Actual source code: mmsbaij.c
petsc-3.4.2 2013-07-02
2: /*
3: Support for the parallel SBAIJ matrix vector multiply
4: */
5: #include <../src/mat/impls/sbaij/mpi/mpisbaij.h>
7: extern PetscErrorCode MatSetValues_SeqSBAIJ(Mat,PetscInt,const PetscInt [],PetscInt,const PetscInt [],const PetscScalar [],InsertMode);
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,*ec_owner,k;
23: const PetscInt *sowners;
24: PetscScalar *ptr;
27: VecScatterDestroy(&sbaij->sMvctx);
29: /* For the first stab we make an array as long as the number of columns */
30: /* mark those columns that are in sbaij->B */
31: PetscMalloc(Nbs*sizeof(PetscInt),&indices);
32: PetscMemzero(indices,Nbs*sizeof(PetscInt));
33: for (i=0; i<mbs; i++) {
34: for (j=0; j<B->ilen[i]; j++) {
35: if (!indices[aj[B->i[i] + j]]) ec++;
36: indices[aj[B->i[i] + j]] = 1;
37: }
38: }
40: /* form arrays of columns we need */
41: PetscMalloc(ec*sizeof(PetscInt),&garray);
42: PetscMalloc2(2*ec,PetscInt,&sgarray,ec,PetscInt,&ec_owner);
44: ec = 0;
45: for (j=0; j<size; j++) {
46: for (i=owners[j]; i<owners[j+1]; i++) {
47: if (indices[i]) {
48: garray[ec] = i;
49: ec_owner[ec] = j;
50: ec++;
51: }
52: }
53: }
55: /* make indices now point into garray */
56: for (i=0; i<ec; i++) indices[garray[i]] = i;
58: /* compact out the extra columns in B */
59: for (i=0; i<mbs; i++) {
60: for (j=0; j<B->ilen[i]; j++) aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
61: }
62: B->nbs = ec;
64: sbaij->B->cmap->n = sbaij->B->cmap->N = ec*mat->rmap->bs;
66: PetscLayoutSetUp((sbaij->B->cmap));
67: PetscFree(indices);
69: /* create local vector that is used to scatter into */
70: VecCreateSeq(PETSC_COMM_SELF,ec*bs,&sbaij->lvec);
72: /* create two temporary index sets for building scatter-gather */
73: PetscMalloc(2*ec*sizeof(PetscInt),&stmp);
74: ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,PETSC_COPY_VALUES,&from);
75: for (i=0; i<ec; i++) stmp[i] = i;
76: ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_COPY_VALUES,&to);
78: /* generate the scatter context
79: -- Mvctx and lvec are not used by MatMult_MPISBAIJ(), but usefule for some applications */
80: VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);
81: VecScatterCreate(gvec,from,sbaij->lvec,to,&sbaij->Mvctx);
82: VecDestroy(&gvec);
84: sbaij->garray = garray;
86: PetscLogObjectParent(mat,sbaij->Mvctx);
87: PetscLogObjectParent(mat,sbaij->lvec);
88: PetscLogObjectParent(mat,from);
89: PetscLogObjectParent(mat,to);
91: ISDestroy(&from);
92: ISDestroy(&to);
94: /* create parallel vector that is used by SBAIJ matrix to scatter from/into */
95: lsize = (mbs + ec)*bs;
96: VecCreateMPI(PetscObjectComm((PetscObject)mat),lsize,PETSC_DETERMINE,&sbaij->slvec0);
97: VecDuplicate(sbaij->slvec0,&sbaij->slvec1);
98: VecGetSize(sbaij->slvec0,&vec_size);
100: VecGetOwnershipRanges(sbaij->slvec0,&sowners);
102: /* x index in the IS sfrom */
103: for (i=0; i<ec; i++) {
104: j = ec_owner[i];
105: sgarray[i] = garray[i] + (sowners[j]/bs - owners[j]);
106: }
107: /* b index in the IS sfrom */
108: k = sowners[rank]/bs + mbs;
109: for (i=ec,j=0; i< 2*ec; i++,j++) sgarray[i] = k + j;
110: ISCreateBlock(PETSC_COMM_SELF,bs,2*ec,sgarray,PETSC_COPY_VALUES,&from);
112: /* x index in the IS sto */
113: k = sowners[rank]/bs + mbs;
114: for (i=0; i<ec; i++) stmp[i] = (k + i);
115: /* b index in the IS sto */
116: for (i=ec; i<2*ec; i++) stmp[i] = sgarray[i-ec];
118: ISCreateBlock(PETSC_COMM_SELF,bs,2*ec,stmp,PETSC_COPY_VALUES,&to);
120: VecScatterCreate(sbaij->slvec0,from,sbaij->slvec1,to,&sbaij->sMvctx);
122: VecGetLocalSize(sbaij->slvec1,&nt);
123: VecGetArray(sbaij->slvec1,&ptr);
124: VecCreateSeqWithArray(PETSC_COMM_SELF,1,bs*mbs,ptr,&sbaij->slvec1a);
125: VecCreateSeqWithArray(PETSC_COMM_SELF,1,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec1b);
126: VecRestoreArray(sbaij->slvec1,&ptr);
128: VecGetArray(sbaij->slvec0,&ptr);
129: VecCreateSeqWithArray(PETSC_COMM_SELF,1,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec0b);
130: VecRestoreArray(sbaij->slvec0,&ptr);
132: PetscFree(stmp);
133: MPI_Barrier(PetscObjectComm((PetscObject)mat));
135: PetscLogObjectParent(mat,sbaij->sMvctx);
136: PetscLogObjectParent(mat,sbaij->slvec0);
137: PetscLogObjectParent(mat,sbaij->slvec1);
138: PetscLogObjectParent(mat,sbaij->slvec0b);
139: PetscLogObjectParent(mat,sbaij->slvec1a);
140: PetscLogObjectParent(mat,sbaij->slvec1b);
141: PetscLogObjectParent(mat,from);
142: PetscLogObjectParent(mat,to);
144: PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
145: ISDestroy(&from);
146: ISDestroy(&to);
147: PetscFree2(sgarray,ec_owner);
148: return(0);
149: }
153: PetscErrorCode MatSetUpMultiply_MPISBAIJ_2comm(Mat mat)
154: {
155: Mat_MPISBAIJ *baij = (Mat_MPISBAIJ*)mat->data;
156: Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)(baij->B->data);
158: PetscInt i,j,*aj = B->j,ec = 0,*garray;
159: PetscInt bs = mat->rmap->bs,*stmp;
160: IS from,to;
161: Vec gvec;
162: #if defined(PETSC_USE_CTABLE)
163: PetscTable gid1_lid1;
164: PetscTablePosition tpos;
165: PetscInt gid,lid;
166: #else
167: PetscInt Nbs = baij->Nbs,*indices;
168: #endif
171: #if defined(PETSC_USE_CTABLE)
172: /* use a table - Mark Adams */
173: PetscTableCreate(B->mbs,baij->Nbs+1,&gid1_lid1);
174: for (i=0; i<B->mbs; i++) {
175: for (j=0; j<B->ilen[i]; j++) {
176: PetscInt data,gid1 = aj[B->i[i]+j] + 1;
177: PetscTableFind(gid1_lid1,gid1,&data);
178: if (!data) {
179: /* one based table */
180: PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);
181: }
182: }
183: }
184: /* form array of columns we need */
185: PetscMalloc(ec*sizeof(PetscInt),&garray);
186: PetscTableGetHeadPosition(gid1_lid1,&tpos);
187: while (tpos) {
188: PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
189: gid--; lid--;
190: garray[lid] = gid;
191: }
192: PetscSortInt(ec,garray);
193: PetscTableRemoveAll(gid1_lid1);
194: for (i=0; i<ec; i++) {
195: PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);
196: }
197: /* compact out the extra columns in B */
198: for (i=0; i<B->mbs; i++) {
199: for (j=0; j<B->ilen[i]; j++) {
200: PetscInt gid1 = aj[B->i[i] + j] + 1;
201: PetscTableFind(gid1_lid1,gid1,&lid);
202: lid--;
203: aj[B->i[i]+j] = lid;
204: }
205: }
206: B->nbs = ec;
208: baij->B->cmap->n = baij->B->cmap->N = ec*mat->rmap->bs;
210: PetscLayoutSetUp((baij->B->cmap));
211: PetscTableDestroy(&gid1_lid1);
212: #else
213: /* For the first stab we make an array as long as the number of columns */
214: /* mark those columns that are in baij->B */
215: PetscMalloc(Nbs*sizeof(PetscInt),&indices);
216: PetscMemzero(indices,Nbs*sizeof(PetscInt));
217: for (i=0; i<B->mbs; i++) {
218: for (j=0; j<B->ilen[i]; j++) {
219: if (!indices[aj[B->i[i] + j]]) ec++;
220: indices[aj[B->i[i] + j]] = 1;
221: }
222: }
224: /* form array of columns we need */
225: PetscMalloc(ec*sizeof(PetscInt),&garray);
226: ec = 0;
227: for (i=0; i<Nbs; i++) {
228: if (indices[i]) {
229: garray[ec++] = i;
230: }
231: }
233: /* make indices now point into garray */
234: for (i=0; i<ec; i++) indices[garray[i]] = i;
236: /* compact out the extra columns in B */
237: for (i=0; i<B->mbs; i++) {
238: for (j=0; j<B->ilen[i]; j++) {
239: aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
240: }
241: }
242: B->nbs = ec;
244: baij->B->cmap->n = ec*mat->rmap->bs;
246: PetscFree(indices);
247: #endif
249: /* create local vector that is used to scatter into */
250: VecCreateSeq(PETSC_COMM_SELF,ec*bs,&baij->lvec);
252: /* create two temporary index sets for building scatter-gather */
253: ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,PETSC_COPY_VALUES,&from);
255: PetscMalloc(ec*sizeof(PetscInt),&stmp);
256: for (i=0; i<ec; i++) stmp[i] = i;
257: ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_OWN_POINTER,&to);
259: /* create temporary global vector to generate scatter context */
260: VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);
261: VecScatterCreate(gvec,from,baij->lvec,to,&baij->Mvctx);
262: VecDestroy(&gvec);
264: PetscLogObjectParent(mat,baij->Mvctx);
265: PetscLogObjectParent(mat,baij->lvec);
266: PetscLogObjectParent(mat,from);
267: PetscLogObjectParent(mat,to);
269: baij->garray = garray;
271: PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
272: ISDestroy(&from);
273: ISDestroy(&to);
274: return(0);
275: }
277: /*
278: Takes the local part of an already assembled MPISBAIJ matrix
279: and disassembles it. This is to allow new nonzeros into the matrix
280: that require more communication in the matrix vector multiply.
281: Thus certain data-structures must be rebuilt.
283: Kind of slow! But that's what application programmers get when
284: they are sloppy.
285: */
288: PetscErrorCode MatDisAssemble_MPISBAIJ(Mat A)
289: {
290: Mat_MPISBAIJ *baij = (Mat_MPISBAIJ*)A->data;
291: Mat B = baij->B,Bnew;
292: Mat_SeqBAIJ *Bbaij = (Mat_SeqBAIJ*)B->data;
294: PetscInt i,j,mbs=Bbaij->mbs,n = A->cmap->N,col,*garray=baij->garray;
295: PetscInt k,bs=A->rmap->bs,bs2=baij->bs2,*rvals,*nz,ec,m=A->rmap->n;
296: MatScalar *a = Bbaij->a;
297: PetscScalar *atmp;
298: #if defined(PETSC_USE_REAL_MAT_SINGLE)
299: PetscInt l;
300: #endif
303: #if defined(PETSC_USE_REAL_MAT_SINGLE)
304: PetscMalloc(A->rmap->bs*sizeof(PetscScalar),&atmp);
305: #endif
306: /* free stuff related to matrix-vec multiply */
307: VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
308: VecDestroy(&baij->lvec);
309: VecScatterDestroy(&baij->Mvctx);
311: VecDestroy(&baij->slvec0);
312: VecDestroy(&baij->slvec0b);
313: VecDestroy(&baij->slvec1);
314: VecDestroy(&baij->slvec1a);
315: VecDestroy(&baij->slvec1b);
317: if (baij->colmap) {
318: #if defined(PETSC_USE_CTABLE)
319: PetscTableDestroy(&baij->colmap);
320: #else
321: PetscFree(baij->colmap);
322: PetscLogObjectMemory(A,-Bbaij->nbs*sizeof(PetscInt));
323: #endif
324: }
326: /* make sure that B is assembled so we can access its values */
327: MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
328: MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
330: /* invent new B and copy stuff over */
331: PetscMalloc(mbs*sizeof(PetscInt),&nz);
332: for (i=0; i<mbs; i++) {
333: nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
334: }
335: MatCreate(PETSC_COMM_SELF,&Bnew);
336: MatSetSizes(Bnew,m,n,m,n);
337: MatSetType(Bnew,((PetscObject)B)->type_name);
338: MatSeqBAIJSetPreallocation(Bnew,B->rmap->bs,0,nz);
340: ((Mat_SeqSBAIJ*)Bnew->data)->nonew = Bbaij->nonew; /* Inherit insertion error options. */
342: PetscFree(nz);
344: PetscMalloc(bs*sizeof(PetscInt),&rvals);
345: for (i=0; i<mbs; i++) {
346: rvals[0] = bs*i;
347: for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1;
348: for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
349: col = garray[Bbaij->j[j]]*bs;
350: for (k=0; k<bs; k++) {
351: #if defined(PETSC_USE_REAL_MAT_SINGLE)
352: for (l=0; l<bs; l++) atmp[l] = a[j*bs2+l];
353: #else
354: atmp = a+j*bs2 + k*bs;
355: #endif
356: MatSetValues_SeqSBAIJ(Bnew,bs,rvals,1,&col,atmp,B->insertmode);
357: col++;
358: }
359: }
360: }
361: #if defined(PETSC_USE_REAL_MAT_SINGLE)
362: PetscFree(atmp);
363: #endif
364: PetscFree(baij->garray);
366: baij->garray = 0;
368: PetscFree(rvals);
369: PetscLogObjectMemory(A,-ec*sizeof(PetscInt));
370: MatDestroy(&B);
371: PetscLogObjectParent(A,Bnew);
373: baij->B = Bnew;
375: A->was_assembled = PETSC_FALSE;
376: return(0);
377: }