2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team,
6 * Copyright (c) 2013, 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.
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.
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.
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.
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.
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.
51 #include "gmx_fatal.h"
60 #include "gromacs/legacyheaders/thread_mpi/threads.h"
62 #include "gmxfio_int.h"
64 /* This is the new improved and thread safe version of gmxfio. */
68 /* the list of open files is a linked list, with a dummy element at its head;
69 it is initialized when the first file is opened. */
70 static t_fileio *open_files = NULL;
73 /* this mutex locks the open_files structure so that no two threads can
76 For now, we use this as a coarse grained lock on all file
77 insertion/deletion operations because it makes avoiding deadlocks
78 easier, and adds almost no overhead: the only overhead is during
79 opening and closing of files, or during global operations like
80 iterating along all open files. All these cases should be rare
81 during the simulation. */
82 static tMPI_Thread_mutex_t open_file_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
85 /* These simple lists define the I/O type for these files */
86 static const int ftpXDR[] =
87 { efTPR, efTRR, efEDR, efXTC, efMTX, efCPT };
88 static const int ftpASC[] =
89 { efTPA, efGRO, efPDB };
90 static const int ftpBIN[] =
93 static const int ftpXML[] =
97 const char *itemstr[eitemNR] =
99 "[header]", "[inputrec]", "[box]", "[topology]", "[coordinates]",
100 "[velocities]", "[forces]"
103 const char *eioNames[eioNR] =
105 "REAL", "INT", "GMX_STE_T", "UCHAR", "NUCHAR", "USHORT", "RVEC", "NRVEC",
111 /* Comment strings for TPA only */
112 const char *comment_str[eitemNR] = {
113 "; The header holds information on the number of atoms etc. and on whether\n"
114 "; certain items are present in the file or not.\n"
117 "; DO NOT EDIT THIS FILE BY HAND\n"
118 "; The GROMACS preprocessor performs a lot of checks on your input that\n"
119 "; you ignore when editing this. Your simulation may crash because of this\n",
120 "; The inputrec holds the parameters for MD such as the number of steps,\n"
121 "; the timestep and the cut-offs.\n",
122 "; The simulation box in nm.\n",
123 "; The topology section describes the topology of the molecules\n"
124 "; i.e. bonds, angles and dihedrals etc. and also holds the force field\n"
126 "; The atomic coordinates in nm\n",
127 "; The atomic velocities in nm/ps\n",
128 "; The forces on the atoms in nm/ps^2\n"
134 /******************************************************************
136 * Internal functions:
138 ******************************************************************/
140 static int gmx_fio_int_flush(t_fileio* fio)
146 rc = fflush(fio->fp);
150 rc = fflush((FILE *) fio->xdr->x_private);
156 /* returns TRUE if the file type ftp is in the set set */
157 static gmx_bool in_ftpset(int ftp, int nset, const int set[])
163 for (i = 0; (i < nset); i++)
176 extern void gmx_fio_set_comment(t_fileio *fio, const char *comment)
178 fio->comment = comment;
181 extern void gmx_fio_unset_comment(t_fileio *fio)
187 const char *gmx_fio_dbgstr(t_fileio *fio, const char *desc, char *buf)
191 /* set to empty string */
196 snprintf(buf, GMX_FIO_BUFLEN, " ; %s %s", fio->comment ? fio->comment : "", desc);
202 /* check the number of items given against the type */
203 void gmx_fio_check_nitem(int eio, int nitem, const char *file, int line)
205 if ((nitem != 1) && !((eio == eioNRVEC) || (eio == eioNUCHAR)))
208 "nitem (%d) may differ from 1 only for %s or %s, not for %s"
209 "(%s, %d)", nitem, eioNames[eioNUCHAR], eioNames[eioNRVEC],
210 eioNames[eio], file, line);
215 /* output a data type error. */
216 void gmx_fio_fe(t_fileio *fio, int eio, const char *desc,
217 const char *srcfile, int line)
220 gmx_fatal(FARGS, "Trying to %s %s type %d (%s), src %s, line %d",
221 fio->bRead ? "read" : "write", desc, eio,
222 ((eio >= 0) && (eio < eioNR)) ? eioNames[eio] : "unknown",
227 /* set the reader/writer functions based on the file type */
228 static void gmx_fio_set_iotype(t_fileio *fio)
230 if (in_ftpset(fio->iFTP, asize(ftpXDR), ftpXDR))
233 fio->iotp = &xdr_iotype;
235 gmx_fatal(FARGS, "Sorry, no XDR");
238 else if (in_ftpset(fio->iFTP, asize(ftpASC), ftpASC))
240 fio->iotp = &asc_iotype;
242 else if (in_ftpset(fio->iFTP, asize(ftpBIN), ftpBIN))
244 fio->iotp = &bin_iotype;
247 else if (in_ftpset(fio->iFTP, asize(ftpXML), ftpXML))
249 fio->iotp = &dummy_iotype;
254 fio->iotp = &dummy_iotype;
259 /* lock the mutex associated with this fio. This needs to be done for every
260 type of access to the fio's elements. */
261 void gmx_fio_lock(t_fileio *fio)
263 tMPI_Lock_lock(&(fio->mtx));
265 /* unlock the mutex associated with this fio. */
266 void gmx_fio_unlock(t_fileio *fio)
268 tMPI_Lock_unlock(&(fio->mtx));
271 /* make a dummy head element, assuming we locked everything. */
272 static void gmx_fio_make_dummy(void)
277 open_files->fp = NULL;
278 open_files->fn = NULL;
279 open_files->next = open_files;
280 open_files->prev = open_files;
281 tMPI_Lock_init(&(open_files->mtx));
291 /***********************************************************************
293 * FILE LIST OPERATIONS
295 ***********************************************************************/
298 /* insert a new t_fileio into the list */
299 static void gmx_fio_insert(t_fileio *fio)
302 /* first lock the big open_files mutex. */
303 tMPI_Thread_mutex_lock(&open_file_mutex);
304 /* now check whether the dummy element has been allocated,
305 and allocate it if it hasn't */
306 gmx_fio_make_dummy();
308 /* and lock the fio we got and the list's head **/
310 gmx_fio_lock(open_files);
311 prev = open_files->prev;
312 /* lock the element after the current one */
313 if (prev != open_files)
318 /* now do the actual insertion: */
319 fio->next = open_files;
320 open_files->prev = fio;
324 /* now unlock all our locks */
325 if (prev != open_files)
327 gmx_fio_unlock(prev);
329 gmx_fio_unlock(open_files);
332 /* now unlock the big open_files mutex. */
333 tMPI_Thread_mutex_unlock(&open_file_mutex);
336 /* remove a t_fileio into the list. We assume the fio is locked, and we leave
338 NOTE: We also assume that the open_file_mutex has been locked */
339 static void gmx_fio_remove(t_fileio *fio)
343 /* lock prev, because we're changing it */
344 gmx_fio_lock(fio->prev);
346 /* now set the prev's pointer */
347 fio->prev->next = fio->next;
348 gmx_fio_unlock(fio->prev);
350 /* with the next ptr, we can simply lock while the original was locked */
351 gmx_fio_lock(fio->next);
352 fio->next->prev = fio->prev;
353 gmx_fio_unlock(fio->next);
355 /* and make sure we point nowhere in particular */
356 fio->next = fio->prev = fio;
360 /* get the first open file, or NULL if there is none.
361 Returns a locked fio. */
362 static t_fileio *gmx_fio_get_first(void)
365 /* first lock the big open_files mutex and the dummy's mutex */
367 /* first lock the big open_files mutex. */
368 tMPI_Thread_mutex_lock(&open_file_mutex);
369 gmx_fio_make_dummy();
371 gmx_fio_lock(open_files);
372 ret = open_files->next;
375 /* check whether there were any to begin with */
376 if (ret == open_files)
378 /* after this, the open_file pointer should never change */
383 gmx_fio_lock(open_files->next);
385 gmx_fio_unlock(open_files);
391 /* get the next open file, or NULL if there is none.
392 Unlocks the previous fio and locks the next one. */
393 static t_fileio *gmx_fio_get_next(t_fileio *fio)
398 /* check if that was the last one */
399 if (fio->next == open_files)
402 tMPI_Thread_mutex_unlock(&open_file_mutex);
413 /* Stop looping through the open_files. Unlocks the global lock. */
414 static void gmx_fio_stop_getting_next(t_fileio *fio)
417 tMPI_Thread_mutex_unlock(&open_file_mutex);
423 /*****************************************************************
427 *****************************************************************/
428 t_fileio *gmx_fio_open(const char *fn, const char *mode)
430 t_fileio *fio = NULL;
433 gmx_bool bRead, bReadWrite;
436 if (fn2ftp(fn) == efTPA)
438 strcpy(newmode, mode);
442 /* sanitize the mode string */
443 if (strncmp(mode, "r+", 2) == 0)
445 strcpy(newmode, "r+");
447 else if (mode[0] == 'r')
449 strcpy(newmode, "r");
451 else if (strncmp(mode, "w+", 2) == 0)
453 strcpy(newmode, "w+");
455 else if (mode[0] == 'w')
457 strcpy(newmode, "w");
459 else if (strncmp(mode, "a+", 2) == 0)
461 strcpy(newmode, "a+");
463 else if (mode[0] == 'a')
465 strcpy(newmode, "a");
469 gmx_fatal(FARGS, "DEATH HORROR in gmx_fio_open, mode is '%s'", mode);
473 /* Check if it should be opened as a binary file */
474 if (strncmp(ftp2ftype(fn2ftp(fn)), "ASCII", 5))
476 /* Not ascii, add b to file mode */
477 if ((strchr(newmode, 'b') == NULL) && (strchr(newmode, 'B') == NULL))
479 strcat(newmode, "b");
484 tMPI_Lock_init(&(fio->mtx));
485 bRead = (newmode[0] == 'r' && newmode[1] != '+');
486 bReadWrite = (newmode[1] == '+');
491 fio->iFTP = fn2ftp(fn);
492 fio->fn = strdup(fn);
495 /* If this file type is in the list of XDR files, open it like that */
496 if (in_ftpset(fio->iFTP, asize(ftpXDR), ftpXDR))
498 /* First check whether we have to make a backup,
499 * only for writing, not for read or append.
501 if (newmode[0] == 'w')
504 /* only make backups for normal gromacs */
510 /* Check whether file exists */
517 fio->fp = ffopen(fn, newmode);
519 /* determine the XDR direction */
520 if (newmode[0] == 'w' || newmode[0] == 'a')
522 fio->xdrmode = XDR_ENCODE;
526 fio->xdrmode = XDR_DECODE;
530 xdrstdio_create(fio->xdr, fio->fp, fio->xdrmode);
534 /* If it is not, open it as a regular file */
535 fio->fp = ffopen(fn, newmode);
538 /* for appending seek to end of file to make sure ftell gives correct position
539 * important for checkpointing */
540 if (newmode[0] == 'a')
542 gmx_fseek(fio->fp, 0, SEEK_END);
547 /* Use stdin/stdout for I/O */
549 fio->fp = bRead ? stdin : stdout;
550 fio->fn = strdup("STDIO");
554 fio->bReadWrite = bReadWrite;
555 fio->bDouble = (sizeof(real) == sizeof(double));
559 /* set the reader/writer functions */
560 gmx_fio_set_iotype(fio);
562 /* and now insert this file into the list of open files. */
567 static int gmx_fio_close_locked(t_fileio *fio)
573 gmx_fatal(FARGS, "File %s closed twice!\n", fio->fn);
576 if (in_ftpset(fio->iFTP, asize(ftpXDR), ftpXDR))
578 xdr_destroy(fio->xdr);
582 /* Don't close stdin and stdout! */
583 if (!fio->bStdio && fio->fp != NULL)
585 rc = ffclose(fio->fp); /* fclose returns 0 if happy */
593 int gmx_fio_close(t_fileio *fio)
597 /* first lock the big open_files mutex. */
598 /* We don't want two processes operating on the list at the same time */
599 tMPI_Thread_mutex_lock(&open_file_mutex);
602 /* first remove it from the list */
604 rc = gmx_fio_close_locked(fio);
610 tMPI_Thread_mutex_unlock(&open_file_mutex);
615 /* close only fp but keep FIO entry. */
616 int gmx_fio_fp_close(t_fileio *fio)
620 if (!in_ftpset(fio->iFTP, asize(ftpXDR), ftpXDR) && !fio->bStdio)
622 rc = ffclose(fio->fp); /* fclose returns 0 if happy */
630 FILE * gmx_fio_fopen(const char *fn, const char *mode)
635 fio = gmx_fio_open(fn, mode);
643 int gmx_fio_fclose(FILE *fp)
646 t_fileio *found = NULL;
649 cur = gmx_fio_get_first();
654 rc = gmx_fio_close_locked(cur);
656 gmx_fio_stop_getting_next(cur);
661 cur = gmx_fio_get_next(cur);
667 /* internal variant of get_file_md5 that operates on a locked file */
668 static int gmx_fio_int_get_file_md5(t_fileio *fio, gmx_off_t offset,
669 unsigned char digest[])
671 /*1MB: large size important to catch almost identical files */
672 #define CPT_CHK_LEN 1048576
674 unsigned char buf[CPT_CHK_LEN];
676 gmx_off_t seek_offset;
679 seek_offset = offset - CPT_CHK_LEN;
684 read_len = offset - seek_offset;
687 if (fio->fp && fio->bReadWrite)
689 ret = gmx_fseek(fio->fp, seek_offset, SEEK_SET);
692 gmx_fseek(fio->fp, 0, SEEK_END);
695 if (ret) /*either no fp, not readwrite, or fseek not successful */
700 /* the read puts the file position back to offset */
701 if ((gmx_off_t)fread(buf, 1, read_len, fio->fp) != read_len)
703 /* not fatal: md5sum check to prevent overwriting files
704 * works (less safe) without
708 fprintf(stderr, "\nTrying to get md5sum: %s: %s\n", fio->fn,
711 else if (feof(fio->fp))
714 * For long runs that checkpoint frequently but write e.g. logs
715 * infrequently we don't want to issue lots of warnings before we
716 * have written anything to the log.
720 fprintf(stderr, "\nTrying to get md5sum: EOF: %s\n", fio->fn);
727 "\nTrying to get md5sum: Unknown reason for short read: %s\n",
731 gmx_fseek(fio->fp, 0, SEEK_END);
735 gmx_fseek(fio->fp, 0, SEEK_END); /*is already at end, but under windows
736 it gives problems otherwise*/
740 fprintf(debug, "chksum %s readlen %ld\n", fio->fn, (long int)read_len);
746 md5_append(&state, buf, read_len);
747 md5_finish(&state, digest);
758 * fio: file to compute md5 for
759 * offset: starting pointer of region to use for md5
760 * digest: return array of md5 sum
762 int gmx_fio_get_file_md5(t_fileio *fio, gmx_off_t offset,
763 unsigned char digest[])
768 ret = gmx_fio_int_get_file_md5(fio, offset, digest);
774 /* The fio_mutex should ALWAYS be locked when this function is called */
775 static int gmx_fio_int_get_file_position(t_fileio *fio, gmx_off_t *offset)
779 /* Flush the file, so we are sure it is written */
780 if (gmx_fio_int_flush(fio))
785 "Cannot write file '%s'; maybe you are out of disk space?",
790 /* We cannot count on XDR being able to write 64-bit integers,
791 so separate into high/low 32-bit values.
792 In case the filesystem has 128-bit offsets we only care
793 about the first 64 bits - we'll have to fix
794 this when exabyte-size output files are common...
796 *offset = gmx_ftell(fio->fp);
801 int gmx_fio_get_output_file_positions(gmx_file_position_t **p_outputfiles,
804 int i, nfiles, rc, nalloc;
807 gmx_file_position_t * outputfiles;
813 /* pre-allocate 100 files */
815 snew(outputfiles, nalloc);
817 cur = gmx_fio_get_first();
820 /* Skip the checkpoint files themselves, since they could be open when
821 we call this routine... */
822 /* also skip debug files (shoud be the only iFTP==efNR) */
826 cur->iFTP != efCPT &&
830 /* This is an output file currently open for writing, add it */
831 if (nfiles == nalloc)
834 srenew(outputfiles, nalloc);
837 strncpy(outputfiles[nfiles].filename, cur->fn, STRLEN - 1);
839 /* Get the file position */
840 gmx_fio_int_get_file_position(cur, &outputfiles[nfiles].offset);
842 outputfiles[nfiles].chksum_size
843 = gmx_fio_int_get_file_md5(cur,
844 outputfiles[nfiles].offset,
845 outputfiles[nfiles].chksum);
850 cur = gmx_fio_get_next(cur);
853 *p_outputfiles = outputfiles;
859 void gmx_fio_checktype(t_fileio *fio)
861 if (in_ftpset(fio->iFTP, asize(ftpXDR), ftpXDR))
865 else if (in_ftpset(fio->iFTP, asize(ftpASC), ftpASC))
869 else if (in_ftpset(fio->iFTP, asize(ftpBIN), ftpBIN))
874 else if (in_ftpset(fio->iFTP, asize(ftpXML), ftpXML))
881 gmx_fatal(FARGS, "Can not read/write topologies to file type %s",
888 void gmx_fio_setprecision(t_fileio *fio, gmx_bool bDouble)
891 fio->bDouble = bDouble;
895 gmx_bool gmx_fio_getdebug(t_fileio *fio)
906 void gmx_fio_setdebug(t_fileio *fio, gmx_bool bDebug)
909 fio->bDebug = bDebug;
913 char *gmx_fio_getname(t_fileio *fio)
923 int gmx_fio_getftp(t_fileio* fio)
934 void gmx_fio_rewind(t_fileio* fio)
940 xdr_destroy(fio->xdr);
942 xdrstdio_create(fio->xdr, fio->fp, fio->xdrmode);
952 int gmx_fio_flush(t_fileio* fio)
957 ret = gmx_fio_int_flush(fio);
965 static int gmx_fio_int_fsync(t_fileio *fio)
973 rc = gmx_fsync(fio->fp);
975 else if (fio->xdr) /* this should normally not happen */
977 rc = gmx_fsync((FILE*) fio->xdr->x_private);
978 /* ^ is this actually OK? */
985 int gmx_fio_fsync(t_fileio *fio)
990 rc = gmx_fio_int_fsync(fio);
998 t_fileio *gmx_fio_all_output_fsync(void)
1000 t_fileio *ret = NULL;
1003 cur = gmx_fio_get_first();
1006 /* skip debug files (shoud be the only iFTP==efNR) */
1012 /* if any of them fails, return failure code */
1013 int rc = gmx_fio_int_fsync(cur);
1014 if (rc != 0 && !ret)
1019 cur = gmx_fio_get_next(cur);
1022 /* in addition, we force these to be written out too, if they're being
1023 redirected. We don't check for errors because errors most likely mean
1024 that they're not redirected. */
1027 #if (defined(HAVE_FSYNC))
1028 /* again, fahcore defines HAVE_FSYNC and fsync() */
1029 fsync(STDOUT_FILENO);
1030 fsync(STDERR_FILENO);
1037 gmx_off_t gmx_fio_ftell(t_fileio* fio)
1044 ret = gmx_ftell(fio->fp);
1046 gmx_fio_unlock(fio);
1050 int gmx_fio_seek(t_fileio* fio, gmx_off_t fpos)
1057 rc = gmx_fseek(fio->fp, fpos, SEEK_SET);
1064 gmx_fio_unlock(fio);
1068 FILE *gmx_fio_getfp(t_fileio *fio)
1077 gmx_fio_unlock(fio);
1081 XDR *gmx_fio_getxdr(t_fileio* fio)
1090 gmx_fio_unlock(fio);
1095 gmx_bool gmx_fio_getread(t_fileio* fio)
1101 gmx_fio_unlock(fio);
1106 int xtc_seek_frame(t_fileio *fio, int frame, int natoms)
1111 ret = xdr_xtc_seek_frame(frame, fio->fp, fio->xdr, natoms);
1112 gmx_fio_unlock(fio);
1117 int xtc_seek_time(t_fileio *fio, real time, int natoms, gmx_bool bSeekForwardOnly)
1122 ret = xdr_xtc_seek_time(time, fio->fp, fio->xdr, natoms, bSeekForwardOnly);
1123 gmx_fio_unlock(fio);