sequenzo 0.1.18__cp312-cp312-win_amd64.whl → 0.1.20__cp312-cp312-win_amd64.whl

sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h

@@ -1,573 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-
-#include <iostream>
-#include <fstream>
-#include <Eigen/SparseCore>
-#include <bench/BenchTimer.h>
-#include <cstdlib>
-#include <string>
-#include <Eigen/Cholesky>
-#include <Eigen/Jacobi>
-#include <Eigen/Householder>
-#include <Eigen/IterativeLinearSolvers>
-#include <unsupported/Eigen/IterativeSolvers>
-#include <Eigen/LU>
-#include <unsupported/Eigen/SparseExtra>
-#include <Eigen/SparseLU>
-
-#include "spbenchstyle.h"
-
-#ifdef EIGEN_METIS_SUPPORT
-#include <Eigen/MetisSupport>
-#endif
-
-#ifdef EIGEN_CHOLMOD_SUPPORT
-#include <Eigen/CholmodSupport>
-#endif
-
-#ifdef EIGEN_UMFPACK_SUPPORT
-#include <Eigen/UmfPackSupport>
-#endif
-
-#ifdef EIGEN_KLU_SUPPORT
-#include <Eigen/KLUSupport>
-#endif
-
-#ifdef EIGEN_PARDISO_SUPPORT
-#include <Eigen/PardisoSupport>
-#endif
-
-#ifdef EIGEN_SUPERLU_SUPPORT
-#include <Eigen/SuperLUSupport>
-#endif
-
-#ifdef EIGEN_PASTIX_SUPPORT
-#include <Eigen/PaStiXSupport>
-#endif
-
-// CONSTANTS
-#define EIGEN_UMFPACK  10
-#define EIGEN_KLU  11
-#define EIGEN_SUPERLU  20
-#define EIGEN_PASTIX  30
-#define EIGEN_PARDISO  40
-#define EIGEN_SPARSELU_COLAMD 50
-#define EIGEN_SPARSELU_METIS 51
-#define EIGEN_BICGSTAB  60
-#define EIGEN_BICGSTAB_ILUT  61
-#define EIGEN_GMRES 70
-#define EIGEN_GMRES_ILUT 71
-#define EIGEN_SIMPLICIAL_LDLT  80
-#define EIGEN_CHOLMOD_LDLT  90
-#define EIGEN_PASTIX_LDLT  100
-#define EIGEN_PARDISO_LDLT  110
-#define EIGEN_SIMPLICIAL_LLT  120
-#define EIGEN_CHOLMOD_SUPERNODAL_LLT  130
-#define EIGEN_CHOLMOD_SIMPLICIAL_LLT  140
-#define EIGEN_PASTIX_LLT  150
-#define EIGEN_PARDISO_LLT  160
-#define EIGEN_CG  170
-#define EIGEN_CG_PRECOND  180
-
-using namespace Eigen;
-using namespace std; 
-
-
-// Global variables for input parameters
-int MaximumIters; // Maximum number of iterations
-double RelErr; // Relative error of the computed solution
-double best_time_val; // Current best time overall solvers 
-int best_time_id; //  id of the best solver for the current system 
-
-template<typename T> inline typename NumTraits<T>::Real test_precision() { return NumTraits<T>::dummy_precision(); }
-template<> inline float test_precision<float>() { return 1e-3f; }                                                             
-template<> inline double test_precision<double>() { return 1e-6; }                                                            
-template<> inline float test_precision<std::complex<float> >() { return test_precision<float>(); }
-template<> inline double test_precision<std::complex<double> >() { return test_precision<double>(); }
-
-void printStatheader(std::ofstream& out)
-{
-  // Print XML header
-  // NOTE It would have been much easier to write these XML documents using external libraries like tinyXML or Xerces-C++.
-  
-  out << "<?xml version='1.0' encoding='UTF-8'?> \n";
-  out << "<?xml-stylesheet type='text/xsl' href='#stylesheet' ?> \n"; 
-  out << "<!DOCTYPE BENCH  [\n<!ATTLIST xsl:stylesheet\n id\t ID  #REQUIRED>\n]>";
-  out << "\n\n<!-- Generated by the Eigen library -->\n"; 
-  
-  out << "\n<BENCH> \n" ; //root XML element 
-  // Print the xsl style section
-  printBenchStyle(out); 
-  // List all available solvers 
-  out << " <AVAILSOLVER> \n";
-#ifdef EIGEN_UMFPACK_SUPPORT
-  out <<"  <SOLVER ID='" << EIGEN_UMFPACK << "'>\n"; 
-  out << "   <TYPE> LU </TYPE> \n";
-  out << "   <PACKAGE> UMFPACK </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-#endif
-#ifdef EIGEN_KLU_SUPPORT
-  out <<"  <SOLVER ID='" << EIGEN_KLU << "'>\n";
-  out << "   <TYPE> LU </TYPE> \n";
-  out << "   <PACKAGE> KLU </PACKAGE> \n";
-  out << "  </SOLVER> \n";
-#endif
-#ifdef EIGEN_SUPERLU_SUPPORT
-  out <<"  <SOLVER ID='" << EIGEN_SUPERLU << "'>\n"; 
-  out << "   <TYPE> LU </TYPE> \n";
-  out << "   <PACKAGE> SUPERLU </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-#endif
-#ifdef EIGEN_CHOLMOD_SUPPORT
-  out <<"  <SOLVER ID='" << EIGEN_CHOLMOD_SIMPLICIAL_LLT << "'>\n"; 
-  out << "   <TYPE> LLT SP</TYPE> \n";
-  out << "   <PACKAGE> CHOLMOD </PACKAGE> \n";
-  out << "  </SOLVER> \n"; 
-  
-  out <<"  <SOLVER ID='" << EIGEN_CHOLMOD_SUPERNODAL_LLT << "'>\n"; 
-  out << "   <TYPE> LLT</TYPE> \n";
-  out << "   <PACKAGE> CHOLMOD </PACKAGE> \n";
-  out << "  </SOLVER> \n";
-  
-  out <<"  <SOLVER ID='" << EIGEN_CHOLMOD_LDLT << "'>\n"; 
-  out << "   <TYPE> LDLT </TYPE> \n";
-  out << "   <PACKAGE> CHOLMOD </PACKAGE> \n";  
-  out << "  </SOLVER> \n"; 
-#endif
-#ifdef EIGEN_PARDISO_SUPPORT
-  out <<"  <SOLVER ID='" << EIGEN_PARDISO << "'>\n"; 
-  out << "   <TYPE> LU </TYPE> \n";
-  out << "   <PACKAGE> PARDISO </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-  
-  out <<"  <SOLVER ID='" << EIGEN_PARDISO_LLT << "'>\n"; 
-  out << "   <TYPE> LLT </TYPE> \n";
-  out << "   <PACKAGE> PARDISO </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-  
-  out <<"  <SOLVER ID='" << EIGEN_PARDISO_LDLT << "'>\n"; 
-  out << "   <TYPE> LDLT </TYPE> \n";
-  out << "   <PACKAGE> PARDISO </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-#endif
-#ifdef EIGEN_PASTIX_SUPPORT
-  out <<"  <SOLVER ID='" << EIGEN_PASTIX << "'>\n"; 
-  out << "   <TYPE> LU </TYPE> \n";
-  out << "   <PACKAGE> PASTIX </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-  
-  out <<"  <SOLVER ID='" << EIGEN_PASTIX_LLT << "'>\n"; 
-  out << "   <TYPE> LLT </TYPE> \n";
-  out << "   <PACKAGE> PASTIX </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-  
-  out <<"  <SOLVER ID='" << EIGEN_PASTIX_LDLT << "'>\n"; 
-  out << "   <TYPE> LDLT </TYPE> \n";
-  out << "   <PACKAGE> PASTIX </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-#endif
-  
-  out <<"  <SOLVER ID='" << EIGEN_BICGSTAB << "'>\n"; 
-  out << "   <TYPE> BICGSTAB </TYPE> \n";
-  out << "   <PACKAGE> EIGEN </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-  
-  out <<"  <SOLVER ID='" << EIGEN_BICGSTAB_ILUT << "'>\n"; 
-  out << "   <TYPE> BICGSTAB_ILUT </TYPE> \n";
-  out << "   <PACKAGE> EIGEN </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-  
-  out <<"  <SOLVER ID='" << EIGEN_GMRES_ILUT << "'>\n"; 
-  out << "   <TYPE> GMRES_ILUT </TYPE> \n";
-  out << "   <PACKAGE> EIGEN </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-  
-  out <<"  <SOLVER ID='" << EIGEN_SIMPLICIAL_LDLT << "'>\n"; 
-  out << "   <TYPE> LDLT </TYPE> \n";
-  out << "   <PACKAGE> EIGEN </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-  
-  out <<"  <SOLVER ID='" << EIGEN_SIMPLICIAL_LLT << "'>\n"; 
-  out << "   <TYPE> LLT </TYPE> \n";
-  out << "   <PACKAGE> EIGEN </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-  
-  out <<"  <SOLVER ID='" << EIGEN_CG << "'>\n"; 
-  out << "   <TYPE> CG </TYPE> \n";
-  out << "   <PACKAGE> EIGEN </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-  
-  out <<"  <SOLVER ID='" << EIGEN_SPARSELU_COLAMD << "'>\n"; 
-  out << "   <TYPE> LU_COLAMD </TYPE> \n";
-  out << "   <PACKAGE> EIGEN </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-  
-#ifdef EIGEN_METIS_SUPPORT
-  out <<"  <SOLVER ID='" << EIGEN_SPARSELU_METIS << "'>\n"; 
-  out << "   <TYPE> LU_METIS </TYPE> \n";
-  out << "   <PACKAGE> EIGEN </PACKAGE> \n"; 
-  out << "  </SOLVER> \n"; 
-#endif
-  out << " </AVAILSOLVER> \n"; 
-  
-}
-
-
-template<typename Solver, typename Scalar>
-void call_solver(Solver &solver, const int solver_id, const typename Solver::MatrixType& A, const Matrix<Scalar, Dynamic, 1>& b, const Matrix<Scalar, Dynamic, 1>& refX,std::ofstream& statbuf)
-{
-  
-  double total_time;
-  double compute_time;
-  double solve_time; 
-  double rel_error;
-  Matrix<Scalar, Dynamic, 1> x; 
-  BenchTimer timer; 
-  timer.reset();
-  timer.start();
-  solver.compute(A); 
-  if (solver.info() != Success)
-  {
-    std::cerr << "Solver failed ... \n";
-    return;
-  }
-  timer.stop();
-  compute_time = timer.value();
-  statbuf << "    <TIME>\n"; 
-  statbuf << "     <COMPUTE> " << timer.value() << "</COMPUTE>\n";
-  std::cout<< "COMPUTE TIME : " << timer.value() <<std::endl; 
-    
-  timer.reset();
-  timer.start();
-  x = solver.solve(b); 
-  if (solver.info() == NumericalIssue)
-  {
-    std::cerr << "Solver failed ... \n";
-    return;
-  }
-  timer.stop();
-  solve_time = timer.value();
-  statbuf << "     <SOLVE> " << timer.value() << "</SOLVE>\n"; 
-  std::cout<< "SOLVE TIME : " << timer.value() <<std::endl; 
-  
-  total_time = solve_time + compute_time;
-  statbuf << "     <TOTAL> " << total_time << "</TOTAL>\n"; 
-  std::cout<< "TOTAL TIME : " << total_time <<std::endl; 
-  statbuf << "    </TIME>\n"; 
-  
-  // Verify the relative error
-  if(refX.size() != 0)
-    rel_error = (refX - x).norm()/refX.norm();
-  else 
-  {
-    // Compute the relative residual norm
-    Matrix<Scalar, Dynamic, 1> temp; 
-    temp = A * x; 
-    rel_error = (b-temp).norm()/b.norm();
-  }
-  statbuf << "    <ERROR> " << rel_error << "</ERROR>\n"; 
-  std::cout<< "REL. ERROR : " << rel_error << "\n\n" ;
-  if ( rel_error <= RelErr )
-  {
-    // check the best time if convergence
-    if(!best_time_val || (best_time_val > total_time))
-    {
-      best_time_val = total_time;
-      best_time_id = solver_id;
-    }
-  }
-}
-
-template<typename Solver, typename Scalar>
-void call_directsolver(Solver& solver, const int solver_id, const typename Solver::MatrixType& A, const Matrix<Scalar, Dynamic, 1>& b, const Matrix<Scalar, Dynamic, 1>& refX, std::string& statFile)
-{
-    std::ofstream statbuf(statFile.c_str(), std::ios::app);
-    statbuf << "   <SOLVER_STAT ID='" << solver_id <<"'>\n"; 
-    call_solver(solver, solver_id, A, b, refX,statbuf);
-    statbuf << "   </SOLVER_STAT>\n";
-    statbuf.close();
-}
-
-template<typename Solver, typename Scalar>
-void call_itersolver(Solver &solver, const int solver_id, const typename Solver::MatrixType& A, const Matrix<Scalar, Dynamic, 1>& b, const Matrix<Scalar, Dynamic, 1>& refX, std::string& statFile)
-{
-  solver.setTolerance(RelErr); 
-  solver.setMaxIterations(MaximumIters);
-  
-  std::ofstream statbuf(statFile.c_str(), std::ios::app);
-  statbuf << " <SOLVER_STAT ID='" << solver_id <<"'>\n"; 
-  call_solver(solver, solver_id, A, b, refX,statbuf); 
-  statbuf << "   <ITER> "<< solver.iterations() << "</ITER>\n";
-  statbuf << " </SOLVER_STAT>\n";
-  std::cout << "ITERATIONS : " << solver.iterations() <<"\n\n\n"; 
-  
-}
-
-
-template <typename Scalar>
-void SelectSolvers(const SparseMatrix<Scalar>&A, unsigned int sym, Matrix<Scalar, Dynamic, 1>& b, const Matrix<Scalar, Dynamic, 1>& refX, std::string& statFile)
-{
-  typedef SparseMatrix<Scalar, ColMajor> SpMat; 
-  // First, deal with Nonsymmetric and symmetric matrices
-  best_time_id = 0; 
-  best_time_val = 0.0;
-  //UMFPACK
-  #ifdef EIGEN_UMFPACK_SUPPORT
-  {
-    cout << "Solving with UMFPACK LU ... \n"; 
-    UmfPackLU<SpMat> solver; 
-    call_directsolver(solver, EIGEN_UMFPACK, A, b, refX,statFile); 
-  }
-  #endif
-  //KLU
-  #ifdef EIGEN_KLU_SUPPORT
-  {
-    cout << "Solving with KLU LU ... \n";
-    KLU<SpMat> solver;
-    call_directsolver(solver, EIGEN_KLU, A, b, refX,statFile);
-  }
-  #endif
-    //SuperLU
-  #ifdef EIGEN_SUPERLU_SUPPORT
-  {
-    cout << "\nSolving with SUPERLU ... \n"; 
-    SuperLU<SpMat> solver;
-    call_directsolver(solver, EIGEN_SUPERLU, A, b, refX,statFile); 
-  }
-  #endif
-    
-   // PaStix LU
-  #ifdef EIGEN_PASTIX_SUPPORT
-  {
-    cout << "\nSolving with PASTIX LU ... \n"; 
-    PastixLU<SpMat> solver; 
-    call_directsolver(solver, EIGEN_PASTIX, A, b, refX,statFile) ;
-  }
-  #endif
-
-   //PARDISO LU
-  #ifdef EIGEN_PARDISO_SUPPORT
-  {
-    cout << "\nSolving with PARDISO LU ... \n"; 
-    PardisoLU<SpMat>  solver; 
-    call_directsolver(solver, EIGEN_PARDISO, A, b, refX,statFile);
-  }
-  #endif
-  
-  // Eigen SparseLU METIS
-  cout << "\n Solving with Sparse LU AND COLAMD ... \n";
-  SparseLU<SpMat, COLAMDOrdering<int> >   solver;
-  call_directsolver(solver, EIGEN_SPARSELU_COLAMD, A, b, refX, statFile); 
-  // Eigen SparseLU METIS
-  #ifdef EIGEN_METIS_SUPPORT
-  {
-    cout << "\n Solving with Sparse LU AND METIS ... \n";
-    SparseLU<SpMat, MetisOrdering<int> >   solver;
-    call_directsolver(solver, EIGEN_SPARSELU_METIS, A, b, refX, statFile); 
-  }
-  #endif
-  
-  //BiCGSTAB
-  {
-    cout << "\nSolving with BiCGSTAB ... \n"; 
-    BiCGSTAB<SpMat> solver; 
-    call_itersolver(solver, EIGEN_BICGSTAB, A, b, refX,statFile);
-  }
-  //BiCGSTAB+ILUT
-  {
-    cout << "\nSolving with BiCGSTAB and ILUT ... \n"; 
-    BiCGSTAB<SpMat, IncompleteLUT<Scalar> > solver; 
-    call_itersolver(solver, EIGEN_BICGSTAB_ILUT, A, b, refX,statFile); 
-  }
-  
-   
-  //GMRES
-//   {
-//     cout << "\nSolving with GMRES ... \n"; 
-//     GMRES<SpMat> solver; 
-//     call_itersolver(solver, EIGEN_GMRES, A, b, refX,statFile); 
-//   }
-  //GMRES+ILUT
-  {
-    cout << "\nSolving with GMRES and ILUT ... \n"; 
-    GMRES<SpMat, IncompleteLUT<Scalar> > solver; 
-    call_itersolver(solver, EIGEN_GMRES_ILUT, A, b, refX,statFile);
-  }
-  
-  // Hermitian and not necessarily positive-definites
-  if (sym != NonSymmetric)
-  {
-    // Internal Cholesky
-    {
-      cout << "\nSolving with Simplicial LDLT ... \n"; 
-      SimplicialLDLT<SpMat, Lower> solver;
-      call_directsolver(solver, EIGEN_SIMPLICIAL_LDLT, A, b, refX,statFile); 
-    }
-    
-    // CHOLMOD
-    #ifdef EIGEN_CHOLMOD_SUPPORT
-    {
-      cout << "\nSolving with CHOLMOD LDLT ... \n"; 
-      CholmodDecomposition<SpMat, Lower> solver;
-      solver.setMode(CholmodLDLt);
-       call_directsolver(solver,EIGEN_CHOLMOD_LDLT, A, b, refX,statFile);
-    }
-    #endif
-    
-    //PASTIX LLT
-    #ifdef EIGEN_PASTIX_SUPPORT
-    {
-      cout << "\nSolving with PASTIX LDLT ... \n"; 
-      PastixLDLT<SpMat, Lower> solver; 
-      call_directsolver(solver,EIGEN_PASTIX_LDLT, A, b, refX,statFile); 
-    }
-    #endif
-    
-    //PARDISO LLT
-    #ifdef EIGEN_PARDISO_SUPPORT
-    {
-      cout << "\nSolving with PARDISO LDLT ... \n"; 
-      PardisoLDLT<SpMat, Lower> solver; 
-      call_directsolver(solver,EIGEN_PARDISO_LDLT, A, b, refX,statFile); 
-    }
-    #endif
-  }
-
-   // Now, symmetric POSITIVE DEFINITE matrices
-  if (sym == SPD)
-  {
-    
-    //Internal Sparse Cholesky
-    {
-      cout << "\nSolving with SIMPLICIAL LLT ... \n"; 
-      SimplicialLLT<SpMat, Lower> solver; 
-      call_directsolver(solver,EIGEN_SIMPLICIAL_LLT, A, b, refX,statFile); 
-    }
-    
-    // CHOLMOD
-    #ifdef EIGEN_CHOLMOD_SUPPORT
-    {
-      // CholMOD SuperNodal LLT
-      cout << "\nSolving with CHOLMOD LLT (Supernodal)... \n"; 
-      CholmodDecomposition<SpMat, Lower> solver;
-      solver.setMode(CholmodSupernodalLLt);
-       call_directsolver(solver,EIGEN_CHOLMOD_SUPERNODAL_LLT, A, b, refX,statFile);
-      // CholMod Simplicial LLT
-      cout << "\nSolving with CHOLMOD LLT (Simplicial) ... \n"; 
-      solver.setMode(CholmodSimplicialLLt);
-      call_directsolver(solver,EIGEN_CHOLMOD_SIMPLICIAL_LLT, A, b, refX,statFile);
-    }
-    #endif
-    
-    //PASTIX LLT
-    #ifdef EIGEN_PASTIX_SUPPORT
-    {
-      cout << "\nSolving with PASTIX LLT ... \n"; 
-      PastixLLT<SpMat, Lower> solver; 
-      call_directsolver(solver,EIGEN_PASTIX_LLT, A, b, refX,statFile);
-    }
-    #endif
-    
-    //PARDISO LLT
-    #ifdef EIGEN_PARDISO_SUPPORT
-    {
-      cout << "\nSolving with PARDISO LLT ... \n"; 
-      PardisoLLT<SpMat, Lower> solver; 
-      call_directsolver(solver,EIGEN_PARDISO_LLT, A, b, refX,statFile); 
-    }
-    #endif
-    
-    // Internal CG
-    {
-      cout << "\nSolving with CG ... \n"; 
-      ConjugateGradient<SpMat, Lower> solver; 
-      call_itersolver(solver,EIGEN_CG, A, b, refX,statFile);
-    }
-    //CG+IdentityPreconditioner
-//     {
-//       cout << "\nSolving with CG and IdentityPreconditioner ... \n"; 
-//       ConjugateGradient<SpMat, Lower, IdentityPreconditioner> solver; 
-//       call_itersolver(solver,EIGEN_CG_PRECOND, A, b, refX,statFile);
-//     }
-  } // End SPD matrices 
-}
-
-/* Browse all the matrices available in the specified folder 
- * and solve the associated linear system.
- * The results of each solve are printed in the standard output
- * and optionally in the provided html file
- */
-template <typename Scalar>
-void Browse_Matrices(const string folder, bool statFileExists, std::string& statFile, int maxiters, double tol)
-{
-  MaximumIters = maxiters; // Maximum number of iterations, global variable 
-  RelErr = tol;  //Relative residual error  as stopping criterion for iterative solvers
-  MatrixMarketIterator<Scalar> it(folder);
-  for ( ; it; ++it)
-  {
-    //print the infos for this linear system 
-    if(statFileExists)
-    {
-      std::ofstream statbuf(statFile.c_str(), std::ios::app);
-      statbuf << "<LINEARSYSTEM> \n";
-      statbuf << "   <MATRIX> \n";
-      statbuf << "     <NAME> " << it.matname() << " </NAME>\n"; 
-      statbuf << "     <SIZE> " << it.matrix().rows() << " </SIZE>\n"; 
-      statbuf << "     <ENTRIES> " << it.matrix().nonZeros() << "</ENTRIES>\n";
-      if (it.sym()!=NonSymmetric)
-      {
-        statbuf << "     <SYMMETRY> Symmetric </SYMMETRY>\n" ; 
-        if (it.sym() == SPD) 
-          statbuf << "     <POSDEF> YES </POSDEF>\n"; 
-        else 
-          statbuf << "     <POSDEF> NO </POSDEF>\n"; 
-          
-      }
-      else
-      {
-        statbuf << "     <SYMMETRY> NonSymmetric </SYMMETRY>\n" ; 
-        statbuf << "     <POSDEF> NO </POSDEF>\n"; 
-      }
-      statbuf << "   </MATRIX> \n";
-      statbuf.close();
-    }
-    
-    cout<< "\n\n===================================================== \n";
-    cout<< " ======  SOLVING WITH MATRIX " << it.matname() << " ====\n";
-    cout<< " =================================================== \n\n";
-    Matrix<Scalar, Dynamic, 1> refX;
-    if(it.hasrefX()) refX = it.refX();
-    // Call all suitable solvers for this linear system 
-    SelectSolvers<Scalar>(it.matrix(), it.sym(), it.rhs(), refX, statFile);
-    
-    if(statFileExists)
-    {
-      std::ofstream statbuf(statFile.c_str(), std::ios::app);
-      statbuf << "  <BEST_SOLVER ID='"<< best_time_id
-              << "'></BEST_SOLVER>\n"; 
-      statbuf << " </LINEARSYSTEM> \n"; 
-      statbuf.close();
-    }
-  } 
-} 
-
-bool get_options(int argc, char **args, string option, string* value=0)
-{
-  int idx = 1, found=false; 
-  while (idx<argc && !found){
-    if (option.compare(args[idx]) == 0){
-      found = true; 
-      if(value) *value = args[idx+1];
-    }
-    idx+=2;
-  }
-  return found; 
-}

sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h

@@ -1,95 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef SPBENCHSTYLE_H
-#define SPBENCHSTYLE_H
-
-void printBenchStyle(std::ofstream& out)
-{
-  out << "<xsl:stylesheet id='stylesheet' version='1.0' \
-      xmlns:xsl='http://www.w3.org/1999/XSL/Transform' >\n \
-      <xsl:template match='xsl:stylesheet' />\n \
-      <xsl:template match='/'> <!-- Root of the document -->\n \
-      <html>\n \
-        <head> \n \
-          <style type='text/css'> \n \
-            td { white-space: nowrap;}\n \
-          </style>\n \
-        </head>\n \
-        <body>";
-  out<<"<table border='1' width='100%' height='100%'>\n \
-        <TR> <!-- Write the table header -->\n \
-        <TH>Matrix</TH> <TH>N</TH> <TH> NNZ</TH>  <TH> Sym</TH>  <TH> SPD</TH> <TH> </TH>\n \
-          <xsl:for-each select='BENCH/AVAILSOLVER/SOLVER'>\n \
-            <xsl:sort select='@ID' data-type='number'/>\n \
-            <TH>\n \
-              <xsl:value-of select='TYPE' />\n \
-              <xsl:text></xsl:text>\n \
-              <xsl:value-of select='PACKAGE' />\n \
-              <xsl:text></xsl:text>\n \
-            </TH>\n \
-          </xsl:for-each>\n \
-        </TR>";
-        
-  out<<"  <xsl:for-each select='BENCH/LINEARSYSTEM'>\n \
-          <TR> <!-- print statistics for one linear system-->\n \
-            <TH rowspan='4'> <xsl:value-of select='MATRIX/NAME' /> </TH>\n \
-            <TD rowspan='4'> <xsl:value-of select='MATRIX/SIZE' /> </TD>\n \
-            <TD rowspan='4'> <xsl:value-of select='MATRIX/ENTRIES' /> </TD>\n \
-            <TD rowspan='4'> <xsl:value-of select='MATRIX/SYMMETRY' /> </TD>\n \
-            <TD rowspan='4'> <xsl:value-of select='MATRIX/POSDEF' /> </TD>\n \
-            <TH> Compute Time </TH>\n \
-            <xsl:for-each select='SOLVER_STAT'>\n \
-              <xsl:sort select='@ID' data-type='number'/>\n \
-              <TD> <xsl:value-of select='TIME/COMPUTE' /> </TD>\n \
-            </xsl:for-each>\n \
-          </TR>";
-  out<<"  <TR>\n \
-            <TH> Solve Time </TH>\n \
-            <xsl:for-each select='SOLVER_STAT'>\n \
-              <xsl:sort select='@ID' data-type='number'/>\n \
-              <TD> <xsl:value-of select='TIME/SOLVE' /> </TD>\n \
-            </xsl:for-each>\n \
-          </TR>\n \
-          <TR>\n \
-            <TH> Total Time </TH>\n \
-            <xsl:for-each select='SOLVER_STAT'>\n \
-              <xsl:sort select='@ID' data-type='number'/>\n \
-              <xsl:choose>\n \
-                <xsl:when test='@ID=../BEST_SOLVER/@ID'>\n \
-                  <TD style='background-color:red'> <xsl:value-of select='TIME/TOTAL' />  </TD>\n \
-                </xsl:when>\n \
-                <xsl:otherwise>\n \
-                  <TD>  <xsl:value-of select='TIME/TOTAL' /></TD>\n \
-                </xsl:otherwise>\n \
-              </xsl:choose>\n \
-            </xsl:for-each>\n \
-          </TR>";
-  out<<"  <TR>\n \
-              <TH> Error </TH>\n \
-              <xsl:for-each select='SOLVER_STAT'>\n \
-                <xsl:sort select='@ID' data-type='number'/>\n \
-                <TD> <xsl:value-of select='ERROR' />\n \
-                <xsl:if test='ITER'>\n \
-                  <xsl:text>(</xsl:text>\n \
-                  <xsl:value-of select='ITER' />\n \
-                  <xsl:text>)</xsl:text>\n \
-                </xsl:if> </TD>\n \
-              </xsl:for-each>\n \
-            </TR>\n \
-          </xsl:for-each>\n \
-      </table>\n \
-    </body>\n \
-    </html>\n \
-  </xsl:template>\n \
-  </xsl:stylesheet>\n\n";
-  
-}
-
-#endif