-/* -*- 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.
+ *
+ * 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.
*
- * If you want to redistribute modifications, 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 www.gromacs.org.
+ * 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.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * 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.
*
- * For more info, check our website at http://www.gromacs.org
+ * 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.
*
- * And Hey:
- * GROningen Mixture of Alchemy and Childrens' Stories
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include "gromacs/utility/gmx_header_config.h"
+#include "gmxpre.h"
+
+#include "config.h"
#include <stdio.h>
#include <stdlib.h>
#ifdef HAVE_SYS_TIME_H
#include <sys/time.h>
#endif
-
-#include "smalloc.h"
-#include "gmx_fatal.h"
-#include "network.h"
-#include "main.h"
-#include "macros.h"
-#include "futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "string2.h"
-#include "copyrite.h"
-
-#ifdef GMX_THREAD_MPI
-#include "thread_mpi.h"
-#endif
-
-#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/programinfo.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
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxmpi.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. */
+
+#define BUFSIZE 1024
static void par_fn(char *base, int ftp, const t_commrec *cr,
gmx_bool bAppendSimId, gmx_bool bAppendNodeId,
}
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))
- {
- /* 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+" );
- }
- else if (!bAppendFiles)
+ if (!bAppendFiles)
{
- fp = gmx_fio_fopen(tmpnm, bAppendFiles ? "a+" : "w+" );
+ fp = gmx_fio_fopen(lognm, bAppendFiles ? "a+" : "w+" );
}
- sfree(tmpnm);
-
gmx_fatal_set_log_file(fp);
/* Get some machine parameters */
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);
MPI_Comm_create(MPI_COMM_WORLD, ms->mpi_group_masters,
&ms->mpi_comm_masters);
-#if !defined(GMX_THREAD_MPI) && !defined(MPI_IN_PLACE_EXISTS)
+#if !defined(MPI_IN_PLACE_EXISTS)
/* initialize the MPI_IN_PLACE replacement buffers */
snew(ms->mpb, 1);
ms->mpb->ibuf = NULL;
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]);
}
}
}
-
-t_commrec *init_par()
-{
- t_commrec *cr;
-
- snew(cr, 1);
-
-#if defined GMX_MPI && !defined GMX_THREAD_MPI
- if (!gmx_mpi_initialized())
- {
- gmx_comm("MPI has not been initialized properly");
- }
- cr->nnodes = gmx_node_num();
- cr->sim_nodeid = gmx_node_rank();
- if (!PAR(cr) && (cr->sim_nodeid != 0))
- {
- gmx_comm("(!PAR(cr) && (cr->sim_nodeid != 0))");
- }
-
- cr->mpi_comm_mysim = MPI_COMM_WORLD;
- cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
-#else
- /* These should never be accessed */
- cr->mpi_comm_mysim = NULL;
- cr->mpi_comm_mygroup = NULL;
- cr->nnodes = 1;
- cr->sim_nodeid = 0;
-#endif
-
- cr->nodeid = cr->sim_nodeid;
-
- cr->duty = (DUTY_PP | DUTY_PME);
-
-#ifdef GMX_MPI
-#if !defined(GMX_THREAD_MPI) && !defined(MPI_IN_PLACE_EXISTS)
- /* initialize the MPI_IN_PLACE replacement buffers */
- snew(cr->mpb, 1);
- cr->mpb->ibuf = NULL;
- cr->mpb->libuf = NULL;
- cr->mpb->fbuf = NULL;
- cr->mpb->dbuf = NULL;
- cr->mpb->ibuf_alloc = 0;
- cr->mpb->libuf_alloc = 0;
- cr->mpb->fbuf_alloc = 0;
- cr->mpb->dbuf_alloc = 0;
-#endif
-#endif
-
- return cr;
-}
-
-t_commrec *init_par_threads(const t_commrec *cro)
-{
-#ifdef GMX_THREAD_MPI
- int initialized;
- t_commrec *cr;
-
- /* make a thread-specific commrec */
- snew(cr, 1);
- /* now copy the whole thing, so settings like the number of PME nodes
- get propagated. */
- *cr = *cro;
-
- /* and we start setting our own thread-specific values for things */
- MPI_Initialized(&initialized);
- if (!initialized)
- {
- gmx_comm("Initializing threads without comm");
- }
- /* once threads will be used together with MPI, we'll
- fill the cr structure with distinct data here. This might even work: */
- cr->sim_nodeid = gmx_setup(0, NULL, &cr->nnodes);
-
- cr->mpi_comm_mysim = MPI_COMM_WORLD;
- cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
- cr->nodeid = cr->sim_nodeid;
- cr->duty = (DUTY_PP | DUTY_PME);
-
- return cr;
-#else
- return NULL;
-#endif
-}