Homec4science
Diffusion lammps (lammm-master) Browse

lammps/src/balance.cpp
1111c8ba93c9lammm-master

Last Change
Raw File

balance.cpp
View Options

/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
//#define BALANCE_DEBUG 1
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "balance.h"
#include "atom.h"
#include "comm.h"
#include "rcb.h"
#include "irregular.h"
#include "domain.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{XYZ,SHIFT,BISECTION};
enum{NONE,UNIFORM,USER};
enum{X,Y,Z};
enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
/* ---------------------------------------------------------------------- */
Balance::Balance(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
memory->create(proccount,nprocs,"balance:proccount");
memory->create(allproccount,nprocs,"balance:allproccount");
user_xsplit = user_ysplit = user_zsplit = NULL;
shift_allocate = 0;
rcb = NULL;
fp = NULL;
firststep = 1;
}
/* ---------------------------------------------------------------------- */
Balance::~Balance()
{
memory->destroy(proccount);
memory->destroy(allproccount);
delete [] user_xsplit;
delete [] user_ysplit;
delete [] user_zsplit;
if (shift_allocate) {
delete [] bdim;
delete [] count;
delete [] sum;
delete [] target;
delete [] onecount;
delete [] lo;
delete [] hi;
delete [] losum;
delete [] hisum;
}
delete rcb;
if (fp) fclose(fp);
}
/* ----------------------------------------------------------------------
called as balance command in input script
------------------------------------------------------------------------- */
void Balance::command(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all(FLERR,"Balance command before simulation box is defined");
if (comm->me == 0 && screen) fprintf(screen,"Balancing ...\n");
// parse arguments
if (narg < 2) error->all(FLERR,"Illegal balance command");
thresh = force->numeric(FLERR,arg[0]);
int dimension = domain->dimension;
int *procgrid = comm->procgrid;
style = -1;
xflag = yflag = zflag = NONE;
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"x") == 0) {
if (style != -1 && style != XYZ)
error->all(FLERR,"Illegal balance command");
style = XYZ;
if (strcmp(arg[iarg+1],"uniform") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
xflag = UNIFORM;
iarg += 2;
} else {
if (1 + procgrid[0]-1 > narg)
error->all(FLERR,"Illegal balance command");
xflag = USER;
delete [] user_xsplit;
user_xsplit = new double[procgrid[0]+1];
user_xsplit[0] = 0.0;
iarg++;
for (int i = 1; i < procgrid[0]; i++)
user_xsplit[i] = force->numeric(FLERR,arg[iarg++]);
user_xsplit[procgrid[0]] = 1.0;
}
} else if (strcmp(arg[iarg],"y") == 0) {
if (style != -1 && style != XYZ)
error->all(FLERR,"Illegal balance command");
style = XYZ;
if (strcmp(arg[iarg+1],"uniform") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
yflag = UNIFORM;
iarg += 2;
} else {
if (1 + procgrid[1]-1 > narg)
error->all(FLERR,"Illegal balance command");
yflag = USER;
delete [] user_ysplit;
user_ysplit = new double[procgrid[1]+1];
user_ysplit[0] = 0.0;
iarg++;
for (int i = 1; i < procgrid[1]; i++)
user_ysplit[i] = force->numeric(FLERR,arg[iarg++]);
user_ysplit[procgrid[1]] = 1.0;
}
} else if (strcmp(arg[iarg],"z") == 0) {
if (style != -1 && style != XYZ)
error->all(FLERR,"Illegal balance command");
style = XYZ;
if (strcmp(arg[iarg+1],"uniform") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
zflag = UNIFORM;
iarg += 2;
} else {
if (1 + procgrid[2]-1 > narg)
error->all(FLERR,"Illegal balance command");
zflag = USER;
delete [] user_zsplit;
user_zsplit = new double[procgrid[2]+1];
user_zsplit[0] = 0.0;
iarg++;
for (int i = 1; i < procgrid[2]; i++)
user_zsplit[i] = force->numeric(FLERR,arg[iarg++]);
user_zsplit[procgrid[2]] = 1.0;
}
} else if (strcmp(arg[iarg],"shift") == 0) {
if (style != -1) error->all(FLERR,"Illegal balance command");
if (iarg+4 > narg) error->all(FLERR,"Illegal balance command");
style = SHIFT;
if (strlen(arg[iarg+1]) > 3) error->all(FLERR,"Illegal balance command");
strcpy(bstr,arg[iarg+1]);
nitermax = force->inumeric(FLERR,arg[iarg+2]);
if (nitermax <= 0) error->all(FLERR,"Illegal balance command");
stopthresh = force->numeric(FLERR,arg[iarg+3]);
if (stopthresh < 1.0) error->all(FLERR,"Illegal balance command");
iarg += 4;
} else if (strcmp(arg[iarg],"rcb") == 0) {
if (style != -1) error->all(FLERR,"Illegal balance command");
style = BISECTION;
iarg++;
} else break;
}
// optional keywords
outflag = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"out") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal balance command");
if (outflag) error->all(FLERR,"Illegal balance command");
outflag = 1;
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) error->one(FLERR,"Cannot open balance output file");
}
iarg += 2;
} else error->all(FLERR,"Illegal balance command");
}
// error check
if (style == XYZ) {
if (zflag != NONE && dimension == 2)
error->all(FLERR,"Cannot balance in z dimension for 2d simulation");
if (xflag == USER)
for (int i = 1; i <= procgrid[0]; i++)
if (user_xsplit[i-1] >= user_xsplit[i])
error->all(FLERR,"Illegal balance command");
if (yflag == USER)
for (int i = 1; i <= procgrid[1]; i++)
if (user_ysplit[i-1] >= user_ysplit[i])
error->all(FLERR,"Illegal balance command");
if (zflag == USER)
for (int i = 1; i <= procgrid[2]; i++)
if (user_zsplit[i-1] >= user_zsplit[i])
error->all(FLERR,"Illegal balance command");
}
if (style == SHIFT) {
const int blen=strlen(bstr);
for (int i = 0; i < blen; i++) {
if (bstr[i] != 'x' && bstr[i] != 'y' && bstr[i] != 'z')
error->all(FLERR,"Balance shift string is invalid");
if (bstr[i] == 'z' && dimension == 2)
error->all(FLERR,"Balance shift string is invalid");
for (int j = i+1; j < blen; j++)
if (bstr[i] == bstr[j])
error->all(FLERR,"Balance shift string is invalid");
}
}
if (style == BISECTION && comm->style == 0)
error->all(FLERR,"Balance rcb cannot be used with comm_style brick");
// insure atoms are in current box & update box via shrink-wrap
// init entire system since comm->setup is done
// comm::init needs neighbor::init needs pair::init needs kspace::init, etc
lmp->init();
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
domain->reset_box();
comm->setup();
comm->exchange();
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// imbinit = initial imbalance
int maxinit;
double imbinit = imbalance_nlocal(maxinit);
// no load-balance if imbalance doesn't exceed threshhold
// unless switching from tiled to non tiled layout, then force rebalance
if (comm->layout == LAYOUT_TILED && style != BISECTION) {
} else if (imbinit < thresh) return;
// debug output of initial state
#ifdef BALANCE_DEBUG
if (outflag) dumpout(update->ntimestep,fp);
#endif
int niter = 0;
// perform load-balance
// style XYZ = explicit setting of cutting planes of logical 3d grid
if (style == XYZ) {
if (comm->layout == LAYOUT_UNIFORM) {
if (xflag == USER || yflag == USER || zflag == USER)
comm->layout = LAYOUT_NONUNIFORM;
} else if (comm->style == LAYOUT_NONUNIFORM) {
if (xflag == UNIFORM && yflag == UNIFORM && zflag == UNIFORM)
comm->layout = LAYOUT_UNIFORM;
} else if (comm->style == LAYOUT_TILED) {
if (xflag == UNIFORM && yflag == UNIFORM && zflag == UNIFORM)
comm->layout = LAYOUT_UNIFORM;
else comm->layout = LAYOUT_NONUNIFORM;
}
if (xflag == UNIFORM) {
for (int i = 0; i < procgrid[0]; i++)
comm->xsplit[i] = i * 1.0/procgrid[0];
comm->xsplit[procgrid[0]] = 1.0;
} else if (xflag == USER)
for (int i = 0; i <= procgrid[0]; i++) comm->xsplit[i] = user_xsplit[i];
if (yflag == UNIFORM) {
for (int i = 0; i < procgrid[1]; i++)
comm->ysplit[i] = i * 1.0/procgrid[1];
comm->ysplit[procgrid[1]] = 1.0;
} else if (yflag == USER)
for (int i = 0; i <= procgrid[1]; i++) comm->ysplit[i] = user_ysplit[i];
if (zflag == UNIFORM) {
for (int i = 0; i < procgrid[2]; i++)
comm->zsplit[i] = i * 1.0/procgrid[2];
comm->zsplit[procgrid[2]] = 1.0;
} else if (zflag == USER)
for (int i = 0; i <= procgrid[2]; i++) comm->zsplit[i] = user_zsplit[i];
}
// style SHIFT = adjust cutting planes of logical 3d grid
if (style == SHIFT) {
comm->layout = LAYOUT_NONUNIFORM;
shift_setup_static(bstr);
niter = shift();
}
// style BISECTION = recursive coordinate bisectioning
if (style == BISECTION) {
comm->layout = LAYOUT_TILED;
bisection(1);
}
// reset proc sub-domains
// for either brick or tiled comm style
if (domain->triclinic) domain->set_lamda_box();
domain->set_local_box();
// move atoms to new processors via irregular()
if (domain->triclinic) domain->x2lamda(atom->nlocal);
Irregular *irregular = new Irregular(lmp);
if (style == BISECTION) irregular->migrate_atoms(1,1,rcb->sendproc);
else irregular->migrate_atoms(1);
delete irregular;
if (domain->triclinic) domain->lamda2x(atom->nlocal);
// output of final result
if (outflag) dumpout(update->ntimestep,fp);
// check if any atoms were lost
bigint natoms;
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (natoms != atom->natoms) {
char str[128];
sprintf(str,"Lost atoms via balance: original " BIGINT_FORMAT
" current " BIGINT_FORMAT,atom->natoms,natoms);
error->all(FLERR,str);
}
// imbfinal = final imbalance based on final nlocal
int maxfinal;
double imbfinal = imbalance_nlocal(maxfinal);
if (me == 0) {
if (screen) {
fprintf(screen," iteration count = %d\n",niter);
fprintf(screen," initial/final max atoms/proc = %d %d\n",
maxinit,maxfinal);
fprintf(screen," initial/final imbalance factor = %g %g\n",
imbinit,imbfinal);
}
if (logfile) {
fprintf(logfile," iteration count = %d\n",niter);
fprintf(logfile," initial/final max atoms/proc = %d %d\n",
maxinit,maxfinal);
fprintf(logfile," initial/final imbalance factor = %g %g\n",
imbinit,imbfinal);
}
}
if (style != BISECTION) {
if (me == 0) {
if (screen) {
fprintf(screen," x cuts:");
for (int i = 0; i <= comm->procgrid[0]; i++)
fprintf(screen," %g",comm->xsplit[i]);
fprintf(screen,"\n");
fprintf(screen," y cuts:");
for (int i = 0; i <= comm->procgrid[1]; i++)
fprintf(screen," %g",comm->ysplit[i]);
fprintf(screen,"\n");
fprintf(screen," z cuts:");
for (int i = 0; i <= comm->procgrid[2]; i++)
fprintf(screen," %g",comm->zsplit[i]);
fprintf(screen,"\n");
}
if (logfile) {
fprintf(logfile," x cuts:");
for (int i = 0; i <= comm->procgrid[0]; i++)
fprintf(logfile," %g",comm->xsplit[i]);
fprintf(logfile,"\n");
fprintf(logfile," y cuts:");
for (int i = 0; i <= comm->procgrid[1]; i++)
fprintf(logfile," %g",comm->ysplit[i]);
fprintf(logfile,"\n");
fprintf(logfile," z cuts:");
for (int i = 0; i <= comm->procgrid[2]; i++)
fprintf(logfile," %g",comm->zsplit[i]);
fprintf(logfile,"\n");
}
}
}
}
/* ----------------------------------------------------------------------
calculate imbalance based on nlocal
return max = max atom per proc
return imbalance factor = max atom per proc / ave atom per proc
------------------------------------------------------------------------- */
double Balance::imbalance_nlocal(int &max)
{
MPI_Allreduce(&atom->nlocal,&max,1,MPI_INT,MPI_MAX,world);
double imbalance = 1.0;
if (max) imbalance = max / (1.0 * atom->natoms / nprocs);
return imbalance;
}
/* ----------------------------------------------------------------------
calculate imbalance based on processor splits in 3 dims
atoms must be in lamda coords (0-1) before called
map atoms to 3d grid of procs
return max = max atom per proc
return imbalance factor = max atom per proc / ave atom per proc
------------------------------------------------------------------------- */
double Balance::imbalance_splits(int &max)
{
double *xsplit = comm->xsplit;
double *ysplit = comm->ysplit;
double *zsplit = comm->zsplit;
int nx = comm->procgrid[0];
int ny = comm->procgrid[1];
int nz = comm->procgrid[2];
for (int i = 0; i < nprocs; i++) proccount[i] = 0;
double **x = atom->x;
int nlocal = atom->nlocal;
int ix,iy,iz;
for (int i = 0; i < nlocal; i++) {
ix = binary(x[i][0],nx,xsplit);
iy = binary(x[i][1],ny,ysplit);
iz = binary(x[i][2],nz,zsplit);
proccount[iz*nx*ny + iy*nx + ix]++;
}
MPI_Allreduce(proccount,allproccount,nprocs,MPI_INT,MPI_SUM,world);
max = 0;
for (int i = 0; i < nprocs; i++) max = MAX(max,allproccount[i]);
double imbalance = 1.0;
if (max) imbalance = max / (1.0 * atom->natoms / nprocs);
return imbalance;
}
/* ----------------------------------------------------------------------
perform balancing via RCB class
sortflag = flag for sorting order of received messages by proc ID
------------------------------------------------------------------------- */
int *Balance::bisection(int sortflag)
{
if (!rcb) rcb = new RCB(lmp);
// NOTE: this logic is specific to orthogonal boxes, not triclinic
int dim = domain->dimension;
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
double *prd = domain->prd;
// shrink-wrap simulation box around atoms for input to RCB
// leads to better-shaped sub-boxes when atoms are far from box boundaries
double shrink[6],shrinkall[6];
shrink[0] = boxhi[0]; shrink[1] = boxhi[1]; shrink[2] = boxhi[2];
shrink[3] = boxlo[0]; shrink[4] = boxlo[1]; shrink[5] = boxlo[2];
double **x = atom->x;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
shrink[0] = MIN(shrink[0],x[i][0]);
shrink[1] = MIN(shrink[1],x[i][1]);
shrink[2] = MIN(shrink[2],x[i][2]);
shrink[3] = MAX(shrink[3],x[i][0]);
shrink[4] = MAX(shrink[4],x[i][1]);
shrink[5] = MAX(shrink[5],x[i][2]);
}
shrink[3] = -shrink[3]; shrink[4] = -shrink[4]; shrink[5] = -shrink[5];
MPI_Allreduce(shrink,shrinkall,6,MPI_DOUBLE,MPI_MIN,world);
shrinkall[3] = -shrinkall[3];
shrinkall[4] = -shrinkall[4];
shrinkall[5] = -shrinkall[5];
double *shrinklo = &shrinkall[0];
double *shrinkhi = &shrinkall[3];
// invoke RCB
// then invert() to create list of proc assignements for my atoms
//rcb->compute(dim,atom->nlocal,atom->x,NULL,boxlo,boxhi);
rcb->compute(dim,atom->nlocal,atom->x,NULL,shrinklo,shrinkhi);
rcb->invert(sortflag);
// reset RCB lo/hi bounding box to full simulation box as needed
double *lo = rcb->lo;
double *hi = rcb->hi;
if (lo[0] == shrinklo[0]) lo[0] = boxlo[0];
if (lo[1] == shrinklo[1]) lo[1] = boxlo[1];
if (lo[2] == shrinklo[2]) lo[2] = boxlo[2];
if (hi[0] == shrinkhi[0]) hi[0] = boxhi[0];
if (hi[1] == shrinkhi[1]) hi[1] = boxhi[1];
if (hi[2] == shrinkhi[2]) hi[2] = boxhi[2];
// store RCB cut, dim, lo/hi box in CommTiled
// cut and lo/hi need to be in fractional form so can
// OK if changes by epsilon from what RCB used since particles
// will subsequently migrate to new owning procs by exchange() anyway
// ditto for particles exactly on lo/hi RCB box boundaries due to ties
comm->rcbnew = 1;
int idim = rcb->cutdim;
if (idim >= 0) comm->rcbcutfrac = (rcb->cut - boxlo[idim]) / prd[idim];
else comm->rcbcutfrac = 0.0;
comm->rcbcutdim = idim;
double (*mysplit)[2] = comm->mysplit;
mysplit[0][0] = (lo[0] - boxlo[0]) / prd[0];
if (hi[0] == boxhi[0]) mysplit[0][1] = 1.0;
else mysplit[0][1] = (hi[0] - boxlo[0]) / prd[0];
mysplit[1][0] = (lo[1] - boxlo[1]) / prd[1];
if (hi[1] == boxhi[1]) mysplit[1][1] = 1.0;
else mysplit[1][1] = (hi[1] - boxlo[1]) / prd[1];
mysplit[2][0] = (lo[2] - boxlo[2]) / prd[2];
if (hi[2] == boxhi[2]) mysplit[2][1] = 1.0;
else mysplit[2][1] = (hi[2] - boxlo[2]) / prd[2];
// return list of procs to send my atoms to
return rcb->sendproc;
}
/* ----------------------------------------------------------------------
setup static load balance operations
called from command and indirectly initially from fix balance
set rho = 0 for static balancing
------------------------------------------------------------------------- */
void Balance::shift_setup_static(char *str)
{
shift_allocate = 1;
ndim = strlen(str);
bdim = new int[ndim];
for (int i = 0; i < ndim; i++) {
if (str[i] == 'x') bdim[i] = X;
if (str[i] == 'y') bdim[i] = Y;
if (str[i] == 'z') bdim[i] = Z;
}
int max = MAX(comm->procgrid[0],comm->procgrid[1]);
max = MAX(max,comm->procgrid[2]);
count = new bigint[max];
onecount = new bigint[max];
sum = new bigint[max+1];
target = new bigint[max+1];
lo = new double[max+1];
hi = new double[max+1];
losum = new bigint[max+1];
hisum = new bigint[max+1];
// if current layout is TILED, set initial uniform splits in Comm
// this gives starting point to subsequent shift balancing
if (comm->layout == LAYOUT_TILED) {
int *procgrid = comm->procgrid;
double *xsplit = comm->xsplit;
double *ysplit = comm->ysplit;
double *zsplit = comm->zsplit;
for (int i = 0; i < procgrid[0]; i++) xsplit[i] = i * 1.0/procgrid[0];
for (int i = 0; i < procgrid[1]; i++) ysplit[i] = i * 1.0/procgrid[1];
for (int i = 0; i < procgrid[2]; i++) zsplit[i] = i * 1.0/procgrid[2];
xsplit[procgrid[0]] = ysplit[procgrid[1]] = zsplit[procgrid[2]] = 1.0;
}
rho = 0;
}
/* ----------------------------------------------------------------------
setup shift load balance operations
called from fix balance
set rho = 1 to do dynamic balancing after call to shift_setup_static()
------------------------------------------------------------------------- */
void Balance::shift_setup(char *str, int nitermax_in, double thresh_in)
{
shift_setup_static(str);
nitermax = nitermax_in;
stopthresh = thresh_in;
rho = 1;
}
/* ----------------------------------------------------------------------
load balance by changing xyz split proc boundaries in Comm
called one time from input script command or many times from fix balance
return niter = iteration count
------------------------------------------------------------------------- */
int Balance::shift()
{
int i,j,k,m,np,max;
double *split;
// no balancing if no atoms
bigint natoms = atom->natoms;
if (natoms == 0) return 0;
// set delta for 1d balancing = root of threshhold
// root = # of dimensions being balanced on
double delta = pow(stopthresh,1.0/ndim) - 1.0;
int *procgrid = comm->procgrid;
// all balancing done in lamda coords
domain->x2lamda(atom->nlocal);
// loop over dimensions in balance string
int niter = 0;
for (int idim = 0; idim < ndim; idim++) {
// split = ptr to xyz split in Comm
if (bdim[idim] == X) split = comm->xsplit;
else if (bdim[idim] == Y) split = comm->ysplit;
else if (bdim[idim] == Z) split = comm->zsplit;
else continue;
// intial count and sum
np = procgrid[bdim[idim]];
tally(bdim[idim],np,split);
// target[i] = desired sum at split I
for (i = 0; i < np; i++)
target[i] = static_cast<int> (1.0*natoms/np * i + 0.5);
target[np] = natoms;
// lo[i] = closest split <= split[i] with a sum <= target
// hi[i] = closest split >= split[i] with a sum >= target
lo[0] = hi[0] = 0.0;
lo[np] = hi[np] = 1.0;
losum[0] = hisum[0] = 0;
losum[np] = hisum[np] = natoms;
for (i = 1; i < np; i++) {
for (j = i; j >= 0; j--)
if (sum[j] <= target[i]) {
lo[i] = split[j];
losum[i] = sum[j];
break;
}
for (j = i; j <= np; j++)
if (sum[j] >= target[i]) {
hi[i] = split[j];
hisum[i] = sum[j];
break;
}
}
// iterate until balanced
#ifdef BALANCE_DEBUG
if (me == 0) debug_shift_output(idim,0,np,split);
#endif
int doneflag;
int change = 1;
for (m = 0; m < nitermax; m++) {
change = adjust(np,split);
tally(bdim[idim],np,split);
niter++;
#ifdef BALANCE_DEBUG
if (me == 0) debug_shift_output(idim,m+1,np,split);
if (outflag) dumpout(update->ntimestep,fp);
#endif
// stop if no change in splits, b/c all targets are met exactly
if (!change) break;
// stop if all split sums are within delta of targets
// this is a 1d test of particle count per slice
// assumption is that this is sufficient accuracy
// for 3d imbalance factor to reach threshhold
doneflag = 1;
for (i = 1; i < np; i++)
if (fabs(1.0*(sum[i]-target[i]))/target[i] > delta) doneflag = 0;
if (doneflag) break;
}
// eliminate final adjacent splits that are duplicates
// can happen if particle distribution is narrow and Nitermax is small
// set lo = midpt between splits
// spread duplicates out evenly between bounding midpts with non-duplicates
// i,j = lo/hi indices of set of duplicate splits
// delta = new spacing between duplicates
// bounding midpts = lo[i-1] and lo[j]
int duplicate = 0;
for (i = 1; i < np-1; i++)
if (split[i] == split[i+1]) duplicate = 1;
if (duplicate) {
for (i = 0; i < np; i++)
lo[i] = 0.5 * (split[i] + split[i+1]);
i = 1;
while (i < np-1) {
j = i+1;
while (split[j] == split[i]) j++;
j--;
if (j > i) {
delta = (lo[j] - lo[i-1]) / (j-i+2);
for (k = i; k <= j; k++)
split[k] = lo[i-1] + (k-i+1)*delta;
}
i = j+1;
}
}
// sanity check on bad duplicate or inverted splits
// zero or negative width sub-domains will break Comm class
// should never happen if recursive multisection algorithm is correct
int bad = 0;
for (i = 0; i < np; i++)
if (split[i] >= split[i+1]) bad = 1;
if (bad) error->all(FLERR,"Balance produced bad splits");
/*
if (me == 0) {
printf("BAD SPLITS %d %d %d\n",np+1,niter,delta);
for (i = 0; i < np+1; i++)
printf(" %g",split[i]);
printf("\n");
}
*/
// stop at this point in bstr if imbalance factor < threshhold
// this is a true 3d test of particle count per processor
double imbfactor = imbalance_splits(max);
if (imbfactor <= stopthresh) break;
}
// restore real coords
domain->lamda2x(atom->nlocal);
return niter;
}
/* ----------------------------------------------------------------------
count atoms in each slice, based on their dim coordinate
N = # of slices
split = N+1 cuts between N slices
return updated count = particles per slice
retrun updated sum = cummulative count below each of N+1 splits
use binary search to find which slice each atom is in
------------------------------------------------------------------------- */
void Balance::tally(int dim, int n, double *split)
{
for (int i = 0; i < n; i++) onecount[i] = 0;
double **x = atom->x;
int nlocal = atom->nlocal;
int index;
for (int i = 0; i < nlocal; i++) {
index = binary(x[i][dim],n,split);
onecount[index]++;
}
MPI_Allreduce(onecount,count,n,MPI_LMP_BIGINT,MPI_SUM,world);
sum[0] = 0;
for (int i = 1; i < n+1; i++)
sum[i] = sum[i-1] + count[i-1];
}
/* ----------------------------------------------------------------------
adjust cuts between N slices in a dim via recursive multisectioning method
split = current N+1 cuts, with 0.0 and 1.0 at end points
sum = cummulative count up to each split
target = desired cummulative count up to each split
lo/hi = split values that bound current split
update lo/hi to reflect sums at current split values
overwrite split with new cuts
guaranteed that splits will remain in ascending order,
though adjacent values may be identical
recursive bisectioning zooms in on each cut by halving lo/hi
return 0 if no changes in any splits, b/c they are all perfect
------------------------------------------------------------------------- */
int Balance::adjust(int n, double *split)
{
int i;
double fraction;
// reset lo/hi based on current sum and splits
// insure lo is monotonically increasing, ties are OK
// insure hi is monotonically decreasing, ties are OK
// this effectively uses info from nearby splits
// to possibly tighten bounds on lo/hi
for (i = 1; i < n; i++) {
if (sum[i] <= target[i]) {
lo[i] = split[i];
losum[i] = sum[i];
}
if (sum[i] >= target[i]) {
hi[i] = split[i];
hisum[i] = sum[i];
}
}
for (i = 1; i < n; i++)
if (lo[i] < lo[i-1]) {
lo[i] = lo[i-1];
losum[i] = losum[i-1];
}
for (i = n-1; i > 0; i--)
if (hi[i] > hi[i+1]) {
hi[i] = hi[i+1];
hisum[i] = hisum[i+1];
}
int change = 0;
for (int i = 1; i < n; i++)
if (sum[i] != target[i]) {
change = 1;
if (rho == 0) split[i] = 0.5 * (lo[i]+hi[i]);
else {
fraction = 1.0*(target[i]-losum[i]) / (hisum[i]-losum[i]);
split[i] = lo[i] + fraction * (hi[i]-lo[i]);
}
}
return change;
}
/* ----------------------------------------------------------------------
binary search for where value falls in N-length vec
note that vec actually has N+1 values, but ignore last one
values in vec are monotonically increasing, but adjacent values can be ties
value may be outside range of vec limits
always return index from 0 to N-1 inclusive
return 0 if value < vec[0]
reutrn N-1 if value >= vec[N-1]
return index = 1 to N-2 inclusive if vec[index] <= value < vec[index+1]
note that for adjacent tie values, index of lower tie is not returned
since never satisfies 2nd condition that value < vec[index+1]
------------------------------------------------------------------------- */
int Balance::binary(double value, int n, double *vec)
{
int lo = 0;
int hi = n-1;
if (value < vec[lo]) return lo;
if (value >= vec[hi]) return hi;
// insure vec[lo] <= value < vec[hi] at every iteration
// done when lo,hi are adjacent
int index = (lo+hi)/2;
while (lo < hi-1) {
if (value < vec[index]) hi = index;
else if (value >= vec[index]) lo = index;
index = (lo+hi)/2;
}
return index;
}
/* ----------------------------------------------------------------------
write dump snapshot of line segments in Pizza.py mdump mesh format
write xy lines around each proc's sub-domain for 2d
write xyz cubes around each proc's sub-domain for 3d
only called by proc 0
NOTE: only implemented for orthogonal boxes, not triclinic
------------------------------------------------------------------------- */
void Balance::dumpout(bigint tstep, FILE *fp)
{
int dimension = domain->dimension;
int triclinic = domain->triclinic;
// Allgather each proc's sub-box
// could use Gather, but that requires MPI to alloc memory
double *lo,*hi;
if (triclinic == 0) {
lo = domain->sublo;
hi = domain->subhi;
} else {
lo = domain->sublo_lamda;
hi = domain->subhi_lamda;
}
double box[6];
box[0] = lo[0]; box[1] = lo[1]; box[2] = lo[2];
box[3] = hi[0]; box[4] = hi[1]; box[5] = hi[2];
double **boxall;
memory->create(boxall,nprocs,6,"balance:dumpout");
MPI_Allgather(box,6,MPI_DOUBLE,&boxall[0][0],6,MPI_DOUBLE,world);
if (me) {
memory->destroy(boxall);
return;
}
// proc 0 writes out nodal coords
// some will be duplicates
double *boxlo = domain->boxlo;
double *boxhi = domain->boxhi;
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,BIGINT_FORMAT "\n",tstep);
fprintf(fp,"ITEM: NUMBER OF NODES\n");
if (dimension == 2) fprintf(fp,"%d\n",4*nprocs);
else fprintf(fp,"%d\n",8*nprocs);
fprintf(fp,"ITEM: BOX BOUNDS\n");
fprintf(fp,"%g %g\n",boxlo[0],boxhi[0]);
fprintf(fp,"%g %g\n",boxlo[1],boxhi[1]);
fprintf(fp,"%g %g\n",boxlo[2],boxhi[2]);
fprintf(fp,"ITEM: NODES\n");
if (triclinic == 0) {
if (dimension == 2) {
int m = 0;
for (int i = 0; i < nprocs; i++) {
fprintf(fp,"%d %d %g %g %g\n",m+1,1,boxall[i][0],boxall[i][1],0.0);
fprintf(fp,"%d %d %g %g %g\n",m+2,1,boxall[i][3],boxall[i][1],0.0);
fprintf(fp,"%d %d %g %g %g\n",m+3,1,boxall[i][3],boxall[i][4],0.0);
fprintf(fp,"%d %d %g %g %g\n",m+4,1,boxall[i][0],boxall[i][4],0.0);
m += 4;
}
} else {
int m = 0;
for (int i = 0; i < nprocs; i++) {
fprintf(fp,"%d %d %g %g %g\n",m+1,1,
boxall[i][0],boxall[i][1],boxall[i][2]);
fprintf(fp,"%d %d %g %g %g\n",m+2,1,
boxall[i][3],boxall[i][1],boxall[i][2]);
fprintf(fp,"%d %d %g %g %g\n",m+3,1,
boxall[i][3],boxall[i][4],boxall[i][2]);
fprintf(fp,"%d %d %g %g %g\n",m+4,1,
boxall[i][0],boxall[i][4],boxall[i][2]);
fprintf(fp,"%d %d %g %g %g\n",m+5,1,
boxall[i][0],boxall[i][1],boxall[i][5]);
fprintf(fp,"%d %d %g %g %g\n",m+6,1,
boxall[i][3],boxall[i][1],boxall[i][5]);
fprintf(fp,"%d %d %g %g %g\n",m+7,1,
boxall[i][3],boxall[i][4],boxall[i][5]);
fprintf(fp,"%d %d %g %g %g\n",m+8,1,
boxall[i][0],boxall[i][4],boxall[i][5]);
m += 8;
}
}
} else {
double (*bc)[3] = domain->corners;
if (dimension == 2) {
int m = 0;
for (int i = 0; i < nprocs; i++) {
domain->lamda_box_corners(&boxall[i][0],&boxall[i][3]);
fprintf(fp,"%d %d %g %g %g\n",m+1,1,bc[0][0],bc[0][1],0.0);
fprintf(fp,"%d %d %g %g %g\n",m+2,1,bc[1][0],bc[1][1],0.0);
fprintf(fp,"%d %d %g %g %g\n",m+3,1,bc[2][0],bc[2][1],0.0);
fprintf(fp,"%d %d %g %g %g\n",m+4,1,bc[3][0],bc[3][1],0.0);
m += 4;
}
} else {
int m = 0;
for (int i = 0; i < nprocs; i++) {
domain->lamda_box_corners(&boxall[i][0],&boxall[i][3]);
fprintf(fp,"%d %d %g %g %g\n",m+1,1,bc[0][0],bc[0][1],bc[0][1]);
fprintf(fp,"%d %d %g %g %g\n",m+2,1,bc[1][0],bc[1][1],bc[1][1]);
fprintf(fp,"%d %d %g %g %g\n",m+3,1,bc[2][0],bc[2][1],bc[2][1]);
fprintf(fp,"%d %d %g %g %g\n",m+4,1,bc[3][0],bc[3][1],bc[3][1]);
fprintf(fp,"%d %d %g %g %g\n",m+5,1,bc[4][0],bc[4][1],bc[4][1]);
fprintf(fp,"%d %d %g %g %g\n",m+6,1,bc[5][0],bc[5][1],bc[5][1]);
fprintf(fp,"%d %d %g %g %g\n",m+7,1,bc[6][0],bc[6][1],bc[6][1]);
fprintf(fp,"%d %d %g %g %g\n",m+8,1,bc[7][0],bc[7][1],bc[7][1]);
m += 8;
}
}
}
// write out one square/cube per processor for 2d/3d
fprintf(fp,"ITEM: TIMESTEP\n");
fprintf(fp,BIGINT_FORMAT "\n",tstep);
if (dimension == 2) fprintf(fp,"ITEM: NUMBER OF SQUARES\n");
else fprintf(fp,"ITEM: NUMBER OF CUBES\n");
fprintf(fp,"%d\n",nprocs);
if (dimension == 2) fprintf(fp,"ITEM: SQUARES\n");
else fprintf(fp,"ITEM: CUBES\n");
if (dimension == 2) {
int m = 0;
for (int i = 0; i < nprocs; i++) {
fprintf(fp,"%d %d %d %d %d %d\n",i+1,1,m+1,m+2,m+3,m+4);
m += 4;
}
} else {
int m = 0;
for (int i = 0; i < nprocs; i++) {
fprintf(fp,"%d %d %d %d %d %d %d %d %d %d\n",
i+1,1,m+1,m+2,m+3,m+4,m+5,m+6,m+7,m+8);
m += 8;
}
}
memory->destroy(boxall);
}
/* ----------------------------------------------------------------------
debug output for Idim and count
only called by proc 0
------------------------------------------------------------------------- */
#ifdef BALANCE_DEBUG
void Balance::debug_shift_output(int idim, int m, int np, double *split)
{
int i;
const char *dim = NULL;
double *boxlo = domain->boxlo;
double *prd = domain->prd;
if (bdim[idim] == X) dim = "X";
else if (bdim[idim] == Y) dim = "Y";
else if (bdim[idim] == Z) dim = "Z";
fprintf(stderr,"Dimension %s, Iteration %d\n",dim,m);
fprintf(stderr," Count:");
for (i = 0; i < np; i++) fprintf(stderr," " BIGINT_FORMAT,count[i]);
fprintf(stderr,"\n");
fprintf(stderr," Sum:");
for (i = 0; i <= np; i++) fprintf(stderr," " BIGINT_FORMAT,sum[i]);
fprintf(stderr,"\n");
fprintf(stderr," Target:");
for (i = 0; i <= np; i++) fprintf(stderr," " BIGINT_FORMAT,target[i]);
fprintf(stderr,"\n");
fprintf(stderr," Actual cut:");
for (i = 0; i <= np; i++)
fprintf(stderr," %g",boxlo[bdim[idim]] + split[i]*prd[bdim[idim]]);
fprintf(stderr,"\n");
fprintf(stderr," Split:");
for (i = 0; i <= np; i++) fprintf(stderr," %g",split[i]);
fprintf(stderr,"\n");
fprintf(stderr," Low:");
for (i = 0; i <= np; i++) fprintf(stderr," %g",lo[i]);
fprintf(stderr,"\n");
fprintf(stderr," Low-sum:");
for (i = 0; i <= np; i++) fprintf(stderr," " BIGINT_FORMAT,losum[i]);
fprintf(stderr,"\n");
fprintf(stderr," Hi:");
for (i = 0; i <= np; i++) fprintf(stderr," %g",hi[i]);
fprintf(stderr,"\n");
fprintf(stderr," Hi-sum:");
for (i = 0; i <= np; i++) fprintf(stderr," " BIGINT_FORMAT,hisum[i]);
fprintf(stderr,"\n");
fprintf(stderr," Delta:");
for (i = 0; i < np; i++) fprintf(stderr," %g",split[i+1]-split[i]);
fprintf(stderr,"\n");
bigint max = 0;
for (i = 0; i < np; i++) max = MAX(max,count[i]);
fprintf(stderr," Imbalance factor: %g\n",1.0*max*np/target[np]);
}
#endif
c4science · Help