Ifpack_SupportGraph.h

/*@HEADER
// ***********************************************************************
//
//       Ifpack: Object-Oriented Algebraic Preconditioner Package
//                 Copyright (2002) Sandia Corporation
//
// Under terms of Contract DE-AC04-94AL85000, there is a non-exclusive
// license for use of this work by or on behalf of the U.S. Government.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// 1. Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the Corporation nor the names of the
// contributors may be used to endorse or promote products derived from
// this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// Questions? Contact Michael A. Heroux (maherou@sandia.gov)
//
// ***********************************************************************
//@HEADER
*/
 
#ifndef IFPACK_SUPPORTGRAPH_H
#define IFPACK_SUPPORTGRAPH_H
 
#if defined(Ifpack_SHOW_DEPRECATED_WARNINGS)
#ifdef __GNUC__
#warning "The Ifpack package is deprecated"
#endif
#endif
 
#include "Ifpack_ConfigDefs.h"
#include "Ifpack_Condest.h"
#include "Ifpack_Preconditioner.h"
#include "Ifpack_Amesos.h"
#include "Ifpack_Condest.h"
#include "Epetra_Map.h"
#include "Epetra_Comm.h"
#include "Epetra_Time.h"
#include "Epetra_Vector.h"
#include "Epetra_MultiVector.h"
#include "Epetra_LinearProblem.h"
#include "Epetra_RowMatrix.h"
#include "Epetra_CrsMatrix.h"
 
#include "Teuchos_ParameterList.hpp"
#include "Teuchos_RefCountPtr.hpp"
 
#include <boost/graph/adjacency_list.hpp>
#include <boost/graph/kruskal_min_spanning_tree.hpp>
#include <boost/graph/prim_minimum_spanning_tree.hpp>
#include <boost/config.hpp>
 
using Teuchos::RefCountPtr;
using Teuchos::rcp;
typedef std::pair<int, int> E;
using namespace boost;
 
typedef adjacency_list < vecS, vecS, undirectedS,
  no_property, property < edge_weight_t, double > > Graph;
typedef graph_traits < Graph >::edge_descriptor Edge;
typedef graph_traits < Graph >::vertex_descriptor Vertex;
 
 
 
template<typename T=Ifpack_Amesos> class Ifpack_SupportGraph :
public virtual Ifpack_Preconditioner
{
 
 public:
 
 
 Ifpack_SupportGraph(Epetra_RowMatrix* Matrix_in);
 
 
 
 
 virtual int SetUseTranspose(bool UseTranspose_in);
 
 
 
 
 
 virtual int Apply(const Epetra_MultiVector& X, Epetra_MultiVector& Y) const;
 
 
 virtual int ApplyInverse(const Epetra_MultiVector& X, Epetra_MultiVector& Y) const;
 
 virtual double NormInf() const {return(0.0);}
 
 
 
 
 virtual const char * Label() const;
 
 virtual bool UseTranspose() const {return(UseTranspose_);};
 
 virtual bool HasNormInf() const {return(false);};
 
 virtual const Epetra_Comm & Comm() const {return(Matrix_->Comm());};
 
 virtual const Epetra_Map & OperatorDomainMap() const {return(Matrix_->OperatorDomainMap());};
 
 virtual const Epetra_Map & OperatorRangeMap() const {return(Matrix_->OperatorRangeMap());};
 
 
 
 
 virtual bool IsInitialized() const
 {
   return(IsInitialized_);
 }
 
 virtual bool IsComputed() const
 {
   return(IsComputed_);
 }
 
 
 virtual int SetParameters(Teuchos::ParameterList& List);
 
 
 virtual int Initialize();
 
 virtual int Compute();
 
 
 
 
 
 
 virtual double Condest(const Ifpack_CondestType CT = Ifpack_Cheap,
                        const int MaxIters = 1550,
                        const double Tol = 1e-9,
                        Epetra_RowMatrix* Matrix_in = 0);
 
 virtual double Condest() const
 {
   return(Condest_);
 }
 
 virtual const Epetra_RowMatrix& Matrix() const
 {
   return(*Matrix_);
 }
 
 virtual std::ostream& Print(std::ostream&) const;
 
 virtual int NumInitialize() const
 {
   return(NumInitialize_);
 }
 
 virtual int NumCompute() const
 {
   return(NumCompute_);
 }
 
 virtual int NumApplyInverse() const
 {
   return(NumApplyInverse_);
 }
 
 virtual double InitializeTime() const
 {
   return(InitializeTime_);
 }
 
 virtual double ComputeTime() const
 {
   return(ComputeTime_);
 }
 
 virtual double ApplyInverseTime() const
 {
   return(ApplyInverseTime_);
 }
 
 virtual double InitializeFlops() const
 {
   return(InitializeFlops_);
 }
 
 virtual double ComputeFlops() const
 {
   return(ComputeFlops_);
 }
 
 virtual double ApplyInverseFlops() const
 {
   return(ApplyInverseFlops_);
 }
 
 
 
 protected:
 
 int FindSupport();
 
 Teuchos::RefCountPtr<const Epetra_RowMatrix> Matrix_;
 
 Teuchos::RefCountPtr<Epetra_CrsMatrix> Support_;
 
 std::string Label_;
 
 bool IsInitialized_;
 
 bool IsComputed_;
 
 bool UseTranspose_;
 
 Teuchos::ParameterList List_;
 
 double Condest_;
 
 int NumInitialize_;
 
 int NumCompute_;
 
 mutable int NumApplyInverse_;
 
 double InitializeTime_;
 
 double ComputeTime_;
 
 mutable double ApplyInverseTime_;
 
 double InitializeFlops_;
 
 double ComputeFlops_;
 
 mutable double ApplyInverseFlops_;
 
 Teuchos::RefCountPtr<Epetra_Time> Time_;
 
 Teuchos::RefCountPtr<T> Inverse_;
 
 int NumForests_;
 
 double DiagPertRel_;
 
 double DiagPertAbs_;
 
 double KeepDiag_;
 
 int Randomize_;
 
}; // class Ifpack_SupportGraph<T>
 
 
 
//==============================================================================
template<typename T>
Ifpack_SupportGraph<T>::Ifpack_SupportGraph(Epetra_RowMatrix* Matrix_in):
Matrix_(rcp(Matrix_in,false)),
  IsInitialized_(false),
  IsComputed_(false),
  UseTranspose_(false),
  Condest_(-1.0),
  NumInitialize_(0),
  NumCompute_(0),
  NumApplyInverse_(0),
  InitializeTime_(0.0),
  ComputeTime_(0.0),
  ApplyInverseTime_(0.0),
  InitializeFlops_(0.0),
  ComputeFlops_(0.0),
  ApplyInverseFlops_(0.0),
  NumForests_(1),
  DiagPertRel_(1.0),
  DiagPertAbs_(0.0),
  KeepDiag_(1.0),
  Randomize_(0)
{
 
  Teuchos::ParameterList List_in;
  SetParameters(List_in);
}
//==============================================================================
template<typename T>
int Ifpack_SupportGraph<T>::FindSupport()
{
 
  // Extract matrix dimensions
  long long rows = (*Matrix_).NumGlobalRows64();
  long long cols = (*Matrix_).NumGlobalCols64();
  int num_edges  = ((*Matrix_).NumMyNonzeros() - (*Matrix_).NumMyDiagonals())/2;
  std::cout << "global num rows " << rows << std::endl;
 
  // Assert square matrix
  IFPACK_CHK_ERR((rows == cols));
 
  if(rows > std::numeric_limits<int>::max())
  {
    std::cerr << "Ifpack_SupportGraph<T>::FindSupport: global num rows won't fit an int. " << rows << std::endl;
    IFPACK_CHK_ERR(1);
  }
 
  // Rename for clarity
  int num_verts = (int) rows;
 
  // Create data structures for the BGL code and temp data structures for extraction
  E *edge_array = new E[num_edges];
  double *weights = new double[num_edges];
 
  int num_entries;
  int max_num_entries = (*Matrix_).MaxNumEntries();
  double *values = new double[max_num_entries];
  int *indices = new int[max_num_entries];
 
  double * diagonal = new double[num_verts];
 
 
  for(int i = 0; i < max_num_entries; i++)
    {
      values[i]=0;
      indices[i]=0;
    }
 
  // Extract from the epetra matrix keeping only one edge per pair (assume symmetric)
  int k = 0;
  for(int i = 0; i < num_verts; i++)
    {
      (*Matrix_).ExtractMyRowCopy(i,max_num_entries,num_entries,values,indices);
 
      for(int j = 0; j < num_entries; j++)
        {
 
          if(i == indices[j])
            {
              diagonal[i] = values[j];
              // Diagonal pertubation, only if requested
              if (DiagPertRel_)
                 diagonal[i] *= DiagPertRel_;
              if (DiagPertAbs_)
                 diagonal[i] += DiagPertAbs_;
            }
 
          if(i < indices[j])
            {
              edge_array[k] = E(i,indices[j]);
              weights[k] = values[j];
              if (Randomize_)
              {
                // Add small random pertubation.
                weights[k] *= (1.0 + 1e-8 * drand48());
              }
 
              k++;
            }
        }
    }
 
  // Create BGL graph
  Graph g(edge_array, edge_array + num_edges, weights, num_verts);
 
 
  property_map < Graph, edge_weight_t >::type weight = get(edge_weight, g);
 
  std::vector < Edge > spanning_tree;
 
  // Run Kruskal, actually maximal weight ST since edges are negative
  kruskal_minimum_spanning_tree(g, std::back_inserter(spanning_tree));
 
 
  std::vector<int> NumNz(num_verts,1);
 
  //Find the degree of all the vertices
  for (std::vector < Edge >::iterator ei = spanning_tree.begin();
       ei != spanning_tree.end(); ++ei)
    {
      NumNz[source(*ei,g)] = NumNz[source(*ei,g)] + 1;
      NumNz[target(*ei,g)] = NumNz[target(*ei,g)] + 1;
    }
 
 
  // Create an stl vector of stl vectors to hold indices and values (neighbour edges)
  std::vector< std::vector< int > > Indices(num_verts);
  // TODO: Optimize for performance, may use arrays instead of vectors
  //std::vector<int> Indices[num_verts];
  //std::vector<double> Values[num_verts];
 
  std::vector< std::vector< double > > Values(num_verts);
 
  for(int i = 0; i < num_verts; i++)
    {
      std::vector<int> temp(NumNz[i],0);
      std::vector<double> temp2(NumNz[i],0);
      Indices[i] = temp;
      Values[i] = temp2;
    }
 
  int *l = new int[num_verts];
  for(int i = 0; i < num_verts; i++)
    {
      Indices[i][0] = i;
      l[i] = 1;
    }
 
  // Add each spanning forest (tree) to the support graph and
  // remove it from original graph
  for(int i = 0; i < NumForests_; i++)
    {
      if(i > 0)
        {
          spanning_tree.clear();
          kruskal_minimum_spanning_tree(g,std::back_inserter(spanning_tree));
          for(std::vector < Edge >::iterator ei = spanning_tree.begin();
              ei != spanning_tree.end(); ++ei)
            {
              NumNz[source(*ei,g)] = NumNz[source(*ei,g)] + 1;
              NumNz[target(*ei,g)] = NumNz[target(*ei,g)] + 1;
            }
          for(int i = 0; i < num_verts; i++)
            {
              Indices[i].resize(NumNz[i]);
              Values[i].resize(NumNz[i]);
            }
        }
 
      for (std::vector < Edge >::iterator ei = spanning_tree.begin();
           ei != spanning_tree.end(); ++ei)
        {
          // Assume standard Laplacian with constant row-sum.
          // Edge weights are negative, so subtract to make diagonal positive
          Indices[source(*ei,g)][0] = source(*ei,g);
          Values[source(*ei,g)][0] = Values[source(*ei,g)][0] - weight[*ei];
          Indices[target(*ei,g)][0] = target(*ei,g);
          Values[target(*ei,g)][0] = Values[target(*ei,g)][0] - weight[*ei];
 
          Indices[source(*ei,g)][l[source(*ei,g)]] = target(*ei,g);
          Values[source(*ei,g)][l[source(*ei,g)]] = weight[*ei];
          l[source(*ei,g)] = l[source(*ei,g)] + 1;
 
          Indices[target(*ei,g)][l[target(*ei,g)]] = source(*ei,g);
          Values[target(*ei,g)][l[target(*ei,g)]] = weight[*ei];
          l[target(*ei,g)] = l[target(*ei,g)] + 1;
 
          remove_edge(*ei,g);
        }
 
    }
 
 
  // Set diagonal to weighted average of Laplacian preconditioner
  // and the original matrix
 
  // First compute the "diagonal surplus" (in the original input matrix)
  // If input is a (pure, Dirichlet) graph Laplacian , this will be 0
  Epetra_Vector ones(Matrix_->OperatorDomainMap());
  Epetra_Vector surplus(Matrix_->OperatorRangeMap());
 
  ones.PutScalar(1.0);
  Matrix_->Multiply(false, ones, surplus);
 
  for(int i = 0; i < num_verts; i++)
     {
          Values[i][0] += surplus[i];
          Values[i][0] = KeepDiag_*diagonal[i] +
                         (1.-KeepDiag_) * Values[i][0];
     }
 
  // Create the CrsMatrix for the support graph
  Support_ = rcp(new Epetra_CrsMatrix(Copy, Matrix().RowMatrixRowMap(),l, false));
 
#ifndef EPETRA_NO_64BIT_GLOBAL_INDICES
  if((*Matrix_).RowMatrixRowMap().GlobalIndicesLongLong())
  {
    // Fill in the matrix with the stl vectors for each row
    for(int i = 0; i < num_verts; i++)
      {
        std::vector<long long> IndicesLL(l[i]);
        for(int k = 0; k < l[i]; ++k)
           IndicesLL[k] = Indices[i][k];
 
        (*Support_).InsertGlobalValues(i,l[i],&Values[i][0],&IndicesLL[0]);
      }
  }
  else
#endif
#ifndef EPETRA_NO_32BIT_GLOBAL_INDICES
  if((*Matrix_).RowMatrixRowMap().GlobalIndicesInt())
  {
    // Fill in the matrix with the stl vectors for each row
    for(int i = 0; i < num_verts; i++)
      {
        (*Support_).InsertGlobalValues(i,l[i],&Values[i][0],&Indices[i][0]);
      }
  }
  else
#endif
  throw "Ifpack_SupportGraph::FindSupport: GlobalIndices unknown.";;
 
  (*Support_).FillComplete();
 
  delete edge_array;
  delete weights;
  delete values;
  delete indices;
  delete l;
  delete diagonal;
 
  return(0);
}
//==============================================================================
template<typename T>
int Ifpack_SupportGraph<T>::SetParameters(Teuchos::ParameterList& List_in)
{
  List_ = List_in;
  NumForests_ = List_in.get("MST: forest number", NumForests_);
  KeepDiag_ = List_in.get("MST: keep diagonal", KeepDiag_);
  Randomize_ = List_in.get("MST: randomize", Randomize_);
  // Diagonal pertubation parameters have weird names to be compatible with rest of Ifpack!
  DiagPertRel_ = List_in.get("fact: relative threshold", DiagPertRel_);
  DiagPertAbs_ = List_in.get("fact: absolute threshold", DiagPertAbs_);
 
  return(0);
}
//==============================================================================
template<typename T>
int Ifpack_SupportGraph<T>::Initialize()
{
  IsInitialized_ = false;
  IsComputed_ = false;
 
 
  if (Time_ == Teuchos::null)
    {
      Time_ = Teuchos::rcp( new Epetra_Time(Comm()) );
    }
 
 
  Time_->ResetStartTime();
 
  FindSupport();
 
  Inverse_ = Teuchos::rcp(new T(Support_.get()));
 
  IFPACK_CHK_ERR(Inverse_->Initialize());
 
  IsInitialized_ = true;
  ++NumInitialize_;
  InitializeTime_ += Time_->ElapsedTime();
 
  return(0);
 
}
//==============================================================================
template<typename T>
int Ifpack_SupportGraph<T>::Compute()
{
  if (IsInitialized() == false)
    IFPACK_CHK_ERR(Initialize());
 
  Time_->ResetStartTime();
  IsComputed_ = false;
  Condest_ = -1.0;
 
  IFPACK_CHK_ERR(Inverse_->Compute());
 
  IsComputed_ = true;
  ++NumCompute_;
  ComputeTime_ += Time_->ElapsedTime();
 
 
  return(0);
}
//==============================================================================
template<typename T>
int Ifpack_SupportGraph<T>::SetUseTranspose(bool UseTranspose_in)
{
  // store the flag -- it will be set in Initialize() if Inverse_ does not
  // exist.
  UseTranspose_ = UseTranspose_in;
 
  // If Inverse_ exists, pass it right now.
  if (Inverse_!=Teuchos::null)
    IFPACK_CHK_ERR(Inverse_->SetUseTranspose(UseTranspose_in));
 
  return(0);
}
//==============================================================================
template<typename T>
int Ifpack_SupportGraph<T>::
Apply(const Epetra_MultiVector& X, Epetra_MultiVector& Y) const
{
  IFPACK_CHK_ERR(Matrix_->Apply(X,Y));
  return(0);
}
//==============================================================================
template<typename T>
const char * Ifpack_SupportGraph<T>::Label() const
{
  return(Label_.c_str());
}
//==============================================================================
template<typename T>
int Ifpack_SupportGraph<T>::
ApplyInverse(const Epetra_MultiVector& X, Epetra_MultiVector& Y) const
{
  if (!IsComputed())
    IFPACK_CHK_ERR(-3);
 
  Time_->ResetStartTime();
 
 
  Inverse_->ApplyInverse(X,Y);
 
  ++NumApplyInverse_;
  ApplyInverseTime_ += Time_->ElapsedTime();
 
  return(0);
}
//==============================================================================
template<typename T>
std::ostream& Ifpack_SupportGraph<T>::
Print(std::ostream& os) const
{
  os << "================================================================================" << std::endl;
   os << "Ifpack_SupportGraph: " << Label () << std::endl << std::endl;
  os << "Condition number estimate = " << Condest() << std::endl;
  os << "Global number of rows            = " << Matrix_->NumGlobalRows64() << std::endl;
  os << "Number of edges in support graph     = " << (Support_->NumGlobalNonzeros64()-Support_->NumGlobalDiagonals64())/2 << std::endl;
  os << "Fraction of off diagonals of support graph/off diagonals of original     = "
     << ((double)Support_->NumGlobalNonzeros64()-Support_->NumGlobalDiagonals64())/(Matrix_->NumGlobalNonzeros64()-Matrix_->NumGlobalDiagonals64());
  os << std::endl;
  os << "Phase           # calls   Total Time (s)       Total MFlops     MFlops/s" << std::endl;
  os << "-----           -------   --------------       ------------     --------" << std::endl;
  os << "Initialize()    "   << std::setw(10) << NumInitialize_
     << "  " << std::setw(15) << InitializeTime_
     << "        0.0              0.0" << std::endl;
  os << "Compute()       "   << std::setw(10) << NumCompute_
     << "  " << std::setw(22) << ComputeTime_
     << "  " << std::setw(15) << 1.0e-6 * ComputeFlops_;
  if (ComputeTime_ != 0.0)
    os << "  " << std::setw(15) << 1.0e-6 * ComputeFlops_ / ComputeTime_ << std::endl;
  else
    os << "     " << std::setw(15) << 0.0 << std::endl;
  os << "ApplyInverse()  "   << std::setw(10) << NumApplyInverse_
     << "  " << std::setw(22) << ApplyInverseTime_
     << "  " << std::setw(15) << 1.0e-6 * ApplyInverseFlops_;
  if (ApplyInverseTime_ != 0.0)
    os << "  " << std::setw(15) << 1.0e-6 * ApplyInverseFlops_ / ApplyInverseTime_ << std::endl;
  else
    os << "  " << std::setw(15) << 0.0 << std::endl;
 
  os << std::endl << std::endl;
  os << "Now calling the underlying preconditioner's print()" << std::endl;
 
  Inverse_->Print(os);
 
  return os;
}
//==============================================================================
template<typename T>
double Ifpack_SupportGraph<T>::
Condest(const Ifpack_CondestType CT, const int MaxIters,
        const double Tol, Epetra_RowMatrix* Matrix_in)
{
  if (!IsComputed()) // cannot compute right now
    {
      return(-1.0);
    }
 
  Condest_ = Ifpack_Condest(*this, CT, MaxIters, Tol, Matrix_in);
 
  return(Condest_);
}
 
#endif // IFPACK_SUPPORTGRAPH_H