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17602b4c26fa94e02e204b3e8e85a48cecc65569
lammps/src/comm.cpp
Stan Moore 73fa8d4055 Rename Kokkos variables
2019-06-07 16:30:02 -06:00

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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 <cstdlib>
#include <cstring>
#include "comm.h"
#include "universe.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "pair.h"
#include "modify.h"
#include "fix.h"
#include "compute.h"
#include "domain.h"
#include "output.h"
#include "dump.h"
#include "group.h"
#include "procmap.h"
#include "irregular.h"
#include "accelerator_kokkos.h"
#include "memory.h"
#include "error.h"
#ifdef _OPENMP
#include <omp.h>
#endif
using namespace LAMMPS_NS;
#define BUFMIN 1000 // also in comm styles
enum{ONELEVEL,TWOLEVEL,NUMA,CUSTOM};
enum{CART,CARTREORDER,XYZ};
/* ---------------------------------------------------------------------- */
Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
mode = 0;
bordergroup = 0;
cutghostuser = 0.0;
cutusermulti = NULL;
ghost_velocity = 0;
user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0;
coregrid[0] = coregrid[1] = coregrid[2] = 1;
gridflag = ONELEVEL;
mapflag = CART;
customfile = NULL;
outfile = NULL;
recv_from_partition = send_to_partition = -1;
otherflag = 0;
maxexchange_atom = maxexchange_fix = 0;
grid2proc = NULL;
xsplit = ysplit = zsplit = NULL;
rcbnew = 0;
// use of OpenMP threads
// query OpenMP for number of threads/process set by user at run-time
// if the OMP_NUM_THREADS environment variable is not set, we default
// to using 1 thread. This follows the principle of the least surprise,
// while practically all OpenMP implementations violate it by using
// as many threads as there are (virtual) CPU cores by default.
nthreads = 1;
#ifdef _OPENMP
if (lmp->kokkos) {
nthreads = lmp->kokkos->nthreads * lmp->kokkos->numa;
} else if (getenv("OMP_NUM_THREADS") == NULL) {
nthreads = 1;
if (me == 0)
error->message(FLERR,"OMP_NUM_THREADS environment is not set. "
"Defaulting to 1 thread.");
} else {
nthreads = omp_get_max_threads();
}
// enforce consistent number of threads across all MPI tasks
MPI_Bcast(&nthreads,1,MPI_INT,0,world);
if (!lmp->kokkos) omp_set_num_threads(nthreads);
if (me == 0) {
if (screen)
fprintf(screen," using %d OpenMP thread(s) per MPI task\n",nthreads);
if (logfile)
fprintf(logfile," using %d OpenMP thread(s) per MPI task\n",nthreads);
}
#endif
}
/* ---------------------------------------------------------------------- */
Comm::~Comm()
{
memory->destroy(grid2proc);
memory->destroy(xsplit);
memory->destroy(ysplit);
memory->destroy(zsplit);
memory->destroy(cutusermulti);
delete [] customfile;
delete [] outfile;
}
/* ----------------------------------------------------------------------
deep copy of arrays from old Comm class to new one
all public/protected vectors/arrays in parent Comm class must be copied
called from alternate constructor of child classes
when new comm style is created from Input
------------------------------------------------------------------------- */
void Comm::copy_arrays(Comm *oldcomm)
{
if (oldcomm->grid2proc) {
memory->create(grid2proc,procgrid[0],procgrid[1],procgrid[2],
"comm:grid2proc");
memcpy(&grid2proc[0][0][0],&oldcomm->grid2proc[0][0][0],
(procgrid[0]*procgrid[1]*procgrid[2])*sizeof(int));
memory->create(xsplit,procgrid[0]+1,"comm:xsplit");
memory->create(ysplit,procgrid[1]+1,"comm:ysplit");
memory->create(zsplit,procgrid[2]+1,"comm:zsplit");
memcpy(xsplit,oldcomm->xsplit,(procgrid[0]+1)*sizeof(double));
memcpy(ysplit,oldcomm->ysplit,(procgrid[1]+1)*sizeof(double));
memcpy(zsplit,oldcomm->zsplit,(procgrid[2]+1)*sizeof(double));
}
if (oldcomm->cutusermulti) {
memory->create(cutusermulti,atom->ntypes+1,"comm:cutusermulti");
memcpy(cutusermulti,oldcomm->cutusermulti,atom->ntypes+1);
}
if (customfile) {
int n = strlen(oldcomm->customfile) + 1;
customfile = new char[n];
strcpy(customfile,oldcomm->customfile);
}
if (outfile) {
int n = strlen(oldcomm->outfile) + 1;
outfile = new char[n];
strcpy(outfile,oldcomm->outfile);
}
}
/* ----------------------------------------------------------------------
common to all Comm styles
------------------------------------------------------------------------- */
void Comm::init()
{
triclinic = domain->triclinic;
map_style = atom->map_style;
// check warn if any proc's subbox is smaller than neigh skin
// since may lead to lost atoms in exchange()
// really should check every exchange() in case box size is shrinking
// but seems overkill to do that (fix balance does perform this check)
domain->subbox_too_small_check(neighbor->skin);
// comm_only = 1 if only x,f are exchanged in forward/reverse comm
// comm_x_only = 0 if ghost_velocity since velocities are added
comm_x_only = atom->avec->comm_x_only;
comm_f_only = atom->avec->comm_f_only;
if (ghost_velocity) comm_x_only = 0;
// set per-atom sizes for forward/reverse/border comm
// augment by velocity and fix quantities if needed
size_forward = atom->avec->size_forward;
size_reverse = atom->avec->size_reverse;
size_border = atom->avec->size_border;
if (ghost_velocity) size_forward += atom->avec->size_velocity;
if (ghost_velocity) size_border += atom->avec->size_velocity;
for (int i = 0; i < modify->nfix; i++)
size_border += modify->fix[i]->comm_border;
// per-atom limits for communication
// maxexchange = max # of datums in exchange comm, set in exchange()
// maxforward = # of datums in largest forward comm
// maxreverse = # of datums in largest reverse comm
// query pair,fix,compute,dump for their requirements
// pair style can force reverse comm even if newton off
maxforward = MAX(size_forward,size_border);
maxreverse = size_reverse;
if (force->pair) maxforward = MAX(maxforward,force->pair->comm_forward);
if (force->pair) maxreverse = MAX(maxreverse,force->pair->comm_reverse);
for (int i = 0; i < modify->nfix; i++) {
maxforward = MAX(maxforward,modify->fix[i]->comm_forward);
maxreverse = MAX(maxreverse,modify->fix[i]->comm_reverse);
}
for (int i = 0; i < modify->ncompute; i++) {
maxforward = MAX(maxforward,modify->compute[i]->comm_forward);
maxreverse = MAX(maxreverse,modify->compute[i]->comm_reverse);
}
for (int i = 0; i < output->ndump; i++) {
maxforward = MAX(maxforward,output->dump[i]->comm_forward);
maxreverse = MAX(maxreverse,output->dump[i]->comm_reverse);
}
if (force->newton == 0) maxreverse = 0;
if (force->pair) maxreverse = MAX(maxreverse,force->pair->comm_reverse_off);
}
/* ----------------------------------------------------------------------
modify communication params
invoked from input script by comm_modify command
------------------------------------------------------------------------- */
void Comm::modify_params(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal comm_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"mode") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command");
if (strcmp(arg[iarg+1],"single") == 0) {
// need to reset cutghostuser when switching comm mode
if (mode == Comm::MULTI) cutghostuser = 0.0;
memory->destroy(cutusermulti);
cutusermulti = NULL;
mode = Comm::SINGLE;
} else if (strcmp(arg[iarg+1],"multi") == 0) {
// need to reset cutghostuser when switching comm mode
if (mode == Comm::SINGLE) cutghostuser = 0.0;
mode = Comm::MULTI;
} else error->all(FLERR,"Illegal comm_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"group") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command");
bordergroup = group->find(arg[iarg+1]);
if (bordergroup < 0)
error->all(FLERR,"Invalid group in comm_modify command");
if (bordergroup && (atom->firstgroupname == NULL ||
strcmp(arg[iarg+1],atom->firstgroupname) != 0))
error->all(FLERR,"Comm_modify group != atom_modify first group");
iarg += 2;
} else if (strcmp(arg[iarg],"cutoff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command");
if (mode == Comm::MULTI)
error->all(FLERR,
"Use cutoff/multi keyword to set cutoff in multi mode");
cutghostuser = force->numeric(FLERR,arg[iarg+1]);
if (cutghostuser < 0.0)
error->all(FLERR,"Invalid cutoff in comm_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"cutoff/multi") == 0) {
int i,nlo,nhi;
double cut;
if (mode == Comm::SINGLE)
error->all(FLERR,"Use cutoff keyword to set cutoff in single mode");
if (domain->box_exist == 0)
error->all(FLERR,
"Cannot set cutoff/multi before simulation box is defined");
const int ntypes = atom->ntypes;
if (iarg+3 > narg)
error->all(FLERR,"Illegal comm_modify command");
if (cutusermulti == NULL) {
memory->create(cutusermulti,ntypes+1,"comm:cutusermulti");
for (i=0; i < ntypes+1; ++i)
cutusermulti[i] = -1.0;
}
force->bounds(FLERR,arg[iarg+1],ntypes,nlo,nhi,1);
cut = force->numeric(FLERR,arg[iarg+2]);
cutghostuser = MAX(cutghostuser,cut);
if (cut < 0.0)
error->all(FLERR,"Invalid cutoff in comm_modify command");
for (i=nlo; i<=nhi; ++i)
cutusermulti[i] = cut;
iarg += 3;
} else if (strcmp(arg[iarg],"vel") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) ghost_velocity = 1;
else if (strcmp(arg[iarg+1],"no") == 0) ghost_velocity = 0;
else error->all(FLERR,"Illegal comm_modify command");
iarg += 2;
} else error->all(FLERR,"Illegal comm_modify command");
}
}
/* ----------------------------------------------------------------------
set dimensions for 3d grid of processors, and associated flags
invoked from input script by processors command
------------------------------------------------------------------------- */
void Comm::set_processors(int narg, char **arg)
{
if (narg < 3) error->all(FLERR,"Illegal processors command");
if (strcmp(arg[0],"*") == 0) user_procgrid[0] = 0;
else user_procgrid[0] = force->inumeric(FLERR,arg[0]);
if (strcmp(arg[1],"*") == 0) user_procgrid[1] = 0;
else user_procgrid[1] = force->inumeric(FLERR,arg[1]);
if (strcmp(arg[2],"*") == 0) user_procgrid[2] = 0;
else user_procgrid[2] = force->inumeric(FLERR,arg[2]);
if (user_procgrid[0] < 0 || user_procgrid[1] < 0 || user_procgrid[2] < 0)
error->all(FLERR,"Illegal processors command");
int p = user_procgrid[0]*user_procgrid[1]*user_procgrid[2];
if (p && p != nprocs)
error->all(FLERR,"Specified processors != physical processors");
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"grid") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal processors command");
if (strcmp(arg[iarg+1],"onelevel") == 0) {
gridflag = ONELEVEL;
} else if (strcmp(arg[iarg+1],"twolevel") == 0) {
if (iarg+6 > narg) error->all(FLERR,"Illegal processors command");
gridflag = TWOLEVEL;
ncores = force->inumeric(FLERR,arg[iarg+2]);
if (strcmp(arg[iarg+3],"*") == 0) user_coregrid[0] = 0;
else user_coregrid[0] = force->inumeric(FLERR,arg[iarg+3]);
if (strcmp(arg[iarg+4],"*") == 0) user_coregrid[1] = 0;
else user_coregrid[1] = force->inumeric(FLERR,arg[iarg+4]);
if (strcmp(arg[iarg+5],"*") == 0) user_coregrid[2] = 0;
else user_coregrid[2] = force->inumeric(FLERR,arg[iarg+5]);
if (ncores <= 0 || user_coregrid[0] < 0 ||
user_coregrid[1] < 0 || user_coregrid[2] < 0)
error->all(FLERR,"Illegal processors command");
iarg += 4;
} else if (strcmp(arg[iarg+1],"numa") == 0) {
gridflag = NUMA;
} else if (strcmp(arg[iarg+1],"custom") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal processors command");
gridflag = CUSTOM;
delete [] customfile;
int n = strlen(arg[iarg+2]) + 1;
customfile = new char[n];
strcpy(customfile,arg[iarg+2]);
iarg += 1;
} else error->all(FLERR,"Illegal processors command");
iarg += 2;
} else if (strcmp(arg[iarg],"map") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal processors command");
if (strcmp(arg[iarg+1],"cart") == 0) mapflag = CART;
else if (strcmp(arg[iarg+1],"cart/reorder") == 0) mapflag = CARTREORDER;
else if (strcmp(arg[iarg+1],"xyz") == 0 ||
strcmp(arg[iarg+1],"xzy") == 0 ||
strcmp(arg[iarg+1],"yxz") == 0 ||
strcmp(arg[iarg+1],"yzx") == 0 ||
strcmp(arg[iarg+1],"zxy") == 0 ||
strcmp(arg[iarg+1],"zyx") == 0) {
mapflag = XYZ;
strncpy(xyz,arg[iarg+1],3);
} else error->all(FLERR,"Illegal processors command");
iarg += 2;
} else if (strcmp(arg[iarg],"part") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal processors command");
if (universe->nworlds == 1)
error->all(FLERR,
"Cannot use processors part command "
"without using partitions");
int isend = force->inumeric(FLERR,arg[iarg+1]);
int irecv = force->inumeric(FLERR,arg[iarg+2]);
if (isend < 1 || isend > universe->nworlds ||
irecv < 1 || irecv > universe->nworlds || isend == irecv)
error->all(FLERR,"Invalid partitions in processors part command");
if (isend-1 == universe->iworld) {
if (send_to_partition >= 0)
error->all(FLERR,
"Sending partition in processors part command "
"is already a sender");
send_to_partition = irecv-1;
}
if (irecv-1 == universe->iworld) {
if (recv_from_partition >= 0)
error->all(FLERR,
"Receiving partition in processors part command "
"is already a receiver");
recv_from_partition = isend-1;
}
// only receiver has otherflag dependency
if (strcmp(arg[iarg+3],"multiple") == 0) {
if (universe->iworld == irecv-1) {
otherflag = 1;
other_style = Comm::MULTIPLE;
}
} else error->all(FLERR,"Illegal processors command");
iarg += 4;
} else if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal processors command");
delete [] outfile;
int n = strlen(arg[iarg+1]) + 1;
outfile = new char[n];
strcpy(outfile,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal processors command");
}
// error checks
if (gridflag == NUMA && mapflag != CART)
error->all(FLERR,"Processors grid numa and map style are incompatible");
if (otherflag && (gridflag == NUMA || gridflag == CUSTOM))
error->all(FLERR,
"Processors part option and grid style are incompatible");
}
/* ----------------------------------------------------------------------
create a 3d grid of procs based on Nprocs and box size & shape
map processors to grid, setup xyz split for a uniform grid
------------------------------------------------------------------------- */
void Comm::set_proc_grid(int outflag)
{
// recv 3d proc grid of another partition if my 3d grid depends on it
if (recv_from_partition >= 0) {
if (me == 0) {
MPI_Recv(other_procgrid,3,MPI_INT,
universe->root_proc[recv_from_partition],0,
universe->uworld,MPI_STATUS_IGNORE);
MPI_Recv(other_coregrid,3,MPI_INT,
universe->root_proc[recv_from_partition],0,
universe->uworld,MPI_STATUS_IGNORE);
}
MPI_Bcast(other_procgrid,3,MPI_INT,0,world);
MPI_Bcast(other_coregrid,3,MPI_INT,0,world);
}
// create ProcMap class to create 3d grid and map procs to it
ProcMap *pmap = new ProcMap(lmp);
// create 3d grid of processors
// produces procgrid and coregrid (if relevant)
if (gridflag == ONELEVEL) {
pmap->onelevel_grid(nprocs,user_procgrid,procgrid,
otherflag,other_style,other_procgrid,other_coregrid);
} else if (gridflag == TWOLEVEL) {
pmap->twolevel_grid(nprocs,user_procgrid,procgrid,
ncores,user_coregrid,coregrid,
otherflag,other_style,other_procgrid,other_coregrid);
} else if (gridflag == NUMA) {
pmap->numa_grid(nprocs,user_procgrid,procgrid,coregrid);
} else if (gridflag == CUSTOM) {
pmap->custom_grid(customfile,nprocs,user_procgrid,procgrid);
}
// error check on procgrid
// should not be necessary due to ProcMap
if (procgrid[0]*procgrid[1]*procgrid[2] != nprocs)
error->all(FLERR,"Bad grid of processors");
if (domain->dimension == 2 && procgrid[2] != 1)
error->all(FLERR,"Processor count in z must be 1 for 2d simulation");
// grid2proc[i][j][k] = proc that owns i,j,k location in 3d grid
if (grid2proc) memory->destroy(grid2proc);
memory->create(grid2proc,procgrid[0],procgrid[1],procgrid[2],
"comm:grid2proc");
// map processor IDs to 3d processor grid
// produces myloc, procneigh, grid2proc
if (gridflag == ONELEVEL) {
if (mapflag == CART)
pmap->cart_map(0,procgrid,myloc,procneigh,grid2proc);
else if (mapflag == CARTREORDER)
pmap->cart_map(1,procgrid,myloc,procneigh,grid2proc);
else if (mapflag == XYZ)
pmap->xyz_map(xyz,procgrid,myloc,procneigh,grid2proc);
} else if (gridflag == TWOLEVEL) {
if (mapflag == CART)
pmap->cart_map(0,procgrid,ncores,coregrid,myloc,procneigh,grid2proc);
else if (mapflag == CARTREORDER)
pmap->cart_map(1,procgrid,ncores,coregrid,myloc,procneigh,grid2proc);
else if (mapflag == XYZ)
pmap->xyz_map(xyz,procgrid,ncores,coregrid,myloc,procneigh,grid2proc);
} else if (gridflag == NUMA) {
pmap->numa_map(0,coregrid,myloc,procneigh,grid2proc);
} else if (gridflag == CUSTOM) {
pmap->custom_map(procgrid,myloc,procneigh,grid2proc);
}
// print 3d grid info to screen and logfile
if (outflag && me == 0) {
if (screen) {
fprintf(screen," %d by %d by %d MPI processor grid\n",
procgrid[0],procgrid[1],procgrid[2]);
if (gridflag == NUMA || gridflag == TWOLEVEL)
fprintf(screen," %d by %d by %d core grid within node\n",
coregrid[0],coregrid[1],coregrid[2]);
}
if (logfile) {
fprintf(logfile," %d by %d by %d MPI processor grid\n",
procgrid[0],procgrid[1],procgrid[2]);
if (gridflag == NUMA || gridflag == TWOLEVEL)
fprintf(logfile," %d by %d by %d core grid within node\n",
coregrid[0],coregrid[1],coregrid[2]);
}
}
// print 3d grid details to outfile
if (outfile) pmap->output(outfile,procgrid,grid2proc);
// free ProcMap class
delete pmap;
// set xsplit,ysplit,zsplit for uniform spacings
memory->destroy(xsplit);
memory->destroy(ysplit);
memory->destroy(zsplit);
memory->create(xsplit,procgrid[0]+1,"comm:xsplit");
memory->create(ysplit,procgrid[1]+1,"comm:ysplit");
memory->create(zsplit,procgrid[2]+1,"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;
// set lamda box params after procs are assigned
// only set once unless load-balancing occurs
if (domain->triclinic) domain->set_lamda_box();
// send my 3d proc grid to another partition if requested
if (send_to_partition >= 0) {
if (me == 0) {
MPI_Send(procgrid,3,MPI_INT,
universe->root_proc[send_to_partition],0,
universe->uworld);
MPI_Send(coregrid,3,MPI_INT,
universe->root_proc[send_to_partition],0,
universe->uworld);
}
}
}
/* ----------------------------------------------------------------------
determine which proc owns atom with coord x[3] based on current decomp
x will be in box (orthogonal) or lamda coords (triclinic)
if layout = UNIFORM, calculate owning proc directly
if layout = NONUNIFORM, iteratively find owning proc via binary search
if layout = TILED, CommTiled has its own method
return owning proc ID via grid2proc
return igx,igy,igz = logical grid loc of owing proc within 3d grid of procs
------------------------------------------------------------------------- */
int Comm::coord2proc(double *x, int &igx, int &igy, int &igz)
{
double *prd = domain->prd;
double *boxlo = domain->boxlo;
// initialize triclinic b/c coord2proc can be called before Comm::init()
// via Irregular::migrate_atoms()
triclinic = domain->triclinic;
if (layout == Comm::LAYOUT_UNIFORM) {
if (triclinic == 0) {
igx = static_cast<int> (procgrid[0] * (x[0]-boxlo[0]) / prd[0]);
igy = static_cast<int> (procgrid[1] * (x[1]-boxlo[1]) / prd[1]);
igz = static_cast<int> (procgrid[2] * (x[2]-boxlo[2]) / prd[2]);
} else {
igx = static_cast<int> (procgrid[0] * x[0]);
igy = static_cast<int> (procgrid[1] * x[1]);
igz = static_cast<int> (procgrid[2] * x[2]);
}
} else if (layout == Comm::LAYOUT_NONUNIFORM) {
if (triclinic == 0) {
igx = binary((x[0]-boxlo[0])/prd[0],procgrid[0],xsplit);
igy = binary((x[1]-boxlo[1])/prd[1],procgrid[1],ysplit);
igz = binary((x[2]-boxlo[2])/prd[2],procgrid[2],zsplit);
} else {
igx = binary(x[0],procgrid[0],xsplit);
igy = binary(x[1],procgrid[1],ysplit);
igz = binary(x[2],procgrid[2],zsplit);
}
}
if (igx < 0) igx = 0;
if (igx >= procgrid[0]) igx = procgrid[0] - 1;
if (igy < 0) igy = 0;
if (igy >= procgrid[1]) igy = procgrid[1] - 1;
if (igz < 0) igz = 0;
if (igz >= procgrid[2]) igz = procgrid[2] - 1;
return grid2proc[igx][igy][igz];
}
/* ----------------------------------------------------------------------
binary search for value in N-length ascending vec
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 if vec[index] <= value < vec[index+1]
------------------------------------------------------------------------- */
int Comm::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;
}
/* ----------------------------------------------------------------------
communicate inbuf around full ring of processors with messtag
nbytes = size of inbuf = n datums * nper bytes
callback() is invoked to allow caller to process/update each proc's inbuf
if self=1 (default), then callback() is invoked on final iteration
using original inbuf, which may have been updated
for non-NULL outbuf, final updated inbuf is copied to it
ok to specify outbuf = inbuf
the ptr argument is a pointer to the instance of calling class
------------------------------------------------------------------------- */
void Comm::ring(int n, int nper, void *inbuf, int messtag,
void (*callback)(int, char *, void *),
void *outbuf, void *ptr, int self)
{
MPI_Request request;
MPI_Status status;
int nbytes = n*nper;
int maxbytes;
MPI_Allreduce(&nbytes,&maxbytes,1,MPI_INT,MPI_MAX,world);
// no need to communicate without data
if (maxbytes == 0) return;
// sanity check
if ((nbytes > 0) && inbuf == NULL)
error->one(FLERR,"Cannot put data on ring from NULL pointer");
char *buf,*bufcopy;
memory->create(buf,maxbytes,"comm:buf");
memory->create(bufcopy,maxbytes,"comm:bufcopy");
if (nbytes && inbuf) memcpy(buf,inbuf,nbytes);
int next = me + 1;
int prev = me - 1;
if (next == nprocs) next = 0;
if (prev < 0) prev = nprocs - 1;
for (int loop = 0; loop < nprocs; loop++) {
if (me != next) {
MPI_Irecv(bufcopy,maxbytes,MPI_CHAR,prev,messtag,world,&request);
MPI_Send(buf,nbytes,MPI_CHAR,next,messtag,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_CHAR,&nbytes);
if (nbytes) memcpy(buf,bufcopy,nbytes);
}
if (self || loop < nprocs-1) callback(nbytes/nper,buf,ptr);
}
if (nbytes && outbuf) memcpy(outbuf,buf,nbytes);
memory->destroy(buf);
memory->destroy(bufcopy);
}
/* ----------------------------------------------------------------------
rendezvous communication operation
three stages:
first comm sends inbuf from caller decomp to rvous decomp
callback operates on data in rendevous decomp
second comm sends outbuf from rvous decomp back to caller decomp
inputs:
which = perform (0) irregular or (1) MPI_All2allv communication
n = # of datums in inbuf
inbuf = vector of input datums
insize = byte size of each input datum
inorder = 0 for inbuf in random proc order, 1 for datums ordered by proc
procs: inorder 0 = proc to send each datum to, 1 = # of datums/proc,
callback = caller function to invoke in rendezvous decomposition
takes input datums, returns output datums
outorder = same as inorder, but for datums returned by callback()
ptr = pointer to caller class, passed to callback()
outputs:
nout = # of output datums (function return)
outbuf = vector of output datums
outsize = byte size of each output datum
callback inputs:
nrvous = # of rvous decomp datums in inbuf_rvous
inbuf_rvous = vector of rvous decomp input datums
ptr = pointer to caller class
callback outputs:
nrvous_out = # of rvous decomp output datums (function return)
flag = 0 for no second comm, 1 for outbuf_rvous = inbuf_rvous,
2 for second comm with new outbuf_rvous
procs_rvous = outorder 0 = proc to send each datum to, 1 = # of datums/proc
allocated
outbuf_rvous = vector of rvous decomp output datums
NOTE: could use MPI_INT or MPI_DOUBLE insead of MPI_CHAR
to avoid checked-for overflow in MPI_Alltoallv?
------------------------------------------------------------------------- */
int Comm::
rendezvous(int which, int n, char *inbuf, int insize,
int inorder, int *procs,
int (*callback)(int, char *, int &, int *&, char *&, void *),
int outorder, char *&outbuf, int outsize, void *ptr, int statflag)
{
if (which == 0)
return rendezvous_irregular(n,inbuf,insize,inorder,procs,callback,
outorder,outbuf,outsize,ptr,statflag);
else
return rendezvous_all2all(n,inbuf,insize,inorder,procs,callback,
outorder,outbuf,outsize,ptr,statflag);
}
/* ---------------------------------------------------------------------- */
int Comm::
rendezvous_irregular(int n, char *inbuf, int insize, int inorder, int *procs,
int (*callback)(int, char *, int &, int *&, char *&, void *),
int outorder, char *&outbuf,
int outsize, void *ptr, int statflag)
{
// irregular comm of inbuf from caller decomp to rendezvous decomp
Irregular *irregular = new Irregular(lmp);
int nrvous;
if (inorder) nrvous = irregular->create_data_grouped(n,procs);
else nrvous = irregular->create_data(n,procs);
char *inbuf_rvous = (char *) memory->smalloc((bigint) nrvous*insize,
"rendezvous:inbuf");
irregular->exchange_data(inbuf,insize,inbuf_rvous);
bigint irregular1_bytes = irregular->memory_usage();
irregular->destroy_data();
delete irregular;
// peform rendezvous computation via callback()
// callback() allocates/populates proclist_rvous and outbuf_rvous
int flag;
int *procs_rvous;
char *outbuf_rvous;
int nrvous_out = callback(nrvous,inbuf_rvous,flag,
procs_rvous,outbuf_rvous,ptr);
if (flag != 1) memory->sfree(inbuf_rvous); // outbuf_rvous = inbuf_vous
if (flag == 0) {
if (statflag) rendezvous_stats(n,0,nrvous,nrvous_out,insize,outsize,
(bigint) nrvous_out*sizeof(int) +
irregular1_bytes);
return 0; // all nout_rvous are 0, no 2nd comm stage
}
// irregular comm of outbuf from rendezvous decomp back to caller decomp
// caller will free outbuf
irregular = new Irregular(lmp);
int nout;
if (outorder)
nout = irregular->create_data_grouped(nrvous_out,procs_rvous);
else nout = irregular->create_data(nrvous_out,procs_rvous);
outbuf = (char *) memory->smalloc((bigint) nout*outsize,
"rendezvous:outbuf");
irregular->exchange_data(outbuf_rvous,outsize,outbuf);
bigint irregular2_bytes = irregular->memory_usage();
irregular->destroy_data();
delete irregular;
memory->destroy(procs_rvous);
memory->sfree(outbuf_rvous);
// return number of output datums
// last arg to stats() = memory for procs_rvous + irregular comm
if (statflag) rendezvous_stats(n,nout,nrvous,nrvous_out,insize,outsize,
(bigint) nrvous_out*sizeof(int) +
MAX(irregular1_bytes,irregular2_bytes));
return nout;
}
/* ---------------------------------------------------------------------- */
int Comm::
rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
int (*callback)(int, char *, int &, int *&, char *&, void *),
int outorder, char *&outbuf, int outsize, void *ptr,
int statflag)
{
int iproc;
bigint all2all1_bytes,all2all2_bytes;
int *sendcount,*sdispls,*recvcount,*rdispls;
int *procs_a2a;
bigint *offsets;
char *inbuf_a2a,*outbuf_a2a;
// create procs and inbuf for All2all if necesary
if (!inorder) {
memory->create(procs_a2a,nprocs,"rendezvous:procs");
inbuf_a2a = (char *) memory->smalloc((bigint) n*insize,
"rendezvous:inbuf");
memory->create(offsets,nprocs,"rendezvous:offsets");
for (int i = 0; i < nprocs; i++) procs_a2a[i] = 0;
for (int i = 0; i < n; i++) procs_a2a[procs[i]]++;
offsets[0] = 0;
for (int i = 1; i < nprocs; i++)
offsets[i] = offsets[i-1] + insize*procs_a2a[i-1];
bigint offset = 0;
for (int i = 0; i < n; i++) {
iproc = procs[i];
memcpy(&inbuf_a2a[offsets[iproc]],&inbuf[offset],insize);
offsets[iproc] += insize;
offset += insize;
}
all2all1_bytes = nprocs*sizeof(int) + nprocs*sizeof(bigint) + n*insize;
} else {
procs_a2a = procs;
inbuf_a2a = inbuf;
all2all1_bytes = 0;
}
// create args for MPI_Alltoallv() on input data
memory->create(sendcount,nprocs,"rendezvous:sendcount");
memcpy(sendcount,procs_a2a,nprocs*sizeof(int));
memory->create(recvcount,nprocs,"rendezvous:recvcount");
MPI_Alltoall(sendcount,1,MPI_INT,recvcount,1,MPI_INT,world);
memory->create(sdispls,nprocs,"rendezvous:sdispls");
memory->create(rdispls,nprocs,"rendezvous:rdispls");
sdispls[0] = rdispls[0] = 0;
for (int i = 1; i < nprocs; i++) {
sdispls[i] = sdispls[i-1] + sendcount[i-1];
rdispls[i] = rdispls[i-1] + recvcount[i-1];
}
int nrvous = rdispls[nprocs-1] + recvcount[nprocs-1];
// test for overflow of input data due to imbalance or insize
// means that individual sdispls or rdispls values overflow
int overflow = 0;
if ((bigint) n*insize > MAXSMALLINT) overflow = 1;
if ((bigint) nrvous*insize > MAXSMALLINT) overflow = 1;
int overflowall;
MPI_Allreduce(&overflow,&overflowall,1,MPI_INT,MPI_MAX,world);
if (overflowall) error->all(FLERR,"Overflow input size in rendezvous_a2a");
for (int i = 0; i < nprocs; i++) {
sendcount[i] *= insize;
sdispls[i] *= insize;
recvcount[i] *= insize;
rdispls[i] *= insize;
}
// all2all comm of inbuf from caller decomp to rendezvous decomp
char *inbuf_rvous = (char *) memory->smalloc((bigint) nrvous*insize,
"rendezvous:inbuf");
MPI_Alltoallv(inbuf_a2a,sendcount,sdispls,MPI_CHAR,
inbuf_rvous,recvcount,rdispls,MPI_CHAR,world);
if (!inorder) {
memory->destroy(procs_a2a);
memory->sfree(inbuf_a2a);
memory->destroy(offsets);
}
// peform rendezvous computation via callback()
// callback() allocates/populates proclist_rvous and outbuf_rvous
int flag;
int *procs_rvous;
char *outbuf_rvous;
int nrvous_out = callback(nrvous,inbuf_rvous,flag,
procs_rvous,outbuf_rvous,ptr);
if (flag != 1) memory->sfree(inbuf_rvous); // outbuf_rvous = inbuf_vous
if (flag == 0) {
memory->destroy(sendcount);
memory->destroy(recvcount);
memory->destroy(sdispls);
memory->destroy(rdispls);
if (statflag) rendezvous_stats(n,0,nrvous,nrvous_out,insize,outsize,
(bigint) nrvous_out*sizeof(int) +
4*nprocs*sizeof(int) + all2all1_bytes);
return 0; // all nout_rvous are 0, no 2nd irregular
}
// create procs and outbuf for All2all if necesary
if (!outorder) {
memory->create(procs_a2a,nprocs,"rendezvous_a2a:procs");
outbuf_a2a = (char *) memory->smalloc((bigint) nrvous_out*outsize,
"rendezvous:outbuf");
memory->create(offsets,nprocs,"rendezvous:offsets");
for (int i = 0; i < nprocs; i++) procs_a2a[i] = 0;
for (int i = 0; i < nrvous_out; i++) procs_a2a[procs_rvous[i]]++;
offsets[0] = 0;
for (int i = 1; i < nprocs; i++)
offsets[i] = offsets[i-1] + outsize*procs_a2a[i-1];
bigint offset = 0;
for (int i = 0; i < nrvous_out; i++) {
iproc = procs_rvous[i];
memcpy(&outbuf_a2a[offsets[iproc]],&outbuf_rvous[offset],outsize);
offsets[iproc] += outsize;
offset += outsize;
}
all2all2_bytes = nprocs*sizeof(int) + nprocs*sizeof(bigint) +
nrvous_out*outsize;
} else {
procs_a2a = procs_rvous;
outbuf_a2a = outbuf_rvous;
all2all2_bytes = 0;
}
// comm outbuf from rendezvous decomposition back to caller
memcpy(sendcount,procs_a2a,nprocs*sizeof(int));
MPI_Alltoall(sendcount,1,MPI_INT,recvcount,1,MPI_INT,world);
sdispls[0] = rdispls[0] = 0;
for (int i = 1; i < nprocs; i++) {
sdispls[i] = sdispls[i-1] + sendcount[i-1];
rdispls[i] = rdispls[i-1] + recvcount[i-1];
}
int nout = rdispls[nprocs-1] + recvcount[nprocs-1];
// test for overflow of outbuf due to imbalance or outsize
// means that individual sdispls or rdispls values overflow
overflow = 0;
if ((bigint) nrvous*outsize > MAXSMALLINT) overflow = 1;
if ((bigint) nout*outsize > MAXSMALLINT) overflow = 1;
MPI_Allreduce(&overflow,&overflowall,1,MPI_INT,MPI_MAX,world);
if (overflowall) error->all(FLERR,"Overflow output in rendezvous_a2a");
for (int i = 0; i < nprocs; i++) {
sendcount[i] *= outsize;
sdispls[i] *= outsize;
recvcount[i] *= outsize;
rdispls[i] *= outsize;
}
// all2all comm of outbuf from rendezvous decomp back to caller decomp
// caller will free outbuf
outbuf = (char *) memory->smalloc((bigint) nout*outsize,"rendezvous:outbuf");
MPI_Alltoallv(outbuf_a2a,sendcount,sdispls,MPI_CHAR,
outbuf,recvcount,rdispls,MPI_CHAR,world);
memory->destroy(procs_rvous);
memory->sfree(outbuf_rvous);
if (!outorder) {
memory->destroy(procs_a2a);
memory->sfree(outbuf_a2a);
memory->destroy(offsets);
}
// clean up
memory->destroy(sendcount);
memory->destroy(recvcount);
memory->destroy(sdispls);
memory->destroy(rdispls);
// return number of output datums
// last arg to stats() = mem for procs_rvous + per-proc vecs + reordering ops
if (statflag) rendezvous_stats(n,nout,nrvous,nrvous_out,insize,outsize,
(bigint) nrvous_out*sizeof(int) +
4*nprocs*sizeof(int) +
MAX(all2all1_bytes,all2all2_bytes));
return nout;
}
/* ----------------------------------------------------------------------
print balance and memory info for rendezvous operation
useful for debugging
------------------------------------------------------------------------- */
void Comm::rendezvous_stats(int n, int nout, int nrvous, int nrvous_out,
int insize, int outsize, bigint commsize)
{
bigint size_in_all,size_in_max,size_in_min;
bigint size_out_all,size_out_max,size_out_min;
bigint size_inrvous_all,size_inrvous_max,size_inrvous_min;
bigint size_outrvous_all,size_outrvous_max,size_outrvous_min;
bigint size_comm_all,size_comm_max,size_comm_min;
bigint size = (bigint) n*insize;
MPI_Allreduce(&size,&size_in_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
MPI_Allreduce(&size,&size_in_max,1,MPI_LMP_BIGINT,MPI_MAX,world);
MPI_Allreduce(&size,&size_in_min,1,MPI_LMP_BIGINT,MPI_MIN,world);
size = (bigint) nout*outsize;
MPI_Allreduce(&size,&size_out_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
MPI_Allreduce(&size,&size_out_max,1,MPI_LMP_BIGINT,MPI_MAX,world);
MPI_Allreduce(&size,&size_out_min,1,MPI_LMP_BIGINT,MPI_MIN,world);
size = (bigint) nrvous*insize;
MPI_Allreduce(&size,&size_inrvous_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
MPI_Allreduce(&size,&size_inrvous_max,1,MPI_LMP_BIGINT,MPI_MAX,world);
MPI_Allreduce(&size,&size_inrvous_min,1,MPI_LMP_BIGINT,MPI_MIN,world);
size = (bigint) nrvous_out*insize;
MPI_Allreduce(&size,&size_outrvous_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
MPI_Allreduce(&size,&size_outrvous_max,1,MPI_LMP_BIGINT,MPI_MAX,world);
MPI_Allreduce(&size,&size_outrvous_min,1,MPI_LMP_BIGINT,MPI_MIN,world);
size = commsize;
MPI_Allreduce(&size,&size_comm_all,1,MPI_LMP_BIGINT,MPI_SUM,world);
MPI_Allreduce(&size,&size_comm_max,1,MPI_LMP_BIGINT,MPI_MAX,world);
MPI_Allreduce(&size,&size_comm_min,1,MPI_LMP_BIGINT,MPI_MIN,world);
int mbytes = 1024*1024;
if (me == 0) {
if (screen) {
fprintf(screen,"Rendezvous balance and memory info: (tot,ave,max,min) \n");
fprintf(screen," input datum count: "
BIGINT_FORMAT " %g " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
size_in_all/insize,1.0*size_in_all/nprocs/insize,
size_in_max/insize,size_in_min/insize);
fprintf(screen," input data (MB): %g %g %g %g\n",
1.0*size_in_all/mbytes,1.0*size_in_all/nprocs/mbytes,
1.0*size_in_max/mbytes,1.0*size_in_min/mbytes);
if (outsize)
fprintf(screen," output datum count: "
BIGINT_FORMAT " %g " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
size_out_all/outsize,1.0*size_out_all/nprocs/outsize,
size_out_max/outsize,size_out_min/outsize);
else
fprintf(screen," output datum count: %d %g %d %d\n",0,0.0,0,0);
fprintf(screen," output data (MB): %g %g %g %g\n",
1.0*size_out_all/mbytes,1.0*size_out_all/nprocs/mbytes,
1.0*size_out_max/mbytes,1.0*size_out_min/mbytes);
fprintf(screen," input rvous datum count: "
BIGINT_FORMAT " %g " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
size_inrvous_all/insize,1.0*size_inrvous_all/nprocs/insize,
size_inrvous_max/insize,size_inrvous_min/insize);
fprintf(screen," input rvous data (MB): %g %g %g %g\n",
1.0*size_inrvous_all/mbytes,1.0*size_inrvous_all/nprocs/mbytes,
1.0*size_inrvous_max/mbytes,1.0*size_inrvous_min/mbytes);
if (outsize)
fprintf(screen," output rvous datum count: "
BIGINT_FORMAT " %g " BIGINT_FORMAT " " BIGINT_FORMAT "\n",
size_outrvous_all/outsize,1.0*size_outrvous_all/nprocs/outsize,
size_outrvous_max/outsize,size_outrvous_min/outsize);
else
fprintf(screen," output rvous datum count: %d %g %d %d\n",0,0.0,0,0);
fprintf(screen," output rvous data (MB): %g %g %g %g\n",
1.0*size_outrvous_all/mbytes,1.0*size_outrvous_all/nprocs/mbytes,
1.0*size_outrvous_max/mbytes,1.0*size_outrvous_min/mbytes);
fprintf(screen," rvous comm (MB): %g %g %g %g\n",
1.0*size_comm_all/mbytes,1.0*size_comm_all/nprocs/mbytes,
1.0*size_comm_max/mbytes,1.0*size_comm_min/mbytes);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads Nlines from file into buf and bcasts buf to all procs
caller allocates buf to max size needed
each line is terminated by newline, even if last line in file is not
return 0 if successful, 1 if get EOF error before read is complete
------------------------------------------------------------------------- */
int Comm::read_lines_from_file(FILE *fp, int nlines, int maxline, char *buf)
{
int m;
if (me == 0) {
m = 0;
for (int i = 0; i < nlines; i++) {
if (!fgets(&buf[m],maxline,fp)) {
m = 0;
break;
}
m += strlen(&buf[m]);
}
if (m) {
if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
m++;
}
}
MPI_Bcast(&m,1,MPI_INT,0,world);
if (m == 0) return 1;
MPI_Bcast(buf,m,MPI_CHAR,0,world);
return 0;
}
/* ----------------------------------------------------------------------
proc 0 reads Nlines from file into buf and bcasts buf to all procs
caller allocates buf to max size needed
each line is terminated by newline, even if last line in file is not
return 0 if successful, 1 if get EOF error before read is complete
------------------------------------------------------------------------- */
int Comm::read_lines_from_file_universe(FILE *fp, int nlines, int maxline,
char *buf)
{
int m;
int me_universe = universe->me;
MPI_Comm uworld = universe->uworld;
if (me_universe == 0) {
m = 0;
for (int i = 0; i < nlines; i++) {
if (!fgets(&buf[m],maxline,fp)) {
m = 0;
break;
}
m += strlen(&buf[m]);
}
if (m) {
if (buf[m-1] != '\n') strcpy(&buf[m++],"\n");
m++;
}
}
MPI_Bcast(&m,1,MPI_INT,0,uworld);
if (m == 0) return 1;
MPI_Bcast(buf,m,MPI_CHAR,0,uworld);
return 0;
}
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