-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
+ *
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+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
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*
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+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
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+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
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*
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/main.h"
+#include <limits.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
-#include <limits.h>
#include <time.h>
+#include "config.h"
+
+#ifdef GMX_NATIVE_WINDOWS
+#include <process.h>
+#endif
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
+#ifdef HAVE_UNISTD_H
+#include <unistd.h>
+#endif
-#include "smalloc.h"
-#include "gmx_fatal.h"
-#include "network.h"
-#include "main.h"
-#include "macros.h"
-#include "gromacs/fileio/futil.h"
#include "gromacs/fileio/filenm.h"
#include "gromacs/fileio/gmxfio.h"
-#include "string2.h"
-#include "copyrite.h"
-
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/utility/programinfo.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
-
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
-
-#ifdef GMX_NATIVE_WINDOWS
-#include <process.h>
-#endif
-
#define BUFSIZE 1024
-
static void par_fn(char *base, int ftp, const t_commrec *cr,
gmx_bool bAppendSimId, gmx_bool bAppendNodeId,
char buf[], int bufsize)
}
if (bAppendNodeId)
{
- strcat(buf, "_node");
+ strcat(buf, "_rank");
sprintf(buf+strlen(buf), "%d", cr->nodeid);
}
strcat(buf, ".");
/* Add extension again */
- strcat(buf, (ftp == efTPX) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
+ strcat(buf, (ftp == efTPR) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
if (debug)
{
- fprintf(debug, "node %d par_fn '%s'\n", cr->nodeid, buf);
+ fprintf(debug, "rank %d par_fn '%s'\n", cr->nodeid, buf);
if (fn2ftp(buf) == efLOG)
{
fprintf(debug, "log\n");
sfree(ibuf);
}
-void check_multi_large_int(FILE *log, const gmx_multisim_t *ms,
- gmx_large_int_t val, const char *name,
- gmx_bool bQuiet)
+void check_multi_int64(FILE *log, const gmx_multisim_t *ms,
+ gmx_int64_t val, const char *name,
+ gmx_bool bQuiet)
{
- gmx_large_int_t *ibuf;
+ gmx_int64_t *ibuf;
int p;
gmx_bool bCompatible;
char strbuf[255];
/* first make the format string */
snprintf(strbuf, 255, " subsystem %%d: %s\n",
- gmx_large_int_pfmt);
+ "%" GMX_PRId64);
fprintf(log, strbuf, p, ibuf[p]);
}
}
}
-char *gmx_gethostname(char *name, size_t len)
-{
- if (len < 8)
- {
- gmx_incons("gmx_gethostname called with len<8");
- }
-#ifdef HAVE_UNISTD_H
- if (gethostname(name, len-1) != 0)
- {
- strncpy(name, "unknown", 8);
- }
-#else
- strncpy(name, "unknown", 8);
-#endif
-
- return name;
-}
-
-
-void gmx_log_open(const char *lognm, const t_commrec *cr, gmx_bool bMasterOnly,
+void gmx_log_open(const char *lognm, const t_commrec *cr,
gmx_bool bAppendFiles, FILE** fplog)
{
- int len, pid;
- char buf[256], host[256];
+ int pid;
+ char host[256];
time_t t;
char timebuf[STRLEN];
FILE *fp = *fplog;
- char *tmpnm;
-
- debug_gmx();
-
- /* Communicate the filename for logfile */
- if (cr->nnodes > 1 && !bMasterOnly
-#ifdef GMX_THREAD_MPI
- /* With thread MPI the non-master log files are opened later
- * when the files names are already known on all nodes.
- */
- && FALSE
-#endif
- )
- {
- if (MASTER(cr))
- {
- len = strlen(lognm) + 1;
- }
- gmx_bcast(sizeof(len), &len, cr);
- if (!MASTER(cr))
- {
- snew(tmpnm, len+8);
- }
- else
- {
- tmpnm = gmx_strdup(lognm);
- }
- gmx_bcast(len*sizeof(*tmpnm), tmpnm, cr);
- }
- else
- {
- tmpnm = gmx_strdup(lognm);
- }
debug_gmx();
- if (!bMasterOnly && !MASTER(cr))
+ if (!bAppendFiles)
{
- /* Since log always ends with '.log' let's use this info */
- par_fn(tmpnm, efLOG, cr, FALSE, !bMasterOnly, buf, 255);
- fp = gmx_fio_fopen(buf, bAppendFiles ? "a+" : "w+" );
+ fp = gmx_fio_fopen(lognm, bAppendFiles ? "a+" : "w+" );
}
- else if (!bAppendFiles)
- {
- fp = gmx_fio_fopen(tmpnm, bAppendFiles ? "a+" : "w+" );
- }
-
- sfree(tmpnm);
gmx_fatal_set_log_file(fp);
fprintf(fp,
"Log file opened on %s"
- "Host: %s pid: %d nodeid: %d nnodes: %d\n",
+ "Host: %s pid: %d rank ID: %d number of ranks: %d\n",
timebuf, host, pid, cr->nodeid, cr->nnodes);
try
{
gmx::BinaryInformationSettings settings;
settings.extendedInfo(true);
settings.copyright(!bAppendFiles);
- gmx::printBinaryInformation(fp, gmx::ProgramInfo::getInstance(), settings);
+ gmx::printBinaryInformation(fp, gmx::getProgramContext(), settings);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
fprintf(fp, "\n\n");
nnodes = cr->nnodes;
if (nnodes % nsim != 0)
{
- gmx_fatal(FARGS, "The number of nodes (%d) is not a multiple of the number of simulations (%d)", nnodes, nsim);
+ gmx_fatal(FARGS, "The number of ranks (%d) is not a multiple of the number of simulations (%d)", nnodes, nsim);
}
nnodpersim = nnodes/nsim;
if (debug)
{
- fprintf(debug, "We have %d simulations, %d nodes per simulation, local simulation is %d\n", nsim, nnodpersim, sim);
+ fprintf(debug, "We have %d simulations, %d ranks per simulation, local simulation is %d\n", nsim, nnodpersim, sim);
}
snew(ms, 1);
fprintf(debug, "This is simulation %d", cr->ms->sim);
if (PAR(cr))
{
- fprintf(debug, ", local number of nodes %d, local nodeid %d",
+ fprintf(debug, ", local number of ranks %d, local rank ID %d",
cr->nnodes, cr->sim_nodeid);
}
fprintf(debug, "\n\n");
* at the actual file name
*/
if (is_output(&fnm[i]) ||
- fnm[i].ftp == efTPX || fnm[i].ftp == efCPT ||
+ fnm[i].ftp == efTPR || fnm[i].ftp == efCPT ||
strcmp(fnm[i].opt, "-rerun") == 0)
{
ftp = fn2ftp(fnm[i].fns[0]);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff