src/gromacs/utility/smalloc.h

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  37 /*! \file
  38  * \brief
  39  * C-style memory allocation routines for \Gromacs.
  40  *
  41  * This header provides macros snew(), srenew(), smalloc(), and sfree() for
  42  * C-style 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  * \inpublicapi
  61  * \ingroup module_utility
  62  */
  63 #ifndef GMX_UTILITY_SMALLOC_H
  64 #define GMX_UTILITY_SMALLOC_H
  65
  66 #include <stddef.h>
  67
  68 #include "gromacs/utility/basedefinitions.h"
  69
  70 /*! \brief
  71  * \Gromacs wrapper for malloc().
  72  *
  73  * \param[in] name   Variable name identifying the allocation.
  74  * \param[in] file   Source code file where the allocation originates from.
  75  * \param[in] line   Source code line where the allocation originates from.
  76  * \param[in] size   Number of bytes to allocate.
  77  * \returns   Pointer to the allocated space.
  78  *
  79  * This should generally be called through smalloc(), not directly.
  80  */
  81 void* save_malloc(const char* name, const char* file, int line, size_t size);
  82 /*! \brief
  83  * \Gromacs wrapper for calloc().
  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] nelem  Number of elements to allocate.
  89  * \param[in] elsize Number of bytes per element.
  90  * \returns   Pointer to the allocated space.
  91  *
  92  * This should generally be called through snew(), not directly.
  93  */
  94 void* save_calloc(const char* name, const char* file, int line, size_t nelem, size_t elsize);
  95 /*! \brief
  96  * \Gromacs wrapper for realloc().
  97  *
  98  * \param[in] name   Variable name identifying the allocation.
  99  * \param[in] file   Source code file where the allocation originates from.
 100  * \param[in] line   Source code line where the allocation originates from.
 101  * \param[in] ptr    Pointer to the previously allocated memory (can be NULL).
 102  * \param[in] nelem  Number of elements to allocate.
 103  * \param[in] elsize Number of bytes per element.
 104  * \returns   Pointer to the allocated space.
 105  *
 106  * As with realloc(), if \p ptr is NULL, memory is allocated as if malloc() was
 107  * called.
 108  * This should generally be called through srenew(), not directly.
 109  *
 110  * Note that the allocated memory is not initialized to zero.
 111  */
 112 void* save_realloc(const char* name, const char* file, int line, void* ptr, size_t nelem, size_t elsize);
 113 /*! \brief
 114  * \Gromacs wrapper for free().
 115  *
 116  * \param[in] name   Variable name identifying the deallocation.
 117  * \param[in] file   Source code file where the deallocation originates from.
 118  * \param[in] line   Source code line where the deallocation originates from.
 119  * \param[in] ptr    Pointer to the allocated memory (can be NULL).
 120  *
 121  * If \p ptr is NULL, does nothing.
 122  * This should generally be called through sfree(), not directly.
 123  * This never fails.
 124  */
 125 void save_free(const char* name, const char* file, int line, void* ptr);
 126
 127 /*! \brief
 128  * \Gromacs wrapper for allocating aligned memory.
 129  *
 130  * \param[in] name   Variable name identifying the allocation.
 131  * \param[in] file   Source code file where the allocation originates from.
 132  * \param[in] line   Source code line where the allocation originates from.
 133  * \param[in] nelem  Number of elements to allocate.
 134  * \param[in] elsize Number of bytes per element.
 135  * \param[in] alignment Requested alignment in bytes.
 136  * \returns   Pointer to the allocated space, aligned at `alignment`-byte
 137  *     boundary.
 138  *
 139  * There is no macro that invokes this function.
 140  *
 141  * The returned pointer should only be freed with a call to save_free_aligned().
 142  */
 143 void* save_malloc_aligned(const char* name, const char* file, int line, size_t nelem, size_t elsize, size_t alignment);
 144 /*! \brief
 145  * \Gromacs wrapper for allocating zero-initialized aligned memory.
 146  *
 147  * \param[in] name   Variable name identifying the allocation.
 148  * \param[in] file   Source code file where the allocation originates from.
 149  * \param[in] line   Source code line where the allocation originates from.
 150  * \param[in] nelem  Number of elements to allocate.
 151  * \param[in] elsize Number of bytes per element.
 152  * \param[in] alignment Requested alignment in bytes.
 153  * \returns   Pointer to the allocated space, aligned at `alignment`-byte
 154  *     boundary.
 155  *
 156  * This should generally be called through snew_aligned(), not directly.
 157  *
 158  * The returned pointer should only be freed with a call to save_free_aligned().
 159  */
 160 void* save_calloc_aligned(const char* name, const char* file, int line, size_t nelem, size_t elsize, size_t alignment);
 161 /*! \brief
 162  * \Gromacs wrapper for freeing aligned memory.
 163  *
 164  * \param[in] name   Variable name identifying the deallocation.
 165  * \param[in] file   Source code file where the deallocation originates from.
 166  * \param[in] line   Source code line where the deallocation originates from.
 167  * \param[in] ptr    Pointer to the allocated memory (can be NULL).
 168  *
 169  * If \p ptr is NULL, does nothing.
 170  * \p ptr should have been allocated with save_malloc_aligned() or
 171  * save_calloc_aligned().
 172  * This should generally be called through sfree_aligned(), not directly.
 173  * This never fails.
 174  */
 175 void save_free_aligned(const char* name, const char* file, int line, void* ptr);
 176
 177 #include <type_traits>
 178
 179 /*! \cond internal */
 180 /*! \name Implementation templates for C++ memory allocation macros
 181  *
 182  * These templates are used to implement the snew() etc. macros for C++, where
 183  * an explicit cast is needed from `void *` (the return value of the allocation
 184  * wrapper functions) to the type of \p ptr.
 185  *
 186  * Having these as `static` avoid some obscure bugs if several files define
 187  * distinct data structures with identical names and allocate memory for them
 188  * using snew().  By the C++ standard, such declarations cause undefined
 189  * behavior, but can be difficult to spot in the existing C code.
 190  * Without the `static` (and if the compiler does not inline the calls), the
 191  * linker cannot that data structures with identical names are actually
 192  * different and links calls to these template functions incorrectly, which can
 193  * result in allocation of an incorrect amount of memory if the element size is
 194  * computed within the function.
 195  *
 196  * The size cannot be passed as a parameter to the function either, since that
 197  * provokes warnings from cppcheck for some invocations, where a complex
 198  * expression is passed as \p ptr.
 199  */
 200 /*! \{ */
 201 /** C++ helper for snew(). */
 202 template<typename T>
 203 static inline void gmx_snew_impl(const char* name, const char* file, int line, T*& ptr, size_t nelem)
 204 {
 205     // TODO: Use std::is_pod_v when CUDA 11 is a requirement.
 206     static_assert(std::is_pod<T>::value, "snew() called on C++ type");
 207     // NOLINTNEXTLINE bugprone-sizeof-expression
 208     ptr = static_cast<T*>(save_calloc(name, file, line, nelem, sizeof(T)));
 209 }
 210 /** C++ helper for srenew(). */
 211 template<typename T>
 212 static inline void gmx_srenew_impl(const char* name, const char* file, int line, T*& ptr, size_t nelem)
 213 {
 214     // TODO: Use std::is_pod_v when CUDA 11 is a requirement.
 215     static_assert(std::is_pod<T>::value, "srenew() called on C++ type");
 216     // NOLINTNEXTLINE bugprone-sizeof-expression
 217     ptr = static_cast<T*>(save_realloc(name, file, line, ptr, nelem, sizeof(T)));
 218 }
 219 /** C++ helper for smalloc(). */
 220 template<typename T>
 221 static inline void gmx_smalloc_impl(const char* name, const char* file, int line, T*& ptr, size_t size)
 222 {
 223     // TODO: Use std::is_pod_v when CUDA 11 is a requirement.
 224     static_assert(std::is_pod<T>::value, "smalloc() called on C++ type");
 225     ptr = static_cast<T*>(save_malloc(name, file, line, size));
 226 }
 227 /** C++ helper for snew_aligned(). */
 228 template<typename T>
 229 static inline void
 230 gmx_snew_aligned_impl(const char* name, const char* file, int line, T*& ptr, size_t nelem, size_t alignment)
 231 {
 232     // TODO: Use std::is_pod_v when CUDA 11 is a requirement.
 233     static_assert(std::is_pod<T>::value, "snew_aligned() called on C++ type");
 234     ptr = static_cast<T*>(save_calloc_aligned(name, file, line, nelem, sizeof(T), alignment));
 235 }
 236 /** C++ helper for sfree(). */
 237 template<typename T>
 238 static inline void gmx_sfree_impl(const char* name, const char* file, int line, T* ptr)
 239 {
 240     // TODO: Use std::is_pod_v and std::is_void_v when CUDA 11 is a requirement.
 241     static_assert(std::is_pod<T>::value || std::is_void<T>::value, "sfree() called on C++ type");
 242     save_free(name, file, line, ptr);
 243 }
 244 /** C++ helper for sfree_aligned(). */
 245 template<typename T>
 246 static inline void gmx_sfree_aligned_impl(const char* name, const char* file, int line, T* ptr)
 247 {
 248     // TODO: Use std::is_pod_v and std::is_void_v when CUDA 11 is a requirement.
 249     static_assert(std::is_pod<T>::value || std::is_void<T>::value,
 250                   "sfree_aligned() called on C++ type");
 251     save_free_aligned(name, file, line, ptr);
 252 }
 253 /*! \} */
 254 /*! \endcond */
 255
 256 /*! \def snew
 257  * \brief
 258  * Allocates memory for a given number of elements.
 259  *
 260  * \param[out] ptr   Pointer to allocate.
 261  * \param[in]  nelem Number of elements to allocate.
 262  *
 263  * Allocates memory for \p nelem elements of type \p *ptr and sets this to
 264  * \p ptr.  The allocated memory is initialized to zeros.
 265  *
 266  * \hideinitializer
 267  */
 268 /*! \def srenew
 269  * \brief
 270  * Reallocates memory for a given number of elements.
 271  *
 272  * \param[in,out] ptr   Pointer to allocate/reallocate.
 273  * \param[in]     nelem Number of elements to allocate.
 274  *
 275  * (Re)allocates memory for \p ptr such that it can hold \p nelem elements of
 276  * type \p *ptr, and sets the new pointer to \p ptr.
 277  * If \p ptr is `NULL`, memory is allocated as if it was new.
 278  * If \p nelem is zero, \p ptr is freed (if not `NULL`).
 279  * Note that the allocated memory is not initialized, unlike with snew().
 280  *
 281  * \hideinitializer
 282  */
 283 /*! \def smalloc
 284  * \brief
 285  * Allocates memory for a given number of bytes.
 286  *
 287  * \param[out] ptr  Pointer to allocate.
 288  * \param[in]  size Number of bytes to allocate.
 289  *
 290  * Allocates memory for \p size bytes and sets this to \p ptr.
 291  * The allocated memory is initialized to zero.
 292  *
 293  * \hideinitializer
 294  */
 295 /*! \def snew_aligned
 296  * \brief
 297  * Allocates aligned memory for a given number of elements.
 298  *
 299  * \param[out] ptr       Pointer to allocate.
 300  * \param[in]  nelem     Number of elements to allocate.
 301  * \param[in]  alignment Requested alignment in bytes.
 302  *
 303  * Allocates memory for \p nelem elements of type \p *ptr and sets this to
 304  * \p ptr.  The returned pointer is `alignment`-byte aligned.
 305  * The allocated memory is initialized to zeros.
 306  *
 307  * The returned pointer should only be freed with sfree_aligned().
 308  *
 309  * \hideinitializer
 310  */
 311 /*! \def sfree
 312  * \brief
 313  * Frees memory referenced by \p ptr.
 314  *
 315  * \p ptr is allowed to be NULL, in which case nothing is done.
 316  *
 317  * \hideinitializer
 318  */
 319 /*! \def sfree_aligned
 320  * \brief
 321  * Frees aligned memory referenced by \p ptr.
 322  *
 323  * This must only be called with a pointer obtained through snew_aligned().
 324  * \p ptr is allowed to be NULL, in which case nothing is done.
 325  *
 326  * \hideinitializer
 327  */
 328
 329 /* C++ implementation */
 330 #define snew(ptr, nelem) gmx_snew_impl(#ptr, __FILE__, __LINE__, (ptr), (nelem))
 331 #define srenew(ptr, nelem) gmx_srenew_impl(#ptr, __FILE__, __LINE__, (ptr), (nelem))
 332 #define smalloc(ptr, size) gmx_smalloc_impl(#ptr, __FILE__, __LINE__, (ptr), (size))
 333 #define snew_aligned(ptr, nelem, alignment) \
 334     gmx_snew_aligned_impl(#ptr, __FILE__, __LINE__, (ptr), (nelem), alignment)
 335 #define sfree(ptr) gmx_sfree_impl(#ptr, __FILE__, __LINE__, (ptr))
 336 #define sfree_aligned(ptr) gmx_sfree_aligned_impl(#ptr, __FILE__, __LINE__, (ptr))
 337
 338 /*! \brief
 339  * Over allocation factor for memory allocations.
 340  *
 341  * Memory (re)allocation can be VERY slow, especially with some
 342  * MPI libraries that replace the standard malloc and realloc calls.
 343  * To avoid slow memory allocation we use over_alloc to set the memory
 344  * allocation size for large data blocks. Since this scales the size
 345  * with a factor, we use log(n) realloc calls instead of n.
 346  * This can reduce allocation times from minutes to seconds.
 347  *
 348  * This factor leads to 4 realloc calls to double the array size.
 349  */
 350 constexpr float OVER_ALLOC_FAC = 1.19F;
 351
 352 /*! \brief
 353  * Turns over allocation for variable size atoms/cg/top arrays on or off,
 354  * default is off.
 355  *
 356  * \todo
 357  * This is mdrun-specific, so it might be better to put this and
 358  * over_alloc_dd() much higher up.
 359  */
 360 void set_over_alloc_dd(gmx_bool set);
 361
 362 /*! \brief
 363  * Returns new allocation count for domain decomposition allocations.
 364  *
 365  * Returns n when domain decomposition over allocation is off.
 366  * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
 367  * This is to avoid frequent reallocation during domain decomposition in mdrun.
 368  */
 369 int over_alloc_dd(int n);
 370
 371 /** Over allocation for small data types: int, real etc. */
 372 template<typename T>
 373 constexpr T over_alloc_small(T n)
 374 {
 375     return OVER_ALLOC_FAC * n + 8000;
 376 }
 377
 378 /** Over allocation for large data types: complex structs */
 379 template<typename T>
 380 constexpr T over_alloc_large(T n)
 381 {
 382     return OVER_ALLOC_FAC * n + 1000;
 383 }
 384
 385 #endif