/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
*
- *
+ *
* 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.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* 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.
- *
+ *
* 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.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* GROningen Mixture of Alchemy and Childrens' Stories
*/
#include "thread_mpi.h"
#endif
-/* The source code in this file should be thread-safe.
+/* The source code in this file should be thread-safe.
Please keep it that way. */
/* Portable version of ctime_r implemented in src/gmxlib/string2.c, but we do not want it declared in public installed headers */
char *
-gmx_ctime_r(const time_t *clock,char *buf, int n);
+gmx_ctime_r(const time_t *clock, char *buf, int n);
-#define BUFSIZE 1024
+#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)
+static void par_fn(char *base, int ftp, const t_commrec *cr,
+ gmx_bool bAppendSimId, gmx_bool bAppendNodeId,
+ char buf[], int bufsize)
{
- int n;
-
- if((size_t)bufsize<(strlen(base)+10))
- gmx_mem("Character buffer too small!");
-
- /* Copy to buf, and strip extension */
- strcpy(buf,base);
- buf[strlen(base) - strlen(ftp2ext(fn2ftp(base))) - 1] = '\0';
-
- if (bAppendSimId) {
- sprintf(buf+strlen(buf),"%d",cr->ms->sim);
- }
- if (bAppendNodeId) {
- strcat(buf,"_node");
- sprintf(buf+strlen(buf),"%d",cr->nodeid);
- }
- strcat(buf,".");
-
- /* Add extension again */
- strcat(buf,(ftp == efTPX) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
- if (debug)
- {
- fprintf(debug, "node %d par_fn '%s'\n",cr->nodeid,buf);
- if (fn2ftp(buf) == efLOG)
- {
- fprintf(debug,"log\n");
- }
- }
+ int n;
+
+ if ((size_t)bufsize < (strlen(base)+10))
+ {
+ gmx_mem("Character buffer too small!");
+ }
+
+ /* Copy to buf, and strip extension */
+ strcpy(buf, base);
+ buf[strlen(base) - strlen(ftp2ext(fn2ftp(base))) - 1] = '\0';
+
+ if (bAppendSimId)
+ {
+ sprintf(buf+strlen(buf), "%d", cr->ms->sim);
+ }
+ if (bAppendNodeId)
+ {
+ strcat(buf, "_node");
+ sprintf(buf+strlen(buf), "%d", cr->nodeid);
+ }
+ strcat(buf, ".");
+
+ /* Add extension again */
+ strcat(buf, (ftp == efTPX) ? "tpr" : (ftp == efEDR) ? "edr" : ftp2ext(ftp));
+ if (debug)
+ {
+ fprintf(debug, "node %d par_fn '%s'\n", cr->nodeid, buf);
+ if (fn2ftp(buf) == efLOG)
+ {
+ fprintf(debug, "log\n");
+ }
+ }
}
-void check_multi_int(FILE *log,const gmx_multisim_t *ms,int val,
+void check_multi_int(FILE *log, const gmx_multisim_t *ms, int val,
const char *name,
gmx_bool bQuiet)
{
- int *ibuf,p;
- gmx_bool bCompatible;
-
- if (NULL != log && !bQuiet)
- fprintf(log,"Multi-checking %s ... ",name);
-
- if (ms == NULL)
- gmx_fatal(FARGS,
- "check_multi_int called with a NULL communication pointer");
-
- snew(ibuf,ms->nsim);
- ibuf[ms->sim] = val;
- gmx_sumi_sim(ms->nsim,ibuf,ms);
-
- bCompatible = TRUE;
- for(p=1; p<ms->nsim; p++)
- bCompatible = bCompatible && (ibuf[p-1] == ibuf[p]);
-
- if (bCompatible)
- {
- if (NULL != log && !bQuiet)
- fprintf(log,"OK\n");
- }
- else
- {
- if (NULL != log)
- {
- fprintf(log,"\n%s is not equal for all subsystems\n",name);
- for(p=0; p<ms->nsim; p++)
- fprintf(log," subsystem %d: %d\n",p,ibuf[p]);
- }
- gmx_fatal(FARGS,"The %d subsystems are not compatible\n",ms->nsim);
- }
-
- sfree(ibuf);
+ int *ibuf, p;
+ gmx_bool bCompatible;
+
+ if (NULL != log && !bQuiet)
+ {
+ fprintf(log, "Multi-checking %s ... ", name);
+ }
+
+ if (ms == NULL)
+ {
+ gmx_fatal(FARGS,
+ "check_multi_int called with a NULL communication pointer");
+ }
+
+ snew(ibuf, ms->nsim);
+ ibuf[ms->sim] = val;
+ gmx_sumi_sim(ms->nsim, ibuf, ms);
+
+ bCompatible = TRUE;
+ for (p = 1; p < ms->nsim; p++)
+ {
+ bCompatible = bCompatible && (ibuf[p-1] == ibuf[p]);
+ }
+
+ if (bCompatible)
+ {
+ if (NULL != log && !bQuiet)
+ {
+ fprintf(log, "OK\n");
+ }
+ }
+ else
+ {
+ if (NULL != log)
+ {
+ fprintf(log, "\n%s is not equal for all subsystems\n", name);
+ for (p = 0; p < ms->nsim; p++)
+ {
+ fprintf(log, " subsystem %d: %d\n", p, ibuf[p]);
+ }
+ }
+ gmx_fatal(FARGS, "The %d subsystems are not compatible\n", ms->nsim);
+ }
+
+ sfree(ibuf);
}
-void check_multi_large_int(FILE *log,const gmx_multisim_t *ms,
+void check_multi_large_int(FILE *log, const gmx_multisim_t *ms,
gmx_large_int_t val, const char *name,
gmx_bool bQuiet)
{
- gmx_large_int_t *ibuf;
- int p;
- gmx_bool bCompatible;
-
- if (NULL != log && !bQuiet)
- fprintf(log,"Multi-checking %s ... ",name);
-
- if (ms == NULL)
- gmx_fatal(FARGS,
- "check_multi_int called with a NULL communication pointer");
-
- snew(ibuf,ms->nsim);
- ibuf[ms->sim] = val;
- gmx_sumli_sim(ms->nsim,ibuf,ms);
-
- bCompatible = TRUE;
- for(p=1; p<ms->nsim; p++)
- bCompatible = bCompatible && (ibuf[p-1] == ibuf[p]);
-
- if (bCompatible)
- {
- if (NULL != log && !bQuiet)
- fprintf(log,"OK\n");
- }
- else
- {
- if (NULL != log)
- {
- fprintf(log,"\n%s is not equal for all subsystems\n",name);
- for(p=0; p<ms->nsim; p++)
- {
- char strbuf[255];
- /* first make the format string */
- snprintf(strbuf, 255, " subsystem %%d: %s\n",
- gmx_large_int_pfmt);
- fprintf(log,strbuf,p,ibuf[p]);
- }
- }
- gmx_fatal(FARGS,"The %d subsystems are not compatible\n",ms->nsim);
- }
-
- sfree(ibuf);
+ gmx_large_int_t *ibuf;
+ int p;
+ gmx_bool bCompatible;
+
+ if (NULL != log && !bQuiet)
+ {
+ fprintf(log, "Multi-checking %s ... ", name);
+ }
+
+ if (ms == NULL)
+ {
+ gmx_fatal(FARGS,
+ "check_multi_int called with a NULL communication pointer");
+ }
+
+ snew(ibuf, ms->nsim);
+ ibuf[ms->sim] = val;
+ gmx_sumli_sim(ms->nsim, ibuf, ms);
+
+ bCompatible = TRUE;
+ for (p = 1; p < ms->nsim; p++)
+ {
+ bCompatible = bCompatible && (ibuf[p-1] == ibuf[p]);
+ }
+
+ if (bCompatible)
+ {
+ if (NULL != log && !bQuiet)
+ {
+ fprintf(log, "OK\n");
+ }
+ }
+ else
+ {
+ if (NULL != log)
+ {
+ fprintf(log, "\n%s is not equal for all subsystems\n", name);
+ for (p = 0; p < ms->nsim; p++)
+ {
+ char strbuf[255];
+ /* first make the format string */
+ snprintf(strbuf, 255, " subsystem %%d: %s\n",
+ gmx_large_int_pfmt);
+ fprintf(log, strbuf, p, ibuf[p]);
+ }
+ }
+ gmx_fatal(FARGS, "The %d subsystems are not compatible\n", ms->nsim);
+ }
+
+ sfree(ibuf);
}
#ifdef HAVE_UNISTD_H
if (gethostname(name, len-1) != 0)
{
- strncpy(name, "unknown",8);
+ strncpy(name, "unknown", 8);
}
#else
- strncpy(name, "unknown",8);
+ 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 bMasterOnly,
gmx_bool bAppendFiles, FILE** fplog)
{
- int len,testlen,pid;
- char buf[256],host[256];
+ int len, testlen, pid;
+ char buf[256], host[256];
time_t t;
- char timebuf[STRLEN];
- FILE *fp=*fplog;
- char *tmpnm;
-
+ char timebuf[STRLEN];
+ FILE *fp = *fplog;
+ char *tmpnm;
+
debug_gmx();
-
+
/* Communicate the filename for logfile */
if (cr->nnodes > 1 && !bMasterOnly
#ifdef GMX_THREAD_MPI
{
len = strlen(lognm) + 1;
}
- gmx_bcast(sizeof(len),&len,cr);
+ gmx_bcast(sizeof(len), &len, cr);
if (!MASTER(cr))
{
- snew(tmpnm,len+8);
+ snew(tmpnm, len+8);
}
else
{
- tmpnm=gmx_strdup(lognm);
+ tmpnm = gmx_strdup(lognm);
}
- gmx_bcast(len*sizeof(*tmpnm),tmpnm,cr);
+ gmx_bcast(len*sizeof(*tmpnm), tmpnm, cr);
}
else
{
- tmpnm=gmx_strdup(lognm);
+ 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);
+ par_fn(tmpnm, efLOG, cr, FALSE, !bMasterOnly, buf, 255);
fp = gmx_fio_fopen(buf, bAppendFiles ? "a+" : "w+" );
}
else if (!bAppendFiles)
sfree(tmpnm);
gmx_fatal_set_log_file(fp);
-
+
/* Get some machine parameters */
- gmx_gethostname(host,256);
+ gmx_gethostname(host, 256);
time(&t);
pid = getpid();
# endif
#else
- pid = 0;
+ pid = 0;
#endif
if (bAppendFiles)
"-----------------------------------------------------------\n"
"Restarting from checkpoint, appending to previous log file.\n"
"\n"
- );
+ );
}
-
- gmx_ctime_r(&t,timebuf,STRLEN);
+
+ gmx_ctime_r(&t, timebuf, STRLEN);
fprintf(fp,
"Log file opened on %s"
"Host: %s pid: %d nodeid: %d nnodes: %d\n",
- timebuf,host,pid,cr->nodeid,cr->nnodes);
+ timebuf, host, pid, cr->nodeid, cr->nnodes);
gmx_print_version_info(fp);
fprintf(fp, "\n\n");
void gmx_log_close(FILE *fp)
{
- if (fp) {
- gmx_fatal_set_log_file(NULL);
- gmx_fio_fclose(fp);
- }
+ if (fp)
+ {
+ gmx_fatal_set_log_file(NULL);
+ gmx_fio_fclose(fp);
+ }
}
-static void comm_args(const t_commrec *cr,int *argc,char ***argv)
+static void comm_args(const t_commrec *cr, int *argc, char ***argv)
{
- int i,len;
-
- if (PAR(cr))
- gmx_bcast(sizeof(*argc),argc,cr);
-
- if (!MASTER(cr))
- snew(*argv,*argc+1);
- if (debug)
- {
- fprintf(debug,"NODEID=%d argc=%d\n",cr->nodeid,*argc);
- }
- for(i=0; (i<*argc); i++) {
- if (MASTER(cr))
- len = strlen((*argv)[i])+1;
- gmx_bcast(sizeof(len),&len,cr);
+ int i, len;
+
+ if (PAR(cr))
+ {
+ gmx_bcast(sizeof(*argc), argc, cr);
+ }
+
if (!MASTER(cr))
- snew((*argv)[i],len);
- /*gmx_bcast(len*sizeof((*argv)[i][0]),(*argv)[i],cr);*/
- gmx_bcast(len*sizeof(char),(*argv)[i],cr);
- }
- debug_gmx();
+ {
+ snew(*argv, *argc+1);
+ }
+ if (debug)
+ {
+ fprintf(debug, "NODEID=%d argc=%d\n", cr->nodeid, *argc);
+ }
+ for (i = 0; (i < *argc); i++)
+ {
+ if (MASTER(cr))
+ {
+ len = strlen((*argv)[i])+1;
+ }
+ gmx_bcast(sizeof(len), &len, cr);
+ if (!MASTER(cr))
+ {
+ snew((*argv)[i], len);
+ }
+ /*gmx_bcast(len*sizeof((*argv)[i][0]),(*argv)[i],cr);*/
+ gmx_bcast(len*sizeof(char), (*argv)[i], cr);
+ }
+ debug_gmx();
}
-void init_multisystem(t_commrec *cr,int nsim, char **multidirs,
- int nfile, const t_filenm fnm[],gmx_bool bParFn)
+void init_multisystem(t_commrec *cr, int nsim, char **multidirs,
+ int nfile, const t_filenm fnm[], gmx_bool bParFn)
{
gmx_multisim_t *ms;
- int nnodes,nnodpersim,sim,i,ftp;
- char buf[256];
+ int nnodes, nnodpersim, sim, i, ftp;
+ char buf[256];
#ifdef GMX_MPI
- MPI_Group mpi_group_world;
-#endif
- int *rank;
+ MPI_Group mpi_group_world;
+#endif
+ int *rank;
#ifndef GMX_MPI
if (nsim > 1)
{
- gmx_fatal(FARGS,"This binary is compiled without MPI support, can not do multiple simulations.");
+ gmx_fatal(FARGS, "This binary is compiled without MPI support, can not do multiple simulations.");
}
#endif
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 nodes (%d) is not a multiple of the number of simulations (%d)", nnodes, nsim);
}
nnodpersim = nnodes/nsim;
- sim = cr->nodeid/nnodpersim;
+ sim = cr->nodeid/nnodpersim;
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 nodes per simulation, local simulation is %d\n", nsim, nnodpersim, sim);
}
- snew(ms,1);
- cr->ms = ms;
+ snew(ms, 1);
+ cr->ms = ms;
ms->nsim = nsim;
ms->sim = sim;
#ifdef GMX_MPI
/* Create a communicator for the master nodes */
- snew(rank,ms->nsim);
- for(i=0; i<ms->nsim; i++)
+ snew(rank, ms->nsim);
+ for (i = 0; i < ms->nsim; i++)
{
rank[i] = i*nnodpersim;
}
- MPI_Comm_group(MPI_COMM_WORLD,&mpi_group_world);
- MPI_Group_incl(mpi_group_world,nsim,rank,&ms->mpi_group_masters);
+ MPI_Comm_group(MPI_COMM_WORLD, &mpi_group_world);
+ MPI_Group_incl(mpi_group_world, nsim, rank, &ms->mpi_group_masters);
sfree(rank);
- MPI_Comm_create(MPI_COMM_WORLD,ms->mpi_group_masters,
+ MPI_Comm_create(MPI_COMM_WORLD, ms->mpi_group_masters,
&ms->mpi_comm_masters);
#if !defined(GMX_THREAD_MPI) && !defined(MPI_IN_PLACE_EXISTS)
/* initialize the MPI_IN_PLACE replacement buffers */
snew(ms->mpb, 1);
- ms->mpb->ibuf=NULL;
- ms->mpb->libuf=NULL;
- ms->mpb->fbuf=NULL;
- ms->mpb->dbuf=NULL;
- ms->mpb->ibuf_alloc=0;
- ms->mpb->libuf_alloc=0;
- ms->mpb->fbuf_alloc=0;
- ms->mpb->dbuf_alloc=0;
+ ms->mpb->ibuf = NULL;
+ ms->mpb->libuf = NULL;
+ ms->mpb->fbuf = NULL;
+ ms->mpb->dbuf = NULL;
+ ms->mpb->ibuf_alloc = 0;
+ ms->mpb->libuf_alloc = 0;
+ ms->mpb->fbuf_alloc = 0;
+ ms->mpb->dbuf_alloc = 0;
#endif
#endif
/* Reduce the intra-simulation communication */
cr->sim_nodeid = cr->nodeid % nnodpersim;
- cr->nnodes = nnodpersim;
+ cr->nnodes = nnodpersim;
#ifdef GMX_MPI
- MPI_Comm_split(MPI_COMM_WORLD,sim,cr->sim_nodeid,&cr->mpi_comm_mysim);
+ MPI_Comm_split(MPI_COMM_WORLD, sim, cr->sim_nodeid, &cr->mpi_comm_mysim);
cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
- cr->nodeid = cr->sim_nodeid;
+ cr->nodeid = cr->sim_nodeid;
#endif
if (debug)
{
- fprintf(debug,"This is simulation %d",cr->ms->sim);
+ fprintf(debug, "This is simulation %d", cr->ms->sim);
if (PAR(cr))
{
- fprintf(debug,", local number of nodes %d, local nodeid %d",
- cr->nnodes,cr->sim_nodeid);
+ fprintf(debug, ", local number of nodes %d, local nodeid %d",
+ cr->nnodes, cr->sim_nodeid);
}
- fprintf(debug,"\n\n");
+ fprintf(debug, "\n\n");
}
if (multidirs)
int ret;
if (debug)
{
- fprintf(debug,"Changing to directory %s\n",multidirs[cr->ms->sim]);
+ fprintf(debug, "Changing to directory %s\n", multidirs[cr->ms->sim]);
}
gmx_chdir(multidirs[cr->ms->sim]);
}
else if (bParFn)
{
/* Patch output and tpx, cpt and rerun input file names */
- for(i=0; (i<nfile); i++)
+ for (i = 0; (i < nfile); i++)
{
- /* Because of possible multiple extensions per type we must look
- * at the actual file name
+ /* Because of possible multiple extensions per type we must look
+ * at the actual file name
*/
if (is_output(&fnm[i]) ||
fnm[i].ftp == efTPX || fnm[i].ftp == efCPT ||
- strcmp(fnm[i].opt,"-rerun") == 0)
+ strcmp(fnm[i].opt, "-rerun") == 0)
{
ftp = fn2ftp(fnm[i].fns[0]);
- par_fn(fnm[i].fns[0],ftp,cr,TRUE,FALSE,buf,255);
+ par_fn(fnm[i].fns[0], ftp, cr, TRUE, FALSE, buf, 255);
sfree(fnm[i].fns[0]);
fnm[i].fns[0] = gmx_strdup(buf);
}
}
}
-t_commrec *init_par(int *argc,char ***argv_ptr)
+t_commrec *init_par(int *argc, char ***argv_ptr)
{
- t_commrec *cr;
- char **argv;
- int i;
- gmx_bool pe=FALSE;
+ t_commrec *cr;
+ char **argv;
+ int i;
+ gmx_bool pe = FALSE;
- snew(cr,1);
+ snew(cr, 1);
argv = argv_ptr ? *argv_ptr : NULL;
#if defined GMX_MPI && !defined GMX_THREAD_MPI
- cr->sim_nodeid = gmx_setup(argc,argv,&cr->nnodes);
+ cr->sim_nodeid = gmx_setup(argc, argv, &cr->nnodes);
if (!PAR(cr) && (cr->sim_nodeid != 0))
{
#ifndef GMX_THREAD_MPI
if (PAR(cr))
{
- comm_args(cr,argc,argv_ptr);
+ comm_args(cr, argc, argv_ptr);
}
#endif /* GMX_THREAD_MPI */
#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;
+ /* 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
t_commrec *init_par_threads(const t_commrec *cro)
{
#ifdef GMX_THREAD_MPI
- int initialized;
+ int initialized;
t_commrec *cr;
/* make a thread-specific commrec */
- snew(cr,1);
+ snew(cr, 1);
/* now copy the whole thing, so settings like the number of PME nodes
get propagated. */
- *cr=*cro;
+ *cr = *cro;
/* and we start setting our own thread-specific values for things */
MPI_Initialized(&initialized);
}
/* 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->sim_nodeid = gmx_setup(0, NULL, &cr->nnodes);
- cr->mpi_comm_mysim = MPI_COMM_WORLD;
+ 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);
+ cr->nodeid = cr->sim_nodeid;
+ cr->duty = (DUTY_PP | DUTY_PME);
return cr;
#else
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff