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lammps/src/comm.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author (triclinic) : Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "string.h"
#include "stdio.h"
#include "stdlib.h"
#include "comm.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
#include "neighbor.h"
#include "modify.h"
#include "fix.h"
#include "group.h"
#include "compute.h"
#include "error.h"
#include "memory.h"
using namespace LAMMPS_NS;
#define BUFFACTOR 1.5
#define BUFMIN 1000
#define BUFEXTRA 1000
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define BIG 1.0e20
enum{SINGLE,MULTI};
/* ----------------------------------------------------------------------
setup MPI and allocate buffer space
------------------------------------------------------------------------- */
Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0;
grid2proc = NULL;
bordergroup = 0;
style = SINGLE;
multilo = multihi = NULL;
cutghostmulti = NULL;
cutghostuser = 0.0;
ghost_velocity = 0;
// initialize comm buffers & exchange memory
maxsend = BUFMIN;
memory->create(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
maxrecv = BUFMIN;
memory->create(buf_recv,maxrecv,"comm:buf_recv");
maxswap = 6;
allocate_swap(maxswap);
sendlist = (int **) memory->smalloc(maxswap*sizeof(int *),"sendlist");
memory->create(maxsendlist,maxswap,"maxsendlist");
for (int i = 0; i < maxswap; i++) {
maxsendlist[i] = BUFMIN;
memory->create(sendlist[i],BUFMIN,"sendlist[i]");
}
maxforward_fix = maxreverse_fix = 0;
maxforward_pair = maxreverse_pair = 0;
}
/* ---------------------------------------------------------------------- */
Comm::~Comm()
{
if (grid2proc) memory->destroy(grid2proc);
free_swap();
if (style == MULTI) {
free_multi();
memory->destroy(cutghostmulti);
}
memory->destroy(maxsendlist);
if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]);
memory->sfree(sendlist);
memory->destroy(buf_send);
memory->destroy(buf_recv);
}
/* ----------------------------------------------------------------------
setup 3d grid of procs based on box size
------------------------------------------------------------------------- */
void Comm::set_procs()
{
procs2box();
if (procgrid[0]*procgrid[1]*procgrid[2] != nprocs)
error->all("Bad grid of processors");
if (domain->dimension == 2 && procgrid[2] != 1)
error->all("Processor count in z must be 1 for 2d simulation");
if (grid2proc) memory->destroy(grid2proc);
memory->create(grid2proc,procgrid[0],procgrid[1],procgrid[2],
"comm:grid2proc");
// use MPI Cartesian routines to setup 3d grid of procs
// grid2proc[i][j][k] = proc that owns i,j,k location in grid
// let MPI compute it instead of LAMMPS in case it is machine optimized
int reorder = 0;
int periods[3];
periods[0] = periods[1] = periods[2] = 1;
MPI_Comm cartesian;
MPI_Cart_create(world,3,procgrid,periods,reorder,&cartesian);
MPI_Cart_get(cartesian,3,procgrid,periods,myloc);
MPI_Cart_shift(cartesian,0,1,&procneigh[0][0],&procneigh[0][1]);
MPI_Cart_shift(cartesian,1,1,&procneigh[1][0],&procneigh[1][1]);
MPI_Cart_shift(cartesian,2,1,&procneigh[2][0],&procneigh[2][1]);
int coords[3];
int i,j,k;
for (i = 0; i < procgrid[0]; i++)
for (j = 0; j < procgrid[1]; j++)
for (k = 0; k < procgrid[2]; k++) {
coords[0] = i; coords[1] = j; coords[2] = k;
MPI_Cart_rank(cartesian,coords,&grid2proc[i][j][k]);
}
MPI_Comm_free(&cartesian);
// set lamda box params after procs are assigned
if (domain->triclinic) domain->set_lamda_box();
if (me == 0) {
if (screen) fprintf(screen," %d by %d by %d processor grid\n",
procgrid[0],procgrid[1],procgrid[2]);
if (logfile) fprintf(logfile," %d by %d by %d processor grid\n",
procgrid[0],procgrid[1],procgrid[2]);
}
}
/* ---------------------------------------------------------------------- */
void Comm::init()
{
triclinic = domain->triclinic;
map_style = atom->map_style;
// 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 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;
// maxforward = # of datums in largest forward communication
// maxreverse = # of datums in largest reverse communication
// query pair,fix,compute for their requirements
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);
}
if (force->newton == 0) maxreverse = 0;
// memory for multi-style communication
if (style == MULTI && multilo == NULL) {
allocate_multi(maxswap);
memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti");
}
if (style == SINGLE && multilo) {
free_multi();
memory->destroy(cutghostmulti);
}
}
/* ----------------------------------------------------------------------
setup spatial-decomposition communication patterns
function of neighbor cutoff(s) & cutghostuser & current box size
single style sets slab boundaries (slablo,slabhi) based on max cutoff
multi style sets type-dependent slab boundaries (multilo,multihi)
------------------------------------------------------------------------- */
void Comm::setup()
{
// cutghost[] = max distance at which ghost atoms need to be acquired
// for orthogonal:
// cutghost is in box coords = neigh->cutghost in all 3 dims
// for triclinic:
// neigh->cutghost = distance between tilted planes in box coords
// cutghost is in lamda coords = distance between those planes
// for multi:
// cutghostmulti = same as cutghost, only for each atom type
int i;
int ntypes = atom->ntypes;
double *prd,*sublo,*subhi;
double cut = MAX(neighbor->cutneighmax,cutghostuser);
if (triclinic == 0) {
prd = domain->prd;
sublo = domain->sublo;
subhi = domain->subhi;
cutghost[0] = cutghost[1] = cutghost[2] = cut;
if (style == MULTI) {
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++)
cutghostmulti[i][0] = cutghostmulti[i][1] = cutghostmulti[i][2] =
cuttype[i];
}
} else {
prd = domain->prd_lamda;
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
double *h_inv = domain->h_inv;
double length0,length1,length2;
length0 = sqrt(h_inv[0]*h_inv[0] + h_inv[5]*h_inv[5] + h_inv[4]*h_inv[4]);
cutghost[0] = cut * length0;
length1 = sqrt(h_inv[1]*h_inv[1] + h_inv[3]*h_inv[3]);
cutghost[1] = cut * length1;
length2 = h_inv[2];
cutghost[2] = cut * length2;
if (style == MULTI) {
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++) {
cutghostmulti[i][0] = cuttype[i] * length0;
cutghostmulti[i][1] = cuttype[i] * length1;
cutghostmulti[i][2] = cuttype[i] * length2;
}
}
}
// need = # of procs I need atoms from in each dim based on max cutoff
// for 2d, don't communicate in z
need[0] = static_cast<int> (cutghost[0] * procgrid[0] / prd[0]) + 1;
need[1] = static_cast<int> (cutghost[1] * procgrid[1] / prd[1]) + 1;
need[2] = static_cast<int> (cutghost[2] * procgrid[2] / prd[2]) + 1;
if (domain->dimension == 2) need[2] = 0;
// if non-periodic, do not communicate further than procgrid-1 away
// this enables very large cutoffs in non-periodic systems
int *periodicity = domain->periodicity;
if (periodicity[0] == 0) need[0] = MIN(need[0],procgrid[0]-1);
if (periodicity[1] == 0) need[1] = MIN(need[1],procgrid[1]-1);
if (periodicity[2] == 0) need[2] = MIN(need[2],procgrid[2]-1);
// allocate comm memory
nswap = 2 * (need[0]+need[1]+need[2]);
if (nswap > maxswap) grow_swap(nswap);
// setup parameters for each exchange:
// sendproc = proc to send to at each swap
// recvproc = proc to recv from at each swap
// for style SINGLE:
// slablo/slabhi = boundaries for slab of atoms to send at each swap
// use -BIG/midpt/BIG to insure all atoms included even if round-off occurs
// if round-off, atoms recvd across PBC can be < or > than subbox boundary
// note that borders() only loops over subset of atoms during each swap
// set slablo > slabhi for swaps across non-periodic boundaries
// this insures no atoms are swapped
// only for procs owning sub-box at non-periodic end of global box
// for style MULTI:
// multilo/multihi is same as slablo/slabhi, only for each atom type
// pbc_flag: 0 = nothing across a boundary, 1 = something across a boundary
// pbc = -1/0/1 for PBC factor in each of 3/6 orthog/triclinic dirs
// for triclinic, slablo/hi and pbc_border will be used in lamda (0-1) coords
// 1st part of if statement is sending to the west/south/down
// 2nd part of if statement is sending to the east/north/up
int dim,ineed;
int iswap = 0;
for (dim = 0; dim < 3; dim++) {
for (ineed = 0; ineed < 2*need[dim]; ineed++) {
pbc_flag[iswap] = 0;
pbc[iswap][0] = pbc[iswap][1] = pbc[iswap][2] =
pbc[iswap][3] = pbc[iswap][4] = pbc[iswap][5] = 0;
if (ineed % 2 == 0) {
sendproc[iswap] = procneigh[dim][0];
recvproc[iswap] = procneigh[dim][1];
if (style == SINGLE) {
if (ineed < 2) slablo[iswap] = -BIG;
else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
slabhi[iswap] = sublo[dim] + cutghost[dim];
} else {
for (i = 1; i <= ntypes; i++) {
if (ineed < 2) multilo[iswap][i] = -BIG;
else multilo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
multihi[iswap][i] = sublo[dim] + cutghostmulti[i][dim];
}
}
if (myloc[dim] == 0) {
if (periodicity[dim] == 0) {
if (style == SINGLE) slabhi[iswap] = slablo[iswap] - 1.0;
else
for (i = 1; i <= ntypes; i++)
multihi[iswap][i] = multilo[iswap][i] - 1.0;
} else {
pbc_flag[iswap] = 1;
pbc[iswap][dim] = 1;
if (triclinic) {
if (dim == 1) pbc[iswap][5] = 1;
else if (dim == 2) pbc[iswap][4] = pbc[iswap][3] = 1;
}
}
}
} else {
sendproc[iswap] = procneigh[dim][1];
recvproc[iswap] = procneigh[dim][0];
if (style == SINGLE) {
slablo[iswap] = subhi[dim] - cutghost[dim];
if (ineed < 2) slabhi[iswap] = BIG;
else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
} else {
for (i = 1; i <= ntypes; i++) {
multilo[iswap][i] = subhi[dim] - cutghostmulti[i][dim];
if (ineed < 2) multihi[iswap][i] = BIG;
else multihi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
}
}
if (myloc[dim] == procgrid[dim]-1) {
if (periodicity[dim] == 0) {
if (style == SINGLE) slabhi[iswap] = slablo[iswap] - 1.0;
else
for (i = 1; i <= ntypes; i++)
multihi[iswap][i] = multilo[iswap][i] - 1.0;
} else {
pbc_flag[iswap] = 1;
pbc[iswap][dim] = -1;
if (triclinic) {
if (dim == 1) pbc[iswap][5] = -1;
else if (dim == 2) pbc[iswap][4] = pbc[iswap][3] = -1;
}
}
}
}
iswap++;
}
}
}
/* ----------------------------------------------------------------------
forward communication of atom coords every timestep
other per-atom attributes may also be sent via pack/unpack routines
------------------------------------------------------------------------- */
void Comm::forward_comm()
{
int n;
MPI_Request request;
MPI_Status status;
AtomVec *avec = atom->avec;
double **x = atom->x;
double *buf;
// exchange data with another proc
// if other proc is self, just copy
// if comm_x_only set, exchange or copy directly to x, don't unpack
for (int iswap = 0; iswap < nswap; iswap++) {
if (sendproc[iswap] != me) {
if (comm_x_only) {
if (size_forward_recv[iswap]) buf = x[firstrecv[iswap]];
else buf = NULL;
MPI_Irecv(buf,size_forward_recv[iswap],MPI_DOUBLE,
recvproc[iswap],0,world,&request);
n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
buf_send,pbc_flag[iswap],pbc[iswap]);
MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
MPI_Wait(&request,&status);
} else if (ghost_velocity) {
MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
recvproc[iswap],0,world,&request);
n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],
buf_send,pbc_flag[iswap],pbc[iswap]);
MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
MPI_Wait(&request,&status);
avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_recv);
} else {
MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
recvproc[iswap],0,world,&request);
n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
buf_send,pbc_flag[iswap],pbc[iswap]);
MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
MPI_Wait(&request,&status);
avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
}
} else {
if (comm_x_only) {
if (sendnum[iswap])
n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
x[firstrecv[iswap]],pbc_flag[iswap],
pbc[iswap]);
} else if (ghost_velocity) {
n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],
buf_send,pbc_flag[iswap],pbc[iswap]);
avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_send);
} else {
n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
buf_send,pbc_flag[iswap],pbc[iswap]);
avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send);
}
}
}
}
/* ----------------------------------------------------------------------
reverse communication of forces on atoms every timestep
other per-atom attributes may also be sent via pack/unpack routines
------------------------------------------------------------------------- */
void Comm::reverse_comm()
{
int n;
MPI_Request request;
MPI_Status status;
AtomVec *avec = atom->avec;
double **f = atom->f;
double *buf;
// exchange data with another proc
// if other proc is self, just copy
// if comm_f_only set, exchange or copy directly from f, don't pack
for (int iswap = nswap-1; iswap >= 0; iswap--) {
if (sendproc[iswap] != me) {
if (comm_f_only) {
MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,
sendproc[iswap],0,world,&request);
if (size_reverse_send[iswap]) buf = f[firstrecv[iswap]];
else buf = NULL;
MPI_Send(buf,size_reverse_send[iswap],MPI_DOUBLE,
recvproc[iswap],0,world);
MPI_Wait(&request,&status);
} else {
MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,
sendproc[iswap],0,world,&request);
n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world);
MPI_Wait(&request,&status);
}
avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_recv);
} else {
if (comm_f_only) {
if (sendnum[iswap])
avec->unpack_reverse(sendnum[iswap],sendlist[iswap],
f[firstrecv[iswap]]);
} else {
n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_send);
}
}
}
}
/* ----------------------------------------------------------------------
exchange: move atoms to correct processors
atoms exchanged with all 6 stencil neighbors
send out atoms that have left my box, receive ones entering my box
atoms will be lost if not inside some proc's box
can happen if atom moves outside of non-periodic bounary
or if atom moves more than one proc away
this routine called before every reneighboring
for triclinic, atoms must be in lamda coords (0-1) before exchange is called
------------------------------------------------------------------------- */
void Comm::exchange()
{
int i,m,nsend,nrecv,nrecv1,nrecv2,nlocal;
double lo,hi,value;
double **x;
double *sublo,*subhi,*buf;
MPI_Request request;
MPI_Status status;
AtomVec *avec = atom->avec;
// clear global->local map for owned and ghost atoms
// b/c atoms migrate to new procs in exchange() and
// new ghosts are created in borders()
// map_set() is done at end of borders()
if (map_style) atom->map_clear();
// subbox bounds for orthogonal or triclinic
if (triclinic == 0) {
sublo = domain->sublo;
subhi = domain->subhi;
} else {
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
// loop over dimensions
for (int dim = 0; dim < 3; dim++) {
// fill buffer with atoms leaving my box, using < and >=
// when atom is deleted, fill it in with last atom
x = atom->x;
lo = sublo[dim];
hi = subhi[dim];
nlocal = atom->nlocal;
i = nsend = 0;
while (i < nlocal) {
if (x[i][dim] < lo || x[i][dim] >= hi) {
if (nsend > maxsend) grow_send(nsend,1);
nsend += avec->pack_exchange(i,&buf_send[nsend]);
avec->copy(nlocal-1,i);
nlocal--;
} else i++;
}
atom->nlocal = nlocal;
// send/recv atoms in both directions
// if 1 proc in dimension, no send/recv, set recv buf to send buf
// if 2 procs in dimension, single send/recv
// if more than 2 procs in dimension, send/recv to both neighbors
if (procgrid[dim] == 1) {
nrecv = nsend;
buf = buf_send;
} else {
MPI_Sendrecv(&nsend,1,MPI_INT,procneigh[dim][0],0,
&nrecv1,1,MPI_INT,procneigh[dim][1],0,world,&status);
nrecv = nrecv1;
if (procgrid[dim] > 2) {
MPI_Sendrecv(&nsend,1,MPI_INT,procneigh[dim][1],0,
&nrecv2,1,MPI_INT,procneigh[dim][0],0,world,&status);
nrecv += nrecv2;
}
if (nrecv > maxrecv) grow_recv(nrecv);
MPI_Irecv(buf_recv,nrecv1,MPI_DOUBLE,procneigh[dim][1],0,
world,&request);
MPI_Send(buf_send,nsend,MPI_DOUBLE,procneigh[dim][0],0,world);
MPI_Wait(&request,&status);
if (procgrid[dim] > 2) {
MPI_Irecv(&buf_recv[nrecv1],nrecv2,MPI_DOUBLE,procneigh[dim][0],0,
world,&request);
MPI_Send(buf_send,nsend,MPI_DOUBLE,procneigh[dim][1],0,world);
MPI_Wait(&request,&status);
}
buf = buf_recv;
}
// check incoming atoms to see if they are in my box
// if so, add to my list
m = 0;
while (m < nrecv) {
value = buf[m+dim+1];
if (value >= lo && value < hi) m += avec->unpack_exchange(&buf[m]);
else m += static_cast<int> (buf[m]);
}
}
if (atom->firstgroupname) atom->first_reorder();
}
/* ----------------------------------------------------------------------
borders: list nearby atoms to send to neighboring procs at every timestep
one list is created for every swap that will be made
as list is made, actually do swaps
this does equivalent of a communicate (so don't need to explicitly
call communicate routine on reneighboring timestep)
this routine is called before every reneighboring
for triclinic, atoms must be in lamda coords (0-1) before borders is called
------------------------------------------------------------------------- */
void Comm::borders()
{
int i,n,itype,iswap,dim,ineed,maxneed,smax,rmax;
int nsend,nrecv,nfirst,nlast,ngroup;
double lo,hi;
int *type;
double **x;
double *buf,*mlo,*mhi;
MPI_Request request;
MPI_Status status;
AtomVec *avec = atom->avec;
// clear old ghosts
atom->nghost = 0;
// do swaps over all 3 dimensions
iswap = 0;
smax = rmax = 0;
for (dim = 0; dim < 3; dim++) {
nlast = 0;
maxneed = 2*need[dim];
for (ineed = 0; ineed < maxneed; ineed++) {
// find atoms within slab boundaries lo/hi using <= and >=
// check atoms between nfirst and nlast
// for first swaps in a dim, check owned and ghost
// for later swaps in a dim, only check newly arrived ghosts
// store sent atom indices in list for use in future timesteps
x = atom->x;
if (style == SINGLE) {
lo = slablo[iswap];
hi = slabhi[iswap];
} else {
type = atom->type;
mlo = multilo[iswap];
mhi = multihi[iswap];
}
if (ineed % 2 == 0) {
nfirst = nlast;
nlast = atom->nlocal + atom->nghost;
}
nsend = 0;
// find send atoms according to SINGLE vs MULTI
// all atoms eligible versus atoms in bordergroup
// only need to limit loop to bordergroup for first sends (ineed < 2)
// on these sends, break loop in two: owned (in group) and ghost
if (!bordergroup || ineed >= 2) {
if (style == SINGLE) {
for (i = nfirst; i < nlast; i++)
if (x[i][dim] >= lo && x[i][dim] <= hi) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
} else {
for (i = nfirst; i < nlast; i++) {
itype = type[i];
if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
}
}
} else {
if (style == SINGLE) {
ngroup = atom->nfirst;
for (i = 0; i < ngroup; i++)
if (x[i][dim] >= lo && x[i][dim] <= hi) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
for (i = atom->nlocal; i < nlast; i++)
if (x[i][dim] >= lo && x[i][dim] <= hi) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
} else {
ngroup = atom->nfirst;
for (i = 0; i < ngroup; i++) {
itype = type[i];
if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
}
for (i = atom->nlocal; i < nlast; i++) {
itype = type[i];
if (x[i][dim] >= mlo[itype] && x[i][dim] <= mhi[itype]) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
sendlist[iswap][nsend++] = i;
}
}
}
}
// pack up list of border atoms
if (nsend*size_border > maxsend)
grow_send(nsend*size_border,0);
if (ghost_velocity)
n = avec->pack_border_vel(nsend,sendlist[iswap],buf_send,
pbc_flag[iswap],pbc[iswap]);
else
n = avec->pack_border(nsend,sendlist[iswap],buf_send,
pbc_flag[iswap],pbc[iswap]);
// swap atoms with other proc
// put incoming ghosts at end of my atom arrays
// if swapping with self, simply copy, no messages
if (sendproc[iswap] != me) {
MPI_Sendrecv(&nsend,1,MPI_INT,sendproc[iswap],0,
&nrecv,1,MPI_INT,recvproc[iswap],0,world,&status);
if (nrecv*size_border > maxrecv)
grow_recv(nrecv*size_border);
MPI_Irecv(buf_recv,nrecv*size_border,MPI_DOUBLE,
recvproc[iswap],0,world,&request);
MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
MPI_Wait(&request,&status);
buf = buf_recv;
} else {
nrecv = nsend;
buf = buf_send;
}
// unpack buffer
if (ghost_velocity)
avec->unpack_border_vel(nrecv,atom->nlocal+atom->nghost,buf);
else
avec->unpack_border(nrecv,atom->nlocal+atom->nghost,buf);
// set all pointers & counters
smax = MAX(smax,nsend);
rmax = MAX(rmax,nrecv);
sendnum[iswap] = nsend;
recvnum[iswap] = nrecv;
size_forward_recv[iswap] = nrecv*size_forward;
size_reverse_send[iswap] = nrecv*size_reverse;
size_reverse_recv[iswap] = nsend*size_reverse;
firstrecv[iswap] = atom->nlocal + atom->nghost;
atom->nghost += nrecv;
iswap++;
}
}
// insure send/recv buffers are long enough for all forward & reverse comm
int max = MAX(maxforward*smax,maxreverse*rmax);
if (max > maxsend) grow_send(max,0);
max = MAX(maxforward*rmax,maxreverse*smax);
if (max > maxrecv) grow_recv(max);
// reset global->local map
if (map_style) atom->map_set();
}
/* ----------------------------------------------------------------------
forward communication invoked by a Pair
------------------------------------------------------------------------- */
void Comm::forward_comm_pair(Pair *pair)
{
int iswap,n;
double *buf;
MPI_Request request;
MPI_Status status;
for (iswap = 0; iswap < nswap; iswap++) {
// pack buffer
n = pair->pack_comm(sendnum[iswap],sendlist[iswap],
buf_send,pbc_flag[iswap],pbc[iswap]);
// exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
MPI_Irecv(buf_recv,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,
world,&request);
MPI_Send(buf_send,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
// unpack buffer
pair->unpack_comm(recvnum[iswap],firstrecv[iswap],buf);
}
}
/* ----------------------------------------------------------------------
reverse communication invoked by a Pair
------------------------------------------------------------------------- */
void Comm::reverse_comm_pair(Pair *pair)
{
int iswap,n;
double *buf;
MPI_Request request;
MPI_Status status;
for (iswap = nswap-1; iswap >= 0; iswap--) {
// pack buffer
n = pair->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send);
// exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
MPI_Irecv(buf_recv,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,
world,&request);
MPI_Send(buf_send,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world);
MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
// unpack buffer
pair->unpack_reverse_comm(sendnum[iswap],sendlist[iswap],buf);
}
}
/* ----------------------------------------------------------------------
forward communication invoked by a Fix
------------------------------------------------------------------------- */
void Comm::forward_comm_fix(Fix *fix)
{
int iswap,n;
double *buf;
MPI_Request request;
MPI_Status status;
for (iswap = 0; iswap < nswap; iswap++) {
// pack buffer
n = fix->pack_comm(sendnum[iswap],sendlist[iswap],
buf_send,pbc_flag[iswap],pbc[iswap]);
// exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
MPI_Irecv(buf_recv,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,
world,&request);
MPI_Send(buf_send,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
// unpack buffer
fix->unpack_comm(recvnum[iswap],firstrecv[iswap],buf);
}
}
/* ----------------------------------------------------------------------
reverse communication invoked by a Fix
------------------------------------------------------------------------- */
void Comm::reverse_comm_fix(Fix *fix)
{
int iswap,n;
double *buf;
MPI_Request request;
MPI_Status status;
for (iswap = nswap-1; iswap >= 0; iswap--) {
// pack buffer
n = fix->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send);
// exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
MPI_Irecv(buf_recv,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,
world,&request);
MPI_Send(buf_send,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world);
MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
// unpack buffer
fix->unpack_reverse_comm(sendnum[iswap],sendlist[iswap],buf);
}
}
/* ----------------------------------------------------------------------
forward communication invoked by a Compute
------------------------------------------------------------------------- */
void Comm::forward_comm_compute(Compute *compute)
{
int iswap,n;
double *buf;
MPI_Request request;
MPI_Status status;
for (iswap = 0; iswap < nswap; iswap++) {
// pack buffer
n = compute->pack_comm(sendnum[iswap],sendlist[iswap],
buf_send,pbc_flag[iswap],pbc[iswap]);
// exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
MPI_Irecv(buf_recv,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,
world,&request);
MPI_Send(buf_send,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,world);
MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
// unpack buffer
compute->unpack_comm(recvnum[iswap],firstrecv[iswap],buf);
}
}
/* ----------------------------------------------------------------------
reverse communication invoked by a Compute
------------------------------------------------------------------------- */
void Comm::reverse_comm_compute(Compute *compute)
{
int iswap,n;
double *buf;
MPI_Request request;
MPI_Status status;
for (iswap = nswap-1; iswap >= 0; iswap--) {
// pack buffer
n = compute->pack_reverse_comm(recvnum[iswap],firstrecv[iswap],buf_send);
// exchange with another proc
// if self, set recv buffer to send buffer
if (sendproc[iswap] != me) {
MPI_Irecv(buf_recv,n*sendnum[iswap],MPI_DOUBLE,sendproc[iswap],0,
world,&request);
MPI_Send(buf_send,n*recvnum[iswap],MPI_DOUBLE,recvproc[iswap],0,world);
MPI_Wait(&request,&status);
buf = buf_recv;
} else buf = buf_send;
// unpack buffer
compute->unpack_reverse_comm(sendnum[iswap],sendlist[iswap],buf);
}
}
/* ----------------------------------------------------------------------
assign nprocs to 3d xprd,yprd,zprd box so as to minimize surface area
area = surface area of each of 3 faces of simulation box
for triclinic, area = cross product of 2 edge vectors stored in h matrix
------------------------------------------------------------------------- */
void Comm::procs2box()
{
procgrid[0] = user_procgrid[0];
procgrid[1] = user_procgrid[1];
procgrid[2] = user_procgrid[2];
// all 3 proc counts are specified
if (procgrid[0] && procgrid[1] && procgrid[2]) return;
// 2 out of 3 proc counts are specified
if (procgrid[0] > 0 && procgrid[1] > 0) {
procgrid[2] = nprocs/(procgrid[0]*procgrid[1]);
return;
} else if (procgrid[0] > 0 && procgrid[2] > 0) {
procgrid[1] = nprocs/(procgrid[0]*procgrid[2]);
return;
} else if (procgrid[1] > 0 && procgrid[2] > 0) {
procgrid[0] = nprocs/(procgrid[1]*procgrid[2]);
return;
}
// determine cross-sectional areas for orthogonal and triclinic boxes
// area[0] = xy, area[1] = xz, area[2] = yz
double area[3];
if (domain->triclinic == 0) {
area[0] = domain->xprd * domain->yprd;
area[1] = domain->xprd * domain->zprd;
area[2] = domain->yprd * domain->zprd;
} else {
double *h = domain->h;
double x,y,z;
cross(h[0],0.0,0.0,h[5],h[1],0.0,x,y,z);
area[0] = sqrt(x*x + y*y + z*z);
cross(h[0],0.0,0.0,h[4],h[3],h[2],x,y,z);
area[1] = sqrt(x*x + y*y + z*z);
cross(h[5],h[1],0.0,h[4],h[3],h[2],x,y,z);
area[2] = sqrt(x*x + y*y + z*z);
}
double bestsurf = 2.0 * (area[0]+area[1]+area[2]);
// loop thru all possible factorizations of nprocs
// only consider valid cases that match procgrid settings
// surf = surface area of a proc sub-domain
int ipx,ipy,ipz,valid;
double surf;
ipx = 1;
while (ipx <= nprocs) {
valid = 1;
if (user_procgrid[0] && ipx != user_procgrid[0]) valid = 0;
if (nprocs % ipx) valid = 0;
if (!valid) {
ipx++;
continue;
}
ipy = 1;
while (ipy <= nprocs/ipx) {
valid = 1;
if (user_procgrid[1] && ipy != user_procgrid[1]) valid = 0;
if ((nprocs/ipx) % ipy) valid = 0;
if (!valid) {
ipy++;
continue;
}
ipz = nprocs/ipx/ipy;
valid = 1;
if (user_procgrid[2] && ipz != user_procgrid[2]) valid = 0;
if (domain->dimension == 2 && ipz != 1) valid = 0;
if (!valid) {
ipy++;
continue;
}
surf = area[0]/ipx/ipy + area[1]/ipx/ipz + area[2]/ipy/ipz;
if (surf < bestsurf) {
bestsurf = surf;
procgrid[0] = ipx;
procgrid[1] = ipy;
procgrid[2] = ipz;
}
ipy++;
}
ipx++;
}
}
/* ----------------------------------------------------------------------
vector cross product: c = a x b
------------------------------------------------------------------------- */
void Comm::cross(double ax, double ay, double az,
double bx, double by, double bz,
double &cx, double &cy, double &cz)
{
cx = ay*bz - az*by;
cy = az*bx - ax*bz;
cz = ax*by - ay*bx;
}
/* ----------------------------------------------------------------------
realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA
if flag = 1, realloc
if flag = 0, don't need to realloc with copy, just free/malloc
------------------------------------------------------------------------- */
void Comm::grow_send(int n, int flag)
{
maxsend = static_cast<int> (BUFFACTOR * n);
if (flag)
memory->grow(buf_send,(maxsend+BUFEXTRA),"comm:buf_send");
else {
memory->destroy(buf_send);
memory->create(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
}
}
/* ----------------------------------------------------------------------
free/malloc the size of the recv buffer as needed with BUFFACTOR
------------------------------------------------------------------------- */
void Comm::grow_recv(int n)
{
maxrecv = static_cast<int> (BUFFACTOR * n);
memory->destroy(buf_recv);
memory->create(buf_recv,maxrecv,"comm:buf_recv");
}
/* ----------------------------------------------------------------------
realloc the size of the iswap sendlist as needed with BUFFACTOR
------------------------------------------------------------------------- */
void Comm::grow_list(int iswap, int n)
{
maxsendlist[iswap] = static_cast<int> (BUFFACTOR * n);
memory->grow(sendlist[iswap],maxsendlist[iswap],"comm:sendlist[iswap]");
}
/* ----------------------------------------------------------------------
realloc the buffers needed for swaps
------------------------------------------------------------------------- */
void Comm::grow_swap(int n)
{
free_swap();
allocate_swap(n);
if (style == MULTI) {
free_multi();
allocate_multi(n);
}
sendlist = (int **)
memory->srealloc(sendlist,n*sizeof(int *),"comm:sendlist");
memory->grow(maxsendlist,n,"comm:maxsendlist");
for (int i = maxswap; i < n; i++) {
maxsendlist[i] = BUFMIN;
memory->create(sendlist[i],BUFMIN,"comm:sendlist[i]");
}
maxswap = n;
}
/* ----------------------------------------------------------------------
allocation of swap info
------------------------------------------------------------------------- */
void Comm::allocate_swap(int n)
{
memory->create(sendnum,n,"comm:sendnum");
memory->create(recvnum,n,"comm:recvnum");
memory->create(sendproc,n,"comm:sendproc");
memory->create(recvproc,n,"comm:recvproc");
memory->create(size_forward_recv,n,"comm:size");
memory->create(size_reverse_send,n,"comm:size");
memory->create(size_reverse_recv,n,"comm:size");
memory->create(slablo,n,"comm:slablo");
memory->create(slabhi,n,"comm:slabhi");
memory->create(firstrecv,n,"comm:firstrecv");
memory->create(pbc_flag,n,"comm:pbc_flag");
memory->create(pbc,n,6,"comm:pbc");
}
/* ----------------------------------------------------------------------
allocation of multi-type swap info
------------------------------------------------------------------------- */
void Comm::allocate_multi(int n)
{
multilo = memory->create(multilo,n,atom->ntypes+1,"comm:multilo");
multihi = memory->create(multihi,n,atom->ntypes+1,"comm:multihi");
}
/* ----------------------------------------------------------------------
free memory for swaps
------------------------------------------------------------------------- */
void Comm::free_swap()
{
memory->destroy(sendnum);
memory->destroy(recvnum);
memory->destroy(sendproc);
memory->destroy(recvproc);
memory->destroy(size_forward_recv);
memory->destroy(size_reverse_send);
memory->destroy(size_reverse_recv);
memory->destroy(slablo);
memory->destroy(slabhi);
memory->destroy(firstrecv);
memory->destroy(pbc_flag);
memory->destroy_2d_int_array(pbc);
}
/* ----------------------------------------------------------------------
free memory for multi-type swaps
------------------------------------------------------------------------- */
void Comm::free_multi()
{
memory->destroy(multilo);
memory->destroy(multihi);
}
/* ----------------------------------------------------------------------
set communication style
------------------------------------------------------------------------- */
void Comm::set(int narg, char **arg)
{
if (narg < 1) error->all("Illegal communicate command");
if (strcmp(arg[0],"single") == 0) style = SINGLE;
else if (strcmp(arg[0],"multi") == 0) style = MULTI;
else error->all("Illegal communicate command");
int iarg = 1;
while (iarg < narg) {
if (strcmp(arg[iarg],"group") == 0) {
if (iarg+2 > narg) error->all("Illegal communicate command");
bordergroup = group->find(arg[iarg+1]);
if (bordergroup < 0)
error->all("Invalid group in communicate command");
if (bordergroup && (atom->firstgroupname == NULL ||
strcmp(arg[iarg+1],atom->firstgroupname) != 0))
error->all("Communicate group != atom_modify first group");
iarg += 2;
} else if (strcmp(arg[iarg],"cutoff") == 0) {
if (iarg+2 > narg) error->all("Illegal communicate command");
cutghostuser = atof(arg[iarg+1]);
if (cutghostuser < 0.0)
error->all("Invalid cutoff in communicate command");
iarg += 2;
} else if (strcmp(arg[iarg],"vel") == 0) {
if (iarg+2 > narg) error->all("Illegal communicate command");
if (strcmp(arg[iarg+1],"yes") == 0) ghost_velocity = 1;
else if (strcmp(arg[iarg+1],"yes") == 0) ghost_velocity = 0;
else error->all("Illegal communicate command");
iarg += 2;
} else error->all("Illegal communicate command");
}
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
double Comm::memory_usage()
{
double bytes = 0.0;
for (int i = 0; i < nswap; i++) bytes += maxsendlist[i] * sizeof(int);
bytes += maxsend * sizeof(double);
bytes += maxrecv * sizeof(double);
return bytes;
}
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