2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
37 #include "gromacs/utility/smalloc.h"
52 #include "gromacs/utility/fatalerror.h"
54 #include "gromacs/utility/gmxmpi.h"
58 #include "thread_mpi/threads.h"
60 static void log_action(int bMal, const char *what, const char *file, int line,
61 int nelem, int size, void *ptr)
73 tMPI_Thread_mutex_lock(&gmx_logfile_mtx);
75 /* This total memory count is not correct, since with realloc
76 * it adds the whole size again, not just the increment.
78 /* This static variable is protected by the mutex too... */
82 if (debug && (bytes != 0))
84 fprintf(debug, "%s:%d kB (%7d kB) [%s, line %d, nelem %d, size %d]\n",
85 what ? what : NN, bytes, btot/1024,
86 file ? file : NN, line, nelem, size);
88 /* Print to stderr for things larger than 1 MB */
89 if (bytes >= 1024 || bytes <= -1024)
94 fname = strrchr(file, DIR_SEPARATOR);
104 printf("%s: %.1f MB [%s, line %d, nelem %d, size %d]\n",
105 what ? what : NN, bytes/1024.0,
106 file ? fname : NN, line, nelem, size);
108 tMPI_Thread_mutex_unlock(&gmx_logfile_mtx);
112 void *save_malloc(const char *name, const char *file, int line, size_t size)
123 if ((p = malloc(size)) == NULL)
125 gmx_fatal(errno, __FILE__, __LINE__,
126 "Not enough memory. Failed to malloc %"GMX_PRId64 " bytes for %s\n"
127 "(called from file %s, line %d)",
128 (gmx_int64_t)size, name, file, line);
130 (void) memset(p, 0, size);
133 log_action(1, name, file, line, 1, size, p);
138 void *save_calloc(const char *name, const char *file, int line,
139 size_t nelem, size_t elsize)
144 if ((nelem == 0) || (elsize == 0))
150 #ifdef PRINT_ALLOC_KB
152 if (nelem*elsize >= PRINT_ALLOC_KB*1024)
155 MPI_Comm_rank(MPI_COMM_WORLD, &rank);
157 printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
158 nelem*elsize/1048576.0, name, file, line, rank);
161 #ifdef GMX_BROKEN_CALLOC
162 /* emulate calloc(3) with malloc/memset on machines with
163 a broken calloc, e.g. in -lgmalloc on cray xt3. */
164 if ((p = malloc((size_t)nelem*(size_t)elsize)) == NULL)
166 gmx_fatal(errno, __FILE__, __LINE__,
167 "Not enough memory. Failed to calloc %"GMX_PRId64
168 " elements of size %"GMX_PRId64
169 " for %s\n(called from file %s, line %d)",
170 (gmx_int64_t)nelem, (gmx_int64_t)elsize,
173 memset(p, 0, (size_t) (nelem * elsize));
175 if ((p = calloc((size_t)nelem, (size_t)elsize)) == NULL)
177 gmx_fatal(errno, __FILE__, __LINE__,
178 "Not enough memory. Failed to calloc %"GMX_PRId64
179 " elements of size %"GMX_PRId64
180 " for %s\n(called from file %s, line %d)",
181 (gmx_int64_t)nelem, (gmx_int64_t)elsize, name, file, line);
186 log_action(1, name, file, line, nelem, elsize, p);
191 void *save_realloc(const char *name, const char *file, int line, void *ptr,
192 size_t nelem, size_t elsize)
195 size_t size = nelem*elsize;
200 save_free(name, file, line, ptr);
204 #ifdef PRINT_ALLOC_KB
206 if (size >= PRINT_ALLOC_KB*1024)
209 MPI_Comm_rank(MPI_COMM_WORLD, &rank);
211 printf("Reallocating %.1f MB for %s (called from file %s, line %d on %d)\n",
212 size/1048576.0, name, file, line, rank);
217 p = malloc((size_t)size);
221 p = realloc(ptr, (size_t)size);
225 gmx_fatal(errno, __FILE__, __LINE__,
226 "Not enough memory. Failed to realloc %"GMX_PRId64 " bytes for %s, %s=%x\n"
227 "(called from file %s, line %d)",
228 (gmx_int64_t)size, name, name, ptr, file, line);
231 log_action(1, name, file, line, 1, size, p);
237 void save_free(const char gmx_unused *name, const char gmx_unused *file, int gmx_unused line, void *ptr)
240 log_action(0, name, file, line, 0, 0, ptr);
248 /* If we don't have useful routines for allocating aligned memory,
249 * then we have to use the old-style GROMACS approach bitwise-ANDing
250 * pointers to ensure alignment. We store the pointer to the originally
251 * allocated region in the space before the returned pointer */
253 /* we create a positive define for the absence of an system-provided memalign */
254 #if (!defined HAVE_POSIX_MEMALIGN && !defined HAVE_MEMALIGN && \
255 !defined HAVE__ALIGNED_MALLOC)
256 #define GMX_OWN_MEMALIGN
260 /* Pointers allocated with this routine should only be freed
261 * with save_free_aligned, however this will only matter
262 * on systems that lack posix_memalign() and memalign() when
263 * freeing memory that needed to be adjusted to achieve
264 * the necessary alignment. */
265 void *save_malloc_aligned(const char *name, const char *file, int line,
266 size_t nelem, size_t elsize, size_t alignment)
268 void **aligned = NULL;
269 void *malloced = NULL;
270 gmx_bool allocate_fail;
274 gmx_fatal(errno, __FILE__, __LINE__,
275 "Cannot allocate aligned memory with alignment of zero!\n(called from file %s, line %d)", file, line);
279 if (nelem == 0 || elsize == 0)
285 #ifdef PRINT_ALLOC_KB
286 if (nelem*elsize >= PRINT_ALLOC_KB*1024)
288 printf("Allocating %.1f MB for %s\n",
289 nelem*elsize/(PRINT_ALLOC_KB*1024.0), name);
293 allocate_fail = FALSE; /* stop compiler warnings */
294 #ifdef HAVE_POSIX_MEMALIGN
295 allocate_fail = (0 != posix_memalign(&malloced, alignment, nelem*elsize));
296 #elif defined HAVE_MEMALIGN
297 allocate_fail = ((malloced = memalign(alignment, nelem*elsize)) == NULL);
298 #elif defined HAVE__ALIGNED_MALLOC
299 allocate_fail = ((malloced = _aligned_malloc(nelem*elsize, alignment))
302 allocate_fail = ((malloced = malloc(nelem*elsize+alignment+
303 sizeof(void*))) == NULL);
307 gmx_fatal(errno, __FILE__, __LINE__,
308 "Not enough memory. Failed to allocate %u aligned elements of size %u for %s\n(called from file %s, line %d)", nelem, elsize, name, file, line);
310 /* we start with the original pointer */
311 aligned = (void**)malloced;
313 #ifdef GMX_OWN_MEMALIGN
314 /* Make the aligned pointer, and save the underlying pointer that
315 * we're allowed to free(). */
317 /* we first make space to store that underlying pointer: */
318 aligned = aligned + 1;
319 /* then we apply a bit mask */
320 aligned = (void *) (((size_t) aligned + alignment - 1) &
321 (~((size_t) (alignment-1))));
322 /* and we store the original pointer in the area just before the
323 pointer we're going to return */
324 aligned[-1] = malloced;
327 return (void*)aligned;
330 void *save_calloc_aligned(const char *name, const char *file, int line,
331 size_t nelem, size_t elsize, size_t alignment)
333 void *aligned = save_malloc_aligned(name, file, line, nelem, elsize, alignment);
336 memset(aligned, 0, (size_t)(nelem * elsize));
341 /* This routine can NOT be called with any pointer */
342 void save_free_aligned(const char *name, const char *file, int line, void *ptr)
349 #ifdef GMX_OWN_MEMALIGN
350 /* we get the pointer from just before the memaligned pointer */
351 free = ((void**)ptr)[-1];
354 #ifndef HAVE__ALIGNED_MALLOC
355 /* (Now) we're allowed to use a normal free() on this pointer. */
356 save_free(name, file, line, free);