/*$Id: mpibaij.c,v 1.234 2001/09/25 22:56:49 balay Exp $*/ #include "src/mat/impls/baij/mpi/mpibaij.h" /*I "petscmat.h" I*/ #include "src/vec/vecimpl.h" EXTERN int MatSetUpMultiply_MPIBAIJ(Mat); EXTERN int DisAssemble_MPIBAIJ(Mat); EXTERN int MatIncreaseOverlap_MPIBAIJ(Mat,int,IS *,int); EXTERN int MatGetSubMatrices_MPIBAIJ(Mat,int,IS *,IS *,MatReuse,Mat **); EXTERN int MatGetValues_SeqBAIJ(Mat,int,int *,int,int *,PetscScalar *); EXTERN int MatSetValues_SeqBAIJ(Mat,int,int *,int,int *,PetscScalar *,InsertMode); EXTERN int MatSetValuesBlocked_SeqBAIJ(Mat,int,int*,int,int*,PetscScalar*,InsertMode); EXTERN int MatGetRow_SeqBAIJ(Mat,int,int*,int**,PetscScalar**); EXTERN int MatRestoreRow_SeqBAIJ(Mat,int,int*,int**,PetscScalar**); EXTERN int MatPrintHelp_SeqBAIJ(Mat); EXTERN int MatZeroRows_SeqBAIJ(Mat,IS,PetscScalar*); /* UGLY, ugly, ugly When MatScalar == PetscScalar the function MatSetValuesBlocked_MPIBAIJ_MatScalar() does not exist. Otherwise ..._MatScalar() takes matrix elements in single precision and inserts them into the single precision data structure. The function MatSetValuesBlocked_MPIBAIJ() converts the entries into single precision and then calls ..._MatScalar() to put them into the single precision data structures. */ #if defined(PETSC_USE_MAT_SINGLE) EXTERN int MatSetValuesBlocked_SeqBAIJ_MatScalar(Mat,int,int*,int,int*,MatScalar*,InsertMode); EXTERN int MatSetValues_MPIBAIJ_MatScalar(Mat,int,int*,int,int*,MatScalar*,InsertMode); EXTERN int MatSetValuesBlocked_MPIBAIJ_MatScalar(Mat,int,int*,int,int*,MatScalar*,InsertMode); EXTERN int MatSetValues_MPIBAIJ_HT_MatScalar(Mat,int,int*,int,int*,MatScalar*,InsertMode); EXTERN int MatSetValuesBlocked_MPIBAIJ_HT_MatScalar(Mat,int,int*,int,int*,MatScalar*,InsertMode); #else #define MatSetValuesBlocked_SeqBAIJ_MatScalar MatSetValuesBlocked_SeqBAIJ #define MatSetValues_MPIBAIJ_MatScalar MatSetValues_MPIBAIJ #define MatSetValuesBlocked_MPIBAIJ_MatScalar MatSetValuesBlocked_MPIBAIJ #define MatSetValues_MPIBAIJ_HT_MatScalar MatSetValues_MPIBAIJ_HT #define MatSetValuesBlocked_MPIBAIJ_HT_MatScalar MatSetValuesBlocked_MPIBAIJ_HT #endif #undef __FUNCT__ #define __FUNCT__ "MatGetRowMax_MPIBAIJ" int MatGetRowMax_MPIBAIJ(Mat A,Vec v) { Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; int ierr,i; PetscScalar *va,*vb; Vec vtmp; PetscFunctionBegin; ierr = MatGetRowMax(a->A,v);CHKERRQ(ierr); ierr = VecGetArray(v,&va);CHKERRQ(ierr); ierr = VecCreateSeq(PETSC_COMM_SELF,A->m,&vtmp);CHKERRQ(ierr); ierr = MatGetRowMax(a->B,vtmp);CHKERRQ(ierr); ierr = VecGetArray(vtmp,&vb);CHKERRQ(ierr); for (i=0; im; i++){ if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) va[i] = vb[i]; } ierr = VecRestoreArray(v,&va);CHKERRQ(ierr); ierr = VecRestoreArray(vtmp,&vb);CHKERRQ(ierr); ierr = VecDestroy(vtmp);CHKERRQ(ierr); PetscFunctionReturn(0); } EXTERN_C_BEGIN #undef __FUNCT__ #define __FUNCT__ "MatStoreValues_MPIBAIJ" int MatStoreValues_MPIBAIJ(Mat mat) { Mat_MPIBAIJ *aij = (Mat_MPIBAIJ *)mat->data; int ierr; PetscFunctionBegin; ierr = MatStoreValues(aij->A);CHKERRQ(ierr); ierr = MatStoreValues(aij->B);CHKERRQ(ierr); PetscFunctionReturn(0); } EXTERN_C_END EXTERN_C_BEGIN #undef __FUNCT__ #define __FUNCT__ "MatRetrieveValues_MPIBAIJ" int MatRetrieveValues_MPIBAIJ(Mat mat) { Mat_MPIBAIJ *aij = (Mat_MPIBAIJ *)mat->data; int ierr; PetscFunctionBegin; ierr = MatRetrieveValues(aij->A);CHKERRQ(ierr); ierr = MatRetrieveValues(aij->B);CHKERRQ(ierr); PetscFunctionReturn(0); } EXTERN_C_END /* Local utility routine that creates a mapping from the global column number to the local number in the off-diagonal part of the local storage of the matrix. This is done in a non scable way since the length of colmap equals the global matrix length. */ #undef __FUNCT__ #define __FUNCT__ "CreateColmap_MPIBAIJ_Private" static int CreateColmap_MPIBAIJ_Private(Mat mat) { Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; Mat_SeqBAIJ *B = (Mat_SeqBAIJ*)baij->B->data; int nbs = B->nbs,i,bs=B->bs,ierr; PetscFunctionBegin; #if defined (PETSC_USE_CTABLE) ierr = PetscTableCreate(baij->nbs,&baij->colmap);CHKERRQ(ierr); for (i=0; icolmap,baij->garray[i]+1,i*bs+1);CHKERRQ(ierr); } #else ierr = PetscMalloc((baij->Nbs+1)*sizeof(int),&baij->colmap);CHKERRQ(ierr); PetscLogObjectMemory(mat,baij->Nbs*sizeof(int)); ierr = PetscMemzero(baij->colmap,baij->Nbs*sizeof(int));CHKERRQ(ierr); for (i=0; icolmap[baij->garray[i]] = i*bs+1; #endif PetscFunctionReturn(0); } #define CHUNKSIZE 10 #define MatSetValues_SeqBAIJ_A_Private(row,col,value,addv) \ { \ \ brow = row/bs; \ rp = aj + ai[brow]; ap = aa + bs2*ai[brow]; \ rmax = aimax[brow]; nrow = ailen[brow]; \ bcol = col/bs; \ ridx = row % bs; cidx = col % bs; \ low = 0; high = nrow; \ while (high-low > 3) { \ t = (low+high)/2; \ if (rp[t] > bcol) high = t; \ else low = t; \ } \ for (_i=low; _i bcol) break; \ if (rp[_i] == bcol) { \ bap = ap + bs2*_i + bs*cidx + ridx; \ if (addv == ADD_VALUES) *bap += value; \ else *bap = value; \ goto a_noinsert; \ } \ } \ if (a->nonew == 1) goto a_noinsert; \ else if (a->nonew == -1) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero into matrix"); \ if (nrow >= rmax) { \ /* there is no extra room in row, therefore enlarge */ \ int new_nz = ai[a->mbs] + CHUNKSIZE,len,*new_i,*new_j; \ MatScalar *new_a; \ \ if (a->nonew == -2) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero in the matrix"); \ \ /* malloc new storage space */ \ len = new_nz*(sizeof(int)+bs2*sizeof(MatScalar))+(a->mbs+1)*sizeof(int); \ ierr = PetscMalloc(len,&new_a);CHKERRQ(ierr); \ new_j = (int*)(new_a + bs2*new_nz); \ new_i = new_j + new_nz; \ \ /* copy over old data into new slots */ \ for (ii=0; iimbs+1; ii++) {new_i[ii] = ai[ii]+CHUNKSIZE;} \ ierr = PetscMemcpy(new_j,aj,(ai[brow]+nrow)*sizeof(int));CHKERRQ(ierr); \ len = (new_nz - CHUNKSIZE - ai[brow] - nrow); \ ierr = PetscMemcpy(new_j+ai[brow]+nrow+CHUNKSIZE,aj+ai[brow]+nrow,len*sizeof(int));CHKERRQ(ierr); \ ierr = PetscMemcpy(new_a,aa,(ai[brow]+nrow)*bs2*sizeof(MatScalar));CHKERRQ(ierr); \ ierr = PetscMemzero(new_a+bs2*(ai[brow]+nrow),bs2*CHUNKSIZE*sizeof(PetscScalar));CHKERRQ(ierr); \ ierr = PetscMemcpy(new_a+bs2*(ai[brow]+nrow+CHUNKSIZE), \ aa+bs2*(ai[brow]+nrow),bs2*len*sizeof(MatScalar));CHKERRQ(ierr); \ /* free up old matrix storage */ \ ierr = PetscFree(a->a);CHKERRQ(ierr); \ if (!a->singlemalloc) { \ ierr = PetscFree(a->i);CHKERRQ(ierr); \ ierr = PetscFree(a->j);CHKERRQ(ierr);\ } \ aa = a->a = new_a; ai = a->i = new_i; aj = a->j = new_j; \ a->singlemalloc = PETSC_TRUE; \ \ rp = aj + ai[brow]; ap = aa + bs2*ai[brow]; \ rmax = aimax[brow] = aimax[brow] + CHUNKSIZE; \ PetscLogObjectMemory(A,CHUNKSIZE*(sizeof(int) + bs2*sizeof(MatScalar))); \ a->maxnz += bs2*CHUNKSIZE; \ a->reallocs++; \ a->nz++; \ } \ N = nrow++ - 1; \ /* shift up all the later entries in this row */ \ for (ii=N; ii>=_i; ii--) { \ rp[ii+1] = rp[ii]; \ ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); \ } \ if (N>=_i) { ierr = PetscMemzero(ap+bs2*_i,bs2*sizeof(MatScalar));CHKERRQ(ierr); } \ rp[_i] = bcol; \ ap[bs2*_i + bs*cidx + ridx] = value; \ a_noinsert:; \ ailen[brow] = nrow; \ } #define MatSetValues_SeqBAIJ_B_Private(row,col,value,addv) \ { \ brow = row/bs; \ rp = bj + bi[brow]; ap = ba + bs2*bi[brow]; \ rmax = bimax[brow]; nrow = bilen[brow]; \ bcol = col/bs; \ ridx = row % bs; cidx = col % bs; \ low = 0; high = nrow; \ while (high-low > 3) { \ t = (low+high)/2; \ if (rp[t] > bcol) high = t; \ else low = t; \ } \ for (_i=low; _i bcol) break; \ if (rp[_i] == bcol) { \ bap = ap + bs2*_i + bs*cidx + ridx; \ if (addv == ADD_VALUES) *bap += value; \ else *bap = value; \ goto b_noinsert; \ } \ } \ if (b->nonew == 1) goto b_noinsert; \ else if (b->nonew == -1) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero into matrix"); \ if (nrow >= rmax) { \ /* there is no extra room in row, therefore enlarge */ \ int new_nz = bi[b->mbs] + CHUNKSIZE,len,*new_i,*new_j; \ MatScalar *new_a; \ \ if (b->nonew == -2) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero in the matrix"); \ \ /* malloc new storage space */ \ len = new_nz*(sizeof(int)+bs2*sizeof(MatScalar))+(b->mbs+1)*sizeof(int); \ ierr = PetscMalloc(len,&new_a);CHKERRQ(ierr); \ new_j = (int*)(new_a + bs2*new_nz); \ new_i = new_j + new_nz; \ \ /* copy over old data into new slots */ \ for (ii=0; iimbs+1; ii++) {new_i[ii] = bi[ii]+CHUNKSIZE;} \ ierr = PetscMemcpy(new_j,bj,(bi[brow]+nrow)*sizeof(int));CHKERRQ(ierr); \ len = (new_nz - CHUNKSIZE - bi[brow] - nrow); \ ierr = PetscMemcpy(new_j+bi[brow]+nrow+CHUNKSIZE,bj+bi[brow]+nrow,len*sizeof(int));CHKERRQ(ierr); \ ierr = PetscMemcpy(new_a,ba,(bi[brow]+nrow)*bs2*sizeof(MatScalar));CHKERRQ(ierr); \ ierr = PetscMemzero(new_a+bs2*(bi[brow]+nrow),bs2*CHUNKSIZE*sizeof(MatScalar));CHKERRQ(ierr); \ ierr = PetscMemcpy(new_a+bs2*(bi[brow]+nrow+CHUNKSIZE), \ ba+bs2*(bi[brow]+nrow),bs2*len*sizeof(MatScalar));CHKERRQ(ierr); \ /* free up old matrix storage */ \ ierr = PetscFree(b->a);CHKERRQ(ierr); \ if (!b->singlemalloc) { \ ierr = PetscFree(b->i);CHKERRQ(ierr); \ ierr = PetscFree(b->j);CHKERRQ(ierr); \ } \ ba = b->a = new_a; bi = b->i = new_i; bj = b->j = new_j; \ b->singlemalloc = PETSC_TRUE; \ \ rp = bj + bi[brow]; ap = ba + bs2*bi[brow]; \ rmax = bimax[brow] = bimax[brow] + CHUNKSIZE; \ PetscLogObjectMemory(B,CHUNKSIZE*(sizeof(int) + bs2*sizeof(MatScalar))); \ b->maxnz += bs2*CHUNKSIZE; \ b->reallocs++; \ b->nz++; \ } \ N = nrow++ - 1; \ /* shift up all the later entries in this row */ \ for (ii=N; ii>=_i; ii--) { \ rp[ii+1] = rp[ii]; \ ierr = PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));CHKERRQ(ierr); \ } \ if (N>=_i) { ierr = PetscMemzero(ap+bs2*_i,bs2*sizeof(MatScalar));CHKERRQ(ierr);} \ rp[_i] = bcol; \ ap[bs2*_i + bs*cidx + ridx] = value; \ b_noinsert:; \ bilen[brow] = nrow; \ } #if defined(PETSC_USE_MAT_SINGLE) #undef __FUNCT__ #define __FUNCT__ "MatSetValues_MPIBAIJ" int MatSetValues_MPIBAIJ(Mat mat,int m,int *im,int n,int *in,PetscScalar *v,InsertMode addv) { Mat_MPIBAIJ *b = (Mat_MPIBAIJ*)mat->data; int ierr,i,N = m*n; MatScalar *vsingle; PetscFunctionBegin; if (N > b->setvalueslen) { if (b->setvaluescopy) {ierr = PetscFree(b->setvaluescopy);CHKERRQ(ierr);} ierr = PetscMalloc(N*sizeof(MatScalar),&b->setvaluescopy);CHKERRQ(ierr); b->setvalueslen = N; } vsingle = b->setvaluescopy; for (i=0; idata; int ierr,i,N = m*n*b->bs2; MatScalar *vsingle; PetscFunctionBegin; if (N > b->setvalueslen) { if (b->setvaluescopy) {ierr = PetscFree(b->setvaluescopy);CHKERRQ(ierr);} ierr = PetscMalloc(N*sizeof(MatScalar),&b->setvaluescopy);CHKERRQ(ierr); b->setvalueslen = N; } vsingle = b->setvaluescopy; for (i=0; idata; int ierr,i,N = m*n; MatScalar *vsingle; PetscFunctionBegin; if (N > b->setvalueslen) { if (b->setvaluescopy) {ierr = PetscFree(b->setvaluescopy);CHKERRQ(ierr);} ierr = PetscMalloc(N*sizeof(MatScalar),&b->setvaluescopy);CHKERRQ(ierr); b->setvalueslen = N; } vsingle = b->setvaluescopy; for (i=0; idata; int ierr,i,N = m*n*b->bs2; MatScalar *vsingle; PetscFunctionBegin; if (N > b->setvalueslen) { if (b->setvaluescopy) {ierr = PetscFree(b->setvaluescopy);CHKERRQ(ierr);} ierr = PetscMalloc(N*sizeof(MatScalar),&b->setvaluescopy);CHKERRQ(ierr); b->setvalueslen = N; } vsingle = b->setvaluescopy; for (i=0; idata; MatScalar value; PetscTruth roworiented = baij->roworiented; int ierr,i,j,row,col; int rstart_orig=baij->rstart_bs; int rend_orig=baij->rend_bs,cstart_orig=baij->cstart_bs; int cend_orig=baij->cend_bs,bs=baij->bs; /* Some Variables required in the macro */ Mat A = baij->A; Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)(A)->data; int *aimax=a->imax,*ai=a->i,*ailen=a->ilen,*aj=a->j; MatScalar *aa=a->a; Mat B = baij->B; Mat_SeqBAIJ *b = (Mat_SeqBAIJ*)(B)->data; int *bimax=b->imax,*bi=b->i,*bilen=b->ilen,*bj=b->j; MatScalar *ba=b->a; int *rp,ii,nrow,_i,rmax,N,brow,bcol; int low,high,t,ridx,cidx,bs2=a->bs2; MatScalar *ap,*bap; PetscFunctionBegin; for (i=0; i= mat->M) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Row too large"); #endif if (im[i] >= rstart_orig && im[i] < rend_orig) { row = im[i] - rstart_orig; for (j=0; j= cstart_orig && in[j] < cend_orig){ col = in[j] - cstart_orig; if (roworiented) value = v[i*n+j]; else value = v[i+j*m]; MatSetValues_SeqBAIJ_A_Private(row,col,value,addv); /* ierr = MatSetValues_SeqBAIJ(baij->A,1,&row,1,&col,&value,addv);CHKERRQ(ierr); */ } else if (in[j] < 0) continue; #if defined(PETSC_USE_BOPT_g) else if (in[j] >= mat->N) {SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Column too large");} #endif else { if (mat->was_assembled) { if (!baij->colmap) { ierr = CreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); } #if defined (PETSC_USE_CTABLE) ierr = PetscTableFind(baij->colmap,in[j]/bs + 1,&col);CHKERRQ(ierr); col = col - 1; #else col = baij->colmap[in[j]/bs] - 1; #endif if (col < 0 && !((Mat_SeqBAIJ*)(baij->A->data))->nonew) { ierr = DisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); col = in[j]; /* Reinitialize the variables required by MatSetValues_SeqBAIJ_B_Private() */ B = baij->B; b = (Mat_SeqBAIJ*)(B)->data; bimax=b->imax;bi=b->i;bilen=b->ilen;bj=b->j; ba=b->a; } else col += in[j]%bs; } else col = in[j]; if (roworiented) value = v[i*n+j]; else value = v[i+j*m]; MatSetValues_SeqBAIJ_B_Private(row,col,value,addv); /* ierr = MatSetValues_SeqBAIJ(baij->B,1,&row,1,&col,&value,addv);CHKERRQ(ierr); */ } } } else { if (!baij->donotstash) { if (roworiented) { ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n);CHKERRQ(ierr); } else { ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m);CHKERRQ(ierr); } } } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSetValuesBlocked_MPIBAIJ_MatScalar" int MatSetValuesBlocked_MPIBAIJ_MatScalar(Mat mat,int m,int *im,int n,int *in,MatScalar *v,InsertMode addv) { Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; MatScalar *value,*barray=baij->barray; PetscTruth roworiented = baij->roworiented; int ierr,i,j,ii,jj,row,col,rstart=baij->rstart; int rend=baij->rend,cstart=baij->cstart,stepval; int cend=baij->cend,bs=baij->bs,bs2=baij->bs2; PetscFunctionBegin; if(!barray) { ierr = PetscMalloc(bs2*sizeof(MatScalar),&barray);CHKERRQ(ierr); baij->barray = barray; } if (roworiented) { stepval = (n-1)*bs; } else { stepval = (m-1)*bs; } for (i=0; i= baij->Mbs) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Row too large, row %d max %d",im[i],baij->Mbs); #endif if (im[i] >= rstart && im[i] < rend) { row = im[i] - rstart; for (j=0; j= cstart && in[j] < cend){ col = in[j] - cstart; ierr = MatSetValuesBlocked_SeqBAIJ_MatScalar(baij->A,1,&row,1,&col,barray,addv);CHKERRQ(ierr); } else if (in[j] < 0) continue; #if defined(PETSC_USE_BOPT_g) else if (in[j] >= baij->Nbs) {SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column too large, col %d max %d",in[j],baij->Nbs);} #endif else { if (mat->was_assembled) { if (!baij->colmap) { ierr = CreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); } #if defined(PETSC_USE_BOPT_g) #if defined (PETSC_USE_CTABLE) { int data; ierr = PetscTableFind(baij->colmap,in[j]+1,&data);CHKERRQ(ierr); if ((data - 1) % bs) SETERRQ(PETSC_ERR_PLIB,"Incorrect colmap"); } #else if ((baij->colmap[in[j]] - 1) % bs) SETERRQ(PETSC_ERR_PLIB,"Incorrect colmap"); #endif #endif #if defined (PETSC_USE_CTABLE) ierr = PetscTableFind(baij->colmap,in[j]+1,&col);CHKERRQ(ierr); col = (col - 1)/bs; #else col = (baij->colmap[in[j]] - 1)/bs; #endif if (col < 0 && !((Mat_SeqBAIJ*)(baij->A->data))->nonew) { ierr = DisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); col = in[j]; } } else col = in[j]; ierr = MatSetValuesBlocked_SeqBAIJ_MatScalar(baij->B,1,&row,1,&col,barray,addv);CHKERRQ(ierr); } } } else { if (!baij->donotstash) { if (roworiented) { ierr = MatStashValuesRowBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); } else { ierr = MatStashValuesColBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); } } } } PetscFunctionReturn(0); } #define HASH_KEY 0.6180339887 #define HASH(size,key,tmp) (tmp = (key)*HASH_KEY,(int)((size)*(tmp-(int)tmp))) /* #define HASH(size,key) ((int)((size)*fmod(((key)*HASH_KEY),1))) */ /* #define HASH(size,key,tmp) ((int)((size)*fmod(((key)*HASH_KEY),1))) */ #undef __FUNCT__ #define __FUNCT__ "MatSetValues_MPIBAIJ_HT_MatScalar" int MatSetValues_MPIBAIJ_HT_MatScalar(Mat mat,int m,int *im,int n,int *in,MatScalar *v,InsertMode addv) { Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; PetscTruth roworiented = baij->roworiented; int ierr,i,j,row,col; int rstart_orig=baij->rstart_bs; int rend_orig=baij->rend_bs,Nbs=baij->Nbs; int h1,key,size=baij->ht_size,bs=baij->bs,*HT=baij->ht,idx; PetscReal tmp; MatScalar **HD = baij->hd,value; #if defined(PETSC_USE_BOPT_g) int total_ct=baij->ht_total_ct,insert_ct=baij->ht_insert_ct; #endif PetscFunctionBegin; for (i=0; i= mat->M) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Row too large"); #endif row = im[i]; if (row >= rstart_orig && row < rend_orig) { for (j=0; jdonotstash) { if (roworiented) { ierr = MatStashValuesRow_Private(&mat->stash,im[i],n,in,v+i*n);CHKERRQ(ierr); } else { ierr = MatStashValuesCol_Private(&mat->stash,im[i],n,in,v+i,m);CHKERRQ(ierr); } } } } #if defined(PETSC_USE_BOPT_g) baij->ht_total_ct = total_ct; baij->ht_insert_ct = insert_ct; #endif PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSetValuesBlocked_MPIBAIJ_HT_MatScalar" int MatSetValuesBlocked_MPIBAIJ_HT_MatScalar(Mat mat,int m,int *im,int n,int *in,MatScalar *v,InsertMode addv) { Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; PetscTruth roworiented = baij->roworiented; int ierr,i,j,ii,jj,row,col; int rstart=baij->rstart ; int rend=baij->rend,stepval,bs=baij->bs,bs2=baij->bs2; int h1,key,size=baij->ht_size,idx,*HT=baij->ht,Nbs=baij->Nbs; PetscReal tmp; MatScalar **HD = baij->hd,*baij_a; MatScalar *v_t,*value; #if defined(PETSC_USE_BOPT_g) int total_ct=baij->ht_total_ct,insert_ct=baij->ht_insert_ct; #endif PetscFunctionBegin; if (roworiented) { stepval = (n-1)*bs; } else { stepval = (m-1)*bs; } for (i=0; i= baij->Mbs) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Row too large"); #endif row = im[i]; v_t = v + i*bs2; if (row >= rstart && row < rend) { for (j=0; jdonotstash) { if (roworiented) { ierr = MatStashValuesRowBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); } else { ierr = MatStashValuesColBlocked_Private(&mat->bstash,im[i],n,in,v,m,n,i);CHKERRQ(ierr); } } } } #if defined(PETSC_USE_BOPT_g) baij->ht_total_ct = total_ct; baij->ht_insert_ct = insert_ct; #endif PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatGetValues_MPIBAIJ" int MatGetValues_MPIBAIJ(Mat mat,int m,int *idxm,int n,int *idxn,PetscScalar *v) { Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; int bs=baij->bs,ierr,i,j,bsrstart = baij->rstart*bs,bsrend = baij->rend*bs; int bscstart = baij->cstart*bs,bscend = baij->cend*bs,row,col,data; PetscFunctionBegin; for (i=0; i= mat->M) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Row too large"); if (idxm[i] >= bsrstart && idxm[i] < bsrend) { row = idxm[i] - bsrstart; for (j=0; j= mat->N) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Column too large"); if (idxn[j] >= bscstart && idxn[j] < bscend){ col = idxn[j] - bscstart; ierr = MatGetValues_SeqBAIJ(baij->A,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); } else { if (!baij->colmap) { ierr = CreateColmap_MPIBAIJ_Private(mat);CHKERRQ(ierr); } #if defined (PETSC_USE_CTABLE) ierr = PetscTableFind(baij->colmap,idxn[j]/bs+1,&data);CHKERRQ(ierr); data --; #else data = baij->colmap[idxn[j]/bs]-1; #endif if((data < 0) || (baij->garray[data/bs] != idxn[j]/bs)) *(v+i*n+j) = 0.0; else { col = data + idxn[j]%bs; ierr = MatGetValues_SeqBAIJ(baij->B,1,&row,1,&col,v+i*n+j);CHKERRQ(ierr); } } } } else { SETERRQ(PETSC_ERR_SUP,"Only local values currently supported"); } } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatNorm_MPIBAIJ" int MatNorm_MPIBAIJ(Mat mat,NormType type,PetscReal *nrm) { Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; Mat_SeqBAIJ *amat = (Mat_SeqBAIJ*)baij->A->data,*bmat = (Mat_SeqBAIJ*)baij->B->data; int ierr,i,bs2=baij->bs2; PetscReal sum = 0.0; MatScalar *v; PetscFunctionBegin; if (baij->size == 1) { ierr = MatNorm(baij->A,type,nrm);CHKERRQ(ierr); } else { if (type == NORM_FROBENIUS) { v = amat->a; for (i=0; inz*bs2; i++) { #if defined(PETSC_USE_COMPLEX) sum += PetscRealPart(PetscConj(*v)*(*v)); v++; #else sum += (*v)*(*v); v++; #endif } v = bmat->a; for (i=0; inz*bs2; i++) { #if defined(PETSC_USE_COMPLEX) sum += PetscRealPart(PetscConj(*v)*(*v)); v++; #else sum += (*v)*(*v); v++; #endif } ierr = MPI_Allreduce(&sum,nrm,1,MPIU_REAL,MPI_SUM,mat->comm);CHKERRQ(ierr); *nrm = sqrt(*nrm); } else { SETERRQ(PETSC_ERR_SUP,"No support for this norm yet"); } } PetscFunctionReturn(0); } /* Creates the hash table, and sets the table This table is created only once. If new entried need to be added to the matrix then the hash table has to be destroyed and recreated. */ #undef __FUNCT__ #define __FUNCT__ "MatCreateHashTable_MPIBAIJ_Private" int MatCreateHashTable_MPIBAIJ_Private(Mat mat,PetscReal factor) { Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; Mat A = baij->A,B=baij->B; Mat_SeqBAIJ *a=(Mat_SeqBAIJ *)A->data,*b=(Mat_SeqBAIJ *)B->data; int i,j,k,nz=a->nz+b->nz,h1,*ai=a->i,*aj=a->j,*bi=b->i,*bj=b->j; int size,bs2=baij->bs2,rstart=baij->rstart,ierr; int cstart=baij->cstart,*garray=baij->garray,row,col,Nbs=baij->Nbs; int *HT,key; MatScalar **HD; PetscReal tmp; #if defined(PETSC_USE_BOPT_g) int ct=0,max=0; #endif PetscFunctionBegin; baij->ht_size=(int)(factor*nz); size = baij->ht_size; if (baij->ht) { PetscFunctionReturn(0); } /* Allocate Memory for Hash Table */ ierr = PetscMalloc((size)*(sizeof(int)+sizeof(MatScalar*))+1,&baij->hd);CHKERRQ(ierr); baij->ht = (int*)(baij->hd + size); HD = baij->hd; HT = baij->ht; ierr = PetscMemzero(HD,size*(sizeof(int)+sizeof(PetscScalar*)));CHKERRQ(ierr); /* Loop Over A */ for (i=0; imbs; i++) { for (j=ai[i]; ja + j*bs2; break; #if defined(PETSC_USE_BOPT_g) } else { ct++; #endif } } #if defined(PETSC_USE_BOPT_g) if (k> max) max = k; #endif } } /* Loop Over B */ for (i=0; imbs; i++) { for (j=bi[i]; ja + j*bs2; break; #if defined(PETSC_USE_BOPT_g) } else { ct++; #endif } } #if defined(PETSC_USE_BOPT_g) if (k> max) max = k; #endif } } /* Print Summary */ #if defined(PETSC_USE_BOPT_g) for (i=0,j=0; idata; int ierr,nstash,reallocs; InsertMode addv; PetscFunctionBegin; if (baij->donotstash) { PetscFunctionReturn(0); } /* make sure all processors are either in INSERTMODE or ADDMODE */ ierr = MPI_Allreduce(&mat->insertmode,&addv,1,MPI_INT,MPI_BOR,mat->comm);CHKERRQ(ierr); if (addv == (ADD_VALUES|INSERT_VALUES)) { SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"Some processors inserted others added"); } mat->insertmode = addv; /* in case this processor had no cache */ ierr = MatStashScatterBegin_Private(&mat->stash,baij->rowners_bs);CHKERRQ(ierr); ierr = MatStashScatterBegin_Private(&mat->bstash,baij->rowners);CHKERRQ(ierr); ierr = MatStashGetInfo_Private(&mat->stash,&nstash,&reallocs);CHKERRQ(ierr); PetscLogInfo(0,"MatAssemblyBegin_MPIBAIJ:Stash has %d entries,uses %d mallocs.\n",nstash,reallocs); ierr = MatStashGetInfo_Private(&mat->bstash,&nstash,&reallocs);CHKERRQ(ierr); PetscLogInfo(0,"MatAssemblyBegin_MPIBAIJ:Block-Stash has %d entries, uses %d mallocs.\n",nstash,reallocs); PetscFunctionReturn(0); } EXTERN int MatUseDSCPACK_MPIBAIJ(Mat); #undef __FUNCT__ #define __FUNCT__ "MatAssemblyEnd_MPIBAIJ" int MatAssemblyEnd_MPIBAIJ(Mat mat,MatAssemblyType mode) { Mat_MPIBAIJ *baij=(Mat_MPIBAIJ*)mat->data; Mat_SeqBAIJ *a=(Mat_SeqBAIJ*)baij->A->data,*b=(Mat_SeqBAIJ*)baij->B->data; int i,j,rstart,ncols,n,ierr,flg,bs2=baij->bs2; int *row,*col,other_disassembled; PetscTruth r1,r2,r3; MatScalar *val; InsertMode addv = mat->insertmode; #if defined(PETSC_HAVE_DSCPACK) PetscTruth flag; #endif PetscFunctionBegin; if (!baij->donotstash) { while (1) { ierr = MatStashScatterGetMesg_Private(&mat->stash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); if (!flg) break; for (i=0; istash);CHKERRQ(ierr); /* Now process the block-stash. Since the values are stashed column-oriented, set the roworiented flag to column oriented, and after MatSetValues() restore the original flags */ r1 = baij->roworiented; r2 = a->roworiented; r3 = b->roworiented; baij->roworiented = PETSC_FALSE; a->roworiented = PETSC_FALSE; b->roworiented = PETSC_FALSE; while (1) { ierr = MatStashScatterGetMesg_Private(&mat->bstash,&n,&row,&col,&val,&flg);CHKERRQ(ierr); if (!flg) break; for (i=0; ibstash);CHKERRQ(ierr); baij->roworiented = r1; a->roworiented = r2; b->roworiented = r3; } ierr = MatAssemblyBegin(baij->A,mode);CHKERRQ(ierr); ierr = MatAssemblyEnd(baij->A,mode);CHKERRQ(ierr); /* determine if any processor has disassembled, if so we must also disassemble ourselfs, in order that we may reassemble. */ /* if nonzero structure of submatrix B cannot change then we know that no processor disassembled thus we can skip this stuff */ if (!((Mat_SeqBAIJ*)baij->B->data)->nonew) { ierr = MPI_Allreduce(&mat->was_assembled,&other_disassembled,1,MPI_INT,MPI_PROD,mat->comm);CHKERRQ(ierr); if (mat->was_assembled && !other_disassembled) { ierr = DisAssemble_MPIBAIJ(mat);CHKERRQ(ierr); } } if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) { ierr = MatSetUpMultiply_MPIBAIJ(mat);CHKERRQ(ierr); } ierr = MatAssemblyBegin(baij->B,mode);CHKERRQ(ierr); ierr = MatAssemblyEnd(baij->B,mode);CHKERRQ(ierr); #if defined(PETSC_USE_BOPT_g) if (baij->ht && mode== MAT_FINAL_ASSEMBLY) { PetscLogInfo(0,"MatAssemblyEnd_MPIBAIJ:Average Hash Table Search in MatSetValues = %5.2f\n",((PetscReal)baij->ht_total_ct)/baij->ht_insert_ct); baij->ht_total_ct = 0; baij->ht_insert_ct = 0; } #endif if (baij->ht_flag && !baij->ht && mode == MAT_FINAL_ASSEMBLY) { ierr = MatCreateHashTable_MPIBAIJ_Private(mat,baij->ht_fact);CHKERRQ(ierr); mat->ops->setvalues = MatSetValues_MPIBAIJ_HT; mat->ops->setvaluesblocked = MatSetValuesBlocked_MPIBAIJ_HT; } if (baij->rowvalues) { ierr = PetscFree(baij->rowvalues);CHKERRQ(ierr); baij->rowvalues = 0; } #if defined(PETSC_HAVE_DSCPACK) ierr = PetscOptionsHasName(PETSC_NULL,"-mat_baij_dscpack",&flag);CHKERRQ(ierr); if (flag) { ierr = MatUseDSCPACK_MPIBAIJ(mat);CHKERRQ(ierr); } #endif PetscFunctionReturn(0); } extern int MatMPIBAIJFactorInfo_DSCPACK(Mat,PetscViewer); #undef __FUNCT__ #define __FUNCT__ "MatView_MPIBAIJ_ASCIIorDraworSocket" static int MatView_MPIBAIJ_ASCIIorDraworSocket(Mat mat,PetscViewer viewer) { Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; int ierr,bs = baij->bs,size = baij->size,rank = baij->rank; PetscTruth isascii,isdraw; PetscViewer sviewer; PetscViewerFormat format; PetscFunctionBegin; ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_ASCII,&isascii);CHKERRQ(ierr); ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_DRAW,&isdraw);CHKERRQ(ierr); if (isascii) { ierr = PetscViewerGetFormat(viewer,&format);CHKERRQ(ierr); if (format == PETSC_VIEWER_ASCII_INFO_LONG) { MatInfo info; ierr = MPI_Comm_rank(mat->comm,&rank);CHKERRQ(ierr); ierr = MatGetInfo(mat,MAT_LOCAL,&info);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] Local rows %d nz %d nz alloced %d bs %d mem %d\n", rank,mat->m,(int)info.nz_used*bs,(int)info.nz_allocated*bs, baij->bs,(int)info.memory);CHKERRQ(ierr); ierr = MatGetInfo(baij->A,MAT_LOCAL,&info);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] on-diagonal part: nz %d \n",rank,(int)info.nz_used*bs);CHKERRQ(ierr); ierr = MatGetInfo(baij->B,MAT_LOCAL,&info);CHKERRQ(ierr); ierr = PetscViewerASCIISynchronizedPrintf(viewer,"[%d] off-diagonal part: nz %d \n",rank,(int)info.nz_used*bs);CHKERRQ(ierr); ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); ierr = VecScatterView(baij->Mvctx,viewer);CHKERRQ(ierr); PetscFunctionReturn(0); } else if (format == PETSC_VIEWER_ASCII_INFO) { ierr = PetscViewerASCIIPrintf(viewer," block size is %d\n",bs);CHKERRQ(ierr); PetscFunctionReturn(0); } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { #if defined(PETSC_HAVE_DSCPACK) && !defined(PETSC_USE_SINGLE) && !defined(PETSC_USE_COMPLEX) ierr = MatMPIBAIJFactorInfo_DSCPACK(mat,viewer);CHKERRQ(ierr); #endif PetscFunctionReturn(0); } } if (isdraw) { PetscDraw draw; PetscTruth isnull; ierr = PetscViewerDrawGetDraw(viewer,0,&draw);CHKERRQ(ierr); ierr = PetscDrawIsNull(draw,&isnull);CHKERRQ(ierr); if (isnull) PetscFunctionReturn(0); } if (size == 1) { ierr = PetscObjectSetName((PetscObject)baij->A,mat->name);CHKERRQ(ierr); ierr = MatView(baij->A,viewer);CHKERRQ(ierr); } else { /* assemble the entire matrix onto first processor. */ Mat A; Mat_SeqBAIJ *Aloc; int M = mat->M,N = mat->N,*ai,*aj,col,i,j,k,*rvals,mbs = baij->mbs; MatScalar *a; if (!rank) { ierr = MatCreateMPIBAIJ(mat->comm,baij->bs,M,N,M,N,0,PETSC_NULL,0,PETSC_NULL,&A);CHKERRQ(ierr); } else { ierr = MatCreateMPIBAIJ(mat->comm,baij->bs,0,0,M,N,0,PETSC_NULL,0,PETSC_NULL,&A);CHKERRQ(ierr); } PetscLogObjectParent(mat,A); /* copy over the A part */ Aloc = (Mat_SeqBAIJ*)baij->A->data; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; ierr = PetscMalloc(bs*sizeof(int),&rvals);CHKERRQ(ierr); for (i=0; irstart + i); for (j=1; jcstart+aj[j])*bs; for (k=0; kB->data; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; for (i=0; irstart + i); for (j=1; jgarray[aj[j]]*bs; for (k=0; kdata))->A,mat->name);CHKERRQ(ierr); ierr = MatView(((Mat_MPIBAIJ*)(A->data))->A,sviewer);CHKERRQ(ierr); } ierr = PetscViewerRestoreSingleton(viewer,&sviewer);CHKERRQ(ierr); ierr = MatDestroy(A);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatView_MPIBAIJ" int MatView_MPIBAIJ(Mat mat,PetscViewer viewer) { int ierr; PetscTruth isascii,isdraw,issocket,isbinary; PetscFunctionBegin; ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_ASCII,&isascii);CHKERRQ(ierr); ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_DRAW,&isdraw);CHKERRQ(ierr); ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_SOCKET,&issocket);CHKERRQ(ierr); ierr = PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_BINARY,&isbinary);CHKERRQ(ierr); if (isascii || isdraw || issocket || isbinary) { ierr = MatView_MPIBAIJ_ASCIIorDraworSocket(mat,viewer);CHKERRQ(ierr); } else { SETERRQ1(1,"Viewer type %s not supported by MPIBAIJ matrices",((PetscObject)viewer)->type_name); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatDestroy_MPIBAIJ" int MatDestroy_MPIBAIJ(Mat mat) { Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; int ierr; PetscFunctionBegin; #if defined(PETSC_USE_LOG) PetscLogObjectState((PetscObject)mat,"Rows=%d,Cols=%d",mat->M,mat->N); #endif ierr = MatStashDestroy_Private(&mat->stash);CHKERRQ(ierr); ierr = MatStashDestroy_Private(&mat->bstash);CHKERRQ(ierr); ierr = PetscFree(baij->rowners);CHKERRQ(ierr); ierr = MatDestroy(baij->A);CHKERRQ(ierr); ierr = MatDestroy(baij->B);CHKERRQ(ierr); #if defined (PETSC_USE_CTABLE) if (baij->colmap) {ierr = PetscTableDelete(baij->colmap);CHKERRQ(ierr);} #else if (baij->colmap) {ierr = PetscFree(baij->colmap);CHKERRQ(ierr);} #endif if (baij->garray) {ierr = PetscFree(baij->garray);CHKERRQ(ierr);} if (baij->lvec) {ierr = VecDestroy(baij->lvec);CHKERRQ(ierr);} if (baij->Mvctx) {ierr = VecScatterDestroy(baij->Mvctx);CHKERRQ(ierr);} if (baij->rowvalues) {ierr = PetscFree(baij->rowvalues);CHKERRQ(ierr);} if (baij->barray) {ierr = PetscFree(baij->barray);CHKERRQ(ierr);} if (baij->hd) {ierr = PetscFree(baij->hd);CHKERRQ(ierr);} #if defined(PETSC_USE_MAT_SINGLE) if (baij->setvaluescopy) {ierr = PetscFree(baij->setvaluescopy);CHKERRQ(ierr);} #endif ierr = PetscFree(baij);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatMult_MPIBAIJ" int MatMult_MPIBAIJ(Mat A,Vec xx,Vec yy) { Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; int ierr,nt; PetscFunctionBegin; ierr = VecGetLocalSize(xx,&nt);CHKERRQ(ierr); if (nt != A->n) { SETERRQ(PETSC_ERR_ARG_SIZ,"Incompatible partition of A and xx"); } ierr = VecGetLocalSize(yy,&nt);CHKERRQ(ierr); if (nt != A->m) { SETERRQ(PETSC_ERR_ARG_SIZ,"Incompatible parition of A and yy"); } ierr = VecScatterBegin(xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD,a->Mvctx);CHKERRQ(ierr); ierr = (*a->A->ops->mult)(a->A,xx,yy);CHKERRQ(ierr); ierr = VecScatterEnd(xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD,a->Mvctx);CHKERRQ(ierr); ierr = (*a->B->ops->multadd)(a->B,a->lvec,yy,yy);CHKERRQ(ierr); ierr = VecScatterPostRecvs(xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD,a->Mvctx);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatMultAdd_MPIBAIJ" int MatMultAdd_MPIBAIJ(Mat A,Vec xx,Vec yy,Vec zz) { Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; int ierr; PetscFunctionBegin; ierr = VecScatterBegin(xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD,a->Mvctx);CHKERRQ(ierr); ierr = (*a->A->ops->multadd)(a->A,xx,yy,zz);CHKERRQ(ierr); ierr = VecScatterEnd(xx,a->lvec,INSERT_VALUES,SCATTER_FORWARD,a->Mvctx);CHKERRQ(ierr); ierr = (*a->B->ops->multadd)(a->B,a->lvec,zz,zz);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatMultTranspose_MPIBAIJ" int MatMultTranspose_MPIBAIJ(Mat A,Vec xx,Vec yy) { Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; int ierr; PetscFunctionBegin; /* do nondiagonal part */ ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); /* send it on its way */ ierr = VecScatterBegin(a->lvec,yy,ADD_VALUES,SCATTER_REVERSE,a->Mvctx);CHKERRQ(ierr); /* do local part */ ierr = (*a->A->ops->multtranspose)(a->A,xx,yy);CHKERRQ(ierr); /* receive remote parts: note this assumes the values are not actually */ /* inserted in yy until the next line, which is true for my implementation*/ /* but is not perhaps always true. */ ierr = VecScatterEnd(a->lvec,yy,ADD_VALUES,SCATTER_REVERSE,a->Mvctx);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatMultTransposeAdd_MPIBAIJ" int MatMultTransposeAdd_MPIBAIJ(Mat A,Vec xx,Vec yy,Vec zz) { Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; int ierr; PetscFunctionBegin; /* do nondiagonal part */ ierr = (*a->B->ops->multtranspose)(a->B,xx,a->lvec);CHKERRQ(ierr); /* send it on its way */ ierr = VecScatterBegin(a->lvec,zz,ADD_VALUES,SCATTER_REVERSE,a->Mvctx);CHKERRQ(ierr); /* do local part */ ierr = (*a->A->ops->multtransposeadd)(a->A,xx,yy,zz);CHKERRQ(ierr); /* receive remote parts: note this assumes the values are not actually */ /* inserted in yy until the next line, which is true for my implementation*/ /* but is not perhaps always true. */ ierr = VecScatterEnd(a->lvec,zz,ADD_VALUES,SCATTER_REVERSE,a->Mvctx);CHKERRQ(ierr); PetscFunctionReturn(0); } /* This only works correctly for square matrices where the subblock A->A is the diagonal block */ #undef __FUNCT__ #define __FUNCT__ "MatGetDiagonal_MPIBAIJ" int MatGetDiagonal_MPIBAIJ(Mat A,Vec v) { Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; int ierr; PetscFunctionBegin; if (A->M != A->N) SETERRQ(PETSC_ERR_SUP,"Supports only square matrix where A->A is diag block"); ierr = MatGetDiagonal(a->A,v);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatScale_MPIBAIJ" int MatScale_MPIBAIJ(PetscScalar *aa,Mat A) { Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; int ierr; PetscFunctionBegin; ierr = MatScale(aa,a->A);CHKERRQ(ierr); ierr = MatScale(aa,a->B);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatGetRow_MPIBAIJ" int MatGetRow_MPIBAIJ(Mat matin,int row,int *nz,int **idx,PetscScalar **v) { Mat_MPIBAIJ *mat = (Mat_MPIBAIJ*)matin->data; PetscScalar *vworkA,*vworkB,**pvA,**pvB,*v_p; int bs = mat->bs,bs2 = mat->bs2,i,ierr,*cworkA,*cworkB,**pcA,**pcB; int nztot,nzA,nzB,lrow,brstart = mat->rstart*bs,brend = mat->rend*bs; int *cmap,*idx_p,cstart = mat->cstart; PetscFunctionBegin; if (mat->getrowactive == PETSC_TRUE) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"Already active"); mat->getrowactive = PETSC_TRUE; if (!mat->rowvalues && (idx || v)) { /* allocate enough space to hold information from the longest row. */ Mat_SeqBAIJ *Aa = (Mat_SeqBAIJ*)mat->A->data,*Ba = (Mat_SeqBAIJ*)mat->B->data; int max = 1,mbs = mat->mbs,tmp; for (i=0; ii[i+1] - Aa->i[i] + Ba->i[i+1] - Ba->i[i]; if (max < tmp) { max = tmp; } } ierr = PetscMalloc(max*bs2*(sizeof(int)+sizeof(PetscScalar)),&mat->rowvalues);CHKERRQ(ierr); mat->rowindices = (int*)(mat->rowvalues + max*bs2); } if (row < brstart || row >= brend) SETERRQ(PETSC_ERR_SUP,"Only local rows") lrow = row - brstart; pvA = &vworkA; pcA = &cworkA; pvB = &vworkB; pcB = &cworkB; if (!v) {pvA = 0; pvB = 0;} if (!idx) {pcA = 0; if (!v) pcB = 0;} ierr = (*mat->A->ops->getrow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); ierr = (*mat->B->ops->getrow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); nztot = nzA + nzB; cmap = mat->garray; if (v || idx) { if (nztot) { /* Sort by increasing column numbers, assuming A and B already sorted */ int imark = -1; if (v) { *v = v_p = mat->rowvalues; for (i=0; irowindices; if (imark > -1) { for (i=0; iA->ops->restorerow)(mat->A,lrow,&nzA,pcA,pvA);CHKERRQ(ierr); ierr = (*mat->B->ops->restorerow)(mat->B,lrow,&nzB,pcB,pvB);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatRestoreRow_MPIBAIJ" int MatRestoreRow_MPIBAIJ(Mat mat,int row,int *nz,int **idx,PetscScalar **v) { Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; PetscFunctionBegin; if (baij->getrowactive == PETSC_FALSE) { SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"MatGetRow not called"); } baij->getrowactive = PETSC_FALSE; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatGetBlockSize_MPIBAIJ" int MatGetBlockSize_MPIBAIJ(Mat mat,int *bs) { Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)mat->data; PetscFunctionBegin; *bs = baij->bs; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatZeroEntries_MPIBAIJ" int MatZeroEntries_MPIBAIJ(Mat A) { Mat_MPIBAIJ *l = (Mat_MPIBAIJ*)A->data; int ierr; PetscFunctionBegin; ierr = MatZeroEntries(l->A);CHKERRQ(ierr); ierr = MatZeroEntries(l->B);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatGetInfo_MPIBAIJ" int MatGetInfo_MPIBAIJ(Mat matin,MatInfoType flag,MatInfo *info) { Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)matin->data; Mat A = a->A,B = a->B; int ierr; PetscReal isend[5],irecv[5]; PetscFunctionBegin; info->block_size = (PetscReal)a->bs; ierr = MatGetInfo(A,MAT_LOCAL,info);CHKERRQ(ierr); isend[0] = info->nz_used; isend[1] = info->nz_allocated; isend[2] = info->nz_unneeded; isend[3] = info->memory; isend[4] = info->mallocs; ierr = MatGetInfo(B,MAT_LOCAL,info);CHKERRQ(ierr); isend[0] += info->nz_used; isend[1] += info->nz_allocated; isend[2] += info->nz_unneeded; isend[3] += info->memory; isend[4] += info->mallocs; if (flag == MAT_LOCAL) { info->nz_used = isend[0]; info->nz_allocated = isend[1]; info->nz_unneeded = isend[2]; info->memory = isend[3]; info->mallocs = isend[4]; } else if (flag == MAT_GLOBAL_MAX) { ierr = MPI_Allreduce(isend,irecv,5,MPIU_REAL,MPI_MAX,matin->comm);CHKERRQ(ierr); info->nz_used = irecv[0]; info->nz_allocated = irecv[1]; info->nz_unneeded = irecv[2]; info->memory = irecv[3]; info->mallocs = irecv[4]; } else if (flag == MAT_GLOBAL_SUM) { ierr = MPI_Allreduce(isend,irecv,5,MPIU_REAL,MPI_SUM,matin->comm);CHKERRQ(ierr); info->nz_used = irecv[0]; info->nz_allocated = irecv[1]; info->nz_unneeded = irecv[2]; info->memory = irecv[3]; info->mallocs = irecv[4]; } else { SETERRQ1(1,"Unknown MatInfoType argument %d",flag); } info->rows_global = (PetscReal)A->M; info->columns_global = (PetscReal)A->N; info->rows_local = (PetscReal)A->m; info->columns_local = (PetscReal)A->N; info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ info->fill_ratio_needed = 0; info->factor_mallocs = 0; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSetOption_MPIBAIJ" int MatSetOption_MPIBAIJ(Mat A,MatOption op) { Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; int ierr; PetscFunctionBegin; switch (op) { case MAT_NO_NEW_NONZERO_LOCATIONS: case MAT_YES_NEW_NONZERO_LOCATIONS: case MAT_COLUMNS_UNSORTED: case MAT_COLUMNS_SORTED: case MAT_NEW_NONZERO_ALLOCATION_ERR: case MAT_KEEP_ZEROED_ROWS: case MAT_NEW_NONZERO_LOCATION_ERR: ierr = MatSetOption(a->A,op);CHKERRQ(ierr); ierr = MatSetOption(a->B,op);CHKERRQ(ierr); break; case MAT_ROW_ORIENTED: a->roworiented = PETSC_TRUE; ierr = MatSetOption(a->A,op);CHKERRQ(ierr); ierr = MatSetOption(a->B,op);CHKERRQ(ierr); break; case MAT_ROWS_SORTED: case MAT_ROWS_UNSORTED: case MAT_YES_NEW_DIAGONALS: case MAT_USE_SINGLE_PRECISION_SOLVES: PetscLogInfo(A,"Info:MatSetOption_MPIBAIJ:Option ignored\n"); break; case MAT_COLUMN_ORIENTED: a->roworiented = PETSC_FALSE; ierr = MatSetOption(a->A,op);CHKERRQ(ierr); ierr = MatSetOption(a->B,op);CHKERRQ(ierr); break; case MAT_IGNORE_OFF_PROC_ENTRIES: a->donotstash = PETSC_TRUE; break; case MAT_NO_NEW_DIAGONALS: SETERRQ(PETSC_ERR_SUP,"MAT_NO_NEW_DIAGONALS"); case MAT_USE_HASH_TABLE: a->ht_flag = PETSC_TRUE; break; default: SETERRQ(PETSC_ERR_SUP,"unknown option"); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatTranspose_MPIBAIJ(" int MatTranspose_MPIBAIJ(Mat A,Mat *matout) { Mat_MPIBAIJ *baij = (Mat_MPIBAIJ*)A->data; Mat_SeqBAIJ *Aloc; Mat B; int ierr,M=A->M,N=A->N,*ai,*aj,i,*rvals,j,k,col; int bs=baij->bs,mbs=baij->mbs; MatScalar *a; PetscFunctionBegin; if (!matout && M != N) SETERRQ(PETSC_ERR_ARG_SIZ,"Square matrix only for in-place"); ierr = MatCreateMPIBAIJ(A->comm,baij->bs,A->n,A->m,N,M,0,PETSC_NULL,0,PETSC_NULL,&B);CHKERRQ(ierr); /* copy over the A part */ Aloc = (Mat_SeqBAIJ*)baij->A->data; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; ierr = PetscMalloc(bs*sizeof(int),&rvals);CHKERRQ(ierr); for (i=0; irstart + i); for (j=1; jcstart+aj[j])*bs; for (k=0; kB->data; ai = Aloc->i; aj = Aloc->j; a = Aloc->a; for (i=0; irstart + i); for (j=1; jgarray[aj[j]]*bs; for (k=0; kdata; Mat a = baij->A,b = baij->B; int ierr,s1,s2,s3; PetscFunctionBegin; ierr = MatGetLocalSize(mat,&s2,&s3);CHKERRQ(ierr); if (rr) { ierr = VecGetLocalSize(rr,&s1);CHKERRQ(ierr); if (s1!=s3) SETERRQ(PETSC_ERR_ARG_SIZ,"right vector non-conforming local size"); /* Overlap communication with computation. */ ierr = VecScatterBegin(rr,baij->lvec,INSERT_VALUES,SCATTER_FORWARD,baij->Mvctx);CHKERRQ(ierr); } if (ll) { ierr = VecGetLocalSize(ll,&s1);CHKERRQ(ierr); if (s1!=s2) SETERRQ(PETSC_ERR_ARG_SIZ,"left vector non-conforming local size"); ierr = (*b->ops->diagonalscale)(b,ll,PETSC_NULL);CHKERRQ(ierr); } /* scale the diagonal block */ ierr = (*a->ops->diagonalscale)(a,ll,rr);CHKERRQ(ierr); if (rr) { /* Do a scatter end and then right scale the off-diagonal block */ ierr = VecScatterEnd(rr,baij->lvec,INSERT_VALUES,SCATTER_FORWARD,baij->Mvctx);CHKERRQ(ierr); ierr = (*b->ops->diagonalscale)(b,PETSC_NULL,baij->lvec);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatZeroRows_MPIBAIJ" int MatZeroRows_MPIBAIJ(Mat A,IS is,PetscScalar *diag) { Mat_MPIBAIJ *l = (Mat_MPIBAIJ*)A->data; int i,ierr,N,*rows,*owners = l->rowners,size = l->size; int *procs,*nprocs,j,idx,nsends,*work,row; int nmax,*svalues,*starts,*owner,nrecvs,rank = l->rank; int *rvalues,tag = A->tag,count,base,slen,n,*source; int *lens,imdex,*lrows,*values,bs=l->bs,rstart_bs=l->rstart_bs; MPI_Comm comm = A->comm; MPI_Request *send_waits,*recv_waits; MPI_Status recv_status,*send_status; IS istmp; PetscTruth found; PetscFunctionBegin; ierr = ISGetLocalSize(is,&N);CHKERRQ(ierr); ierr = ISGetIndices(is,&rows);CHKERRQ(ierr); /* first count number of contributors to each processor */ ierr = PetscMalloc(2*size*sizeof(int),&nprocs);CHKERRQ(ierr); ierr = PetscMemzero(nprocs,2*size*sizeof(int));CHKERRQ(ierr); procs = nprocs + size; ierr = PetscMalloc((N+1)*sizeof(int),&owner);CHKERRQ(ierr); /* see note*/ for (i=0; i= owners[j]*bs && idx < owners[j+1]*bs) { nprocs[j]++; procs[j] = 1; owner[i] = j; found = PETSC_TRUE; break; } } if (!found) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Index out of range"); } nsends = 0; for (i=0; iB before l->A because the (diag) case below may put values into l->B*/ ierr = MatZeroRows_SeqBAIJ(l->B,istmp,0);CHKERRQ(ierr); if (diag && (l->A->M == l->A->N)) { ierr = MatZeroRows_SeqBAIJ(l->A,istmp,diag);CHKERRQ(ierr); } else if (diag) { ierr = MatZeroRows_SeqBAIJ(l->A,istmp,0);CHKERRQ(ierr); if (((Mat_SeqBAIJ*)l->A->data)->nonew) { SETERRQ(PETSC_ERR_SUP,"MatZeroRows() on rectangular matrices cannot be used with the Mat options \n\ MAT_NO_NEW_NONZERO_LOCATIONS,MAT_NEW_NONZERO_LOCATION_ERR,MAT_NEW_NONZERO_ALLOCATION_ERR"); } for (i=0; iA,istmp,0);CHKERRQ(ierr); } ierr = ISDestroy(istmp);CHKERRQ(ierr); ierr = PetscFree(lrows);CHKERRQ(ierr); /* wait on sends */ if (nsends) { ierr = PetscMalloc(nsends*sizeof(MPI_Status),&send_status);CHKERRQ(ierr); ierr = MPI_Waitall(nsends,send_waits,send_status);CHKERRQ(ierr); ierr = PetscFree(send_status);CHKERRQ(ierr); } ierr = PetscFree(send_waits);CHKERRQ(ierr); ierr = PetscFree(svalues);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatPrintHelp_MPIBAIJ" int MatPrintHelp_MPIBAIJ(Mat A) { Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; MPI_Comm comm = A->comm; static int called = 0; int ierr; PetscFunctionBegin; if (!a->rank) { ierr = MatPrintHelp_SeqBAIJ(a->A);CHKERRQ(ierr); } if (called) {PetscFunctionReturn(0);} else called = 1; ierr = (*PetscHelpPrintf)(comm," Options for MATMPIBAIJ matrix format (the defaults):\n");CHKERRQ(ierr); ierr = (*PetscHelpPrintf)(comm," -mat_use_hash_table : Use hashtable for efficient matrix assembly\n");CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSetUnfactored_MPIBAIJ" int MatSetUnfactored_MPIBAIJ(Mat A) { Mat_MPIBAIJ *a = (Mat_MPIBAIJ*)A->data; int ierr; PetscFunctionBegin; ierr = MatSetUnfactored(a->A);CHKERRQ(ierr); PetscFunctionReturn(0); } static int MatDuplicate_MPIBAIJ(Mat,MatDuplicateOption,Mat *); #undef __FUNCT__ #define __FUNCT__ "MatEqual_MPIBAIJ" int MatEqual_MPIBAIJ(Mat A,Mat B,PetscTruth *flag) { Mat_MPIBAIJ *matB = (Mat_MPIBAIJ*)B->data,*matA = (Mat_MPIBAIJ*)A->data; Mat a,b,c,d; PetscTruth flg; int ierr; PetscFunctionBegin; ierr = PetscTypeCompare((PetscObject)B,MATMPIBAIJ,&flg);CHKERRQ(ierr); if (!flg) SETERRQ(PETSC_ERR_ARG_INCOMP,"Matrices must be same type"); a = matA->A; b = matA->B; c = matB->A; d = matB->B; ierr = MatEqual(a,c,&flg);CHKERRQ(ierr); if (flg == PETSC_TRUE) { ierr = MatEqual(b,d,&flg);CHKERRQ(ierr); } ierr = MPI_Allreduce(&flg,flag,1,MPI_INT,MPI_LAND,A->comm);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatSetUpPreallocation_MPIBAIJ" int MatSetUpPreallocation_MPIBAIJ(Mat A) { int ierr; PetscFunctionBegin; ierr = MatMPIBAIJSetPreallocation(A,1,PETSC_DEFAULT,0,PETSC_DEFAULT,0);CHKERRQ(ierr); PetscFunctionReturn(0); } /* -------------------------------------------------------------------*/ static struct _MatOps MatOps_Values = { MatSetValues_MPIBAIJ, MatGetRow_MPIBAIJ, MatRestoreRow_MPIBAIJ, MatMult_MPIBAIJ, MatMultAdd_MPIBAIJ, MatMultTranspose_MPIBAIJ, MatMultTransposeAdd_MPIBAIJ, 0, 0, 0, 0, 0, 0, 0, MatTranspose_MPIBAIJ, MatGetInfo_MPIBAIJ, MatEqual_MPIBAIJ, MatGetDiagonal_MPIBAIJ, MatDiagonalScale_MPIBAIJ, MatNorm_MPIBAIJ, MatAssemblyBegin_MPIBAIJ, MatAssemblyEnd_MPIBAIJ, 0, MatSetOption_MPIBAIJ, MatZeroEntries_MPIBAIJ, MatZeroRows_MPIBAIJ, 0, 0, 0, 0, MatSetUpPreallocation_MPIBAIJ, 0, 0, 0, 0, MatDuplicate_MPIBAIJ, 0, 0, 0, 0, 0, MatGetSubMatrices_MPIBAIJ, MatIncreaseOverlap_MPIBAIJ, MatGetValues_MPIBAIJ, 0, MatPrintHelp_MPIBAIJ, MatScale_MPIBAIJ, 0, 0, 0, MatGetBlockSize_MPIBAIJ, 0, 0, 0, 0, 0, 0, MatSetUnfactored_MPIBAIJ, 0, MatSetValuesBlocked_MPIBAIJ, 0, MatDestroy_MPIBAIJ, MatView_MPIBAIJ, MatGetPetscMaps_Petsc, 0, 0, 0, 0, 0, 0, MatGetRowMax_MPIBAIJ}; EXTERN_C_BEGIN #undef __FUNCT__ #define __FUNCT__ "MatGetDiagonalBlock_MPIBAIJ" int MatGetDiagonalBlock_MPIBAIJ(Mat A,PetscTruth *iscopy,MatReuse reuse,Mat *a) { PetscFunctionBegin; *a = ((Mat_MPIBAIJ *)A->data)->A; *iscopy = PETSC_FALSE; PetscFunctionReturn(0); } EXTERN_C_END EXTERN_C_BEGIN #undef __FUNCT__ #define __FUNCT__ "MatCreate_MPIBAIJ" int MatCreate_MPIBAIJ(Mat B) { Mat_MPIBAIJ *b; int ierr; PetscTruth flg; PetscFunctionBegin; ierr = PetscNew(Mat_MPIBAIJ,&b);CHKERRQ(ierr); B->data = (void*)b; ierr = PetscMemzero(b,sizeof(Mat_MPIBAIJ));CHKERRQ(ierr); ierr = PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));CHKERRQ(ierr); B->mapping = 0; B->factor = 0; B->assembled = PETSC_FALSE; B->insertmode = NOT_SET_VALUES; ierr = MPI_Comm_rank(B->comm,&b->rank);CHKERRQ(ierr); ierr = MPI_Comm_size(B->comm,&b->size);CHKERRQ(ierr); /* build local table of row and column ownerships */ ierr = PetscMalloc(3*(b->size+2)*sizeof(int),&b->rowners);CHKERRQ(ierr); PetscLogObjectMemory(B,3*(b->size+2)*sizeof(int)+sizeof(struct _p_Mat)+sizeof(Mat_MPIBAIJ)); b->cowners = b->rowners + b->size + 2; b->rowners_bs = b->cowners + b->size + 2; /* build cache for off array entries formed */ ierr = MatStashCreate_Private(B->comm,1,&B->stash);CHKERRQ(ierr); b->donotstash = PETSC_FALSE; b->colmap = PETSC_NULL; b->garray = PETSC_NULL; b->roworiented = PETSC_TRUE; #if defined(PETSC_USE_MAT_SINGLE) /* stuff for MatSetValues_XXX in single precision */ b->setvalueslen = 0; b->setvaluescopy = PETSC_NULL; #endif /* stuff used in block assembly */ b->barray = 0; /* stuff used for matrix vector multiply */ b->lvec = 0; b->Mvctx = 0; /* stuff for MatGetRow() */ b->rowindices = 0; b->rowvalues = 0; b->getrowactive = PETSC_FALSE; /* hash table stuff */ b->ht = 0; b->hd = 0; b->ht_size = 0; b->ht_flag = PETSC_FALSE; b->ht_fact = 0; b->ht_total_ct = 0; b->ht_insert_ct = 0; ierr = PetscOptionsHasName(PETSC_NULL,"-mat_use_hash_table",&flg);CHKERRQ(ierr); if (flg) { PetscReal fact = 1.39; ierr = MatSetOption(B,MAT_USE_HASH_TABLE);CHKERRQ(ierr); ierr = PetscOptionsGetReal(PETSC_NULL,"-mat_use_hash_table",&fact,PETSC_NULL);CHKERRQ(ierr); if (fact <= 1.0) fact = 1.39; ierr = MatMPIBAIJSetHashTableFactor(B,fact);CHKERRQ(ierr); PetscLogInfo(0,"MatCreateMPIBAIJ:Hash table Factor used %5.2f\n",fact); } ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatStoreValues_C", "MatStoreValues_MPIBAIJ", MatStoreValues_MPIBAIJ);CHKERRQ(ierr); ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatRetrieveValues_C", "MatRetrieveValues_MPIBAIJ", MatRetrieveValues_MPIBAIJ);CHKERRQ(ierr); ierr = PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetDiagonalBlock_C", "MatGetDiagonalBlock_MPIBAIJ", MatGetDiagonalBlock_MPIBAIJ);CHKERRQ(ierr); PetscFunctionReturn(0); } EXTERN_C_END #undef __FUNCT__ #define __FUNCT__ "MatMPIBAIJSetPreallocation" /*@C MatMPIBAIJSetPreallocation - Creates a sparse parallel matrix in block AIJ format (block compressed row). For good matrix assembly performance the user should preallocate the matrix storage by setting the parameters d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, performance can be increased by more than a factor of 50. Collective on Mat Input Parameters: + A - the matrix . bs - size of blockk . d_nz - number of block nonzeros per block row in diagonal portion of local submatrix (same for all local rows) . d_nnz - array containing the number of block nonzeros in the various block rows of the in diagonal portion of the local (possibly different for each block row) or PETSC_NULL. You must leave room for the diagonal entry even if it is zero. . o_nz - number of block nonzeros per block row in the off-diagonal portion of local submatrix (same for all local rows). - o_nnz - array containing the number of nonzeros in the various block rows of the off-diagonal portion of the local submatrix (possibly different for each block row) or PETSC_NULL. Output Parameter: Options Database Keys: . -mat_no_unroll - uses code that does not unroll the loops in the block calculations (much slower) . -mat_block_size - size of the blocks to use Notes: If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one processor than it must be used on all processors that share the object for that argument. Storage Information: For a square global matrix we define each processor's diagonal portion to be its local rows and the corresponding columns (a square submatrix); each processor's off-diagonal portion encompasses the remainder of the local matrix (a rectangular submatrix). The user can specify preallocated storage for the diagonal part of the local submatrix with either d_nz or d_nnz (not both). Set d_nz=PETSC_DEFAULT and d_nnz=PETSC_NULL for PETSc to control dynamic memory allocation. Likewise, specify preallocated storage for the off-diagonal part of the local submatrix with o_nz or o_nnz (not both). Consider a processor that owns rows 3, 4 and 5 of a parallel matrix. In the figure below we depict these three local rows and all columns (0-11). .vb 0 1 2 3 4 5 6 7 8 9 10 11 ------------------- row 3 | o o o d d d o o o o o o row 4 | o o o d d d o o o o o o row 5 | o o o d d d o o o o o o ------------------- .ve Thus, any entries in the d locations are stored in the d (diagonal) submatrix, and any entries in the o locations are stored in the o (off-diagonal) submatrix. Note that the d and the o submatrices are stored simply in the MATSEQBAIJ format for compressed row storage. Now d_nz should indicate the number of block nonzeros per row in the d matrix, and o_nz should indicate the number of block nonzeros per row in the o matrix. In general, for PDE problems in which most nonzeros are near the diagonal, one expects d_nz >> o_nz. For large problems you MUST preallocate memory or you will get TERRIBLE performance; see the users' manual chapter on matrices. Level: intermediate .keywords: matrix, block, aij, compressed row, sparse, parallel .seealso: MatCreate(), MatCreateSeqBAIJ(), MatSetValues(), MatCreateMPIBAIJ() @*/ int MatMPIBAIJSetPreallocation(Mat B,int bs,int d_nz,int *d_nnz,int o_nz,int *o_nnz) { Mat_MPIBAIJ *b; int ierr,i; PetscTruth flg2; PetscFunctionBegin; ierr = PetscTypeCompare((PetscObject)B,MATMPIBAIJ,&flg2);CHKERRQ(ierr); if (!flg2) PetscFunctionReturn(0); B->preallocated = PETSC_TRUE; ierr = PetscOptionsGetInt(PETSC_NULL,"-mat_block_size",&bs,PETSC_NULL);CHKERRQ(ierr); if (bs < 1) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Invalid block size specified, must be positive"); if (d_nz == PETSC_DEFAULT || d_nz == PETSC_DECIDE) d_nz = 5; if (o_nz == PETSC_DEFAULT || o_nz == PETSC_DECIDE) o_nz = 2; if (d_nz < 0) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"d_nz cannot be less than 0: value %d",d_nz); if (o_nz < 0) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"o_nz cannot be less than 0: value %d",o_nz); if (d_nnz) { for (i=0; im/bs; i++) { if (d_nnz[i] < 0) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"d_nnz cannot be less than -1: local row %d value %d",i,d_nnz[i]); } } if (o_nnz) { for (i=0; im/bs; i++) { if (o_nnz[i] < 0) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"o_nnz cannot be less than -1: local row %d value %d",i,o_nnz[i]); } } ierr = PetscSplitOwnershipBlock(B->comm,bs,&B->m,&B->M);CHKERRQ(ierr); ierr = PetscSplitOwnershipBlock(B->comm,bs,&B->n,&B->N);CHKERRQ(ierr); ierr = PetscMapCreateMPI(B->comm,B->m,B->M,&B->rmap);CHKERRQ(ierr); ierr = PetscMapCreateMPI(B->comm,B->n,B->N,&B->cmap);CHKERRQ(ierr); b = (Mat_MPIBAIJ*)B->data; b->bs = bs; b->bs2 = bs*bs; b->mbs = B->m/bs; b->nbs = B->n/bs; b->Mbs = B->M/bs; b->Nbs = B->N/bs; ierr = MPI_Allgather(&b->mbs,1,MPI_INT,b->rowners+1,1,MPI_INT,B->comm);CHKERRQ(ierr); b->rowners[0] = 0; for (i=2; i<=b->size; i++) { b->rowners[i] += b->rowners[i-1]; } b->rstart = b->rowners[b->rank]; b->rend = b->rowners[b->rank+1]; ierr = MPI_Allgather(&b->nbs,1,MPI_INT,b->cowners+1,1,MPI_INT,B->comm);CHKERRQ(ierr); b->cowners[0] = 0; for (i=2; i<=b->size; i++) { b->cowners[i] += b->cowners[i-1]; } b->cstart = b->cowners[b->rank]; b->cend = b->cowners[b->rank+1]; for (i=0; i<=b->size; i++) { b->rowners_bs[i] = b->rowners[i]*bs; } b->rstart_bs = b->rstart*bs; b->rend_bs = b->rend*bs; b->cstart_bs = b->cstart*bs; b->cend_bs = b->cend*bs; ierr = MatCreateSeqBAIJ(PETSC_COMM_SELF,bs,B->m,B->n,d_nz,d_nnz,&b->A);CHKERRQ(ierr); PetscLogObjectParent(B,b->A); ierr = MatCreateSeqBAIJ(PETSC_COMM_SELF,bs,B->m,B->N,o_nz,o_nnz,&b->B);CHKERRQ(ierr); PetscLogObjectParent(B,b->B); ierr = MatStashCreate_Private(B->comm,bs,&B->bstash);CHKERRQ(ierr); PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatCreateMPIBAIJ" /*@C MatCreateMPIBAIJ - Creates a sparse parallel matrix in block AIJ format (block compressed row). For good matrix assembly performance the user should preallocate the matrix storage by setting the parameters d_nz (or d_nnz) and o_nz (or o_nnz). By setting these parameters accurately, performance can be increased by more than a factor of 50. Collective on MPI_Comm Input Parameters: + comm - MPI communicator . bs - size of blockk . m - number of local rows (or PETSC_DECIDE to have calculated if M is given) This value should be the same as the local size used in creating the y vector for the matrix-vector product y = Ax. . n - number of local columns (or PETSC_DECIDE to have calculated if N is given) This value should be the same as the local size used in creating the x vector for the matrix-vector product y = Ax. . M - number of global rows (or PETSC_DETERMINE to have calculated if m is given) . N - number of global columns (or PETSC_DETERMINE to have calculated if n is given) . d_nz - number of nonzero blocks per block row in diagonal portion of local submatrix (same for all local rows) . d_nnz - array containing the number of nonzero blocks in the various block rows of the in diagonal portion of the local (possibly different for each block row) or PETSC_NULL. You must leave room for the diagonal entry even if it is zero. . o_nz - number of nonzero blocks per block row in the off-diagonal portion of local submatrix (same for all local rows). - o_nnz - array containing the number of nonzero blocks in the various block rows of the off-diagonal portion of the local submatrix (possibly different for each block row) or PETSC_NULL. Output Parameter: . A - the matrix Options Database Keys: . -mat_no_unroll - uses code that does not unroll the loops in the block calculations (much slower) . -mat_block_size - size of the blocks to use Notes: A nonzero block is any block that as 1 or more nonzeros in it The user MUST specify either the local or global matrix dimensions (possibly both). If PETSC_DECIDE or PETSC_DETERMINE is used for a particular argument on one processor than it must be used on all processors that share the object for that argument. Storage Information: For a square global matrix we define each processor's diagonal portion to be its local rows and the corresponding columns (a square submatrix); each processor's off-diagonal portion encompasses the remainder of the local matrix (a rectangular submatrix). The user can specify preallocated storage for the diagonal part of the local submatrix with either d_nz or d_nnz (not both). Set d_nz=PETSC_DEFAULT and d_nnz=PETSC_NULL for PETSc to control dynamic memory allocation. Likewise, specify preallocated storage for the off-diagonal part of the local submatrix with o_nz or o_nnz (not both). Consider a processor that owns rows 3, 4 and 5 of a parallel matrix. In the figure below we depict these three local rows and all columns (0-11). .vb 0 1 2 3 4 5 6 7 8 9 10 11 ------------------- row 3 | o o o d d d o o o o o o row 4 | o o o d d d o o o o o o row 5 | o o o d d d o o o o o o ------------------- .ve Thus, any entries in the d locations are stored in the d (diagonal) submatrix, and any entries in the o locations are stored in the o (off-diagonal) submatrix. Note that the d and the o submatrices are stored simply in the MATSEQBAIJ format for compressed row storage. Now d_nz should indicate the number of block nonzeros per row in the d matrix, and o_nz should indicate the number of block nonzeros per row in the o matrix. In general, for PDE problems in which most nonzeros are near the diagonal, one expects d_nz >> o_nz. For large problems you MUST preallocate memory or you will get TERRIBLE performance; see the users' manual chapter on matrices. Level: intermediate .keywords: matrix, block, aij, compressed row, sparse, parallel .seealso: MatCreate(), MatCreateSeqBAIJ(), MatSetValues(), MatCreateMPIBAIJ() @*/ int MatCreateMPIBAIJ(MPI_Comm comm,int bs,int m,int n,int M,int N,int d_nz,int *d_nnz,int o_nz,int *o_nnz,Mat *A) { int ierr,size; PetscFunctionBegin; ierr = MatCreate(comm,m,n,M,N,A);CHKERRQ(ierr); ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); if (size > 1) { ierr = MatSetType(*A,MATMPIBAIJ);CHKERRQ(ierr); ierr = MatMPIBAIJSetPreallocation(*A,bs,d_nz,d_nnz,o_nz,o_nnz);CHKERRQ(ierr); } else { ierr = MatSetType(*A,MATSEQBAIJ);CHKERRQ(ierr); ierr = MatSeqBAIJSetPreallocation(*A,bs,d_nz,d_nnz);CHKERRQ(ierr); } PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatDuplicate_MPIBAIJ" static int MatDuplicate_MPIBAIJ(Mat matin,MatDuplicateOption cpvalues,Mat *newmat) { Mat mat; Mat_MPIBAIJ *a,*oldmat = (Mat_MPIBAIJ*)matin->data; int ierr,len=0; PetscFunctionBegin; *newmat = 0; ierr = MatCreate(matin->comm,matin->m,matin->n,matin->M,matin->N,&mat);CHKERRQ(ierr); ierr = MatSetType(mat,MATMPIBAIJ);CHKERRQ(ierr); mat->preallocated = PETSC_TRUE; mat->assembled = PETSC_TRUE; a = (Mat_MPIBAIJ*)mat->data; a->bs = oldmat->bs; a->bs2 = oldmat->bs2; a->mbs = oldmat->mbs; a->nbs = oldmat->nbs; a->Mbs = oldmat->Mbs; a->Nbs = oldmat->Nbs; a->rstart = oldmat->rstart; a->rend = oldmat->rend; a->cstart = oldmat->cstart; a->cend = oldmat->cend; a->size = oldmat->size; a->rank = oldmat->rank; a->donotstash = oldmat->donotstash; a->roworiented = oldmat->roworiented; a->rowindices = 0; a->rowvalues = 0; a->getrowactive = PETSC_FALSE; a->barray = 0; a->rstart_bs = oldmat->rstart_bs; a->rend_bs = oldmat->rend_bs; a->cstart_bs = oldmat->cstart_bs; a->cend_bs = oldmat->cend_bs; /* hash table stuff */ a->ht = 0; a->hd = 0; a->ht_size = 0; a->ht_flag = oldmat->ht_flag; a->ht_fact = oldmat->ht_fact; a->ht_total_ct = 0; a->ht_insert_ct = 0; ierr = PetscMemcpy(a->rowners,oldmat->rowners,3*(a->size+2)*sizeof(int));CHKERRQ(ierr); ierr = MatStashCreate_Private(matin->comm,1,&mat->stash);CHKERRQ(ierr); ierr = MatStashCreate_Private(matin->comm,oldmat->bs,&mat->bstash);CHKERRQ(ierr); if (oldmat->colmap) { #if defined (PETSC_USE_CTABLE) ierr = PetscTableCreateCopy(oldmat->colmap,&a->colmap);CHKERRQ(ierr); #else ierr = PetscMalloc((a->Nbs)*sizeof(int),&a->colmap);CHKERRQ(ierr); PetscLogObjectMemory(mat,(a->Nbs)*sizeof(int)); ierr = PetscMemcpy(a->colmap,oldmat->colmap,(a->Nbs)*sizeof(int));CHKERRQ(ierr); #endif } else a->colmap = 0; if (oldmat->garray && (len = ((Mat_SeqBAIJ*)(oldmat->B->data))->nbs)) { ierr = PetscMalloc(len*sizeof(int),&a->garray);CHKERRQ(ierr); PetscLogObjectMemory(mat,len*sizeof(int)); ierr = PetscMemcpy(a->garray,oldmat->garray,len*sizeof(int));CHKERRQ(ierr); } else a->garray = 0; ierr = VecDuplicate(oldmat->lvec,&a->lvec);CHKERRQ(ierr); PetscLogObjectParent(mat,a->lvec); ierr = VecScatterCopy(oldmat->Mvctx,&a->Mvctx);CHKERRQ(ierr); PetscLogObjectParent(mat,a->Mvctx); ierr = MatDuplicate(oldmat->A,cpvalues,&a->A);CHKERRQ(ierr); PetscLogObjectParent(mat,a->A); ierr = MatDuplicate(oldmat->B,cpvalues,&a->B);CHKERRQ(ierr); PetscLogObjectParent(mat,a->B); ierr = PetscFListDuplicate(matin->qlist,&mat->qlist);CHKERRQ(ierr); *newmat = mat; PetscFunctionReturn(0); } #include "petscsys.h" EXTERN_C_BEGIN #undef __FUNCT__ #define __FUNCT__ "MatLoad_MPIBAIJ" int MatLoad_MPIBAIJ(PetscViewer viewer,MatType type,Mat *newmat) { Mat A; int i,nz,ierr,j,rstart,rend,fd; PetscScalar *vals,*buf; MPI_Comm comm = ((PetscObject)viewer)->comm; MPI_Status status; int header[4],rank,size,*rowlengths = 0,M,N,m,*rowners,*browners,maxnz,*cols; int *locrowlens,*sndcounts = 0,*procsnz = 0,jj,*mycols,*ibuf; int tag = ((PetscObject)viewer)->tag,bs=1,Mbs,mbs,extra_rows; int *dlens,*odlens,*mask,*masked1,*masked2,rowcount,odcount; int dcount,kmax,k,nzcount,tmp; PetscFunctionBegin; ierr = PetscOptionsGetInt(PETSC_NULL,"-matload_block_size",&bs,PETSC_NULL);CHKERRQ(ierr); ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); if (!rank) { ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); ierr = PetscBinaryRead(fd,(char *)header,4,PETSC_INT);CHKERRQ(ierr); if (header[0] != MAT_FILE_COOKIE) SETERRQ(PETSC_ERR_FILE_UNEXPECTED,"not matrix object"); if (header[3] < 0) { SETERRQ(PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as MPIBAIJ"); } } ierr = MPI_Bcast(header+1,3,MPI_INT,0,comm);CHKERRQ(ierr); M = header[1]; N = header[2]; if (M != N) SETERRQ(PETSC_ERR_SUP,"Can only do square matrices"); /* This code adds extra rows to make sure the number of rows is divisible by the blocksize */ Mbs = M/bs; extra_rows = bs - M + bs*(Mbs); if (extra_rows == bs) extra_rows = 0; else Mbs++; if (extra_rows &&!rank) { PetscLogInfo(0,"MatLoad_MPIBAIJ:Padding loaded matrix to match blocksize\n"); } /* determine ownership of all rows */ mbs = Mbs/size + ((Mbs % size) > rank); m = mbs*bs; ierr = PetscMalloc(2*(size+2)*sizeof(int),&rowners);CHKERRQ(ierr); browners = rowners + size + 1; ierr = MPI_Allgather(&mbs,1,MPI_INT,rowners+1,1,MPI_INT,comm);CHKERRQ(ierr); rowners[0] = 0; for (i=2; i<=size; i++) rowners[i] += rowners[i-1]; for (i=0; i<=size; i++) browners[i] = rowners[i]*bs; rstart = rowners[rank]; rend = rowners[rank+1]; /* distribute row lengths to all processors */ ierr = PetscMalloc((rend-rstart)*bs*sizeof(int),&locrowlens);CHKERRQ(ierr); if (!rank) { ierr = PetscMalloc((M+extra_rows)*sizeof(int),&rowlengths);CHKERRQ(ierr); ierr = PetscBinaryRead(fd,rowlengths,M,PETSC_INT);CHKERRQ(ierr); for (i=0; i= rend) masked2[odcount++] = tmp; else masked1[dcount++] = tmp; } } rowcount++; } dlens[i] = dcount; odlens[i] = odcount; /* zero out the mask elements we set */ for (j=0; jtag,comm);CHKERRQ(ierr); } /* the last proc */ if (size != 1){ nz = procsnz[i] - extra_rows; vals = buf; ierr = PetscBinaryRead(fd,vals,nz,PETSC_SCALAR);CHKERRQ(ierr); for (i=0; itag,comm);CHKERRQ(ierr); } ierr = PetscFree(procsnz);CHKERRQ(ierr); } else { /* receive numeric values */ ierr = PetscMalloc(nz*sizeof(PetscScalar),&buf);CHKERRQ(ierr); /* receive message of values*/ vals = buf; mycols = ibuf; ierr = MPI_Recv(vals,nz,MPIU_SCALAR,0,A->tag,comm,&status);CHKERRQ(ierr); ierr = MPI_Get_count(&status,MPIU_SCALAR,&maxnz);CHKERRQ(ierr); if (maxnz != nz) SETERRQ(PETSC_ERR_FILE_UNEXPECTED,"something is wrong with file"); /* insert into matrix */ jj = rstart*bs; for (i=0; idata; baij->ht_fact = fact; PetscFunctionReturn(0); } #undef __FUNCT__ #define __FUNCT__ "MatMPIBAIJGetSeqBAIJ" int MatMPIBAIJGetSeqBAIJ(Mat A,Mat *Ad,Mat *Ao,int **colmap) { Mat_MPIBAIJ *a = (Mat_MPIBAIJ *)A->data; PetscFunctionBegin; *Ad = a->A; *Ao = a->B; *colmap = a->garray; PetscFunctionReturn(0); }