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37 #include "gromacs/utility/smalloc.h"
52 #include "gromacs/legacyheaders/gmx_fatal.h"
55 #include "gromacs/legacyheaders/network.h"
56 #include "gromacs/utility/gmxmpi.h"
60 #include "thread_mpi/threads.h"
62 static void log_action(int bMal, const char *what, const char *file, int line,
63 int nelem, int size, void *ptr)
75 tMPI_Thread_mutex_lock(&gmx_logfile_mtx);
77 /* This total memory count is not correct, since with realloc
78 * it adds the whole size again, not just the increment.
80 /* This static variable is protected by the mutex too... */
84 if (debug && (bytes != 0))
86 fprintf(debug, "%s:%d kB (%7d kB) [%s, line %d, nelem %d, size %d]\n",
87 what ? what : NN, bytes, btot/1024,
88 file ? file : NN, line, nelem, size);
90 /* Print to stderr for things larger than 1 MB */
91 if (bytes >= 1024 || bytes <= -1024)
96 fname = strrchr(file, DIR_SEPARATOR);
106 printf("%s: %.1f MB [%s, line %d, nelem %d, size %d]\n",
107 what ? what : NN, bytes/1024.0,
108 file ? fname : NN, line, nelem, size);
110 tMPI_Thread_mutex_unlock(&gmx_logfile_mtx);
114 void *save_malloc(const char *name, const char *file, int line, size_t size)
125 if ((p = malloc(size)) == NULL)
127 gmx_fatal(errno, __FILE__, __LINE__,
128 "Not enough memory. Failed to malloc %"GMX_PRId64 " bytes for %s\n"
129 "(called from file %s, line %d)",
130 (gmx_int64_t)size, name, file, line);
132 (void) memset(p, 0, size);
135 log_action(1, name, file, line, 1, size, p);
140 void *save_calloc(const char *name, const char *file, int line,
141 size_t nelem, size_t elsize)
146 if ((nelem == 0) || (elsize == 0))
152 #ifdef PRINT_ALLOC_KB
153 if (nelem*elsize >= PRINT_ALLOC_KB*1024)
155 int rank = gmx_node_rank();
156 printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
157 nelem*elsize/1048576.0, name, file, line, rank);
160 #ifdef GMX_BROKEN_CALLOC
161 /* emulate calloc(3) with malloc/memset on machines with
162 a broken calloc, e.g. in -lgmalloc on cray xt3. */
163 if ((p = malloc((size_t)nelem*(size_t)elsize)) == NULL)
165 gmx_fatal(errno, __FILE__, __LINE__,
166 "Not enough memory. Failed to calloc %"GMX_PRId64
167 " elements of size %"GMX_PRId64
168 " for %s\n(called from file %s, line %d)",
169 (gmx_int64_t)nelem, (gmx_int64_t)elsize,
172 memset(p, 0, (size_t) (nelem * elsize));
174 if ((p = calloc((size_t)nelem, (size_t)elsize)) == NULL)
176 gmx_fatal(errno, __FILE__, __LINE__,
177 "Not enough memory. Failed to calloc %"GMX_PRId64
178 " elements of size %"GMX_PRId64
179 " for %s\n(called from file %s, line %d)",
180 (gmx_int64_t)nelem, (gmx_int64_t)elsize, name, file, line);
185 log_action(1, name, file, line, nelem, elsize, p);
190 void *save_realloc(const char *name, const char *file, int line, void *ptr,
191 size_t nelem, size_t elsize)
194 size_t size = nelem*elsize;
199 save_free(name, file, line, ptr);
203 #ifdef PRINT_ALLOC_KB
204 if (size >= PRINT_ALLOC_KB*1024)
206 int rank = gmx_node_rank();
207 printf("Reallocating %.1f MB for %s (called from file %s, line %d on %d)\n",
208 size/1048576.0, name, file, line, rank);
213 p = malloc((size_t)size);
217 p = realloc(ptr, (size_t)size);
221 gmx_fatal(errno, __FILE__, __LINE__,
222 "Not enough memory. Failed to realloc %"GMX_PRId64 " bytes for %s, %s=%x\n"
223 "(called from file %s, line %d)",
224 (gmx_int64_t)size, name, name, ptr, file, line);
227 log_action(1, name, file, line, 1, size, p);
233 void save_free(const char gmx_unused *name, const char gmx_unused *file, int gmx_unused line, void *ptr)
236 log_action(0, name, file, line, 0, 0, ptr);
244 /* If we don't have useful routines for allocating aligned memory,
245 * then we have to use the old-style GROMACS approach bitwise-ANDing
246 * pointers to ensure alignment. We store the pointer to the originally
247 * allocated region in the space before the returned pointer */
249 /* we create a positive define for the absence of an system-provided memalign */
250 #if (!defined HAVE_POSIX_MEMALIGN && !defined HAVE_MEMALIGN && \
251 !defined HAVE__ALIGNED_MALLOC)
252 #define GMX_OWN_MEMALIGN
256 /* Pointers allocated with this routine should only be freed
257 * with save_free_aligned, however this will only matter
258 * on systems that lack posix_memalign() and memalign() when
259 * freeing memory that needed to be adjusted to achieve
260 * the necessary alignment. */
261 void *save_malloc_aligned(const char *name, const char *file, int line,
262 size_t nelem, size_t elsize, size_t alignment)
264 void **aligned = NULL;
265 void *malloced = NULL;
266 gmx_bool allocate_fail;
270 gmx_fatal(errno, __FILE__, __LINE__,
271 "Cannot allocate aligned memory with alignment of zero!\n(called from file %s, line %d)", file, line);
275 if (nelem == 0 || elsize == 0)
281 #ifdef PRINT_ALLOC_KB
282 if (nelem*elsize >= PRINT_ALLOC_KB*1024)
284 int rank = gmx_node_rank();
285 printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
286 nelem*elsize/1048576.0, name, file, line, rank);
290 allocate_fail = FALSE; /* stop compiler warnings */
291 #ifdef HAVE_POSIX_MEMALIGN
292 allocate_fail = (0 != posix_memalign(&malloced, alignment, nelem*elsize));
293 #elif defined HAVE_MEMALIGN
294 allocate_fail = ((malloced = memalign(alignment, nelem*elsize)) == NULL);
295 #elif defined HAVE__ALIGNED_MALLOC
296 allocate_fail = ((malloced = _aligned_malloc(nelem*elsize, alignment))
299 allocate_fail = ((malloced = malloc(nelem*elsize+alignment+
300 sizeof(void*))) == NULL);
304 gmx_fatal(errno, __FILE__, __LINE__,
305 "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);
307 /* we start with the original pointer */
308 aligned = (void**)malloced;
310 #ifdef GMX_OWN_MEMALIGN
311 /* Make the aligned pointer, and save the underlying pointer that
312 * we're allowed to free(). */
314 /* we first make space to store that underlying pointer: */
315 aligned = aligned + 1;
316 /* then we apply a bit mask */
317 aligned = (void *) (((size_t) aligned + alignment - 1) &
318 (~((size_t) (alignment-1))));
319 /* and we store the original pointer in the area just before the
320 pointer we're going to return */
321 aligned[-1] = malloced;
324 return (void*)aligned;
327 void *save_calloc_aligned(const char *name, const char *file, int line,
328 size_t nelem, size_t elsize, size_t alignment)
330 void *aligned = save_malloc_aligned(name, file, line, nelem, elsize, alignment);
333 memset(aligned, 0, (size_t)(nelem * elsize));
338 /* This routine can NOT be called with any pointer */
339 void save_free_aligned(const char *name, const char *file, int line, void *ptr)
346 #ifdef GMX_OWN_MEMALIGN
347 /* we get the pointer from just before the memaligned pointer */
348 free = ((void**)ptr)[-1];
351 #ifndef HAVE__ALIGNED_MALLOC
352 /* (Now) we're allowed to use a normal free() on this pointer. */
353 save_free(name, file, line, free);