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];
#ifdef GMX_MPI
MPI_Group mpi_group_world;
int *rank;
#endif
#ifndef GMX_MPI
if (nsim > 1)
{
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 ranks (%d) is not a multiple of the number of simulations (%d)", nnodes, nsim);
}
nnodpersim = nnodes/nsim;
sim = cr->nodeid/nnodpersim;
if (debug)
{
fprintf(debug, "We have %d simulations, %d ranks per simulation, local simulation is %d\n", nsim, nnodpersim, sim);
}
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++)
{
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);
sfree(rank);
MPI_Comm_create(MPI_COMM_WORLD, ms->mpi_group_masters,
&ms->mpi_comm_masters);
#if !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;
#endif
#endif
/* Reduce the intra-simulation communication */
cr->sim_nodeid = cr->nodeid % nnodpersim;
cr->nnodes = nnodpersim;
#ifdef GMX_MPI
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;
#endif
if (debug)
{
fprintf(debug, "This is simulation %d", cr->ms->sim);
if (PAR(cr))
{
fprintf(debug, ", local number of ranks %d, local rank ID %d",
cr->nnodes, cr->sim_nodeid);
}
fprintf(debug, "\n\n");
}
if (multidirs)
{
if (debug)
{
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++)
{
/* 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)
{
ftp = fn2ftp(fnm[i].fns[0]);
par_fn(fnm[i].fns[0], ftp, cr, TRUE, FALSE, buf, 255);
sfree(fnm[i].fns[0]);
fnm[i].fns[0] = gmx_strdup(buf);
}
}
}
}
void init_multisystem(t_commrec *cr,int nsim,
int nfile,t_filenm fnm[],bool bParFn)
{
gmx_multisim_t *ms;
int nnodes,nnodpersim,sim,i,ftp;
char buf[256];
#ifdef GMX_MPI
MPI_Group mpi_group_world;
#endif
int *rank;
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);
nnodpersim = nnodes/nsim;
sim = cr->nodeid/nnodpersim;
if (debug)
fprintf(debug,"We have %d simulations, %d nodes per simulation, local simulation is %d\n",nsim,nnodpersim,sim);
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++)
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);
sfree(rank);
MPI_Comm_create(MPI_COMM_WORLD,ms->mpi_group_masters,
&ms->mpi_comm_masters);
#endif
/* Reduce the intra-simulation communication */
cr->sim_nodeid = cr->nodeid % nnodpersim;
cr->nnodes = nnodpersim;
#ifdef GMX_MPI
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;
#endif
if (debug) {
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,"\n\n");
}
if (bParFn) {
/* Patch output and tpx file names (except log which has been done already)
*/
for(i=0; (i<nfile); i++) {
/* 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) {
ftp = fn2ftp(fnm[i].fns[0]);
par_fn(fnm[i].fns[0],ftp,cr,FALSE,buf,255);
sfree(fnm[i].fns[0]);
fnm[i].fns[0] = strdup(buf);
}
}
}
}
void gmx_log_open(const char *lognm, const t_commrec *cr, gmx_bool bMasterOnly,
gmx_bool bAppendFiles, FILE** fplog)
{
int len, pid;
char buf[256], 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)
{
fp = gmx_fio_fopen(tmpnm, bAppendFiles ? "a+" : "w+" );
}
sfree(tmpnm);
gmx_fatal_set_log_file(fp);
/* Get some machine parameters */
gmx_gethostname(host, 256);
time(&t);
#ifndef NO_GETPID
# ifdef GMX_NATIVE_WINDOWS
pid = _getpid();
# else
pid = getpid();
# endif
#else
pid = 0;
#endif
if (bAppendFiles)
{
fprintf(fp,
"\n"
"\n"
"-----------------------------------------------------------\n"
"Restarting from checkpoint, appending to previous log file.\n"
"\n"
);
}
gmx_ctime_r(&t, timebuf, STRLEN);
fprintf(fp,
"Log file opened on %s"
"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::getProgramContext(), settings);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
fprintf(fp, "\n\n");
fflush(fp);
debug_gmx();
*fplog = fp;
}
FILE *gmx_log_open(char *lognm,const t_commrec *cr,bool bMasterOnly, unsigned long Flags)
{
int len,testlen,pid;
char buf[256],host[256];
time_t t;
FILE *fp;
bool bAppend = Flags & MD_APPENDFILES;
debug_gmx();
/* Communicate the filename for logfile */
if (cr->nnodes > 1 && !bMasterOnly) {
if (MASTER(cr))
len = strlen(lognm)+1;
gmx_bcast(sizeof(len),&len,cr);
if (!MASTER(cr))
snew(lognm,len+8);
gmx_bcast(len*sizeof(*lognm),lognm,cr);
}
debug_gmx();
if (PAR(cr) && !bMasterOnly) {
/* Since log always ends with '.log' let's use this info */
par_fn(lognm,efLOG,cr,cr->ms!=NULL,buf,255);
fp = gmx_fio_fopen(buf, bAppend ? "a" : "w" );
} else {
fp = gmx_fio_fopen(lognm, bAppend ? "a" : "w" );
}
gmx_fatal_set_log_file(fp);
/* Get some machine parameters */
#ifdef HAVE_UNISTD_H
if( gethostname(host,255) != 0)
sprintf(host,"unknown");
#else
sprintf(host,"unknown");
#endif
time(&t);
#ifndef NO_GETPID
# if ((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__)
pid = _getpid();
# else
pid = getpid();
# endif
#else
pid = 0;
#endif
if(bAppend)
{
fprintf(fp,
"\n\n"
"-----------------------------------------------------------\n"
"Restarting from checkpoint, appending to previous log file.\n\n"
);
}
fprintf(fp,
"Log file opened on %s"
"Host: %s pid: %d nodeid: %d nnodes: %d\n",
ctime(&t),host,pid,cr->nodeid,cr->nnodes);
#if (defined BUILD_MACHINE && defined BUILD_TIME && defined BUILD_USER)
fprintf(fp,
"The Gromacs distribution was built %s by\n"
"%s (%s)\n\n\n",BUILD_TIME,BUILD_USER,BUILD_MACHINE);
#endif
fflush(fp);
debug_gmx();
return fp;
}