This file is indexed.

/usr/include/trilinos/Tsqr_Matrix.hpp is in libtrilinos-tpetra-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
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
//@HEADER
// ************************************************************************
//
//          Kokkos: Node API and Parallel Node Kernels
//              Copyright (2008) 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

#ifndef __TSQR_Tsqr_Matrix_hpp
#define __TSQR_Tsqr_Matrix_hpp

#include <Tsqr_Util.hpp>
#include <Tsqr_MatView.hpp>

#include <stdexcept>
#include <sstream>
#include <limits>
#include <vector>

////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////

namespace TSQR {

  /// \class Matrix
  /// \brief A column-oriented dense matrix
  /// \author Mark Hoemmen
  ///
  /// A column-oriented dense matrix, with indices of type Ordinal and
  /// elements of type Scalar.
  ///
  /// \note This class resembles Teuchos::SerialDenseMatrix.  It
  ///   existed originally because there was a need for TSQR to build
  ///   independently of Teuchos.  That requirement no longer exists,
  ///   but for various reasons it has been helpful to keep Matrix
  ///   around.  In particular, I can change the interface of Matrix
  ///   without affecting other Teuchos users.
  template<class Ordinal, class Scalar>
  class Matrix {
  public:
    typedef MatView<Ordinal, Scalar> mat_view_type;
    typedef ConstMatView<Ordinal, Scalar> const_mat_view_type;

  private:
    static bool
    fits_in_size_t (const Ordinal& ord)
    {
      const Ordinal result = static_cast< Ordinal > (static_cast< size_t > (ord));
      return (ord == result);
    }

    /// Check whether num_rows*num_cols makes sense as an amount of
    /// storage (for the num_rows by num_cols dense matrix).  Not
    /// making sense includes negative values for either parameter (if
    /// they are signed types), or overflow when computing their
    /// product.  Throw an exception of the appropriate type for any
    /// of these cases.  Otherwise, return num_rows*num_cols as a
    /// size_t.
    ///
    /// \param num_rows [in] Number of rows in the matrix
    /// \param num_cols [in] Number of columns in the matrix
    /// \return num_rows*num_cols
    size_t
    verified_alloc_size (const Ordinal num_rows,
                         const Ordinal num_cols) const
    {
      if (! std::numeric_limits< Ordinal >::is_integer)
        throw std::logic_error("Ordinal must be an integer type");

      // Quick exit also checks for zero num_cols (which prevents
      // division by zero in the tests below).
      if (num_rows == 0 || num_cols == 0)
        return size_t(0);

      // If Ordinal is signed, make sure that num_rows and num_cols
      // are nonnegative.
      if (std::numeric_limits< Ordinal >::is_signed)
        {
          if (num_rows < 0)
            {
              std::ostringstream os;
              os << "# rows (= " << num_rows << ") < 0";
              throw std::logic_error (os.str());
            }
          else if (num_cols < 0)
            {
              std::ostringstream os;
              os << "# columns (= " << num_cols << ") < 0";
              throw std::logic_error (os.str());
            }
        }

      // If Ordinal is bigger than a size_t, do special range
      // checking.  The compiler warns (comparison of signed and
      // unsigned) if Ordinal is a signed type and we try to do
      // "numeric_limits<size_t>::max() <
      // std::numeric_limits<Ordinal>::max()", so instead we cast each
      // of num_rows and num_cols to size_t and back to Ordinal again,
      // and see if we get the same result.  If not, then we
      // definitely can't return a size_t product of num_rows and
      // num_cols.
      if (! fits_in_size_t (num_rows))
        {
          std::ostringstream os;
          os << "# rows (= " << num_rows << ") > max size_t value (= "
             << std::numeric_limits<size_t>::max() << ")";
          throw std::range_error (os.str());
        }
      else if (! fits_in_size_t (num_cols))
        {
          std::ostringstream os;
          os << "# columns (= " << num_cols << ") > max size_t value (= "
             << std::numeric_limits<size_t>::max() << ")";
          throw std::range_error (os.str());
        }

      // Both num_rows and num_cols fit in a size_t, and are
      // nonnegative.  Now check whether their product also fits in a
      // size_t.
      //
      // Note: This may throw a SIGFPE (floating-point exception) if
      // num_cols is zero.  Be sure to check first (above).
      if (static_cast<size_t>(num_rows) >
          std::numeric_limits<size_t>::max() / static_cast<size_t>(num_cols))
        {
          std::ostringstream os;
          os << "num_rows (= " << num_rows << ") * num_cols (= "
             << num_cols << ") > max size_t value (= "
             << std::numeric_limits<size_t>::max() << ")";
          throw std::range_error (os.str());
        }
      return static_cast<size_t>(num_rows) * static_cast<size_t>(num_cols);
    }

  public:
    typedef Scalar scalar_type;
    typedef Ordinal ordinal_type;
    typedef Scalar* pointer_type;

    //! Constructor with dimensions.
    Matrix (const Ordinal num_rows,
            const Ordinal num_cols) :
      nrows_ (num_rows),
      ncols_ (num_cols),
      A_ (verified_alloc_size (num_rows, num_cols))
    {}

    //! Constructor with dimensions and fill datum.
    Matrix (const Ordinal num_rows,
            const Ordinal num_cols,
            const Scalar& value) :
      nrows_ (num_rows),
      ncols_ (num_cols),
      A_ (verified_alloc_size (num_rows, num_cols), value)
    {}

    /// \brief Copy constructor.
    ///
    /// We need an explicit copy constructor, because otherwise the
    /// default copy constructor would override the generic matrix
    /// view "copy constructor" below.
    Matrix (const Matrix& in) :
      nrows_ (in.nrows()),
      ncols_ (in.ncols()),
      A_ (verified_alloc_size (in.nrows(), in.ncols()))
    {
      if (! in.empty())
        copy_matrix (nrows(), ncols(), get(), lda(), in.get(), in.lda());
    }

    //! Default constructor (constructs an empty matrix).
    Matrix () : nrows_(0), ncols_(0), A_(0) {}

    //! Trivial destructor.
    ~Matrix () {}

    /// \brief "Copy constructor" from a matrix view type.
    ///
    /// This constructor allocates a new matrix and copies the
    /// elements of the input view into the resulting new matrix.
    /// MatrixViewType must have nrows(), ncols(), get(), and lda()
    /// methods that match MatView's methods.
    template<class MatrixViewType>
    Matrix (const MatrixViewType& in) :
      nrows_ (in.nrows()),
      ncols_ (in.ncols()),
      A_ (verified_alloc_size (in.nrows(), in.ncols()))
    {
      if (A_.size() != 0)
        copy_matrix (nrows(), ncols(), get(), lda(), in.get(), in.lda());
    }

    //! Fill all entries of the matrix with the given value.
    void
    fill (const Scalar value)
    {
      fill_matrix (nrows(), ncols(), get(), lda(), value);
    }

    /// \brief Non-const reference to element (i,j) of the matrix.
    ///
    /// \param i [in] Zero-based row index of the matrix.
    /// \param j [in] Zero-based column index of the matrix.
    Scalar& operator() (const Ordinal i, const Ordinal j) {
      return A_[i + j*lda()];
    }

    /// \brief Const reference to element (i,j) of the matrix.
    ///
    /// \param i [in] Zero-based row index of the matrix.
    /// \param j [in] Zero-based column index of the matrix.
    const Scalar& operator() (const Ordinal i, const Ordinal j) const {
      return A_[i + j*lda()];
    }

    //! 1-D std::vector - style access.
    Scalar& operator[] (const Ordinal i) {
      return A_[i];
    }

    //! Equality: ONLY compares dimensions and pointers (shallow).
    template<class MatrixViewType>
    bool operator== (const MatrixViewType& B) const
    {
      if (get() != B.get() || nrows() != B.nrows() || ncols() != B.ncols() || lda() != B.lda()) {
        return false;
      } else {
        return true;
      }
    }

    //! Number of rows in the matrix.
    Ordinal nrows() const { return nrows_; }

    //! Number of columns in the matrix.
    Ordinal ncols() const { return ncols_; }

    //! Leading dimension (a.k.a. stride) of the matrix.
    Ordinal lda() const { return nrows_; }

    //! Whether the matrix is empty (has either zero rows or zero columns).
    bool empty() const { return nrows() == 0 || ncols() == 0; }

    //! A non-const pointer to the matrix data.
    Scalar*
    get()
    {
      if (A_.size() > 0)
        return &A_[0];
      else
        return static_cast<Scalar*> (NULL);
    }

    //! A const pointer to the matrix data.
    const Scalar*
    get() const
    {
      if (A_.size() > 0)
        return &A_[0];
      else
        return static_cast<const Scalar*> (NULL);
    }

    //! A non-const view of the matrix.
    mat_view_type view () {
      return mat_view_type (nrows(), ncols(), get(), lda());
    }

    //! A const view of the matrix.
    const_mat_view_type const_view () const {
      return const_mat_view_type (nrows(), ncols(),
                                  const_cast<const Scalar*> (get()), lda());
    }

    /// Change the dimensions of the matrix.  Reallocate if necessary.
    /// Existing data in the matrix is invalidated.
    ///
    /// \param num_rows [in] New number of rows in the matrix
    /// \param num_cols [in] New number of columns in the matrix
    ///
    /// \warning This does <it>not</it> do the same thing as the
    ///   Matlab function of the same name.  In particular, it does
    ///   not reinterpret the existing matrix data using different
    ///   dimensions.
    void
    reshape (const Ordinal num_rows, const Ordinal num_cols)
    {
      if (num_rows == nrows() && num_cols == ncols())
        return; // no need to reallocate or do anything else

      const size_t alloc_size = verified_alloc_size (num_rows, num_cols);
      nrows_ = num_rows;
      ncols_ = num_cols;
      A_.resize (alloc_size);
    }

  private:
    //! Number of rows in the matrix.
    Ordinal nrows_;
    //! Number of columns in the matrix.
    Ordinal ncols_;
    /// \brief Where the entries of the matrix are stored.
    ///
    /// The matrix is stored using one-dimensional storage with
    /// column-major (Fortran-style) indexing.  This makes Matrix
    /// compatible with the BLAS and LAPACK.
    std::vector<Scalar> A_;
  };

} // namespace TSQR

#endif // __TSQR_Tsqr_Matrix_hpp