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50 #include <sys/types.h>
55 #if GMX_NATIVE_WINDOWS
56 #include <direct.h> // For _chdir() and _getcwd()
61 #include "gromacs/utility/cstringutil.h"
62 #include "gromacs/utility/datafilefinder.h"
63 #include "gromacs/utility/dir_separator.h"
64 #include "gromacs/utility/exceptions.h"
65 #include "gromacs/utility/fatalerror.h"
66 #include "gromacs/utility/mutex.h"
67 #include "gromacs/utility/path.h"
68 #include "gromacs/utility/programcontext.h"
69 #include "gromacs/utility/smalloc.h"
70 #include "gromacs/utility/stringutil.h"
72 /* we keep a linked list of all files opened through pipes (i.e.
73 compressed or .gzipped files. This way we can distinguish between them
74 without having to change the semantics of reading from/writing to files)
76 typedef struct t_pstack {
78 struct t_pstack *prev;
81 static t_pstack *pstack = nullptr;
82 static bool bUnbuffered = false;
83 static int s_maxBackupCount = 0;
85 /* this linked list is an intrinsically globally shared object, so we have
86 to protect it with mutexes */
87 static gmx::Mutex pstack_mutex;
89 using Lock = gmx::lock_guard<gmx::Mutex>;
95 //! Global library file finder; stores the object set with setLibraryFileFinder().
96 const DataFileFinder *g_libFileFinder;
97 //! Default library file finder if nothing is set.
98 const DataFileFinder g_defaultLibFileFinder;
101 const DataFileFinder &getLibraryFileFinder()
103 if (g_libFileFinder != nullptr)
105 return *g_libFileFinder;
107 return g_defaultLibFileFinder;
110 void setLibraryFileFinder(const DataFileFinder *finder)
112 g_libFileFinder = finder;
117 void gmx_disable_file_buffering(void)
122 void gmx_set_max_backup_count(int count)
126 const char *env = getenv("GMX_MAXBACKUP");
129 // TODO: Check that the value is converted properly.
130 count = strtol(env, nullptr, 10);
138 // Use a reasonably low value for countmax; we might
139 // generate 4-5 files in each round, and we don't
140 // want to hit directory limits of 1024 or 2048 files.
144 s_maxBackupCount = count;
147 static void push_ps(FILE *fp)
151 Lock pstackLock(pstack_mutex);
160 /* don't use pipes!*/
161 #define popen fah_fopen
162 #define pclose fah_fclose
168 #if (!HAVE_PIPES && !defined(__native_client__))
169 static FILE *popen(const char *nm, const char *mode)
171 gmx_impl("Sorry no pipes...");
176 static int pclose(FILE *fp)
178 gmx_impl("Sorry no pipes...");
182 #endif /* !HAVE_PIPES && !defined(__native_client__) */
183 #endif /* GMX_FAHCORE */
185 int gmx_ffclose(FILE *fp)
193 Lock pstackLock(pstack_mutex);
203 else if (ps->fp == fp)
209 pstack = pstack->prev;
214 while ((ps->prev != nullptr) && (ps->prev->fp != fp))
218 if ((ps->prev != nullptr) && ps->prev->fp == fp)
220 if (ps->prev->fp != nullptr)
222 ret = pclose(ps->prev->fp);
225 ps->prev = ps->prev->prev;
242 void frewind(FILE *fp)
244 Lock pstackLock(pstack_mutex);
246 t_pstack *ps = pstack;
247 while (ps != nullptr)
251 fprintf(stderr, "Cannot rewind compressed file!\n");
259 int gmx_fseek(FILE *stream, gmx_off_t offset, int whence)
262 return fseeko(stream, offset, whence);
265 return _fseeki64(stream, offset, whence);
267 return fseek(stream, offset, whence);
272 gmx_off_t gmx_ftell(FILE *stream)
275 return ftello(stream);
279 return _ftelli64(stream);
281 return ftello64(stream);
284 return ftell(stream);
289 int gmx_truncate(const char *filename, gmx_off_t length)
291 #if GMX_NATIVE_WINDOWS
292 FILE *fp = fopen(filename, "rb+");
298 int rc = _chsize_s(fileno(fp), length);
300 int rc = _chsize(fileno(fp), length);
305 return truncate(filename, length);
309 static FILE *uncompress(const char *fn, const char *mode)
314 sprintf(buf, "uncompress -c < %s", fn);
315 fprintf(stderr, "Going to execute '%s'\n", buf);
316 if ((fp = popen(buf, mode)) == nullptr)
325 static FILE *gunzip(const char *fn, const char *mode)
330 sprintf(buf, "gunzip -c < %s", fn);
331 fprintf(stderr, "Going to execute '%s'\n", buf);
332 if ((fp = popen(buf, mode)) == nullptr)
341 gmx_bool gmx_fexist(const char *fname)
345 if (fname == nullptr)
349 test = fopen(fname, "r");
352 /*Windows doesn't allow fopen of directory - so we need to check this seperately */
353 #if GMX_NATIVE_WINDOWS
354 DWORD attr = GetFileAttributes(fname);
355 return (attr != INVALID_FILE_ATTRIBUTES) && (attr & FILE_ATTRIBUTE_DIRECTORY);
367 static char *backup_fn(const char *file)
370 char *directory, *fn;
373 smalloc(buf, GMX_PATH_MAX);
375 for (i = strlen(file)-1; ((i > 0) && (file[i] != DIR_SEPARATOR)); i--)
379 /* Must check whether i > 0, i.e. whether there is a directory
380 * in the file name. In that case we overwrite the / sign with
381 * a '\0' to end the directory string .
385 directory = gmx_strdup(file);
387 fn = gmx_strdup(file+i+1);
391 directory = gmx_strdup(".");
392 fn = gmx_strdup(file);
396 sprintf(buf, "%s/#%s.%d#", directory, fn, count);
399 while ((count <= s_maxBackupCount) && gmx_fexist(buf));
401 /* Arbitrarily bail out */
402 if (count > s_maxBackupCount)
404 /* TODO: The error message is only accurate for code that starts with
405 * Gromacs command-line interface. */
406 gmx_fatal(FARGS, "Won't make more than %d backups of %s for you.\n"
407 "The env.var. GMX_MAXBACKUP controls this maximum, -1 disables backups.",
408 s_maxBackupCount, fn);
417 void make_backup(const char *name)
419 if (s_maxBackupCount <= 0)
423 if (gmx_fexist(name))
425 char *backup = backup_fn(name);
426 if (rename(name, backup) == 0)
428 fprintf(stderr, "\nBack Off! I just backed up %s to %s\n",
433 fprintf(stderr, "\nSorry couldn't backup %s to %s\n", name, backup);
439 FILE *gmx_ffopen(const char *file, const char *mode)
442 return fopen(file, mode);
445 char buf[256], *bufsize = nullptr, *ptr;
460 bRead = (mode[0] == 'r' && mode[1] != '+');
462 if (!bRead || gmx_fexist(buf))
464 if ((ff = fopen(buf, mode)) == nullptr)
469 /* Check whether we should be using buffering (default) or not
472 if (bUnbuffered || ((bufsize = getenv("GMX_LOG_BUFFER")) != nullptr))
474 /* Check whether to use completely unbuffered */
481 bs = strtol(bufsize, nullptr, 10);
490 if (setvbuf(ff, ptr, _IOFBF, bs) != 0)
492 gmx_file("Buffering File");
500 sprintf(buf, "%s.Z", file);
503 ff = uncompress(buf, mode);
507 sprintf(buf, "%s.gz", file);
510 ff = gunzip(buf, mode);
523 char *low_gmxlibfn(const char *file, gmx_bool bAddCWD, gmx_bool bFatal)
527 const gmx::DataFileFinder &finder = gmx::getLibraryFileFinder();
529 finder.findFile(gmx::DataFileOptions(file)
530 .includeCurrentDir(bAddCWD)
531 .throwIfNotFound(bFatal));
534 return gmx_strdup(result.c_str());
537 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
541 FILE *low_libopen(const char *file, gmx_bool bFatal)
545 const gmx::DataFileFinder &finder = gmx::getLibraryFileFinder();
547 finder.openFile(gmx::DataFileOptions(file)
548 .includeCurrentDir(true)
549 .throwIfNotFound(bFatal));
552 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
556 char *gmxlibfn(const char *file)
558 return low_gmxlibfn(file, TRUE, TRUE);
561 FILE *libopen(const char *file)
563 return low_libopen(file, TRUE);
566 void gmx_tmpnam(char *buf)
570 if ((len = strlen(buf)) < 7)
572 gmx_fatal(FARGS, "Buf passed to gmx_tmpnam must be at least 7 bytes long");
574 for (i = len-6; (i < len); i++)
578 /* mktemp is dangerous and we should use mkstemp instead, but
579 * since windows doesnt support it we have to separate the cases.
580 * 20090307: mktemp deprecated, use iso c++ _mktemp instead.
582 #if GMX_NATIVE_WINDOWS
586 gmx_fatal(FARGS, "Error creating temporary file %s: %s", buf,
590 int fd = mkstemp(buf);
594 gmx_fatal(FARGS, "Error creating temporary file %s: %s", buf,
601 /* name in Buf should now be OK and file is CLOSED */
606 FILE *gmx_fopen_temporary(char *buf)
609 FILE *fpout = nullptr;
611 if ((len = strlen(buf)) < 7)
613 gmx_fatal(FARGS, "Buf passed to gmx_fopentmp must be at least 7 bytes long");
615 for (i = len-6; (i < len); i++)
619 /* mktemp is dangerous and we should use mkstemp instead, but
620 * since windows doesnt support it we have to separate the cases.
621 * 20090307: mktemp deprecated, use iso c++ _mktemp instead.
623 #if GMX_NATIVE_WINDOWS
627 gmx_fatal(FARGS, "Error creating temporary file %s: %s", buf,
630 if ((fpout = fopen(buf, "w")) == NULL)
632 gmx_fatal(FARGS, "Cannot open temporary file %s", buf);
635 int fd = mkstemp(buf);
638 gmx_fatal(FARGS, "Error creating temporary file %s: %s", buf,
641 if ((fpout = fdopen(fd, "w")) == nullptr)
643 gmx_fatal(FARGS, "Cannot open temporary file %s", buf);
646 /* name in Buf should now be OK and file is open */
651 int gmx_file_rename(const char *oldname, const char *newname)
653 #if !GMX_NATIVE_WINDOWS
654 /* under unix, rename() is atomic (at least, it should be). */
655 return rename(oldname, newname);
657 if (MoveFileEx(oldname, newname,
658 MOVEFILE_REPLACE_EXISTING|MOVEFILE_WRITE_THROUGH))
669 int gmx_file_copy(const char *oldname, const char *newname, gmx_bool copy_if_empty)
671 /* the full copy buffer size: */
672 #define FILECOPY_BUFSIZE (1<<16)
677 snew(buf, FILECOPY_BUFSIZE);
679 in = fopen(oldname, "rb");
685 /* If we don't copy when empty, we postpone opening the file
686 until we're actually ready to write. */
689 out = fopen(newname, "wb");
700 nread = fread(buf, sizeof(char), FILECOPY_BUFSIZE, in);
706 /* so this is where we open when copy_if_empty is false:
707 here we know we read something. */
708 out = fopen(newname, "wb");
714 ret = fwrite(buf, sizeof(char), nread, out);
740 #undef FILECOPY_BUFSIZE
744 int gmx_fsync(FILE *fp)
749 /* the fahcore defines its own os-independent fsync */
751 #else /* GMX_FAHCORE */
755 /* get the file number */
764 /* do the actual fsync */
774 #endif /* GMX_FAHCORE */
776 /* We check for these error codes this way because POSIX requires them
777 to be defined, and using anything other than macros is unlikely: */
779 /* we don't want to report an error just because fsync() caught a signal.
780 For our purposes, we can just ignore this. */
781 if (rc && errno == EINTR)
787 /* we don't want to report an error just because we tried to fsync()
788 stdout, a socket or a pipe. */
789 if (rc && errno == EINVAL)
797 void gmx_chdir(const char *directory)
799 #if GMX_NATIVE_WINDOWS
800 int rc = _chdir(directory);
802 int rc = chdir(directory);
806 gmx_fatal(FARGS, "Cannot change directory to '%s'. Reason: %s",
807 directory, strerror(errno));
811 void gmx_getcwd(char *buffer, size_t size)
813 #if GMX_NATIVE_WINDOWS
814 char *pdum = _getcwd(buffer, size);
816 char *pdum = getcwd(buffer, size);
820 gmx_fatal(FARGS, "Cannot get working directory. Reason: %s",