Actual source code: mmbaij.c
petsc-3.4.2 2013-07-02
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> /* needed because accesses data structure of ISLocalToGlobalMapping directly */
8: extern PetscErrorCode MatSetValuesBlocked_SeqBAIJ(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode);
12: PetscErrorCode MatSetUpMultiply_MPIBAIJ(Mat mat)
13: {
14: Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data;
15: Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)(baij->B->data);
17: PetscInt i,j,*aj = B->j,ec = 0,*garray;
18: PetscInt bs = mat->rmap->bs,*stmp;
19: IS from,to;
20: Vec gvec;
21: #if defined(PETSC_USE_CTABLE)
22: PetscTable gid1_lid1;
23: PetscTablePosition tpos;
24: PetscInt gid,lid;
25: #else
26: PetscInt Nbs = baij->Nbs,*indices;
27: #endif
30: #if defined(PETSC_USE_CTABLE)
31: /* use a table - Mark Adams */
32: PetscTableCreate(B->mbs,baij->Nbs+1,&gid1_lid1);
33: for (i=0; i<B->mbs; i++) {
34: for (j=0; j<B->ilen[i]; j++) {
35: PetscInt data,gid1 = aj[B->i[i]+j] + 1;
36: PetscTableFind(gid1_lid1,gid1,&data);
37: if (!data) {
38: /* one based table */
39: PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);
40: }
41: }
42: }
43: /* form array of columns we need */
44: PetscMalloc((ec+1)*sizeof(PetscInt),&garray);
45: PetscTableGetHeadPosition(gid1_lid1,&tpos);
46: while (tpos) {
47: PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
48: gid--; lid--;
49: garray[lid] = gid;
50: }
51: PetscSortInt(ec,garray);
52: PetscTableRemoveAll(gid1_lid1);
53: for (i=0; i<ec; i++) {
54: PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);
55: }
56: /* compact out the extra columns in B */
57: for (i=0; i<B->mbs; i++) {
58: for (j=0; j<B->ilen[i]; j++) {
59: PetscInt gid1 = aj[B->i[i] + j] + 1;
60: PetscTableFind(gid1_lid1,gid1,&lid);
61: lid--;
62: aj[B->i[i]+j] = lid;
63: }
64: }
65: B->nbs = ec;
66: baij->B->cmap->n = baij->B->cmap->N = ec*mat->rmap->bs;
68: PetscLayoutSetUp((baij->B->cmap));
69: PetscTableDestroy(&gid1_lid1);
70: #else
71: /* Make an array as long as the number of columns */
72: /* mark those columns that are in baij->B */
73: PetscMalloc((Nbs+1)*sizeof(PetscInt),&indices);
74: PetscMemzero(indices,Nbs*sizeof(PetscInt));
75: for (i=0; i<B->mbs; i++) {
76: for (j=0; j<B->ilen[i]; j++) {
77: if (!indices[aj[B->i[i] + j]]) ec++;
78: indices[aj[B->i[i] + j]] = 1;
79: }
80: }
82: /* form array of columns we need */
83: PetscMalloc((ec+1)*sizeof(PetscInt),&garray);
84: ec = 0;
85: for (i=0; i<Nbs; i++) {
86: if (indices[i]) {
87: garray[ec++] = i;
88: }
89: }
91: /* make indices now point into garray */
92: for (i=0; i<ec; i++) {
93: indices[garray[i]] = i;
94: }
96: /* compact out the extra columns in B */
97: for (i=0; i<B->mbs; i++) {
98: for (j=0; j<B->ilen[i]; j++) {
99: aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
100: }
101: }
102: B->nbs = ec;
103: baij->B->cmap->n = baij->B->cmap->N = ec*mat->rmap->bs;
105: PetscLayoutSetUp((baij->B->cmap));
106: PetscFree(indices);
107: #endif
109: /* create local vector that is used to scatter into */
110: VecCreateSeq(PETSC_COMM_SELF,ec*bs,&baij->lvec);
112: /* create two temporary index sets for building scatter-gather */
113: ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,PETSC_COPY_VALUES,&from);
115: PetscMalloc((ec+1)*sizeof(PetscInt),&stmp);
116: for (i=0; i<ec; i++) stmp[i] = i;
117: ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_OWN_POINTER,&to);
119: /* create temporary global vector to generate scatter context */
120: VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);
122: VecScatterCreate(gvec,from,baij->lvec,to,&baij->Mvctx);
124: PetscLogObjectParent(mat,baij->Mvctx);
125: PetscLogObjectParent(mat,baij->lvec);
126: PetscLogObjectParent(mat,from);
127: PetscLogObjectParent(mat,to);
129: baij->garray = garray;
131: PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
132: ISDestroy(&from);
133: ISDestroy(&to);
134: VecDestroy(&gvec);
135: return(0);
136: }
138: /*
139: Takes the local part of an already assembled MPIBAIJ matrix
140: and disassembles it. This is to allow new nonzeros into the matrix
141: that require more communication in the matrix vector multiply.
142: Thus certain data-structures must be rebuilt.
144: Kind of slow! But that's what application programmers get when
145: they are sloppy.
146: */
149: PetscErrorCode MatDisAssemble_MPIBAIJ(Mat A)
150: {
151: Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)A->data;
152: Mat B = baij->B,Bnew;
153: Mat_SeqBAIJ *Bbaij = (Mat_SeqBAIJ*)B->data;
155: PetscInt i,j,mbs=Bbaij->mbs,n = A->cmap->N,col,*garray=baij->garray;
156: PetscInt bs2 = baij->bs2,*nz,ec,m = A->rmap->n;
157: MatScalar *a = Bbaij->a;
158: MatScalar *atmp;
162: /* free stuff related to matrix-vec multiply */
163: VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
164: VecDestroy(&baij->lvec); baij->lvec = 0;
165: VecScatterDestroy(&baij->Mvctx); baij->Mvctx = 0;
166: if (baij->colmap) {
167: #if defined(PETSC_USE_CTABLE)
168: PetscTableDestroy(&baij->colmap);
169: #else
170: PetscFree(baij->colmap);
171: PetscLogObjectMemory(A,-Bbaij->nbs*sizeof(PetscInt));
172: #endif
173: }
175: /* make sure that B is assembled so we can access its values */
176: MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
177: MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
179: /* invent new B and copy stuff over */
180: PetscMalloc(mbs*sizeof(PetscInt),&nz);
181: for (i=0; i<mbs; i++) {
182: nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
183: }
184: MatCreate(PetscObjectComm((PetscObject)B),&Bnew);
185: MatSetSizes(Bnew,m,n,m,n);
186: MatSetType(Bnew,((PetscObject)B)->type_name);
187: MatSeqBAIJSetPreallocation(Bnew,B->rmap->bs,0,nz);
189: ((Mat_SeqBAIJ*)Bnew->data)->nonew = Bbaij->nonew; /* Inherit insertion error options. */
191: MatSetOption(Bnew,MAT_ROW_ORIENTED,PETSC_FALSE);
193: for (i=0; i<mbs; i++) {
194: for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
195: col = garray[Bbaij->j[j]];
196: atmp = a + j*bs2;
197: MatSetValuesBlocked_SeqBAIJ(Bnew,1,&i,1,&col,atmp,B->insertmode);
198: }
199: }
200: MatSetOption(Bnew,MAT_ROW_ORIENTED,PETSC_TRUE);
202: PetscFree(nz);
203: PetscFree(baij->garray);
204: PetscLogObjectMemory(A,-ec*sizeof(PetscInt));
205: MatDestroy(&B);
206: PetscLogObjectParent(A,Bnew);
208: baij->B = Bnew;
209: A->was_assembled = PETSC_FALSE;
210: A->assembled = PETSC_FALSE;
211: return(0);
212: }
214: /* ugly stuff added for Glenn someday we should fix this up */
216: static PetscInt *uglyrmapd = 0,*uglyrmapo = 0; /* mapping from the local ordering to the "diagonal" and "off-diagonal" parts of the local matrix */
217: static Vec uglydd = 0,uglyoo = 0; /* work vectors used to scale the two parts of the local matrix */
222: PetscErrorCode MatMPIBAIJDiagonalScaleLocalSetUp(Mat inA,Vec scale)
223: {
224: Mat_MPIBAIJ *ina = (Mat_MPIBAIJ*) inA->data; /*access private part of matrix */
225: Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)ina->B->data;
227: PetscInt bs = inA->rmap->bs,i,n,nt,j,cstart,cend,no,*garray = ina->garray,*lindices;
228: PetscInt *r_rmapd,*r_rmapo;
231: MatGetOwnershipRange(inA,&cstart,&cend);
232: MatGetSize(ina->A,NULL,&n);
233: PetscMalloc((inA->rmap->bmapping->n+1)*sizeof(PetscInt),&r_rmapd);
234: PetscMemzero(r_rmapd,inA->rmap->bmapping->n*sizeof(PetscInt));
235: nt = 0;
236: for (i=0; i<inA->rmap->bmapping->n; i++) {
237: if (inA->rmap->bmapping->indices[i]*bs >= cstart && inA->rmap->bmapping->indices[i]*bs < cend) {
238: nt++;
239: r_rmapd[i] = inA->rmap->bmapping->indices[i] + 1;
240: }
241: }
242: if (nt*bs != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Hmm nt*bs %D n %D",nt*bs,n);
243: PetscMalloc((n+1)*sizeof(PetscInt),&uglyrmapd);
244: for (i=0; i<inA->rmap->bmapping->n; i++) {
245: if (r_rmapd[i]) {
246: for (j=0; j<bs; j++) {
247: uglyrmapd[(r_rmapd[i]-1)*bs+j-cstart] = i*bs + j;
248: }
249: }
250: }
251: PetscFree(r_rmapd);
252: VecCreateSeq(PETSC_COMM_SELF,n,&uglydd);
254: PetscMalloc((ina->Nbs+1)*sizeof(PetscInt),&lindices);
255: PetscMemzero(lindices,ina->Nbs*sizeof(PetscInt));
256: for (i=0; i<B->nbs; i++) {
257: lindices[garray[i]] = i+1;
258: }
259: no = inA->rmap->bmapping->n - nt;
260: PetscMalloc((inA->rmap->bmapping->n+1)*sizeof(PetscInt),&r_rmapo);
261: PetscMemzero(r_rmapo,inA->rmap->bmapping->n*sizeof(PetscInt));
262: nt = 0;
263: for (i=0; i<inA->rmap->bmapping->n; i++) {
264: if (lindices[inA->rmap->bmapping->indices[i]]) {
265: nt++;
266: r_rmapo[i] = lindices[inA->rmap->bmapping->indices[i]];
267: }
268: }
269: if (nt > no) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Hmm nt %D no %D",nt,n);
270: PetscFree(lindices);
271: PetscMalloc((nt*bs+1)*sizeof(PetscInt),&uglyrmapo);
272: for (i=0; i<inA->rmap->bmapping->n; i++) {
273: if (r_rmapo[i]) {
274: for (j=0; j<bs; j++) {
275: uglyrmapo[(r_rmapo[i]-1)*bs+j] = i*bs + j;
276: }
277: }
278: }
279: PetscFree(r_rmapo);
280: VecCreateSeq(PETSC_COMM_SELF,nt*bs,&uglyoo);
281: return(0);
282: }
286: PetscErrorCode MatMPIBAIJDiagonalScaleLocal(Mat A,Vec scale)
287: {
288: /* This routine should really be abandoned as it duplicates MatDiagonalScaleLocal */
292: PetscTryMethod(A,"MatDiagonalScaleLocal_C",(Mat,Vec),(A,scale));
293: return(0);
294: }
298: PetscErrorCode MatDiagonalScaleLocal_MPIBAIJ(Mat A,Vec scale)
299: {
300: Mat_MPIBAIJ *a = (Mat_MPIBAIJ*) A->data; /*access private part of matrix */
302: PetscInt n,i;
303: PetscScalar *d,*o,*s;
306: if (!uglyrmapd) {
307: MatMPIBAIJDiagonalScaleLocalSetUp(A,scale);
308: }
310: VecGetArray(scale,&s);
312: VecGetLocalSize(uglydd,&n);
313: VecGetArray(uglydd,&d);
314: for (i=0; i<n; i++) {
315: d[i] = s[uglyrmapd[i]]; /* copy "diagonal" (true local) portion of scale into dd vector */
316: }
317: VecRestoreArray(uglydd,&d);
318: /* column scale "diagonal" portion of local matrix */
319: MatDiagonalScale(a->A,NULL,uglydd);
321: VecGetLocalSize(uglyoo,&n);
322: VecGetArray(uglyoo,&o);
323: for (i=0; i<n; i++) {
324: o[i] = s[uglyrmapo[i]]; /* copy "off-diagonal" portion of scale into oo vector */
325: }
326: VecRestoreArray(scale,&s);
327: VecRestoreArray(uglyoo,&o);
328: /* column scale "off-diagonal" portion of local matrix */
329: MatDiagonalScale(a->B,NULL,uglyoo);
330: return(0);
331: }