xref: /petsc/src/ksp/pc/impls/gamg/gamg.c (revision b2a4f308a067d4334e0f98f83bfed4d44e1338a5)

/*
 GAMG geometric-algebric multigrid PC - Mark Adams 2011
 */
#include "private/matimpl.h"
#include <../src/ksp/pc/impls/gamg/gamg.h>           /*I "petscpc.h" I*/
#include <private/kspimpl.h>

#if defined PETSC_USE_LOG
PetscLogEvent gamg_setup_events[NUM_SET];
#endif
#define GAMG_MAXLEVELS 30

/* #define GAMG_STAGES */
#if (defined PETSC_USE_LOG && defined GAMG_STAGES)
static PetscLogStage gamg_stages[GAMG_MAXLEVELS];
#endif

static PetscFList GAMGList = 0;

/* ----------------------------------------------------------------------------- */
#undef __FUNCT__
#define __FUNCT__ "PCReset_GAMG"
PetscErrorCode PCReset_GAMG(PC pc)
{
  PetscErrorCode  ierr;
  PC_MG           *mg = (PC_MG*)pc->data;
  PC_GAMG         *pc_gamg = (PC_GAMG*)mg->innerctx;

  PetscFunctionBegin;
  if( pc_gamg->data != 0 ) { /* this should not happen, cleaned up in SetUp */
    ierr = PetscFree(pc_gamg->data); CHKERRQ(ierr);
  }
  pc_gamg->data = 0; pc_gamg->data_sz = 0;
  PetscFunctionReturn(0);
}

/* -------------------------------------------------------------------------- */
/*
   createLevel: create coarse op with RAP.  repartition and/or reduce number
     of active processors.

   Input Parameter:
   . pc - parameters
   . Amat_fine - matrix on this fine (k) level
   . cbs - coarse block size
   . isLast -
   In/Output Parameter:
   . a_P_inout - prolongation operator to the next level (k-1)
   . a_nactive_proc - number of active procs
   Output Parameter:
   . a_Amat_crs - coarse matrix that is created (k-1)
*/

#undef __FUNCT__
#define __FUNCT__ "createLevel"
PetscErrorCode createLevel( const PC pc,
                            const Mat Amat_fine,
                            const PetscInt cbs,
                            const PetscBool isLast,
                            Mat *a_P_inout,
                            PetscMPIInt *a_nactive_proc,
                            Mat *a_Amat_crs
                            )
{
  PC_MG           *mg = (PC_MG*)pc->data;
  PC_GAMG         *pc_gamg = (PC_GAMG*)mg->innerctx;
  const PetscBool  repart = pc_gamg->repart;
  const PetscInt   min_eq_proc = pc_gamg->min_eq_proc, coarse_max = pc_gamg->coarse_eq_limit;
  PetscErrorCode   ierr;
  Mat              Cmat,Pnew,Pold=*a_P_inout;
  IS               new_indices,isnum;
  MPI_Comm         wcomm = ((PetscObject)Amat_fine)->comm;
  PetscMPIInt      mype,npe,new_npe,nactive = *a_nactive_proc;
  PetscInt         neq,NN,Istart,Iend,Istart0,Iend0,ncrs_new,ncrs0,rfactor;

  PetscFunctionBegin;
  ierr = MPI_Comm_rank( wcomm, &mype ); CHKERRQ(ierr);
  ierr = MPI_Comm_size( wcomm, &npe );  CHKERRQ(ierr);

  /* RAP */
#ifdef USE_R
  /* make R wih brute force for now */
  ierr = MatTranspose( Pold, Pnew );
  ierr = MatDestroy( &Pold );  CHKERRQ(ierr);
  ierr = MatRARt( Amat_fine, Pnew, MAT_INITIAL_MATRIX, 2.0, &Cmat ); CHKERRQ(ierr);
  Pold = Pnew;
#else
  ierr = MatPtAP( Amat_fine, Pold, MAT_INITIAL_MATRIX, 2.0, &Cmat ); CHKERRQ(ierr);
#endif
  ierr = MatSetBlockSize( Cmat, cbs );      CHKERRQ(ierr);
  ierr = MatGetOwnershipRange( Cmat, &Istart0, &Iend0 ); CHKERRQ(ierr);
  ncrs0 = (Iend0-Istart0)/cbs; assert((Iend0-Istart0)%cbs == 0);

  /* get number of PEs to make active, reduce */
  ierr = MatGetSize( Cmat, &neq, &NN );  CHKERRQ(ierr);
  new_npe = (PetscMPIInt)((float)neq/(float)min_eq_proc + 0.5); /* hardwire min. number of eq/proc */
  if( new_npe == 0 || neq < coarse_max ) new_npe = 1;
  else if (new_npe >= nactive ) new_npe = nactive; /* no change, rare */
  if( isLast ) new_npe = 1;

  if( !repart && new_npe==nactive ) {
    *a_Amat_crs = Cmat; /* output - no repartitioning or reduction */
  }
  else {
    /* Repartition Cmat_{k} and move colums of P^{k}_{k-1} and coordinates accordingly */
    const PetscInt *idx,ndata_rows=pc_gamg->data_cell_rows,ndata_cols=pc_gamg->data_cell_cols,data_sz=ndata_rows*ndata_cols;
    const PetscInt  stride0=ncrs0*pc_gamg->data_cell_rows;
    PetscInt        *counts,is_sz,*newproc_idx,ii,jj,kk,strideNew,*tidx,inpe,targetPE;
    IS              isnewproc;
    VecScatter      vecscat;
    PetscScalar    *array;
    Vec             src_crd, dest_crd;
    IS              isscat;

    ierr = PetscMalloc( npe*sizeof(PetscInt), &counts ); CHKERRQ(ierr);
#if defined PETSC_USE_LOG
      ierr = PetscLogEventBegin(gamg_setup_events[SET12],0,0,0,0);CHKERRQ(ierr);
#endif
    if( repart ) {
      /* create sub communicator  */
      Mat             adj;

      if (pc_gamg->verbose) PetscPrintf(wcomm,"\t[%d]%s repartition: npe (active): %d --> %d, neq = %d\n",mype,__FUNCT__,*a_nactive_proc,new_npe,neq);

      /* MatPartitioningApply call MatConvert, which is collective */
      if( cbs == 1 ) {
	ierr = MatConvert( Cmat, MATMPIADJ, MAT_INITIAL_MATRIX, &adj );   CHKERRQ(ierr);
      }
      else{
	/* make a scalar matrix to partition */
	Mat tMat;
	PetscInt ncols,jj,Ii;
	const PetscScalar *vals;
	const PetscInt *idx;
	PetscInt *d_nnz, *o_nnz;
	static PetscInt llev = 0;

	ierr = PetscMalloc( ncrs0*sizeof(PetscInt), &d_nnz ); CHKERRQ(ierr);
	ierr = PetscMalloc( ncrs0*sizeof(PetscInt), &o_nnz ); CHKERRQ(ierr);
	for ( Ii = Istart0, jj = 0 ; Ii < Iend0 ; Ii += cbs, jj++ ) {
	  ierr = MatGetRow(Cmat,Ii,&ncols,0,0); CHKERRQ(ierr);
	  d_nnz[jj] = ncols/cbs;
	  o_nnz[jj] = ncols/cbs;
	  ierr = MatRestoreRow(Cmat,Ii,&ncols,0,0); CHKERRQ(ierr);
	  if( d_nnz[jj] > ncrs0 ) d_nnz[jj] = ncrs0;
	  if( o_nnz[jj] > (neq/cbs-ncrs0) ) o_nnz[jj] = neq/cbs-ncrs0;
	}

	ierr = MatCreateMPIAIJ( wcomm, ncrs0, ncrs0,
				PETSC_DETERMINE, PETSC_DETERMINE,
				0, d_nnz, 0, o_nnz,
				&tMat );
	CHKERRQ(ierr);
	ierr = PetscFree( d_nnz ); CHKERRQ(ierr);
	ierr = PetscFree( o_nnz ); CHKERRQ(ierr);

	for ( ii = Istart0; ii < Iend0; ii++ ) {
	  PetscInt dest_row = ii/cbs;
	  ierr = MatGetRow(Cmat,ii,&ncols,&idx,&vals); CHKERRQ(ierr);
	  for( jj = 0 ; jj < ncols ; jj++ ){
	    PetscInt dest_col = idx[jj]/cbs;
	    PetscScalar v = 1.0;
	    ierr = MatSetValues(tMat,1,&dest_row,1,&dest_col,&v,ADD_VALUES); CHKERRQ(ierr);
	  }
	  ierr = MatRestoreRow(Cmat,ii,&ncols,&idx,&vals); CHKERRQ(ierr);
	}
	ierr = MatAssemblyBegin(tMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
	ierr = MatAssemblyEnd(tMat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

	if( llev++ == -1 ) {
	  PetscViewer viewer; char fname[32];
	  sprintf(fname,"part_mat_%d.mat",llev);
	  PetscViewerBinaryOpen(wcomm,fname,FILE_MODE_WRITE,&viewer);
	  ierr = MatView( tMat, viewer ); CHKERRQ(ierr);
	  ierr = PetscViewerDestroy( &viewer );
	}

	ierr = MatConvert( tMat, MATMPIADJ, MAT_INITIAL_MATRIX, &adj );   CHKERRQ(ierr);

	ierr = MatDestroy( &tMat );  CHKERRQ(ierr);
      }

      { /* partition: get newproc_idx, set is_sz */
	char prefix[256];
	const char *pcpre;
	const PetscInt *is_idx;
	MatPartitioning  mpart;
	IS proc_is;

	ierr = MatPartitioningCreate( wcomm, &mpart ); CHKERRQ(ierr);
	ierr = MatPartitioningSetAdjacency( mpart, adj ); CHKERRQ(ierr);
	ierr = PCGetOptionsPrefix( pc, &pcpre );CHKERRQ(ierr);
	ierr = PetscSNPrintf(prefix,sizeof prefix,"%spc_gamg_",pcpre?pcpre:"");CHKERRQ(ierr);
	ierr = PetscObjectSetOptionsPrefix((PetscObject)mpart,prefix);CHKERRQ(ierr);
	ierr = MatPartitioningSetFromOptions( mpart );    CHKERRQ(ierr);
	ierr = MatPartitioningSetNParts( mpart, new_npe );CHKERRQ(ierr);
	ierr = MatPartitioningApply( mpart, &proc_is ); CHKERRQ(ierr);
	ierr = MatPartitioningDestroy( &mpart );          CHKERRQ(ierr);

	/* collect IS info */
	ierr = ISGetLocalSize( proc_is, &is_sz );       CHKERRQ(ierr);
	ierr = PetscMalloc( cbs*is_sz*sizeof(PetscInt), &newproc_idx ); CHKERRQ(ierr);
	ierr = ISGetIndices( proc_is, &is_idx );        CHKERRQ(ierr);
	NN = 1; /* bring to "front" of machine */
	/*NN = npe/new_npe;*/ /* spread partitioning across machine */
	for( kk = jj = 0 ; kk < is_sz ; kk++ ){
	  for( ii = 0 ; ii < cbs ; ii++, jj++ ){
	    newproc_idx[jj] = is_idx[kk] * NN; /* distribution */
	  }
	}
	ierr = ISRestoreIndices( proc_is, &is_idx );     CHKERRQ(ierr);
	ierr = ISDestroy( &proc_is );                    CHKERRQ(ierr);

	is_sz *= cbs;
      }
      ierr = MatDestroy( &adj );                       CHKERRQ(ierr);

      ierr = ISCreateGeneral( wcomm, is_sz, newproc_idx, PETSC_COPY_VALUES, &isnewproc );
      CHKERRQ(ierr);
      if( newproc_idx != 0 ) {
	ierr = PetscFree( newproc_idx );  CHKERRQ(ierr);
      }
    }
    else { /* simple aggreagtion of parts */
      /* find factor */
      if( new_npe == 1 ) rfactor = npe; /* easy */
      else {
	PetscReal best_fact = 0.;
	jj = -1;
	for( kk = 1 ; kk <= npe ; kk++ ){
	  if( npe%kk==0 ) { /* a candidate */
	    PetscReal nactpe = (PetscReal)npe/(PetscReal)kk, fact = nactpe/(PetscReal)new_npe;
	    if(fact > 1.0) fact = 1./fact; /* keep fact < 1 */
	    if( fact > best_fact ) {
	      best_fact = fact; jj = kk;
	    }
	  }
	}
	if(jj!=-1) rfactor = jj;
	else rfactor = 1; /* prime? */
      }
      new_npe = npe/rfactor;

      if( new_npe==nactive ) {
	*a_Amat_crs = Cmat; /* output - no repartitioning or reduction */
	ierr = PetscFree( counts );  CHKERRQ(ierr);
	*a_nactive_proc = new_npe; /* output */
	if (pc_gamg->verbose) PetscPrintf(wcomm,"\t[%d]%s aggregate processors noop: new_npe=%d, neq=%d\n",mype,__FUNCT__,new_npe,neq);
	PetscFunctionReturn(0);
      }

      /* reduce - isnewproc */
      targetPE = mype/rfactor;

      if (pc_gamg->verbose) PetscPrintf(wcomm,"\t[%d]%s aggregate processors: npe: %d --> %d, neq=%d\n",mype,__FUNCT__,*a_nactive_proc,new_npe,neq);
      is_sz = ncrs0*cbs;
      ierr = ISCreateStride( wcomm, is_sz, targetPE, 0, &isnewproc );
      CHKERRQ(ierr);
    }

    /*
      Create an index set from the isnewproc index set to indicate the mapping TO
    */
    ierr = ISPartitioningToNumbering( isnewproc, &isnum ); CHKERRQ(ierr);
    /*
      Determine how many elements are assigned to each processor
    */
    inpe = npe;
    ierr = ISPartitioningCount( isnewproc, inpe, counts ); CHKERRQ(ierr);
    ierr = ISDestroy( &isnewproc );                       CHKERRQ(ierr);
    ncrs_new = counts[mype]/cbs;
    strideNew = ncrs_new*ndata_rows;
#if defined PETSC_USE_LOG
      ierr = PetscLogEventEnd(gamg_setup_events[SET12],0,0,0,0);   CHKERRQ(ierr);
#endif
    /* Create a vector to contain the newly ordered element information */
    ierr = VecCreate( wcomm, &dest_crd );
    ierr = VecSetSizes( dest_crd, data_sz*ncrs_new, PETSC_DECIDE ); CHKERRQ(ierr);
    ierr = VecSetFromOptions( dest_crd ); CHKERRQ(ierr); /* this is needed! */
    /*
     There are 'ndata_rows*ndata_cols' data items per node, (one can think of the vectors of having
     a block size of ...).  Note, ISs are expanded into equation space by 'cbs'.
     */
    ierr = PetscMalloc( (ncrs0*data_sz)*sizeof(PetscInt), &tidx ); CHKERRQ(ierr);
    ierr = ISGetIndices( isnum, &idx ); CHKERRQ(ierr);
    for(ii=0,jj=0; ii<ncrs0 ; ii++) {
      PetscInt id = idx[ii*cbs]/cbs; /* get node back */
      for( kk=0; kk<data_sz ; kk++, jj++) tidx[jj] = id*data_sz + kk;
    }
    ierr = ISRestoreIndices( isnum, &idx ); CHKERRQ(ierr);
    ierr = ISCreateGeneral( wcomm, data_sz*ncrs0, tidx, PETSC_COPY_VALUES, &isscat );
    CHKERRQ(ierr);
    ierr = PetscFree( tidx );  CHKERRQ(ierr);
    /*
     Create a vector to contain the original vertex information for each element
     */
    ierr = VecCreateSeq( PETSC_COMM_SELF, data_sz*ncrs0, &src_crd ); CHKERRQ(ierr);
    for( jj=0; jj<ndata_cols ; jj++ ) {
      for( ii=0 ; ii<ncrs0 ; ii++) {
	for( kk=0; kk<ndata_rows ; kk++ ) {
	  PetscInt ix = ii*ndata_rows + kk + jj*stride0, jx = ii*data_sz + kk*ndata_cols + jj;
          PetscScalar tt = (PetscScalar)pc_gamg->data[ix];
	  ierr = VecSetValues( src_crd, 1, &jx, &tt, INSERT_VALUES );  CHKERRQ(ierr);
	}
      }
    }
    ierr = VecAssemblyBegin(src_crd); CHKERRQ(ierr);
    ierr = VecAssemblyEnd(src_crd); CHKERRQ(ierr);
    /*
      Scatter the element vertex information (still in the original vertex ordering)
      to the correct processor
    */
    ierr = VecScatterCreate( src_crd, PETSC_NULL, dest_crd, isscat, &vecscat);
    CHKERRQ(ierr);
    ierr = ISDestroy( &isscat );       CHKERRQ(ierr);
    ierr = VecScatterBegin(vecscat,src_crd,dest_crd,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = VecScatterEnd(vecscat,src_crd,dest_crd,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = VecScatterDestroy( &vecscat );       CHKERRQ(ierr);
    ierr = VecDestroy( &src_crd );       CHKERRQ(ierr);
    /*
      Put the element vertex data into a new allocation of the gdata->ele
    */
    ierr = PetscFree( pc_gamg->data );    CHKERRQ(ierr);
    ierr = PetscMalloc( data_sz*ncrs_new*sizeof(PetscReal), &pc_gamg->data );    CHKERRQ(ierr);
    pc_gamg->data_sz = data_sz*ncrs_new;
    ierr = VecGetArray( dest_crd, &array );    CHKERRQ(ierr);
    for( jj=0; jj<ndata_cols ; jj++ ) {
      for( ii=0 ; ii<ncrs_new ; ii++) {
	for( kk=0; kk<ndata_rows ; kk++ ) {
	  PetscInt ix = ii*ndata_rows + kk + jj*strideNew, jx = ii*data_sz + kk*ndata_cols + jj;
	  pc_gamg->data[ix] = PetscRealPart(array[jx]);
	  array[jx] = 1.e300;
	}
      }
    }
    ierr = VecRestoreArray( dest_crd, &array );    CHKERRQ(ierr);
    ierr = VecDestroy( &dest_crd );    CHKERRQ(ierr);
#if defined PETSC_USE_LOG
    ierr = PetscLogEventBegin(gamg_setup_events[SET13],0,0,0,0);CHKERRQ(ierr);
#endif
    /*
      Invert for MatGetSubMatrix
    */
    ierr = ISInvertPermutation( isnum, ncrs_new*cbs, &new_indices ); CHKERRQ(ierr);
    ierr = ISSort( new_indices ); CHKERRQ(ierr); /* is this needed? */
    ierr = ISDestroy( &isnum ); CHKERRQ(ierr);
#if defined PETSC_USE_LOG
    ierr = PetscLogEventEnd(gamg_setup_events[SET13],0,0,0,0);CHKERRQ(ierr);
    ierr = PetscLogEventBegin(gamg_setup_events[SET14],0,0,0,0);CHKERRQ(ierr);
#endif
    /* A_crs output */
    ierr = MatGetSubMatrix( Cmat, new_indices, new_indices, MAT_INITIAL_MATRIX, a_Amat_crs );
    CHKERRQ(ierr);

    ierr = MatDestroy( &Cmat ); CHKERRQ(ierr);
    Cmat = *a_Amat_crs; /* output */
    ierr = MatSetBlockSize( Cmat, cbs );      CHKERRQ(ierr);
#if defined PETSC_USE_LOG
    ierr = PetscLogEventEnd(gamg_setup_events[SET14],0,0,0,0);CHKERRQ(ierr);
#endif
    /* prolongator */
    ierr = MatGetOwnershipRange( Pold, &Istart, &Iend );    CHKERRQ(ierr);
    {
      IS findices;
#if defined PETSC_USE_LOG
      ierr = PetscLogEventBegin(gamg_setup_events[SET15],0,0,0,0);CHKERRQ(ierr);
#endif
      ierr = ISCreateStride(wcomm,Iend-Istart,Istart,1,&findices);   CHKERRQ(ierr);
#ifdef USE_R
      ierr = MatGetSubMatrix( Pold, new_indices, findices, MAT_INITIAL_MATRIX, &Pnew );
#else
      ierr = MatGetSubMatrix( Pold, findices, new_indices, MAT_INITIAL_MATRIX, &Pnew );
#endif
      CHKERRQ(ierr);
      ierr = ISDestroy( &findices ); CHKERRQ(ierr);
#if defined PETSC_USE_LOG
      ierr = PetscLogEventEnd(gamg_setup_events[SET15],0,0,0,0);CHKERRQ(ierr);
#endif
    }
    ierr = MatDestroy( a_P_inout ); CHKERRQ(ierr);
    *a_P_inout = Pnew; /* output - repartitioned */
    ierr = ISDestroy( &new_indices ); CHKERRQ(ierr);
    ierr = PetscFree( counts );  CHKERRQ(ierr);
  }

  *a_nactive_proc = new_npe; /* output */

  if( !PETSC_TRUE ) {
    PetscViewer viewer; char fname[32]; static int llev=0; Cmat = *a_Amat_crs;
    if(llev==0) {
      sprintf(fname,"Cmat_%d.m",llev++);
      PetscViewerASCIIOpen(wcomm,fname,&viewer);
      ierr = PetscViewerSetFormat( viewer, PETSC_VIEWER_ASCII_MATLAB);  CHKERRQ(ierr);
      ierr = MatView(Amat_fine, viewer ); CHKERRQ(ierr);
      ierr = PetscViewerDestroy( &viewer );
    }
    sprintf(fname,"Cmat_%d.m",llev++);
    PetscViewerASCIIOpen(wcomm,fname,&viewer);
    ierr = PetscViewerSetFormat( viewer, PETSC_VIEWER_ASCII_MATLAB);  CHKERRQ(ierr);
    ierr = MatView(Cmat, viewer ); CHKERRQ(ierr);
    ierr = PetscViewerDestroy( &viewer );
  }

  PetscFunctionReturn(0);
}

/* -------------------------------------------------------------------------- */
/*
   PCSetUp_GAMG - Prepares for the use of the GAMG preconditioner
                    by setting data structures and options.

   Input Parameter:
.  pc - the preconditioner context

   Application Interface Routine: PCSetUp()

   Notes:
   The interface routine PCSetUp() is not usually called directly by
   the user, but instead is called by PCApply() if necessary.
*/
#undef __FUNCT__
#define __FUNCT__ "PCSetUp_GAMG"
PetscErrorCode PCSetUp_GAMG( PC pc )
{
  PetscErrorCode  ierr;
  PC_MG           *mg = (PC_MG*)pc->data;
  PC_GAMG         *pc_gamg = (PC_GAMG*)mg->innerctx;
  PC_MG_Levels   **mglevels = mg->levels;
  Mat              Amat = pc->mat, Pmat = pc->pmat;
  PetscInt         fine_level,level,level1,M,N,bs,nloc,lidx,Istart,Iend;
  MPI_Comm         wcomm = ((PetscObject)pc)->comm;
  PetscMPIInt      mype,npe,nactivepe;
  Mat              Aarr[GAMG_MAXLEVELS], Parr[GAMG_MAXLEVELS];
  PetscReal        emaxs[GAMG_MAXLEVELS];
  PetscLogDouble   nnz0,nnztot;
  MatInfo          info;

  PetscFunctionBegin;
  pc_gamg->setup_count++;
  if( pc->setupcalled > 0 ) {
    /* just do Galerkin grids */
    Mat B,dA,dB;

    /* PCSetUp_MG seems to insists on setting this to GMRES */
    ierr = KSPSetType( mglevels[0]->smoothd, KSPPREONLY ); CHKERRQ(ierr);

    if( pc_gamg->Nlevels > 1 ) {
      /* currently only handle case where mat and pmat are the same on coarser levels */
      ierr = KSPGetOperators(mglevels[pc_gamg->Nlevels-1]->smoothd,&dA,&dB,PETSC_NULL);CHKERRQ(ierr);
      /* (re)set to get dirty flag */
      ierr = KSPSetOperators(mglevels[pc_gamg->Nlevels-1]->smoothd,dA,dB,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
      ierr = KSPSetUp( mglevels[pc_gamg->Nlevels-1]->smoothd ); CHKERRQ(ierr);

      for (level=pc_gamg->Nlevels-2; level>-1; level--) {
        ierr = KSPGetOperators(mglevels[level]->smoothd,PETSC_NULL,&B,PETSC_NULL);CHKERRQ(ierr);
        /* the first time through the matrix structure has changed from repartitioning */
        if( pc_gamg->setup_count == 2 ) {
          ierr = MatDestroy( &B );  CHKERRQ(ierr);
          ierr = MatPtAP(dB,mglevels[level+1]->interpolate,MAT_INITIAL_MATRIX,1.0,&B);CHKERRQ(ierr);
          mglevels[level]->A = B;
        }
        else {
          ierr = MatPtAP(dB,mglevels[level+1]->interpolate,MAT_REUSE_MATRIX,1.0,&B);CHKERRQ(ierr);
        }
        ierr = KSPSetOperators(mglevels[level]->smoothd,B,B,SAME_NONZERO_PATTERN); CHKERRQ(ierr);
        dB = B;
        /* setup KSP/PC */
        ierr = KSPSetUp( mglevels[level]->smoothd ); CHKERRQ(ierr);
      }
    }

    pc->setupcalled = 2;

    PetscFunctionReturn(0);
  }

  ierr = MPI_Comm_rank(wcomm,&mype);CHKERRQ(ierr);
  ierr = MPI_Comm_size(wcomm,&npe);CHKERRQ(ierr);
  /* GAMG requires input of fine-grid matrix. It determines nlevels. */
  ierr = MatGetBlockSize( Amat, &bs ); CHKERRQ(ierr);
  ierr = MatGetSize( Amat, &M, &N );CHKERRQ(ierr);
  ierr = MatGetOwnershipRange( Amat, &Istart, &Iend ); CHKERRQ(ierr);
  nloc = (Iend-Istart)/bs; assert((Iend-Istart)%bs == 0);

  if( pc_gamg->data == 0 && nloc > 0 ) {
    if(!pc_gamg->createdefaultdata){
      SETERRQ(((PetscObject)pc)->comm,PETSC_ERR_LIB,"'createdefaultdata' not set?!?! need to support NULL data!!!");
    }
    ierr = pc_gamg->createdefaultdata( pc ); CHKERRQ(ierr);
  }

  /* Get A_i and R_i */
  if (pc_gamg->verbose) {
    if(pc_gamg->verbose==1) ierr =  MatGetInfo(Amat,MAT_LOCAL,&info);
    else ierr =  MatGetInfo(Amat,MAT_GLOBAL_SUM,&info);
    CHKERRQ(ierr);
    nnz0 = info.nz_used;
    nnztot = info.nz_used;
    PetscPrintf(wcomm,"\t[%d]%s level %d N=%d, n data rows=%d, n data cols=%d, nnz/row (ave)=%d, np=%d\n",
                mype,__FUNCT__,0,N,pc_gamg->data_cell_rows,pc_gamg->data_cell_cols,
                (int)(nnz0/(PetscReal)N),npe);
  }
  for ( level=0, Aarr[0] = Pmat, nactivepe = npe; /* hard wired stopping logic */
        level < (pc_gamg->Nlevels-1) && (level==0 || M>pc_gamg->coarse_eq_limit); /* && (npe==1 || nactivepe>1); */
        level++ ){
    level1 = level + 1;
#if (defined PETSC_USE_LOG && defined GAMG_STAGES)
    ierr = PetscLogStagePush(gamg_stages[level]); CHKERRQ( ierr );
#endif
#if defined PETSC_USE_LOG
    ierr = PetscLogEventBegin(gamg_setup_events[SET1],0,0,0,0); CHKERRQ(ierr);
#endif
    { /* construct prolongator */
      Mat Gmat;   assert(pc_gamg->graph);
      IS selected, llist;   assert(pc_gamg->coarsen);

      ierr = pc_gamg->graph( pc, Aarr[level], &Gmat ); CHKERRQ(ierr);
      ierr = pc_gamg->coarsen( pc, Gmat, &selected, &llist ); CHKERRQ(ierr);
      ierr = pc_gamg->prolongator( pc, Aarr[level], Gmat, selected, llist, &Parr[level1] );
      CHKERRQ(ierr);

      if( Parr[level1] ){
          /* get new block size of coarse matrices */
        if( pc_gamg->col_bs_id != -1 ){
          PetscBool flag;
          ierr = PetscObjectComposedDataGetInt( (PetscObject)Parr[level1], pc_gamg->col_bs_id, bs, flag );
          CHKERRQ( ierr ); assert(flag);
        }
      }

      if( pc_gamg->optprol && Parr[level1] ){
        /* smooth */
        ierr = pc_gamg->optprol( pc, Aarr[level], &Parr[level1] ); CHKERRQ(ierr);
      }

      ierr = MatDestroy( &Gmat );  CHKERRQ(ierr);
      ierr = ISDestroy( &selected );  CHKERRQ(ierr);
      ierr = ISDestroy( &llist );  CHKERRQ(ierr);
    }
#if defined PETSC_USE_LOG
    ierr = PetscLogEventEnd(gamg_setup_events[SET1],0,0,0,0);CHKERRQ(ierr);
#endif
    /* cache eigen estimate */
    if( pc_gamg->emax_id != -1 ){
      PetscBool flag;
      ierr = PetscObjectComposedDataGetReal( (PetscObject)Aarr[level], pc_gamg->emax_id, emaxs[level], flag );
      CHKERRQ( ierr );
      if( !flag ) emaxs[level] = -1.;
    }
    else emaxs[level] = -1.;
    if(level==0) Aarr[0] = Amat; /* use Pmat for finest level setup, but use mat for solver */
    if( !Parr[level1] ) {
      if (pc_gamg->verbose) PetscPrintf(wcomm,"\t[%d]%s stop gridding, level %d\n",mype,__FUNCT__,level);
      break;
    }
#if defined PETSC_USE_LOG
    ierr = PetscLogEventBegin(gamg_setup_events[SET2],0,0,0,0);CHKERRQ(ierr);
#endif
    ierr = createLevel( pc, Aarr[level], bs,
                        (PetscBool)(level==pc_gamg->Nlevels-2),
                        &Parr[level1], &nactivepe, &Aarr[level1] );
    CHKERRQ(ierr);
#if defined PETSC_USE_LOG
    ierr = PetscLogEventEnd(gamg_setup_events[SET2],0,0,0,0);CHKERRQ(ierr);
#endif
    ierr = MatGetSize( Aarr[level1], &M, &N );CHKERRQ(ierr);
    ierr = MatGetInfo( Aarr[level1], MAT_GLOBAL_SUM, &info ); CHKERRQ(ierr);
    if (pc_gamg->verbose){
      PetscPrintf(wcomm,"\t\t[%d]%s %d) N=%d, n data cols=%d, nnz/row (ave)=%d, %d active pes\n",
                  mype,__FUNCT__,(int)level1,N,pc_gamg->data_cell_cols,
                  (int)(info.nz_used/(PetscReal)N),nactivepe);
    }
    /* stop if one node */
    if( M/pc_gamg->data_cell_cols < 2 ) {
      level++;
      break;
    }
    /* Vec diag; PetscScalar *data_arr,v; PetscInt Istart,Iend,kk,nloceq,id; */
    /* v = 1.e-10; /\* LU factor has hard wired numbers for small diags so this needs to match (yuk) *\/ */
    /* ierr = MatGetOwnershipRange(Aarr[level1], &Istart, &Iend); CHKERRQ(ierr); */
    /* nloceq = Iend-Istart; */
    /* ierr = MatGetVecs( Aarr[level1], &diag, 0 );    CHKERRQ(ierr); */
    /* ierr = MatGetDiagonal( Aarr[level1], diag );    CHKERRQ(ierr); */
    /* ierr = VecGetArray( diag, &data_arr );   CHKERRQ(ierr); */
    /* for(kk=0;kk<nloceq;kk++){ */
    /*   if(data_arr[kk]==0.0) { */
    /*     id = kk + Istart; */
    /*     ierr = MatSetValues(Aarr[level1],1,&id,1,&id,&v,INSERT_VALUES); */
    /*     CHKERRQ(ierr); */
    /*     PetscPrintf(PETSC_COMM_SELF,"\t[%d]%s warning: added zero to diag (%d) on level %d \n",mype,__FUNCT__,id,level1); */
    /*   } */
    /* } */
    /* ierr = VecRestoreArray( diag, &data_arr ); CHKERRQ(ierr); */
    /* ierr = VecDestroy( &diag );                CHKERRQ(ierr); */
    ierr = MatAssemblyBegin(Aarr[level1],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(Aarr[level1],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

#if (defined PETSC_USE_LOG && defined GAMG_STAGES)
    ierr = PetscLogStagePop(); CHKERRQ( ierr );
#endif
    if(pc_gamg->verbose){
      if(pc_gamg->verbose==1) ierr =  MatGetInfo(Aarr[level1],MAT_LOCAL,&info);
      else ierr =  MatGetInfo(Aarr[level1],MAT_GLOBAL_SUM,&info);
      CHKERRQ(ierr);
      nnztot += info.nz_used;
    }
  } /* levels */

  if( pc_gamg->data ) {
    ierr = PetscFree( pc_gamg->data ); CHKERRQ( ierr );
    pc_gamg->data = 0;
  }

  if (pc_gamg->verbose) PetscPrintf(wcomm,"\t[%d]%s %d levels, grid compexity = %g\n",0,__FUNCT__,level+1,nnztot/nnz0);
  pc_gamg->Nlevels = level + 1;
  fine_level = level;
  ierr = PCMGSetLevels(pc,pc_gamg->Nlevels,PETSC_NULL);CHKERRQ(ierr);

  if( pc_gamg->Nlevels > 1 ) { /* don't setup MG if  */
  /* set default smoothers */
  for ( lidx = 1, level = pc_gamg->Nlevels-2;
        lidx <= fine_level;
        lidx++, level--) {
    PetscReal emax, emin;
    KSP smoother; PC subpc;
    PetscBool isCheb;
    /* set defaults */
    ierr = PCMGGetSmoother( pc, lidx, &smoother ); CHKERRQ(ierr);
    ierr = KSPSetType( smoother, KSPCHEBYCHEV );CHKERRQ(ierr);
    ierr = KSPGetPC( smoother, &subpc ); CHKERRQ(ierr);
    /* ierr = KSPSetTolerances(smoother,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,2); CHKERRQ(ierr); */
    ierr = PCSetType( subpc, PCJACOBI ); CHKERRQ(ierr);
    ierr = KSPSetNormType( smoother, KSP_NORM_NONE ); CHKERRQ(ierr);
    /* overide defaults with input parameters */
    ierr = KSPSetFromOptions( smoother ); CHKERRQ(ierr);

    ierr = KSPSetOperators( smoother, Aarr[level], Aarr[level], SAME_NONZERO_PATTERN );   CHKERRQ(ierr);
    /* do my own cheby */
    ierr = PetscTypeCompare( (PetscObject)smoother, KSPCHEBYCHEV, &isCheb ); CHKERRQ(ierr);

    if( isCheb ) {
      ierr = PetscTypeCompare( (PetscObject)subpc, PCJACOBI, &isCheb ); CHKERRQ(ierr);
      if( isCheb && emaxs[level] > 0.0 ) emax=emaxs[level]; /* eigen estimate only for diagnal PC */
      else{ /* eigen estimate 'emax' */
        KSP eksp; Mat Lmat = Aarr[level];
        Vec bb, xx;

        ierr = MatGetVecs( Lmat, &bb, 0 );         CHKERRQ(ierr);
        ierr = MatGetVecs( Lmat, &xx, 0 );         CHKERRQ(ierr);
        {
          PetscRandom    rctx;
          ierr = PetscRandomCreate(wcomm,&rctx);CHKERRQ(ierr);
          ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
          ierr = VecSetRandom(bb,rctx);CHKERRQ(ierr);
          ierr = PetscRandomDestroy( &rctx ); CHKERRQ(ierr);
        }
        ierr = KSPCreate(wcomm,&eksp);CHKERRQ(ierr);
        ierr = KSPSetTolerances( eksp, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT, 10 );
        CHKERRQ(ierr);
        ierr = KSPSetNormType( eksp, KSP_NORM_NONE );                 CHKERRQ(ierr);

        ierr = KSPAppendOptionsPrefix( eksp, "est_");         CHKERRQ(ierr);
        ierr = KSPSetFromOptions( eksp );    CHKERRQ(ierr);

        ierr = KSPSetInitialGuessNonzero( eksp, PETSC_FALSE ); CHKERRQ(ierr);
        ierr = KSPSetOperators( eksp, Lmat, Lmat, SAME_NONZERO_PATTERN ); CHKERRQ( ierr );
        ierr = KSPSetComputeSingularValues( eksp,PETSC_TRUE ); CHKERRQ(ierr);

        { /* set PC type to be same as smoother - does not get all parameters!!! */
          const PCType type;    PC pc;
          ierr = PCGetType( subpc, &type );   CHKERRQ(ierr);
          ierr = KSPGetPC( eksp, &pc );CHKERRQ( ierr );
          ierr = PCSetType( pc, type ); CHKERRQ(ierr);
        }

	/* solve - keep stuff out of logging */
	ierr = PetscLogEventDeactivate(KSP_Solve);CHKERRQ(ierr);
	ierr = PetscLogEventDeactivate(PC_Apply);CHKERRQ(ierr);
        ierr = KSPSolve( eksp, bb, xx ); CHKERRQ(ierr);
	ierr = PetscLogEventActivate(KSP_Solve);CHKERRQ(ierr);
	ierr = PetscLogEventActivate(PC_Apply);CHKERRQ(ierr);

        ierr = KSPComputeExtremeSingularValues( eksp, &emax, &emin ); CHKERRQ(ierr);

        ierr = VecDestroy( &xx );       CHKERRQ(ierr);
        ierr = VecDestroy( &bb );       CHKERRQ(ierr);
        ierr = KSPDestroy( &eksp );       CHKERRQ(ierr);

        if (pc_gamg->verbose) {
          PetscPrintf(wcomm,"\t\t\t%s PC setup max eigen=%e min=%e\n",__FUNCT__,emax,emin);
        }
      }
      {
        PetscInt N1, N0, tt;
        ierr = MatGetSize( Aarr[level], &N1, &tt );         CHKERRQ(ierr);
        ierr = MatGetSize( Aarr[level+1], &N0, &tt );       CHKERRQ(ierr);
        /* heuristic - is this crap? */
        emin = 1.*emax/((PetscReal)N1/(PetscReal)N0);
        emax *= 1.05;
      }
      ierr = KSPChebychevSetEigenvalues( smoother, emax, emin );CHKERRQ(ierr);
    }
  }
  {
    /* coarse grid */
    KSP smoother,*k2; PC subpc,pc2; PetscInt ii,first;
    Mat Lmat = Aarr[pc_gamg->Nlevels-1];
    ierr = PCMGGetSmoother( pc, 0, &smoother ); CHKERRQ(ierr);
    ierr = KSPSetOperators( smoother, Lmat, Lmat, SAME_NONZERO_PATTERN ); CHKERRQ(ierr);
    ierr = KSPSetNormType( smoother, KSP_NORM_NONE ); CHKERRQ(ierr);
    ierr = KSPGetPC( smoother, &subpc ); CHKERRQ(ierr);
    ierr = PCSetType( subpc, PCBJACOBI ); CHKERRQ(ierr);
    ierr = PCSetUp( subpc ); CHKERRQ(ierr);
    ierr = PCBJacobiGetSubKSP(subpc,&ii,&first,&k2);CHKERRQ(ierr);
    assert(ii==1);
    ierr = KSPGetPC(k2[0],&pc2);CHKERRQ(ierr);
    ierr = PCSetType( pc2, PCLU ); CHKERRQ(ierr);
  }

  /* should be called in PCSetFromOptions_GAMG(), but cannot be called prior to PCMGSetLevels() */
  ierr = PetscObjectOptionsBegin((PetscObject)pc);CHKERRQ(ierr);
  ierr = PCSetFromOptions_MG(pc); CHKERRQ(ierr);
  ierr = PetscOptionsEnd();CHKERRQ(ierr);
  if (mg->galerkin != 2) SETERRQ(wcomm,PETSC_ERR_USER,"GAMG does Galerkin manually so the -pc_mg_galerkin option must not be used.");

  /* set interpolation between the levels, clean up */
  for (lidx=0,level=pc_gamg->Nlevels-1;
       lidx<fine_level;
       lidx++, level--){
    ierr = PCMGSetInterpolation( pc, lidx+1, Parr[level] );CHKERRQ(ierr);
    ierr = MatDestroy( &Parr[level] );  CHKERRQ(ierr);
    ierr = MatDestroy( &Aarr[level] );  CHKERRQ(ierr);
  }

  /* setupcalled is set to 0 so that MG is setup from scratch */
  pc->setupcalled = 0;
  ierr = PCSetUp_MG( pc );CHKERRQ( ierr );
  pc->setupcalled = 1; /* use 1 as signal that this has not been re-setup */

  {
    KSP smoother;  /* PCSetUp_MG seems to insists on setting this to GMRES on coarse grid */
    ierr = PCMGGetSmoother( pc, 0, &smoother ); CHKERRQ(ierr);
    ierr = KSPSetType( smoother, KSPPREONLY ); CHKERRQ(ierr);
    ierr = KSPSetUp( smoother ); CHKERRQ(ierr);
  }
  }
  else {
    KSP smoother;
    if (pc_gamg->verbose) PetscPrintf(wcomm,"\t[%d]%s one level solver used (system is seen as DD). Using default solver.\n",mype,__FUNCT__);
    ierr = PCMGGetSmoother( pc, 0, &smoother ); CHKERRQ(ierr);
    ierr = KSPSetOperators( smoother, Aarr[0], Aarr[0], SAME_NONZERO_PATTERN );   CHKERRQ(ierr);
    ierr = KSPSetType( smoother, KSPPREONLY ); CHKERRQ(ierr);
    /* setupcalled is set to 0 so that MG is setup from scratch */
    pc->setupcalled = 0;
    ierr = PCSetUp_MG( pc );CHKERRQ( ierr );
    pc->setupcalled = 1; /* use 1 as signal that this has not been re-setup */
  }
  PetscFunctionReturn(0);
}

/* ------------------------------------------------------------------------- */
/*
   PCDestroy_GAMG - Destroys the private context for the GAMG preconditioner
   that was created with PCCreate_GAMG().

   Input Parameter:
.  pc - the preconditioner context

   Application Interface Routine: PCDestroy()
*/
#undef __FUNCT__
#define __FUNCT__ "PCDestroy_GAMG"
PetscErrorCode PCDestroy_GAMG( PC pc )
{
  PetscErrorCode  ierr;
  PC_MG           *mg = (PC_MG*)pc->data;
  PC_GAMG         *pc_gamg= (PC_GAMG*)mg->innerctx;

  PetscFunctionBegin;
  ierr = PCReset_GAMG( pc );CHKERRQ(ierr);
  ierr = PetscFree( pc_gamg );CHKERRQ(ierr);
  ierr = PCDestroy_MG( pc );CHKERRQ(ierr);
  PetscFunctionReturn(0);
}


#undef __FUNCT__
#define __FUNCT__ "PCGAMGSetProcEqLim"
/*@
   PCGAMGSetProcEqLim - Set number of equations to aim for on coarse grids via
   processor reduction.

   Not Collective on PC

   Input Parameters:
.  pc - the preconditioner context


   Options Database Key:
.  -pc_gamg_process_eq_limit

   Level: intermediate

   Concepts: Unstructured multrigrid preconditioner

.seealso: ()
@*/
PetscErrorCode  PCGAMGSetProcEqLim(PC pc, PetscInt n)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(pc,PC_CLASSID,1);
  ierr = PetscTryMethod(pc,"PCGAMGSetProcEqLim_C",(PC,PetscInt),(pc,n));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "PCGAMGSetProcEqLim_GAMG"
PetscErrorCode PCGAMGSetProcEqLim_GAMG(PC pc, PetscInt n)
{
  PC_MG           *mg = (PC_MG*)pc->data;
  PC_GAMG         *pc_gamg = (PC_GAMG*)mg->innerctx;

  PetscFunctionBegin;
  if(n>0) pc_gamg->min_eq_proc = n;
  PetscFunctionReturn(0);
}
EXTERN_C_END

#undef __FUNCT__
#define __FUNCT__ "PCGAMGSetCoarseEqLim"
/*@
   PCGAMGSetCoarseEqLim - Set max number of equations on coarse grids.

 Collective on PC

   Input Parameters:
.  pc - the preconditioner context


   Options Database Key:
.  -pc_gamg_coarse_eq_limit

   Level: intermediate

   Concepts: Unstructured multrigrid preconditioner

.seealso: ()
 @*/
PetscErrorCode PCGAMGSetCoarseEqLim(PC pc, PetscInt n)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(pc,PC_CLASSID,1);
  ierr = PetscTryMethod(pc,"PCGAMGSetCoarseEqLim_C",(PC,PetscInt),(pc,n));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "PCGAMGSetCoarseEqLim_GAMG"
PetscErrorCode PCGAMGSetCoarseEqLim_GAMG(PC pc, PetscInt n)
{
  PC_MG           *mg = (PC_MG*)pc->data;
  PC_GAMG         *pc_gamg = (PC_GAMG*)mg->innerctx;

  PetscFunctionBegin;
  if(n>0) pc_gamg->coarse_eq_limit = n;
  PetscFunctionReturn(0);
}
EXTERN_C_END

#undef __FUNCT__
#define __FUNCT__ "PCGAMGSetRepartitioning"
/*@
   PCGAMGSetRepartitioning - Repartition the coarse grids

   Collective on PC

   Input Parameters:
.  pc - the preconditioner context


   Options Database Key:
.  -pc_gamg_repartition

   Level: intermediate

   Concepts: Unstructured multrigrid preconditioner

.seealso: ()
@*/
PetscErrorCode PCGAMGSetRepartitioning(PC pc, PetscBool n)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(pc,PC_CLASSID,1);
  ierr = PetscTryMethod(pc,"PCGAMGSetRepartitioning_C",(PC,PetscBool),(pc,n));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "PCGAMGSetRepartitioning_GAMG"
PetscErrorCode PCGAMGSetRepartitioning_GAMG(PC pc, PetscBool n)
{
  PC_MG           *mg = (PC_MG*)pc->data;
  PC_GAMG         *pc_gamg = (PC_GAMG*)mg->innerctx;

  PetscFunctionBegin;
  pc_gamg->repart = n;
  PetscFunctionReturn(0);
}
EXTERN_C_END

#undef __FUNCT__
#define __FUNCT__ "PCGAMGSetNlevels"
/*@
   PCGAMGSetNlevels -

   Not collective on PC

   Input Parameters:
.  pc - the preconditioner context


   Options Database Key:
.  -pc_mg_levels

   Level: intermediate

   Concepts: Unstructured multrigrid preconditioner

.seealso: ()
@*/
PetscErrorCode PCGAMGSetNlevels(PC pc, PetscInt n)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(pc,PC_CLASSID,1);
  ierr = PetscTryMethod(pc,"PCGAMGSetNlevels_C",(PC,PetscInt),(pc,n));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "PCGAMGSetNlevels_GAMG"
PetscErrorCode PCGAMGSetNlevels_GAMG(PC pc, PetscInt n)
{
  PC_MG           *mg = (PC_MG*)pc->data;
  PC_GAMG         *pc_gamg = (PC_GAMG*)mg->innerctx;

  PetscFunctionBegin;
  pc_gamg->Nlevels = n;
  PetscFunctionReturn(0);
}
EXTERN_C_END

#undef __FUNCT__
#define __FUNCT__ "PCGAMGSetThreshold"
/*@
   PCGAMGSetThreshold - Relative threshold to use for dropping edges in aggregation graph

   Not collective on PC

   Input Parameters:
.  pc - the preconditioner context


   Options Database Key:
.  -pc_gamg_threshold

   Level: intermediate

   Concepts: Unstructured multrigrid preconditioner

.seealso: ()
@*/
PetscErrorCode PCGAMGSetThreshold(PC pc, PetscReal n)
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(pc,PC_CLASSID,1);
  ierr = PetscTryMethod(pc,"PCGAMGSetThreshold_C",(PC,PetscReal),(pc,n));CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "PCGAMGSetThreshold_GAMG"
PetscErrorCode PCGAMGSetThreshold_GAMG(PC pc, PetscReal n)
{
  PC_MG           *mg = (PC_MG*)pc->data;
  PC_GAMG         *pc_gamg = (PC_GAMG*)mg->innerctx;

  PetscFunctionBegin;
  pc_gamg->threshold = n;
  PetscFunctionReturn(0);
}
EXTERN_C_END

#undef __FUNCT__
#define __FUNCT__ "PCGAMGSetType"
/*@
   PCGAMGSetType - Set solution method - calls sub create method

   Collective on PC

   Input Parameters:
.  pc - the preconditioner context


   Options Database Key:
.  -pc_gamg_type

   Level: intermediate

   Concepts: Unstructured multrigrid preconditioner

.seealso: ()
@*/
PetscErrorCode PCGAMGSetType( PC pc, const PCGAMGType type )
{
  PetscErrorCode ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(pc,PC_CLASSID,1);
  ierr = PetscTryMethod(pc,"PCGAMGSetType_C",(PC,const PCGAMGType),(pc,type));
  CHKERRQ(ierr);
  PetscFunctionReturn(0);
}

EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "PCGAMGSetType_GAMG"
PetscErrorCode PCGAMGSetType_GAMG( PC pc, const PCGAMGType type )
{
  PetscErrorCode ierr,(*r)(PC);

  PetscFunctionBegin;
  ierr = PetscFListFind(GAMGList,((PetscObject)pc)->comm,type,PETSC_FALSE,(PetscVoidStarFunction)&r);
  CHKERRQ(ierr);

  if (!r) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_UNKNOWN_TYPE,"Unknown GAMG type %s given",type);

  /* call sub create method */
  ierr = (*r)(pc); CHKERRQ(ierr);

  PetscFunctionReturn(0);
}
EXTERN_C_END

#undef __FUNCT__
#define __FUNCT__ "PCSetFromOptions_GAMG"
PetscErrorCode PCSetFromOptions_GAMG( PC pc )
{
  PetscErrorCode  ierr;
  PC_MG           *mg = (PC_MG*)pc->data;
  PC_GAMG         *pc_gamg = (PC_GAMG*)mg->innerctx;
  PetscBool        flag;
  MPI_Comm         wcomm = ((PetscObject)pc)->comm;

  PetscFunctionBegin;
  ierr = PetscOptionsHead("GAMG options"); CHKERRQ(ierr);
  {
    /* -pc_gamg_verbose */
    ierr = PetscOptionsInt("-pc_gamg_verbose","Verbose (debugging) output for PCGAMG",
                           "none", pc_gamg->verbose,
                           &pc_gamg->verbose, PETSC_NULL );
    CHKERRQ(ierr);

    /* -pc_gamg_repartition */
    ierr = PetscOptionsBool("-pc_gamg_repartition",
                            "Repartion coarse grids (false)",
                            "PCGAMGRepartitioning",
                            pc_gamg->repart,
                            &pc_gamg->repart,
                            &flag);
    CHKERRQ(ierr);

    /* -pc_gamg_process_eq_limit */
    ierr = PetscOptionsInt("-pc_gamg_process_eq_limit",
                           "Limit (goal) on number of equations per process on coarse grids",
                           "PCGAMGSetProcEqLim",
                           pc_gamg->min_eq_proc,
                           &pc_gamg->min_eq_proc,
                           &flag );
    CHKERRQ(ierr);

    /* -pc_gamg_coarse_eq_limit */
    ierr = PetscOptionsInt("-pc_gamg_coarse_eq_limit",
                           "Limit on number of equations for the coarse grid",
                           "PCGAMGSetCoarseEqLim",
                           pc_gamg->coarse_eq_limit,
                           &pc_gamg->coarse_eq_limit,
                           &flag );
    CHKERRQ(ierr);

    /* -pc_gamg_threshold */
    ierr = PetscOptionsReal("-pc_gamg_threshold",
                            "Relative threshold to use for dropping edges in aggregation graph",
                            "PCGAMGSetThreshold",
                            pc_gamg->threshold,
                            &pc_gamg->threshold,
                            &flag );
    CHKERRQ(ierr);
    if(flag && pc_gamg->verbose) PetscPrintf(wcomm,"\t[%d]%s threshold set %e\n",0,__FUNCT__,pc_gamg->threshold);

    ierr = PetscOptionsInt("-pc_mg_levels",
                           "Set number of MG levels",
                           "PCGAMGSetNlevels",
                           pc_gamg->Nlevels,
                           &pc_gamg->Nlevels,
                           &flag );
  }
  ierr = PetscOptionsTail();CHKERRQ(ierr);

  PetscFunctionReturn(0);
}

/* -------------------------------------------------------------------------- */
/*MC
     PCCreate_GAMG - Geometric algebraic multigrid (AMG) preconditioning framework.
       - This is the entry point to GAMG, registered in pcregis.c

   Options Database Keys:
   Multigrid options(inherited)
+  -pc_mg_cycles <1>: 1 for V cycle, 2 for W-cycle (PCMGSetCycleType)
.  -pc_mg_smoothup <1>: Number of post-smoothing steps (PCMGSetNumberSmoothUp)
.  -pc_mg_smoothdown <1>: Number of pre-smoothing steps (PCMGSetNumberSmoothDown)
-  -pc_mg_type <multiplicative>: (one of) additive multiplicative full cascade kascade

  Level: intermediate

  Concepts: multigrid

.seealso:  PCCreate(), PCSetType(), PCType (for list of available types), PC, PCMGType,
           PCMGSetLevels(), PCMGGetLevels(), PCMGSetType(), PCMGSetCycleType(), PCMGSetNumberSmoothDown(),
           PCMGSetNumberSmoothUp(), PCMGGetCoarseSolve(), PCMGSetResidual(), PCMGSetInterpolation(),
           PCMGSetRestriction(), PCMGGetSmoother(), PCMGGetSmootherUp(), PCMGGetSmootherDown(),
           PCMGSetCyclesOnLevel(), PCMGSetRhs(), PCMGSetX(), PCMGSetR()
M*/
EXTERN_C_BEGIN
#undef __FUNCT__
#define __FUNCT__ "PCCreate_GAMG"
PetscErrorCode  PCCreate_GAMG( PC pc )
{
  PetscErrorCode  ierr;
  PC_GAMG         *pc_gamg;
  PC_MG           *mg;
  PetscClassId     cookie;

#if defined PETSC_USE_LOG
  static long count = 0;
#endif

  PetscFunctionBegin;
  /* PCGAMG is an inherited class of PCMG. Initialize pc as PCMG */
  ierr = PCSetType( pc, PCMG );  CHKERRQ(ierr); /* calls PCCreate_MG() and MGCreate_Private() */
  ierr = PetscObjectChangeTypeName( (PetscObject)pc, PCGAMG ); CHKERRQ(ierr);

  /* create a supporting struct and attach it to pc */
  ierr = PetscNewLog( pc, PC_GAMG, &pc_gamg ); CHKERRQ(ierr);
  mg = (PC_MG*)pc->data;
  mg->galerkin = 2;             /* Use Galerkin, but it is computed externally */
  mg->innerctx = pc_gamg;

  pc_gamg->setup_count = 0;
  /* these should be in subctx but repartitioning needs simple arrays */
  pc_gamg->data_sz = 0;
  pc_gamg->data = 0;

  /* register AMG type */
  if( !GAMGList ){
    ierr = PetscFListAdd(&GAMGList,GAMGGEO,"PCCreateGAMG_GEO",(void(*)(void))PCCreateGAMG_GEO);CHKERRQ(ierr);
    ierr = PetscFListAdd(&GAMGList,GAMGAGG,"PCCreateGAMG_AGG",(void(*)(void))PCCreateGAMG_AGG);CHKERRQ(ierr);
  }

  /* overwrite the pointers of PCMG by the functions of base class PCGAMG */
  pc->ops->setfromoptions = PCSetFromOptions_GAMG;
  pc->ops->setup          = PCSetUp_GAMG;
  pc->ops->reset          = PCReset_GAMG;
  pc->ops->destroy        = PCDestroy_GAMG;

  ierr = PetscObjectComposeFunctionDynamic( (PetscObject)pc,
					    "PCGAMGSetProcEqLim_C",
					    "PCGAMGSetProcEqLim_GAMG",
					    PCGAMGSetProcEqLim_GAMG);
  CHKERRQ(ierr);

  ierr = PetscObjectComposeFunctionDynamic( (PetscObject)pc,
					    "PCGAMGSetCoarseEqLim_C",
					    "PCGAMGSetCoarseEqLim_GAMG",
					    PCGAMGSetCoarseEqLim_GAMG);
  CHKERRQ(ierr);

  ierr = PetscObjectComposeFunctionDynamic( (PetscObject)pc,
					    "PCGAMGSetRepartitioning_C",
					    "PCGAMGSetRepartitioning_GAMG",
					    PCGAMGSetRepartitioning_GAMG);
  CHKERRQ(ierr);

  ierr = PetscObjectComposeFunctionDynamic( (PetscObject)pc,
					    "PCGAMGSetThreshold_C",
					    "PCGAMGSetThreshold_GAMG",
					    PCGAMGSetThreshold_GAMG);
  CHKERRQ(ierr);

  ierr = PetscObjectComposeFunctionDynamic( (PetscObject)pc,
					    "PCGAMGSetType_C",
					    "PCGAMGSetType_GAMG",
					    PCGAMGSetType_GAMG);
  CHKERRQ(ierr);

  pc_gamg->repart = PETSC_FALSE;
  pc_gamg->min_eq_proc = 100;
  pc_gamg->coarse_eq_limit = 800;
  pc_gamg->threshold = 0.05;
  pc_gamg->Nlevels = GAMG_MAXLEVELS;
  pc_gamg->verbose = 0;
  pc_gamg->emax_id = -1;
  pc_gamg->col_bs_id = -1;

  /* instantiate derived type */
  ierr = PetscOptionsHead("GAMG options"); CHKERRQ(ierr);
  {
    char tname[256] = GAMGAGG;
    ierr = PetscOptionsList("-pc_gamg_type","Type of GAMG method","PCGAMGSetType",
                            GAMGList, tname, tname, sizeof(tname), PETSC_NULL );
    CHKERRQ(ierr);
    ierr = PCGAMGSetType( pc, tname ); CHKERRQ(ierr);
  }
  ierr = PetscOptionsTail();CHKERRQ(ierr);

#if defined PETSC_USE_LOG
  if( count++ == 0 ) {
    PetscClassIdRegister("GAMG Setup",&cookie);
    PetscLogEventRegister("GAMG: createProl", cookie, &gamg_setup_events[SET1]);
    PetscLogEventRegister("  Graph", cookie, &gamg_setup_events[GRAPH]);
    /* PetscLogEventRegister("    G.Mat", cookie, &gamg_setup_events[GRAPH_MAT]); */
    /* PetscLogEventRegister("    G.Filter", cookie, &gamg_setup_events[GRAPH_FILTER]); */
    /* PetscLogEventRegister("    G.Square", cookie, &gamg_setup_events[GRAPH_SQR]); */
    PetscLogEventRegister("  MIS/Agg", cookie, &gamg_setup_events[SET4]);
    PetscLogEventRegister("  geo: growSupp", cookie, &gamg_setup_events[SET5]);
    PetscLogEventRegister("  geo: triangle", cookie, &gamg_setup_events[SET6]);
    PetscLogEventRegister("    search&set", cookie, &gamg_setup_events[FIND_V]);
    PetscLogEventRegister("  SA: colect data", cookie, &gamg_setup_events[SET7]);
    PetscLogEventRegister("  SA: frmProl0", cookie, &gamg_setup_events[SET8]);
    PetscLogEventRegister("  SA: smooth", cookie, &gamg_setup_events[SET9]);
    PetscLogEventRegister("GAMG: partLevel", cookie, &gamg_setup_events[SET2]);
    PetscLogEventRegister("  repartition", cookie, &gamg_setup_events[SET12]);
    PetscLogEventRegister("  Invert-Sort", cookie, &gamg_setup_events[SET13]);
    PetscLogEventRegister("  Move A", cookie, &gamg_setup_events[SET14]);
    PetscLogEventRegister("  Move P", cookie, &gamg_setup_events[SET15]);

    /* PetscLogEventRegister(" PL move data", cookie, &gamg_setup_events[SET13]); */
    /* PetscLogEventRegister("GAMG: fix", cookie, &gamg_setup_events[SET10]); */
    /* PetscLogEventRegister("GAMG: set levels", cookie, &gamg_setup_events[SET11]); */
    /* create timer stages */
#if defined GAMG_STAGES
    {
      char str[32];
      sprintf(str,"MG Level %d (finest)",0);
      PetscLogStageRegister(str, &gamg_stages[0]);
      PetscInt lidx;
      for (lidx=1;lidx<9;lidx++){
	sprintf(str,"MG Level %d",lidx);
	PetscLogStageRegister(str, &gamg_stages[lidx]);
      }
    }
#endif
  }
#endif
  PetscFunctionReturn(0);
}
EXTERN_C_END