1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
4 * This source code is part of
8 * GROningen MAchine for Chemical Simulations
11 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
12 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
13 * Copyright (c) 2001-2004, The GROMACS development team,
14 * check out http://www.gromacs.org for more information.
16 * This program is free software; you can redistribute it and/or
17 * modify it under the terms of the GNU General Public License
18 * as published by the Free Software Foundation; either version 2
19 * of the License, or (at your option) any later version.
21 * If you want to redistribute modifications, please consider that
22 * scientific software is very special. Version control is crucial -
23 * bugs must be traceable. We will be happy to consider code for
24 * inclusion in the official distribution, but derived work must not
25 * be called official GROMACS. Details are found in the README & COPYING
26 * files - if they are missing, get the official version at www.gromacs.org.
28 * To help us fund GROMACS development, we humbly ask that you cite
29 * the papers on the package - you can find them in the top README file.
31 * For more info, check our website at http://www.gromacs.org
34 * GROningen Mixture of Alchemy and Childrens' Stories
43 #include <sys/types.h>
56 #ifdef GMX_NATIVE_WINDOWS
65 #include "gmx_fatal.h"
71 #include "thread_mpi.h"
74 /* Windows file stuff, only necessary for visual studio */
79 /* we keep a linked list of all files opened through pipes (i.e.
80 compressed or .gzipped files. This way we can distinguish between them
81 without having to change the semantics of reading from/writing to files)
83 typedef struct t_pstack {
85 struct t_pstack *prev;
88 static t_pstack *pstack=NULL;
89 static gmx_bool bUnbuffered=FALSE;
92 /* this linked list is an intrinsically globally shared object, so we have
93 to protect it with mutexes */
94 static tMPI_Thread_mutex_t pstack_mutex=TMPI_THREAD_MUTEX_INITIALIZER;
102 void push_ps(FILE *fp)
106 #ifdef GMX_THREAD_MPI
107 tMPI_Thread_mutex_lock(&pstack_mutex);
114 #ifdef GMX_THREAD_MPI
115 tMPI_Thread_mutex_unlock(&pstack_mutex);
120 /* don't use pipes!*/
121 #define popen fah_fopen
122 #define pclose fah_fclose
132 static FILE *popen(const char *nm,const char *mode)
134 gmx_impl("Sorry no pipes...");
139 static int pclose(FILE *fp)
141 gmx_impl("Sorry no pipes...");
148 int ffclose(FILE *fp)
155 #ifdef GMX_THREAD_MPI
156 tMPI_Thread_mutex_lock(&pstack_mutex);
164 else if (ps->fp == fp) {
171 while ((ps->prev != NULL) && (ps->prev->fp != fp))
173 if ((ps->prev != NULL) && ps->prev->fp == fp) {
174 if (ps->prev->fp != NULL)
175 ret = pclose(ps->prev->fp);
177 ps->prev=ps->prev->prev;
185 #ifdef GMX_THREAD_MPI
186 tMPI_Thread_mutex_unlock(&pstack_mutex);
197 void frewind(FILE *fp)
200 #ifdef GMX_THREAD_MPI
201 tMPI_Thread_mutex_lock(&pstack_mutex);
207 fprintf(stderr,"Cannot rewind compressed file!\n");
208 #ifdef GMX_THREAD_MPI
209 tMPI_Thread_mutex_unlock(&pstack_mutex);
216 #ifdef GMX_THREAD_MPI
217 tMPI_Thread_mutex_unlock(&pstack_mutex);
221 int gmx_fseek(FILE *stream, gmx_off_t offset, int whence)
224 return fseeko(stream, offset, whence);
226 #ifdef HAVE__FSEEKI64
227 return _fseeki64(stream, offset, whence);
229 return fseek(stream, offset, whence);
234 gmx_off_t gmx_ftell(FILE *stream)
237 return ftello(stream);
239 #ifdef HAVE__FSEEKI64
240 return _ftelli64(stream);
242 return ftell(stream);
248 gmx_bool is_pipe(FILE *fp)
251 #ifdef GMX_THREAD_MPI
252 tMPI_Thread_mutex_lock(&pstack_mutex);
258 #ifdef GMX_THREAD_MPI
259 tMPI_Thread_mutex_unlock(&pstack_mutex);
265 #ifdef GMX_THREAD_MPI
266 tMPI_Thread_mutex_unlock(&pstack_mutex);
272 static FILE *uncompress(const char *fn,const char *mode)
277 sprintf(buf,"uncompress -c < %s",fn);
278 fprintf(stderr,"Going to execute '%s'\n",buf);
279 if ((fp=popen(buf,mode)) == NULL)
286 static FILE *gunzip(const char *fn,const char *mode)
291 sprintf(buf,"gunzip -c < %s",fn);
292 fprintf(stderr,"Going to execute '%s'\n",buf);
293 if ((fp=popen(buf,mode)) == NULL)
300 gmx_bool gmx_fexist(const char *fname)
306 test=fopen(fname,"r");
308 /*Windows doesn't allow fopen of directory - so we need to check this seperately */
309 #ifdef GMX_NATIVE_WINDOWS
310 DWORD attr = GetFileAttributes(fname);
311 return (attr != INVALID_FILE_ATTRIBUTES) && (attr & FILE_ATTRIBUTE_DIRECTORY);
321 static gmx_bool gmx_is_file(const char *fname)
327 test=fopen(fname,"r");
335 /*Windows doesn't allow fopen of directory - so we don't need to check this seperately */
336 #if (!((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__))
340 status = stat (fname, &st_buf);
341 if (status != 0 || !S_ISREG(st_buf.st_mode))
352 gmx_bool gmx_fexist_master(const char *fname, t_commrec *cr)
358 bExist = gmx_fexist(fname);
362 gmx_bcast(sizeof(bExist),&bExist,cr);
367 gmx_bool gmx_eof(FILE *fp)
375 if ((beof=fread(data,1,1,fp))==1)
376 gmx_fseek(fp,-1,SEEK_CUR);
381 static char *backup_fn(const char *file,int count_max)
383 /* Use a reasonably low value for countmax; we might
384 * generate 4-5 files in each round, and we dont
385 * want to hit directory limits of 1024 or 2048 files.
394 count_max = COUNTMAX;
397 smalloc(buf, GMX_PATH_MAX);
399 for(i=strlen(file)-1; ((i > 0) && (file[i] != DIR_SEPARATOR)); i--)
401 /* Must check whether i > 0, i.e. whether there is a directory
402 * in the file name. In that case we overwrite the / sign with
403 * a '\0' to end the directory string .
406 directory = gmx_strdup(file);
408 fn = gmx_strdup(file+i+1);
411 directory = gmx_strdup(".");
412 fn = gmx_strdup(file);
415 sprintf(buf,"%s/#%s.%d#",directory,fn,count);
417 } while ((count <= count_max) && gmx_fexist(buf));
419 /* Arbitrarily bail out */
420 if (count > count_max)
421 gmx_fatal(FARGS,"Won't make more than %d backups of %s for you.\n"
422 "The env.var. GMX_MAXBACKUP controls this maximum, -1 disables backups.",
431 gmx_bool make_backup(const char * name)
438 return FALSE; /* skip making backups */
441 if (gmx_fexist(name))
443 env = getenv("GMX_MAXBACKUP");
447 sscanf(env,"%d",&count_max);
450 /* Do not make backups and possibly overwrite old files */
456 /* Use the default maximum */
459 backup = backup_fn(name,count_max);
460 if(rename(name, backup) == 0) {
461 fprintf(stderr, "\nBack Off! I just backed up %s to %s\n",
464 fprintf(stderr, "Sorry couldn't backup %s to %s\n", name, backup);
473 FILE *ffopen(const char *file,const char *mode)
476 return fopen(file,mode);
479 char buf[256],*bf,*bufsize=0,*ptr;
493 bRead= (mode[0]=='r'&&mode[1]!='+');
495 if (!bRead || gmx_fexist(buf)) {
496 if ((ff=fopen(buf,mode))==NULL)
499 /* Check whether we should be using buffering (default) or not
502 if (bUnbuffered || ((bufsize=getenv("LOG_BUFS")) != NULL)) {
503 /* Check whether to use completely unbuffered */
507 bs=strtol(bufsize, NULL, 10);
512 if (setvbuf(ff,ptr,_IOFBF,bs) != 0)
513 gmx_file("Buffering File");
519 sprintf(buf,"%s.Z",file);
520 if (gmx_fexist(buf)) {
521 ff=uncompress(buf,mode);
524 sprintf(buf,"%s.gz",file);
525 if (gmx_fexist(buf)) {
536 /* Our own implementation of dirent-like functionality to scan directories. */
541 #elif (defined GMX_NATIVE_WINDOWS)
542 intptr_t windows_handle;
543 struct _finddata_t finddata;
552 gmx_directory_open(gmx_directory_t *p_gmxdir,const char *dirname)
554 struct gmx_directory * gmxdir;
562 if( (gmxdir->dirent_handle = opendir(dirname)) != NULL)
572 #elif (defined GMX_NATIVE_WINDOWS)
574 if(dirname!=NULL && strlen(dirname)>0)
580 len = strlen(dirname);
583 strncpy(tmpname,dirname,len+1);
585 /* Remove possible trailing directory separator */
586 if(tmpname[len]=='/' || tmpname[len]=='\\')
592 strcat(tmpname,"/*");
595 if( (gmxdir->windows_handle=_findfirst(tmpname,&gmxdir->finddata))>0L)
619 "Source compiled without POSIX dirent or windows support - cannot scan directories.\n"
620 "In the very unlikely event this is not a compile-time mistake you could consider\n"
621 "implementing support for your platform in futil.c, but contact the developers\n"
622 "to make sure it's really necessary!\n");
630 gmx_directory_nextfile(gmx_directory_t gmxdir,char *name,int maxlength_name)
636 struct dirent * direntp_large;
640 if(gmxdir!=NULL && gmxdir->dirent_handle!=NULL)
642 /* On some platforms no space is present for d_name in dirent.
643 * Since d_name is guaranteed to be the last entry, allocating
644 * extra space for dirent will allow more size for d_name.
645 * GMX_MAX_PATH should always be >= the max possible d_name.
647 smalloc(direntp_large, sizeof(*direntp_large) + GMX_PATH_MAX);
648 rc = readdir_r(gmxdir->dirent_handle,direntp_large,&p);
652 strncpy(name,direntp_large->d_name,maxlength_name);
659 sfree(direntp_large);
667 #elif (defined GMX_NATIVE_WINDOWS)
671 if(gmxdir->windows_handle<=0)
677 else if(gmxdir->first==1)
679 strncpy(name,gmxdir->finddata.name,maxlength_name);
685 if(_findnext(gmxdir->windows_handle,&gmxdir->finddata)==0)
687 strncpy(name,gmxdir->finddata.name,maxlength_name);
700 "Source compiled without POSIX dirent or windows support - cannot scan directories.\n");
708 gmx_directory_close(gmx_directory_t gmxdir)
712 rc = (gmxdir != NULL) ? closedir(gmxdir->dirent_handle) : EINVAL;
713 #elif (defined GMX_NATIVE_WINDOWS)
714 rc = (gmxdir != NULL) ? _findclose(gmxdir->windows_handle) : EINVAL;
717 "Source compiled without POSIX dirent or windows support - cannot scan directories.\n");
726 static gmx_bool search_subdirs(const char *parent, char *libdir)
731 /* Search a few common subdirectory names for the gromacs library dir */
732 sprintf(libdir,"%s%cshare%ctop%cgurgle.dat",parent,
733 DIR_SEPARATOR,DIR_SEPARATOR,DIR_SEPARATOR);
734 found=gmx_fexist(libdir);
736 sprintf(libdir,"%s%cshare%cgromacs%ctop%cgurgle.dat",parent,
737 DIR_SEPARATOR,DIR_SEPARATOR,
738 DIR_SEPARATOR,DIR_SEPARATOR);
739 found=gmx_fexist(libdir);
742 sprintf(libdir,"%s%cshare%cgromacs-%s%ctop%cgurgle.dat",parent,
743 DIR_SEPARATOR,DIR_SEPARATOR,VERSION,
744 DIR_SEPARATOR,DIR_SEPARATOR);
745 found=gmx_fexist(libdir);
748 sprintf(libdir,"%s%cshare%cgromacs%cgromacs-%s%ctop%cgurgle.dat",parent,
749 DIR_SEPARATOR,DIR_SEPARATOR,DIR_SEPARATOR,
750 VERSION,DIR_SEPARATOR,DIR_SEPARATOR);
751 found=gmx_fexist(libdir);
754 /* Remove the gurgle.dat part from libdir if we found something */
756 ptr=strrchr(libdir,DIR_SEPARATOR); /* slash or backslash always present, no check necessary */
763 /* Check if the program name begins with "/" on unix/cygwin, or
764 * with "\" or "X:\" on windows. If not, the program name
765 * is relative to the current directory.
767 static gmx_bool filename_is_absolute(char *name)
769 #ifdef GMX_NATIVE_WINDOWS
770 return ((name[0] == DIR_SEPARATOR) || ((strlen(name)>3) && strncmp(name+1,":\\",2)) == 0);
772 return (name[0] == DIR_SEPARATOR);
776 gmx_bool get_libdir(char *libdir)
778 #define GMX_BINNAME_MAX 512
779 char bin_name[GMX_BINNAME_MAX];
780 char buf[GMX_BINNAME_MAX];
781 char full_path[GMX_PATH_MAX+GMX_BINNAME_MAX];
782 char system_path[GMX_PATH_MAX];
783 char *dir,*ptr,*s,*pdum;
784 gmx_bool found=FALSE;
787 if (Program() != NULL)
790 /* First - detect binary name */
791 if (strlen(Program()) >= GMX_BINNAME_MAX)
793 gmx_fatal(FARGS,"The name of the binary is longer than the allowed buffer size (%d):\n'%s'",GMX_BINNAME_MAX,Program());
795 strncpy(bin_name,Program(),GMX_BINNAME_MAX-1);
797 /* On windows & cygwin we need to add the .exe extension
798 * too, or we wont be able to detect that the file exists
800 #if (defined GMX_NATIVE_WINDOWS || defined GMX_CYGWIN)
801 if(strlen(bin_name)<3 || gmx_strncasecmp(bin_name+strlen(bin_name)-4,".exe",4))
802 strcat(bin_name,".exe");
805 /* Only do the smart search part if we got a real name */
806 if (NULL!=bin_name && strncmp(bin_name,"GROMACS",GMX_BINNAME_MAX)) {
808 if (!strchr(bin_name,DIR_SEPARATOR)) {
809 /* No slash or backslash in name means it must be in the path - search it! */
810 /* Add the local dir since it is not in the path on windows */
811 gmx_getcwd(system_path, sizeof(system_path));
812 sprintf(full_path,"%s%c%s",system_path,DIR_SEPARATOR,bin_name);
813 found = gmx_is_file(full_path);
814 if (!found && (s=getenv("PATH")) != NULL)
818 dupped=gmx_strdup(s);
820 while(!found && (dir=gmx_strsep(&s, PATH_SEPARATOR)) != NULL)
822 sprintf(full_path,"%s%c%s",dir,DIR_SEPARATOR,bin_name);
823 found = gmx_is_file(full_path);
831 } else if (!filename_is_absolute(bin_name)) {
832 /* name contains directory separators, but
833 * it does not start at the root, i.e.
834 * name is relative to the current dir
836 gmx_getcwd(buf, sizeof(buf));
837 sprintf(full_path,"%s%c%s",buf,DIR_SEPARATOR,bin_name);
839 strncpy(full_path,bin_name,GMX_PATH_MAX);
842 /* Now we should have a full path and name in full_path,
843 * but on unix it might be a link, or a link to a link to a link..
845 #ifndef GMX_NATIVE_WINDOWS
846 while( (i=readlink(full_path,buf,sizeof(buf)-1)) > 0 ) {
848 /* If it doesn't start with "/" it is relative */
849 if (buf[0]!=DIR_SEPARATOR) {
850 strncpy(strrchr(full_path,DIR_SEPARATOR)+1,buf,GMX_PATH_MAX);
852 strncpy(full_path,buf,GMX_PATH_MAX);
856 /* If running directly from the build tree, try to use the source
859 #if (defined CMAKE_SOURCE_DIR && defined CMAKE_BINARY_DIR)
860 if (strncmp(full_path, CMAKE_BINARY_DIR, strlen(CMAKE_BINARY_DIR)) == 0)
862 if (search_subdirs(CMAKE_SOURCE_DIR, libdir))
869 /* Remove the executable name - it always contains at least one slash */
870 *(strrchr(full_path,DIR_SEPARATOR)+1)='\0';
871 /* Now we have the full path to the gromacs executable.
872 * Use it to find the library dir.
875 while(!found && ( (ptr=strrchr(full_path,DIR_SEPARATOR)) != NULL ) ) {
877 found=search_subdirs(full_path,libdir);
881 /* End of smart searching. If we didn't find it in our parent tree,
882 * or if the program name wasn't set, at least try some standard
883 * locations before giving up, in case we are running from e.g.
884 * a users home directory. This only works on unix or cygwin...
886 #ifndef GMX_NATIVE_WINDOWS
888 found=search_subdirs("/usr/local",libdir);
890 found=search_subdirs("/usr",libdir);
892 found=search_subdirs("/opt",libdir);
898 char *low_gmxlibfn(const char *file, gmx_bool bAddCWD, gmx_bool bFatal)
903 char libpath[GMX_PATH_MAX];
904 gmx_bool env_is_set=FALSE;
905 char *s,tmppath[GMX_PATH_MAX];
907 /* GMXLIB can be a path now */
908 lib=getenv("GMXLIB");
912 strncpy(libpath,lib,GMX_PATH_MAX);
914 else if (!get_libdir(libpath))
916 strncpy(libpath,GMXLIBDIR,GMX_PATH_MAX);
920 if (bAddCWD && gmx_fexist(file))
922 ret = gmx_strdup(file);
926 strncpy(tmppath,libpath,GMX_PATH_MAX);
928 while(ret == NULL && (dir=gmx_strsep(&s, PATH_SEPARATOR)) != NULL )
930 sprintf(buf,"%s%c%s",dir,DIR_SEPARATOR,file);
933 ret = gmx_strdup(buf);
936 if (ret == NULL && bFatal)
941 "Library file %s not found %sin your GMXLIB path.",
942 file, bAddCWD ? "in current dir nor " : "");
947 "Library file %s not found %sin default directories.\n"
948 "(You can set the directories to search with the GMXLIB path variable)",
949 file, bAddCWD ? "in current dir nor " : "");
961 FILE *low_libopen(const char *file,gmx_bool bFatal)
966 fn=low_gmxlibfn(file,TRUE,bFatal);
972 fprintf(debug,"Opening library file %s\n",fn);
980 char *gmxlibfn(const char *file)
982 return low_gmxlibfn(file,TRUE,TRUE);
985 FILE *libopen(const char *file)
987 return low_libopen(file,TRUE);
990 void gmx_tmpnam(char *buf)
994 if ((len = strlen(buf)) < 7)
995 gmx_fatal(FARGS,"Buf passed to gmx_tmpnam must be at least 7 bytes long");
996 for(i=len-6; (i<len); i++) {
999 /* mktemp is dangerous and we should use mkstemp instead, but
1000 * since windows doesnt support it we have to separate the cases.
1001 * 20090307: mktemp deprecated, use iso c++ _mktemp instead.
1003 #ifdef GMX_NATIVE_WINDOWS
1010 gmx_fatal(FARGS,"Invalid template %s for mkstemp",buf);
1013 gmx_fatal(FARGS,"mkstemp created existing file",buf);
1016 gmx_fatal(FARGS,"Permission denied for opening %s",buf);
1023 /* name in Buf should now be OK */
1026 int gmx_truncatefile(char *path, gmx_off_t length)
1029 /* Microsoft visual studio does not have "truncate" */
1031 LARGE_INTEGER win_length;
1033 win_length.QuadPart = length;
1035 fh = CreateFile(path,GENERIC_READ | GENERIC_WRITE,0,NULL,
1036 OPEN_EXISTING,0,NULL);
1037 SetFilePointerEx(fh,win_length,NULL,FILE_BEGIN);
1043 return truncate(path,length);
1048 int gmx_file_rename(const char *oldname, const char *newname)
1050 #ifndef GMX_NATIVE_WINDOWS
1051 /* under unix, rename() is atomic (at least, it should be). */
1052 return rename(oldname, newname);
1054 if (MoveFileEx(oldname, newname,
1055 MOVEFILE_REPLACE_EXISTING|MOVEFILE_WRITE_THROUGH))
1062 int gmx_file_copy(const char *oldname, const char *newname, gmx_bool copy_if_empty)
1064 /* the full copy buffer size: */
1065 #define FILECOPY_BUFSIZE (1<<16)
1070 snew(buf, FILECOPY_BUFSIZE);
1072 in=fopen(oldname, "rb");
1076 /* If we don't copy when empty, we postpone opening the file
1077 until we're actually ready to write. */
1080 out=fopen(newname, "wb");
1089 nread=fread(buf, sizeof(char), FILECOPY_BUFSIZE, in);
1095 /* so this is where we open when copy_if_empty is false:
1096 here we know we read something. */
1097 out=fopen(newname, "wb");
1101 ret=fwrite(buf, sizeof(char), nread, out);
1121 #undef FILECOPY_BUFSIZE
1125 int gmx_fsync(FILE *fp)
1130 /* the fahcore defines its own os-independent fsync */
1132 #else /* GMX_FAHCORE */
1136 /* get the file number */
1137 #if defined(HAVE_FILENO)
1139 #elif defined(HAVE__FILENO)
1143 /* do the actual fsync */
1146 #if (defined(HAVE_FSYNC))
1148 #elif (defined(HAVE__COMMIT))
1153 #endif /* GMX_FAHCORE */
1155 /* We check for these error codes this way because POSIX requires them
1156 to be defined, and using anything other than macros is unlikely: */
1158 /* we don't want to report an error just because fsync() caught a signal.
1159 For our purposes, we can just ignore this. */
1160 if (rc && errno==EINTR)
1164 /* we don't want to report an error just because we tried to fsync()
1165 stdout, a socket or a pipe. */
1166 if (rc && errno==EINVAL)
1172 void gmx_chdir(const char *directory)
1174 #ifdef GMX_NATIVE_WINDOWS
1175 int rc = _chdir(directory);
1177 int rc = chdir(directory);
1181 gmx_fatal(FARGS, "Cannot change directory to '%s'. Reason: %s",
1182 directory, strerror(errno));
1186 void gmx_getcwd(char *buffer, size_t size)
1188 #ifdef GMX_NATIVE_WINDOWS
1189 char *pdum = _getcwd(buffer, size);
1191 char *pdum = getcwd(buffer, size);
1195 gmx_fatal(FARGS, "Cannot get working directory. Reason: %s",