Actual source code: mmbaij.c
petsc-3.6.1 2015-08-06
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: PetscMalloc1(ec+1,&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: PetscCalloc1(Nbs+1,&indices);
74: for (i=0; i<B->mbs; i++) {
75: for (j=0; j<B->ilen[i]; j++) {
76: if (!indices[aj[B->i[i] + j]]) ec++;
77: indices[aj[B->i[i] + j]] = 1;
78: }
79: }
81: /* form array of columns we need */
82: PetscMalloc1(ec+1,&garray);
83: ec = 0;
84: for (i=0; i<Nbs; i++) {
85: if (indices[i]) {
86: garray[ec++] = i;
87: }
88: }
90: /* make indices now point into garray */
91: for (i=0; i<ec; i++) {
92: indices[garray[i]] = i;
93: }
95: /* compact out the extra columns in B */
96: for (i=0; i<B->mbs; i++) {
97: for (j=0; j<B->ilen[i]; j++) {
98: aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
99: }
100: }
101: B->nbs = ec;
102: baij->B->cmap->n = baij->B->cmap->N = ec*mat->rmap->bs;
104: PetscLayoutSetUp((baij->B->cmap));
105: PetscFree(indices);
106: #endif
108: /* create local vector that is used to scatter into */
109: VecCreateSeq(PETSC_COMM_SELF,ec*bs,&baij->lvec);
111: /* create two temporary index sets for building scatter-gather */
112: ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,PETSC_COPY_VALUES,&from);
114: PetscMalloc1(ec+1,&stmp);
115: for (i=0; i<ec; i++) stmp[i] = i;
116: ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_OWN_POINTER,&to);
118: /* create temporary global vector to generate scatter context */
119: VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);
121: VecScatterCreate(gvec,from,baij->lvec,to,&baij->Mvctx);
123: PetscLogObjectParent((PetscObject)mat,(PetscObject)baij->Mvctx);
124: PetscLogObjectParent((PetscObject)mat,(PetscObject)baij->lvec);
125: PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
126: PetscLogObjectParent((PetscObject)mat,(PetscObject)to);
128: baij->garray = garray;
130: PetscLogObjectMemory((PetscObject)mat,(ec+1)*sizeof(PetscInt));
131: ISDestroy(&from);
132: ISDestroy(&to);
133: VecDestroy(&gvec);
134: return(0);
135: }
137: /*
138: Takes the local part of an already assembled MPIBAIJ matrix
139: and disassembles it. This is to allow new nonzeros into the matrix
140: that require more communication in the matrix vector multiply.
141: Thus certain data-structures must be rebuilt.
143: Kind of slow! But that's what application programmers get when
144: they are sloppy.
145: */
148: PetscErrorCode MatDisAssemble_MPIBAIJ(Mat A)
149: {
150: Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)A->data;
151: Mat B = baij->B,Bnew;
152: Mat_SeqBAIJ *Bbaij = (Mat_SeqBAIJ*)B->data;
154: PetscInt i,j,mbs=Bbaij->mbs,n = A->cmap->N,col,*garray=baij->garray;
155: PetscInt bs2 = baij->bs2,*nz,ec,m = A->rmap->n;
156: MatScalar *a = Bbaij->a;
157: MatScalar *atmp;
161: /* free stuff related to matrix-vec multiply */
162: VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
163: VecDestroy(&baij->lvec); baij->lvec = 0;
164: VecScatterDestroy(&baij->Mvctx); baij->Mvctx = 0;
165: if (baij->colmap) {
166: #if defined(PETSC_USE_CTABLE)
167: PetscTableDestroy(&baij->colmap);
168: #else
169: PetscFree(baij->colmap);
170: PetscLogObjectMemory((PetscObject)A,-Bbaij->nbs*sizeof(PetscInt));
171: #endif
172: }
174: /* make sure that B is assembled so we can access its values */
175: MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
176: MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
178: /* invent new B and copy stuff over */
179: PetscMalloc1(mbs,&nz);
180: for (i=0; i<mbs; i++) {
181: nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
182: }
183: MatCreate(PetscObjectComm((PetscObject)B),&Bnew);
184: MatSetSizes(Bnew,m,n,m,n);
185: MatSetType(Bnew,((PetscObject)B)->type_name);
186: MatSeqBAIJSetPreallocation(Bnew,B->rmap->bs,0,nz);
188: ((Mat_SeqBAIJ*)Bnew->data)->nonew = Bbaij->nonew; /* Inherit insertion error options. */
190: MatSetOption(Bnew,MAT_ROW_ORIENTED,PETSC_FALSE);
191: /*
192: Ensure that B's nonzerostate is monotonically increasing.
193: Or should this follow the MatSetValuesBlocked() loop to preserve B's nonzerstate across a MatDisAssemble() call?
194: */
195: Bnew->nonzerostate = B->nonzerostate;
197: for (i=0; i<mbs; i++) {
198: for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
199: col = garray[Bbaij->j[j]];
200: atmp = a + j*bs2;
201: MatSetValuesBlocked_SeqBAIJ(Bnew,1,&i,1,&col,atmp,B->insertmode);
202: }
203: }
204: MatSetOption(Bnew,MAT_ROW_ORIENTED,PETSC_TRUE);
206: PetscFree(nz);
207: PetscFree(baij->garray);
208: PetscLogObjectMemory((PetscObject)A,-ec*sizeof(PetscInt));
209: MatDestroy(&B);
210: PetscLogObjectParent((PetscObject)A,(PetscObject)Bnew);
212: baij->B = Bnew;
213: A->was_assembled = PETSC_FALSE;
214: A->assembled = PETSC_FALSE;
215: return(0);
216: }
218: /* ugly stuff added for Glenn someday we should fix this up */
220: static PetscInt *uglyrmapd = 0,*uglyrmapo = 0; /* mapping from the local ordering to the "diagonal" and "off-diagonal" parts of the local matrix */
221: static Vec uglydd = 0,uglyoo = 0; /* work vectors used to scale the two parts of the local matrix */
226: PetscErrorCode MatMPIBAIJDiagonalScaleLocalSetUp(Mat inA,Vec scale)
227: {
228: Mat_MPIBAIJ *ina = (Mat_MPIBAIJ*) inA->data; /*access private part of matrix */
229: Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)ina->B->data;
231: PetscInt bs = inA->rmap->bs,i,n,nt,j,cstart,cend,no,*garray = ina->garray,*lindices;
232: PetscInt *r_rmapd,*r_rmapo;
235: MatGetOwnershipRange(inA,&cstart,&cend);
236: MatGetSize(ina->A,NULL,&n);
237: PetscCalloc1(inA->rmap->mapping->n+1,&r_rmapd);
238: nt = 0;
239: for (i=0; i<inA->rmap->mapping->n; i++) {
240: if (inA->rmap->mapping->indices[i]*bs >= cstart && inA->rmap->mapping->indices[i]*bs < cend) {
241: nt++;
242: r_rmapd[i] = inA->rmap->mapping->indices[i] + 1;
243: }
244: }
245: if (nt*bs != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Hmm nt*bs %D n %D",nt*bs,n);
246: PetscMalloc1(n+1,&uglyrmapd);
247: for (i=0; i<inA->rmap->mapping->n; i++) {
248: if (r_rmapd[i]) {
249: for (j=0; j<bs; j++) {
250: uglyrmapd[(r_rmapd[i]-1)*bs+j-cstart] = i*bs + j;
251: }
252: }
253: }
254: PetscFree(r_rmapd);
255: VecCreateSeq(PETSC_COMM_SELF,n,&uglydd);
257: PetscCalloc1(ina->Nbs+1,&lindices);
258: for (i=0; i<B->nbs; i++) {
259: lindices[garray[i]] = i+1;
260: }
261: no = inA->rmap->mapping->n - nt;
262: PetscCalloc1(inA->rmap->mapping->n+1,&r_rmapo);
263: nt = 0;
264: for (i=0; i<inA->rmap->mapping->n; i++) {
265: if (lindices[inA->rmap->mapping->indices[i]]) {
266: nt++;
267: r_rmapo[i] = lindices[inA->rmap->mapping->indices[i]];
268: }
269: }
270: if (nt > no) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Hmm nt %D no %D",nt,n);
271: PetscFree(lindices);
272: PetscMalloc1(nt*bs+1,&uglyrmapo);
273: for (i=0; i<inA->rmap->mapping->n; i++) {
274: if (r_rmapo[i]) {
275: for (j=0; j<bs; j++) {
276: uglyrmapo[(r_rmapo[i]-1)*bs+j] = i*bs + j;
277: }
278: }
279: }
280: PetscFree(r_rmapo);
281: VecCreateSeq(PETSC_COMM_SELF,nt*bs,&uglyoo);
282: return(0);
283: }
287: PetscErrorCode MatMPIBAIJDiagonalScaleLocal(Mat A,Vec scale)
288: {
289: /* This routine should really be abandoned as it duplicates MatDiagonalScaleLocal */
293: PetscTryMethod(A,"MatDiagonalScaleLocal_C",(Mat,Vec),(A,scale));
294: return(0);
295: }
299: PetscErrorCode MatDiagonalScaleLocal_MPIBAIJ(Mat A,Vec scale)
300: {
301: Mat_MPIBAIJ *a = (Mat_MPIBAIJ*) A->data; /*access private part of matrix */
303: PetscInt n,i;
304: PetscScalar *d,*o,*s;
307: if (!uglyrmapd) {
308: MatMPIBAIJDiagonalScaleLocalSetUp(A,scale);
309: }
311: VecGetArray(scale,&s);
313: VecGetLocalSize(uglydd,&n);
314: VecGetArray(uglydd,&d);
315: for (i=0; i<n; i++) {
316: d[i] = s[uglyrmapd[i]]; /* copy "diagonal" (true local) portion of scale into dd vector */
317: }
318: VecRestoreArray(uglydd,&d);
319: /* column scale "diagonal" portion of local matrix */
320: MatDiagonalScale(a->A,NULL,uglydd);
322: VecGetLocalSize(uglyoo,&n);
323: VecGetArray(uglyoo,&o);
324: for (i=0; i<n; i++) {
325: o[i] = s[uglyrmapo[i]]; /* copy "off-diagonal" portion of scale into oo vector */
326: }
327: VecRestoreArray(scale,&s);
328: VecRestoreArray(uglyoo,&o);
329: /* column scale "off-diagonal" portion of local matrix */
330: MatDiagonalScale(a->B,NULL,uglyoo);
331: return(0);
332: }