This file is indexed.

/usr/include/trilinos/Ifpack_ShyLU.h is in libtrilinos-shylu-dev 12.4.2-2.

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
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
//@HEADER
// ************************************************************************
//
//               ShyLU: Hybrid preconditioner package
//                 Copyright 2012 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 Ifpack_ShyLU.h

    \brief Use ShyLU as a preconditioner within IFPACK.

    \author Siva Rajamanickam

*/

#ifndef IFPACK_SHYLU_H
#define IFPACK_SHYLU_H

#include <assert.h>
#include <iostream>
#include <sstream>
#include <string>

/* This define will make S block diagonal, To make this happen even some
   zero columns/rows of C and R will be stored.
   */
#define BLOCK_DIAGONAL_Si

#include "ShyLUCore_config.h"

// Epetra includes
#ifdef HAVE_SHYLUCORE_MPI
#include "Epetra_MpiComm.h"
#else
#include "Epetra_SerialComm.h"
#endif
#include "Epetra_SerialComm.h"
#include "Epetra_Time.h"
#include "Epetra_CrsMatrix.h"
#include "Epetra_Map.h"
#include "Epetra_MultiVector.h"
#include "Epetra_LinearProblem.h"
#include "Epetra_Import.h"
#include "Epetra_Export.h"

// Teuchos includes
#include "Teuchos_GlobalMPISession.hpp"
#include "Teuchos_XMLParameterListHelpers.hpp"
#include "Teuchos_LAPACK.hpp"

// AztecOO includes
#include "AztecOO.h"

#include "shylu.h"
#include "shylu_util.h"

// Ifpack includes
#include "Ifpack_Preconditioner.h"

//Isorropia includes
#include "Isorropia_Epetra.hpp"
#include "Isorropia_EpetraRedistributor.hpp"
#include "Isorropia_EpetraPartitioner.hpp"

// EpetraExt includes
#include "EpetraExt_MultiVectorOut.h"
#include "EpetraExt_RowMatrixOut.h"

// Amesos includes
#include "Amesos.h"
#include "Amesos_BaseSolver.h"

using namespace std;

/** \brief ShyLU's interface to be used as an Ifpack Preconditioner
 *
 */
class Ifpack_ShyLU: public Ifpack_Preconditioner
{
    public:
    // @{ Constructors and destructors.
    //! Constructor
    Ifpack_ShyLU(Epetra_CrsMatrix* A);

    //! Destructor
    ~Ifpack_ShyLU()
    {
        Destroy();
    }

    // @}
    // @{ Construction methods

    //! Initialize the preconditioner, does not touch matrix values.
    int Initialize();

    //! Returns \c true if the preconditioner has been successfully initialized.
    bool IsInitialized() const
    {
        return(IsInitialized_);
    }

    //! Compute ILU factors L and U using the specified parameters.
    int Compute();

    //! If factor is completed, this query returns true, otherwise it returns false.
    bool IsComputed() const
    {
        return(IsComputed_);
    }

    //! Set parameters using a Teuchos::ParameterList object.
    /* This method is only available if the Teuchos package is enabled.
     This method recognizes four parameter names: relax_value,
     absolute_threshold, relative_threshold and overlap_mode. These names are
     case insensitive, and in each case except overlap_mode, the ParameterEntry
     must have type double. For overlap_mode, the ParameterEntry must have
     type Epetra_CombineMode.
    */
    int SetParameters(Teuchos::ParameterList& parameterlist);

    int SetUseTranspose(bool UseTranspose_in) {
        UseTranspose_ = UseTranspose_in;
     return(0);
     };

    //! Returns the current UseTranspose setting.
    bool UseTranspose() const {return(UseTranspose_);};




    // @}

    // @{ Mathematical functions.
    // Applies the matrix to X, returns the result in Y.
    int Apply(const Epetra_MultiVector& X,
           Epetra_MultiVector& Y) const
    {
    return(Multiply(false,X,Y));
    }

    int Multiply(bool Trans, const Epetra_MultiVector& X,
           Epetra_MultiVector& Y) const{return A_->Multiply(Trans,X,Y);}

    //! Returns the result of a Epetra_Operator inverse applied to an Epetra_MultiVector X in Y.
    /*!
    \param
       X - (In) A Epetra_MultiVector of dimension NumVectors to solve for.
    \param Out
       Y - (Out) A Epetra_MultiVector of dimension NumVectors containing result.

    \return Integer error code, set to 0 if successful.
    */
    int ApplyInverse(const Epetra_MultiVector& X, Epetra_MultiVector& Y) const;

    //! Computes the estimated condition number and returns the value.
    double Condest(const Ifpack_CondestType CT = Ifpack_Cheap,
                 const int MaxIters = 1550,
                 const double Tol = 1e-9,
         Epetra_RowMatrix* Matrix_in = 0);

    //! Returns the computed estimated condition number, or -1.0 if not computed.
int JustTryIt() ;

    double Condest() const
    {
        return(Condest_);
    }

    // @}
    // @{ Query methods

    //! Returns a character string describing the operator
    const char* Label() const {return(Label_.c_str());}

    //! Sets label for \c this object.
    int SetLabel(std::string Label_in)
    {
        Label_ = Label_in;
        return(0);
    }


    //! Returns 0.0 because this class cannot compute Inf-norm.
    double NormInf() const {return(0.0);};

    //! Returns false because this class cannot compute an Inf-norm.
    bool HasNormInf() const {return(false);};

    //! Returns the Epetra_Map object associated with the domain of this operator.
    const Epetra_Map & OperatorDomainMap() const {return(A_->OperatorDomainMap());};

    //! Returns the Epetra_Map object associated with the range of this operator.
    const Epetra_Map & OperatorRangeMap() const{return(A_->OperatorRangeMap());};

    //! Returns the Epetra_BlockMap object associated with the range of this matrix operator.
    const Epetra_Comm & Comm() const{return(A_->Comm());};

    //! Returns a reference to the matrix to be preconditioned.
    const Epetra_RowMatrix& Matrix() const
    {
        return(*A_);
    }

    //! Prints on stream basic information about \c this object.
    virtual ostream& Print(ostream& os) const;

    //! Returns the number of calls to Initialize().
    virtual int NumInitialize() const
    {
        return(NumInitialize_);
    }

    //! Returns the number of calls to Compute().
    virtual int NumCompute() const
    {
        return(NumCompute_);
    }

    //! Returns the number of calls to ApplyInverse().
    virtual int NumApplyInverse() const
    {
        return(NumApplyInverse_);
    }

    //! Returns the time spent in Initialize().
    virtual double InitializeTime() const
    {
        return(InitializeTime_);
    }

    //! Returns the time spent in Compute().
    virtual double ComputeTime() const
    {
        return(ComputeTime_);
    }

    //! Returns the time spent in ApplyInverse().
    virtual double ApplyInverseTime() const
    {
        return(ApplyInverseTime_);
    }

    //! Returns the number of flops in the initialization phase.
    virtual double InitializeFlops() const
    {
        return(0.0);
    }

    virtual double ComputeFlops() const
    {
        return(ComputeFlops_);
    }

    virtual double ApplyInverseFlops() const
    {
        return(ApplyInverseFlops_);
    }

    private:

    // @}
    // @{ Private methods

    //! Copy constructor (should never be used)
    Ifpack_ShyLU(const Ifpack_ShyLU& RHS) :
    Time_(RHS.Comm())
    {}

    //! operator= (should never be used)
    Ifpack_ShyLU& operator=(const Ifpack_ShyLU& RHS)
    {
        return(*this);
    }

    //! Destroys all internal data
    void Destroy();

    //! Returns the number of global matrix rows.
    int NumGlobalRows() const {return(A_->NumGlobalRows());};

    //! Returns the number of global matrix columns.
    int NumGlobalCols() const {return(A_->NumGlobalCols());};

    //! Returns the number of local matrix rows.
    int NumMyRows() const {return(A_->NumMyRows());};

    //! Returns the number of local matrix columns.
    int NumMyCols() const {return(A_->NumMyCols());};

    // @}
    // @{ Internal data

    //! Pointer to the Epetra_RowMatrix to factorize
    Epetra_CrsMatrix *A_;

    Teuchos::ParameterList List_;
    //mutable AztecOO *solver_; // Ugh !!! Mutable ! To workaround AztecOO bug
    mutable shylu_data slu_data_; // More mutable !!!
    mutable shylu_config slu_config_; // More mutable !!
    mutable shylu_symbolic slu_sym_; // More mutable !!

    //fpr later use
    // Isorropia::Epetra::Partitioner *partitioner_; // unused
    // Isorropia::Epetra::Redistributor *rd_; // unused

    bool UseTranspose_;

    double Condest_;

    bool IsParallel_;
    //! If \c true, the preconditioner has been successfully initialized.
    bool IsInitialized_;
    //! If \c true, the preconditioner has been successfully computed.
    bool IsComputed_;
    //! Label of \c this object.
    std::string Label_;
    //! Contains the number of successful calls to Initialize().
    int NumInitialize_;
    //! Contains the number of successful call to Compute().
    int NumCompute_;

    //! Contains the number of successful call to ApplyInverse().
    mutable int NumApplyInverse_;
    //! Contains the time for all successful calls to Initialize().
    double InitializeTime_;
    //! Contains the time for all successful calls to Compute().
    double ComputeTime_;
    //! Contains the time for all successful calls to ApplyInverse().
    mutable double ApplyInverseTime_;
    //! Contains the number of flops for Compute().
    double ComputeFlops_;
    //! Contain sthe number of flops for ApplyInverse().
    mutable double ApplyInverseFlops_;
    //! Used for timing issues
    mutable Epetra_Time Time_;
    // @}

};

#endif /* IFPACK_SHYLU_H */