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Tue, Sep 3, 02:13

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 "atom.h"
#include "force.h"
#include "kspace.h"
#include "update.h"
#include "min.h"
#include "neighbor.h"
#include "output.h"
#include "memory.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Finish::Finish(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void Finish::end(int flag)
{
int i;
int histo[10];
double time,tmp,ave,max,min;
int me,nprocs;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
// deduce time_other
double time_other = timer->array[TIME_LOOP] -
(timer->array[TIME_PAIR] + timer->array[TIME_BOND] +
timer->array[TIME_KSPACE] + timer->array[TIME_NEIGHBOR] +
timer->array[TIME_COMM] + timer->array[TIME_OUTPUT]);
double time_loop = timer->array[TIME_LOOP];
MPI_Allreduce(&time_loop,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time_loop = tmp/nprocs;
// overall loop time
// use actual natoms, in case atoms were lost
double natoms;
double rlocal = atom->nlocal;
MPI_Allreduce(&rlocal,&natoms,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen)
fprintf(screen,
"Loop time of %g on %d procs for %d steps with %.15g atoms\n",
time_loop,nprocs,update->nsteps,natoms);
if (logfile)
fprintf(logfile,
"Loop time of %g on %d procs for %d steps with %.15g atoms\n",
time_loop,nprocs,update->nsteps,natoms);
}
if (flag == 0) return;
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
// minimization stats
if (update->whichflag == 1) {
if (me == 0) {
if (screen) {
fprintf(screen,"Minimization stats:\n");
fprintf(screen," E initial, next-to-last, final = %g %g %g\n",
update->minimize->einitial,update->minimize->eprevious,
update->minimize->efinal);
fprintf(screen," Gradient 2-norm init/final= %g %g\n",
update->minimize->gnorm2_init,update->minimize->gnorm2_final);
fprintf(screen," Gradient inf-norm init/final= %g %g\n",
update->minimize->gnorminf_init,
update->minimize->gnorminf_final);
fprintf(screen," Iterations = %d\n",update->minimize->niter);
fprintf(screen," Force evaluations = %d\n",update->minimize->neval);
}
if (logfile) {
fprintf(logfile,"Minimization stats:\n");
fprintf(logfile," E initial, next-to-last, final = %g %g %g\n",
update->minimize->einitial,update->minimize->eprevious,
update->minimize->efinal);
fprintf(logfile," Gradient 2-norm init/final= %g %g\n",
update->minimize->gnorm2_init,update->minimize->gnorm2_final);
fprintf(logfile," Gradient inf-norm init/final= %g %g\n",
update->minimize->gnorminf_init,
update->minimize->gnorminf_final);
fprintf(logfile," Iterations = %d\n",update->minimize->niter);
fprintf(logfile," Force evaluations = %d\n",update->minimize->neval);
}
}
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
}
// timing breakdowns
if (time_loop == 0.0) time_loop = 1.0;
time = timer->array[TIME_PAIR];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Pair time (%%) = %g (%g)\n",time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Pair time (%%) = %g (%g)\n",time,time/time_loop*100.0);
}
if (atom->molecular) {
time = timer->array[TIME_BOND];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Bond time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Bond time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
}
if (force->kspace) {
time = timer->array[TIME_KSPACE];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Kspce time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Kspce time (%%) = %g (%g)\n",
time,time/time_loop*100.0);
}
}
time = timer->array[TIME_NEIGHBOR];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Neigh time (%%) = %g (%g)\n",time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Neigh time (%%) = %g (%g)\n",time,time/time_loop*100.0);
}
time = timer->array[TIME_COMM];
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->array[TIME_OUTPUT];
MPI_Allreduce(&time,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time = tmp/nprocs;
if (me == 0) {
if (screen)
fprintf(screen,"Outpt time (%%) = %g (%g)\n",time,time/time_loop*100.0);
if (logfile)
fprintf(logfile,"Outpt 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);
}
// FFT timing statistics
// time3d,time1d = total time during run for 3d and 1d FFTs
if (strstr(force->kspace_style,"pppm")) {
if (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
int nsteps = update->nsteps;
int nsample = 5;
double time3d,time1d;
force->kspace->timing(nsample,time3d,time1d);
time3d = nsteps * time3d / nsample;
MPI_Allreduce(&time3d,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time3d = tmp/nprocs;
time1d = nsteps * time1d / nsample;
MPI_Allreduce(&time1d,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
time1d = tmp/nprocs;
double time_kspace = timer->array[TIME_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) {
fraction = time3d/time_kspace*100.0;
flop3 = nflops/1.0e9/(time3d/4.0/nsteps);
flop1 = nflops/1.0e9/(time1d/4.0/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,time3d/time_kspace*100.0);
fprintf(logfile,"FFT Gflps 3d 1d-only = %g %g\n",
nflops/1.0e9/(time3d/4.0/nsteps),
nflops/1.0e9/(time1d/4.0/nsteps));
}
}
}
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");
}
}
int nneigh = 0;
if (neighbor->half_every)
for (i = 0; i < atom->nlocal; i++) nneigh += neighbor->numneigh[i];
else if (neighbor->full_every)
for (i = 0; i < atom->nlocal; i++) nneigh += neighbor->numneigh_full[i];
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");
}
}
if (neighbor->half_every && neighbor->full_every) {
nneigh = 0;
for (i = 0; i < atom->nlocal; i++) nneigh += neighbor->numneigh_full[i];
tmp = nneigh;
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 (me == 0) {
if (screen) fprintf(screen,"\n");
if (logfile) fprintf(logfile,"\n");
}
tmp = nneigh;
double nall;
MPI_Allreduce(&tmp,&nall,1,MPI_DOUBLE,MPI_SUM,world);
int nspec;
double nspec_all;
if (atom->molecular) {
nspec = 0;
for (i = 0; i < atom->nlocal; i++) nspec += atom->nspecial[i][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 (natoms > 0) fprintf(screen,"Ave neighs/atom = %g\n",nall/natoms);
if (atom->molecular && natoms > 0)
fprintf(screen,"Ave special neighs/atom = %g\n",nspec_all/natoms);
fprintf(screen,"Neighbor list builds = %d\n",neighbor->ncalls);
fprintf(screen,"Dangerous builds = %d\n",neighbor->ndanger);
}
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 (natoms > 0) fprintf(logfile,"Ave neighs/atom = %g\n",nall/natoms);
if (atom->molecular && natoms > 0)
fprintf(logfile,"Ave special neighs/atom = %g\n",nspec_all/natoms);
fprintf(logfile,"Neighbor list builds = %d\n",neighbor->ncalls);
fprintf(logfile,"Dangerous builds = %d\n",neighbor->ndanger);
}
}
}
/* ---------------------------------------------------------------------- */
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]++;
}
histotmp = (int *) memory->smalloc(nhisto*sizeof(int),"finish:histotmp");
MPI_Allreduce(histo,histotmp,nhisto,MPI_INT,MPI_SUM,world);
for (i = 0; i < nhisto; i++) histo[i] = histotmp[i];
memory->sfree(histotmp);
*pave = ave;
*pmax = max;
*pmin = min;
}

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