add_subdirectory(fft)
add_subdirectory(linearalgebra)
add_subdirectory(math)
+add_subdirectory(mdrunutility)
add_subdirectory(random)
add_subdirectory(onlinehelp)
add_subdirectory(options)
done_state(&state);
}
-
-static gmx_bool exist_output_file(const char *fnm_cp, int nfile, const t_filenm fnm[])
-{
- int i;
-
- /* Check if the output file name stored in the checkpoint file
- * is one of the output file names of mdrun.
- */
- i = 0;
- while (i < nfile &&
- !(is_output(&fnm[i]) && strcmp(fnm_cp, fnm[i].fns[0]) == 0))
- {
- i++;
- }
-
- return (i < nfile && gmx_fexist(fnm_cp));
-}
-
/* This routine cannot print tons of data, since it is called before the log file is opened. */
-gmx_bool read_checkpoint_simulation_part(const char *filename, int *simulation_part,
- t_commrec *cr,
- gmx_bool bAppendReq,
- int nfile, const t_filenm fnm[],
- const char *part_suffix, gmx_bool *bAddPart)
+void
+read_checkpoint_simulation_part_and_filenames(t_fileio *fp,
+ int *simulation_part,
+ int *nfiles,
+ gmx_file_position_t **outputfiles)
{
- t_fileio *fp;
- gmx_int64_t step = 0;
- double t;
- /* This next line is nasty because the sub-structures of t_state
- * cannot be assumed to be zeroed (or even initialized in ways the
- * rest of the code might assume). Using snew would be better, but
- * this will all go away for 5.0. */
- t_state state;
- int nfiles;
- gmx_file_position_t *outputfiles;
- int nexist, f;
- gmx_bool bAppend;
- char *fn, suf_up[STRLEN];
-
- bAppend = FALSE;
+ gmx_int64_t step = 0;
+ double t;
+ t_state state;
- if (SIMMASTER(cr))
- {
- if (!gmx_fexist(filename) || (!(fp = gmx_fio_open(filename, "r")) ))
- {
- *simulation_part = 0;
- }
- else
- {
- init_state(&state, 0, 0, 0, 0, 0);
-
- read_checkpoint_data(fp, simulation_part, &step, &t, &state,
- &nfiles, &outputfiles);
- if (gmx_fio_close(fp) != 0)
- {
- gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
- }
- done_state(&state);
-
- if (bAppendReq)
- {
- nexist = 0;
- for (f = 0; f < nfiles; f++)
- {
- if (exist_output_file(outputfiles[f].filename, nfile, fnm))
- {
- nexist++;
- }
- }
- if (nexist == nfiles)
- {
- bAppend = bAppendReq;
- }
- else if (nexist > 0)
- {
- 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",
- filename);
- fprintf(stderr, "output files present:");
- for (f = 0; f < nfiles; f++)
- {
- if (exist_output_file(outputfiles[f].filename,
- nfile, fnm))
- {
- fprintf(stderr, " %s", outputfiles[f].filename);
- }
- }
- fprintf(stderr, "\n");
- fprintf(stderr, "output files not present or named differently:");
- for (f = 0; f < nfiles; f++)
- {
- if (!exist_output_file(outputfiles[f].filename,
- nfile, fnm))
- {
- fprintf(stderr, " %s", 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);
- }
- }
-
- if (bAppend)
- {
- if (nfiles == 0)
- {
- gmx_fatal(FARGS, "File appending requested, but no output file information is stored in the checkpoint file");
- }
- fn = outputfiles[0].filename;
- if (strlen(fn) < 4 ||
- gmx_strcasecmp(fn+strlen(fn)-4, ftp2ext(efLOG)) == 0)
- {
- gmx_fatal(FARGS, "File appending requested, but the log file is not the first file listed in the checkpoint file");
- }
- /* Set bAddPart to whether the suffix string '.part' is present
- * in the log file name.
- */
- strcpy(suf_up, part_suffix);
- upstring(suf_up);
- *bAddPart = (strstr(fn, part_suffix) != NULL ||
- strstr(fn, suf_up) != NULL);
- }
+ init_state(&state, 0, 0, 0, 0, 0);
- sfree(outputfiles);
- }
- }
- if (PAR(cr))
+ read_checkpoint_data(fp, simulation_part, &step, &t, &state,
+ nfiles, outputfiles);
+ if (gmx_fio_close(fp) != 0)
{
- gmx_bcast(sizeof(*simulation_part), simulation_part, cr);
-
- if (*simulation_part > 0 && bAppendReq)
- {
- gmx_bcast(sizeof(bAppend), &bAppend, cr);
- gmx_bcast(sizeof(*bAddPart), bAddPart, cr);
- }
+ gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
}
-
- return bAppend;
+ done_state(&state);
}
int *simulation_part,
gmx_int64_t *step);
-/* Read just the simulation 'generation' and with bAppendReq check files.
- * This is necessary already at the beginning of mdrun,
- * to be able to rename the logfile correctly.
- * When file appending is requested, checks which output files are present:
- * all present: return TRUE,
- * none present: return FALSE,
- * part present: fatal error.
- * When TRUE is returned, bAddPart will tell whether the simulation part
- * needs to be added to the output file name.
+/* ! \brief Read simulation part and output filenames from a checkpoint file
+ *
+ * Used by mdrun to handle restarts
+ *
+ * \param[in] fp Handle to open checkpoint file
+ * \param[out] simulation_part The part of the simulation that wrote the checkpoint
+ * \param[out] nfiles Number of output files from the previous run
+ * \param[out] outputfiles Pointer to array of output file names from the previous run. Pointer is allocated in this function.
*/
-gmx_bool read_checkpoint_simulation_part(const char *filename, int *simulation_part,
- t_commrec *cr,
- gmx_bool bAppendReq,
- int nfile, const t_filenm fnm[],
- const char *part_suffix, gmx_bool *bAddPart);
+void
+read_checkpoint_simulation_part_and_filenames(t_fileio *fp,
+ int *simulation_part,
+ int *nfiles,
+ gmx_file_position_t **outputfiles);
#ifdef __cplusplus
}
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2015, 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.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+file(GLOB MDRUNUTILITY_SOURCES *.cpp)
+set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${MDRUNUTILITY_SOURCES} PARENT_SCOPE)
+
+if (BUILD_TESTING)
+# add_subdirectory(tests)
+endif()
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2015, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file declares functions for mdrun to call to manage the
+ * details of doing a restart (ie. reading checkpoints, appending
+ * output files).
+ *
+ * \todo Clean up the error-prone logic here. Add doxygen.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author Erik Lindahl <erik@kth.se>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_mdrunutility
+ */
+
+#include "gmxpre.h"
+
+#include "handlerestart.h"
+
+#include <string.h>
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/smalloc.h"
+
+/*! \brief Search for \p fnm_cp in fnm and return true iff found
+ *
+ * \todo This could be implemented sanely with a for loop. */
+static gmx_bool exist_output_file(const char *fnm_cp, int nfile, const t_filenm fnm[])
+{
+ int i;
+
+ /* Check if the output file name stored in the checkpoint file
+ * is one of the output file names of mdrun.
+ */
+ i = 0;
+ while (i < nfile &&
+ !(is_output(&fnm[i]) && strcmp(fnm_cp, fnm[i].fns[0]) == 0))
+ {
+ i++;
+ }
+
+ return (i < nfile && gmx_fexist(fnm_cp));
+}
+
+/*! \brief Support handling restarts
+ *
+ * \todo Clean this up (next patch)
+ *
+ * Read just the simulation 'generation' and with bTryToAppendFiles check files.
+ * 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.
+ *
+ * This routine cannot print tons of data, since it is called before
+ * the log file is opened. */
+static void
+read_checkpoint_data(const char *filename, int *simulation_part,
+ t_commrec *cr,
+ gmx_bool bTryToAppendFiles,
+ int nfile, const t_filenm fnm[],
+ const char *part_suffix,
+ gmx_bool *bAddPart,
+ gmx_bool *bDoAppendFiles)
+{
+ t_fileio *fp;
+ int nfiles;
+ gmx_file_position_t *outputfiles;
+ int nexist, f;
+ char *fn, suf_up[STRLEN];
+
+ *bDoAppendFiles = FALSE;
+
+ if (SIMMASTER(cr))
+ {
+ if (!gmx_fexist(filename) || (!(fp = gmx_fio_open(filename, "r")) ))
+ {
+ *simulation_part = 0;
+ }
+ else
+ {
+ read_checkpoint_simulation_part_and_filenames(fp,
+ simulation_part,
+ &nfiles,
+ &outputfiles);
+
+ if (bTryToAppendFiles)
+ {
+ nexist = 0;
+ for (f = 0; f < nfiles; f++)
+ {
+ if (exist_output_file(outputfiles[f].filename, nfile, fnm))
+ {
+ nexist++;
+ }
+ }
+ if (nexist == nfiles)
+ {
+ *bDoAppendFiles = bTryToAppendFiles;
+ }
+ else if (nexist > 0)
+ {
+ 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",
+ filename);
+ fprintf(stderr, "output files present:");
+ for (f = 0; f < nfiles; f++)
+ {
+ if (exist_output_file(outputfiles[f].filename,
+ nfile, fnm))
+ {
+ fprintf(stderr, " %s", outputfiles[f].filename);
+ }
+ }
+ fprintf(stderr, "\n");
+ fprintf(stderr, "output files not present or named differently:");
+ for (f = 0; f < nfiles; f++)
+ {
+ if (!exist_output_file(outputfiles[f].filename,
+ nfile, fnm))
+ {
+ fprintf(stderr, " %s", 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);
+ }
+ }
+
+ if (*bDoAppendFiles)
+ {
+ if (nfiles == 0)
+ {
+ gmx_fatal(FARGS, "File appending requested, but no output file information is stored in the checkpoint file");
+ }
+ fn = outputfiles[0].filename;
+ if (strlen(fn) < 4 ||
+ gmx_strcasecmp(fn+strlen(fn)-4, ftp2ext(efLOG)) == 0)
+ {
+ gmx_fatal(FARGS, "File appending requested, but the log file is not the first file listed in the checkpoint file");
+ }
+ /* Set bAddPart to whether the suffix string '.part' is present
+ * in the log file name.
+ */
+ strcpy(suf_up, part_suffix);
+ upstring(suf_up);
+ *bAddPart = (strstr(fn, part_suffix) != NULL ||
+ strstr(fn, suf_up) != NULL);
+ }
+
+ sfree(outputfiles);
+ }
+ }
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(*simulation_part), simulation_part, cr);
+
+ if (*simulation_part > 0 && bTryToAppendFiles)
+ {
+ gmx_bcast(sizeof(*bDoAppendFiles), bDoAppendFiles, cr);
+ gmx_bcast(sizeof(*bAddPart), bAddPart, cr);
+ }
+ }
+}
+
+/* This routine cannot print tons of data, since it is called before the log file is opened. */
+void
+handleRestart(t_commrec *cr,
+ gmx_bool bTryToAppendFiles,
+ const int NFILE,
+ t_filenm fnm[],
+ gmx_bool *bDoAppendFiles,
+ gmx_bool *bStartFromCpt)
+{
+ gmx_bool bAddPart;
+ int sim_part, sim_part_fn;
+ 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))
+ {
+ read_checkpoint_data(opt2fn_master("-cpi", NFILE, fnm, cr),
+ &sim_part_fn, cr,
+ bTryToAppendFiles, NFILE, fnm,
+ 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
+ {
+ sim_part = sim_part_fn + 1;
+ }
+
+ if (MULTISIM(cr) && MASTER(cr))
+ {
+ if (MULTIMASTER(cr))
+ {
+ /* Log file is not yet available, so if there's a
+ * problem we can only write to stderr. */
+ fpmulti = stderr;
+ }
+ else
+ {
+ fpmulti = NULL;
+ }
+ check_multi_int(fpmulti, cr->ms, sim_part, "simulation part", TRUE);
+ }
+ }
+ else
+ {
+ *bDoAppendFiles = FALSE;
+ }
+ *bStartFromCpt = sim_part > 1;
+
+ if (!*bDoAppendFiles)
+ {
+ sim_part_fn = sim_part;
+ }
+
+ if (bAddPart)
+ {
+ char suffix[STRLEN];
+
+ /* Rename all output files (except checkpoint files) */
+ /* create new part name first (zero-filled) */
+ sprintf(suffix, "%s%04d", part_suffix, sim_part_fn);
+
+ add_suffix_to_output_names(fnm, NFILE, suffix);
+ if (MULTIMASTER(cr))
+ {
+ fprintf(stdout, "Checkpoint file is from part %d, new output files will be suffixed '%s'.\n", sim_part-1, suffix);
+ }
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2015, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \defgroup module_mdrunutility Implementation of mdrun utility functionality
+ * \ingroup group_mdrun
+ *
+ * \brief This module contains code that implements general
+ * infrastructure for mdrun that does not suit any other module.
+ */
+/*! \libinternal \file
+ *
+ * \brief This file declares functions for mdrun to call to manage the
+ * details of doing a restart (ie. reading checkpoints, appending
+ * output files).
+ *
+ * \todo There may be other code in runner.cpp etc. that can usefully
+ * live here
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author Erik Lindahl <erik@kth.se>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \inlibraryapi
+ * \ingroup module_mdrunutility
+ */
+
+#ifndef GMX_MDRUNUTILITY_HANDLERESTART_H
+#define GMX_MDRUNUTILITY_HANDLERESTART_H
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/basedefinitions.h"
+
+/*! \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.
+ *
+ * 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] 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
+ */
+void handleRestart(t_commrec *cr,
+ gmx_bool bTryToAppendFiles,
+ const int NFILE,
+ t_filenm fnm[],
+ gmx_bool *bDoAppendFiles,
+ gmx_bool *bStartFromCpt);
+
+#endif
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/filenm.h"
-#include "gromacs/legacyheaders/checkpoint.h"
#include "gromacs/legacyheaders/macros.h"
#include "gromacs/legacyheaders/main.h"
#include "gromacs/legacyheaders/mdrun.h"
#include "gromacs/legacyheaders/readinp.h"
#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/mdrunutility/handlerestart.h"
#include "gromacs/utility/fatalerror.h"
#include "mdrun_main.h"
real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
real cpt_period = 15.0, max_hours = -1;
- gmx_bool bAppendFiles = TRUE;
+ gmx_bool bTryToAppendFiles = TRUE;
gmx_bool bKeepAndNumCPT = FALSE;
gmx_bool bResetCountersHalfWay = FALSE;
output_env_t oenv = NULL;
"Checkpoint interval (minutes)" },
{ "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
"Keep and number checkpoint files" },
- { "-append", FALSE, etBOOL, {&bAppendFiles},
+ { "-append", FALSE, etBOOL, {&bTryToAppendFiles},
"Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
{ "-nsteps", FALSE, etINT64, {&nsteps},
"Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option, smaller is invalid)" },
unsigned long Flags;
ivec ddxyz;
int dd_node_order;
- gmx_bool bAddPart;
- FILE *fplog, *fpmulti;
- int sim_part, sim_part_fn;
- const char *part_suffix = ".part";
- char suffix[STRLEN];
+ gmx_bool bDoAppendFiles, bStartFromCpt;
+ FILE *fplog;
int rc;
char **multidir = NULL;
#endif
}
- bAddPart = !bAppendFiles;
-
- /* Check if there is ANY checkpoint file available */
- sim_part = 1;
- sim_part_fn = sim_part;
- if (opt2bSet("-cpi", NFILE, fnm))
- {
- bAppendFiles =
- read_checkpoint_simulation_part(opt2fn_master("-cpi", NFILE,
- fnm, cr),
- &sim_part_fn, cr,
- bAppendFiles, NFILE, fnm,
- part_suffix, &bAddPart);
- if (sim_part_fn == 0 && MULTIMASTER(cr))
- {
- fprintf(stdout, "No previous checkpoint file present, assuming this is a new run.\n");
- }
- else
- {
- sim_part = sim_part_fn + 1;
- }
-
- if (MULTISIM(cr) && MASTER(cr))
- {
- if (MULTIMASTER(cr))
- {
- /* Log file is not yet available, so if there's a
- * problem we can only write to stderr. */
- fpmulti = stderr;
- }
- else
- {
- fpmulti = NULL;
- }
- check_multi_int(fpmulti, cr->ms, sim_part, "simulation part", TRUE);
- }
- }
- else
- {
- bAppendFiles = FALSE;
- }
-
- if (!bAppendFiles)
- {
- sim_part_fn = sim_part;
- }
-
- if (bAddPart)
- {
- /* Rename all output files (except checkpoint files) */
- /* create new part name first (zero-filled) */
- sprintf(suffix, "%s%04d", part_suffix, sim_part_fn);
-
- add_suffix_to_output_names(fnm, NFILE, suffix);
- if (MULTIMASTER(cr))
- {
- fprintf(stdout, "Checkpoint file is from part %d, new output files will be suffixed '%s'.\n", sim_part-1, suffix);
- }
- }
+ 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 | (bAppendFiles ? 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 | (sim_part > 1 ? MD_STARTFROMCPT : 0);
+ Flags = Flags | (bStartFromCpt ? MD_STARTFROMCPT : 0);
Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
Flags = Flags | (bIMDwait ? MD_IMDWAIT : 0);
Flags = Flags | (bIMDterm ? MD_IMDTERM : 0);
/* We postpone opening the log file if we are appending, so we can
first truncate the old log file and append to the correct position
there instead. */
- if (MASTER(cr) && !bAppendFiles)
+ if (MASTER(cr) && !bDoAppendFiles)
{
gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
Flags & MD_APPENDFILES, &fplog);
/* Log file has to be closed in mdrunner if we are appending to it
(fplog not set here) */
- if (MASTER(cr) && !bAppendFiles)
+ if (MASTER(cr) && !bDoAppendFiles)
{
gmx_log_close(fplog);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff