Actual source code: mmsell.c

petsc-3.9.0 2018-04-07
Report Typos and Errors
  1: /*
  2:    Support for the parallel SELL matrix vector multiply
  3: */
  4:  #include <../src/mat/impls/sell/mpi/mpisell.h>
  5:  #include <petsc/private/isimpl.h>

  7: /*
  8:    Takes the local part of an already assembled MPISELL matrix
  9:    and disassembles it. This is to allow new nonzeros into the matrix
 10:    that require more communication in the matrix vector multiply.
 11:    Thus certain data-structures must be rebuilt.

 13:    Kind of slow! But that's what application programmers get when
 14:    they are sloppy.
 15: */
 16: PetscErrorCode MatDisAssemble_MPISELL(Mat A)
 17: {
 18:   Mat_MPISELL    *sell=(Mat_MPISELL*)A->data;
 19:   Mat            B=sell->B,Bnew;
 20:   Mat_SeqSELL    *Bsell=(Mat_SeqSELL*)B->data;
 21:   PetscInt       i,j,totalslices,N=A->cmap->N,ec,row;
 22:   PetscBool      isnonzero;

 26:   /* free stuff related to matrix-vec multiply */
 27:   VecGetSize(sell->lvec,&ec); /* needed for PetscLogObjectMemory below */
 28:   VecDestroy(&sell->lvec);
 29:   VecScatterDestroy(&sell->Mvctx);
 30:   if (sell->colmap) {
 31: #if defined(PETSC_USE_CTABLE)
 32:     PetscTableDestroy(&sell->colmap);
 33: #else
 34:     PetscFree(sell->colmap);
 35:     PetscLogObjectMemory((PetscObject)A,-sell->B->cmap->n*sizeof(PetscInt));
 36: #endif
 37:   }

 39:   /* make sure that B is assembled so we can access its values */
 40:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
 41:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

 43:   /* invent new B and copy stuff over */
 44:   MatCreate(PETSC_COMM_SELF,&Bnew);
 45:   MatSetSizes(Bnew,B->rmap->n,N,B->rmap->n,N);
 46:   MatSetBlockSizesFromMats(Bnew,A,A);
 47:   MatSetType(Bnew,((PetscObject)B)->type_name);
 48:   MatSeqSELLSetPreallocation(Bnew,0,Bsell->rlen);
 49:   ((Mat_SeqSELL*)Bnew->data)->nonew = Bsell->nonew; /* Inherit insertion error options. */

 51:   /*
 52:    Ensure that B's nonzerostate is monotonically increasing.
 53:    Or should this follow the MatSetValues() loop to preserve B's nonzerstate across a MatDisAssemble() call?
 54:    */
 55:   Bnew->nonzerostate = B->nonzerostate;

 57:   totalslices = B->rmap->n/8+((B->rmap->n & 0x07)?1:0); /* floor(n/8) */
 58:   for (i=0; i<totalslices; i++) { /* loop over slices */
 59:     for (j=Bsell->sliidx[i],row=0; j<Bsell->sliidx[i+1]; j++,row=((row+1)&0x07)) {
 60:       isnonzero = (PetscBool)((j-Bsell->sliidx[i])/8 < Bsell->rlen[8*i+row]);
 61:       if (isnonzero) {
 62:         MatSetValue(Bnew,8*i+row,sell->garray[Bsell->colidx[j]],Bsell->val[j],B->insertmode);
 63:       }
 64:     }
 65:   }

 67:   PetscFree(sell->garray);
 68:   PetscLogObjectMemory((PetscObject)A,-ec*sizeof(PetscInt));
 69:   MatDestroy(&B);
 70:   PetscLogObjectParent((PetscObject)A,(PetscObject)Bnew);

 72:   sell->B          = Bnew;
 73:   A->was_assembled = PETSC_FALSE;
 74:   A->assembled     = PETSC_FALSE;
 75:   return(0);
 76: }

 78: PetscErrorCode MatSetUpMultiply_MPISELL(Mat mat)
 79: {
 80:   Mat_MPISELL    *sell=(Mat_MPISELL*)mat->data;
 81:   Mat_SeqSELL    *B=(Mat_SeqSELL*)(sell->B->data);
 83:   PetscInt       i,j,*bcolidx=B->colidx,ec=0,*garray,totalslices;
 84:   IS             from,to;
 85:   Vec            gvec;
 86:   PetscBool      isnonzero;
 87: #if defined(PETSC_USE_CTABLE)
 88:   PetscTable         gid1_lid1;
 89:   PetscTablePosition tpos;
 90:   PetscInt           gid,lid;
 91: #else
 92:   PetscInt N = mat->cmap->N,*indices;
 93: #endif

 96:   totalslices = sell->B->rmap->n/8+((sell->B->rmap->n & 0x07)?1:0); /* floor(n/8) */

 98:   /* ec counts the number of columns that contain nonzeros */
 99: #if defined(PETSC_USE_CTABLE)
100:   /* use a table */
101:   PetscTableCreate(sell->B->rmap->n,mat->cmap->N+1,&gid1_lid1);
102:   for (i=0; i<totalslices; i++) { /* loop over slices */
103:     for (j=B->sliidx[i]; j<B->sliidx[i+1]; j++) {
104:       isnonzero = (PetscBool)((j-B->sliidx[i])/8 < B->rlen[(i<<3)+(j&0x07)]);
105:       if (isnonzero) { /* check the mask bit */
106:         PetscInt data,gid1 = bcolidx[j] + 1;
107:         PetscTableFind(gid1_lid1,gid1,&data);
108:         if (!data) {
109:           /* one based table */
110:           PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);
111:         }
112:       }
113:     }
114:   }

116:   /* form array of columns we need */
117:   PetscMalloc1(ec+1,&garray);
118:   PetscTableGetHeadPosition(gid1_lid1,&tpos);
119:   while (tpos) {
120:     PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
121:     gid--;
122:     lid--;
123:     garray[lid] = gid;
124:   }
125:   PetscSortInt(ec,garray); /* sort, and rebuild */
126:   PetscTableRemoveAll(gid1_lid1);
127:   for (i=0; i<ec; i++) {
128:     PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);
129:   }

131:   /* compact out the extra columns in B */
132:   for (i=0; i<totalslices; i++) { /* loop over slices */
133:     for (j=B->sliidx[i]; j<B->sliidx[i+1]; j++) {
134:       isnonzero = (PetscBool)((j-B->sliidx[i])/8 < B->rlen[(i<<3)+(j&0x07)]);
135:       if (isnonzero) {
136:         PetscInt gid1 = bcolidx[j] + 1;
137:         PetscTableFind(gid1_lid1,gid1,&lid);
138:         lid--;
139:         bcolidx[j] = lid;
140:       }
141:     }
142:   }
143:   sell->B->cmap->n = sell->B->cmap->N = ec;
144:   sell->B->cmap->bs = 1;

146:   PetscLayoutSetUp((sell->B->cmap));
147:   PetscTableDestroy(&gid1_lid1);
148: #else
149:   /* Make an array as long as the number of columns */
150:   PetscCalloc1(N+1,&indices);
151:   /* mark those columns that are in sell->B */
152:   for (i=0; i<totalslices; i++) { /* loop over slices */
153:     for (j=B->sliidx[i]; j<B->sliidx[i+1]; j++) {
154:       isnonzero = (PetscBool)((j-B->sliidx[i])/8 < B->rlen[(i<<3)+(j&0x07)]);
155:       if (isnonzero) {
156:         if (!indices[bcolidx[j]]) ec++;
157:         indices[bcolidx[j]] = 1;
158:       }
159:     }
160:   }

162:   /* form array of columns we need */
163:   PetscMalloc1(ec+1,&garray);
164:   ec   = 0;
165:   for (i=0; i<N; i++) {
166:     if (indices[i]) garray[ec++] = i;
167:   }

169:   /* make indices now point into garray */
170:   for (i=0; i<ec; i++) {
171:     indices[garray[i]] = i;
172:   }

174:   /* compact out the extra columns in B */
175:   for (i=0; i<totalslices; i++) { /* loop over slices */
176:     for (j=B->sliidx[i]; j<B->sliidx[i+1]; j++) {
177:       isnonzero = (PetscBool)((j-B->sliidx[i])/8 < B->rlen[(i<<3)+(j&0x07)]);
178:       if (isnonzero) bcolidx[j] = indices[bcolidx[j]];
179:     }
180:   }
181:   sell->B->cmap->n = sell->B->cmap->N = ec; /* number of columns that are not all zeros */
182:   sell->B->cmap->bs = 1;

184:   PetscLayoutSetUp((sell->B->cmap));
185:   PetscFree(indices);
186: #endif
187:   /* create local vector that is used to scatter into */
188:   VecCreateSeq(PETSC_COMM_SELF,ec,&sell->lvec);
189:   /* create two temporary Index sets for build scatter gather */
190:   ISCreateGeneral(((PetscObject)mat)->comm,ec,garray,PETSC_COPY_VALUES,&from);
191:   ISCreateStride(PETSC_COMM_SELF,ec,0,1,&to);

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

197:   /* generate the scatter context */
198:   VecScatterCreate(gvec,from,sell->lvec,to,&sell->Mvctx);
199:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sell->Mvctx);
200:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sell->lvec);
201:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
202:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);

204:   sell->garray = garray;

206:   PetscLogObjectMemory((PetscObject)mat,(ec+1)*sizeof(PetscInt));
207:   ISDestroy(&from);
208:   ISDestroy(&to);
209:   VecDestroy(&gvec);
210:   return(0);
211: }

213: /*      ugly stuff added for Glenn someday we should fix this up */
214: static PetscInt *auglyrmapd = 0,*auglyrmapo = 0; /* mapping from the local ordering to the "diagonal" and "off-diagonal" parts of the local matrix */
215: static Vec auglydd          = 0,auglyoo     = 0; /* work vectors used to scale the two parts of the local matrix */

217: PetscErrorCode MatMPISELLDiagonalScaleLocalSetUp(Mat inA,Vec scale)
218: {
219:   Mat_MPISELL    *ina=(Mat_MPISELL*)inA->data; /*access private part of matrix */
221:   PetscInt       i,n,nt,cstart,cend,no,*garray=ina->garray,*lindices;
222:   PetscInt       *r_rmapd,*r_rmapo;

225:   MatGetOwnershipRange(inA,&cstart,&cend);
226:   MatGetSize(ina->A,NULL,&n);
227:   PetscCalloc1(inA->rmap->mapping->n+1,&r_rmapd);
228:   nt   = 0;
229:   for (i=0; i<inA->rmap->mapping->n; i++) {
230:     if (inA->rmap->mapping->indices[i] >= cstart && inA->rmap->mapping->indices[i] < cend) {
231:       nt++;
232:       r_rmapd[i] = inA->rmap->mapping->indices[i] + 1;
233:     }
234:   }
235:   if (nt != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Hmm nt %D n %D",nt,n);
236:   PetscMalloc1(n+1,&auglyrmapd);
237:   for (i=0; i<inA->rmap->mapping->n; i++) {
238:     if (r_rmapd[i]) {
239:       auglyrmapd[(r_rmapd[i]-1)-cstart] = i;
240:     }
241:   }
242:   PetscFree(r_rmapd);
243:   VecCreateSeq(PETSC_COMM_SELF,n,&auglydd);
244:   PetscCalloc1(inA->cmap->N+1,&lindices);
245:   for (i=0; i<ina->B->cmap->n; i++) {
246:     lindices[garray[i]] = i+1;
247:   }
248:   no   = inA->rmap->mapping->n - nt;
249:   PetscCalloc1(inA->rmap->mapping->n+1,&r_rmapo);
250:   nt   = 0;
251:   for (i=0; i<inA->rmap->mapping->n; i++) {
252:     if (lindices[inA->rmap->mapping->indices[i]]) {
253:       nt++;
254:       r_rmapo[i] = lindices[inA->rmap->mapping->indices[i]];
255:     }
256:   }
257:   if (nt > no) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Hmm nt %D no %D",nt,n);
258:   PetscFree(lindices);
259:   PetscMalloc1(nt+1,&auglyrmapo);
260:   for (i=0; i<inA->rmap->mapping->n; i++) {
261:     if (r_rmapo[i]) {
262:       auglyrmapo[(r_rmapo[i]-1)] = i;
263:     }
264:   }
265:   PetscFree(r_rmapo);
266:   VecCreateSeq(PETSC_COMM_SELF,nt,&auglyoo);
267:   return(0);
268: }

270: PetscErrorCode MatDiagonalScaleLocal_MPISELL(Mat A,Vec scale)
271: {
272:   Mat_MPISELL       *a=(Mat_MPISELL*)A->data; /*access private part of matrix */
273:   PetscErrorCode    ierr;
274:   PetscInt          n,i;
275:   PetscScalar       *d,*o;
276:   const PetscScalar *s;

279:   if (!auglyrmapd) {
280:     MatMPISELLDiagonalScaleLocalSetUp(A,scale);
281:   }
282:   VecGetArrayRead(scale,&s);
283:   VecGetLocalSize(auglydd,&n);
284:   VecGetArray(auglydd,&d);
285:   for (i=0; i<n; i++) {
286:     d[i] = s[auglyrmapd[i]]; /* copy "diagonal" (true local) portion of scale into dd vector */
287:   }
288:   VecRestoreArray(auglydd,&d);
289:   /* column scale "diagonal" portion of local matrix */
290:   MatDiagonalScale(a->A,NULL,auglydd);
291:   VecGetLocalSize(auglyoo,&n);
292:   VecGetArray(auglyoo,&o);
293:   for (i=0; i<n; i++) {
294:     o[i] = s[auglyrmapo[i]]; /* copy "off-diagonal" portion of scale into oo vector */
295:   }
296:   VecRestoreArrayRead(scale,&s);
297:   VecRestoreArray(auglyoo,&o);
298:   /* column scale "off-diagonal" portion of local matrix */
299:   MatDiagonalScale(a->B,NULL,auglyoo);
300:   return(0);
301: }