src/gromacs/utility/smalloc.h

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  37 /*! \file
  38  * \brief
  39  * C memory allocation routines for \Gromacs.
  40  *
  41  * This header provides macros snew(), srenew(), smalloc(), and sfree() for
  42  * C memory management.  Additionally, snew_aligned() and sfree_aligned() are
  43  * provided for managing memory with a specified byte alignment.
  44  *
  45  * If an allocation fails, the program is halted by calling gmx_fatal(), which
  46  * outputs source file and line number and the name of the variable involved.
  47  * This frees calling code from the trouble of checking the result of the
  48  * allocations everywhere.  It also provides a location for centrally logging
  49  * memory allocations for diagnosing memory usage (currently can only enabled
  50  * by changing the source code).  Additionally, sfree() works also with a
  51  * `NULL` parameter, which standard free() does not.
  52  *
  53  * The macros forward the calls to functions save_malloc(), save_calloc(),
  54  * save_realloc(), save_free(), save_calloc_aligned(), and save_free_aligned().
  55  * There are a few low-level locations in \Gromacs that call these directly,
  56  * but generally the macros should be used.
  57  * save_malloc_aligned() exists for this purpose, although there is no macro to
  58  * invoke it.
  59  *
  60  * \if internal
  61  * As an implementation detail, the macros need a different internal
  62  * implementation for C and C++ code.  This is because C accepts conversions
  63  * from `void *` to any pointer type, but C++ doesn't.  And in order to cast
  64  * the returned pointer to a correct type, a C++ template needs to be used to
  65  * get access to the type.
  66  * \endif
  67  *
  68  * \inpublicapi
  69  * \ingroup module_utility
  70  */
  71 #ifndef GMX_UTILITY_SMALLOC_H
  72 #define GMX_UTILITY_SMALLOC_H
  73
  74 #include <stddef.h>
  75
  76 #include "gromacs/utility/basedefinitions.h"
  77
  78 #ifdef __cplusplus
  79 extern "C" {
  80 #endif
  81
  82 /*! \brief
  83  * \Gromacs wrapper for malloc().
  84  *
  85  * \param[in] name   Variable name identifying the allocation.
  86  * \param[in] file   Source code file where the allocation originates from.
  87  * \param[in] line   Source code line where the allocation originates from.
  88  * \param[in] size   Number of bytes to allocate.
  89  * \returns   Pointer to the allocated space.
  90  *
  91  * This should generally be called through smalloc(), not directly.
  92  */
  93 void *save_malloc(const char *name, const char *file, int line, size_t size);
  94 /*! \brief
  95  * \Gromacs wrapper for calloc().
  96  *
  97  * \param[in] name   Variable name identifying the allocation.
  98  * \param[in] file   Source code file where the allocation originates from.
  99  * \param[in] line   Source code line where the allocation originates from.
 100  * \param[in] nelem  Number of elements to allocate.
 101  * \param[in] elsize Number of bytes per element.
 102  * \returns   Pointer to the allocated space.
 103  *
 104  * This should generally be called through snew(), not directly.
 105  */
 106 void *save_calloc(const char *name, const char *file, int line,
 107                   size_t nelem, size_t elsize);
 108 /*! \brief
 109  * \Gromacs wrapper for realloc().
 110  *
 111  * \param[in] name   Variable name identifying the allocation.
 112  * \param[in] file   Source code file where the allocation originates from.
 113  * \param[in] line   Source code line where the allocation originates from.
 114  * \param[in] ptr    Pointer to the previously allocated memory (can be NULL).
 115  * \param[in] nelem  Number of elements to allocate.
 116  * \param[in] elsize Number of bytes per element.
 117  * \returns   Pointer to the allocated space.
 118  *
 119  * As with realloc(), if \p ptr is NULL, memory is allocated as if malloc() was
 120  * called.
 121  * This should generally be called through srenew(), not directly.
 122  *
 123  * Note that the allocated memory is not initialized to zero.
 124  */
 125 void *save_realloc(const char *name, const char *file, int line,
 126                    void *ptr, size_t nelem, size_t elsize);
 127 /*! \brief
 128  * \Gromacs wrapper for free().
 129  *
 130  * \param[in] name   Variable name identifying the deallocation.
 131  * \param[in] file   Source code file where the deallocation originates from.
 132  * \param[in] line   Source code line where the deallocation originates from.
 133  * \param[in] ptr    Pointer to the allocated memory (can be NULL).
 134  *
 135  * If \p ptr is NULL, does nothing.
 136  * This should generally be called through sfree(), not directly.
 137  * This never fails.
 138  */
 139 void save_free(const char *name, const char *file, int line, void *ptr);
 140
 141 /*! \brief
 142  * \Gromacs wrapper for allocating aligned memory.
 143  *
 144  * \param[in] name   Variable name identifying the allocation.
 145  * \param[in] file   Source code file where the allocation originates from.
 146  * \param[in] line   Source code line where the allocation originates from.
 147  * \param[in] nelem  Number of elements to allocate.
 148  * \param[in] elsize Number of bytes per element.
 149  * \param[in] alignment Requested alignment in bytes.
 150  * \returns   Pointer to the allocated space, aligned at `alignment`-byte
 151  *     boundary.
 152  *
 153  * There is no macro that invokes this function.
 154  *
 155  * The returned pointer should only be freed with a call to save_free_aligned().
 156  */
 157 void *save_malloc_aligned(const char *name, const char *file, int line,
 158                           size_t nelem, size_t elsize, size_t alignment);
 159 /*! \brief
 160  * \Gromacs wrapper for allocating zero-initialized aligned memory.
 161  *
 162  * \param[in] name   Variable name identifying the allocation.
 163  * \param[in] file   Source code file where the allocation originates from.
 164  * \param[in] line   Source code line where the allocation originates from.
 165  * \param[in] nelem  Number of elements to allocate.
 166  * \param[in] elsize Number of bytes per element.
 167  * \param[in] alignment Requested alignment in bytes.
 168  * \returns   Pointer to the allocated space, aligned at `alignment`-byte
 169  *     boundary.
 170  *
 171  * This should generally be called through snew_aligned(), not directly.
 172  *
 173  * The returned pointer should only be freed with a call to save_free_aligned().
 174  */
 175 void *save_calloc_aligned(const char *name, const char *file, int line,
 176                           size_t nelem, size_t elsize, size_t alignment);
 177 /*! \brief
 178  * \Gromacs wrapper for freeing aligned memory.
 179  *
 180  * \param[in] name   Variable name identifying the deallocation.
 181  * \param[in] file   Source code file where the deallocation originates from.
 182  * \param[in] line   Source code line where the deallocation originates from.
 183  * \param[in] ptr    Pointer to the allocated memory (can be NULL).
 184  *
 185  * If \p ptr is NULL, does nothing.
 186  * \p ptr should have been allocated with save_malloc_aligned() or
 187  * save_calloc_aligned().
 188  * This should generally be called through sfree_aligned(), not directly.
 189  * This never fails.
 190  */
 191 void save_free_aligned(const char *name, const char *file, int line, void *ptr);
 192
 193 #ifdef __cplusplus
 194 }
 195 #endif
 196
 197 #ifdef __cplusplus
 198
 199 #if GMX_CXX11_COMPILATION
 200 #include <type_traits>
 201 #endif
 202
 203 /*! \cond internal */
 204 /*! \name Implementation templates for C++ memory allocation macros
 205  *
 206  * These templates are used to implement the snew() etc. macros for C++, where
 207  * an explicit cast is needed from `void *` (the return value of the allocation
 208  * wrapper functions) to the thpe of \p ptr.
 209  *
 210  * Having these as `static` avoid some obscure bugs if several files define
 211  * distinct data structures with identical names and allocate memory for them
 212  * using snew().  By the C++ standard, such declarations cause undefined
 213  * behavior, but can be difficult to spot in the existing C code.
 214  * Without the `static` (and if the compiler does not inline the calls), the
 215  * linker cannot that data structures with identical names are actually
 216  * different and links calls to these template functions incorrectly, which can
 217  * result in allocation of an incorrect amount of memory if the element size is
 218  * computed within the function.
 219  *
 220  * The size cannot be passed as a parameter to the function either, since that
 221  * provokes warnings from cppcheck for some invocations, where a complex
 222  * expression is passed as \p ptr.
 223  */
 224 /*! \{ */
 225 /** C++ helper for snew(). */
 226 template <typename T> static inline
 227 void gmx_snew_impl(const char *name, const char *file, int line,
 228                    T * &ptr, size_t nelem)
 229 {
 230 #if GMX_CXX11_COMPILATION
 231     static_assert(std::is_pod<T>::value, "snew() called on C++ type");
 232 #endif
 233     ptr = (T *)save_calloc(name, file, line, nelem, sizeof(T));
 234 }
 235 /** C++ helper for srenew(). */
 236 template <typename T> static inline
 237 void gmx_srenew_impl(const char *name, const char *file, int line,
 238                      T * &ptr, size_t nelem)
 239 {
 240 #if GMX_CXX11_COMPILATION
 241     static_assert(std::is_pod<T>::value, "srenew() called on C++ type");
 242 #endif
 243     ptr = (T *)save_realloc(name, file, line, ptr, nelem, sizeof(T));
 244 }
 245 /** C++ helper for smalloc(). */
 246 template <typename T> static inline
 247 void gmx_smalloc_impl(const char *name, const char *file, int line,
 248                       T * &ptr, size_t size)
 249 {
 250 #if GMX_CXX11_COMPILATION
 251     static_assert(std::is_pod<T>::value, "smalloc() called on C++ type");
 252 #endif
 253     ptr = (T *)save_malloc(name, file, line, size);
 254 }
 255 /** C++ helper for snew_aligned(). */
 256 template <typename T> static inline
 257 void gmx_snew_aligned_impl(const char *name, const char *file, int line,
 258                            T * &ptr, size_t nelem, size_t alignment)
 259 {
 260 #if GMX_CXX11_COMPILATION
 261     static_assert(std::is_pod<T>::value, "snew_aligned() called on C++ type");
 262 #endif
 263     ptr = (T *)save_calloc_aligned(name, file, line, nelem, sizeof(T), alignment);
 264 }
 265 /** C++ helper for sfree(). */
 266 template <typename T> static inline
 267 void gmx_sfree_impl(const char *name, const char *file, int line, T *ptr)
 268 {
 269 #if GMX_CXX11_COMPILATION
 270     static_assert(std::is_pod<T>::value || std::is_void<T>::value,
 271                   "sfree() called on C++ type");
 272 #endif
 273     save_free(name, file, line, ptr);
 274 }
 275 /** C++ helper for sfree_aligned(). */
 276 template <typename T> static inline
 277 void gmx_sfree_aligned_impl(const char *name, const char *file, int line, T *ptr)
 278 {
 279 #if GMX_CXX11_COMPILATION
 280     static_assert(std::is_pod<T>::value || std::is_void<T>::value,
 281                   "sfree_aligned() called on C++ type");
 282 #endif
 283     save_free_aligned(name, file, line, ptr);
 284 }
 285 /*! \} */
 286 /*! \endcond */
 287 #endif /* __cplusplus */
 288
 289 /*! \def snew
 290  * \brief
 291  * Allocates memory for a given number of elements.
 292  *
 293  * \param[out] ptr   Pointer to allocate.
 294  * \param[in]  nelem Number of elements to allocate.
 295  *
 296  * Allocates memory for \p nelem elements of type \p *ptr and sets this to
 297  * \p ptr.  The allocated memory is initialized to zeros.
 298  *
 299  * \hideinitializer
 300  */
 301 /*! \def srenew
 302  * \brief
 303  * Reallocates memory for a given number of elements.
 304  *
 305  * \param[in,out] ptr   Pointer to allocate/reallocate.
 306  * \param[in]     nelem Number of elements to allocate.
 307  *
 308  * (Re)allocates memory for \p ptr such that it can hold \p nelem elements of
 309  * type \p *ptr, and sets the new pointer to \p ptr.
 310  * If \p ptr is `NULL`, memory is allocated as if it was new.
 311  * If \p nelem is zero, \p ptr is freed (if not `NULL`).
 312  * Note that the allocated memory is not initialized, unlike with snew().
 313  *
 314  * \hideinitializer
 315  */
 316 /*! \def smalloc
 317  * \brief
 318  * Allocates memory for a given number of bytes.
 319  *
 320  * \param[out] ptr  Pointer to allocate.
 321  * \param[in]  size Number of bytes to allocate.
 322  *
 323  * Allocates memory for \p size bytes and sets this to \p ptr.
 324  * The allocated memory is initialized to zero.
 325  *
 326  * \hideinitializer
 327  */
 328 /*! \def snew_aligned
 329  * \brief
 330  * Allocates aligned memory for a given number of elements.
 331  *
 332  * \param[out] ptr       Pointer to allocate.
 333  * \param[in]  nelem     Number of elements to allocate.
 334  * \param[in]  alignment Requested alignment in bytes.
 335  *
 336  * Allocates memory for \p nelem elements of type \p *ptr and sets this to
 337  * \p ptr.  The returned pointer is `alignment`-byte aligned.
 338  * The allocated memory is initialized to zeros.
 339  *
 340  * The returned pointer should only be freed with sfree_aligned().
 341  *
 342  * \hideinitializer
 343  */
 344 /*! \def sfree
 345  * \brief
 346  * Frees memory referenced by \p ptr.
 347  *
 348  * \p ptr is allowed to be NULL, in which case nothing is done.
 349  *
 350  * \hideinitializer
 351  */
 352 /*! \def sfree_aligned
 353  * \brief
 354  * Frees aligned memory referenced by \p ptr.
 355  *
 356  * This must only be called with a pointer obtained through snew_aligned().
 357  * \p ptr is allowed to be NULL, in which case nothing is done.
 358  *
 359  * \hideinitializer
 360  */
 361 #ifdef __cplusplus
 362
 363 /* C++ implementation */
 364 #define snew(ptr, nelem) \
 365     gmx_snew_impl(#ptr, __FILE__, __LINE__, (ptr), (nelem))
 366 #define srenew(ptr, nelem) \
 367     gmx_srenew_impl(#ptr, __FILE__, __LINE__, (ptr), (nelem))
 368 #define smalloc(ptr, size) \
 369     gmx_smalloc_impl(#ptr, __FILE__, __LINE__, (ptr), (size))
 370 #define snew_aligned(ptr, nelem, alignment) \
 371     gmx_snew_aligned_impl(#ptr, __FILE__, __LINE__, (ptr), (nelem), alignment)
 372 #define sfree(ptr) \
 373     gmx_sfree_impl(#ptr, __FILE__, __LINE__, (ptr))
 374 #define sfree_aligned(ptr) \
 375     gmx_sfree_aligned_impl(#ptr, __FILE__, __LINE__, (ptr))
 376
 377 #else
 378
 379 /* C implementation */
 380 #define snew(ptr, nelem) \
 381     (ptr) = save_calloc(#ptr, __FILE__, __LINE__, (nelem), sizeof(*(ptr)))
 382 #define srenew(ptr, nelem) \
 383     (ptr) = save_realloc(#ptr, __FILE__, __LINE__, (ptr), (nelem), sizeof(*(ptr)))
 384 #define smalloc(ptr, size) \
 385     (ptr) = save_malloc(#ptr, __FILE__, __LINE__, size)
 386 #define snew_aligned(ptr, nelem, alignment) \
 387     (ptr) = save_calloc_aligned(#ptr, __FILE__, __LINE__, (nelem), sizeof(*(ptr)), alignment)
 388 #define sfree(ptr) save_free(#ptr, __FILE__, __LINE__, (ptr))
 389 #define sfree_aligned(ptr) save_free_aligned(#ptr, __FILE__, __LINE__, (ptr))
 390
 391 #endif
 392
 393 #ifdef __cplusplus
 394 extern "C" {
 395 #endif
 396
 397 /*! \brief
 398  * Over allocation factor for memory allocations.
 399  *
 400  * Memory (re)allocation can be VERY slow, especially with some
 401  * MPI libraries that replace the standard malloc and realloc calls.
 402  * To avoid slow memory allocation we use over_alloc to set the memory
 403  * allocation size for large data blocks. Since this scales the size
 404  * with a factor, we use log(n) realloc calls instead of n.
 405  * This can reduce allocation times from minutes to seconds.
 406  *
 407  * This factor leads to 4 realloc calls to double the array size.
 408  */
 409 #define OVER_ALLOC_FAC 1.19
 410
 411 /*! \brief
 412  * Turns over allocation for variable size atoms/cg/top arrays on or off,
 413  * default is off.
 414  *
 415  * \todo
 416  * This is mdrun-specific, so it might be better to put this and
 417  * over_alloc_dd() much higher up.
 418  */
 419 void set_over_alloc_dd(gmx_bool set);
 420
 421 /*! \brief
 422  * Returns new allocation count for domain decomposition allocations.
 423  *
 424  * Returns n when domain decomposition over allocation is off.
 425  * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
 426  * This is to avoid frequent reallocation during domain decomposition in mdrun.
 427  */
 428 int over_alloc_dd(int n);
 429
 430 /** Over allocation for small data types: int, real etc. */
 431 #define over_alloc_small(n) (int)(OVER_ALLOC_FAC*(n) + 8000)
 432
 433 /** Over allocation for large data types: complex structs */
 434 #define over_alloc_large(n) (int)(OVER_ALLOC_FAC*(n) + 1000)
 435
 436 #ifdef __cplusplus
 437 }
 438 #endif
 439
 440 #endif