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>

  7: PetscErrorCode MatSetUpMultiply_MPISBAIJ(Mat mat)
  8: {
  9:   Mat_MPISBAIJ   *sbaij = (Mat_MPISBAIJ*)mat->data;
 10:   Mat_SeqBAIJ    *B     = (Mat_SeqBAIJ*)(sbaij->B->data);
 11:   PetscInt       Nbs = sbaij->Nbs,i,j,*aj = B->j,ec = 0,*garray,*sgarray;
 12:   PetscInt       bs  = mat->rmap->bs,*stmp,mbs=sbaij->mbs, vec_size,nt;
 13:   IS             from,to;
 14:   Vec            gvec;
 15:   PetscMPIInt    rank = sbaij->rank,lsize;
 16:   PetscInt       *owners = sbaij->rangebs,*ec_owner,k;
 17:   const PetscInt *sowners;
 18:   PetscScalar    *ptr;
 19: #if defined(PETSC_USE_CTABLE)
 20:   PetscTable         gid1_lid1; /* one-based gid to lid table */
 21:   PetscTablePosition tpos;
 22:   PetscInt           gid,lid;
 23: #else
 24:   PetscInt           *indices;
 25: #endif

 27: #if defined(PETSC_USE_CTABLE)
 28:   PetscTableCreate(mbs,Nbs+1,&gid1_lid1);
 29:   for (i=0; i<B->mbs; i++) {
 30:     for (j=0; j<B->ilen[i]; j++) {
 31:       PetscInt data,gid1 = aj[B->i[i]+j] + 1;
 32:       PetscTableFind(gid1_lid1,gid1,&data);
 33:       if (!data) PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);
 34:     }
 35:   }
 36:   /* form array of columns we need */
 37:   PetscMalloc1(ec,&garray);
 38:   PetscTableGetHeadPosition(gid1_lid1,&tpos);
 39:   while (tpos) {
 40:     PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
 41:     gid--; lid--;
 42:     garray[lid] = gid;
 43:   }
 44:   PetscSortInt(ec,garray);
 45:   PetscTableRemoveAll(gid1_lid1);
 46:   for (i=0; i<ec; i++) PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);
 47:   /* compact out the extra columns in B */
 48:   for (i=0; i<B->mbs; i++) {
 49:     for (j=0; j<B->ilen[i]; j++) {
 50:       PetscInt gid1 = aj[B->i[i] + j] + 1;
 51:       PetscTableFind(gid1_lid1,gid1,&lid);
 52:       lid--;
 53:       aj[B->i[i]+j] = lid;
 54:     }
 55:   }
 56:   PetscTableDestroy(&gid1_lid1);
 57:   PetscMalloc2(2*ec,&sgarray,ec,&ec_owner);
 58:   for (i=j=0; i<ec; i++) {
 59:     while (garray[i]>=owners[j+1]) j++;
 60:     ec_owner[i] = j;
 61:   }
 62: #else
 63:   /* For the first stab we make an array as long as the number of columns */
 64:   /* mark those columns that are in sbaij->B */
 65:   PetscCalloc1(Nbs,&indices);
 66:   for (i=0; i<mbs; i++) {
 67:     for (j=0; j<B->ilen[i]; j++) {
 68:       if (!indices[aj[B->i[i] + j]]) ec++;
 69:       indices[aj[B->i[i] + j]] = 1;
 70:     }
 71:   }

 73:   /* form arrays of columns we need */
 74:   PetscMalloc1(ec,&garray);
 75:   PetscMalloc2(2*ec,&sgarray,ec,&ec_owner);

 77:   ec = 0;
 78:   for (j=0; j<sbaij->size; j++) {
 79:     for (i=owners[j]; i<owners[j+1]; i++) {
 80:       if (indices[i]) {
 81:         garray[ec]   = i;
 82:         ec_owner[ec] = j;
 83:         ec++;
 84:       }
 85:     }
 86:   }

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

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

101:   VecScatterDestroy(&sbaij->sMvctx);
102:   /* create local vector that is used to scatter into */
103:   VecCreateSeq(PETSC_COMM_SELF,ec*bs,&sbaij->lvec);

105:   /* create two temporary index sets for building scatter-gather */
106:   PetscMalloc1(2*ec,&stmp);
107:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,PETSC_COPY_VALUES,&from);
108:   for (i=0; i<ec; i++) stmp[i] = i;
109:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_COPY_VALUES,&to);

111:   /* generate the scatter context
112:      -- Mvctx and lvec are not used by MatMult_MPISBAIJ(), but have other uses, such as in MatDiagonalScale_MPISBAIJ */
113:   VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);
114:   VecScatterCreate(gvec,from,sbaij->lvec,to,&sbaij->Mvctx);
115:   VecDestroy(&gvec);

117:   sbaij->garray = garray;

119:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->Mvctx);
120:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->lvec);
121:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
122:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);

124:   ISDestroy(&from);
125:   ISDestroy(&to);

127:   /* create parallel vector that is used by SBAIJ matrix to scatter from/into */
128:   lsize = (mbs + ec)*bs;
129:   VecCreateMPI(PetscObjectComm((PetscObject)mat),lsize,PETSC_DETERMINE,&sbaij->slvec0);
130:   VecDuplicate(sbaij->slvec0,&sbaij->slvec1);
131:   VecGetSize(sbaij->slvec0,&vec_size);

133:   VecGetOwnershipRanges(sbaij->slvec0,&sowners);

135:   /* x index in the IS sfrom */
136:   for (i=0; i<ec; i++) {
137:     j          = ec_owner[i];
138:     sgarray[i] = garray[i] + (sowners[j]/bs - owners[j]);
139:   }
140:   /* b index in the IS sfrom */
141:   k = sowners[rank]/bs + mbs;
142:   for (i=ec,j=0; i< 2*ec; i++,j++) sgarray[i] = k + j;
143:   ISCreateBlock(PETSC_COMM_SELF,bs,2*ec,sgarray,PETSC_COPY_VALUES,&from);

145:   /* x index in the IS sto */
146:   k = sowners[rank]/bs + mbs;
147:   for (i=0; i<ec; i++) stmp[i] = (k + i);
148:   /* b index in the IS sto */
149:   for (i=ec; i<2*ec; i++) stmp[i] = sgarray[i-ec];

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

153:   VecScatterCreate(sbaij->slvec0,from,sbaij->slvec1,to,&sbaij->sMvctx);
154:   VecScatterViewFromOptions(sbaij->sMvctx,(PetscObject)mat,"-matmult_vecscatter_view");

156:   VecGetLocalSize(sbaij->slvec1,&nt);
157:   VecGetArray(sbaij->slvec1,&ptr);
158:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,bs*mbs,ptr,&sbaij->slvec1a);
159:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec1b);
160:   VecRestoreArray(sbaij->slvec1,&ptr);

162:   VecGetArray(sbaij->slvec0,&ptr);
163:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec0b);
164:   VecRestoreArray(sbaij->slvec0,&ptr);

166:   PetscFree(stmp);

168:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->sMvctx);
169:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec0);
170:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec1);
171:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec0b);
172:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec1a);
173:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec1b);
174:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
175:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);

177:   PetscLogObjectMemory((PetscObject)mat,ec*sizeof(PetscInt));
178:   ISDestroy(&from);
179:   ISDestroy(&to);
180:   PetscFree2(sgarray,ec_owner);
181:   return 0;
182: }

184: /*
185:      Takes the local part of an already assembled MPISBAIJ matrix
186:    and disassembles it. This is to allow new nonzeros into the matrix
187:    that require more communication in the matrix vector multiply.
188:    Thus certain data-structures must be rebuilt.

190:    Kind of slow! But that's what application programmers get when
191:    they are sloppy.
192: */
193: PetscErrorCode MatDisAssemble_MPISBAIJ(Mat A)
194: {
195:   Mat_MPISBAIJ   *baij  = (Mat_MPISBAIJ*)A->data;
196:   Mat            B      = baij->B,Bnew;
197:   Mat_SeqBAIJ    *Bbaij = (Mat_SeqBAIJ*)B->data;
198:   PetscInt       i,j,mbs=Bbaij->mbs,n = A->cmap->N,col,*garray=baij->garray;
199:   PetscInt       k,bs=A->rmap->bs,bs2=baij->bs2,*rvals,*nz,ec,m=A->rmap->n;
200:   MatScalar      *a = Bbaij->a;
201:   PetscScalar    *atmp;
202: #if defined(PETSC_USE_REAL_MAT_SINGLE)
203:   PetscInt l;
204: #endif

206: #if defined(PETSC_USE_REAL_MAT_SINGLE)
207:   PetscMalloc1(A->rmap->bs,&atmp);
208: #endif
209:   /* free stuff related to matrix-vec multiply */
210:   VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
211:   VecDestroy(&baij->lvec);
212:   VecScatterDestroy(&baij->Mvctx);

214:   VecDestroy(&baij->slvec0);
215:   VecDestroy(&baij->slvec0b);
216:   VecDestroy(&baij->slvec1);
217:   VecDestroy(&baij->slvec1a);
218:   VecDestroy(&baij->slvec1b);

220:   if (baij->colmap) {
221: #if defined(PETSC_USE_CTABLE)
222:     PetscTableDestroy(&baij->colmap);
223: #else
224:     PetscFree(baij->colmap);
225:     PetscLogObjectMemory((PetscObject)A,-Bbaij->nbs*sizeof(PetscInt));
226: #endif
227:   }

229:   /* make sure that B is assembled so we can access its values */
230:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
231:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

233:   /* invent new B and copy stuff over */
234:   PetscMalloc1(mbs,&nz);
235:   for (i=0; i<mbs; i++) {
236:     nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
237:   }
238:   MatCreate(PETSC_COMM_SELF,&Bnew);
239:   MatSetSizes(Bnew,m,n,m,n);
240:   MatSetType(Bnew,((PetscObject)B)->type_name);
241:   MatSeqBAIJSetPreallocation(Bnew,B->rmap->bs,0,nz);
242:   PetscFree(nz);

244:   if (Bbaij->nonew >= 0) { /* Inherit insertion error options (if positive). */
245:     ((Mat_SeqSBAIJ*)Bnew->data)->nonew = Bbaij->nonew;
246:   }

248:   /*
249:    Ensure that B's nonzerostate is monotonically increasing.
250:    Or should this follow the MatSetValues() loop to preserve B's nonzerstate across a MatDisAssemble() call?
251:    */
252:   Bnew->nonzerostate = B->nonzerostate;
253:   PetscMalloc1(bs,&rvals);
254:   for (i=0; i<mbs; i++) {
255:     rvals[0] = bs*i;
256:     for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1;
257:     for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
258:       col = garray[Bbaij->j[j]]*bs;
259:       for (k=0; k<bs; k++) {
260: #if defined(PETSC_USE_REAL_MAT_SINGLE)
261:         for (l=0; l<bs; l++) atmp[l] = a[j*bs2+l];
262: #else
263:         atmp = a+j*bs2 + k*bs;
264: #endif
265:         MatSetValues_SeqSBAIJ(Bnew,bs,rvals,1,&col,atmp,B->insertmode);
266:         col++;
267:       }
268:     }
269:   }
270: #if defined(PETSC_USE_REAL_MAT_SINGLE)
271:   PetscFree(atmp);
272: #endif
273:   PetscFree(baij->garray);

275:   baij->garray = NULL;

277:   PetscFree(rvals);
278:   PetscLogObjectMemory((PetscObject)A,-ec*sizeof(PetscInt));
279:   MatDestroy(&B);
280:   PetscLogObjectParent((PetscObject)A,(PetscObject)Bnew);

282:   baij->B = Bnew;

284:   A->was_assembled = PETSC_FALSE;
285:   return 0;
286: }