/*@C PCGAMGFilterGraph - filter (remove zero and possibly small values from the) graph and make it symmetric if requested Collective on Mat Input Parameter: + a_Gmat - the graph . vfilter - threshold paramter [0,1) - symm - make the result symmetric Level: developer Notes: This is called before graph coarsers are called. .seealso: PCGAMGSetThreshold() @*/ PetscErrorCode PCGAMGFilterGraph(Mat *a_Gmat,PetscReal vfilter,PetscBool symm) { PetscErrorCode ierr; PetscInt Istart,Iend,Ii,jj,ncols,nnz0,nnz1, NN, MM, nloc; PetscMPIInt rank; Mat Gmat = *a_Gmat, tGmat, matTrans; MPI_Comm comm; const PetscScalar *vals; const PetscInt *idx; PetscInt *d_nnz, *o_nnz; Vec diag; MatType mtype; PetscFunctionBegin; #if defined PETSC_GAMG_USE_LOG ierr = PetscLogEventBegin(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr); #endif /* scale Gmat for all values between -1 and 1 */ ierr = MatCreateVecs(Gmat, &diag, 0);CHKERRQ(ierr); ierr = MatGetDiagonal(Gmat, diag);CHKERRQ(ierr); ierr = VecReciprocal(diag);CHKERRQ(ierr); ierr = VecSqrtAbs(diag);CHKERRQ(ierr); ierr = MatDiagonalScale(Gmat, diag, diag);CHKERRQ(ierr); ierr = VecDestroy(&diag);CHKERRQ(ierr); if (vfilter < 0.0 && !symm) { /* Just use the provided matrix as the graph but make all values positive */ MatInfo info; PetscScalar *avals; PetscBool isaij,ismpiaij; ierr = PetscObjectBaseTypeCompare((PetscObject)Gmat,MATSEQAIJ,&isaij);CHKERRQ(ierr); ierr = PetscObjectBaseTypeCompare((PetscObject)Gmat,MATMPIAIJ,&ismpiaij);CHKERRQ(ierr); if (!isaij && !ismpiaij) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Require (MPI)AIJ matrix type"); if (isaij) { ierr = MatGetInfo(Gmat,MAT_LOCAL,&info);CHKERRQ(ierr); ierr = MatSeqAIJGetArray(Gmat,&avals);CHKERRQ(ierr); for (jj = 0; jj<info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]); ierr = MatSeqAIJRestoreArray(Gmat,&avals);CHKERRQ(ierr); } else { Mat_MPIAIJ *aij = (Mat_MPIAIJ*)Gmat->data; ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr); ierr = MatSeqAIJGetArray(aij->A,&avals);CHKERRQ(ierr); for (jj = 0; jj<info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]); ierr = MatSeqAIJRestoreArray(aij->A,&avals);CHKERRQ(ierr); ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr); ierr = MatSeqAIJGetArray(aij->B,&avals);CHKERRQ(ierr); for (jj = 0; jj<info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]); ierr = MatSeqAIJRestoreArray(aij->B,&avals);CHKERRQ(ierr); } #if defined PETSC_GAMG_USE_LOG ierr = PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr); #endif PetscFunctionReturn(0); } ierr = PetscObjectGetComm((PetscObject)Gmat,&comm);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); ierr = MatGetOwnershipRange(Gmat, &Istart, &Iend);CHKERRQ(ierr); nloc = Iend - Istart; ierr = MatGetSize(Gmat, &MM, &NN);CHKERRQ(ierr); if (symm) { ierr = MatTranspose(Gmat, MAT_INITIAL_MATRIX, &matTrans);CHKERRQ(ierr); } /* Determine upper bound on nonzeros needed in new filtered matrix */ ierr = PetscMalloc2(nloc, &d_nnz,nloc, &o_nnz);CHKERRQ(ierr); for (Ii = Istart, jj = 0; Ii < Iend; Ii++, jj++) { ierr = MatGetRow(Gmat,Ii,&ncols,NULL,NULL);CHKERRQ(ierr); d_nnz[jj] = ncols; o_nnz[jj] = ncols; ierr = MatRestoreRow(Gmat,Ii,&ncols,NULL,NULL);CHKERRQ(ierr); if (symm) { ierr = MatGetRow(matTrans,Ii,&ncols,NULL,NULL);CHKERRQ(ierr); d_nnz[jj] += ncols; o_nnz[jj] += ncols; ierr = MatRestoreRow(matTrans,Ii,&ncols,NULL,NULL);CHKERRQ(ierr); } if (d_nnz[jj] > nloc) d_nnz[jj] = nloc; if (o_nnz[jj] > (MM-nloc)) o_nnz[jj] = MM - nloc; } ierr = MatGetType(Gmat,&mtype);CHKERRQ(ierr); ierr = MatCreate(comm, &tGmat);CHKERRQ(ierr); ierr = MatSetSizes(tGmat,nloc,nloc,MM,MM);CHKERRQ(ierr); ierr = MatSetBlockSizes(tGmat, 1, 1);CHKERRQ(ierr); ierr = MatSetType(tGmat, mtype);CHKERRQ(ierr); ierr = MatSeqAIJSetPreallocation(tGmat,0,d_nnz);CHKERRQ(ierr); ierr = MatMPIAIJSetPreallocation(tGmat,0,d_nnz,0,o_nnz);CHKERRQ(ierr); ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr); if (symm) { ierr = MatDestroy(&matTrans);CHKERRQ(ierr); } else { /* all entries are generated locally so MatAssembly will be slightly faster for large process counts */ ierr = MatSetOption(tGmat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr); } for (Ii = Istart, nnz0 = nnz1 = 0; Ii < Iend; Ii++) { ierr = MatGetRow(Gmat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr); for (jj=0; jj<ncols; jj++,nnz0++) { PetscScalar sv = PetscAbs(PetscRealPart(vals[jj])); if (PetscRealPart(sv) > vfilter) { nnz1++; if (symm) { sv *= 0.5; ierr = MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValues(tGmat,1,&idx[jj],1,&Ii,&sv,ADD_VALUES);CHKERRQ(ierr); } else { ierr = MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);CHKERRQ(ierr); } } } ierr = MatRestoreRow(Gmat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr); } ierr = MatAssemblyBegin(tGmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(tGmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); #if defined PETSC_GAMG_USE_LOG ierr = PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr); #endif #if defined(PETSC_USE_INFO) { double t1 = (!nnz0) ? 1. : 100.*(double)nnz1/(double)nnz0, t2 = (!nloc) ? 1. : (double)nnz0/(double)nloc; ierr = PetscInfo4(*a_Gmat,"\t %g%% nnz after filtering, with threshold %g, %g nnz ave. (N=%D)\n",t1,vfilter,t2,MM);CHKERRQ(ierr); } #endif ierr = MatDestroy(&Gmat);CHKERRQ(ierr); *a_Gmat = tGmat; PetscFunctionReturn(0); }
PetscErrorCode PCGAMGFilterGraph(Mat *a_Gmat,const PetscReal vfilter,const PetscBool symm,const PetscInt verbose) { PetscErrorCode ierr; PetscInt Istart,Iend,Ii,jj,ncols,nnz0,nnz1, NN, MM, nloc; PetscMPIInt rank, size; Mat Gmat = *a_Gmat, tGmat, matTrans; MPI_Comm comm; const PetscScalar *vals; const PetscInt *idx; PetscInt *d_nnz, *o_nnz; Vec diag; PetscFunctionBegin; ierr = PetscObjectGetComm((PetscObject)Gmat,&comm);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); ierr = MatGetOwnershipRange(Gmat, &Istart, &Iend);CHKERRQ(ierr); nloc = Iend - Istart; ierr = MatGetSize(Gmat, &MM, &NN);CHKERRQ(ierr); #if defined PETSC_GAMG_USE_LOG ierr = PetscLogEventBegin(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr); #endif /* scale Gmat so filter works */ ierr = MatGetVecs(Gmat, &diag, 0);CHKERRQ(ierr); ierr = MatGetDiagonal(Gmat, diag);CHKERRQ(ierr); ierr = VecReciprocal(diag);CHKERRQ(ierr); ierr = VecSqrtAbs(diag);CHKERRQ(ierr); ierr = MatDiagonalScale(Gmat, diag, diag);CHKERRQ(ierr); ierr = VecDestroy(&diag);CHKERRQ(ierr); if (symm) { ierr = MatTranspose(Gmat, MAT_INITIAL_MATRIX, &matTrans);CHKERRQ(ierr); } /* filter - dup zeros out matrix */ ierr = PetscMalloc1(nloc, &d_nnz);CHKERRQ(ierr); ierr = PetscMalloc1(nloc, &o_nnz);CHKERRQ(ierr); for (Ii = Istart, jj = 0; Ii < Iend; Ii++, jj++) { ierr = MatGetRow(Gmat,Ii,&ncols,NULL,NULL);CHKERRQ(ierr); d_nnz[jj] = ncols; o_nnz[jj] = ncols; ierr = MatRestoreRow(Gmat,Ii,&ncols,NULL,NULL);CHKERRQ(ierr); if (symm) { ierr = MatGetRow(matTrans,Ii,&ncols,NULL,NULL);CHKERRQ(ierr); d_nnz[jj] += ncols; o_nnz[jj] += ncols; ierr = MatRestoreRow(matTrans,Ii,&ncols,NULL,NULL);CHKERRQ(ierr); } if (d_nnz[jj] > nloc) d_nnz[jj] = nloc; if (o_nnz[jj] > (MM-nloc)) o_nnz[jj] = MM - nloc; } ierr = MatCreateAIJ(comm, nloc, nloc, MM, MM, 0, d_nnz, 0, o_nnz, &tGmat);CHKERRQ(ierr); ierr = PetscFree(d_nnz);CHKERRQ(ierr); ierr = PetscFree(o_nnz);CHKERRQ(ierr); if (symm) { ierr = MatDestroy(&matTrans);CHKERRQ(ierr); } for (Ii = Istart, nnz0 = nnz1 = 0; Ii < Iend; Ii++) { ierr = MatGetRow(Gmat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr); for (jj=0; jj<ncols; jj++,nnz0++) { PetscScalar sv = PetscAbs(PetscRealPart(vals[jj])); if (PetscRealPart(sv) > vfilter) { nnz1++; if (symm) { sv *= 0.5; ierr = MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValues(tGmat,1,&idx[jj],1,&Ii,&sv,ADD_VALUES);CHKERRQ(ierr); } else { ierr = MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);CHKERRQ(ierr); } } } ierr = MatRestoreRow(Gmat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr); } ierr = MatAssemblyBegin(tGmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(tGmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); #if defined PETSC_GAMG_USE_LOG ierr = PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr); #endif if (verbose) { if (verbose == 1) { ierr = PetscPrintf(comm,"\t[%d]%s %g%% nnz after filtering, with threshold %g, %g nnz ave. (N=%d)\n",rank,__FUNCT__, 100.*(double)nnz1/(double)nnz0,vfilter,(double)nnz0/(double)nloc,MM);CHKERRQ(ierr); } else { PetscInt nnz[2],out[2]; nnz[0] = nnz0; nnz[1] = nnz1; ierr = MPI_Allreduce(nnz, out, 2, MPIU_INT, MPI_SUM, comm);CHKERRQ(ierr); ierr = PetscPrintf(comm,"\t[%d]%s %g%% nnz after filtering, with threshold %g, %g nnz ave. (N=%d)\n",rank,__FUNCT__, 100.*(double)out[1]/(double)out[0],vfilter,(double)out[0]/(double)MM,MM);CHKERRQ(ierr); } } ierr = MatDestroy(&Gmat);CHKERRQ(ierr); *a_Gmat = tGmat; PetscFunctionReturn(0); }
static PetscErrorCode KSPSolve_LSQR(KSP ksp) { PetscErrorCode ierr; PetscInt i,size1,size2; PetscScalar rho,rhobar,phi,phibar,theta,c,s,tmp,tau; PetscReal beta,alpha,rnorm; Vec X,B,V,V1,U,U1,TMP,W,W2,SE,Z = NULL; Mat Amat,Pmat; MatStructure pflag; KSP_LSQR *lsqr = (KSP_LSQR*)ksp->data; PetscBool diagonalscale,nopreconditioner; PetscFunctionBegin; ierr = PCGetDiagonalScale(ksp->pc,&diagonalscale);CHKERRQ(ierr); if (diagonalscale) SETERRQ1(PetscObjectComm((PetscObject)ksp),PETSC_ERR_SUP,"Krylov method %s does not support diagonal scaling",((PetscObject)ksp)->type_name); ierr = PCGetOperators(ksp->pc,&Amat,&Pmat,&pflag);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)ksp->pc,PCNONE,&nopreconditioner);CHKERRQ(ierr); /* nopreconditioner =PETSC_FALSE; */ /* Calculate norm of right hand side */ ierr = VecNorm(ksp->vec_rhs,NORM_2,&lsqr->rhs_norm);CHKERRQ(ierr); /* mark norm of matrix with negative number to indicate it has not yet been computed */ lsqr->anorm = -1.0; /* vectors of length m, where system size is mxn */ B = ksp->vec_rhs; U = lsqr->vwork_m[0]; U1 = lsqr->vwork_m[1]; /* vectors of length n */ X = ksp->vec_sol; W = lsqr->vwork_n[0]; V = lsqr->vwork_n[1]; V1 = lsqr->vwork_n[2]; W2 = lsqr->vwork_n[3]; if (!nopreconditioner) Z = lsqr->vwork_n[4]; /* standard error vector */ SE = lsqr->se; if (SE) { ierr = VecGetSize(SE,&size1);CHKERRQ(ierr); ierr = VecGetSize(X,&size2);CHKERRQ(ierr); if (size1 != size2) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Standard error vector (size %d) does not match solution vector (size %d)",size1,size2); ierr = VecSet(SE,0.0);CHKERRQ(ierr); } /* Compute initial residual, temporarily use work vector u */ if (!ksp->guess_zero) { ierr = KSP_MatMult(ksp,Amat,X,U);CHKERRQ(ierr); /* u <- b - Ax */ ierr = VecAYPX(U,-1.0,B);CHKERRQ(ierr); } else { ierr = VecCopy(B,U);CHKERRQ(ierr); /* u <- b (x is 0) */ } /* Test for nothing to do */ ierr = VecNorm(U,NORM_2,&rnorm);CHKERRQ(ierr); ierr = PetscObjectAMSTakeAccess((PetscObject)ksp);CHKERRQ(ierr); ksp->its = 0; ksp->rnorm = rnorm; ierr = PetscObjectAMSGrantAccess((PetscObject)ksp);CHKERRQ(ierr); ierr = KSPLogResidualHistory(ksp,rnorm);CHKERRQ(ierr); ierr = KSPMonitor(ksp,0,rnorm);CHKERRQ(ierr); ierr = (*ksp->converged)(ksp,0,rnorm,&ksp->reason,ksp->cnvP);CHKERRQ(ierr); if (ksp->reason) PetscFunctionReturn(0); beta = rnorm; ierr = VecScale(U,1.0/beta);CHKERRQ(ierr); ierr = KSP_MatMultTranspose(ksp,Amat,U,V);CHKERRQ(ierr); if (nopreconditioner) { ierr = VecNorm(V,NORM_2,&alpha);CHKERRQ(ierr); } else { ierr = PCApply(ksp->pc,V,Z);CHKERRQ(ierr); ierr = VecDotRealPart(V,Z,&alpha);CHKERRQ(ierr); if (alpha <= 0.0) { ksp->reason = KSP_DIVERGED_BREAKDOWN; PetscFunctionReturn(0); } alpha = PetscSqrtReal(alpha); ierr = VecScale(Z,1.0/alpha);CHKERRQ(ierr); } ierr = VecScale(V,1.0/alpha);CHKERRQ(ierr); if (nopreconditioner) { ierr = VecCopy(V,W);CHKERRQ(ierr); } else { ierr = VecCopy(Z,W);CHKERRQ(ierr); } lsqr->arnorm = alpha * beta; phibar = beta; rhobar = alpha; i = 0; do { if (nopreconditioner) { ierr = KSP_MatMult(ksp,Amat,V,U1);CHKERRQ(ierr); } else { ierr = KSP_MatMult(ksp,Amat,Z,U1);CHKERRQ(ierr); } ierr = VecAXPY(U1,-alpha,U);CHKERRQ(ierr); ierr = VecNorm(U1,NORM_2,&beta);CHKERRQ(ierr); if (beta == 0.0) { ksp->reason = KSP_DIVERGED_BREAKDOWN; break; } ierr = VecScale(U1,1.0/beta);CHKERRQ(ierr); ierr = KSP_MatMultTranspose(ksp,Amat,U1,V1);CHKERRQ(ierr); ierr = VecAXPY(V1,-beta,V);CHKERRQ(ierr); if (nopreconditioner) { ierr = VecNorm(V1,NORM_2,&alpha);CHKERRQ(ierr); } else { ierr = PCApply(ksp->pc,V1,Z);CHKERRQ(ierr); ierr = VecDotRealPart(V1,Z,&alpha);CHKERRQ(ierr); if (alpha <= 0.0) { ksp->reason = KSP_DIVERGED_BREAKDOWN; break; } alpha = PetscSqrtReal(alpha); ierr = VecScale(Z,1.0/alpha);CHKERRQ(ierr); } ierr = VecScale(V1,1.0/alpha);CHKERRQ(ierr); rho = PetscSqrtScalar(rhobar*rhobar + beta*beta); c = rhobar / rho; s = beta / rho; theta = s * alpha; rhobar = -c * alpha; phi = c * phibar; phibar = s * phibar; tau = s * phi; ierr = VecAXPY(X,phi/rho,W);CHKERRQ(ierr); /* x <- x + (phi/rho) w */ if (SE) { ierr = VecCopy(W,W2);CHKERRQ(ierr); ierr = VecSquare(W2);CHKERRQ(ierr); ierr = VecScale(W2,1.0/(rho*rho));CHKERRQ(ierr); ierr = VecAXPY(SE, 1.0, W2);CHKERRQ(ierr); /* SE <- SE + (w^2/rho^2) */ } if (nopreconditioner) { ierr = VecAYPX(W,-theta/rho,V1);CHKERRQ(ierr); /* w <- v - (theta/rho) w */ } else { ierr = VecAYPX(W,-theta/rho,Z);CHKERRQ(ierr); /* w <- z - (theta/rho) w */ } lsqr->arnorm = alpha*PetscAbsScalar(tau); rnorm = PetscRealPart(phibar); ierr = PetscObjectAMSTakeAccess((PetscObject)ksp);CHKERRQ(ierr); ksp->its++; ksp->rnorm = rnorm; ierr = PetscObjectAMSGrantAccess((PetscObject)ksp);CHKERRQ(ierr); ierr = KSPLogResidualHistory(ksp,rnorm);CHKERRQ(ierr); ierr = KSPMonitor(ksp,i+1,rnorm);CHKERRQ(ierr); ierr = (*ksp->converged)(ksp,i+1,rnorm,&ksp->reason,ksp->cnvP);CHKERRQ(ierr); if (ksp->reason) break; SWAP(U1,U,TMP); SWAP(V1,V,TMP); i++; } while (i<ksp->max_it); if (i >= ksp->max_it && !ksp->reason) ksp->reason = KSP_DIVERGED_ITS; /* Finish off the standard error estimates */ if (SE) { tmp = 1.0; ierr = MatGetSize(Amat,&size1,&size2);CHKERRQ(ierr); if (size1 > size2) tmp = size1 - size2; tmp = rnorm / PetscSqrtScalar(tmp); ierr = VecSqrtAbs(SE);CHKERRQ(ierr); ierr = VecScale(SE,tmp);CHKERRQ(ierr); } PetscFunctionReturn(0); }
PetscErrorCode heavyEdgeMatchAgg(IS perm,Mat a_Gmat,PetscInt verbose,PetscCoarsenData **a_locals_llist) { PetscErrorCode ierr; PetscBool isMPI; MPI_Comm wcomm = ((PetscObject)a_Gmat)->comm; PetscInt sub_it,kk,n,ix,*idx,*ii,iter,Iend,my0; PetscMPIInt rank,size; const PetscInt nloc = a_Gmat->rmap->n,n_iter=6; /* need to figure out how to stop this */ PetscInt *lid_cprowID,*lid_gid; PetscBool *lid_matched; Mat_SeqAIJ *matA, *matB=0; Mat_MPIAIJ *mpimat=0; PetscScalar one=1.; PetscCoarsenData *agg_llists = PETSC_NULL,*deleted_list = PETSC_NULL; Mat cMat,tMat,P; MatScalar *ap; PetscMPIInt tag1,tag2; PetscFunctionBegin; ierr = MPI_Comm_rank(wcomm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(wcomm, &size);CHKERRQ(ierr); ierr = MatGetOwnershipRange(a_Gmat, &my0, &Iend);CHKERRQ(ierr); ierr = PetscCommGetNewTag(wcomm, &tag1);CHKERRQ(ierr); ierr = PetscCommGetNewTag(wcomm, &tag2);CHKERRQ(ierr); ierr = PetscMalloc(nloc*sizeof(PetscInt), &lid_gid);CHKERRQ(ierr); /* explicit array needed */ ierr = PetscMalloc(nloc*sizeof(PetscInt), &lid_cprowID);CHKERRQ(ierr); ierr = PetscMalloc(nloc*sizeof(PetscBool), &lid_matched);CHKERRQ(ierr); ierr = PetscCDCreate(nloc, &agg_llists);CHKERRQ(ierr); /* ierr = PetscCDSetChuckSize(agg_llists, nloc+1);CHKERRQ(ierr); */ *a_locals_llist = agg_llists; ierr = PetscCDCreate(size, &deleted_list);CHKERRQ(ierr); ierr = PetscCDSetChuckSize(deleted_list, 100);CHKERRQ(ierr); /* setup 'lid_gid' for scatters and add self to all lists */ for (kk=0;kk<nloc;kk++) { lid_gid[kk] = kk + my0; ierr = PetscCDAppendID(agg_llists, kk, my0+kk);CHKERRQ(ierr); } /* make a copy of the graph, this gets destroyed in iterates */ ierr = MatDuplicate(a_Gmat,MAT_COPY_VALUES,&cMat);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)a_Gmat, MATMPIAIJ, &isMPI);CHKERRQ(ierr); iter = 0; while(iter++ < n_iter) { PetscScalar *cpcol_gid,*cpcol_max_ew,*cpcol_max_pe,*lid_max_ew; PetscBool *cpcol_matched; PetscMPIInt *cpcol_pe,proc; Vec locMaxEdge,locMaxPE,ghostMaxEdge,ghostMaxPE; PetscInt nEdges,n_nz_row,jj; Edge *Edges; PetscInt gid; const PetscInt *perm_ix, n_sub_its = 120; /* get submatrices of cMat */ if (isMPI) { mpimat = (Mat_MPIAIJ*)cMat->data; matA = (Mat_SeqAIJ*)mpimat->A->data; matB = (Mat_SeqAIJ*)mpimat->B->data; /* force compressed storage of B */ matB->compressedrow.check = PETSC_TRUE; ierr = MatCheckCompressedRow(mpimat->B,&matB->compressedrow,matB->i,cMat->rmap->n,-1.0);CHKERRQ(ierr); assert(matB->compressedrow.use); } else { matA = (Mat_SeqAIJ*)cMat->data; } assert(matA && !matA->compressedrow.use); assert(matB==0 || matB->compressedrow.use); /* set max edge on nodes */ ierr = MatGetVecs(cMat, &locMaxEdge, 0);CHKERRQ(ierr); ierr = MatGetVecs(cMat, &locMaxPE, 0);CHKERRQ(ierr); /* get 'cpcol_pe' & 'cpcol_gid' & init. 'cpcol_matched' using 'mpimat->lvec' */ if (mpimat) { Vec vec; PetscScalar vval; ierr = MatGetVecs(cMat, &vec, 0);CHKERRQ(ierr); /* cpcol_pe */ vval = (PetscScalar)(rank); for (kk=0,gid=my0;kk<nloc;kk++,gid++) { ierr = VecSetValues(vec, 1, &gid, &vval, INSERT_VALUES);CHKERRQ(ierr); /* set with GID */ } ierr = VecAssemblyBegin(vec);CHKERRQ(ierr); ierr = VecAssemblyEnd(vec);CHKERRQ(ierr); ierr = VecScatterBegin(mpimat->Mvctx,vec,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(mpimat->Mvctx,vec,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecGetArray(mpimat->lvec, &cpcol_gid);CHKERRQ(ierr); /* get proc ID in 'cpcol_gid' */ ierr = VecGetLocalSize(mpimat->lvec, &n);CHKERRQ(ierr); ierr = PetscMalloc(n*sizeof(PetscInt), &cpcol_pe);CHKERRQ(ierr); for (kk=0;kk<n;kk++) cpcol_pe[kk] = (PetscMPIInt)PetscRealPart(cpcol_gid[kk]); ierr = VecRestoreArray(mpimat->lvec, &cpcol_gid);CHKERRQ(ierr); /* cpcol_gid */ for (kk=0,gid=my0;kk<nloc;kk++,gid++) { vval = (PetscScalar)(gid); ierr = VecSetValues(vec, 1, &gid, &vval, INSERT_VALUES);CHKERRQ(ierr); /* set with GID */ } ierr = VecAssemblyBegin(vec);CHKERRQ(ierr); ierr = VecAssemblyEnd(vec);CHKERRQ(ierr); ierr = VecScatterBegin(mpimat->Mvctx,vec,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(mpimat->Mvctx,vec,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecDestroy(&vec);CHKERRQ(ierr); ierr = VecGetArray(mpimat->lvec, &cpcol_gid);CHKERRQ(ierr); /* get proc ID in 'cpcol_gid' */ /* cpcol_matched */ ierr = VecGetLocalSize(mpimat->lvec, &n);CHKERRQ(ierr); ierr = PetscMalloc(n*sizeof(PetscBool), &cpcol_matched);CHKERRQ(ierr); for (kk=0;kk<n;kk++) cpcol_matched[kk] = PETSC_FALSE; } /* need an inverse map - locals */ for (kk=0;kk<nloc;kk++) lid_cprowID[kk] = -1; /* set index into compressed row 'lid_cprowID' */ if (matB) { ii = matB->compressedrow.i; for (ix=0; ix<matB->compressedrow.nrows; ix++) { lid_cprowID[matB->compressedrow.rindex[ix]] = ix; } } /* get removed IS, use '' */ /* if (iter==1) { */ /* PetscInt *lid_rem,idx; */ /* ierr = PetscMalloc(nloc*sizeof(PetscInt), &lid_rem);CHKERRQ(ierr); */ /* for (kk=idx=0;kk<nloc;kk++){ */ /* PetscInt nn,lid=kk; */ /* ii = matA->i; nn = ii[lid+1] - ii[lid]; */ /* if ((ix=lid_cprowID[lid]) != -1) { /\* if I have any ghost neighbors *\/ */ /* ii = matB->compressedrow.i; */ /* nn += ii[ix+1] - ii[ix]; */ /* } */ /* if (nn < 2) { */ /* lid_rem[idx++] = kk + my0; */ /* } */ /* } */ /* ierr = PetscCDSetRemovedIS(agg_llists, wcomm, idx, lid_rem);CHKERRQ(ierr); */ /* ierr = PetscFree(lid_rem);CHKERRQ(ierr); */ /* } */ /* compute 'locMaxEdge' & 'locMaxPE', and create list of edges, count edges' */ for (nEdges=0,kk=0,gid=my0;kk<nloc;kk++,gid++){ PetscReal max_e = 0., tt; PetscScalar vval; PetscInt lid = kk; PetscMPIInt max_pe=rank,pe; ii = matA->i; n = ii[lid+1] - ii[lid]; idx = matA->j + ii[lid]; ap = matA->a + ii[lid]; for (jj=0; jj<n; jj++) { PetscInt lidj = idx[jj]; if (lidj != lid && PetscRealPart(ap[jj]) > max_e) max_e = PetscRealPart(ap[jj]); if (lidj > lid) nEdges++; } if ((ix=lid_cprowID[lid]) != -1) { /* if I have any ghost neighbors */ ii = matB->compressedrow.i; n = ii[ix+1] - ii[ix]; ap = matB->a + ii[ix]; idx = matB->j + ii[ix]; for (jj=0 ; jj<n ; jj++) { if ((tt=PetscRealPart(ap[jj])) > max_e) max_e = tt; nEdges++; if ((pe=cpcol_pe[idx[jj]]) > max_pe) max_pe = pe; } } vval = max_e; ierr = VecSetValues(locMaxEdge, 1, &gid, &vval, INSERT_VALUES);CHKERRQ(ierr); vval = (PetscScalar)max_pe; ierr = VecSetValues(locMaxPE, 1, &gid, &vval, INSERT_VALUES);CHKERRQ(ierr); } ierr = VecAssemblyBegin(locMaxEdge);CHKERRQ(ierr); ierr = VecAssemblyEnd(locMaxEdge);CHKERRQ(ierr); ierr = VecAssemblyBegin(locMaxPE);CHKERRQ(ierr); ierr = VecAssemblyEnd(locMaxPE);CHKERRQ(ierr); /* get 'cpcol_max_ew' & 'cpcol_max_pe' */ if (mpimat) { ierr = VecDuplicate(mpimat->lvec, &ghostMaxEdge);CHKERRQ(ierr); ierr = VecScatterBegin(mpimat->Mvctx,locMaxEdge,ghostMaxEdge,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(mpimat->Mvctx,locMaxEdge,ghostMaxEdge,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecGetArray(ghostMaxEdge, &cpcol_max_ew);CHKERRQ(ierr); ierr = VecDuplicate(mpimat->lvec, &ghostMaxPE);CHKERRQ(ierr); ierr = VecScatterBegin(mpimat->Mvctx,locMaxPE,ghostMaxPE,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(mpimat->Mvctx,locMaxPE,ghostMaxPE,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecGetArray(ghostMaxPE, &cpcol_max_pe);CHKERRQ(ierr); } /* setup sorted list of edges */ ierr = PetscMalloc(nEdges*sizeof(Edge), &Edges);CHKERRQ(ierr); ierr = ISGetIndices(perm, &perm_ix);CHKERRQ(ierr); for (nEdges=n_nz_row=kk=0;kk<nloc;kk++){ PetscInt nn, lid = perm_ix[kk]; ii = matA->i; nn = n = ii[lid+1] - ii[lid]; idx = matA->j + ii[lid]; ap = matA->a + ii[lid]; for (jj=0; jj<n; jj++) { PetscInt lidj = idx[jj]; assert(PetscRealPart(ap[jj])>0.); if (lidj > lid) { Edges[nEdges].lid0 = lid; Edges[nEdges].gid1 = lidj + my0; Edges[nEdges].cpid1 = -1; Edges[nEdges].weight = PetscRealPart(ap[jj]); nEdges++; } } if ((ix=lid_cprowID[lid]) != -1) { /* if I have any ghost neighbors */ ii = matB->compressedrow.i; n = ii[ix+1] - ii[ix]; ap = matB->a + ii[ix]; idx = matB->j + ii[ix]; nn += n; for (jj=0 ; jj<n ; jj++) { assert(PetscRealPart(ap[jj])>0.); Edges[nEdges].lid0 = lid; Edges[nEdges].gid1 = (PetscInt)PetscRealPart(cpcol_gid[idx[jj]]); Edges[nEdges].cpid1 = idx[jj]; Edges[nEdges].weight = PetscRealPart(ap[jj]); nEdges++; } } if (nn > 1) n_nz_row++; else if (iter == 1){ /* should select this because it is technically in the MIS but lets not */ ierr = PetscCDRemoveAll(agg_llists, lid);CHKERRQ(ierr); } } ierr = ISRestoreIndices(perm,&perm_ix);CHKERRQ(ierr); qsort(Edges, nEdges, sizeof(Edge), gamg_hem_compare); /* projection matrix */ ierr = MatCreateAIJ(wcomm, nloc, nloc, PETSC_DETERMINE, PETSC_DETERMINE, 1, 0, 1, 0, &P);CHKERRQ(ierr); /* clear matched flags */ for (kk=0;kk<nloc;kk++) lid_matched[kk] = PETSC_FALSE; /* process - communicate - process */ for (sub_it=0;sub_it<n_sub_its;sub_it++){ PetscInt nactive_edges; ierr = VecGetArray(locMaxEdge, &lid_max_ew);CHKERRQ(ierr); for (kk=nactive_edges=0;kk<nEdges;kk++){ /* HEM */ const Edge *e = &Edges[kk]; const PetscInt lid0=e->lid0,gid1=e->gid1,cpid1=e->cpid1,gid0=lid0+my0,lid1=gid1-my0; PetscBool isOK = PETSC_TRUE; /* skip if either (local) vertex is done already */ if (lid_matched[lid0] || (gid1>=my0 && gid1<Iend && lid_matched[gid1-my0])) { continue; } /* skip if ghost vertex is done */ if (cpid1 != -1 && cpcol_matched[cpid1]) { continue; } nactive_edges++; /* skip if I have a bigger edge someplace (lid_max_ew gets updated) */ if (PetscRealPart(lid_max_ew[lid0]) > e->weight + 1.e-12) { continue; } if (cpid1 == -1) { if (PetscRealPart(lid_max_ew[lid1]) > e->weight + 1.e-12) { continue; } } else { /* see if edge might get matched on other proc */ PetscReal g_max_e = PetscRealPart(cpcol_max_ew[cpid1]); if (g_max_e > e->weight + 1.e-12) { continue; } else if (e->weight > g_max_e - 1.e-12 && (PetscMPIInt)PetscRealPart(cpcol_max_pe[cpid1]) > rank) { /* check for max_e == to this edge and larger processor that will deal with this */ continue; } } /* check ghost for v0 */ if (isOK){ PetscReal max_e,ew; if ((ix=lid_cprowID[lid0]) != -1) { /* if I have any ghost neighbors */ ii = matB->compressedrow.i; n = ii[ix+1] - ii[ix]; ap = matB->a + ii[ix]; idx = matB->j + ii[ix]; for (jj=0 ; jj<n && isOK; jj++) { PetscInt lidj = idx[jj]; if (cpcol_matched[lidj]) continue; ew = PetscRealPart(ap[jj]); max_e = PetscRealPart(cpcol_max_ew[lidj]); /* check for max_e == to this edge and larger processor that will deal with this */ if (ew > max_e - 1.e-12 && ew > PetscRealPart(lid_max_ew[lid0]) - 1.e-12 && (PetscMPIInt)PetscRealPart(cpcol_max_pe[lidj]) > rank){ isOK = PETSC_FALSE; } } } /* for v1 */ if (cpid1 == -1 && isOK){ if ((ix=lid_cprowID[lid1]) != -1) { /* if I have any ghost neighbors */ ii = matB->compressedrow.i; n = ii[ix+1] - ii[ix]; ap = matB->a + ii[ix]; idx = matB->j + ii[ix]; for (jj=0 ; jj<n && isOK ; jj++) { PetscInt lidj = idx[jj]; if (cpcol_matched[lidj]) continue; ew = PetscRealPart(ap[jj]); max_e = PetscRealPart(cpcol_max_ew[lidj]); /* check for max_e == to this edge and larger processor that will deal with this */ if (ew > max_e - 1.e-12 && ew > PetscRealPart(lid_max_ew[lid1]) - 1.e-12 && (PetscMPIInt)PetscRealPart(cpcol_max_pe[lidj]) > rank) { isOK = PETSC_FALSE; } } } } } /* do it */ if (isOK){ if (cpid1 == -1) { lid_matched[lid1] = PETSC_TRUE; /* keep track of what we've done this round */ ierr = PetscCDAppendRemove(agg_llists, lid0, lid1);CHKERRQ(ierr); } else if (sub_it != n_sub_its-1) { /* add gid1 to list of ghost deleted by me -- I need their children */ proc = cpcol_pe[cpid1]; cpcol_matched[cpid1] = PETSC_TRUE; /* messing with VecGetArray array -- needed??? */ ierr = PetscCDAppendID(deleted_list, proc, cpid1);CHKERRQ(ierr); /* cache to send messages */ ierr = PetscCDAppendID(deleted_list, proc, lid0);CHKERRQ(ierr); } else { continue; } lid_matched[lid0] = PETSC_TRUE; /* keep track of what we've done this round */ /* set projection */ ierr = MatSetValues(P,1,&gid0,1,&gid0,&one,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValues(P,1,&gid1,1,&gid0,&one,INSERT_VALUES);CHKERRQ(ierr); } /* matched */ } /* edge loop */ /* deal with deleted ghost on first pass */ if (size>1 && sub_it != n_sub_its-1){ PetscCDPos pos; PetscBool ise = PETSC_FALSE; PetscInt nSend1, **sbuffs1,nSend2; #define REQ_BF_SIZE 100 MPI_Request *sreqs2[REQ_BF_SIZE],*rreqs2[REQ_BF_SIZE]; MPI_Status status; /* send request */ for (proc=0,nSend1=0;proc<size;proc++){ ierr = PetscCDEmptyAt(deleted_list,proc,&ise);CHKERRQ(ierr); if (!ise) nSend1++; } ierr = PetscMalloc(nSend1*sizeof(PetscInt*), &sbuffs1);CHKERRQ(ierr); /* ierr = PetscMalloc4(nSend1, PetscInt*, sbuffs1, nSend1, PetscInt*, rbuffs1, nSend1, MPI_Request*, sreqs1, nSend1, MPI_Request*, rreqs1);CHKERRQ(ierr); */ /* PetscFree4(sbuffs1,rbuffs1,sreqs1,rreqs1); */ for (proc=0,nSend1=0;proc<size;proc++){ /* count ghosts */ ierr = PetscCDSizeAt(deleted_list,proc,&n);CHKERRQ(ierr); if (n>0){ #define CHUNCK_SIZE 100 PetscInt *sbuff,*pt; MPI_Request *request; assert(n%2==0); n /= 2; ierr = PetscMalloc((2 + 2*n + n*CHUNCK_SIZE)*sizeof(PetscInt) + 2*sizeof(MPI_Request), &sbuff);CHKERRQ(ierr); /* PetscMalloc4(2+2*n,PetscInt,sbuffs1[nSend1],n*CHUNCK_SIZE,PetscInt,rbuffs1[nSend1],1,MPI_Request,rreqs2[nSend1],1,MPI_Request,sreqs2[nSend1]); */ /* save requests */ sbuffs1[nSend1] = sbuff; request = (MPI_Request*)sbuff; sbuff = pt = (PetscInt*)(request+1); *pt++ = n; *pt++ = rank; ierr = PetscCDGetHeadPos(deleted_list,proc,&pos);CHKERRQ(ierr); while(pos){ PetscInt lid0, cpid, gid; ierr = PetscLLNGetID(pos, &cpid);CHKERRQ(ierr); gid = (PetscInt)PetscRealPart(cpcol_gid[cpid]); ierr = PetscCDGetNextPos(deleted_list,proc,&pos);CHKERRQ(ierr); ierr = PetscLLNGetID(pos, &lid0);CHKERRQ(ierr); ierr = PetscCDGetNextPos(deleted_list,proc,&pos);CHKERRQ(ierr); *pt++ = gid; *pt++ = lid0; } /* send request tag1 [n, proc, n*[gid1,lid0] ] */ ierr = MPI_Isend(sbuff, 2*n+2, MPIU_INT, proc, tag1, wcomm, request);CHKERRQ(ierr); /* post recieve */ request = (MPI_Request*)pt; rreqs2[nSend1] = request; /* cache recv request */ pt = (PetscInt*)(request+1); ierr = MPI_Irecv(pt, n*CHUNCK_SIZE, MPIU_INT, proc, tag2, wcomm, request);CHKERRQ(ierr); /* clear list */ ierr = PetscCDRemoveAll(deleted_list, proc);CHKERRQ(ierr); nSend1++; } } /* recieve requests, send response, clear lists */ kk = nactive_edges; ierr = MPI_Allreduce(&kk,&nactive_edges,1,MPIU_INT,MPI_SUM,wcomm);CHKERRQ(ierr); /* not correct syncronization and global */ nSend2 = 0; while(1){ #define BF_SZ 10000 PetscMPIInt flag,count; PetscInt rbuff[BF_SZ],*pt,*pt2,*pt3,count2,*sbuff,count3; MPI_Request *request; ierr = MPI_Iprobe(MPI_ANY_SOURCE, tag1, wcomm, &flag, &status);CHKERRQ(ierr); if (!flag) break; ierr = MPI_Get_count(&status, MPIU_INT, &count);CHKERRQ(ierr); if (count > BF_SZ) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"buffer too small for recieve: %d",count); proc = status.MPI_SOURCE; /* recieve request tag1 [n, proc, n*[gid1,lid0] ] */ ierr = MPI_Recv(rbuff, count, MPIU_INT, proc, tag1, wcomm, &status);CHKERRQ(ierr); /* count sends */ pt = rbuff; count3 = count2 = 0; n = *pt++; kk = *pt++; assert(kk==proc); while(n--){ PetscInt gid1=*pt++, lid1=gid1-my0; kk=*pt++; assert(lid1>=0 && lid1<nloc); if (lid_matched[lid1]){ PetscPrintf(PETSC_COMM_SELF,"\t *** [%d]%s %d) ERROR recieved deleted gid %d, deleted by (lid) %d from proc %d\n",rank,__FUNCT__,sub_it,gid1,kk); PetscSleep(1); } assert(!lid_matched[lid1]); lid_matched[lid1] = PETSC_TRUE; /* keep track of what we've done this round */ ierr = PetscCDSizeAt(agg_llists, lid1, &kk);CHKERRQ(ierr); count2 += kk + 2; count3++; /* number of verts requested (n) */ } assert(pt-rbuff==count); if (count2 > count3*CHUNCK_SIZE) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Irecv will be too small: %d",count2); /* send tag2 *[lid0, n, n*[gid] ] */ ierr = PetscMalloc(count2*sizeof(PetscInt) + sizeof(MPI_Request), &sbuff);CHKERRQ(ierr); request = (MPI_Request*)sbuff; sreqs2[nSend2++] = request; /* cache request */ if (nSend2==REQ_BF_SIZE) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"buffer too small for requests: %d",nSend2); pt2 = sbuff = (PetscInt*)(request+1); pt = rbuff; n = *pt++; kk = *pt++; assert(kk==proc); while(n--){ /* read [n, proc, n*[gid1,lid0] */ PetscInt gid1=*pt++, lid1=gid1-my0, lid0=*pt++; assert(lid1>=0 && lid1<nloc); /* write [lid0, n, n*[gid] ] */ *pt2++ = lid0; pt3 = pt2++; /* save pointer for later */ /* for (pos=PetscCDGetHeadPos(agg_llists,lid1) ; pos ; pos=PetscCDGetNextPos(agg_llists,lid1,pos)){ */ ierr = PetscCDGetHeadPos(agg_llists,lid1,&pos);CHKERRQ(ierr); while(pos){ PetscInt gid; ierr = PetscLLNGetID(pos, &gid);CHKERRQ(ierr); ierr = PetscCDGetNextPos(agg_llists,lid1,&pos);CHKERRQ(ierr); *pt2++ = gid; } *pt3 = (pt2-pt3)-1; /* clear list */ ierr = PetscCDRemoveAll(agg_llists, lid1);CHKERRQ(ierr); } assert(pt2-sbuff==count2); assert(pt-rbuff==count); /* send requested data tag2 *[lid0, n, n*[gid1] ] */ ierr = MPI_Isend(sbuff, count2, MPIU_INT, proc, tag2, wcomm, request);CHKERRQ(ierr); } /* recieve tag2 *[lid0, n, n*[gid] ] */ for (kk=0;kk<nSend1;kk++){ PetscMPIInt count; MPI_Request *request; PetscInt *pt, *pt2; request = rreqs2[kk]; /* no need to free -- buffer is in 'sbuffs1' */ ierr = MPI_Wait(request, &status);CHKERRQ(ierr); ierr = MPI_Get_count(&status, MPIU_INT, &count);CHKERRQ(ierr); pt = pt2 = (PetscInt*)(request+1); while(pt-pt2 < count){ PetscInt lid0 = *pt++, n = *pt++; assert(lid0>=0 && lid0<nloc); while(n--){ PetscInt gid1 = *pt++; ierr = PetscCDAppendID(agg_llists, lid0, gid1);CHKERRQ(ierr); } } assert(pt-pt2==count); } /* wait for tag1 isends */ while(nSend1--){ MPI_Request *request; request = (MPI_Request*)sbuffs1[nSend1]; ierr = MPI_Wait(request, &status);CHKERRQ(ierr); ierr = PetscFree(request);CHKERRQ(ierr); } ierr = PetscFree(sbuffs1);CHKERRQ(ierr); /* wait for tag2 isends */ while(nSend2--){ MPI_Request *request = sreqs2[nSend2]; ierr = MPI_Wait(request, &status);CHKERRQ(ierr); ierr = PetscFree(request);CHKERRQ(ierr); } ierr = VecRestoreArray(ghostMaxEdge, &cpcol_max_ew);CHKERRQ(ierr); ierr = VecRestoreArray(ghostMaxPE, &cpcol_max_pe);CHKERRQ(ierr); /* get 'cpcol_matched' - use locMaxPE, ghostMaxEdge, cpcol_max_ew */ for (kk=0,gid=my0;kk<nloc;kk++,gid++) { PetscScalar vval = lid_matched[kk] ? 1.0 : 0.0; ierr = VecSetValues(locMaxPE, 1, &gid, &vval, INSERT_VALUES);CHKERRQ(ierr); /* set with GID */ } ierr = VecAssemblyBegin(locMaxPE);CHKERRQ(ierr); ierr = VecAssemblyEnd(locMaxPE);CHKERRQ(ierr); ierr = VecScatterBegin(mpimat->Mvctx,locMaxPE,ghostMaxEdge,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(mpimat->Mvctx,locMaxPE,ghostMaxEdge,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecGetArray(ghostMaxEdge, &cpcol_max_ew);CHKERRQ(ierr); ierr = VecGetLocalSize(mpimat->lvec, &n);CHKERRQ(ierr); for (kk=0;kk<n;kk++) { cpcol_matched[kk] = (PetscBool)(PetscRealPart(cpcol_max_ew[kk]) != 0.0); } ierr = VecRestoreArray(ghostMaxEdge, &cpcol_max_ew);CHKERRQ(ierr); } /* size > 1 */ /* compute 'locMaxEdge' */ ierr = VecRestoreArray(locMaxEdge, &lid_max_ew);CHKERRQ(ierr); for (kk=0,gid=my0;kk<nloc;kk++,gid++){ PetscReal max_e = 0.,tt; PetscScalar vval; PetscInt lid = kk; if (lid_matched[lid]) vval = 0.; else { ii = matA->i; n = ii[lid+1] - ii[lid]; idx = matA->j + ii[lid]; ap = matA->a + ii[lid]; for (jj=0; jj<n; jj++) { PetscInt lidj = idx[jj]; if (lid_matched[lidj]) continue; /* this is new - can change local max */ if (lidj != lid && PetscRealPart(ap[jj]) > max_e) max_e = PetscRealPart(ap[jj]); } if (lid_cprowID && (ix=lid_cprowID[lid]) != -1) { /* if I have any ghost neighbors */ ii = matB->compressedrow.i; n = ii[ix+1] - ii[ix]; ap = matB->a + ii[ix]; idx = matB->j + ii[ix]; for (jj=0 ; jj<n ; jj++) { PetscInt lidj = idx[jj]; if (cpcol_matched[lidj]) continue; if ((tt=PetscRealPart(ap[jj])) > max_e) max_e = tt; } } } vval = (PetscScalar)max_e; ierr = VecSetValues(locMaxEdge, 1, &gid, &vval, INSERT_VALUES);CHKERRQ(ierr); /* set with GID */ } ierr = VecAssemblyBegin(locMaxEdge);CHKERRQ(ierr); ierr = VecAssemblyEnd(locMaxEdge);CHKERRQ(ierr); if (size>1 && sub_it != n_sub_its-1){ /* compute 'cpcol_max_ew' */ ierr = VecScatterBegin(mpimat->Mvctx,locMaxEdge,ghostMaxEdge,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(mpimat->Mvctx,locMaxEdge,ghostMaxEdge,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecGetArray(ghostMaxEdge, &cpcol_max_ew);CHKERRQ(ierr); ierr = VecGetArray(locMaxEdge, &lid_max_ew);CHKERRQ(ierr); /* compute 'cpcol_max_pe' */ for (kk=0,gid=my0;kk<nloc;kk++,gid++){ PetscInt lid = kk; PetscReal ew,v1_max_e,v0_max_e=PetscRealPart(lid_max_ew[lid]); PetscScalar vval; PetscMPIInt max_pe=rank,pe; if (lid_matched[lid]) vval = (PetscScalar)rank; else if ((ix=lid_cprowID[lid]) != -1) { /* if I have any ghost neighbors */ ii = matB->compressedrow.i; n = ii[ix+1] - ii[ix]; ap = matB->a + ii[ix]; idx = matB->j + ii[ix]; for (jj=0 ; jj<n ; jj++) { PetscInt lidj = idx[jj]; if (cpcol_matched[lidj]) continue; ew = PetscRealPart(ap[jj]); v1_max_e = PetscRealPart(cpcol_max_ew[lidj]); /* get max pe that has a max_e == to this edge w */ if ((pe=cpcol_pe[idx[jj]]) > max_pe && ew > v1_max_e - 1.e-12 && ew > v0_max_e - 1.e-12) max_pe = pe; assert(ew < v0_max_e + 1.e-12 && ew < v1_max_e + 1.e-12); } vval = (PetscScalar)max_pe; } ierr = VecSetValues(locMaxPE, 1, &gid, &vval, INSERT_VALUES);CHKERRQ(ierr); } ierr = VecAssemblyBegin(locMaxPE);CHKERRQ(ierr); ierr = VecAssemblyEnd(locMaxPE);CHKERRQ(ierr); ierr = VecScatterBegin(mpimat->Mvctx,locMaxPE,ghostMaxPE,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(mpimat->Mvctx,locMaxPE,ghostMaxPE,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecGetArray(ghostMaxPE, &cpcol_max_pe);CHKERRQ(ierr); ierr = VecRestoreArray(locMaxEdge, &lid_max_ew);CHKERRQ(ierr); } /* deal with deleted ghost */ if (verbose>2) PetscPrintf(wcomm,"\t[%d]%s %d.%d: %d active edges.\n", rank,__FUNCT__,iter,sub_it,nactive_edges); if (!nactive_edges) break; } /* sub_it loop */ /* clean up iteration */ ierr = PetscFree(Edges);CHKERRQ(ierr); if (mpimat){ ierr = VecRestoreArray(ghostMaxEdge, &cpcol_max_ew);CHKERRQ(ierr); ierr = VecDestroy(&ghostMaxEdge);CHKERRQ(ierr); ierr = VecRestoreArray(ghostMaxPE, &cpcol_max_pe);CHKERRQ(ierr); ierr = VecDestroy(&ghostMaxPE);CHKERRQ(ierr); ierr = PetscFree(cpcol_pe);CHKERRQ(ierr); ierr = PetscFree(cpcol_matched);CHKERRQ(ierr); } ierr = VecDestroy(&locMaxEdge);CHKERRQ(ierr); ierr = VecDestroy(&locMaxPE);CHKERRQ(ierr); if (mpimat){ ierr = VecRestoreArray(mpimat->lvec, &cpcol_gid);CHKERRQ(ierr); } /* create next G if needed */ if (iter == n_iter) { /* hard wired test - need to look at full surrounded nodes or something */ ierr = MatDestroy(&P);CHKERRQ(ierr); ierr = MatDestroy(&cMat);CHKERRQ(ierr); break; } else { Vec diag; /* add identity for unmatched vertices so they stay alive */ for (kk=0,gid=my0;kk<nloc;kk++,gid++){ if (!lid_matched[kk]) { gid = kk+my0; ierr = MatGetRow(cMat,gid,&n,0,0);CHKERRQ(ierr); if (n>1){ ierr = MatSetValues(P,1,&gid,1,&gid,&one,INSERT_VALUES);CHKERRQ(ierr); } ierr = MatRestoreRow(cMat,gid,&n,0,0);CHKERRQ(ierr); } } ierr = MatAssemblyBegin(P,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(P,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* project to make new graph with colapsed edges */ ierr = MatPtAP(cMat,P,MAT_INITIAL_MATRIX,1.0,&tMat);CHKERRQ(ierr); ierr = MatDestroy(&P);CHKERRQ(ierr); ierr = MatDestroy(&cMat);CHKERRQ(ierr); cMat = tMat; ierr = MatGetVecs(cMat, &diag, 0);CHKERRQ(ierr); ierr = MatGetDiagonal(cMat, diag);CHKERRQ(ierr); /* effectively PCJACOBI */ ierr = VecReciprocal(diag);CHKERRQ(ierr); ierr = VecSqrtAbs(diag);CHKERRQ(ierr); ierr = MatDiagonalScale(cMat, diag, diag);CHKERRQ(ierr); ierr = VecDestroy(&diag);CHKERRQ(ierr); } } /* coarsen iterator */ /* make fake matrix */ if (size>1){ Mat mat; PetscCDPos pos; PetscInt gid, NN, MM, jj = 0, mxsz = 0; for (kk=0;kk<nloc;kk++){ ierr = PetscCDSizeAt(agg_llists, kk, &jj);CHKERRQ(ierr); if (jj > mxsz) mxsz = jj; } ierr = MatGetSize(a_Gmat, &MM, &NN);CHKERRQ(ierr); if (mxsz > MM-nloc) mxsz = MM-nloc; ierr = MatCreateAIJ(wcomm, nloc, nloc,PETSC_DETERMINE, PETSC_DETERMINE,0, 0, mxsz, 0, &mat);CHKERRQ(ierr); /* */ for (kk=0,gid=my0;kk<nloc;kk++,gid++){ /* for (pos=PetscCDGetHeadPos(agg_llists,kk) ; pos ; pos=PetscCDGetNextPos(agg_llists,kk,pos)){ */ ierr = PetscCDGetHeadPos(agg_llists,kk,&pos);CHKERRQ(ierr); while(pos){ PetscInt gid1; ierr = PetscLLNGetID(pos, &gid1);CHKERRQ(ierr); ierr = PetscCDGetNextPos(agg_llists,kk,&pos);CHKERRQ(ierr); if (gid1 < my0 || gid1 >= my0+nloc) { ierr = MatSetValues(mat,1,&gid,1,&gid1,&one,ADD_VALUES);CHKERRQ(ierr); } } } ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = PetscCDSetMat(agg_llists, mat);CHKERRQ(ierr); } ierr = PetscFree(lid_cprowID);CHKERRQ(ierr); ierr = PetscFree(lid_gid);CHKERRQ(ierr); ierr = PetscFree(lid_matched);CHKERRQ(ierr); ierr = PetscCDDestroy(deleted_list);CHKERRQ(ierr); PetscFunctionReturn(0); }