This file is indexed.

/usr/include/CGAL/Taucs_solver_traits.h is in libcgal-dev 4.2-5ubuntu1.

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
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
// Copyright (c) 2005  INRIA (France).
// All rights reserved.
//
// This file is part of CGAL (www.cgal.org).
// You can redistribute it and/or modify it under the terms of the GNU
// General Public License as published by the Free Software Foundation,
// either version 3 of the License, or (at your option) any later version.
//
// Licensees holding a valid commercial license may use this file in
// accordance with the commercial license agreement provided with the software.
//
// This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
// WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
//
// $URL$
// $Id$
//
//
// Author(s)     : Laurent Saboret, Pierre Alliez, Bruno Levy


#ifndef CGAL_TAUCS_SOLVER_TRAITS_H
#define CGAL_TAUCS_SOLVER_TRAITS_H

#include <CGAL/basic.h> // include basic.h before testing #defines

// Uncomment the next line to see libraries selected by auto-link
//#define CGAL_LIB_DIAGNOSTIC
#include <CGAL/auto_link/TAUCS.h>

#include <CGAL/Taucs_matrix.h>
#include <CGAL/Taucs_vector.h>
#include <CGAL/Taucs_fix.h>

#ifdef WIN32
  #include <CGAL/Win32_exception.h>
#endif
    
#include <boost/shared_ptr.hpp>

#include <stdio.h> // For tempnam
#include <cmath>
#include <cfloat>
#include <climits>

#ifdef _MSC_VER
#include <io.h>
#endif

namespace CGAL {

/// @cond SKIP_IN_MANUAL

/// \ingroup  PkgSurfaceParameterizationAlgebra
///
/// The class Taucs_symmetric_solver_traits
/// is a traits class for solving symmetric positive definite sparse linear systems
/// using TAUCS solvers family.
/// The default solver is the Multifrontal Supernodal Cholesky Factorization.
///
/// \cgalModels `SparseLinearAlgebraTraits_d`

template<class T>       // Tested with T = taucs_single or taucs_double
                        // May also work with T = taucs_dcomplex and taucs_scomplex
class Taucs_symmetric_solver_traits
{
// Public types
public:

    typedef Taucs_symmetric_matrix<T>   Matrix;
    typedef Taucs_vector<T>             Vector;
    typedef T                           NT;

// Public operations
public:

    /// Create a TAUCS sparse linear solver for symmetric positive definite matrices.
    /// The default solver is the Multifrontal Supernodal Cholesky Factorization.
    /// See taucs_linsolve() documentation for the meaning of the
    /// 'options' and 'arguments' parameters.
    Taucs_symmetric_solver_traits(
      const char*  options[]   = NULL,  ///< must be persistent
      const void*  arguments[] = NULL)  ///< must be persistent
    {
        static const char* MULTIFRONTAL_LLT[] = {"taucs.factor.LLT=true",
                                                 "taucs.factor.mf=true",
                                                 "taucs.factor.ordering=metis",
                                                 NULL};
        m_options   = (options == NULL) ? MULTIFRONTAL_LLT : options;
        m_arguments = arguments;
    }

    /// Solve the sparse linear system "A*X = B".
    /// Return true on success. The solution is then (1/D) * X.
    ///
    /// \pre A.row_dimension()    == B.dimension().
    /// \pre A.column_dimension() == X.dimension().
    bool linear_solver (const Matrix& A, const Vector& B, Vector& X, NT& D)
    {
        D = 1;          // TAUCS does not support homogeneous coordinates

#ifdef DEBUG_TRACE
        // Turn on TAUCS trace to stderr or to a log file
    #if DEBUG_TRACE >= 2
        std::cerr.flush();
        taucs_logfile((char*)"stderr");
    #else
        taucs_logfile((char*)"taucs.log");
    #endif

//         // Print A and B
//         int n = A.row_dimension();
//         if (n < 20)	// if small matrix, print it entirely
//         {
//           fprintf(stderr, "******************  A:  ******************\n");
//           for (int i=0; i<n; i++)  {
//             for (int j=0; j<n; j++)
//               fprintf(stderr, "%lf\t", (double)A.get_coef(i, j));
//             fprintf(stderr, "\n");
//           }
//           fprintf(stderr, "******************  B:  ******************\n");
//           for (int j=0; j<n; j++)
//             fprintf(stderr, "%lf\t", (double)B[j]);
//           fprintf(stderr, "\n");
//           fprintf(stderr, "******************************************\n");
//         }
//         else		// if large matrix, print only not null elements
//         {
//           fprintf(stderr, "******************  A*X=B  ******************\n");
//           for (int i=0; i<n; i++)  {
//             for (int j=0; j<n; j++)
//               if ( ! IsZero(A.get_coef(i, j)) )
//                 fprintf(stderr, "A[%d][%d] = %lf\t", i, j, (double)A.get_coef(i, j));
//             fprintf(stderr, "\n");
//           }
//           for (int j=0; j<n; j++)
//             if ( ! IsZero(B[j]) )
//               fprintf(stderr, "B[%d] = %lf\t", j, (double)B[j]);
//           fprintf(stderr, "\n");
//           fprintf(stderr, "******************************************\n");
//         }
#endif

#ifdef WIN32
        Win32_exception_handler eh; // catch Win32 structured exceptions
#endif
    
        try
        {
//printf("A[0][0]=%lf\n", (double) A.get_coef(0,0));
//printf("A[77][77]=%lf\n", (double) A.get_coef(77,77));
//printf("taucs_linsolve()\n");
            // Factor, solve and free
            int success = taucs_linsolve((taucs_ccs_matrix*) A.get_taucs_matrix(),
                                         NULL,
                                         1,
                                         X.get_taucs_vector(),
                                         (T*) B.get_taucs_vector(),
                                         (char**) m_options,
                                         (void**) m_arguments);
//printf("A[0][0]=%lf\n", (double) A.get_coef(0,0));
//printf("A[77][77]=%lf\n", (double) A.get_coef(77,77));
            if (success != TAUCS_SUCCESS) {
                taucs_printf((char*)"\tSolving Failed\n");
                return false;
            } else {
                return true;
            }
        }
        catch (...)
        {
            taucs_printf((char*)"\tIncorrect Matrix\n");
            return false;
        }
    }

private:

    // Test if a floating point number is (close to) 0.0.
    static inline bool IsZero(NT a)
    {
        return (CGAL::abs(a) < 10.0 * (std::numeric_limits<NT>::min)());
    }

// Fields
private:
    const char**  m_options;
    const void**  m_arguments;
};


/// \ingroup  PkgSurfaceParameterizationAlgebra
///
/// The class Taucs_solver_traits
/// is a traits class for solving general, that is symmetric and unsymmetric, sparse linear systems
/// using TAUCS out-of-core LU factorization.
///
/// \cgalModels `SparseLinearAlgebraTraits_d`

template<class T>       // Tested with T = taucs_single or taucs_double
                        // May also work with T = taucs_dcomplex and taucs_scomplex
class Taucs_solver_traits
{
// Public types
public:

    typedef Taucs_matrix<T>             Matrix;
    typedef Taucs_vector<T>             Vector;
    typedef T                           NT;

// Public operations
public:

    /// Create a TAUCS sparse linear solver for GENERAL (aka unsymmetric) matrices.
    Taucs_solver_traits()
    {
    }

    /// Solve the sparse linear system "A*X = B".
    /// Return true on success. The solution is then (1/D) * X.
    ///
    /// \pre A.row_dimension()    == B.dimension().
    /// \pre A.column_dimension() == X.dimension().
    bool linear_solver (const Matrix& A, const Vector& B, Vector& X, NT& D)
    {
        D = 1;          // TAUCS does not support homogeneous coordinates

#ifdef DEBUG_TRACE
        // Turn on TAUCS trace to stderr or to a log file
    #if DEBUG_TRACE >= 2
        std::cerr.flush();
        taucs_logfile((char*)"stderr");
    #else
        taucs_logfile((char*)"taucs.log");
    #endif

//         // Print A and B
//         int n = A.row_dimension();
//         if (n < 20)  // if small matrix, print it entirely
//         {
//           fprintf(stderr, "******************  A:  ******************\n");
//           for (int i=0; i<n; i++)  {
//             for (int j=0; j<n; j++)
//               fprintf(stderr, "%lf\t", (double)A.get_coef(i, j));
//             fprintf(stderr, "\n");
//           }
//           fprintf(stderr, "******************  B:  ******************\n");
//           for (int j=0; j<n; j++)
//             fprintf(stderr, "%lf\t", (double)B[j]);
//           fprintf(stderr, "\n");
//           fprintf(stderr, "******************************************\n");
//         }
//         else     // if large matrix, print only not null elements
//         {
//           fprintf(stderr, "******************  A*X=B  ******************\n");
//           for (int i=0; i<n; i++)  {
//             for (int j=0; j<n; j++)
//               if ( ! IsZero(A.get_coef(i, j)) )
//                 fprintf(stderr, "A[%d][%d] = %lf\t", i, j, (double)A.get_coef(i, j));
//             fprintf(stderr, "\n");
//           }
//           for (int j=0; j<n; j++)
//             if ( ! IsZero(B[j]) )
//               fprintf(stderr, "B[%d] = %lf\t", j, (double)B[j]);
//           fprintf(stderr, "\n");
//           fprintf(stderr, "******************************************\n");
//         }
#endif

#ifdef WIN32
        Win32_exception_handler eh; // catch Win32 structured exceptions
#endif
    
        try
        {
            int     success;

            // ordering
            int*    perm_raw = NULL;
            int*    invperm_raw = NULL;
            taucs_ccs_order((taucs_ccs_matrix*) A.get_taucs_matrix(),
                            &perm_raw,
                            &invperm_raw,
                            (char*)"colamd");
            boost::shared_ptr<int> perm(perm_raw, free);
            boost::shared_ptr<int> invperm(invperm_raw, free);
            if ( perm == NULL || invperm == NULL)
                throw std::runtime_error("Ordering Failed");

            // Create multi-file for out-of-core swapping.
            // Note: g++ complains that tempnam() is deprecated. You may safely ignore the warning.
#ifdef _MSC_VER
            char template_name[13] = {'t', 'a', 'u', 'c', 's','.','X','X','X','X','X','X', '\0' };
            char* matrixfile = _mktemp(template_name);
            if (matrixfile == NULL)
                throw std::runtime_error("Cannot Create Multifile");
            boost::shared_ptr<taucs_io_handle> oocL(taucs_io_create_multifile(matrixfile), taucs_io_delete);
#else
            boost::shared_ptr<char> matrixfile(tempnam(NULL, "taucs.L"), free);
            if (matrixfile == NULL)
                throw std::runtime_error("Cannot Create Multifile");
            boost::shared_ptr<taucs_io_handle> oocL(taucs_io_create_multifile(matrixfile.get()), taucs_io_delete);
#endif
            if (oocL == NULL)
                throw std::runtime_error("Cannot Create Multifile");

            // factor
            int memory_mb = int(taucs_available_memory_size()/1048576.0);
            success = taucs_ooc_factor_lu((taucs_ccs_matrix*) A.get_taucs_matrix(),
                                           perm.get(),
                                           oocL.get(),
                                           memory_mb*1048576.0);
            if (success != TAUCS_SUCCESS)
                throw std::runtime_error("Factorization Failed");

            // solve
            success = taucs_ooc_solve_lu(oocL.get(),
                                         X.get_taucs_vector(),
                                        (T*) B.get_taucs_vector());
            if (success != TAUCS_SUCCESS)
                throw std::runtime_error("Solving Failed");

            return true;
        }
        catch (std::exception& e)
        {
            taucs_printf((char*)"\t");
            taucs_printf((char*)(e.what() != NULL ? e.what() : "Incorrect Matrix"));
            taucs_printf((char*)"\n");
            return false;
        }
        catch (...)
        {
            taucs_printf((char*)"\tIncorrect Matrix\n");
            return false;
        }
    }

private:

    // Test if a floating point number is (close to) 0.0.
    static inline bool IsZero(NT a)
    {
        return ( ::CGAL::abs(a) < 10.0 * (std::numeric_limits<NT>::min)());
    }
};
/// @endcond

} //namespace CGAL

#endif // CGAL_TAUCS_SOLVER_TRAITS_H