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.
41 /* This file is completely threadsafe - keep it that way! */
43 #include "gromacs/utility/gmxmpi.h"
48 #include "gmx_fatal.h"
56 #include "gromacs/legacyheaders/thread_mpi/threads.h"
58 static void log_action(int bMal, const char *what, const char *file, int line,
59 int nelem, int size, void *ptr)
71 tMPI_Thread_mutex_lock(&gmx_logfile_mtx);
73 /* This total memory count is not correct, since with realloc
74 * it adds the whole size again, not just the increment.
76 /* This static variable is protected by the mutex too... */
80 if (debug && (bytes != 0))
82 fprintf(debug, "%s:%d kB (%7d kB) [%s, line %d, nelem %d, size %d]\n",
83 what ? what : NN, bytes, btot/1024,
84 file ? file : NN, line, nelem, size);
86 /* Print to stderr for things larger than 1 MB */
87 if (bytes >= 1024 || bytes <= -1024)
92 fname = strrchr(file, DIR_SEPARATOR);
102 printf("%s: %.1f MB [%s, line %d, nelem %d, size %d]\n",
103 what ? what : NN, bytes/1024.0,
104 file ? fname : NN, line, nelem, size);
106 tMPI_Thread_mutex_unlock(&gmx_logfile_mtx);
110 void *save_malloc(const char *name, const char *file, int line, size_t size)
121 if ((p = malloc(size)) == NULL)
123 gmx_fatal(errno, __FILE__, __LINE__,
124 "Not enough memory. Failed to malloc %"GMX_PRId64 " bytes for %s\n"
125 "(called from file %s, line %d)",
126 (gmx_int64_t)size, name, file, line);
128 (void) memset(p, 0, size);
131 log_action(1, name, file, line, 1, size, p);
136 void *save_calloc(const char *name, const char *file, int line,
137 size_t nelem, size_t elsize)
142 if ((nelem == 0) || (elsize == 0))
148 #ifdef PRINT_ALLOC_KB
150 if (nelem*elsize >= PRINT_ALLOC_KB*1024)
153 MPI_Comm_rank(MPI_COMM_WORLD, &rank);
155 printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
156 nelem*elsize/1048576.0, name, file, line, rank);
159 #ifdef GMX_BROKEN_CALLOC
160 /* emulate calloc(3) with malloc/memset on machines with
161 a broken calloc, e.g. in -lgmalloc on cray xt3. */
162 if ((p = malloc((size_t)nelem*(size_t)elsize)) == NULL)
164 gmx_fatal(errno, __FILE__, __LINE__,
165 "Not enough memory. Failed to calloc %"GMX_PRId64
166 " elements of size %"GMX_PRId64
167 " for %s\n(called from file %s, line %d)",
168 (gmx_int64_t)nelem, (gmx_int64_t)elsize,
171 memset(p, 0, (size_t) (nelem * elsize));
173 if ((p = calloc((size_t)nelem, (size_t)elsize)) == NULL)
175 gmx_fatal(errno, __FILE__, __LINE__,
176 "Not enough memory. Failed to calloc %"GMX_PRId64
177 " elements of size %"GMX_PRId64
178 " for %s\n(called from file %s, line %d)",
179 (gmx_int64_t)nelem, (gmx_int64_t)elsize, name, file, line);
184 log_action(1, name, file, line, nelem, elsize, p);
189 void *save_realloc(const char *name, const char *file, int line, void *ptr,
190 size_t nelem, size_t elsize)
193 size_t size = nelem*elsize;
198 save_free(name, file, line, ptr);
202 #ifdef PRINT_ALLOC_KB
204 if (size >= PRINT_ALLOC_KB*1024)
207 MPI_Comm_rank(MPI_COMM_WORLD, &rank);
209 printf("Reallocating %.1f MB for %s (called from file %s, line %d on %d)\n",
210 size/1048576.0, name, file, line, rank);
215 p = malloc((size_t)size);
219 p = realloc(ptr, (size_t)size);
223 gmx_fatal(errno, __FILE__, __LINE__,
224 "Not enough memory. Failed to realloc %"GMX_PRId64 " bytes for %s, %s=%x\n"
225 "(called from file %s, line %d)",
226 (gmx_int64_t)size, name, name, ptr, file, line);
229 log_action(1, name, file, line, 1, size, p);
235 void save_free(const char gmx_unused *name, const char gmx_unused *file, int gmx_unused line, void *ptr)
238 log_action(0, name, file, line, 0, 0, ptr);
246 size_t maxavail(void)
249 size_t low, high, size;
253 while ((high-low) > 4)
256 if ((ptr = (char *)malloc((size_t)size)) == NULL)
269 size_t memavail(void)
277 if ((ptr = (char *)malloc((size_t)size)) != NULL)
286 /* If we don't have useful routines for allocating aligned memory,
287 * then we have to use the old-style GROMACS approach bitwise-ANDing
288 * pointers to ensure alignment. We store the pointer to the originally
289 * allocated region in the space before the returned pointer */
291 /* we create a positive define for the absence of an system-provided memalign */
292 #if (!defined HAVE_POSIX_MEMALIGN && !defined HAVE_MEMALIGN && \
293 !defined HAVE__ALIGNED_MALLOC)
294 #define GMX_OWN_MEMALIGN
298 /* Pointers allocated with this routine should only be freed
299 * with save_free_aligned, however this will only matter
300 * on systems that lack posix_memalign() and memalign() when
301 * freeing memory that needed to be adjusted to achieve
302 * the necessary alignment. */
303 void *save_malloc_aligned(const char *name, const char *file, int line,
304 unsigned nelem, size_t elsize, size_t alignment)
306 void **aligned = NULL;
307 void *malloced = NULL;
308 gmx_bool allocate_fail;
312 gmx_fatal(errno, __FILE__, __LINE__,
313 "Cannot allocate aligned memory with alignment of zero!\n(called from file %s, line %d)", file, line);
317 if (nelem == 0 || elsize == 0)
323 #ifdef PRINT_ALLOC_KB
324 if (nelem*elsize >= PRINT_ALLOC_KB*1024)
326 printf("Allocating %.1f MB for %s\n",
327 nelem*elsize/(PRINT_ALLOC_KB*1024.0), name);
331 allocate_fail = FALSE; /* stop compiler warnings */
332 #ifdef HAVE_POSIX_MEMALIGN
333 allocate_fail = (0 != posix_memalign(&malloced, alignment, nelem*elsize));
334 #elif defined HAVE_MEMALIGN
335 allocate_fail = ((malloced = memalign(alignment, nelem*elsize)) == NULL);
336 #elif defined HAVE__ALIGNED_MALLOC
337 allocate_fail = ((malloced = _aligned_malloc(nelem*elsize, alignment))
340 allocate_fail = ((malloced = malloc(nelem*elsize+alignment+
341 sizeof(void*))) == NULL);
345 gmx_fatal(errno, __FILE__, __LINE__,
346 "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);
348 /* we start with the original pointer */
349 aligned = (void**)malloced;
351 #ifdef GMX_OWN_MEMALIGN
352 /* Make the aligned pointer, and save the underlying pointer that
353 * we're allowed to free(). */
355 /* we first make space to store that underlying pointer: */
356 aligned = aligned + 1;
357 /* then we apply a bit mask */
358 aligned = (void *) (((size_t) aligned + alignment - 1) &
359 (~((size_t) (alignment-1))));
360 /* and we store the original pointer in the area just before the
361 pointer we're going to return */
362 aligned[-1] = malloced;
365 return (void*)aligned;
368 void *save_calloc_aligned(const char *name, const char *file, int line,
369 unsigned nelem, size_t elsize, size_t alignment)
371 void *aligned = save_malloc_aligned(name, file, line, nelem, elsize, alignment);
374 memset(aligned, 0, (size_t)(nelem * elsize));
379 /* This routine can NOT be called with any pointer */
380 void save_free_aligned(const char *name, const char *file, int line, void *ptr)
387 #ifdef GMX_OWN_MEMALIGN
388 /* we get the pointer from just before the memaligned pointer */
389 free = ((void**)ptr)[-1];
392 #ifndef HAVE__ALIGNED_MALLOC
393 /* (Now) we're allowed to use a normal free() on this pointer. */
394 save_free(name, file, line, free);