PetscErrorCode MatPtAPSymbolic_SeqAIJ_SeqAIJ_SparseAxpy(Mat A,Mat P,PetscReal fill,Mat *C) { PetscErrorCode ierr; PetscFreeSpaceList free_space=NULL,current_space=NULL; Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*p = (Mat_SeqAIJ*)P->data,*c; PetscInt *pti,*ptj,*ptJ,*ai=a->i,*aj=a->j,*ajj,*pi=p->i,*pj=p->j,*pjj; PetscInt *ci,*cj,*ptadenserow,*ptasparserow,*ptaj,nspacedouble=0; PetscInt an=A->cmap->N,am=A->rmap->N,pn=P->cmap->N,pm=P->rmap->N; PetscInt i,j,k,ptnzi,arow,anzj,ptanzi,prow,pnzj,cnzi,nlnk,*lnk; MatScalar *ca; PetscBT lnkbt; PetscReal afill; PetscFunctionBegin; /* Get ij structure of P^T */ ierr = MatGetSymbolicTranspose_SeqAIJ(P,&pti,&ptj);CHKERRQ(ierr); ptJ = ptj; /* Allocate ci array, arrays for fill computation and */ /* free space for accumulating nonzero column info */ ierr = PetscMalloc1(pn+1,&ci);CHKERRQ(ierr); ci[0] = 0; ierr = PetscCalloc1(2*an+1,&ptadenserow);CHKERRQ(ierr); ptasparserow = ptadenserow + an; /* create and initialize a linked list */ nlnk = pn+1; ierr = PetscLLCreate(pn,pn,nlnk,lnk,lnkbt);CHKERRQ(ierr); /* Set initial free space to be fill*(nnz(A)+ nnz(P)) */ ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ai[am],pi[pm])),&free_space);CHKERRQ(ierr); current_space = free_space; /* Determine symbolic info for each row of C: */ for (i=0; i<pn; i++) { ptnzi = pti[i+1] - pti[i]; ptanzi = 0; /* Determine symbolic row of PtA: */ for (j=0; j<ptnzi; j++) { arow = *ptJ++; anzj = ai[arow+1] - ai[arow]; ajj = aj + ai[arow]; for (k=0; k<anzj; k++) { if (!ptadenserow[ajj[k]]) { ptadenserow[ajj[k]] = -1; ptasparserow[ptanzi++] = ajj[k]; } } } /* Using symbolic info for row of PtA, determine symbolic info for row of C: */ ptaj = ptasparserow; cnzi = 0; for (j=0; j<ptanzi; j++) { prow = *ptaj++; pnzj = pi[prow+1] - pi[prow]; pjj = pj + pi[prow]; /* add non-zero cols of P into the sorted linked list lnk */ ierr = PetscLLAddSorted(pnzj,pjj,pn,nlnk,lnk,lnkbt);CHKERRQ(ierr); cnzi += nlnk; } /* If free space is not available, make more free space */ /* Double the amount of total space in the list */ if (current_space->local_remaining<cnzi) { ierr = PetscFreeSpaceGet(PetscIntSumTruncate(cnzi,current_space->total_array_size),¤t_space);CHKERRQ(ierr); nspacedouble++; } /* Copy data into free space, and zero out denserows */ ierr = PetscLLClean(pn,pn,cnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); current_space->array += cnzi; current_space->local_used += cnzi; current_space->local_remaining -= cnzi; for (j=0; j<ptanzi; j++) ptadenserow[ptasparserow[j]] = 0; /* Aside: Perhaps we should save the pta info for the numerical factorization. */ /* For now, we will recompute what is needed. */ ci[i+1] = ci[i] + cnzi; } /* nnz is now stored in ci[ptm], column indices are in the list of free space */ /* Allocate space for cj, initialize cj, and */ /* destroy list of free space and other temporary array(s) */ ierr = PetscMalloc1(ci[pn]+1,&cj);CHKERRQ(ierr); ierr = PetscFreeSpaceContiguous(&free_space,cj);CHKERRQ(ierr); ierr = PetscFree(ptadenserow);CHKERRQ(ierr); ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); ierr = PetscCalloc1(ci[pn]+1,&ca);CHKERRQ(ierr); /* put together the new matrix */ ierr = MatCreateSeqAIJWithArrays(PetscObjectComm((PetscObject)A),pn,pn,ci,cj,ca,C);CHKERRQ(ierr); ierr = MatSetBlockSizes(*C,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ /* Since these are PETSc arrays, change flags to free them as necessary. */ c = (Mat_SeqAIJ*)((*C)->data); c->free_a = PETSC_TRUE; c->free_ij = PETSC_TRUE; c->nonew = 0; (*C)->ops->ptapnumeric = MatPtAPNumeric_SeqAIJ_SeqAIJ_SparseAxpy; /* set MatInfo */ afill = (PetscReal)ci[pn]/(ai[am]+pi[pm] + 1.e-5); if (afill < 1.0) afill = 1.0; c->maxnz = ci[pn]; c->nz = ci[pn]; (*C)->info.mallocs = nspacedouble; (*C)->info.fill_ratio_given = fill; (*C)->info.fill_ratio_needed = afill; /* Clean up. */ ierr = MatRestoreSymbolicTranspose_SeqAIJ(P,&pti,&ptj);CHKERRQ(ierr); #if defined(PETSC_USE_INFO) if (ci[pn] != 0) { ierr = PetscInfo3((*C),"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); ierr = PetscInfo1((*C),"Use MatPtAP(A,P,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); } else { ierr = PetscInfo((*C),"Empty matrix product\n");CHKERRQ(ierr); } #endif PetscFunctionReturn(0); }
PetscErrorCode MatLUFactorSymbolic_SeqBAIJ_inplace(Mat B,Mat A,IS isrow,IS iscol,const MatFactorInfo *info) { Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b; PetscInt n =a->mbs,bs = A->rmap->bs,bs2=a->bs2; PetscBool row_identity,col_identity,both_identity; IS isicol; PetscErrorCode ierr; const PetscInt *r,*ic; PetscInt i,*ai=a->i,*aj=a->j; PetscInt *bi,*bj,*ajtmp; PetscInt *bdiag,row,nnz,nzi,reallocs=0,nzbd,*im; PetscReal f; PetscInt nlnk,*lnk,k,**bi_ptr; PetscFreeSpaceList free_space=NULL,current_space=NULL; PetscBT lnkbt; PetscBool missing; PetscFunctionBegin; if (A->rmap->N != A->cmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"matrix must be square"); ierr = MatMissingDiagonal(A,&missing,&i);CHKERRQ(ierr); if (missing) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Matrix is missing diagonal entry %D",i); ierr = ISInvertPermutation(iscol,PETSC_DECIDE,&isicol);CHKERRQ(ierr); ierr = ISGetIndices(isrow,&r);CHKERRQ(ierr); ierr = ISGetIndices(isicol,&ic);CHKERRQ(ierr); /* get new row and diagonal pointers, must be allocated separately because they will be given to the Mat_SeqAIJ and freed separately */ ierr = PetscMalloc1(n+1,&bi);CHKERRQ(ierr); ierr = PetscMalloc1(n+1,&bdiag);CHKERRQ(ierr); bi[0] = bdiag[0] = 0; /* linked list for storing column indices of the active row */ nlnk = n + 1; ierr = PetscLLCreate(n,n,nlnk,lnk,lnkbt);CHKERRQ(ierr); ierr = PetscMalloc2(n+1,&bi_ptr,n+1,&im);CHKERRQ(ierr); /* initial FreeSpace size is f*(ai[n]+1) */ f = info->fill; ierr = PetscFreeSpaceGet(PetscRealIntMultTruncate(f,ai[n]+1),&free_space);CHKERRQ(ierr); current_space = free_space; for (i=0; i<n; i++) { /* copy previous fill into linked list */ nzi = 0; nnz = ai[r[i]+1] - ai[r[i]]; ajtmp = aj + ai[r[i]]; ierr = PetscLLAddPerm(nnz,ajtmp,ic,n,nlnk,lnk,lnkbt);CHKERRQ(ierr); nzi += nlnk; /* add pivot rows into linked list */ row = lnk[n]; while (row < i) { nzbd = bdiag[row] - bi[row] + 1; /* num of entries in the row with column index <= row */ ajtmp = bi_ptr[row] + nzbd; /* points to the entry next to the diagonal */ ierr = PetscLLAddSortedLU(ajtmp,row,nlnk,lnk,lnkbt,i,nzbd,im);CHKERRQ(ierr); nzi += nlnk; row = lnk[row]; } bi[i+1] = bi[i] + nzi; im[i] = nzi; /* mark bdiag */ nzbd = 0; nnz = nzi; k = lnk[n]; while (nnz-- && k < i) { nzbd++; k = lnk[k]; } bdiag[i] = bi[i] + nzbd; /* if free space is not available, make more free space */ if (current_space->local_remaining<nzi) { nnz = PetscIntMultTruncate(n - i,nzi); /* estimated and max additional space needed */ ierr = PetscFreeSpaceGet(nnz,¤t_space);CHKERRQ(ierr); reallocs++; } /* copy data into free space, then initialize lnk */ ierr = PetscLLClean(n,n,nzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); bi_ptr[i] = current_space->array; current_space->array += nzi; current_space->local_used += nzi; current_space->local_remaining -= nzi; } #if defined(PETSC_USE_INFO) if (ai[n] != 0) { PetscReal af = ((PetscReal)bi[n])/((PetscReal)ai[n]); ierr = PetscInfo3(A,"Reallocs %D Fill ratio:given %g needed %g\n",reallocs,(double)f,(double)af);CHKERRQ(ierr); ierr = PetscInfo1(A,"Run with -pc_factor_fill %g or use \n",(double)af);CHKERRQ(ierr); ierr = PetscInfo1(A,"PCFactorSetFill(pc,%g);\n",(double)af);CHKERRQ(ierr); ierr = PetscInfo(A,"for best performance.\n");CHKERRQ(ierr); } else { ierr = PetscInfo(A,"Empty matrix\n");CHKERRQ(ierr); } #endif ierr = ISRestoreIndices(isrow,&r);CHKERRQ(ierr); ierr = ISRestoreIndices(isicol,&ic);CHKERRQ(ierr); /* destroy list of free space and other temporary array(s) */ ierr = PetscMalloc1(bi[n]+1,&bj);CHKERRQ(ierr); ierr = PetscFreeSpaceContiguous(&free_space,bj);CHKERRQ(ierr); ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); ierr = PetscFree2(bi_ptr,im);CHKERRQ(ierr); /* put together the new matrix */ ierr = MatSeqBAIJSetPreallocation_SeqBAIJ(B,bs,MAT_SKIP_ALLOCATION,NULL);CHKERRQ(ierr); ierr = PetscLogObjectParent((PetscObject)B,(PetscObject)isicol);CHKERRQ(ierr); b = (Mat_SeqBAIJ*)(B)->data; b->free_a = PETSC_TRUE; b->free_ij = PETSC_TRUE; b->singlemalloc = PETSC_FALSE; ierr = PetscMalloc1((bi[n]+1)*bs2,&b->a);CHKERRQ(ierr); b->j = bj; b->i = bi; b->diag = bdiag; b->free_diag = PETSC_TRUE; b->ilen = 0; b->imax = 0; b->row = isrow; b->col = iscol; b->pivotinblocks = (info->pivotinblocks) ? PETSC_TRUE : PETSC_FALSE; ierr = PetscObjectReference((PetscObject)isrow);CHKERRQ(ierr); ierr = PetscObjectReference((PetscObject)iscol);CHKERRQ(ierr); b->icol = isicol; ierr = PetscMalloc1(bs*n+bs,&b->solve_work);CHKERRQ(ierr); ierr = PetscLogObjectMemory((PetscObject)B,(bi[n]-n)*(sizeof(PetscInt)+sizeof(PetscScalar)*bs2));CHKERRQ(ierr); b->maxnz = b->nz = bi[n]; (B)->factortype = MAT_FACTOR_LU; (B)->info.factor_mallocs = reallocs; (B)->info.fill_ratio_given = f; if (ai[n] != 0) { (B)->info.fill_ratio_needed = ((PetscReal)bi[n])/((PetscReal)ai[n]); } else { (B)->info.fill_ratio_needed = 0.0; } ierr = ISIdentity(isrow,&row_identity);CHKERRQ(ierr); ierr = ISIdentity(iscol,&col_identity);CHKERRQ(ierr); both_identity = (PetscBool) (row_identity && col_identity); ierr = MatSeqBAIJSetNumericFactorization_inplace(B,both_identity);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode MatPtAPSymbolic_SeqAIJ_SeqAIJ_SparseAxpy2(Mat A,Mat P,PetscReal fill,Mat *C) { PetscErrorCode ierr; PetscFreeSpaceList free_space=PETSC_NULL,current_space=PETSC_NULL; Mat_SeqAIJ *a = (Mat_SeqAIJ*)A->data,*p = (Mat_SeqAIJ*)P->data,*c; PetscInt *pti,*ptj,*ptJ,*ai=a->i,*aj=a->j,*ajj,*pi=p->i,*pj=p->j,*pjj; PetscInt *ci,*cj,*ptadenserow,*ptasparserow,*ptaj,nspacedouble=0; PetscInt an=A->cmap->N,am=A->rmap->N,pn=P->cmap->N; PetscInt i,j,k,ptnzi,arow,anzj,ptanzi,prow,pnzj,cnzi,nlnk,*lnk; MatScalar *ca; PetscBT lnkbt; PetscFunctionBegin; /* Get ij structure of P^T */ ierr = MatGetSymbolicTranspose_SeqAIJ(P,&pti,&ptj);CHKERRQ(ierr); ptJ=ptj; /* Allocate ci array, arrays for fill computation and */ /* free space for accumulating nonzero column info */ ierr = PetscMalloc((pn+1)*sizeof(PetscInt),&ci);CHKERRQ(ierr); ci[0] = 0; ierr = PetscMalloc((2*an+1)*sizeof(PetscInt),&ptadenserow);CHKERRQ(ierr); ierr = PetscMemzero(ptadenserow,(2*an+1)*sizeof(PetscInt));CHKERRQ(ierr); ptasparserow = ptadenserow + an; /* create and initialize a linked list */ nlnk = pn+1; ierr = PetscLLCreate(pn,pn,nlnk,lnk,lnkbt);CHKERRQ(ierr); /* Set initial free space to be fill*nnz(A). */ /* This should be reasonable if sparsity of PtAP is similar to that of A. */ ierr = PetscFreeSpaceGet((PetscInt)(fill*ai[am]),&free_space); current_space = free_space; /* Determine symbolic info for each row of C: */ for (i=0;i<pn;i++) { ptnzi = pti[i+1] - pti[i]; ptanzi = 0; /* Determine symbolic row of PtA: */ for (j=0;j<ptnzi;j++) { arow = *ptJ++; anzj = ai[arow+1] - ai[arow]; ajj = aj + ai[arow]; for (k=0;k<anzj;k++) { if (!ptadenserow[ajj[k]]) { ptadenserow[ajj[k]] = -1; ptasparserow[ptanzi++] = ajj[k]; } } } /* Using symbolic info for row of PtA, determine symbolic info for row of C: */ ptaj = ptasparserow; cnzi = 0; for (j=0;j<ptanzi;j++) { prow = *ptaj++; pnzj = pi[prow+1] - pi[prow]; pjj = pj + pi[prow]; /* add non-zero cols of P into the sorted linked list lnk */ ierr = PetscLLAddSorted(pnzj,pjj,pn,nlnk,lnk,lnkbt);CHKERRQ(ierr); cnzi += nlnk; } /* If free space is not available, make more free space */ /* Double the amount of total space in the list */ if (current_space->local_remaining<cnzi) { ierr = PetscFreeSpaceGet(cnzi+current_space->total_array_size,¤t_space);CHKERRQ(ierr); nspacedouble++; } /* Copy data into free space, and zero out denserows */ ierr = PetscLLClean(pn,pn,cnzi,lnk,current_space->array,lnkbt);CHKERRQ(ierr); current_space->array += cnzi; current_space->local_used += cnzi; current_space->local_remaining -= cnzi; for (j=0;j<ptanzi;j++) { ptadenserow[ptasparserow[j]] = 0; } /* Aside: Perhaps we should save the pta info for the numerical factorization. */ /* For now, we will recompute what is needed. */ ci[i+1] = ci[i] + cnzi; } /* nnz is now stored in ci[ptm], column indices are in the list of free space */ /* Allocate space for cj, initialize cj, and */ /* destroy list of free space and other temporary array(s) */ ierr = PetscMalloc((ci[pn]+1)*sizeof(PetscInt),&cj);CHKERRQ(ierr); ierr = PetscFreeSpaceContiguous(&free_space,cj);CHKERRQ(ierr); ierr = PetscFree(ptadenserow);CHKERRQ(ierr); ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); /* Allocate space for ca */ ierr = PetscMalloc((ci[pn]+1)*sizeof(MatScalar),&ca);CHKERRQ(ierr); ierr = PetscMemzero(ca,(ci[pn]+1)*sizeof(MatScalar));CHKERRQ(ierr); /* put together the new matrix */ ierr = MatCreateSeqAIJWithArrays(((PetscObject)A)->comm,pn,pn,ci,cj,ca,C);CHKERRQ(ierr); (*C)->rmap->bs = P->cmap->bs; (*C)->cmap->bs = P->cmap->bs; PetscPrintf(PETSC_COMM_SELF,"************%s C.bs=%d,%d\n",__FUNCT__,(*C)->rmap->bs,(*C)->cmap->bs); /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ /* Since these are PETSc arrays, change flags to free them as necessary. */ c = (Mat_SeqAIJ *)((*C)->data); c->free_a = PETSC_TRUE; c->free_ij = PETSC_TRUE; c->nonew = 0; A->ops->ptapnumeric = MatPtAPNumeric_SeqAIJ_SeqAIJ_SparseAxpy2; /* should use *C->ops until PtAP insterface is updated to double dispatch as MatMatMult() */ /* Clean up. */ ierr = MatRestoreSymbolicTranspose_SeqAIJ(P,&pti,&ptj);CHKERRQ(ierr); #if defined(PETSC_USE_INFO) if (ci[pn] != 0) { PetscReal afill = ((PetscReal)ci[pn])/ai[am]; if (afill < 1.0) afill = 1.0; ierr = PetscInfo3((*C),"Reallocs %D; Fill ratio: given %G needed %G.\n",nspacedouble,fill,afill);CHKERRQ(ierr); ierr = PetscInfo1((*C),"Use MatPtAP(A,P,MatReuse,%G,&C) for best performance.\n",afill);CHKERRQ(ierr); } else { ierr = PetscInfo((*C),"Empty matrix product\n");CHKERRQ(ierr); } #endif PetscFunctionReturn(0); }
PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) { PetscErrorCode ierr; Mat Cmpi; Mat_PtAPMPI *ptap; PetscFreeSpaceList free_space=NULL,current_space=NULL; Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; Mat_SeqAIJ *p_loc,*p_oth; PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pdti,*pdtj,*poti,*potj,*ptJ; PetscInt *adi=ad->i,*aj,*aoi=ao->i,nnz; PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; PetscInt am=A->rmap->n,pN=P->cmap->N,pm=P->rmap->n,pn=P->cmap->n; PetscBT lnkbt; MPI_Comm comm; PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0; PetscInt **buf_rj,**buf_ri,**buf_ri_k; PetscInt len,proc,*dnz,*onz,*owners; PetscInt nzi,*pti,*ptj; PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; MPI_Request *swaits,*rwaits; MPI_Status *sstatus,rstatus; Mat_Merge_SeqsToMPI *merge; PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,pon,nspacedouble=0,j,ap_rmax=0; PetscReal afill=1.0,afill_tmp; PetscInt rmax; #if defined(PTAP_PROFILE) PetscLogDouble t0,t1,t2,t3,t4; #endif PetscFunctionBegin; ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); #if defined(PTAP_PROFILE) ierr = PetscTime(&t0);CHKERRQ(ierr); #endif /* check if matrix local sizes are compatible */ if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend) { SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Arow (%D, %D) != Prow (%D,%D)",A->rmap->rstart,A->rmap->rend,P->rmap->rstart,P->rmap->rend); } if (A->cmap->rstart != P->rmap->rstart || A->cmap->rend != P->rmap->rend) { SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Acol (%D, %D) != Prow (%D,%D)",A->cmap->rstart,A->cmap->rend,P->rmap->rstart,P->rmap->rend); } ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); /* create struct Mat_PtAPMPI and attached it to C later */ ierr = PetscNew(&ptap);CHKERRQ(ierr); ierr = PetscNew(&merge);CHKERRQ(ierr); ptap->merge = merge; ptap->reuse = MAT_INITIAL_MATRIX; /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); /* get P_loc by taking all local rows of P */ ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; pi_loc = p_loc->i; pj_loc = p_loc->j; pi_oth = p_oth->i; pj_oth = p_oth->j; #if defined(PTAP_PROFILE) ierr = PetscTime(&t1);CHKERRQ(ierr); #endif /* first, compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth */ /*-------------------------------------------------------------------*/ ierr = PetscMalloc1((am+1),&api);CHKERRQ(ierr); api[0] = 0; /* create and initialize a linked list */ ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) -OOM for ex56, np=8k on Intrepid! */ ierr = PetscFreeSpaceGet((PetscInt)(fill*(adi[am]+aoi[am]+pi_loc[pm])),&free_space);CHKERRQ(ierr); current_space = free_space; for (i=0; i<am; i++) { /* diagonal portion of A */ nzi = adi[i+1] - adi[i]; aj = ad->j + adi[i]; for (j=0; j<nzi; j++) { row = aj[j]; pnz = pi_loc[row+1] - pi_loc[row]; Jptr = pj_loc + pi_loc[row]; /* add non-zero cols of P into the sorted linked list lnk */ ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); } /* off-diagonal portion of A */ nzi = aoi[i+1] - aoi[i]; aj = ao->j + aoi[i]; for (j=0; j<nzi; j++) { row = aj[j]; pnz = pi_oth[row+1] - pi_oth[row]; Jptr = pj_oth + pi_oth[row]; ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); } apnz = lnk[0]; api[i+1] = api[i] + apnz; if (ap_rmax < apnz) ap_rmax = apnz; /* if free space is not available, double the total space in the list */ if (current_space->local_remaining<apnz) { ierr = PetscFreeSpaceGet(apnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); nspacedouble++; } /* Copy data into free space, then initialize lnk */ ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); current_space->array += apnz; current_space->local_used += apnz; current_space->local_remaining -= apnz; } /* Allocate space for apj, initialize apj, and */ /* destroy list of free space and other temporary array(s) */ ierr = PetscMalloc1((api[am]+1),&apj);CHKERRQ(ierr); ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); afill_tmp = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1); if (afill_tmp > afill) afill = afill_tmp; #if defined(PTAP_PROFILE) ierr = PetscTime(&t2);CHKERRQ(ierr); #endif /* determine symbolic Co=(p->B)^T*AP - send to others */ /*----------------------------------------------------*/ ierr = MatGetSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);CHKERRQ(ierr); /* then, compute symbolic Co = (p->B)^T*AP */ pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors >= (num of nonzero rows of C_seq) - pn */ ierr = PetscMalloc1((pon+1),&coi);CHKERRQ(ierr); coi[0] = 0; /* set initial free space to be fill*(nnz(p->B) + nnz(AP)) */ nnz = fill*(poti[pon] + api[am]); ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); current_space = free_space; for (i=0; i<pon; i++) { pnz = poti[i+1] - poti[i]; ptJ = potj + poti[i]; for (j=0; j<pnz; j++) { row = ptJ[j]; /* row of AP == col of Pot */ apnz = api[row+1] - api[row]; Jptr = apj + api[row]; /* add non-zero cols of AP into the sorted linked list lnk */ ierr = PetscLLCondensedAddSorted(apnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); } nnz = lnk[0]; /* If free space is not available, double the total space in the list */ if (current_space->local_remaining<nnz) { ierr = PetscFreeSpaceGet(nnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); nspacedouble++; } /* Copy data into free space, and zero out denserows */ ierr = PetscLLCondensedClean(pN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); current_space->array += nnz; current_space->local_used += nnz; current_space->local_remaining -= nnz; coi[i+1] = coi[i] + nnz; } ierr = PetscMalloc1((coi[pon]+1),&coj);CHKERRQ(ierr); ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); afill_tmp = (PetscReal)coi[pon]/(poti[pon] + api[am]+1); if (afill_tmp > afill) afill = afill_tmp; ierr = MatRestoreSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);CHKERRQ(ierr); /* send j-array (coj) of Co to other processors */ /*----------------------------------------------*/ /* determine row ownership */ ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); merge->rowmap->n = pn; merge->rowmap->bs = 1; ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); owners = merge->rowmap->range; /* determine the number of messages to send, their lengths */ ierr = PetscMalloc2(size,&len_si,size,&sstatus);CHKERRQ(ierr); ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); ierr = PetscCalloc1(size,&merge->len_s);CHKERRQ(ierr); len_s = merge->len_s; merge->nsend = 0; ierr = PetscMalloc1((size+2),&owners_co);CHKERRQ(ierr); proc = 0; for (i=0; i<pon; i++) { while (prmap[i] >= owners[proc+1]) proc++; len_si[proc]++; /* num of rows in Co to be sent to [proc] */ len_s[proc] += coi[i+1] - coi[i]; } len = 0; /* max length of buf_si[] */ owners_co[0] = 0; for (proc=0; proc<size; proc++) { owners_co[proc+1] = owners_co[proc] + len_si[proc]; if (len_si[proc]) { merge->nsend++; len_si[proc] = 2*(len_si[proc] + 1); len += len_si[proc]; } } /* determine the number and length of messages to receive for coi and coj */ ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); /* post the Irecv and Isend of coj */ ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); ierr = PetscMalloc1((merge->nsend+1),&swaits);CHKERRQ(ierr); for (proc=0, k=0; proc<size; proc++) { if (!len_s[proc]) continue; i = owners_co[proc]; ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); k++; } /* receives and sends of coj are complete */ for (i=0; i<merge->nrecv; i++) { ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); } ierr = PetscFree(rwaits);CHKERRQ(ierr); if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} /* send and recv coi */ /*-------------------*/ ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); ierr = PetscMalloc1((len+1),&buf_s);CHKERRQ(ierr); buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ for (proc=0,k=0; proc<size; proc++) { if (!len_s[proc]) continue; /* form outgoing message for i-structure: buf_si[0]: nrows to be sent [1:nrows]: row index (global) [nrows+1:2*nrows+1]: i-structure index */ /*-------------------------------------------*/ nrows = len_si[proc]/2 - 1; buf_si_i = buf_si + nrows+1; buf_si[0] = nrows; buf_si_i[0] = 0; nrows = 0; for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { nzi = coi[i+1] - coi[i]; buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ nrows++; } ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); k++; buf_si += len_si[proc]; } i = merge->nrecv; while (i--) { ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); } ierr = PetscFree(rwaits);CHKERRQ(ierr); if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} ierr = PetscFree2(len_si,sstatus);CHKERRQ(ierr); ierr = PetscFree(len_ri);CHKERRQ(ierr); ierr = PetscFree(swaits);CHKERRQ(ierr); ierr = PetscFree(buf_s);CHKERRQ(ierr); #if defined(PTAP_PROFILE) ierr = PetscTime(&t3);CHKERRQ(ierr); #endif /* compute the local portion of C (mpi mat) */ /*------------------------------------------*/ ierr = MatGetSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);CHKERRQ(ierr); /* allocate pti array and free space for accumulating nonzero column info */ ierr = PetscMalloc1((pn+1),&pti);CHKERRQ(ierr); pti[0] = 0; /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ nnz = fill*(pi_loc[pm] + api[am]); ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); current_space = free_space; ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); for (k=0; k<merge->nrecv; k++) { buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ nrows = *buf_ri_k[k]; nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ } ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); rmax = 0; for (i=0; i<pn; i++) { /* add pdt[i,:]*AP into lnk */ pnz = pdti[i+1] - pdti[i]; ptJ = pdtj + pdti[i]; for (j=0; j<pnz; j++) { row = ptJ[j]; /* row of AP == col of Pt */ apnz = api[row+1] - api[row]; Jptr = apj + api[row]; /* add non-zero cols of AP into the sorted linked list lnk */ ierr = PetscLLCondensedAddSorted(apnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); } /* add received col data into lnk */ for (k=0; k<merge->nrecv; k++) { /* k-th received message */ if (i == *nextrow[k]) { /* i-th row */ nzi = *(nextci[k]+1) - *nextci[k]; Jptr = buf_rj[k] + *nextci[k]; ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); nextrow[k]++; nextci[k]++; } } nnz = lnk[0]; /* if free space is not available, make more free space */ if (current_space->local_remaining<nnz) { ierr = PetscFreeSpaceGet(nnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); nspacedouble++; } /* copy data into free space, then initialize lnk */ ierr = PetscLLCondensedClean(pN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); current_space->array += nnz; current_space->local_used += nnz; current_space->local_remaining -= nnz; pti[i+1] = pti[i] + nnz; if (nnz > rmax) rmax = nnz; } ierr = MatRestoreSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);CHKERRQ(ierr); ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); ierr = PetscMalloc1((pti[pn]+1),&ptj);CHKERRQ(ierr); ierr = PetscFreeSpaceContiguous(&free_space,ptj);CHKERRQ(ierr); afill_tmp = (PetscReal)pti[pn]/(pi_loc[pm] + api[am]+1); if (afill_tmp > afill) afill = afill_tmp; ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); /* create symbolic parallel matrix Cmpi */ /*--------------------------------------*/ ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); ierr = MatSetBlockSizes(Cmpi,P->cmap->bs,P->cmap->bs);CHKERRQ(ierr); ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); merge->bi = pti; /* Cseq->i */ merge->bj = ptj; /* Cseq->j */ merge->coi = coi; /* Co->i */ merge->coj = coj; /* Co->j */ merge->buf_ri = buf_ri; merge->buf_rj = buf_rj; merge->owners_co = owners_co; merge->destroy = Cmpi->ops->destroy; merge->duplicate = Cmpi->ops->duplicate; /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ Cmpi->assembled = PETSC_FALSE; Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; /* attach the supporting struct to Cmpi for reuse */ c = (Mat_MPIAIJ*)Cmpi->data; c->ptap = ptap; ptap->api = api; ptap->apj = apj; ptap->rmax = ap_rmax; *C = Cmpi; /* flag 'scalable' determines which implementations to be used: 0: do dense axpy in MatPtAPNumeric() - fast, but requires storage of a nonscalable dense array apa; 1: do sparse axpy in MatPtAPNumeric() - might slow, uses a sparse array apa */ /* set default scalable */ ptap->scalable = PETSC_TRUE; ierr = PetscOptionsGetBool(((PetscObject)Cmpi)->prefix,"-matptap_scalable",&ptap->scalable,NULL);CHKERRQ(ierr); if (!ptap->scalable) { /* Do dense axpy */ ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); } else { ierr = PetscCalloc1(ap_rmax+1,&ptap->apa);CHKERRQ(ierr); } #if defined(PTAP_PROFILE) ierr = PetscTime(&t4);CHKERRQ(ierr); if (rank==1) PetscPrintf(MPI_COMM_SELF," [%d] PtAPSymbolic %g/P + %g/AP + %g/comm + %g/PtAP = %g\n",rank,t1-t0,t2-t1,t3-t2,t4-t3,t4-t0);CHKERRQ(ierr); #endif #if defined(PETSC_USE_INFO) if (pti[pn] != 0) { ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %G needed %G.\n",nspacedouble,fill,afill);CHKERRQ(ierr); ierr = PetscInfo1(Cmpi,"Use MatPtAP(A,P,MatReuse,%G,&C) for best performance.\n",afill);CHKERRQ(ierr); } else { ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); } #endif PetscFunctionReturn(0); }
PetscErrorCode MatApplyPAPt_Symbolic_SeqAIJ_SeqAIJ(Mat A,Mat P,Mat *C) { /* Note: This code is virtually identical to that of MatApplyPtAP_SeqAIJ_Symbolic */ /* and MatMatMult_SeqAIJ_SeqAIJ_Symbolic. Perhaps they could be merged nicely. */ PetscErrorCode ierr; PetscFreeSpaceList free_space=PETSC_NULL,current_space=PETSC_NULL; Mat_SeqAIJ *a=(Mat_SeqAIJ*)A->data,*p=(Mat_SeqAIJ*)P->data,*c; PetscInt *ai=a->i,*aj=a->j,*ajj,*pi=p->i,*pj=p->j,*pti,*ptj,*ptjj; PetscInt *ci,*cj,*paj,*padenserow,*pasparserow,*denserow,*sparserow; PetscInt an=A->cmap->N,am=A->rmap->N,pn=P->cmap->N,pm=P->rmap->N; PetscInt i,j,k,pnzi,arow,anzj,panzi,ptrow,ptnzj,cnzi; MatScalar *ca; PetscFunctionBegin; /* some error checking which could be moved into interface layer */ if (pn!=am) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix dimensions are incompatible, %D != %D",pn,am); if (am!=an) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrix 'A' must be square, %D != %D",am, an); /* Set up timers */ ierr = PetscLogEventBegin(MAT_Applypapt_symbolic,A,P,0,0);CHKERRQ(ierr); /* Create ij structure of P^T */ ierr = MatGetSymbolicTranspose_SeqAIJ(P,&pti,&ptj);CHKERRQ(ierr); /* Allocate ci array, arrays for fill computation and */ /* free space for accumulating nonzero column info */ ierr = PetscMalloc(((pm+1)*1)*sizeof(PetscInt),&ci);CHKERRQ(ierr); ci[0] = 0; ierr = PetscMalloc4(an,PetscInt,&padenserow,an,PetscInt,&pasparserow,pm,PetscInt,&denserow,pm,PetscInt,&sparserow);CHKERRQ(ierr); ierr = PetscMemzero(padenserow,an*sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscMemzero(pasparserow,an*sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscMemzero(denserow,pm*sizeof(PetscInt));CHKERRQ(ierr); ierr = PetscMemzero(sparserow,pm*sizeof(PetscInt));CHKERRQ(ierr); /* Set initial free space to be nnz(A) scaled by aspect ratio of Pt. */ /* This should be reasonable if sparsity of PAPt is similar to that of A. */ ierr = PetscFreeSpaceGet((ai[am]/pn)*pm,&free_space);CHKERRQ(ierr); current_space = free_space; /* Determine fill for each row of C: */ for (i=0;i<pm;i++) { pnzi = pi[i+1] - pi[i]; panzi = 0; /* Get symbolic sparse row of PA: */ for (j=0;j<pnzi;j++) { arow = *pj++; anzj = ai[arow+1] - ai[arow]; ajj = aj + ai[arow]; for (k=0;k<anzj;k++) { if (!padenserow[ajj[k]]) { padenserow[ajj[k]] = -1; pasparserow[panzi++] = ajj[k]; } } } /* Using symbolic row of PA, determine symbolic row of C: */ paj = pasparserow; cnzi = 0; for (j=0;j<panzi;j++) { ptrow = *paj++; ptnzj = pti[ptrow+1] - pti[ptrow]; ptjj = ptj + pti[ptrow]; for (k=0;k<ptnzj;k++) { if (!denserow[ptjj[k]]) { denserow[ptjj[k]] = -1; sparserow[cnzi++] = ptjj[k]; } } } /* sort sparse representation */ ierr = PetscSortInt(cnzi,sparserow);CHKERRQ(ierr); /* If free space is not available, make more free space */ /* Double the amount of total space in the list */ if (current_space->local_remaining<cnzi) { ierr = PetscFreeSpaceGet(cnzi+current_space->total_array_size,¤t_space);CHKERRQ(ierr); } /* Copy data into free space, and zero out dense row */ ierr = PetscMemcpy(current_space->array,sparserow,cnzi*sizeof(PetscInt));CHKERRQ(ierr); current_space->array += cnzi; current_space->local_used += cnzi; current_space->local_remaining -= cnzi; for (j=0;j<panzi;j++) { padenserow[pasparserow[j]] = 0; } for (j=0;j<cnzi;j++) { denserow[sparserow[j]] = 0; } ci[i+1] = ci[i] + cnzi; } /* column indices are in the list of free space */ /* Allocate space for cj, initialize cj, and */ /* destroy list of free space and other temporary array(s) */ ierr = PetscMalloc((ci[pm]+1)*sizeof(PetscInt),&cj);CHKERRQ(ierr); ierr = PetscFreeSpaceContiguous(&free_space,cj);CHKERRQ(ierr); ierr = PetscFree4(padenserow,pasparserow,denserow,sparserow);CHKERRQ(ierr); /* Allocate space for ca */ ierr = PetscMalloc((ci[pm]+1)*sizeof(MatScalar),&ca);CHKERRQ(ierr); ierr = PetscMemzero(ca,(ci[pm]+1)*sizeof(MatScalar));CHKERRQ(ierr); /* put together the new matrix */ ierr = MatCreateSeqAIJWithArrays(((PetscObject)A)->comm,pm,pm,ci,cj,ca,C);CHKERRQ(ierr); (*C)->rmap->bs = P->cmap->bs; (*C)->cmap->bs = P->cmap->bs; /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ /* Since these are PETSc arrays, change flags to free them as necessary. */ c = (Mat_SeqAIJ *)((*C)->data); c->free_a = PETSC_TRUE; c->free_ij = PETSC_TRUE; c->nonew = 0; /* Clean up. */ ierr = MatRestoreSymbolicTranspose_SeqAIJ(P,&pti,&ptj);CHKERRQ(ierr); ierr = PetscLogEventEnd(MAT_Applypapt_symbolic,A,P,0,0);CHKERRQ(ierr); PetscFunctionReturn(0); }