/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* This is is needed at the beginning of mdrun,
* to be able to rename the logfile correctly.
* When file appending is requested, checks which output files are present,
- * and returns TRUE/FALSE in bDoAppendFiles if all or none are present.
- * If only some output files are present, give a fatal error.
- * When bDoAppendFiles is TRUE upon return, bAddPart will tell whether the simulation part
- * needs to be added to the output file name.
+ * and issue a fatal error if some are not.
+ * Upon return, bAddPart will tell whether the simulation part
+ * needs to be added to the output file name, i.e. when we are doing checkpoint
+ * continuation without appending.
*
* This routine cannot print tons of data, since it is called before
* the log file is opened. */
if (!gmx_fexist(filename) || (!(fp = gmx_fio_open(filename, "r")) ))
{
*simulation_part = 0;
+ fprintf(stderr, "Warning: No checkpoint file found with -cpi option. Assuming this is a new run.\n\n");
}
else
{
{
*bDoAppendFiles = bTryToAppendFiles;
}
- else if (nexist > 0)
+ else
{
+ // If we get here, the user requested restarting from a checkpoint file, that checkpoint
+ // file was found (so it is not the first part of a new run), but we are still missing
+ // some or all checkpoint files. In this case we issue a fatal error since there are
+ // so many special cases we cannot keep track of, and better safe than sorry.
fprintf(stderr,
"Output file appending has been requested,\n"
"but some output files listed in the checkpoint file %s\n"
- "are not present or are named differently by the current program:\n",
+ "are not present or not named as the output files by the current program:\n",
filename);
- fprintf(stderr, "output files present:");
+ fprintf(stderr, "Expect output files present:\n");
for (f = 0; f < nfiles; f++)
{
if (exist_output_file(outputfiles[f].filename,
nfile, fnm))
{
- fprintf(stderr, " %s", outputfiles[f].filename);
+ fprintf(stderr, " %s\n", outputfiles[f].filename);
}
}
fprintf(stderr, "\n");
- fprintf(stderr, "output files not present or named differently:");
+ fprintf(stderr, "Expected output files not present or named differently:\n");
for (f = 0; f < nfiles; f++)
{
if (!exist_output_file(outputfiles[f].filename,
nfile, fnm))
{
- fprintf(stderr, " %s", outputfiles[f].filename);
+ fprintf(stderr, " %s\n", outputfiles[f].filename);
}
}
- fprintf(stderr, "\n");
- gmx_fatal(FARGS, "File appending requested, but %d of the %d output files are not present or are named differently", nfiles-nexist, nfiles);
+ gmx_fatal(FARGS,
+ "File appending requested, but %d of the %d output files are not present or are named differently. "
+ "For safety reasons, GROMACS-2016 and later only allows file appending to be used when all files "
+ "have the same names as they had in the original run. "
+ "Checkpointing is merely intended for plain continuation of runs. "
+ "For safety reasons you must specify all file names (e.g. with -deffnm), "
+ "and all these files must match the names used in the run prior to checkpointing "
+ "since we will append to them by default. If the files are not available, you "
+ "can add the -noappend flag to mdrun and write separate new parts. "
+ "For mere concatenation of files, you should use the gmx trjcat tool instead.",
+ nfiles-nexist, nfiles);
}
}
}
if (PAR(cr))
{
+ // Make sure all settings are in sync
gmx_bcast(sizeof(*simulation_part), simulation_part, cr);
if (*simulation_part > 0 && bTryToAppendFiles)
const char *part_suffix = ".part";
FILE *fpmulti;
- bAddPart = !bTryToAppendFiles;
/* Check if there is ANY checkpoint file available */
sim_part = 1;
sim_part_fn = sim_part;
if (opt2bSet("-cpi", NFILE, fnm))
{
+ bAddPart = !bTryToAppendFiles;
+
read_checkpoint_data(opt2fn_master("-cpi", NFILE, fnm, cr),
&sim_part_fn, cr,
bTryToAppendFiles, NFILE, fnm,
- part_suffix, &bAddPart,
- bDoAppendFiles);
+ part_suffix, &bAddPart, bDoAppendFiles);
if (sim_part_fn == 0 && MULTIMASTER(cr))
{
fprintf(stdout, "No previous checkpoint file present, assuming this is a new run.\n");
}
else
{
- *bDoAppendFiles = FALSE;
+ *bDoAppendFiles = false;
+ bAddPart = false;
}
+
*bStartFromCpt = sim_part > 1;
if (!*bDoAppendFiles)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \brief Handle startup of mdrun, particularly regarding -cpi and -append
*
* If there is a checkpoint file, then prepare to start from that
- * state. If there is also appending, then organize the file naming
- * accordingly, if possible. Issues various fatal errors if the input
- * conditions are inconsistent or broken. \p fnm is updated with
- * suffix strings for part numbers if we are doing a restart from
- * checkpoint and are not appending.
+ * state. If restarting from a checkpoint file and appending is requested with
+ * tryToAppendFiles, we will set doAppendFiles to true on return if all files
+ * were found correctly. If some files are not found when appending should be
+ * done, we will instead issue a fatal error to avoid unintentional problems.
*
- * Does communication to coordinate behaviour between all ranks of a
- * simulation, and/or simulations.
+ * If there is no checkpoint file, we assume it is the first part of a new run,
+ * and in this case we silently set doAppendFiles to false on return.
+ *
+ * On return, \p fnm is updated with suffix strings for part numbers if we are
+ * doing a restart from checkpoint and are not appending. The routine also does
+ * communication to coordinate behaviour between all ranks of a simulation,
+ * and/or simulations.
*
* \param[in] cr Communication structure
- * \param[in] bTryToAppendFiles Whether mdrun -append was used
+ * \param[in] bTryToAppendFiles Whether appending is requested (from mdrun)
* \param[in] NFILE Size of fnm struct
* \param[inout] fnm Filename parameters to mdrun
- * \param[out] bDoAppendFiles Whether mdrun will append to files
- * \param[out] bStartFromCpt Whether mdrun will start from the -cpi file
+ * \param[out] bDoAppendFiles True on return if we will do appending.
+ * Note that the routine will generate a fatal
+ * error for some scenarios where appending is
+ * requested but the necessary files not found.
+ * \param[out] bStartFromCpt True on return if we found the checkpoint
+ * and will use it to restart.
*/
void handleRestart(t_commrec *cr,
gmx_bool bTryToAppendFiles,
#endif
}
- handleRestart(cr, bTryToAppendFiles, NFILE, fnm,
- &bDoAppendFiles, &bStartFromCpt);
+ if (!opt2bSet("-cpi", NFILE, fnm))
+ {
+ // If we are not starting from a checkpoint we never allow files to be appended
+ // to, since that has caused a ton of strange behaviour and bugs in the past.
+ if (opt2parg_bSet("-append", asize(pa), pa))
+ {
+ // If the user explicitly used the -append option, explain that it is not possible.
+ gmx_fatal(FARGS, "GROMACS can only append to files when restarting from a checkpoint.");
+ }
+ else
+ {
+ // If the user did not say anything explicit, just disable appending.
+ bTryToAppendFiles = FALSE;
+ }
+ }
+
+ handleRestart(cr, bTryToAppendFiles, NFILE, fnm, &bDoAppendFiles, &bStartFromCpt);
Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
Flags = Flags | (bConfout ? MD_CONFOUT : 0);
Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
- Flags = Flags | (bDoAppendFiles ? MD_APPENDFILES : 0);
+ Flags = Flags | (bDoAppendFiles ? MD_APPENDFILES : 0);
Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
Flags = Flags | (bStartFromCpt ? MD_STARTFROMCPT : 0);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff