This file is indexed.

/usr/include/gromacs/utility/alignedallocator.h is in libgromacs-dev 2018.1-1.

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
/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2017, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */
/*! \file
 * \brief Declares allocation policy classes and allocators that are
 * used to make library containers compatible with alignment
 * requirements of particular hardware, e.g. memory operations for
 * SIMD or accelerators.
 *
 * \author Erik Lindahl <erik.lindahl@gmail.com>
 * \author Mark Abraham <mark.j.abraham@gmail.com>
 * \inpublicapi
 * \ingroup module_utility
 */
#ifndef GMX_UTILITY_ALIGNEDALLOCATOR_H
#define GMX_UTILITY_ALIGNEDALLOCATOR_H

#include <cstddef>

#include "gromacs/utility/allocator.h"

namespace gmx
{

/*! \libinternal \brief Policy class for configuring gmx::Allocator, to manage
 * allocations of aligned memory for SIMD code.
 */
class AlignedAllocationPolicy
{
    public:
        /*! \brief Return the alignment size. */
        static std::size_t
        alignment();
        /*! \brief Allocate memory aligned to alignment() bytes.
         *
         *  \param bytes Amount of memory (bytes) to allocate. It is valid to ask for
         *               0 bytes, which will return a non-null pointer that is properly
         *               aligned and padded (but that you should not use).
         *
         * \return Valid pointer if the allocation worked, otherwise nullptr.
         *
         * The memory will always be aligned to 128 bytes, which is our
         * estimate of the longest cache lines on architectures currently in use.
         * It will also be padded by the same amount at the end of the
         * area, to help avoid false cache sharing.
         *
         *  \note Memory allocated with this routine must be released with
         *        gmx::AlignedAllocationPolicy::free(), and absolutely not the system free().
         */
        static void *
        malloc(std::size_t bytes);
        /*! \brief Free aligned memory
         *
         *  \param p  Memory pointer previously returned from malloc()
         *
         *  \note This routine should only be called with pointers obtained from
         *        gmx::AlignedAllocationPolicy::malloc(), and absolutely not any
         *        pointers obtained the system malloc().
         */
        static void
        free(void *p);
};

/*! \brief Aligned memory allocator.
 *
 *  \tparam T          Type of objects to allocate
 *
 * This convenience partial specialization can be used for the
 * optional allocator template parameter in standard library
 * containers, which is necessary e.g. to use SIMD aligned load and
 * store operations on data in those containers. The memory will
 * always be aligned according to the behavior of
 * AlignedAllocationPolicy.
 */
template <class T>
using AlignedAllocator = Allocator<T, AlignedAllocationPolicy>;


/*! \brief Return the memory page size on this system
 *
 * Implements the "construct on first use" idiom to avoid the static
 * initialization order fiasco where a possible static page-aligned
 * container would be initialized before the alignment variable was.
 *
 * Note that thread-safety is guaranteed by the C++11 language
 * standard. */
std::size_t pageSize();

/*! \libinternal \brief Policy class for configuring gmx::Allocator,
 * to manage allocations of page-aligned memory that can be locked for
 * asynchronous transfer to GPU devices.
 */
class PageAlignedAllocationPolicy
{
    public:
        /*! \brief Return the alignment size of memory pages on this system.
         *
         * Queries sysconf/WinAPI, otherwise guesses 4096. */
        static std::size_t
        alignment();
        /*! \brief Allocate memory aligned to alignment() bytes.
         *
         *  \param bytes Amount of memory (bytes) to allocate. It is valid to ask for
         *               0 bytes, which will return a non-null pointer that is properly
         *               aligned and padded (but that you should not use).
         *
         * \return Valid pointer if the allocation worked, otherwise nullptr.
         *
         *  \note Memory allocated with this routine must be released with
         *        gmx::PageAlignedAllocationPolicy::free(), and absolutely not the system free().
         */
        static void *
        malloc(std::size_t bytes);
        /*! \brief Free aligned memory
         *
         *  \param p  Memory pointer previously returned from malloc()
         *
         *  \note This routine should only be called with pointers obtained from
         *        gmx::PageAlignedAllocationPolicy::malloc(), and absolutely not any
         *        pointers obtained the system malloc().
         */
        static void
        free(void *p);
};

/*! \brief PageAligned memory allocator.
 *
 *  \tparam T          Type of objects to allocate
 *
 * This convenience partial specialization can be used for the
 * optional allocator template parameter in standard library
 * containers, which is necessary for locking memory pages for
 * asynchronous transfer between a GPU device and the host.  The
 * memory will always be aligned according to the behavior of
 * PageAlignedAllocationPolicy.
 */
template <class T>
using PageAlignedAllocator = Allocator<T, PageAlignedAllocationPolicy>;

}      // namespace gmx

#endif // GMX_UTILITY_ALIGNEDALLOCATOR_H