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39 #include "gromacs/utility/smalloc.h"
51 #ifdef HAVE__ALIGNED_MALLOC
55 #include "thread_mpi/threads.h"
57 #include "gromacs/utility/fatalerror.h"
59 #include "gromacs/utility/basenetwork.h"
60 #include "gromacs/utility/gmxmpi.h"
63 static gmx_bool g_bOverAllocDD = FALSE;
64 static tMPI_Thread_mutex_t g_over_alloc_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
67 static void log_action(int bMal, const char *what, const char *file, int line,
68 int nelem, int size, void *ptr)
80 tMPI_Thread_mutex_lock(&gmx_logfile_mtx);
82 /* This total memory count is not correct, since with realloc
83 * it adds the whole size again, not just the increment.
85 /* This static variable is protected by the mutex too... */
89 if (debug && (bytes != 0))
91 fprintf(debug, "%s:%d kB (%7d kB) [%s, line %d, nelem %d, size %d]\n",
92 what ? what : NN, bytes, btot/1024,
93 file ? file : NN, line, nelem, size);
95 /* Print to stderr for things larger than 1 MB */
96 if (bytes >= 1024 || bytes <= -1024)
101 fname = strrchr(file, DIR_SEPARATOR);
111 printf("%s: %.1f MB [%s, line %d, nelem %d, size %d]\n",
112 what ? what : NN, bytes/1024.0,
113 file ? fname : NN, line, nelem, size);
115 tMPI_Thread_mutex_unlock(&gmx_logfile_mtx);
119 void *save_malloc(const char *name, const char *file, int line, size_t size)
130 if ((p = malloc(size)) == NULL)
132 gmx_fatal(errno, __FILE__, __LINE__,
133 "Not enough memory. Failed to malloc %"GMX_PRId64 " bytes for %s\n"
134 "(called from file %s, line %d)",
135 (gmx_int64_t)size, name, file, line);
137 (void) memset(p, 0, size);
140 log_action(1, name, file, line, 1, size, p);
145 void *save_calloc(const char *name, const char *file, int line,
146 size_t nelem, size_t elsize)
151 if ((nelem == 0) || (elsize == 0))
157 #ifdef PRINT_ALLOC_KB
158 if (nelem*elsize >= PRINT_ALLOC_KB*1024)
160 int rank = gmx_node_rank();
161 printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
162 nelem*elsize/1048576.0, name, file, line, rank);
165 #ifdef GMX_BROKEN_CALLOC
166 /* emulate calloc(3) with malloc/memset on machines with
167 a broken calloc, e.g. in -lgmalloc on cray xt3. */
168 if ((p = malloc((size_t)nelem*(size_t)elsize)) == NULL)
170 gmx_fatal(errno, __FILE__, __LINE__,
171 "Not enough memory. Failed to calloc %"GMX_PRId64
172 " elements of size %"GMX_PRId64
173 " for %s\n(called from file %s, line %d)",
174 (gmx_int64_t)nelem, (gmx_int64_t)elsize,
177 memset(p, 0, (size_t) (nelem * elsize));
179 if ((p = calloc((size_t)nelem, (size_t)elsize)) == NULL)
181 gmx_fatal(errno, __FILE__, __LINE__,
182 "Not enough memory. Failed to calloc %"GMX_PRId64
183 " elements of size %"GMX_PRId64
184 " for %s\n(called from file %s, line %d)",
185 (gmx_int64_t)nelem, (gmx_int64_t)elsize, name, file, line);
190 log_action(1, name, file, line, nelem, elsize, p);
195 void *save_realloc(const char *name, const char *file, int line, void *ptr,
196 size_t nelem, size_t elsize)
199 size_t size = nelem*elsize;
204 save_free(name, file, line, ptr);
208 #ifdef PRINT_ALLOC_KB
209 if (size >= PRINT_ALLOC_KB*1024)
211 int rank = gmx_node_rank();
212 printf("Reallocating %.1f MB for %s (called from file %s, line %d on %d)\n",
213 size/1048576.0, name, file, line, rank);
218 p = malloc((size_t)size);
222 p = realloc(ptr, (size_t)size);
226 gmx_fatal(errno, __FILE__, __LINE__,
227 "Not enough memory. Failed to realloc %"GMX_PRId64 " bytes for %s, %s=%x\n"
228 "(called from file %s, line %d)",
229 (gmx_int64_t)size, name, name, ptr, file, line);
232 log_action(1, name, file, line, 1, size, p);
238 void save_free(const char gmx_unused *name, const char gmx_unused *file, int gmx_unused line, void *ptr)
241 log_action(0, name, file, line, 0, 0, ptr);
249 /* If we don't have useful routines for allocating aligned memory,
250 * then we have to use the old-style GROMACS approach bitwise-ANDing
251 * pointers to ensure alignment. We store the pointer to the originally
252 * allocated region in the space before the returned pointer */
254 /* we create a positive define for the absence of an system-provided memalign */
255 #if (!defined HAVE_POSIX_MEMALIGN && !defined HAVE_MEMALIGN && \
256 !defined HAVE__ALIGNED_MALLOC)
257 #define GMX_OWN_MEMALIGN
261 /* Pointers allocated with this routine should only be freed
262 * with save_free_aligned, however this will only matter
263 * on systems that lack posix_memalign() and memalign() when
264 * freeing memory that needed to be adjusted to achieve
265 * the necessary alignment. */
266 void *save_malloc_aligned(const char *name, const char *file, int line,
267 size_t nelem, size_t elsize, size_t alignment)
269 void **aligned = NULL;
270 void *malloced = NULL;
271 gmx_bool allocate_fail;
275 gmx_fatal(errno, __FILE__, __LINE__,
276 "Cannot allocate aligned memory with alignment of zero!\n(called from file %s, line %d)", file, line);
280 if (nelem == 0 || elsize == 0)
286 #ifdef PRINT_ALLOC_KB
287 if (nelem*elsize >= PRINT_ALLOC_KB*1024)
289 int rank = gmx_node_rank();
290 printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
291 nelem*elsize/1048576.0, name, file, line, rank);
295 #ifdef HAVE_POSIX_MEMALIGN
296 allocate_fail = (0 != posix_memalign(&malloced, alignment, nelem*elsize));
297 #elif defined HAVE_MEMALIGN
298 allocate_fail = ((malloced = memalign(alignment, nelem*elsize)) == NULL);
299 #elif defined HAVE__ALIGNED_MALLOC
300 allocate_fail = ((malloced = _aligned_malloc(nelem*elsize, alignment))
303 allocate_fail = ((malloced = malloc(nelem*elsize+alignment+
304 sizeof(void*))) == NULL);
308 gmx_fatal(errno, __FILE__, __LINE__,
309 "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);
311 /* we start with the original pointer */
312 aligned = (void**)malloced;
314 #ifdef GMX_OWN_MEMALIGN
315 /* Make the aligned pointer, and save the underlying pointer that
316 * we're allowed to free(). */
318 /* we first make space to store that underlying pointer: */
319 aligned = aligned + 1;
320 /* then we apply a bit mask */
321 aligned = (void *) (((size_t) aligned + alignment - 1) &
322 (~((size_t) (alignment-1))));
323 /* and we store the original pointer in the area just before the
324 pointer we're going to return */
325 aligned[-1] = malloced;
328 return (void*)aligned;
331 void *save_calloc_aligned(const char *name, const char *file, int line,
332 size_t nelem, size_t elsize, size_t alignment)
334 void *aligned = save_malloc_aligned(name, file, line, nelem, elsize, alignment);
337 memset(aligned, 0, (size_t)(nelem * elsize));
342 /* This routine can NOT be called with any pointer */
343 void save_free_aligned(const char gmx_unused *name, const char gmx_unused *file, int gmx_unused line, void *ptr)
350 #ifdef GMX_OWN_MEMALIGN
351 /* we get the pointer from just before the memaligned pointer */
352 free = ((void**)ptr)[-1];
355 #ifndef HAVE__ALIGNED_MALLOC
356 /* (Now) we're allowed to use a normal free() on this pointer. */
357 save_free(name, file, line, free);
364 void set_over_alloc_dd(gmx_bool set)
366 tMPI_Thread_mutex_lock(&g_over_alloc_mutex);
367 /* we just make sure that we don't set this at the same time.
368 We don't worry too much about reading this rarely-set variable */
369 g_bOverAllocDD = set;
370 tMPI_Thread_mutex_unlock(&g_over_alloc_mutex);
373 int over_alloc_dd(int n)
377 return OVER_ALLOC_FAC*n + 100;