src/gromacs/selection/mempool.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2010,2011,2012,2014,2017 by the GROMACS development team.
   5  * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
   6  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   7  * and including many others, as listed in the AUTHORS file in the
   8  * top-level source directory and at http://www.gromacs.org.
   9  *
  10  * GROMACS is free software; you can redistribute it and/or
  11  * modify it under the terms of the GNU Lesser General Public License
  12  * as published by the Free Software Foundation; either version 2.1
  13  * of the License, or (at your option) any later version.
  14  *
  15  * GROMACS is distributed in the hope that it will be useful,
  16  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  17  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  18  * Lesser General Public License for more details.
  19  *
  20  * You should have received a copy of the GNU Lesser General Public
  21  * License along with GROMACS; if not, see
  22  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  23  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  24  *
  25  * If you want to redistribute modifications to GROMACS, please
  26  * consider that scientific software is very special. Version
  27  * control is crucial - bugs must be traceable. We will be happy to
  28  * consider code for inclusion in the official distribution, but
  29  * derived work must not be called official GROMACS. Details are found
  30  * in the README & COPYING files - if they are missing, get the
  31  * official version at http://www.gromacs.org.
  32  *
  33  * To help us fund GROMACS development, we humbly ask that you cite
  34  * the research papers on the package. Check out http://www.gromacs.org.
  35  */
  36 /*! \internal \file
  37  * \brief
  38  * Implements functions in mempool.h.
  39  *
  40  * \author Teemu Murtola <teemu.murtola@gmail.com>
  41  * \ingroup module_selection
  42  */
  43 #include "gmxpre.h"
  44
  45 #include "mempool.h"
  46
  47 #include <cstdlib>
  48
  49 #include <new>
  50
  51 #include "gromacs/selection/indexutil.h"
  52 #include "gromacs/utility/exceptions.h"
  53 #include "gromacs/utility/gmxassert.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 //! Alignment in bytes for all returned blocks.
  57 #define ALIGN_STEP 8
  58
  59 /*! \internal \brief
  60  * Describes a single block allocated from the memory pool.
  61  */
  62 typedef struct gmx_sel_mempool_block_t
  63 {
  64     //! Pointer to the start of the block (as returned to the user).
  65     void* ptr;
  66     //! Size of the block, including padding required to align next block.
  67     size_t size;
  68 } gmx_sel_mempool_block_t;
  69
  70 /*! \internal \brief
  71  * Describes a memory pool.
  72  */
  73 struct gmx_sel_mempool_t
  74 {
  75     //! Number of bytes currently allocated from the pool.
  76     size_t currsize;
  77     //! Number of bytes free in the pool, or 0 if \a buffer is NULL.
  78     size_t freesize;
  79     //! Memory area allocated for the pool, or NULL if not yet reserved.
  80     char* buffer;
  81     //! Pointer to the first free byte (aligned at ::ALIGN_STEP) in \a buffer.
  82     char* freeptr;
  83     //! Number of blocks allocated from the pool.
  84     int nblocks;
  85     //! Array describing the allocated blocks.
  86     gmx_sel_mempool_block_t* blockstack;
  87     //! Number of elements allocated for the \a blockstack array.
  88     int blockstack_nalloc;
  89     /*! \brief
  90      * Maximum number of bytes that have been reserved from the pool
  91      * simultaneously.
  92      */
  93     size_t maxsize;
  94 };
  95
  96 gmx_sel_mempool_t* _gmx_sel_mempool_create()
  97 {
  98     gmx_sel_mempool_t* mp;
  99
 100     snew(mp, 1);
 101     mp->currsize          = 0;
 102     mp->freesize          = 0;
 103     mp->buffer            = nullptr;
 104     mp->freeptr           = nullptr;
 105     mp->nblocks           = 0;
 106     mp->blockstack        = nullptr;
 107     mp->blockstack_nalloc = 0;
 108     mp->maxsize           = 0;
 109     return mp;
 110 }
 111
 112 void _gmx_sel_mempool_destroy(gmx_sel_mempool_t* mp)
 113 {
 114     if (!mp->buffer)
 115     {
 116         int i;
 117
 118         for (i = 0; i < mp->nblocks; ++i)
 119         {
 120             sfree(mp->blockstack[i].ptr);
 121         }
 122     }
 123     sfree(mp->buffer);
 124     sfree(mp->blockstack);
 125     sfree(mp);
 126 }
 127
 128 void* _gmx_sel_mempool_alloc(gmx_sel_mempool_t* mp, size_t size)
 129 {
 130     void*  ptr = nullptr;
 131     size_t size_walign;
 132
 133     size_walign = ((size + ALIGN_STEP - 1) / ALIGN_STEP) * ALIGN_STEP;
 134     if (mp->buffer)
 135     {
 136         if (mp->freesize < size)
 137         {
 138             GMX_THROW(gmx::InternalError("Out of memory pool memory"));
 139         }
 140         ptr = mp->freeptr;
 141         mp->freeptr += size_walign;
 142         mp->freesize -= size_walign;
 143         mp->currsize += size_walign;
 144     }
 145     else
 146     {
 147         ptr = malloc(size);
 148         if (!ptr)
 149         {
 150             throw std::bad_alloc();
 151         }
 152         mp->currsize += size_walign;
 153         if (mp->currsize > mp->maxsize)
 154         {
 155             mp->maxsize = mp->currsize;
 156         }
 157     }
 158
 159     if (mp->nblocks >= mp->blockstack_nalloc)
 160     {
 161         mp->blockstack_nalloc = mp->nblocks + 10;
 162         srenew(mp->blockstack, mp->blockstack_nalloc);
 163     }
 164     mp->blockstack[mp->nblocks].ptr  = ptr;
 165     mp->blockstack[mp->nblocks].size = size_walign;
 166     mp->nblocks++;
 167
 168     return ptr;
 169 }
 170
 171 void _gmx_sel_mempool_free(gmx_sel_mempool_t* mp, void* ptr)
 172 {
 173     int size;
 174
 175     if (ptr == nullptr)
 176     {
 177         return;
 178     }
 179     GMX_RELEASE_ASSERT(mp->nblocks > 0 && mp->blockstack[mp->nblocks - 1].ptr == ptr,
 180                        "Invalid order of memory pool free calls");
 181     mp->nblocks--;
 182     size = mp->blockstack[mp->nblocks].size;
 183     mp->currsize -= size;
 184     if (mp->buffer)
 185     {
 186         mp->freeptr = static_cast<char*>(ptr);
 187         mp->freesize += size;
 188     }
 189     else
 190     {
 191         sfree(ptr);
 192     }
 193 }
 194
 195 void _gmx_sel_mempool_reserve(gmx_sel_mempool_t* mp, size_t size)
 196 {
 197     GMX_RELEASE_ASSERT(mp->nblocks == 0,
 198                        "Cannot reserve memory pool when there is something allocated");
 199     GMX_RELEASE_ASSERT(!mp->buffer, "Cannot reserve memory pool twice");
 200     if (size == 0)
 201     {
 202         size = mp->maxsize;
 203     }
 204     mp->buffer = static_cast<char*>(malloc(size));
 205     if (!mp->buffer)
 206     {
 207         throw std::bad_alloc();
 208     }
 209     mp->freesize = size;
 210     mp->freeptr  = mp->buffer;
 211 }
 212
 213 void _gmx_sel_mempool_alloc_group(gmx_sel_mempool_t* mp, gmx_ana_index_t* g, int isize)
 214 {
 215     void* ptr = _gmx_sel_mempool_alloc(mp, sizeof(*g->index) * isize);
 216     g->index  = static_cast<int*>(ptr);
 217 }
 218
 219 void _gmx_sel_mempool_free_group(gmx_sel_mempool_t* mp, gmx_ana_index_t* g)
 220 {
 221     _gmx_sel_mempool_free(mp, g->index);
 222     g->index = nullptr;
 223 }