*garray;
 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 N = mat->cmap->N,*indices;
 22: #endif

 25: #if defined(PETSC_USE_CTABLE)
 26:   /* use a table */
 27:   PetscTableCreate(aij->B->rmap->n,mat->cmap->N+1,&gid1_lid1);
 28:   for (i=0; i<aij->B->rmap->n; i++) {
 29:     for (j=0; j<B->ilen[i]; j++) {
 30:       PetscInt data,gid1 = aj[B->i[i] + j] + 1;
 31:       PetscTableFind(gid1_lid1,gid1,&data);
 32:       if (!data) {
 33:         /* one based table */
 34:         PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);
 35:       }
 36:     }
 37:   }
 38:   /* form array of columns we need */
 39:   PetscMalloc1(ec+1,&garray);
 40:   PetscTableGetHeadPosition(gid1_lid1,&tpos);
 41:   while (tpos) {
 42:     PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
 43:     gid--;
 44:     lid--;
 45:     garray[lid] = gid;
 46:   }
 47:   PetscSortInt(ec,garray); /* sort, and rebuild */
 48:   PetscTableRemoveAll(gid1_lid1);
 49:   for (i=0; i<ec; i++) {
 50:     PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);
 51:   }
 52:   /* compact out the extra columns in B */
 53:   for (i=0; i<aij->B->rmap->n; i++) {
 54:     for (j=0; j<B->ilen[i]; j++) {
 55:       PetscInt gid1 = aj[B->i[i] + j] + 1;
 56:       PetscTableFind(gid1_lid1,gid1,&lid);
 57:       lid--;
 58:       aj[B->i[i] + j] = lid;
 59:     }
 60:   }
 61:   aij->B->cmap->n = aij->B->cmap->N = ec;
 62:   aij->B->cmap->bs = 1;

 64:   PetscLayoutSetUp((aij->B->cmap));
 65:   PetscTableDestroy(&gid1_lid1);
 66: #else
 67:   /* Make an array as long as the number of columns */
 68:   /* mark those columns that are in aij->B */
 69:   PetscCalloc1(N+1,&indices);
 70:   for (i=0; i<aij->B->rmap->n; i++) {
 71:     for (j=0; j<B->ilen[i]; j++) {
 72:       if (!indices[aj[B->i[i] + j]]) ec++;
 73:       indices[aj[B->i[i] + j]] = 1;
 74:     }
 75:   }

 77:   /* form array of columns we need */
 78:   PetscMalloc1(ec+1,&garray);
 79:   ec   = 0;
 80:   for (i=0; i<N; i++) {
 81:     if (indices[i]) garray[ec++] = i;
 82:   }

 84:   /* make indices now point into garray */
 85:   for (i=0; i<ec; i++) {
 86:     indices[garray[i]] = i;
 87:   }

 89:   /* compact out the extra columns in B */
 90:   for (i=0; i<aij->B->rmap->n; i++) {
 91:     for (j=0; j<B->ilen[i]; j++) {
 92:       aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
 93:     }
 94:   }
 95:   aij->B->cmap->n = aij->B->cmap->N = ec;
 96:   aij->B->cmap->bs = 1;

 98:   PetscLayoutSetUp((aij->B->cmap));
 99:   PetscFree(indices);
100: #endif
101:   /* create local vector that is used to scatter into */
102:   VecCreateSeq(PETSC_COMM_SELF,ec,&aij->lvec);

104:   /* create two temporary Index sets for build scatter gather */
105:   ISCreateGeneral(((PetscObject)mat)->comm,ec,garray,PETSC_COPY_VALUES,&from);

107:   ISCreateStride(PETSC_COMM_SELF,ec,0,1,&to);

109:   /* create temporary global vector to generate scatter context */
110:   /* This does not allocate the array's memory so is efficient */
111:   VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);

113:   /* generate the scatter context */
114:   VecScatterCreate(gvec,from,aij->lvec,to,&aij->Mvctx);
115:   PetscLogObjectParent((PetscObject)mat,(PetscObject)aij->Mvctx);
116:   PetscLogObjectParent((PetscObject)mat,(PetscObject)aij->lvec);
117:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
118:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);

120:   aij->garray = garray;

122:   PetscLogObjectMemory((PetscObject)mat,(ec+1)*sizeof(PetscInt));
123:   ISDestroy(&from);
124:   ISDestroy(&to);
125:   VecDestroy(&gvec);
126:   return(0);
127: }


130: /*
131:      Takes the local part of an already assembled MPIAIJ 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_MPIAIJ(Mat A)
140: {
141:   Mat_MPIAIJ     *aij  = (Mat_MPIAIJ*)A->data;
142:   Mat            B     = aij->B,Bnew;
143:   Mat_SeqAIJ     *Baij = (Mat_SeqAIJ*)B->data;
145:   PetscInt       i,j,m = B->rmap->n,n = A->cmap->N,col,ct = 0,*garray = aij->garray,*nz,ec;
146:   PetscScalar    v;

149:   /* free stuff related to matrix-vec multiply */
150:   VecGetSize(aij->lvec,&ec); /* needed for PetscLogObjectMemory below */
151:   VecDestroy(&aij->lvec);
152:   VecScatterDestroy(&aij->Mvctx);
153:   if (aij->colmap) {
154: #if defined(PETSC_USE_CTABLE)
155:     PetscTableDestroy(&aij->colmap);
156: #else
157:     PetscFree(aij->colmap);
158:     PetscLogObjectMemory((PetscObject)A,-aij->B->cmap->n*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(m+1,&nz);
168:   for (i=0; i<m; i++) {
169:     nz[i] = Baij->i[i+1] - Baij->i[i];
170:   }
171:   MatCreate(PETSC_COMM_SELF,&Bnew);
172:   MatSetSizes(Bnew,m,n,m,n);
173:   MatSetBlockSizesFromMats(Bnew,A,A);
174:   MatSetType(Bnew,((PetscObject)B)->type_name);
175:   MatSeqAIJSetPreallocation(Bnew,0,nz);

177:   ((Mat_SeqAIJ*)Bnew->data)->nonew = Baij->nonew; /* Inherit insertion error options. */
178:   /*
179:    Ensure that B's nonzerostate is monotonically increasing.
180:    Or should this follow the MatSetValues() loop to preserve B's nonzerstate across a MatDisAssemble() call?
181:    */
182:   Bnew->nonzerostate = B->nonzerostate;

184:   PetscFree(nz);
185:   for (i=0; i<m; i++) {
186:     for (j=Baij->i[i]; j<Baij->i[i+1]; j++) {
187:       col  = garray[Baij->j[ct]];
188:       v    = Baij->a[ct++];
189:       MatSetValues(Bnew,1,&i,1,&col,&v,B->insertmode);
190:     }
191:   }
192:   PetscFree(aij->garray);
193:   PetscLogObjectMemory((PetscObject)A,-ec*sizeof(PetscInt));
194:   MatDestroy(&B);
195:   PetscLogObjectParent((PetscObject)A,(PetscObject)Bnew);

197:   aij->B           = Bnew;
198:   A->was_assembled = PETSC_FALSE;
199:   return(0);
200: }

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

204: static PetscInt *auglyrmapd = 0,*auglyrmapo = 0; /* mapping from the local ordering to the "diagonal" and "off-diagonal" parts of the local matrix */
205: static Vec auglydd          = 0,auglyoo     = 0; /* work vectors used to scale the two parts of the local matrix */


208: PetscErrorCode MatMPIAIJDiagonalScaleLocalSetUp(Mat inA,Vec scale)
209: {
210:   Mat_MPIAIJ     *ina = (Mat_MPIAIJ*) inA->data; /*access private part of matrix */
212:   PetscInt       i,n,nt,cstart,cend,no,*garray = ina->garray,*lindices;
213:   PetscInt       *r_rmapd,*r_rmapo;

216:   MatGetOwnershipRange(inA,&cstart,&cend);
217:   MatGetSize(ina->A,NULL,&n);
218:   PetscCalloc1(inA->rmap->mapping->n+1,&r_rmapd);
219:   nt   = 0;
220:   for (i=0; i<inA->rmap->mapping->n; i++) {
221:     if (inA->rmap->mapping->indices[i] >= cstart && inA->rmap->mapping->indices[i] < cend) {
222:       nt++;
223:       r_rmapd[i] = inA->rmap->mapping->indices[i] + 1;
224:     }
225:   }
226:   if (nt != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Hmm nt %D n %D",nt,n);
227:   PetscMalloc1(n+1,&auglyrmapd);
228:   for (i=0; i<inA->rmap->mapping->n; i++) {
229:     if (r_rmapd[i]) {
230:       auglyrmapd[(r_rmapd[i]-1)-cstart] = i;
231:     }
232:   }
233:   PetscFree(r_rmapd);
234:   VecCreateSeq(PETSC_COMM_SELF,n,&auglydd);

236:   PetscCalloc1(inA->cmap->N+1,&lindices);
237:   for (i=0; i<ina->B->cmap->n; i++) {
238:     lindices[garray[i]] = i+1;
239:   }
240:   no   = inA->rmap->mapping->n - nt;
241:   PetscCalloc1(inA->rmap->mapping->n+1,&r_rmapo);
242:   nt   = 0;
243:   for (i=0; i<inA->rmap->mapping->n; i++) {
244:     if (lindices[inA->rmap->mapping->indices[i]]) {
245:       nt++;
246:       r_rmapo[i] = lindices[inA->rmap->mapping->indices[i]];
247:     }
248:   }
249:   if (nt > no) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Hmm nt %D no %D",nt,n);
250:   PetscFree(lindices);
251:   PetscMalloc1(nt+1,&auglyrmapo);
252:   for (i=0; i<inA->rmap->mapping->n; i++) {
253:     if (r_rmapo[i]) {
254:       auglyrmapo[(r_rmapo[i]-1)] = i;
255:     }
256:   }
257:   PetscFree(r_rmapo);
258:   VecCreateSeq(PETSC_COMM_SELF,nt,&auglyoo);
259:   return(0);
260: }

262: PetscErrorCode MatMPIAIJDiagonalScaleLocal(Mat A,Vec scale)
263: {
264:   /* This routine should really be abandoned as it duplicates MatDiagonalScaleLocal */

268:   PetscTryMethod(A,"MatDiagonalScaleLocal_C",(Mat,Vec),(A,scale));
269:   return(0);
270: }

272: PetscErrorCode  MatDiagonalScaleLocal_MPIAIJ(Mat A,Vec scale)
273: {
274:   Mat_MPIAIJ        *a = (Mat_MPIAIJ*) A->data; /*access private part of matrix */
275:   PetscErrorCode    ierr;
276:   PetscInt          n,i;
277:   PetscScalar       *d,*o;
278:   const PetscScalar *s;

281:   if (!auglyrmapd) {
282:     MatMPIAIJDiagonalScaleLocalSetUp(A,scale);
283:   }

285:   VecGetArrayRead(scale,&s);

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

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