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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12752 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-11-20 18:02:47 +00:00
parent 973b24564e
commit 7f8f2fd3ed
9 changed files with 181 additions and 136 deletions
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88
src/comm_tiled.cpp
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@ -159,30 +159,33 @@ void CommTiled::setup()
// if RCB decomp exists and just changed, gather needed global RCB info
if (rcbnew) {
if (!rcbinfo)
rcbinfo = (RCBinfo *)
memory->smalloc(nprocs*sizeof(RCBinfo),"comm:rcbinfo");
rcbnew = 0;
RCBinfo rcbone;
memcpy(&rcbone.mysplit[0][0],&mysplit[0][0],6*sizeof(double));
rcbone.cutfrac = rcbcutfrac;
rcbone.dim = rcbcutdim;
MPI_Allgather(&rcbone,sizeof(RCBinfo),MPI_CHAR,
rcbinfo,sizeof(RCBinfo),MPI_CHAR,world);
}
if (layout == LAYOUT_TILED) coord2proc_setup();
// set cutoff for comm forward and comm reverse
// check that cutoff < any periodic box length
double cut = MAX(neighbor->cutneighmax,cutghostuser);
cutghost[0] = cutghost[1] = cutghost[2] = cut;
if ((periodicity[0] && cut > prd[0]) ||
(periodicity[1] && cut > prd[1]) ||
(dimension == 3 && periodicity[2] && cut > prd[2]))
error->all(FLERR,"Communication cutoff for comm_style tiled "
"cannot exceed periodic box length");
// if cut = 0.0, set to epsilon to induce nearest neighbor comm
// this is b/c sendproc is used below to infer touching exchange procs
// exchange procs will be empty (leading to lost atoms) if sendproc = 0
// will reset sendproc/etc to 0 after exchange is setup, down below
int cutzero = 0;
if (cut == 0.0) {
cutzero = 1;
cut = MIN(prd[0],prd[1]);
if (dimension == 3) cut = MIN(cut,prd[3]);
cut *= EPSILON*EPSILON;
}
// setup forward/reverse communication
// loop over 6 swap directions
// determine which procs I will send to and receive from in each swap
@ -416,6 +419,15 @@ void CommTiled::setup()
for (i = 0; i < noverlap; i++) exchproc[idim][i] = overlap[i];
}
// reset sendproc/etc to 0 if cut is really 0.0
if (cutzero) {
for (i = 0; i < nswap; i++) {
nsendproc[i] = nrecvproc[i] =
sendother[i] = recvother[i] = sendself[i] = 0;
}
}
// reallocate MPI Requests and Statuses as needed
int nmax = 0;
@ -999,13 +1011,15 @@ void CommTiled::forward_comm_pair(Pair *pair)
nsize*recvnum[iswap][i],
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
}
if (sendother[iswap]) {
for (i = 0; i < nsendproc[iswap]; i++) {
for (i = 0; i < nsend; i++) {
n = pair->pack_forward_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);
}
}
if (sendself[iswap]) {
pair->pack_forward_comm(sendnum[iswap][nsend],sendlist[iswap][nsend],
buf_send,pbc_flag[iswap][nsend],
@ -1098,7 +1112,7 @@ void CommTiled::forward_comm_fix(Fix *fix, int size)
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
}
if (sendother[iswap]) {
for (i = 0; i < nsendproc[iswap]; i++) {
for (i = 0; i < nsend; i++) {
n = fix->pack_forward_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);
@ -1196,7 +1210,7 @@ void CommTiled::forward_comm_compute(Compute *compute)
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
}
if (sendother[iswap]) {
for (i = 0; i < nsendproc[iswap]; i++) {
for (i = 0; i < nsend; i++) {
n = compute->pack_forward_comm(sendnum[iswap][i],sendlist[iswap][i],
buf_send,pbc_flag[iswap][i],
pbc[iswap][i]);
@ -1292,7 +1306,7 @@ void CommTiled::forward_comm_dump(Dump *dump)
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
}
if (sendother[iswap]) {
for (i = 0; i < nsendproc[iswap]; i++) {
for (i = 0; i < nsend; i++) {
n = dump->pack_forward_comm(sendnum[iswap][i],sendlist[iswap][i],
buf_send,pbc_flag[iswap][i],
pbc[iswap][i]);
@ -1394,7 +1408,7 @@ void CommTiled::forward_comm_array(int nsize, double **array)
MPI_DOUBLE,recvproc[iswap][i],0,world,&requests[i]);
}
if (sendother[iswap]) {
for (i = 0; i < nsendproc[iswap]; i++) {
for (i = 0; i < nsend; i++) {
m = 0;
for (iatom = 0; iatom < sendnum[iswap][i]; iatom++) {
j = sendlist[iswap][i][iatom];
@ -1740,7 +1754,7 @@ int CommTiled::point_drop_tiled(int idim, double *x)
}
/* ----------------------------------------------------------------------
recursive form
recursive point drop thru RCB tree
------------------------------------------------------------------------- */
int CommTiled::point_drop_tiled_recurse(double *x,
@ -1786,12 +1800,46 @@ int CommTiled::closer_subbox_edge(int idim, double *x)
return 1;
}
/* ----------------------------------------------------------------------
if RCB decomp exists and just changed, gather needed global RCB info
------------------------------------------------------------------------- */
void CommTiled::coord2proc_setup()
{
if (!rcbnew) return;
if (!rcbinfo)
rcbinfo = (RCBinfo *)
memory->smalloc(nprocs*sizeof(RCBinfo),"comm:rcbinfo");
rcbnew = 0;
RCBinfo rcbone;
memcpy(&rcbone.mysplit[0][0],&mysplit[0][0],6*sizeof(double));
rcbone.cutfrac = rcbcutfrac;
rcbone.dim = rcbcutdim;
MPI_Allgather(&rcbone,sizeof(RCBinfo),MPI_CHAR,
rcbinfo,sizeof(RCBinfo),MPI_CHAR,world);
}
/* ----------------------------------------------------------------------
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 or NONUNIFORM, invoke parent method
if layout = TILED, use point_drop_recurse()
return owning proc ID, ignore igx,igy,igz
------------------------------------------------------------------------- */
int CommTiled::coord2proc(double *x, int &igx, int &igy, int &igz)
{
if (layout != LAYOUT_TILED) return Comm::coord2proc(x,igx,igy,igz);
return point_drop_tiled_recurse(x,0,nprocs-1);
}
/* ----------------------------------------------------------------------
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);