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39 #include "gromacs/utility/smalloc.h"
52 #include "thread_mpi/threads.h"
54 #include "gromacs/utility/fatalerror.h"
56 #include "gromacs/utility/gmxmpi.h"
59 static gmx_bool g_bOverAllocDD = FALSE;
60 static tMPI_Thread_mutex_t g_over_alloc_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
63 static void log_action(int bMal, const char *what, const char *file, int line,
64 int nelem, int size, void *ptr)
76 tMPI_Thread_mutex_lock(&gmx_logfile_mtx);
78 /* This total memory count is not correct, since with realloc
79 * it adds the whole size again, not just the increment.
81 /* This static variable is protected by the mutex too... */
85 if (debug && (bytes != 0))
87 fprintf(debug, "%s:%d kB (%7d kB) [%s, line %d, nelem %d, size %d]\n",
88 what ? what : NN, bytes, btot/1024,
89 file ? file : NN, line, nelem, size);
91 /* Print to stderr for things larger than 1 MB */
92 if (bytes >= 1024 || bytes <= -1024)
97 fname = strrchr(file, DIR_SEPARATOR);
107 printf("%s: %.1f MB [%s, line %d, nelem %d, size %d]\n",
108 what ? what : NN, bytes/1024.0,
109 file ? fname : NN, line, nelem, size);
111 tMPI_Thread_mutex_unlock(&gmx_logfile_mtx);
115 void *save_malloc(const char *name, const char *file, int line, size_t size)
126 if ((p = malloc(size)) == NULL)
128 gmx_fatal(errno, __FILE__, __LINE__,
129 "Not enough memory. Failed to malloc %"GMX_PRId64 " bytes for %s\n"
130 "(called from file %s, line %d)",
131 (gmx_int64_t)size, name, file, line);
133 (void) memset(p, 0, size);
136 log_action(1, name, file, line, 1, size, p);
141 void *save_calloc(const char *name, const char *file, int line,
142 size_t nelem, size_t elsize)
147 if ((nelem == 0) || (elsize == 0))
153 #ifdef PRINT_ALLOC_KB
155 if (nelem*elsize >= PRINT_ALLOC_KB*1024)
158 MPI_Comm_rank(MPI_COMM_WORLD, &rank);
160 printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
161 nelem*elsize/1048576.0, name, file, line, rank);
164 #ifdef GMX_BROKEN_CALLOC
165 /* emulate calloc(3) with malloc/memset on machines with
166 a broken calloc, e.g. in -lgmalloc on cray xt3. */
167 if ((p = malloc((size_t)nelem*(size_t)elsize)) == NULL)
169 gmx_fatal(errno, __FILE__, __LINE__,
170 "Not enough memory. Failed to calloc %"GMX_PRId64
171 " elements of size %"GMX_PRId64
172 " for %s\n(called from file %s, line %d)",
173 (gmx_int64_t)nelem, (gmx_int64_t)elsize,
176 memset(p, 0, (size_t) (nelem * elsize));
178 if ((p = calloc((size_t)nelem, (size_t)elsize)) == NULL)
180 gmx_fatal(errno, __FILE__, __LINE__,
181 "Not enough memory. Failed to calloc %"GMX_PRId64
182 " elements of size %"GMX_PRId64
183 " for %s\n(called from file %s, line %d)",
184 (gmx_int64_t)nelem, (gmx_int64_t)elsize, name, file, line);
189 log_action(1, name, file, line, nelem, elsize, p);
194 void *save_realloc(const char *name, const char *file, int line, void *ptr,
195 size_t nelem, size_t elsize)
198 size_t size = nelem*elsize;
203 save_free(name, file, line, ptr);
207 #ifdef PRINT_ALLOC_KB
209 if (size >= PRINT_ALLOC_KB*1024)
212 MPI_Comm_rank(MPI_COMM_WORLD, &rank);
214 printf("Reallocating %.1f MB for %s (called from file %s, line %d on %d)\n",
215 size/1048576.0, name, file, line, rank);
220 p = malloc((size_t)size);
224 p = realloc(ptr, (size_t)size);
228 gmx_fatal(errno, __FILE__, __LINE__,
229 "Not enough memory. Failed to realloc %"GMX_PRId64 " bytes for %s, %s=%x\n"
230 "(called from file %s, line %d)",
231 (gmx_int64_t)size, name, name, ptr, file, line);
234 log_action(1, name, file, line, 1, size, p);
240 void save_free(const char gmx_unused *name, const char gmx_unused *file, int gmx_unused line, void *ptr)
243 log_action(0, name, file, line, 0, 0, ptr);
251 /* If we don't have useful routines for allocating aligned memory,
252 * then we have to use the old-style GROMACS approach bitwise-ANDing
253 * pointers to ensure alignment. We store the pointer to the originally
254 * allocated region in the space before the returned pointer */
256 /* we create a positive define for the absence of an system-provided memalign */
257 #if (!defined HAVE_POSIX_MEMALIGN && !defined HAVE_MEMALIGN && \
258 !defined HAVE__ALIGNED_MALLOC)
259 #define GMX_OWN_MEMALIGN
263 /* Pointers allocated with this routine should only be freed
264 * with save_free_aligned, however this will only matter
265 * on systems that lack posix_memalign() and memalign() when
266 * freeing memory that needed to be adjusted to achieve
267 * the necessary alignment. */
268 void *save_malloc_aligned(const char *name, const char *file, int line,
269 size_t nelem, size_t elsize, size_t alignment)
271 void **aligned = NULL;
272 void *malloced = NULL;
273 gmx_bool allocate_fail;
277 gmx_fatal(errno, __FILE__, __LINE__,
278 "Cannot allocate aligned memory with alignment of zero!\n(called from file %s, line %d)", file, line);
282 if (nelem == 0 || elsize == 0)
288 #ifdef PRINT_ALLOC_KB
289 if (nelem*elsize >= PRINT_ALLOC_KB*1024)
291 printf("Allocating %.1f MB for %s\n",
292 nelem*elsize/(PRINT_ALLOC_KB*1024.0), name);
296 #ifdef HAVE_POSIX_MEMALIGN
297 allocate_fail = (0 != posix_memalign(&malloced, alignment, nelem*elsize));
298 #elif defined HAVE_MEMALIGN
299 allocate_fail = ((malloced = memalign(alignment, nelem*elsize)) == NULL);
300 #elif defined HAVE__ALIGNED_MALLOC
301 allocate_fail = ((malloced = _aligned_malloc(nelem*elsize, alignment))
304 allocate_fail = ((malloced = malloc(nelem*elsize+alignment+
305 sizeof(void*))) == NULL);
309 gmx_fatal(errno, __FILE__, __LINE__,
310 "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);
312 /* we start with the original pointer */
313 aligned = (void**)malloced;
315 #ifdef GMX_OWN_MEMALIGN
316 /* Make the aligned pointer, and save the underlying pointer that
317 * we're allowed to free(). */
319 /* we first make space to store that underlying pointer: */
320 aligned = aligned + 1;
321 /* then we apply a bit mask */
322 aligned = (void *) (((size_t) aligned + alignment - 1) &
323 (~((size_t) (alignment-1))));
324 /* and we store the original pointer in the area just before the
325 pointer we're going to return */
326 aligned[-1] = malloced;
329 return (void*)aligned;
332 void *save_calloc_aligned(const char *name, const char *file, int line,
333 size_t nelem, size_t elsize, size_t alignment)
335 void *aligned = save_malloc_aligned(name, file, line, nelem, elsize, alignment);
338 memset(aligned, 0, (size_t)(nelem * elsize));
343 /* This routine can NOT be called with any pointer */
344 void save_free_aligned(const char *name, const char *file, int line, void *ptr)
351 #ifdef GMX_OWN_MEMALIGN
352 /* we get the pointer from just before the memaligned pointer */
353 free = ((void**)ptr)[-1];
356 #ifndef HAVE__ALIGNED_MALLOC
357 /* (Now) we're allowed to use a normal free() on this pointer. */
358 save_free(name, file, line, free);
365 void set_over_alloc_dd(gmx_bool set)
367 tMPI_Thread_mutex_lock(&g_over_alloc_mutex);
368 /* we just make sure that we don't set this at the same time.
369 We don't worry too much about reading this rarely-set variable */
370 g_bOverAllocDD = set;
371 tMPI_Thread_mutex_unlock(&g_over_alloc_mutex);
374 int over_alloc_dd(int n)
378 return OVER_ALLOC_FAC*n + 100;