/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* GROningen Mixture of Alchemy and Childrens' Stories
*/
#ifdef GMX_THREAD_MPI
#include "thread_mpi/threads.h"
-#endif
+#endif
#include <stdio.h>
#endif
#ifdef DEBUG
-static void log_action(int bMal,const char *what,const char *file,int line,
- int nelem,int size,void *ptr)
+static void log_action(int bMal, const char *what, const char *file, int line,
+ int nelem, int size, void *ptr)
{
- static int btot=0;
- char *NN = "NULL";
- int bytes;
-
- bytes=size*nelem;
- if (!bMal)
- bytes=-bytes;
-
+ static int btot = 0;
+ char *NN = "NULL";
+ int bytes;
+
+ bytes = size*nelem;
+ if (!bMal)
+ {
+ bytes = -bytes;
+ }
+
#ifdef GMX_THREAD_MPI
- tMPI_Thread_mutex_lock(&gmx_logfile_mtx);
+ tMPI_Thread_mutex_lock(&gmx_logfile_mtx);
#endif
- /* This total memory count is not correct, since with realloc
- * it adds the whole size again, not just the increment.
- */
- /* This static variable is protected by the mutex too... */
- btot+=bytes;
-
- bytes/=1024;
- if (debug && (bytes != 0)) {
- fprintf(debug,"%s:%d kB (%7d kB) [%s, line %d, nelem %d, size %d]\n",
- what ? what : NN,bytes,btot/1024,
- file ? file : NN,line,nelem,size);
- }
- /* Print to stderr for things larger than 1 MB */
- if (bytes >= 1024 || bytes <= -1024) {
- char *fname=NULL;
- if (file) {
- fname = strrchr(file,DIR_SEPARATOR);
- if (fname) {
- fname++;
- } else {
- fname = file;
- }
+ /* This total memory count is not correct, since with realloc
+ * it adds the whole size again, not just the increment.
+ */
+ /* This static variable is protected by the mutex too... */
+ btot += bytes;
+
+ bytes /= 1024;
+ if (debug && (bytes != 0))
+ {
+ fprintf(debug, "%s:%d kB (%7d kB) [%s, line %d, nelem %d, size %d]\n",
+ what ? what : NN, bytes, btot/1024,
+ file ? file : NN, line, nelem, size);
+ }
+ /* Print to stderr for things larger than 1 MB */
+ if (bytes >= 1024 || bytes <= -1024)
+ {
+ char *fname = NULL;
+ if (file)
+ {
+ fname = strrchr(file, DIR_SEPARATOR);
+ if (fname)
+ {
+ fname++;
+ }
+ else
+ {
+ fname = file;
+ }
+ }
+ printf("%s: %.1f MB [%s, line %d, nelem %d, size %d]\n",
+ what ? what : NN, bytes/1024.0,
+ file ? fname : NN, line, nelem, size);
}
- printf("%s: %.1f MB [%s, line %d, nelem %d, size %d]\n",
- what ? what : NN,bytes/1024.0,
- file ? fname : NN,line,nelem,size);
- }
#ifdef GMX_THREAD_MPI
- tMPI_Thread_mutex_unlock(&gmx_logfile_mtx);
+ tMPI_Thread_mutex_unlock(&gmx_logfile_mtx);
#endif
}
#endif
-static char *gmx_large_int_str(gmx_large_int_t i,char *buf)
+static char *gmx_large_int_str(gmx_large_int_t i, char *buf)
{
- sprintf(buf,gmx_large_int_pfmt,i);
+ sprintf(buf, gmx_large_int_pfmt, i);
- return buf;
+ return buf;
}
-void *save_malloc(const char *name,const char *file,int line,size_t size)
+void *save_malloc(const char *name, const char *file, int line, size_t size)
{
- void *p;
-
- p=NULL;
- if (size==0)
- p=NULL;
- else
+ void *p;
+
+ p = NULL;
+ if (size == 0)
{
- if ((p=malloc(size))==NULL) {
- char cbuf[22];
- gmx_fatal(errno,__FILE__,__LINE__,
- "Not enough memory. Failed to malloc %s bytes for %s\n"
- "(called from file %s, line %d)",
- gmx_large_int_str((gmx_large_int_t)size,cbuf),
- name,file,line);
- }
- (void) memset(p,0,size);
+ p = NULL;
+ }
+ else
+ {
+ if ((p = malloc(size)) == NULL)
+ {
+ char cbuf[22];
+ gmx_fatal(errno, __FILE__, __LINE__,
+ "Not enough memory. Failed to malloc %s bytes for %s\n"
+ "(called from file %s, line %d)",
+ gmx_large_int_str((gmx_large_int_t)size, cbuf),
+ name, file, line);
+ }
+ (void) memset(p, 0, size);
}
#ifdef DEBUG
- log_action(1,name,file,line,1,size,p);
+ log_action(1, name, file, line, 1, size, p);
#endif
- return p;
+ return p;
}
-void *save_calloc(const char *name,const char *file,int line,
- size_t nelem,size_t elsize)
+void *save_calloc(const char *name, const char *file, int line,
+ size_t nelem, size_t elsize)
{
- void *p;
-
- p=NULL;
- if ((nelem==0)||(elsize==0))
- p=NULL;
- else
+ void *p;
+
+ p = NULL;
+ if ((nelem == 0) || (elsize == 0))
+ {
+ p = NULL;
+ }
+ else
{
#ifdef PRINT_ALLOC_KB
- int rank=0;
- if (nelem*elsize >= PRINT_ALLOC_KB*1024) {
+ int rank = 0;
+ if (nelem*elsize >= PRINT_ALLOC_KB*1024)
+ {
#ifdef GMX_MPI
#include <mpi.h>
- MPI_Comm_rank(MPI_COMM_WORLD,&rank);
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
#endif
- printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
- nelem*elsize/1048576.0,name,file,line,rank);
- }
+ printf("Allocating %.1f MB for %s (called from file %s, line %d on %d)\n",
+ nelem*elsize/1048576.0, name, file, line, rank);
+ }
#endif
#ifdef GMX_BROKEN_CALLOC
- /* emulate calloc(3) with malloc/memset on machines with
- a broken calloc, e.g. in -lgmalloc on cray xt3. */
- if ((p=malloc((size_t)nelem*(size_t)elsize))==NULL)
- gmx_fatal(errno,__FILE__,__LINE__,
- "Not enough memory. Failed to calloc %"gmx_large_int_fmt
- " elements of size %"gmx_large_int_fmt
- " for %s\n(called from file %s, line %d)",
- (gmx_large_int_t)nelem,(gmx_large_int_t)elsize,
- name,file,line);
- memset(p, 0,(size_t) (nelem * elsize));
+ /* emulate calloc(3) with malloc/memset on machines with
+ a broken calloc, e.g. in -lgmalloc on cray xt3. */
+ if ((p = malloc((size_t)nelem*(size_t)elsize)) == NULL)
+ {
+ gmx_fatal(errno, __FILE__, __LINE__,
+ "Not enough memory. Failed to calloc %"gmx_large_int_fmt
+ " elements of size %"gmx_large_int_fmt
+ " for %s\n(called from file %s, line %d)",
+ (gmx_large_int_t)nelem, (gmx_large_int_t)elsize,
+ name, file, line);
+ }
+ memset(p, 0, (size_t) (nelem * elsize));
#else
- if ((p=calloc((size_t)nelem,(size_t)elsize))==NULL)
- gmx_fatal(errno,__FILE__,__LINE__,
- "Not enough memory. Failed to calloc %"gmx_large_int_fmt
- " elements of size %"gmx_large_int_fmt
- " for %s\n(called from file %s, line %d)",
- (gmx_large_int_t)nelem,(gmx_large_int_t)elsize,name,file,line);
+ if ((p = calloc((size_t)nelem, (size_t)elsize)) == NULL)
+ {
+ gmx_fatal(errno, __FILE__, __LINE__,
+ "Not enough memory. Failed to calloc %"gmx_large_int_fmt
+ " elements of size %"gmx_large_int_fmt
+ " for %s\n(called from file %s, line %d)",
+ (gmx_large_int_t)nelem, (gmx_large_int_t)elsize, name, file, line);
+ }
#endif
}
#ifdef DEBUG
- log_action(1,name,file,line,nelem,elsize,p);
+ log_action(1, name, file, line, nelem, elsize, p);
#endif
- return p;
+ return p;
}
-void *save_realloc(const char *name,const char *file,int line,void *ptr,
- size_t nelem,size_t elsize)
+void *save_realloc(const char *name, const char *file, int line, void *ptr,
+ size_t nelem, size_t elsize)
{
- void *p;
- size_t size = nelem*elsize;
-
- p=NULL;
- if (size==0)
+ void *p;
+ size_t size = nelem*elsize;
+
+ p = NULL;
+ if (size == 0)
{
- save_free(name, file, line, ptr);
+ save_free(name, file, line, ptr);
}
- else
+ else
{
#ifdef PRINT_ALLOC_KB
- int rank=0;
- if (size >= PRINT_ALLOC_KB*1024) {
+ int rank = 0;
+ if (size >= PRINT_ALLOC_KB*1024)
+ {
#ifdef GMX_MPI
#include <mpi.h>
- MPI_Comm_rank(MPI_COMM_WORLD,&rank);
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
#endif
- printf("Reallocating %.1f MB for %s (called from file %s, line %d on %d)\n",
- size/1048576.0,name,file,line,rank);
- }
+ printf("Reallocating %.1f MB for %s (called from file %s, line %d on %d)\n",
+ size/1048576.0, name, file, line, rank);
+ }
#endif
- if (ptr==NULL)
- p=malloc((size_t)size);
- else
- p=realloc(ptr,(size_t)size);
- if (p == NULL) {
- char cbuf[22];
- gmx_fatal(errno,__FILE__,__LINE__,
- "Not enough memory. Failed to realloc %s bytes for %s, %s=%x\n"
- "(called from file %s, line %d)",
- gmx_large_int_str((gmx_large_int_t)size,cbuf),
- name,name,ptr,file,line);
- }
+ if (ptr == NULL)
+ {
+ p = malloc((size_t)size);
+ }
+ else
+ {
+ p = realloc(ptr, (size_t)size);
+ }
+ if (p == NULL)
+ {
+ char cbuf[22];
+ gmx_fatal(errno, __FILE__, __LINE__,
+ "Not enough memory. Failed to realloc %s bytes for %s, %s=%x\n"
+ "(called from file %s, line %d)",
+ gmx_large_int_str((gmx_large_int_t)size, cbuf),
+ name, name, ptr, file, line);
+ }
#ifdef DEBUG
- log_action(1,name,file,line,1,size,p);
+ log_action(1, name, file, line, 1, size, p);
#endif
}
- return p;
+ return p;
}
-void save_free(const char *name,const char *file,int line, void *ptr)
+void save_free(const char *name, const char *file, int line, void *ptr)
{
#ifdef DEBUG
- log_action(0,name,file,line,0,0,ptr);
+ log_action(0, name, file, line, 0, 0, ptr);
#endif
- if (ptr != NULL)
- free(ptr);
+ if (ptr != NULL)
+ {
+ free(ptr);
+ }
}
size_t maxavail(void)
{
- char *ptr;
- size_t low,high,size;
-
- low=0;
- high=256e6;
- while ((high-low) > 4) {
- size=(high+low)/2;
- if ((ptr=(char *)malloc((size_t)size))==NULL)
- high=size;
- else {
- free(ptr);
- low=size;
+ char *ptr;
+ size_t low, high, size;
+
+ low = 0;
+ high = 256e6;
+ while ((high-low) > 4)
+ {
+ size = (high+low)/2;
+ if ((ptr = (char *)malloc((size_t)size)) == NULL)
+ {
+ high = size;
+ }
+ else
+ {
+ free(ptr);
+ low = size;
+ }
}
- }
- return low;
+ return low;
}
size_t memavail(void)
{
- char *ptr;
- size_t size;
-
- size = maxavail();
- if (size != 0) {
- if ((ptr=(char *)malloc((size_t)size)) != NULL) {
- size += memavail();
- free(ptr);
+ char *ptr;
+ size_t size;
+
+ size = maxavail();
+ if (size != 0)
+ {
+ if ((ptr = (char *)malloc((size_t)size)) != NULL)
+ {
+ size += memavail();
+ free(ptr);
+ }
}
- }
- return size;
+ return size;
}
/* If we don't have useful routines for allocating aligned memory,
/* Pointers allocated with this routine should only be freed
* with save_free_aligned, however this will only matter
- * on systems that lack posix_memalign() and memalign() when
+ * on systems that lack posix_memalign() and memalign() when
* freeing memory that needed to be adjusted to achieve
* the necessary alignment. */
-void *save_malloc_aligned(const char *name,const char *file,int line,
- unsigned nelem,size_t elsize,size_t alignment)
+void *save_malloc_aligned(const char *name, const char *file, int line,
+ unsigned nelem, size_t elsize, size_t alignment)
{
- void **aligned=NULL;
- void *malloced=NULL;
+ void **aligned = NULL;
+ void *malloced = NULL;
gmx_bool allocate_fail;
if (alignment == 0)
{
- gmx_fatal(errno,__FILE__,__LINE__,
- "Cannot allocate aligned memory with alignment of zero!\n(called from file %s, line %d)",file,line);
+ gmx_fatal(errno, __FILE__, __LINE__,
+ "Cannot allocate aligned memory with alignment of zero!\n(called from file %s, line %d)", file, line);
}
-
- if (nelem ==0 || elsize == 0)
+
+ if (nelem == 0 || elsize == 0)
{
aligned = NULL;
}
if (nelem*elsize >= PRINT_ALLOC_KB*1024)
{
printf("Allocating %.1f MB for %s\n",
- nelem*elsize/(PRINT_ALLOC_KB*1024.0),name);
+ nelem*elsize/(PRINT_ALLOC_KB*1024.0), name);
}
#endif
allocate_fail = FALSE; /* stop compiler warnings */
#ifdef HAVE_POSIX_MEMALIGN
- allocate_fail = (0!=posix_memalign(&malloced, alignment, nelem*elsize));
+ allocate_fail = (0 != posix_memalign(&malloced, alignment, nelem*elsize));
#elif defined HAVE_MEMALIGN
- allocate_fail = ((malloced=memalign(alignment, nelem*elsize)) == NULL);
+ allocate_fail = ((malloced = memalign(alignment, nelem*elsize)) == NULL);
#elif defined HAVE__ALIGNED_MALLOC
- allocate_fail = ((malloced=_aligned_malloc(nelem*elsize, alignment))
+ allocate_fail = ((malloced = _aligned_malloc(nelem*elsize, alignment))
== NULL);
#else
allocate_fail = ((malloced = malloc(nelem*elsize+alignment+
- sizeof(void*)))==NULL);
+ sizeof(void*))) == NULL);
#endif
if (allocate_fail)
{
- gmx_fatal(errno,__FILE__,__LINE__,
- "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);
+ gmx_fatal(errno, __FILE__, __LINE__,
+ "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);
}
/* we start with the original pointer */
- aligned=(void**)malloced;
-
+ aligned = (void**)malloced;
+
#ifdef GMX_OWN_MEMALIGN
- /* Make the aligned pointer, and save the underlying pointer that
- * we're allowed to free(). */
+ /* Make the aligned pointer, and save the underlying pointer that
+ * we're allowed to free(). */
/* we first make space to store that underlying pointer: */
- aligned = aligned + 1;
+ aligned = aligned + 1;
/* then we apply a bit mask */
- aligned = (void *) (((size_t) aligned + alignment - 1) &
+ aligned = (void *) (((size_t) aligned + alignment - 1) &
(~((size_t) (alignment-1))));
- /* and we store the original pointer in the area just before the
+ /* and we store the original pointer in the area just before the
pointer we're going to return */
aligned[-1] = malloced;
#endif
return (void*)aligned;
}
-void *save_calloc_aligned(const char *name,const char *file,int line,
- unsigned nelem,size_t elsize,size_t alignment)
+void *save_calloc_aligned(const char *name, const char *file, int line,
+ unsigned nelem, size_t elsize, size_t alignment)
{
void *aligned = save_malloc_aligned(name, file, line, nelem, elsize, alignment);
if (aligned != NULL)
}
/* This routine can NOT be called with any pointer */
-void save_free_aligned(const char *name,const char *file,int line,void *ptr)
+void save_free_aligned(const char *name, const char *file, int line, void *ptr)
{
- int i, j;
- void *free=ptr;
+ int i, j;
+ void *free = ptr;
if (NULL != ptr)
{
-#ifdef GMX_OWN_MEMALIGN
+#ifdef GMX_OWN_MEMALIGN
/* we get the pointer from just before the memaligned pointer */
- free= ((void**)ptr)[-1];
+ free = ((void**)ptr)[-1];
#endif
#ifndef HAVE__ALIGNED_MALLOC
/* (Now) we're allowed to use a normal free() on this pointer. */
- save_free(name,file,line,free);
+ save_free(name, file, line, free);
#else
_aligned_free(free);
#endif
}
}
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff