This file is indexed.

/usr/include/trilinos/Amesos2_KLU2_decl.hpp is in libtrilinos-amesos2-dev 12.10.1-3.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
// @HEADER
//
// ***********************************************************************
//
//           Amesos2: Templated Direct Sparse Solver Package
//                  Copyright 2011 Sandia Corporation
//
// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
// the U.S. Government retains certain rights in this software.
//
// 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

/**
  \file   Amesos2_KLU2_decl.hpp
  \author Siva Rajamanickam <srajama@sandia.gov>

  \brief  Amesos2 KLU2 declarations.
*/


#ifndef AMESOS2_KLU2_DECL_HPP
#define AMESOS2_KLU2_DECL_HPP

#include "Amesos2_SolverTraits.hpp"
#include "Amesos2_SolverCore.hpp"
#include "Amesos2_KLU2_FunctionMap.hpp"


namespace Amesos2 {


/** \brief Amesos2 interface to the KLU2 package.
 *
 * See the \ref KLU2_parameters "summary of KLU2 parameters"
 * supported by this Amesos2 interface.
 *
 * \ingroup amesos2_solver_interfaces
 */
template <class Matrix,
          class Vector>
class KLU2 : public SolverCore<Amesos2::KLU2, Matrix, Vector>
{
  friend class SolverCore<Amesos2::KLU2,Matrix,Vector>; // Give our base access
                                                          // to our private
                                                          // implementation funcs
public:

  /// Name of this solver interface.
  static const char* name;      // declaration. Initialization outside.

  typedef KLU2<Matrix,Vector>                                       type;
  typedef SolverCore<Amesos2::KLU2,Matrix,Vector>             super_type;

  // Since typedef's are not inheritted, go grab them
  typedef typename super_type::scalar_type                      scalar_type;
  typedef typename super_type::local_ordinal_type        local_ordinal_type;
  typedef typename super_type::global_ordinal_type      global_ordinal_type;
  typedef typename super_type::global_size_type            global_size_type;

  typedef TypeMap<Amesos2::KLU2,scalar_type>                    type_map;

  /*
   * The KLU2 interface will need two other typedef's, which are:
   * - the KLU2 type that corresponds to scalar_type and
   * - the corresponding type to use for magnitude
   */
  typedef typename type_map::type                                  slu_type;
  typedef typename type_map::magnitude_type                  magnitude_type;

  typedef FunctionMap<Amesos2::KLU2,slu_type>               function_map;

  /// \name Constructor/Destructor methods
  //@{

  /**
   * \brief Initialize from Teuchos::RCP.
   *
   * \warning Should not be called directly!  Use instead
   * Amesos2::create() to initialize a KLU2 interface.
   */
  KLU2(Teuchos::RCP<const Matrix> A,
          Teuchos::RCP<Vector>       X,
          Teuchos::RCP<const Vector> B);


  /// Destructor
  ~KLU2( );

  //@}

private:

  /**
   * \brief Performs pre-ordering on the matrix to increase efficiency.
   *
   * KLU2 does not support pre-ordering, so this method does nothing.
   */
  int preOrdering_impl();


  /**
   * \brief Perform symbolic factorization of the matrix using KLU2.
   *
   * Called first in the sequence before numericFactorization.
   *
   * \throw std::runtime_error KLU2 is not able to factor the matrix.
   */
  int symbolicFactorization_impl();


  /**
   * \brief KLU2 specific numeric factorization
   *
   * \throw std::runtime_error KLU2 is not able to factor the matrix
   */
  int numericFactorization_impl();


  /**
   * \brief KLU2 specific solve.
   *
   * Uses the symbolic and numeric factorizations, along with the RHS
   * vector \c B to solve the sparse system of equations.  The
   * solution is placed in X.
   *
   * \throw std::runtime_error KLU2 is not able to solve the system.
   *
   * \callgraph
   */
  int solve_impl(const Teuchos::Ptr<MultiVecAdapter<Vector> >       X,
                 const Teuchos::Ptr<const MultiVecAdapter<Vector> > B) const;


  /**
   * \brief Determines whether the shape of the matrix is OK for this solver.
   */
  bool matrixShapeOK_impl() const;


  /**
   * Currently, the following KLU2 parameters/options are
   * recognized and acted upon:
   *
   * <ul>
   *   <li> \c "Trans" : { \c "NOTRANS" | \c "TRANS" |
   *     \c "CONJ" }.  Specifies whether to solve with the transpose system.</li>
   *   <li> \c "Equil" : { \c true | \c false }.  Specifies whether
   *     the solver to equilibrate the matrix before solving.</li>
   *   <li> \c "IterRefine" : { \c "NO" | \c "SINGLE" | \c "DOUBLE" | \c "EXTRA"
   *     }. Specifies whether to perform iterative refinement, and in
   *     what precision to compute the residual.</li>
   *   <li> \c "SymmetricMode" : { \c true | \c false }.</li>
   *   <li> \c "DiagPivotThresh" : \c double value. Specifies the threshold
   *     used for a diagonal to be considered an acceptable pivot.</li>
   *   <li> \c "ColPerm" which takes one of the following:
   *     <ul>
   *     <li> \c "NATURAL" : natural ordering.</li>
   *     <li> \c "MMD_AT_PLUS_A" : minimum degree ordering on the structure of
   *       \f$ A^T + A\f$ .</li>
   *     <li> \c "MMD_ATA" : minimum degree ordering on the structure of
   *       \f$ A T A \f$ .</li>
   *     <li> \c "COLAMD" : approximate minimum degree column ordering.
   *       (default)</li>
   *     </ul>
   * </ul>
   */
  void setParameters_impl(
    const Teuchos::RCP<Teuchos::ParameterList> & parameterList );


  /**
   * Hooked in by Amesos2::SolverCore parent class.
   *
   * \return a const Teuchos::ParameterList of all valid parameters for this
   * solver.
   */
  Teuchos::RCP<const Teuchos::ParameterList> getValidParameters_impl() const;


  /**
   * \brief Reads matrix data into internal structures
   *
   * \param [in] current_phase an indication of which solution phase this
   *                           load is being performed for.
   *
   * \return \c true if the matrix was loaded, \c false if not
   */
  bool loadA_impl(EPhase current_phase);

  // struct holds all data necessary for KLU2 factorization or solve call
  mutable struct KLU2Data {
      ::KLU2::klu_symbolic<slu_type, local_ordinal_type> *symbolic_;
      ::KLU2::klu_numeric<slu_type, local_ordinal_type> *numeric_;
      ::KLU2::klu_common<slu_type, local_ordinal_type> common_;
  } data_ ;

  // The following Arrays are persisting storage arrays for A, X, and B
  /// Stores the values of the nonzero entries for KLU2
  Teuchos::Array<slu_type> nzvals_;
  /// Stores the location in \c Ai_ and Aval_ that starts row j
  Teuchos::Array<local_ordinal_type> rowind_;
  /// Stores the row indices of the nonzero entries
  Teuchos::Array<local_ordinal_type> colptr_;

  /// Persisting 1D store for X
  Teuchos::Array<slu_type> xvals_;  local_ordinal_type ldx_;
  /// Persisting 1D store for B
  Teuchos::Array<slu_type> bvals_;  local_ordinal_type ldb_;

  /// Transpose flag
  /// 0: Non-transpose, 1: Transpose, 2: Conjugate-transpose
  int transFlag_;
};                              // End class KLU2


// Specialize solver_traits struct for KLU2
// TODO
template <>
struct solver_traits<KLU2> {
#ifdef HAVE_TEUCHOS_COMPLEX
  typedef Meta::make_list4<float,
                           double,
                           std::complex<float>,
                           std::complex<double> > supported_scalars;
#else
  typedef Meta::make_list2<float, double> supported_scalars;
#endif
};

} // end namespace Amesos2

#endif  // AMESOS2_KLU2_DECL_HPP