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lammps/src/finish.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <string.h>
#include <stdio.h>
#include "finish.h"
#include "timer.h"
#include "universe.h"
#include "accelerator_kokkos.h"
#include "accelerator_omp.h"
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "update.h"
#include "min.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "output.h"
#include "memory.h"
#ifdef LMP_USER_OMP
#include "modify.h"
#include "fix_omp.h"
#include "thr_data.h"
#endif
using namespace LAMMPS_NS;
// local function prototypes, code at end of file
static void mpi_timings(const char *label, Timer *t, enum Timer::ttype tt,
MPI_Comm world, const int nprocs, const int nthreads,
const int me, double time_loop, FILE *scr, FILE *log);
#ifdef LMP_USER_OMP
static void omp_times(FixOMP *fix, const char *label, enum Timer::ttype which,
const int nthreads,FILE *scr, FILE *log);
#endif
/* ---------------------------------------------------------------------- */
Finish::Finish(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void Finish::end(int flag)
{
int i,m,nneigh,nneighfull;
int histo[10];
int minflag,prdflag,tadflag,timeflag,fftflag,histoflag,neighflag;
double time,tmp,ave,max,min;
double time_loop,time_other,cpu_loop;
int me,nprocs;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
const int nthreads = comm->nthreads;
// recompute natoms in case atoms have been lost
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
// choose flavors of statistical output
// flag determines caller
// flag = 0 = just loop summary
// flag = 1 = dynamics or minimization
// flag = 2 = PRD
// flag = 3 = TAD
// turn off neighflag for Kspace partition of verlet/split integrator
minflag = prdflag = tadflag = timeflag = fftflag = histoflag = neighflag = 0;
time_loop = cpu_loop = time_other = 0.0;
if (flag == 1) {
if (update->whichflag == 2) minflag = 1;
timeflag = histoflag = 1;
neighflag = 1;
if (update->whichflag == 1 &&
strncmp(update->integrate_style,"verlet/split",12) == 0 &&
universe->iworld == 1) neighflag = 0;
if (force->kspace && force->kspace_match("pppm",0)
&& force->kspace->fftbench) fftflag = 1;
}
if (flag == 2) prdflag = timeflag = histoflag = neighflag = 1;
if (flag == 3) tadflag = histoflag = neighflag = 1;
// loop stats
if (timer->has_loop()) {
// overall loop time
time_loop = timer->get_wall(Timer::TOTAL);
cpu_loop = timer->get_cpu(Timer::TOTAL);
MPI_Allreduce(&time_loop,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time_loop = tmp/nprocs;
MPI_Allreduce(&cpu_loop,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
cpu_loop = tmp/nprocs;
if (time_loop > 0.0) cpu_loop = cpu_loop/time_loop*100.0;
if (me == 0) {
int ntasks = nprocs * nthreads;
const char fmt1[] = "Loop time of %g on %d procs "
"for %d steps with " BIGINT_FORMAT " atoms\n\n";
if (screen) fprintf(screen,fmt1,time_loop,ntasks,update->nsteps,
atom->natoms);
if (logfile) fprintf(logfile,fmt1,time_loop,ntasks,update->nsteps,
atom->natoms);
// Gromacs/NAMD-style performance metric for suitable unit settings
if ( timeflag && !minflag && !prdflag && !tadflag &&
(update->nsteps > 0) && (update->dt != 0.0) &&
((strcmp(update->unit_style,"lj") == 0) ||
(strcmp(update->unit_style,"metal") == 0) ||
(strcmp(update->unit_style,"micro") == 0) ||
(strcmp(update->unit_style,"nano") == 0) ||
(strcmp(update->unit_style,"electron") == 0) ||
(strcmp(update->unit_style,"real") == 0)) ) {
double one_fs = force->femtosecond;
double t_step = ((double) time_loop) / ((double) update->nsteps);
double step_t = 1.0/t_step;
if (strcmp(update->unit_style,"lj") == 0) {
double tau_day = 24.0*3600.0 / t_step * update->dt / one_fs;
const char perf[] = "Performance: %.3f tau/day, %.3f timesteps/s\n";
if (screen) fprintf(screen,perf,tau_day,step_t);
if (logfile) fprintf(logfile,perf,tau_day,step_t);
} else {
double hrs_ns = t_step / update->dt * 1000000.0 * one_fs / 3600.0;
double ns_day = 24.0*3600.0 / t_step * update->dt / one_fs/1000000.0;
const char perf[] =
"Performance: %.3f ns/day, %.3f hours/ns, %.3f timesteps/s\n";
if (screen) fprintf(screen,perf,ns_day,hrs_ns,step_t);
if (logfile) fprintf(logfile,perf,ns_day,hrs_ns,step_t);
}
}
// CPU use on MPI tasks and OpenMP threads
#ifdef LMP_USER_OMP
const char fmt2[] =
"%.1f%% CPU use with %d MPI tasks x %d OpenMP threads\n";
if (screen) fprintf(screen,fmt2,cpu_loop,nprocs,nthreads);
if (logfile) fprintf(logfile,fmt2,cpu_loop,nprocs,nthreads);
#else
if (lmp->kokkos) {
const char fmt2[] =
"%.1f%% CPU use with %d MPI tasks x %d OpenMP threads\n";
if (screen) fprintf(screen,fmt2,cpu_loop,nprocs,lmp->kokkos->num_threads);
if (logfile) fprintf(logfile,fmt2,cpu_loop,nprocs,lmp->kokkos->num_threads);
} else {
const char fmt2[] =
"%.1f%% CPU use with %d MPI tasks x no OpenMP threads\n";
if (screen) fprintf(screen,fmt2,cpu_loop,nprocs);
if (logfile) fprintf(logfile,fmt2,cpu_loop,nprocs);
}
#endif
}
}
// avoid division by zero for very short runs
if (time_loop == 0.0) time_loop = 1.0;
if (cpu_loop == 0.0) cpu_loop = 100.0;
// get "Other" wall time for later use
if (timer->has_normal())
time_other = timer->get_wall(Timer::TOTAL) - timer->get_wall(Timer::ALL);
// minimization stats
if (minflag) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
if (me == 0) {
if (screen) {
fprintf(screen,"Minimization stats:\n");
fprintf(screen," Stopping criterion = %s\n",
update->minimize->stopstr);
fprintf(screen," Energy initial, next-to-last, final = \n"
" %18.12g %18.12g %18.12g\n",
update->minimize->einitial,update->minimize->eprevious,
update->minimize->efinal);
fprintf(screen," Force two-norm initial, final = %g %g\n",
update->minimize->fnorm2_init,update->minimize->fnorm2_final);
fprintf(screen," Force max component initial, final = %g %g\n",
update->minimize->fnorminf_init,
update->minimize->fnorminf_final);
fprintf(screen," Final line search alpha, max atom move = %g %g\n",
update->minimize->alpha_final,
update->minimize->alpha_final*
update->minimize->fnorminf_final);
fprintf(screen," Iterations, force evaluations = %d %d\n",
update->minimize->niter,update->minimize->neval);
}
if (logfile) {
fprintf(logfile,"Minimization stats:\n");
fprintf(logfile," Stopping criterion = %s\n",
update->minimize->stopstr);
fprintf(logfile," Energy initial, next-to-last, final = \n"
" %18.12g %18.12g %18.12g\n",
update->minimize->einitial,update->minimize->eprevious,
update->minimize->efinal);
fprintf(logfile," Force two-norm initial, final = %g %g\n",
update->minimize->fnorm2_init,update->minimize->fnorm2_final);
fprintf(logfile," Force max component initial, final = %g %g\n",
update->minimize->fnorminf_init,
update->minimize->fnorminf_final);
fprintf(logfile," Final line search alpha, max atom move = %g %g\n",
update->minimize->alpha_final,
update->minimize->alpha_final*
update->minimize->fnorminf_final);
fprintf(logfile," Iterations, force evaluations = %d %d\n",
update->minimize->niter,update->minimize->neval);
}
}
}
// PRD stats using PAIR,BOND,KSPACE for dephase,dynamics,quench
if (prdflag) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
if (screen) fprintf(screen,"PRD stats:\n");
if (logfile) fprintf(logfile,"PRD stats:\n");
time = timer->get_wall(Timer::DEPHASE);
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," Dephase time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Dephase time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = timer->get_wall(Timer::DYNAMICS);
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," Dynamics time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Dynamics time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = timer->get_wall(Timer::QUENCH);
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," Quench time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Quench time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = timer->get_wall(Timer::REPCOMM);
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," Comm time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Comm time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = timer->get_wall(Timer::REPOUT);
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," Output time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Output time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = time_other;
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) { // XXXX: replica comm, replica output
if (screen)
fprintf(screen," Other time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Other time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
}
// TAD stats using PAIR,BOND,KSPACE for neb,dynamics,quench
if (tadflag) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
if (screen) fprintf(screen,"TAD stats:\n");
if (logfile) fprintf(logfile,"TAD stats:\n");
time = timer->get_wall(Timer::NEB);
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," NEB time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," NEB time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = timer->get_wall(Timer::DYNAMICS);
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," Dynamics time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Dynamics time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = timer->get_wall(Timer::QUENCH);
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," Quench time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Quench time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = timer->get_wall(Timer::REPCOMM);
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," Comm time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Comm time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = timer->get_wall(Timer::REPOUT);
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," Output time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Output time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
time = time_other;
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen," Other time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile," Other time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
}
if (timeflag && timer->has_normal()) {
if (timer->has_full()) {
const char hdr[] = "\nMPI task timing breakdown:\n"
"Section | min time | avg time | max time |%varavg| %CPU | %total\n"
"-----------------------------------------------------------------------\n";
if (me == 0) {
if (screen) fputs(hdr,screen);
if (logfile) fputs(hdr,logfile);
}
} else {
const char hdr[] = "\nMPI task timing breakdown:\n"
"Section | min time | avg time | max time |%varavg| %total\n"
"---------------------------------------------------------------\n";
if (me == 0) {
if (screen) fputs(hdr,screen);
if (logfile) fputs(hdr,logfile);
}
}
mpi_timings("Pair",timer,Timer::PAIR, world,nprocs,
nthreads,me,time_loop,screen,logfile);
if (atom->molecular)
mpi_timings("Bond",timer,Timer::BOND,world,nprocs,
nthreads,me,time_loop,screen,logfile);
if (force->kspace)
mpi_timings("Kspace",timer,Timer::KSPACE,world,nprocs,
nthreads,me,time_loop,screen,logfile);
mpi_timings("Neigh",timer,Timer::NEIGH,world,nprocs,
nthreads,me,time_loop,screen,logfile);
mpi_timings("Comm",timer,Timer::COMM,world,nprocs,
nthreads,me,time_loop,screen,logfile);
mpi_timings("Output",timer,Timer::OUTPUT,world,nprocs,
nthreads,me,time_loop,screen,logfile);
mpi_timings("Modify",timer,Timer::MODIFY,world,nprocs,
nthreads,me,time_loop,screen,logfile);
if (timer->has_sync())
mpi_timings("Sync",timer,Timer::SYNC,world,nprocs,
nthreads,me,time_loop,screen,logfile);
time = time_other;
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
const char *fmt;
if (timer->has_full())
fmt = "Other | |%- 12.4g| | | |%6.2f\n";
else
fmt = "Other | |%- 12.4g| | |%6.2f\n";
if (me == 0) {
if (screen) fprintf(screen,fmt,time,time/time_loop*100.0);
if (logfile) fprintf(logfile,fmt,time,time/time_loop*100.0);
}
}
#ifdef LMP_USER_OMP
const char thr_hdr_fmt[] =
"\nThread timing breakdown (MPI rank %d):\nTotal threaded time %.4g / %.1f%%\n";
const char thr_header[] =
"Section | min time | avg time | max time |%varavg| %total\n"
"---------------------------------------------------------------\n";
int ifix = modify->find_fix("package_omp");
// print thread breakdown only with full timer detail
if ((ifix >= 0) && timer->has_full() && me == 0) {
double thr_total = 0.0;
ThrData *td;
FixOMP *fixomp = static_cast<FixOMP *>(lmp->modify->fix[ifix]);
for (i=0; i < nthreads; ++i) {
td = fixomp->get_thr(i);
thr_total += td->get_time(Timer::ALL);
}
thr_total /= (double) nthreads;
if (thr_total > 0.0) {
if (screen) {
fprintf(screen,thr_hdr_fmt,me,thr_total,thr_total/time_loop*100.0);
fputs(thr_header,screen);
}
if (logfile) {
fprintf(logfile,thr_hdr_fmt,me,thr_total,thr_total/time_loop*100.0);
fputs(thr_header,logfile);
}
omp_times(fixomp,"Pair",Timer::PAIR,nthreads,screen,logfile);
if (atom->molecular)
omp_times(fixomp,"Bond",Timer::BOND,nthreads,screen,logfile);
if (force->kspace)
omp_times(fixomp,"Kspace",Timer::KSPACE,nthreads,screen,logfile);
omp_times(fixomp,"Neigh",Timer::NEIGH,nthreads,screen,logfile);
omp_times(fixomp,"Reduce",Timer::COMM,nthreads,screen,logfile);
}
}
#endif
// FFT timing statistics
// time3d,time1d = total time during run for 3d and 1d FFTs
// loop on timing() until nsample FFTs require at least 1.0 CPU sec
// time_kspace may be 0.0 if another partition is doing Kspace
if (fftflag) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
int nsteps = update->nsteps;
double time3d;
int nsample = 1;
int nfft = force->kspace->timing_3d(nsample,time3d);
while (time3d < 1.0) {
nsample *= 2;
nfft = force->kspace->timing_3d(nsample,time3d);
}
time3d = nsteps * time3d / nsample;
MPI_Allreduce(&time3d,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time3d = tmp/nprocs;
double time1d;
nsample = 1;
nfft = force->kspace->timing_1d(nsample,time1d);
while (time1d < 1.0) {
nsample *= 2;
nfft = force->kspace->timing_1d(nsample,time1d);
}
time1d = nsteps * time1d / nsample;
MPI_Allreduce(&time1d,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time1d = tmp/nprocs;
double time_kspace = timer->get_wall(Timer::KSPACE);
MPI_Allreduce(&time_kspace,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time_kspace = tmp/nprocs;
double ntotal = 1.0 * force->kspace->nx_pppm *
force->kspace->ny_pppm * force->kspace->nz_pppm;
double nflops = 5.0 * ntotal * log(ntotal);
double fraction,flop3,flop1;
if (nsteps) {
if (time_kspace) fraction = time3d/time_kspace*100.0;
else fraction = 0.0;
flop3 = nfft*nflops/1.0e9/(time3d/nsteps);
flop1 = nfft*nflops/1.0e9/(time1d/nsteps);
} else fraction = flop3 = flop1 = 0.0;
if (me == 0) {
if (screen) {
fprintf(screen,"FFT time (%% of Kspce) = %g (%g)\n",time3d,fraction);
fprintf(screen,"FFT Gflps 3d (1d only) = %g %g\n",flop3,flop1);
}
if (logfile) {
fprintf(logfile,"FFT time (%% of Kspce) = %g (%g)\n",time3d,fraction);
fprintf(logfile,"FFT Gflps 3d (1d only) = %g %g\n",flop3,flop1);
}
}
}
if (histoflag) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
tmp = atom->nlocal;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
fprintf(screen,"Nlocal: %g ave %g max %g min\n",ave,max,min);
fprintf(screen,"Histogram:");
for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile,"Nlocal: %g ave %g max %g min\n",ave,max,min);
fprintf(logfile,"Histogram:");
for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
fprintf(logfile,"\n");
}
}
tmp = atom->nghost;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
fprintf(screen,"Nghost: %g ave %g max %g min\n",ave,max,min);
fprintf(screen,"Histogram:");
for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile,"Nghost: %g ave %g max %g min\n",ave,max,min);
fprintf(logfile,"Histogram:");
for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
fprintf(logfile,"\n");
}
}
// find a non-skip neighbor list containing half pairwise interactions
// count neighbors in that list for stats purposes
// allow it to be Kokkos neigh list as well
for (m = 0; m < neighbor->old_nrequest; m++) {
if ((neighbor->old_requests[m]->half ||
neighbor->old_requests[m]->gran ||
neighbor->old_requests[m]->respaouter ||
neighbor->old_requests[m]->half_from_full) &&
neighbor->old_requests[m]->skip == 0 &&
neighbor->lists[m] && neighbor->lists[m]->numneigh) {
if (!neighbor->lists[m] && lmp->kokkos &&
lmp->kokkos->neigh_list_kokkos(m)) break;
else break;
}
}
nneigh = 0;
if (m < neighbor->old_nrequest) {
if (neighbor->lists[m]) {
int inum = neighbor->lists[m]->inum;
int *ilist = neighbor->lists[m]->ilist;
int *numneigh = neighbor->lists[m]->numneigh;
for (i = 0; i < inum; i++)
nneigh += numneigh[ilist[i]];
} else if (lmp->kokkos) nneigh = lmp->kokkos->neigh_count(m);
}
tmp = nneigh;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
fprintf(screen,"Neighs: %g ave %g max %g min\n",ave,max,min);
fprintf(screen,"Histogram:");
for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile,"Neighs: %g ave %g max %g min\n",ave,max,min);
fprintf(logfile,"Histogram:");
for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
fprintf(logfile,"\n");
}
}
// find a non-skip neighbor list containing full pairwise interactions
// count neighbors in that list for stats purposes
// allow it to be Kokkos neigh list as well
for (m = 0; m < neighbor->old_nrequest; m++) {
if (neighbor->old_requests[m]->full &&
neighbor->old_requests[m]->skip == 0) {
if (lmp->kokkos && lmp->kokkos->neigh_list_kokkos(m)) break;
else break;
}
}
nneighfull = 0;
if (m < neighbor->old_nrequest) {
if (neighbor->lists[m] && neighbor->lists[m]->numneigh) {
int inum = neighbor->lists[m]->inum;
int *ilist = neighbor->lists[m]->ilist;
int *numneigh = neighbor->lists[m]->numneigh;
for (i = 0; i < inum; i++)
nneighfull += numneigh[ilist[i]];
} else if (!neighbor->lists[m] && lmp->kokkos)
nneighfull = lmp->kokkos->neigh_count(m);
tmp = nneighfull;
stats(1,&tmp,&ave,&max,&min,10,histo);
if (me == 0) {
if (screen) {
fprintf(screen,"FullNghs: %g ave %g max %g min\n",ave,max,min);
fprintf(screen,"Histogram:");
for (i = 0; i < 10; i++) fprintf(screen," %d",histo[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile,"FullNghs: %g ave %g max %g min\n",ave,max,min);
fprintf(logfile,"Histogram:");
for (i = 0; i < 10; i++) fprintf(logfile," %d",histo[i]);
fprintf(logfile,"\n");
}
}
}
}
if (neighflag) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
tmp = MAX(nneigh,nneighfull);
double nall;
MPI_Allreduce(&tmp,&nall,1,MPI_DOUBLE,MPI_SUM,world);
int nspec;
double nspec_all = 0;
if (atom->molecular == 1) {
int **nspecial = atom->nspecial;
int nlocal = atom->nlocal;
nspec = 0;
for (i = 0; i < nlocal; i++) nspec += nspecial[i][2];
tmp = nspec;
MPI_Allreduce(&tmp,&nspec_all,1,MPI_DOUBLE,MPI_SUM,world);
} else if (atom->molecular == 2) {
Molecule **onemols = atom->avec->onemols;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
int nlocal = atom->nlocal;
int imol,iatom;
nspec = 0;
for (i = 0; i < nlocal; i++) {
if (molindex[i] < 0) continue;
imol = molindex[i];
iatom = molatom[i];
nspec += onemols[imol]->nspecial[iatom][2];
}
tmp = nspec;
MPI_Allreduce(&tmp,&nspec_all,1,MPI_DOUBLE,MPI_SUM,world);
}
if (me == 0) {
if (screen) {
if (nall < 2.0e9)
fprintf(screen,
"Total # of neighbors = %d\n",static_cast<int> (nall));
else fprintf(screen,"Total # of neighbors = %g\n",nall);
if (atom->natoms > 0)
fprintf(screen,"Ave neighs/atom = %g\n",nall/atom->natoms);
if (atom->molecular && atom->natoms > 0)
fprintf(screen,"Ave special neighs/atom = %g\n",
nspec_all/atom->natoms);
fprintf(screen,"Neighbor list builds = " BIGINT_FORMAT "\n",
neighbor->ncalls);
if (neighbor->dist_check)
fprintf(screen,"Dangerous builds = " BIGINT_FORMAT "\n",
neighbor->ndanger);
else fprintf(screen,"Dangerous builds not checked\n");
}
if (logfile) {
if (nall < 2.0e9)
fprintf(logfile,
"Total # of neighbors = %d\n",static_cast<int> (nall));
else fprintf(logfile,"Total # of neighbors = %g\n",nall);
if (atom->natoms > 0)
fprintf(logfile,"Ave neighs/atom = %g\n",nall/atom->natoms);
if (atom->molecular && atom->natoms > 0)
fprintf(logfile,"Ave special neighs/atom = %g\n",
nspec_all/atom->natoms);
fprintf(logfile,"Neighbor list builds = " BIGINT_FORMAT "\n",
neighbor->ncalls);
if (neighbor->dist_check)
fprintf(logfile,"Dangerous builds = " BIGINT_FORMAT "\n",
neighbor->ndanger);
else fprintf(logfile,"Dangerous builds not checked\n");
}
}
}
if (logfile) fflush(logfile);
}
/* ---------------------------------------------------------------------- */
void Finish::stats(int n, double *data,
double *pave, double *pmax, double *pmin,
int nhisto, int *histo)
{
int i,m;
int *histotmp;
double min = 1.0e20;
double max = -1.0e20;
double ave = 0.0;
for (i = 0; i < n; i++) {
ave += data[i];
if (data[i] < min) min = data[i];
if (data[i] > max) max = data[i];
}
int ntotal;
MPI_Allreduce(&n,&ntotal,1,MPI_INT,MPI_SUM,world);
double tmp;
MPI_Allreduce(&ave,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
ave = tmp/ntotal;
MPI_Allreduce(&min,&tmp,1,MPI_DOUBLE,MPI_MIN,world);
min = tmp;
MPI_Allreduce(&max,&tmp,1,MPI_DOUBLE,MPI_MAX,world);
max = tmp;
for (i = 0; i < nhisto; i++) histo[i] = 0;
double del = max - min;
for (i = 0; i < n; i++) {
if (del == 0.0) m = 0;
else m = static_cast<int> ((data[i]-min)/del * nhisto);
if (m > nhisto-1) m = nhisto-1;
histo[m]++;
}
memory->create(histotmp,nhisto,"finish:histotmp");
MPI_Allreduce(histo,histotmp,nhisto,MPI_INT,MPI_SUM,world);
for (i = 0; i < nhisto; i++) histo[i] = histotmp[i];
memory->destroy(histotmp);
*pave = ave;
*pmax = max;
*pmin = min;
}
/* ---------------------------------------------------------------------- */
void mpi_timings(const char *label, Timer *t, enum Timer::ttype tt,
MPI_Comm world, const int nprocs, const int nthreads,
const int me, double time_loop, FILE *scr, FILE *log)
{
double tmp, time_max, time_min, time_sq;
double time = t->get_wall(tt);
double time_cpu = t->get_cpu(tt);
if (time/time_loop < 0.001) // insufficient timer resolution!
time_cpu = 1.0;
else
time_cpu = time_cpu / time;
if (time_cpu > nthreads) time_cpu = nthreads;
MPI_Allreduce(&time,&time_min,1,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(&time,&time_max,1,MPI_DOUBLE,MPI_MAX,world);
time_sq = time*time;
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
MPI_Allreduce(&time_sq,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time_sq = tmp/nprocs;
MPI_Allreduce(&time_cpu,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time_cpu = tmp/nprocs*100.0;
// % variance from the average as measure of load imbalance
if (time > 1.0e-10)
time_sq = sqrt(time_sq/time - time)*100.0;
else
time_sq = 0.0;
if (me == 0) {
tmp = time/time_loop*100.0;
if (t->has_full()) {
const char fmt[] = "%-8s|%- 12.5g|%- 12.5g|%- 12.5g|%6.1f |%6.1f |%6.2f\n";
if (scr)
fprintf(scr,fmt,label,time_min,time,time_max,time_sq,time_cpu,tmp);
if (log)
fprintf(log,fmt,label,time_min,time,time_max,time_sq,time_cpu,tmp);
time_loop = 100.0/time_loop;
} else {
const char fmt[] = "%-8s|%- 12.5g|%- 12.5g|%- 12.5g|%6.1f |%6.2f\n";
if (scr)
fprintf(scr,fmt,label,time_min,time,time_max,time_sq,tmp);
if (log)
fprintf(log,fmt,label,time_min,time,time_max,time_sq,tmp);
}
}
}
/* ---------------------------------------------------------------------- */
#ifdef LMP_USER_OMP
void omp_times(FixOMP *fix, const char *label, enum Timer::ttype which,
const int nthreads,FILE *scr, FILE *log)
{
const char fmt[] = "%-8s|%- 12.5g|%- 12.5g|%- 12.5g|%6.1f |%6.2f\n";
double time_min, time_max, time_avg, time_total, time_std;
time_min = 1.0e100;
time_max = -1.0e100;
time_total = time_avg = time_std = 0.0;
for (int i=0; i < nthreads; ++i) {
ThrData *thr = fix->get_thr(i);
double tmp=thr->get_time(which);
time_min = MIN(time_min,tmp);
time_max = MAX(time_max,tmp);
time_avg += tmp;
time_std += tmp*tmp;
time_total += thr->get_time(Timer::ALL);
}
time_avg /= nthreads;
time_std /= nthreads;
time_total /= nthreads;
if (time_avg > 1.0e-10)
time_std = sqrt(time_std/time_avg - time_avg)*100.0;
else
time_std = 0.0;
if (scr) fprintf(scr,fmt,label,time_min,time_avg,time_max,time_std,
time_avg/time_total*100.0);
if (log) fprintf(log,fmt,label,time_min,time_avg,time_max,time_std,
time_avg/time_total*100.0);
}
#endif
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