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38 #ifndef GMX_FILEIO_GMXFIO_H
39 #define GMX_FILEIO_GMXFIO_H
43 #include "gromacs/math/vectypes.h"
44 #include "gromacs/utility/cstringutil.h"
45 #include "gromacs/utility/futil.h"
46 #include "gromacs/utility/real.h"
52 typedef struct t_fileio t_fileio;
54 /* NOTE ABOUT THREAD SAFETY:
56 The functions are all thread-safe, provided that two threads don't
57 do something silly like closing the same file, or one thread
58 accesses a file that has been closed by another.
61 /********************************************************
63 ********************************************************/
65 t_fileio *gmx_fio_open(const char *fn, const char *mode);
66 /* Open a new file for reading or writing.
67 * The file type will be deduced from the file name.
70 int gmx_fio_close(t_fileio *fp);
71 /* Close the file corresponding to fp (if not stdio)
72 * The routine will exit when an invalid fio is handled.
73 * Returns 0 on success.
76 int gmx_fio_fp_close(t_fileio *fp);
77 /* Close the file corresponding to fp without closing the FIO entry
78 * Needed e.g. for trxio because the FIO entries are used to store
80 * NOTE that the fp still needs to be properly closed with gmx_fio_close().
81 * The routine will exit when an invalid fio is handled.
82 * Returns 0 on success.
86 /* Open a file, return a stream, record the entry in internal FIO object */
87 FILE* gmx_fio_fopen(const char *fn, const char *mode);
89 /* Close a file previously opened with gmx_fio_fopen.
90 * Do not mix these calls with standard fopen/fclose ones!
91 * Returns 0 on success. */
92 int gmx_fio_fclose(FILE *fp);
96 /********************************************************
97 * Change properties of the open file
98 ********************************************************/
100 void gmx_fio_setprecision(t_fileio *fio, gmx_bool bDouble);
101 /* Select the floating point precision for reading and writing files */
103 char *gmx_fio_getname(t_fileio *fio);
104 /* Return the filename corresponding to the fio index */
106 int gmx_fio_getftp(t_fileio *fio);
107 /* Return the filetype corresponding to the fio index.
108 There is as of now no corresponding setftp function because the file
109 was opened as a specific file type and changing that midway is most
110 likely an evil hack. */
112 void gmx_fio_setdebug(t_fileio *fio, gmx_bool bDebug);
113 /* Set the debug mode */
115 gmx_bool gmx_fio_getread(t_fileio *fio);
116 /* Return whether read mode is on in fio */
118 /***************************************************
120 ***************************************************/
122 void gmx_fio_rewind(t_fileio *fio);
123 /* Rewind the file in fio */
125 int gmx_fio_flush(t_fileio *fio);
126 /* Flush the fio, returns 0 on success */
128 int gmx_fio_fsync(t_fileio *fio);
129 /* fsync the fio, returns 0 on success.
130 NOTE: don't use fsync function unless you're absolutely sure you need it
131 because it deliberately interferes with the OS's caching mechanisms and
132 can cause dramatically slowed down IO performance. Some OSes (Linux,
133 for example), may implement fsync as a full sync() point. */
135 gmx_off_t gmx_fio_ftell(t_fileio *fio);
136 /* Return file position if possible */
138 int gmx_fio_seek(t_fileio *fio, gmx_off_t fpos);
139 /* Set file position if possible, quit otherwise */
141 FILE *gmx_fio_getfp(t_fileio *fio);
142 /* Return the file pointer itself */
145 /* Element with information about position in a currently open file.
146 * gmx_off_t should be defined by autoconf if your system does not have it.
147 * If you do not have it on some other platform you do not have largefile
148 * support at all, and you can define it to int (or better, find out how to
149 * enable large files). */
150 typedef struct gmx_file_position_t
152 char filename[STRLEN];
154 unsigned char chksum[16];
159 int gmx_fio_get_output_file_positions(gmx_file_position_t ** outputfiles,
161 /* Return the name and file pointer positions for all currently open
162 * output files. This is used for saving in the checkpoint files, so we
163 * can truncate output files upon restart-with-appending.
165 * For the first argument you should use a pointer, which will be set to
166 * point to a list of open files.
169 t_fileio *gmx_fio_all_output_fsync(void);
170 /* fsync all open output files. This is used for checkpointing, where
171 we need to ensure that all output is actually written out to
173 This is most important in the case of some networked file systems,
174 where data is not synced with the file server until close() or
175 fsync(), so data could remain in cache for days.
176 Note the caveats reported with gmx_fio_fsync().
178 returns: NULL if no error occurred, or a pointer to the first file that
179 failed if an error occurred
183 int gmx_fio_get_file_md5(t_fileio *fio, gmx_off_t offset,
184 unsigned char digest[]);
187 int xtc_seek_time(t_fileio *fio, real time, int natoms, gmx_bool bSeekForwardOnly);