src/gromacs/utility/smalloc.cpp

   1 /*
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  37 #include "gmxpre.h"
  38
  39 #include "smalloc.h"
  40
  41 #include "config.h"
  42
  43 #include <errno.h>
  44 #include <stdio.h>
  45 #include <stdlib.h>
  46
  47 #ifdef WITH_DMALLOC
  48 #include <dmalloc.h>
  49 #endif
  50 #ifdef HAVE__ALIGNED_MALLOC
  51 #include <malloc.h>
  52 #endif
  53
  54 #include <cstring>
  55
  56 #include "thread_mpi/threads.h"
  57
  58 #include "gromacs/utility/dir_separator.h"
  59 #include "gromacs/utility/fatalerror.h"
  60 #ifdef PRINT_ALLOC_KB
  61 #include "gromacs/utility/basenetwork.h"
  62 #include "gromacs/utility/gmxmpi.h"
  63 #endif
  64
  65 static gmx_bool            g_bOverAllocDD     = FALSE;
  66 static tMPI_Thread_mutex_t g_over_alloc_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
  67
  68 #ifdef DEBUG
  69 static void log_action(int bMal, const char *what, const char *file, int line,
  70                        int nelem, int size, void *ptr)
  71 {
  72     static int btot = 0;
  73     char      *NN   = "NULL";
  74     int        bytes;
  75
  76     bytes = size*nelem;
  77     if (!bMal)
  78     {
  79         bytes = -bytes;
  80     }
  81
  82     tMPI_Thread_mutex_lock(&gmx_logfile_mtx);
  83
  84     /* This total memory count is not correct, since with realloc
  85      * it adds the whole size again, not just the increment.
  86      */
  87     /* This static variable is protected by the mutex too... */
  88     btot += bytes;
  89
  90     bytes /= 1024;
  91     if (debug && (bytes != 0))
  92     {
  93         fprintf(debug, "%s:%d kB (%7d kB) [%s, line %d, nelem %d, size %d]\n",
  94                 what ? what : NN, bytes, btot/1024,
  95                 file ? file : NN, line, nelem, size);
  96     }
  97     /* Print to stderr for things larger than 1 MB */
  98     if (bytes >= 1024 || bytes <= -1024)
  99     {
 100         char *fname = NULL;
 101         if (file)
 102         {
 103             fname = strrchr(file, DIR_SEPARATOR);
 104             if (fname)
 105             {
 106                 fname++;
 107             }
 108             else
 109             {
 110                 fname = file;
 111             }
 112         }
 113         printf("%s: %.1f MB [%s, line %d, nelem %d, size %d]\n",
 114                what ? what  : NN, bytes/1024.0,
 115                file ? fname : NN, line, nelem, size);
 116     }
 117     tMPI_Thread_mutex_unlock(&gmx_logfile_mtx);
 118 }
 119 #endif
 120
 121 void *save_malloc(const char *name, const char *file, int line, size_t size)
 122 {
 123     void *p;
 124
 125     p = NULL;
 126     if (size == 0)
 127     {
 128         p = NULL;
 129     }
 130     else
 131     {
 132         if ((p = malloc(size)) == NULL)
 133         {
 134             gmx_fatal(errno, __FILE__, __LINE__,
 135                       "Not enough memory. Failed to malloc %" GMX_PRId64 " bytes for %s\n"
 136                       "(called from file %s, line %d)",
 137                       (gmx_int64_t)size, name, file, line);
 138         }
 139         (void) memset(p, 0, size);
 140     }
 141 #ifdef DEBUG
 142     log_action(1, name, file, line, 1, size, p);
 143 #endif
 144     return p;
 145 }
 146
 147 void *save_calloc(const char *name, const char *file, int line,
 148                   size_t nelem, size_t elsize)
 149 {
 150     void *p;
 151
 152     p = NULL;
 153     if ((nelem == 0) || (elsize == 0))
 154     {
 155         p = NULL;
 156     }
 157     else
 158     {
 159 #ifdef PRINT_ALLOC_KB
 160         if (nelem*elsize >= PRINT_ALLOC_KB*1024)
 161         {
 162             int rank = gmx_node_rank();
 163             printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
 164                    nelem*elsize/1048576.0, name, file, line, rank);
 165         }
 166 #endif
 167 #ifdef GMX_BROKEN_CALLOC
 168         /* emulate calloc(3) with malloc/memset on machines with
 169            a broken calloc, e.g. in -lgmalloc on cray xt3. */
 170         if ((p = malloc((size_t)nelem*(size_t)elsize)) == NULL)
 171         {
 172             gmx_fatal(errno, __FILE__, __LINE__,
 173                       "Not enough memory. Failed to calloc %" GMX_PRId64
 174                       " elements of size %" GMX_PRId64
 175                       " for %s\n(called from file %s, line %d)",
 176                       (gmx_int64_t)nelem, (gmx_int64_t)elsize,
 177                       name, file, line);
 178         }
 179         memset(p, 0, (size_t) (nelem * elsize));
 180 #else
 181         if ((p = calloc((size_t)nelem, (size_t)elsize)) == NULL)
 182         {
 183             gmx_fatal(errno, __FILE__, __LINE__,
 184                       "Not enough memory. Failed to calloc %" GMX_PRId64
 185                       " elements of size %" GMX_PRId64
 186                       " for %s\n(called from file %s, line %d)",
 187                       (gmx_int64_t)nelem, (gmx_int64_t)elsize, name, file, line);
 188         }
 189 #endif
 190     }
 191 #ifdef DEBUG
 192     log_action(1, name, file, line, nelem, elsize, p);
 193 #endif
 194     return p;
 195 }
 196
 197 void *save_realloc(const char *name, const char *file, int line, void *ptr,
 198                    size_t nelem, size_t elsize)
 199 {
 200     void  *p;
 201     size_t size = nelem*elsize;
 202
 203     p = NULL;
 204     if (size == 0)
 205     {
 206         save_free(name, file, line, ptr);
 207     }
 208     else
 209     {
 210 #ifdef PRINT_ALLOC_KB
 211         if (size >= PRINT_ALLOC_KB*1024)
 212         {
 213             int rank = gmx_node_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);
 216         }
 217 #endif
 218         if (ptr == NULL)
 219         {
 220             p = malloc((size_t)size);
 221         }
 222         else
 223         {
 224             p = realloc(ptr, (size_t)size);
 225         }
 226         if (p == NULL)
 227         {
 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);
 232         }
 233 #ifdef DEBUG
 234         log_action(1, name, file, line, 1, size, p);
 235 #endif
 236     }
 237     return p;
 238 }
 239
 240 void save_free(const char gmx_unused *name, const char gmx_unused *file, int gmx_unused line, void *ptr)
 241 {
 242 #ifdef DEBUG
 243     log_action(0, name, file, line, 0, 0, ptr);
 244 #endif
 245     if (ptr != NULL)
 246     {
 247         free(ptr);
 248     }
 249 }
 250
 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 */
 255
 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
 260 #endif
 261
 262
 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)
 270 {
 271     void   **aligned  = NULL;
 272     void    *malloced = NULL;
 273     gmx_bool allocate_fail;
 274
 275     if (alignment == 0)
 276     {
 277         gmx_fatal(errno, __FILE__, __LINE__,
 278                   "Cannot allocate aligned memory with alignment of zero!\n(called from file %s, line %d)", file, line);
 279     }
 280
 281
 282     if (nelem == 0 || elsize == 0)
 283     {
 284         aligned  = NULL;
 285     }
 286     else
 287     {
 288 #ifdef PRINT_ALLOC_KB
 289         if (nelem*elsize >= PRINT_ALLOC_KB*1024)
 290         {
 291             int rank = gmx_node_rank();
 292             printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
 293                    nelem*elsize/1048576.0, name, file, line, rank);
 294         }
 295 #endif
 296
 297 #ifdef HAVE_POSIX_MEMALIGN
 298         allocate_fail = (0 != posix_memalign(&malloced, alignment, nelem*elsize));
 299 #elif defined HAVE_MEMALIGN
 300         allocate_fail = ((malloced = memalign(alignment, nelem*elsize)) == NULL);
 301 #elif defined HAVE__ALIGNED_MALLOC
 302         allocate_fail = ((malloced = _aligned_malloc(nelem*elsize, alignment))
 303                          == NULL);
 304 #else
 305         allocate_fail = ((malloced = malloc(nelem*elsize+alignment+
 306                                             sizeof(void*))) == NULL);
 307 #endif
 308         if (allocate_fail)
 309         {
 310             gmx_fatal(errno, __FILE__, __LINE__,
 311                       "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         }
 313         /* we start with the original pointer */
 314         aligned = (void**)malloced;
 315
 316 #ifdef GMX_OWN_MEMALIGN
 317         /* Make the aligned pointer, and save the underlying pointer that
 318          * we're allowed to free(). */
 319
 320         /* we first make space to store that underlying pointer: */
 321         aligned = aligned + 1;
 322         /* then we apply a bit mask */
 323         aligned = (void *) (((size_t) aligned + alignment - 1) &
 324                             (~((size_t) (alignment-1))));
 325         /* and we store the original pointer in the area just before the
 326            pointer we're going to return */
 327         aligned[-1] = malloced;
 328 #endif
 329     }
 330     return (void*)aligned;
 331 }
 332
 333 void *save_calloc_aligned(const char *name, const char *file, int line,
 334                           size_t nelem, size_t elsize, size_t alignment)
 335 {
 336     void *aligned = save_malloc_aligned(name, file, line, nelem, elsize, alignment);
 337     if (aligned != NULL)
 338     {
 339         memset(aligned, 0, (size_t)(nelem * elsize));
 340     }
 341     return aligned;
 342 }
 343
 344 /* This routine can NOT be called with any pointer */
 345 void save_free_aligned(const char gmx_unused *name, const char gmx_unused *file, int gmx_unused line, void *ptr)
 346 {
 347     void *free = ptr;
 348
 349     if (NULL != ptr)
 350     {
 351 #ifdef GMX_OWN_MEMALIGN
 352         /* we get the pointer from just before the memaligned pointer */
 353         free = ((void**)ptr)[-1];
 354 #endif
 355
 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);
 359 #else
 360         _aligned_free(free);
 361 #endif
 362     }
 363 }
 364
 365 void set_over_alloc_dd(gmx_bool set)
 366 {
 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);
 372 }
 373
 374 int over_alloc_dd(int n)
 375 {
 376     if (g_bOverAllocDD)
 377     {
 378         return static_cast<int>(OVER_ALLOC_FAC*n + 100);
 379     }
 380     else
 381     {
 382         return n;
 383     }
 384 }