1 /*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2018,2019,2020, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
10 *
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
15 *
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
20 *
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
25 *
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
33 *
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
36 */
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>
gmx_snew_impl(const char * name,const char * file,int line,T * & ptr,size_t nelem)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>
gmx_srenew_impl(const char * name,const char * file,int line,T * & ptr,size_t nelem)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>
gmx_smalloc_impl(const char * name,const char * file,int line,T * & ptr,size_t size)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
gmx_snew_aligned_impl(const char * name,const char * file,int line,T * & ptr,size_t nelem,size_t alignment)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>
gmx_sfree_impl(const char * name,const char * file,int line,T * ptr)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>
gmx_sfree_aligned_impl(const char * name,const char * file,int line,T * ptr)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>
over_alloc_small(T n)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>
over_alloc_large(T n)380 constexpr T over_alloc_large(T n)
381 {
382 return OVER_ALLOC_FAC * n + 1000;
383 }
384
385 #endif
386