#include <config.h>
#endif
+#ifdef __linux
+#define _GNU_SOURCE
+#include <sched.h>
+#include <sys/syscall.h>
+#endif
#include <signal.h>
#include <stdlib.h>
+
#include "typedefs.h"
#include "smalloc.h"
#include "sysstuff.h"
#include "disre.h"
#include "orires.h"
#include "dihre.h"
-#include "pppm.h"
#include "pme.h"
#include "mdatoms.h"
#include "qmmm.h"
#ifdef GMX_LIB_MPI
#include <mpi.h>
#endif
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
#include "tmpi.h"
#endif
+#ifdef GMX_OPENMP
+#include <omp.h>
+#endif
+
/* afm stuf */
#include "pull.h"
return fver;
}
-void set_inbox(int natom, rvec *x)
-{
- rvec tmp;
- int i;
-
- tmp[XX]=tmp[YY]=tmp[ZZ]=0.0;
- for(i=0;i<natom;i++)
- {
- if(x[i][XX]<tmp[XX]) tmp[XX]=x[i][XX];
- if(x[i][YY]<tmp[YY]) tmp[YY]=x[i][YY];
- if(x[i][ZZ]<tmp[ZZ]) tmp[ZZ]=x[i][ZZ];
- }
-
- for(i=0;i<natom;i++)
- rvec_inc(x[i],tmp);
-}
-
int get_mtype_list(t_block *at, gmx_mtop_t *mtop, t_block *tlist)
{
int i,j,nr,mol_id;
return area;
}
-void init_lip(matrix box, gmx_mtop_t *mtop, lip_t *lip)
-{
- int i;
- real mem_area;
- int mol1=0;
-
- mem_area = box[XX][XX]*box[YY][YY]-box[XX][YY]*box[YY][XX];
- for(i=0;i<mtop->nmolblock;i++)
- {
- if(mtop->molblock[i].type == lip->id)
- {
- lip->nr=mtop->molblock[i].nmol;
- lip->natoms=mtop->molblock[i].natoms_mol;
- }
- }
- lip->area=2.0*mem_area/(double)lip->nr;
-
- for (i=0;i<lip->id;i++)
- mol1+=mtop->molblock[i].nmol;
- lip->mol1=mol1;
-}
-
int init_mem_at(mem_t *mem_p, gmx_mtop_t *mtop, rvec *r, matrix box, pos_ins_t *pos_ins)
{
int i,j,at,mol,nmol,nmolbox,count;
}
}
- fclose(fpout);
+ ffclose(fpout);
+ ffclose(fpin);
/* use ffopen to generate backup of topinout */
fpout=ffopen(topfile,"w");
- fclose(fpout);
+ ffclose(fpout);
rename(TEMP_FILENM,topfile);
#undef TEMP_FILENM
}
/* if (DEFORM(*ir))
{
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
tMPI_Thread_mutex_lock(&deform_init_box_mutex);
#endif
set_deform_reference_box(upd,
deform_init_init_step_tpx,
deform_init_box_tpx);
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
#endif
}*/
/* Check whether everything is still allright */
if (((int)gmx_get_stop_condition() > handled_stop_condition)
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
&& MASTER(cr)
#endif
)
gmx_edsam_t ed=NULL;
t_commrec *cr_old=cr;
int nthreads=1,nthreads_requested=1;
-
+ int omp_nthreads = 1;
char *ins;
int rm_bonded_at,fr_id,fr_i=0,tmp_id,warn=0;
read_tpx_state(ftp2fn(efTPX,nfile,fnm),inputrec,state,NULL,mtop);
/* NOW the threads will be started: */
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
#endif
}
/* END OF CAUTION: cr is now reliable */
gmx_setup_nodecomm(fplog,cr);
}
- wcycle = wallcycle_init(fplog,resetstep,cr);
+ /* get number of OpenMP/PME threads
+ * env variable should be read only on one node to make sure it is identical everywhere */
+#ifdef GMX_OPENMP
+ if (EEL_PME(inputrec->coulombtype))
+ {
+ if (MASTER(cr))
+ {
+ char *ptr;
+ omp_nthreads = omp_get_max_threads();
+ if ((ptr=getenv("GMX_PME_NTHREADS")) != NULL)
+ {
+ sscanf(ptr,"%d",&omp_nthreads);
+ }
+ if (fplog!=NULL)
+ {
+ fprintf(fplog,"Using %d threads for PME\n",omp_nthreads);
+ }
+ }
+ if (PAR(cr))
+ {
+ gmx_bcast_sim(sizeof(omp_nthreads),&omp_nthreads,cr);
+ }
+ }
+#endif
+
+ wcycle = wallcycle_init(fplog,resetstep,cr, omp_nthreads);
if (PAR(cr))
{
/* Master synchronizes its value of reset_counters with all nodes
fr = mk_forcerec();
init_forcerec(fplog,oenv,fr,fcd,inputrec,mtop,cr,box,FALSE,
opt2fn("-table",nfile,fnm),
+ opt2fn("-tabletf",nfile,fnm),
opt2fn("-tablep",nfile,fnm),
opt2fn("-tableb",nfile,fnm),FALSE,pforce);
/* version for PCA_NOT_READ_NODE (see md.c) */
/*init_forcerec(fplog,fr,fcd,inputrec,mtop,cr,box,FALSE,
- "nofile","nofile","nofile",FALSE,pforce);
+ "nofile","nofile","nofile","nofile",FALSE,pforce);
*/
fr->bSepDVDL = ((Flags & MD_SEPPOT) == MD_SEPPOT);
}
}
- /* Initiate PPPM if necessary */
- if (fr->eeltype == eelPPPM)
- {
- if (mdatoms->nChargePerturbed)
- {
- gmx_fatal(FARGS,"Free energy with %s is not implemented",
- eel_names[fr->eeltype]);
- }
- status = gmx_pppm_init(fplog,cr,oenv,FALSE,TRUE,box,
- getenv("GMXGHAT"),inputrec, (Flags & MD_REPRODUCIBLE));
- if (status != 0)
- {
- gmx_fatal(FARGS,"Error %d initializing PPPM",status);
- }
- }
-
if (EEL_PME(fr->eeltype))
{
ewaldcoeff = fr->ewaldcoeff;
/* The PME only nodes need to know nChargePerturbed */
gmx_bcast_sim(sizeof(nChargePerturbed),&nChargePerturbed,cr);
}
+
+
+ /*set CPU affinity*/
+#ifdef GMX_OPENMP
+#ifdef __linux
+#ifdef GMX_LIB_MPI
+ {
+ int core;
+ MPI_Comm comm_intra; /*intra communicator (but different to nc.comm_intra includes PME nodes)*/
+ MPI_Comm_split(MPI_COMM_WORLD,gmx_hostname_num(),gmx_node_rank(),&comm_intra);
+ int local_omp_nthreads = (cr->duty & DUTY_PME) ? omp_nthreads : 1; /*threads on this node*/
+ MPI_Scan(&local_omp_nthreads,&core, 1, MPI_INT, MPI_SUM, comm_intra);
+ core-=local_omp_nthreads; /*make exclusive scan*/
+ #pragma omp parallel firstprivate(core) num_threads(local_omp_nthreads)
+ {
+ cpu_set_t mask;
+ CPU_ZERO(&mask);
+ core+=omp_get_thread_num();
+ CPU_SET(core,&mask);
+ sched_setaffinity((pid_t) syscall (SYS_gettid),sizeof(cpu_set_t),&mask);
+ }
+ }
+#endif /*GMX_MPI*/
+#endif /*__linux*/
+#endif /*GMX_OPENMP*/
+
if (cr->duty & DUTY_PME)
{
status = gmx_pme_init(pmedata,cr,npme_major,npme_minor,inputrec,
mtop ? mtop->natoms : 0,nChargePerturbed,
- (Flags & MD_REPRODUCIBLE));
+ (Flags & MD_REPRODUCIBLE),omp_nthreads);
if (status != 0)
{
gmx_fatal(FARGS,"Error %d initializing PME",status);
dd_node_order = nenum(ddno_opt);
cr->npmenodes = npme;
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
/* now determine the number of threads automatically. The threads are
only started at mdrunner_threads, though. */
if (nthreads<1)
gmx_fatal(FARGS,"Need at least two replicas for replica exchange (option -multi)");
if (nmultisim > 1) {
-#ifndef GMX_THREADS
+#ifndef GMX_THREAD_MPI
gmx_bool bParFn = (multidir == NULL);
init_multisystem(cr,nmultisim,multidir,NFILE,fnm,TRUE);
#else
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff