This file is indexed.

/usr/include/trilinos/shylu.h is in libtrilinos-shylu-dev 12.12.1-5.

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
//@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 shylu.h
    
    \brief Main header file of ShyLU (Include main user calls)

    \author Siva Rajamanickam
*/
#ifndef SHYLU_H
#define SHYLU_H

// Epetra include
#include "Epetra_CrsMatrix.h" 
#include "Epetra_Map.h" 
#include "Epetra_MultiVector.h" 
#include "Epetra_LinearProblem.h" 
#include "Epetra_SerialComm.h"

// Amesos includes
#include "Amesos_BaseSolver.h"

// Ifpack includes
#include "Ifpack.h"
#include "Ifpack_Preconditioner.h"

// AztecOO includes
#include "AztecOO.h"

// Isorropia includes
#include "Isorropia_EpetraProber.hpp"

// Amesos2 includes
#ifdef HAVE_SHYLUCORE_AMESOS2
#include <Amesos2.hpp>
#endif

// Tpetra includes
#ifdef HAVE_SHYLUCORE_TPETRA
#include <Tpetra_CrsMatrix_decl.hpp>
#include <Tpetra_CrsMatrix_def.hpp>
#endif

// Zoltan2 includes
#ifdef HAVE_SHYLUCORE_ZOLTAN2
#include <Zoltan2_XpetraCrsMatrixAdapter.hpp>
#include <Zoltan2_XpetraMultiVectorAdapter.hpp>
#include <Zoltan2_PartitioningProblem.hpp>
#endif


// Shylu includes
#include "shylu_symbolic.h"
#include "shylu_config.h"
#include "shylu_probing_operator.h"
#include "shylu_amesos_schur_operator.h"

#include <IQRSolver.h>

//#include "shylu_debug_manager.hpp"

#define MIN(a, b) (((a) < (b)) ? a : b)
#define MAX(a, b) (((a) > (b)) ? a : b)

/** \brief Main data structure holding needed offset and temp variables
 *
 * This structur contains ...  
 */
typedef struct
{
    int Dnr;                    // #local rows
    int Dnc;                    // #local cols
    int Snr;                    // #remote rows
    int *DRowElems;             // local rows
    int *SRowElems;             // remote rows
    int *DColElems;             // Columns in D
    int *gvals;                 // O(n) array differentiating local/global
                                //  row/col
    //Epetra_SerialComm *SComm;   // Serial comm for block diagonals
    Teuchos::RCP<Epetra_Map> LDRowMap;       // RowMap for block diagonals
    Teuchos::RCP<Epetra_Map> LGRowMap;       // RowMap for G (local)
    Teuchos::RCP<Epetra_Map> GMap;           // Dist Map for G

    Teuchos::RCP<Epetra_Import> BdImporter;
    Teuchos::RCP<Epetra_Import> DistImporter;
    Teuchos::RCP<Epetra_Import> BsImporter;
    Teuchos::RCP<Epetra_Import> XsImporter;
    Teuchos::RCP<Epetra_Export> XdExporter;
    Teuchos::RCP<Epetra_Export> XsExporter;

    Teuchos::RCP<Epetra_MultiVector> localrhs;
    Teuchos::RCP<Epetra_MultiVector> temp1;
    Teuchos::RCP<Epetra_MultiVector> temp2;
    Teuchos::RCP<Epetra_MultiVector> Bs;
    Teuchos::RCP<Epetra_MultiVector> Xs;
    Teuchos::RCP<Epetra_MultiVector> LocalXs;
    Teuchos::RCP<Epetra_MultiVector> temp3;
    Teuchos::RCP<Epetra_MultiVector> locallhs;

    // temp timers
    //Teuchos::RCP<Teuchos::Time> importExportTime;
    //Teuchos::RCP<Teuchos::Time> innerIterTime;
    //Teuchos::RCP<Teuchos::Time> fwdTime;
    //Teuchos::RCP<Teuchos::Time> amesosSchurTime;

    //Epetra_CrsMatrix *D;        // Actual D Matrix, not reqd for Amesos_KLU
                                // but required for Amesos_Pardiso
    Teuchos::RCP<IQR::IQRSolver> iqrSolver; // Solver object for IQR func.
    Teuchos::RCP<Epetra_CrsMatrix> Sbar; // Approx Schur complement
    Teuchos::RCP<Epetra_CrsGraph> localSbargraph; // graph of local Sbar
    AztecOO *innersolver;            // inner solver
    Teuchos::RCP<Epetra_MultiVector> Sbarlhs;
    Teuchos::RCP<Epetra_MultiVector> Sbarrhs;
    Teuchos::RCP<Epetra_LinearProblem> LP2;   // Local problem to solve
    Teuchos::RCP<Epetra_LinearProblem> OrigLP2;   // Local problem to solve D
	Teuchos::RCP<EpetraExt::ViewTransform<Epetra_LinearProblem> > ReIdx_LP2;
	Amesos_BaseSolver *dsolver;  // Local Subdomain solver
    Teuchos::RCP<Ifpack_Preconditioner> schur_prec;
    Teuchos::RCP<ShyLU_Probing_Operator> schur_op;
    int lmax;                    // May be this is optimizing too much
    int rmax;                    // May be this is optimizing too much
    Teuchos::RCP<Isorropia::Epetra::Prober> guided_prober;  // Guided Prober for Sbar
    int num_compute;            // # of times Compute() has been called before
                                // or in otherwords #nonlinear iteration-1
} shylu_data;

/** \brief Main function call into ShylU
 *
 * How to use?
 */
int shylu_factor(Epetra_CrsMatrix *A, shylu_symbolic *ssym, shylu_data *data,
                shylu_config *config);

/** \brief Call symbolic factorization on matrix
 *
 */
int shylu_symbolic_factor
(
    Epetra_CrsMatrix *A,    // i/p: A matrix
    shylu_symbolic *ssym,   // symbolic structure
    shylu_data *data,       // numeric structure, TODO: Required ?
    shylu_config *config   // i/p: library configuration
);

/** \brief Call solve on multiple RHS
 *
 */
int shylu_solve(shylu_symbolic *ssym, shylu_data *data, shylu_config *config,
    const Epetra_MultiVector& X, Epetra_MultiVector& Y);

/** \brief Compute an approximate Schur Complement (Narrow Sep)
 *
 *  Computate an approximate Schur Complement either using ...
 */ 

Teuchos::RCP<Epetra_CrsMatrix> computeApproxSchur(shylu_config *config,
    shylu_symbolic *ssym,
    Epetra_CrsMatrix *G, Epetra_CrsMatrix *R,
    Epetra_LinearProblem *LP, Amesos_BaseSolver *solver,
    Ifpack_Preconditioner *ifSolver, Epetra_CrsMatrix *C,
    Epetra_Map *localDRowMap);

/** \brief Compute an approximate Shur Complete (Wide Sep)
 *
 * Compute an approximate Schur Complement based on a wide seperator.
 * Options include ...
 */
Teuchos::RCP<Epetra_CrsMatrix> computeApproxWideSchur(
    shylu_config *config,
    shylu_symbolic *ssym,   // symbolic structure
    Epetra_CrsMatrix *G, Epetra_CrsMatrix *R,
    Epetra_LinearProblem *LP, Amesos_BaseSolver *solver,
    Ifpack_Preconditioner *ifSolver, Epetra_CrsMatrix *C,
    Epetra_Map *localDRowMap);

/** \brief Compute an approximate Schur Complement using the option of Guided Probing
 *
 *  Compute an approximate Schur Complement based on probing of important nonzero values.
 */
Teuchos::RCP<Epetra_CrsMatrix> computeSchur_GuidedProbing
(
    shylu_config *config,
    shylu_symbolic *ssym,   // symbolic structure
    shylu_data *data,       // numeric structure
    Epetra_Map *localDRowMap
);
#endif // SHYLU_H