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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12017 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-05-22 14:38:26 +00:00
parent d45d192091
commit a59a131024
8 changed files with 619 additions and 120 deletions
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657
src/comm_tiled.cpp
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@ -13,10 +13,21 @@
#include "lmptype.h"
#include "comm_tiled.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "pair.h"
#include "modify.h"
#include "fix.h"
#include "compute.h"
#include "dump.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define BUFFACTOR 1.5
enum{SINGLE,MULTI}; // same as in Comm
/* ---------------------------------------------------------------------- */
@ -39,6 +50,28 @@ CommTiled::~CommTiled()
void CommTiled::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 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;
}
/* ----------------------------------------------------------------------
@ -50,6 +83,13 @@ void CommTiled::init()
void CommTiled::setup()
{
// error on triclinic or multi?
// set nswap
// setup neighbor proc info for exchange()
// setup nsendproc and nrecvproc bounts
// setup sendproc and recvproc lists
// setup sendbox
// reallocate requests and statuses
}
/* ----------------------------------------------------------------------
@ -59,83 +99,78 @@ void CommTiled::setup()
void CommTiled::forward_comm(int dummy)
{
/*
int n;
MPI_Request request;
int i,irecv,n;
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
// exchange data with another set of procs in each swap
// if first proc in set is self, then is just self across PBC, 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 (sendproc[iswap][0] != me) {
if (comm_x_only) {
// loop over recvs
if (size_forward_recv[iswap]) buf = x[firstrecv[iswap]];
else buf = NULL;
if (size_forward_recv[iswap])
MPI_Irecv(buf,size_forward_recv[iswap],MPI_DOUBLE,
recvproc[iswap],0,world,&request);
// loop over sends
n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
buf_send,pbc_flag[iswap],pbc[iswap]);
if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
// wait any or all?
if (size_forward_recv[iswap]) MPI_Wait(&request,&status);
for (i = 0; i < nrecvproc[iswap]; i++)
MPI_Irecv(x[firstrecv[iswap][i]],size_forward_recv[iswap][i],
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nsendproc[iswap]; i++) {
n = avec->pack_comm(sendnum[iswap][i],sendlist[iswap][i],
buf_send,pbc_flag[iswap][i],pbc[iswap][i]);
MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap][i],0,world);
}
MPI_Waitall(nrecvproc[iswap],requests,statuses);
} else if (ghost_velocity) {
// loop over recvs
if (size_forward_recv[iswap])
MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
recvproc[iswap],0,world,&request);
// loop over sends
n = avec->pack_comm_vel(sendnum[iswap],sendlist[iswap],
buf_send,pbc_flag[iswap],pbc[iswap]);
if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
// wait any or all?
if (size_forward_recv[iswap]) MPI_Wait(&request,&status);
// loop over recvs and unpack each
avec->unpack_comm_vel(recvnum[iswap],firstrecv[iswap],buf_recv);
for (i = 0; i < nrecvproc[iswap]; i++)
MPI_Irecv(&buf_recv[forward_recv_offset[iswap][i]],
size_forward_recv[iswap][i],
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nsendproc[iswap]; i++) {
n = avec->pack_comm_vel(sendnum[iswap][i],sendlist[iswap][i],
buf_send,pbc_flag[iswap][i],pbc[iswap][i]);
MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap][i],0,world);
}
for (i = 0; i < nrecvproc[iswap]; i++) {
MPI_Waitany(nrecvproc[iswap],requests,&irecv,&status);
avec->unpack_comm_vel(recvnum[iswap][i],firstrecv[iswap][irecv],
&buf_recv[forward_recv_offset[iswap][irecv]]);
}
} else {
// loop over recvs
if (size_forward_recv[iswap])
MPI_Irecv(buf_recv,size_forward_recv[iswap],MPI_DOUBLE,
recvproc[iswap],0,world,&request);
// loop over sends
n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
buf_send,pbc_flag[iswap],pbc[iswap]);
if (n) MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap],0,world);
// wait any or all?
if (size_forward_recv[iswap]) MPI_Wait(&request,&status);
// loop over recvs and unpack each
avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_recv);
for (i = 0; i < nrecvproc[iswap]; i++)
MPI_Irecv(&buf_recv[forward_recv_offset[iswap][i]],
size_forward_recv[iswap][i],
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nsendproc[iswap]; i++) {
n = avec->pack_comm(sendnum[iswap][i],sendlist[iswap][i],
buf_send,pbc_flag[iswap][i],pbc[iswap][i]);
MPI_Send(buf_send,n,MPI_DOUBLE,sendproc[iswap][i],0,world);
}
for (i = 0; i < nrecvproc[iswap]; i++) {
MPI_Waitany(nrecvproc[iswap],requests,&irecv,&status);
avec->unpack_comm(recvnum[iswap][i],firstrecv[iswap][irecv],
&buf_recv[forward_recv_offset[iswap][irecv]]);
}
}
} else {
if (comm_x_only) {
// single copy
if (sendnum[iswap])
n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
x[firstrecv[iswap]],pbc_flag[iswap],
pbc[iswap]);
if (sendnum[iswap][0])
n = avec->pack_comm(sendnum[iswap][0],sendlist[iswap][0],
x[firstrecv[iswap][0]],pbc_flag[iswap][0],
pbc[iswap][0]);
} else if (ghost_velocity) {
// single copy
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);
n = avec->pack_comm_vel(sendnum[iswap][0],sendlist[iswap][0],
buf_send,pbc_flag[iswap][0],pbc[iswap][0]);
avec->unpack_comm_vel(recvnum[iswap][0],firstrecv[iswap][0],buf_send);
} else {
// single copy
n = avec->pack_comm(sendnum[iswap],sendlist[iswap],
buf_send,pbc_flag[iswap],pbc[iswap]);
avec->unpack_comm(recvnum[iswap],firstrecv[iswap],buf_send);
n = avec->pack_comm(sendnum[iswap][0],sendlist[iswap][0],
buf_send,pbc_flag[iswap][0],pbc[iswap][0]);
avec->unpack_comm(recvnum[iswap][0],firstrecv[iswap][0],buf_send);
}
}
}
*/
}
/* ----------------------------------------------------------------------
@ -145,63 +180,60 @@ void CommTiled::forward_comm(int dummy)
void CommTiled::reverse_comm()
{
/*
int n;
int i,irecv,n;
MPI_Request request;
MPI_Status status;
AtomVec *avec = atom->avec;
double **f = atom->f;
double *buf;
// exchange data with other procs in each swap
// if other proc is self, just copy
// exchange data with another set of procs in each swap
// if first proc in set is self, then is just self across PBC, 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 (!selfflag[iswap]) {
if (sendproc[iswap][0] != me) {
if (comm_f_only) {
// loop over recvs
if (size_reverse_recv[iswap])
MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,
sendproc[iswap],0,world,&request);
// loop over sends
if (size_reverse_send[iswap]) buf = f[firstrecv[iswap]];
else buf = NULL;
if (size_reverse_send[iswap])
MPI_Send(buf,size_reverse_send[iswap],MPI_DOUBLE,
recvproc[iswap],0,world);
// wait any or all?
if (size_reverse_recv[iswap]) MPI_Wait(&request,&status);
// loop over recvs and unpack each
avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_recv);
for (i = 0; i < nsendproc[iswap]; i++)
MPI_Irecv(&buf_recv[reverse_recv_offset[iswap][i]],
size_reverse_recv[iswap][i],MPI_DOUBLE,
sendproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nrecvproc[iswap]; i++)
MPI_Send(f[firstrecv[iswap][i]],size_reverse_send[iswap][i],
MPI_DOUBLE,recvproc[iswap][i],0,world);
for (i = 0; i < nsendproc[iswap]; i++) {
MPI_Waitany(nsendproc[iswap],requests,&irecv,&status);
avec->unpack_reverse(sendnum[iswap][irecv],sendlist[iswap][irecv],
&buf_recv[reverse_recv_offset[iswap][irecv]]);
}
} else {
// loop over recvs
if (size_reverse_recv[iswap])
MPI_Irecv(buf_recv,size_reverse_recv[iswap],MPI_DOUBLE,
sendproc[iswap],0,world,&request);
// loop over sends
n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
if (n) MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap],0,world);
// wait any or all?
if (size_reverse_recv[iswap]) MPI_Wait(&request,&status);
// loop over recvs and unpack each
avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_recv);
for (i = 0; i < nsendproc[iswap]; i++)
MPI_Irecv(&buf_recv[reverse_recv_offset[iswap][i]],
size_reverse_recv[iswap][i],MPI_DOUBLE,
sendproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nrecvproc[iswap]; i++) {
n = avec->pack_reverse(recvnum[iswap][i],firstrecv[iswap][i],
buf_send);
MPI_Send(buf_send,n,MPI_DOUBLE,recvproc[iswap][i],0,world);
}
for (i = 0; i < nsendproc[iswap]; i++) {
MPI_Waitany(nsendproc[iswap],requests,&irecv,&status);
avec->unpack_reverse(sendnum[iswap][irecv],sendlist[iswap][irecv],
&buf_recv[reverse_recv_offset[iswap][irecv]]);
}
}
} else {
if (comm_f_only) {
// single copy
if (sendnum[iswap])
avec->unpack_reverse(sendnum[iswap],sendlist[iswap],
f[firstrecv[iswap]]);
if (sendnum[iswap][0])
avec->unpack_reverse(sendnum[iswap][0],sendlist[iswap][0],
f[firstrecv[iswap][0]]);
} else {
// single copy
n = avec->pack_reverse(recvnum[iswap],firstrecv[iswap],buf_send);
avec->unpack_reverse(sendnum[iswap],sendlist[iswap],buf_send);
n = avec->pack_reverse(recvnum[iswap][0],firstrecv[iswap][0],buf_send);
avec->unpack_reverse(sendnum[iswap][0],sendlist[iswap][0],buf_send);
}
}
}
*/
}
/* ----------------------------------------------------------------------
@ -221,32 +253,247 @@ void CommTiled::exchange()
/* ----------------------------------------------------------------------
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
one list is created per swap/proc that will be made
as list is made, actually do communication
this does equivalent of a forward_comm(), so don't need to explicitly
call forward_comm() 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 CommTiled::borders()
{
int i,n,irecv,ngroup,nlast,nsend,rmaxswap;
double xlo,xhi,ylo,yhi,zlo,zhi;
double *bbox;
double **x;
MPI_Status status;
AtomVec *avec = atom->avec;
// smax = max size of single send in a swap/proc
// rmax = max size of recvs from all procs for a swap
int smax = 0;
int rmax = 0;
// loop over all swaps in all dimensions
for (int iswap = 0; iswap < nswap; iswap++) {
// find atoms within rectangles using <= and >=
// for x-dim swaps, check owned atoms
// for yz-dim swaps, check owned and ghost atoms
// store sent atom indices in list for use in future timesteps
// NOTE: assume SINGLE mode, add back in logic for MULTI mode later
x = atom->x;
for (i = 0; i < nsendproc[iswap]; i++) {
bbox = sendbox[iswap][i];
xlo = bbox[0]; xhi = bbox[1];
ylo = bbox[2]; yhi = bbox[3];
zlo = bbox[4]; zhi = bbox[5];
ngroup = atom->nfirst;
if (iswap < 2) nlast = atom->nlocal;
else nlast = atom->nlocal + atom->nghost;
nsend = 0;
for (i = 0; i < ngroup; i++)
if (x[i][0] >= xlo && x[i][0] <= xhi &&
x[i][1] >= ylo && x[i][1] <= yhi &&
x[i][2] >= zlo && x[i][2] <= zhi) {
if (nsend == maxsendlist[iswap][i]) grow_list(iswap,i,nsend);
sendlist[iswap][i][nsend++] = i;
}
for (i = atom->nlocal; i < nlast; i++)
if (x[i][0] >= xlo && x[i][0] <= xhi &&
x[i][1] >= ylo && x[i][1] <= yhi &&
x[i][2] >= zlo && x[i][2] <= zhi) {
if (nsend == maxsendlist[iswap][i]) grow_list(iswap,i,nsend);
sendlist[iswap][i][nsend++] = i;
}
sendnum[iswap][i] = nsend;
smax = MAX(smax,nsend);
}
// send sendnum counts to procs who recv from me
if (sendproc[iswap][0] != me) {
for (i = 0; i < nrecvproc[iswap]; i++)
MPI_Irecv(&recvnum[iswap][i],1,MPI_INT,
recvproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nsendproc[iswap]; i++)
MPI_Send(&sendnum[iswap][i],1,MPI_INT,sendproc[iswap][i],0,world);
MPI_Waitall(nrecvproc[iswap],requests,statuses);
} else recvnum[iswap][0] = sendnum[iswap][0];
// setup other per swap/proc values from sendnum and recvnum
rmaxswap = 0;
for (i = 0; i < nrecvproc[iswap]; i++) {
rmaxswap += recvnum[iswap][i];
size_forward_recv[iswap][i] = recvnum[iswap][i]*size_forward;
size_reverse_send[iswap][i] = recvnum[iswap][i]*size_reverse;
size_reverse_recv[iswap][i] = sendnum[iswap][i]*size_reverse;
if (i == 0) {
firstrecv[iswap][0] = atom->nlocal + atom->nghost;
forward_recv_offset[iswap][0] = 0;
} else {
firstrecv[iswap][i] = firstrecv[iswap][i-1] + recvnum[iswap][i-1];
forward_recv_offset[iswap][i] =
forward_recv_offset[iswap][i-1] + recvnum[iswap][i-1];
}
}
rmax = MAX(rmax,rmaxswap);
// insure send/recv buffers are large enough for border comm
if (smax*size_border > maxsend) grow_send(smax*size_border,0);
if (rmax*size_border > maxrecv) grow_recv(rmax*size_border);
// swap atoms with other procs using pack_border(), unpack_border()
if (sendproc[iswap][0] != me) {
for (i = 0; i < nsendproc[iswap]; i++) {
if (ghost_velocity) {
for (i = 0; i < nrecvproc[iswap]; i++)
MPI_Irecv(&buf_recv[forward_recv_offset[iswap][i]],
recvnum[iswap][i]*size_border,
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nsendproc[iswap]; i++) {
n = avec->pack_border_vel(sendnum[iswap][i],sendlist[iswap][i],
buf_send,pbc_flag[iswap][i],
pbc[iswap][i]);
MPI_Send(buf_send,n*size_border,MPI_DOUBLE,
sendproc[iswap][i],0,world);
}
for (i = 0; i < nrecvproc[iswap]; i++) {
MPI_Waitany(nrecvproc[iswap],requests,&irecv,&status);
avec->unpack_border(recvnum[iswap][i],firstrecv[iswap][irecv],
&buf_recv[forward_recv_offset[iswap][irecv]]);
}
} else {
for (i = 0; i < nrecvproc[iswap]; i++)
MPI_Irecv(&buf_recv[forward_recv_offset[iswap][i]],
recvnum[iswap][i]*size_border,
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nsendproc[iswap]; i++) {
n = avec->pack_border(sendnum[iswap][i],sendlist[iswap][i],
buf_send,pbc_flag[iswap][i],pbc[iswap][i]);
MPI_Send(buf_send,n*size_border,MPI_DOUBLE,
sendproc[iswap][i],0,world);
}
for (i = 0; i < nrecvproc[iswap]; i++) {
MPI_Waitany(nrecvproc[iswap],requests,&irecv,&status);
avec->unpack_border(recvnum[iswap][i],firstrecv[iswap][irecv],
&buf_recv[forward_recv_offset[iswap][irecv]]);
}
}
}
} else {
if (ghost_velocity) {
n = avec->pack_border_vel(sendnum[iswap][0],sendlist[iswap][0],
buf_send,pbc_flag[iswap][0],pbc[iswap][0]);
avec->unpack_border_vel(recvnum[iswap][0],firstrecv[iswap][0],buf_send);
} else {
n = avec->pack_border(sendnum[iswap][0],sendlist[iswap][0],
buf_send,pbc_flag[iswap][0],pbc[iswap][0]);
avec->unpack_border(recvnum[iswap][0],firstrecv[iswap][0],buf_send);
}
}
// increment ghost atoms
n = nrecvproc[iswap];
atom->nghost += forward_recv_offset[iswap][n-1] + recvnum[iswap][n-1];
}
// 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
n = constant number of datums per atom
------------------------------------------------------------------------- */
void CommTiled::forward_comm_pair(Pair *pair)
{
int i,irecv,n;
MPI_Status status;
for (int iswap = 0; iswap < nswap; iswap++) {
if (sendproc[iswap][0] != me) {
for (i = 0; i < nrecvproc[iswap]; i++)
MPI_Irecv(&buf_recv[forward_recv_offset[iswap][i]],
size_forward_recv[iswap][i],
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nsendproc[iswap]; i++) {
n = pair->pack_comm(sendnum[iswap][i],sendlist[iswap][i],
buf_send,pbc_flag[iswap][i],pbc[iswap][i]);
MPI_Send(buf_send,n*sendnum[iswap][i],MPI_DOUBLE,
sendproc[iswap][i],0,world);
}
for (i = 0; i < nrecvproc[iswap]; i++) {
MPI_Waitany(nrecvproc[iswap],requests,&irecv,&status);
pair->unpack_comm(recvnum[iswap][irecv],firstrecv[iswap][irecv],
&buf_recv[forward_recv_offset[iswap][irecv]]);
}
} else {
n = pair->pack_comm(sendnum[iswap][0],sendlist[iswap][0],
buf_send,pbc_flag[iswap][0],pbc[iswap][0]);
pair->unpack_comm(recvnum[iswap][0],firstrecv[iswap][0],buf_send);
}
}
}
/* ----------------------------------------------------------------------
reverse communication invoked by a Pair
n = constant number of datums per atom
------------------------------------------------------------------------- */
void CommTiled::reverse_comm_pair(Pair *pair)
{
int i,irecv,n;
MPI_Status status;
for (int iswap = nswap-1; iswap >= 0; iswap--) {
if (sendproc[iswap][0] != me) {
for (i = 0; i < nsendproc[iswap]; i++)
MPI_Irecv(&buf_recv[reverse_recv_offset[iswap][i]],
size_reverse_recv[iswap][i],MPI_DOUBLE,
sendproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nrecvproc[iswap]; i++) {
n = pair->pack_reverse_comm(recvnum[iswap][i],firstrecv[iswap][i],
buf_send);
MPI_Send(buf_send,n*recvnum[iswap][i],MPI_DOUBLE,
recvproc[iswap][i],0,world);
}
for (i = 0; i < nsendproc[iswap]; i++) {
MPI_Waitany(nsendproc[iswap],requests,&irecv,&status);
pair->unpack_reverse_comm(sendnum[iswap][irecv],sendlist[iswap][irecv],
&buf_recv[reverse_recv_offset[iswap][irecv]]);
}
} else {
n = pair->pack_reverse_comm(recvnum[iswap][0],firstrecv[iswap][0],
buf_send);
pair->unpack_reverse_comm(sendnum[iswap][0],sendlist[iswap][0],buf_send);
}
}
}
/* ----------------------------------------------------------------------
@ -256,6 +503,33 @@ void CommTiled::reverse_comm_pair(Pair *pair)
void CommTiled::forward_comm_fix(Fix *fix)
{
int i,irecv,n;
MPI_Status status;
for (int iswap = 0; iswap < nswap; iswap++) {
if (sendproc[iswap][0] != me) {
for (i = 0; i < nrecvproc[iswap]; i++)
MPI_Irecv(&buf_recv[forward_recv_offset[iswap][i]],
size_forward_recv[iswap][i],
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nsendproc[iswap]; i++) {
n = fix->pack_comm(sendnum[iswap][i],sendlist[iswap][i],
buf_send,pbc_flag[iswap][i],pbc[iswap][i]);
MPI_Send(buf_send,n*sendnum[iswap][i],MPI_DOUBLE,
sendproc[iswap][i],0,world);
}
for (i = 0; i < nrecvproc[iswap]; i++) {
MPI_Waitany(nrecvproc[iswap],requests,&irecv,&status);
fix->unpack_comm(recvnum[iswap][irecv],firstrecv[iswap][irecv],
&buf_recv[forward_recv_offset[iswap][irecv]]);
}
} else {
n = fix->pack_comm(sendnum[iswap][0],sendlist[iswap][0],
buf_send,pbc_flag[iswap][0],pbc[iswap][0]);
fix->unpack_comm(recvnum[iswap][0],firstrecv[iswap][0],buf_send);
}
}
}
/* ----------------------------------------------------------------------
@ -265,11 +539,39 @@ void CommTiled::forward_comm_fix(Fix *fix)
void CommTiled::reverse_comm_fix(Fix *fix)
{
int i,irecv,n;
MPI_Status status;
for (int iswap = nswap-1; iswap >= 0; iswap--) {
if (sendproc[iswap][0] != me) {
for (i = 0; i < nsendproc[iswap]; i++)
MPI_Irecv(&buf_recv[reverse_recv_offset[iswap][i]],
size_reverse_recv[iswap][i],MPI_DOUBLE,
sendproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nrecvproc[iswap]; i++) {
n = fix->pack_reverse_comm(recvnum[iswap][i],firstrecv[iswap][i],
buf_send);
MPI_Send(buf_send,n*recvnum[iswap][i],MPI_DOUBLE,
recvproc[iswap][i],0,world);
}
for (i = 0; i < nsendproc[iswap]; i++) {
MPI_Waitany(nsendproc[iswap],requests,&irecv,&status);
fix->unpack_reverse_comm(sendnum[iswap][irecv],sendlist[iswap][irecv],
&buf_recv[reverse_recv_offset[iswap][irecv]]);
}
} else {
n = fix->pack_reverse_comm(recvnum[iswap][0],firstrecv[iswap][0],
buf_send);
fix->unpack_reverse_comm(sendnum[iswap][0],sendlist[iswap][0],buf_send);
}
}
}
/* ----------------------------------------------------------------------
forward communication invoked by a Fix
n = total datums for all atoms, allows for variable number/atom
NOTE: complicated b/c don't know # to recv a priori
------------------------------------------------------------------------- */
void CommTiled::forward_comm_variable_fix(Fix *fix)
@ -287,34 +589,148 @@ void CommTiled::reverse_comm_variable_fix(Fix *fix)
/* ----------------------------------------------------------------------
forward communication invoked by a Compute
n = constant number of datums per atom
------------------------------------------------------------------------- */
void CommTiled::forward_comm_compute(Compute *compute)
{
int i,irecv,n;
MPI_Status status;
for (int iswap = 0; iswap < nswap; iswap++) {
if (sendproc[iswap][0] != me) {
for (i = 0; i < nrecvproc[iswap]; i++)
MPI_Irecv(&buf_recv[forward_recv_offset[iswap][i]],
size_forward_recv[iswap][i],
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nsendproc[iswap]; i++) {
n = compute->pack_comm(sendnum[iswap][i],sendlist[iswap][i],
buf_send,pbc_flag[iswap][i],pbc[iswap][i]);
MPI_Send(buf_send,n*sendnum[iswap][i],MPI_DOUBLE,
sendproc[iswap][i],0,world);
}
for (i = 0; i < nrecvproc[iswap]; i++) {
MPI_Waitany(nrecvproc[iswap],requests,&irecv,&status);
compute->unpack_comm(recvnum[iswap][irecv],firstrecv[iswap][irecv],
&buf_recv[forward_recv_offset[iswap][irecv]]);
}
} else {
n = compute->pack_comm(sendnum[iswap][0],sendlist[iswap][0],
buf_send,pbc_flag[iswap][0],pbc[iswap][0]);
compute->unpack_comm(recvnum[iswap][0],firstrecv[iswap][0],buf_send);
}
}
}
/* ----------------------------------------------------------------------
reverse communication invoked by a Compute
n = constant number of datums per atom
------------------------------------------------------------------------- */
void CommTiled::reverse_comm_compute(Compute *compute)
{
int i,irecv,n;
MPI_Status status;
for (int iswap = nswap-1; iswap >= 0; iswap--) {
if (sendproc[iswap][0] != me) {
for (i = 0; i < nsendproc[iswap]; i++)
MPI_Irecv(&buf_recv[reverse_recv_offset[iswap][i]],
size_reverse_recv[iswap][i],MPI_DOUBLE,
sendproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nrecvproc[iswap]; i++) {
n = compute->pack_reverse_comm(recvnum[iswap][i],firstrecv[iswap][i],
buf_send);
MPI_Send(buf_send,n*recvnum[iswap][i],MPI_DOUBLE,
recvproc[iswap][i],0,world);
}
for (i = 0; i < nsendproc[iswap]; i++) {
MPI_Waitany(nsendproc[iswap],requests,&irecv,&status);
compute->
unpack_reverse_comm(sendnum[iswap][irecv],sendlist[iswap][irecv],
&buf_recv[reverse_recv_offset[iswap][irecv]]);
}
} else {
n = compute->pack_reverse_comm(recvnum[iswap][0],firstrecv[iswap][0],
buf_send);
compute->unpack_reverse_comm(sendnum[iswap][0],sendlist[iswap][0],
buf_send);
}
}
}
/* ----------------------------------------------------------------------
forward communication invoked by a Dump
n = constant number of datums per atom
------------------------------------------------------------------------- */
void CommTiled::forward_comm_dump(Dump *dump)
{
int i,irecv,n;
MPI_Status status;
for (int iswap = 0; iswap < nswap; iswap++) {
if (sendproc[iswap][0] != me) {
for (i = 0; i < nrecvproc[iswap]; i++)
MPI_Irecv(&buf_recv[forward_recv_offset[iswap][i]],
size_forward_recv[iswap][i],
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nsendproc[iswap]; i++) {
n = dump->pack_comm(sendnum[iswap][i],sendlist[iswap][i],
buf_send,pbc_flag[iswap][i],pbc[iswap][i]);
MPI_Send(buf_send,n*sendnum[iswap][i],MPI_DOUBLE,
sendproc[iswap][i],0,world);
}
for (i = 0; i < nrecvproc[iswap]; i++) {
MPI_Waitany(nrecvproc[iswap],requests,&irecv,&status);
dump->unpack_comm(recvnum[iswap][irecv],firstrecv[iswap][irecv],
&buf_recv[forward_recv_offset[iswap][irecv]]);
}
} else {
n = dump->pack_comm(sendnum[iswap][0],sendlist[iswap][0],
buf_send,pbc_flag[iswap][0],pbc[iswap][0]);
dump->unpack_comm(recvnum[iswap][0],firstrecv[iswap][0],buf_send);
}
}
}
/* ----------------------------------------------------------------------
reverse communication invoked by a Dump
n = constant number of datums per atom
------------------------------------------------------------------------- */
void CommTiled::reverse_comm_dump(Dump *dump)
{
int i,irecv,n;
MPI_Status status;
for (int iswap = nswap-1; iswap >= 0; iswap--) {
if (sendproc[iswap][0] != me) {
for (i = 0; i < nsendproc[iswap]; i++)
MPI_Irecv(&buf_recv[reverse_recv_offset[iswap][i]],
size_reverse_recv[iswap][i],MPI_DOUBLE,
sendproc[iswap][i],0,world,&requests[i]);
for (i = 0; i < nrecvproc[iswap]; i++) {
n = dump->pack_reverse_comm(recvnum[iswap][i],firstrecv[iswap][i],
buf_send);
MPI_Send(buf_send,n*recvnum[iswap][i],MPI_DOUBLE,
recvproc[iswap][i],0,world);
}
for (i = 0; i < nsendproc[iswap]; i++) {
MPI_Waitany(nsendproc[iswap],requests,&irecv,&status);
dump->unpack_reverse_comm(sendnum[iswap][irecv],sendlist[iswap][irecv],
&buf_recv[reverse_recv_offset[iswap][irecv]]);
}
} else {
n = dump->pack_reverse_comm(recvnum[iswap][0],firstrecv[iswap][0],
buf_send);
dump->unpack_reverse_comm(sendnum[iswap][0],sendlist[iswap][0],buf_send);
}
}
}
/* ----------------------------------------------------------------------
@ -335,6 +751,45 @@ int CommTiled::exchange_variable(int n, double *inbuf, double *&outbuf)
return nrecv;
}
/* ----------------------------------------------------------------------
realloc the size of the send buffer as needed with BUFFACTOR and bufextra
if flag = 1, realloc
if flag = 0, don't need to realloc with copy, just free/malloc
------------------------------------------------------------------------- */
void CommTiled::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 CommTiled::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 CommTiled::grow_list(int iswap, int iwhich, int n)
{
maxsendlist[iswap][iwhich] = static_cast<int> (BUFFACTOR * n);
memory->grow(sendlist[iswap][iwhich],maxsendlist[iswap][iwhich],
"comm:sendlist[iswap]");
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */

43
src/comm_tiled.h
View File

@ -44,6 +44,49 @@ class CommTiled : public Comm {
void forward_comm_array(int, double **); // forward comm of array
int exchange_variable(int, double *, double *&); // exchange on neigh stencil
bigint memory_usage();
private:
int nswap; // # of swaps to perform = 2*dim
int *nsendproc,*nrecvproc; // # of procs to send/recv to/from in each swap
int triclinic; // 0 if domain is orthog, 1 if triclinic
int map_style; // non-0 if global->local mapping is done
int size_forward; // # of per-atom datums in forward comm
int size_reverse; // # of datums in reverse comm
int size_border; // # of datums in forward border comm
int **sendnum,**recvnum; // # of atoms to send/recv per swap/proc
int **sendproc,**recvproc; // proc to send/recv to/from per swap/proc
int **size_forward_recv; // # of values to recv in each forward swap/proc
int **firstrecv; // where to put 1st recv atom per swap/proc
int **size_reverse_send; // # to send in each reverse comm per swap/proc
int **size_reverse_recv; // # to recv in each reverse comm per swap/proc
int **forward_recv_offset; // forward comm offsets in buf_recv per swap/proc
int **reverse_recv_offset; // reverse comm offsets in buf_recv per swap/proc
int ***sendlist; // list of atoms to send per swap/proc
int **maxsendlist; // max size of send list per swap/proc
int **pbc_flag; // general flag for sending atoms thru PBC
int ***pbc; // dimension flags for PBC adjustments
double ***sendbox; // bounding box of atoms to send per swap/proc
double *buf_send; // send buffer for all comm
double *buf_recv; // recv buffer for all comm
int maxsend,maxrecv; // current size of send/recv buffer
int maxforward,maxreverse; // max # of datums in forward/reverse comm
int bufextra; // extra space beyond maxsend in send buffer
MPI_Request *requests;
MPI_Status *statuses;
int comm_x_only,comm_f_only; // 1 if only exchange x,f in for/rev comm
void grow_send(int, int); // reallocate send buffer
void grow_recv(int); // free/allocate recv buffer
void grow_list(int, int, int); // reallocate sendlist for one swap/proc
};
}

14
src/dump.cpp
View File

@ -752,13 +752,6 @@ void Dump::modify_params(int narg, char **arg)
output->every_dump[idump] = n;
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) first_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) first_flag = 0;
else error->all(FLERR,"Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"fileper") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (!multiproc)
@ -787,6 +780,13 @@ void Dump::modify_params(int narg, char **arg)
*ptr = '%';
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) first_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) first_flag = 0;
else error->all(FLERR,"Illegal dump_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"flush") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (strcmp(arg[iarg+1],"yes") == 0) flush_flag = 1;

4
src/dump.h
View File

@ -56,8 +56,7 @@ class Dump : protected Pointers {
int compressed; // 1 if dump file is written compressed, 0 no
int binary; // 1 if dump file is written binary, 0 no
int multifile; // 0 = one big file, 1 = one file per timestep
int multiproc; // 0 = proc 0 writes for all
int multiproc; // 0 = proc 0 writes for all,
// else # of procs writing files
int nclusterprocs; // # of procs in my cluster that write to one file
int filewriter; // 1 if this proc writes a file, else 0
@ -99,7 +98,6 @@ class Dump : protected Pointers {
int maxbuf; // size of buf
double *buf; // memory for atom quantities
int maxsbuf; // size of sbuf
char *sbuf; // memory for atom quantities in string format

2
src/neigh_request.cpp
View File

@ -24,6 +24,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
// default ID = 0
id = 0;
unprocessed = 1;
// default is pair request
@ -96,6 +97,7 @@ int NeighRequest::identical(NeighRequest *other)
{
int same = 1;
if (unprocessed) same = 0;
if (requestor != other->requestor) same = 0;
if (id != other->id) same = 0;

2
src/neigh_request.h
View File

@ -23,6 +23,8 @@ class NeighRequest : protected Pointers {
void *requestor; // class that made request
int id; // ID of request
// used to track multiple requests from one class
int unprocessed; // 1 when first requested
// 0 after processed by Neighbor class
// which class is requesting the list, one flag is 1, others are 0

1
src/neighbor.cpp
View File

@ -490,6 +490,7 @@ void Neighbor::init()
// wait to allocate initial pages until copy lists are detected
for (i = 0; i < nrequest; i++) {
requests[i]->unprocessed = 0;
if (requests[i]->kokkos_host || requests[i]->kokkos_device) continue;
lists[i] = new NeighList(lmp);
lists[i]->index = i;

14
src/write_restart.cpp
View File

@ -127,12 +127,13 @@ void WriteRestart::command(int narg, char **arg)
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
// write single restart file
write(file);
delete [] file;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void WriteRestart::multiproc_options(int multiproc_caller, int mpiioflag_caller,
int narg, char **arg)
@ -579,8 +580,7 @@ void WriteRestart::file_layout(int send_size)
// ----------------------------------------------------------------------
// ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void WriteRestart::magic_string()
{
@ -591,8 +591,7 @@ void WriteRestart::magic_string()
delete [] str;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void WriteRestart::endian()
{
@ -600,8 +599,7 @@ void WriteRestart::endian()
fwrite(&endian,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
void WriteRestart::version_numeric()
{