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Merge branch 'master' into multi-comm-tiled

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Conflicts resolved:
    src/comm_tiled.cpp
This commit is contained in:
Richard Berger
2019-11-27 12:12:03 -05:00
parent 0f88513f65 738f155cc4
commit 06964c58de
5666 changed files with 401048 additions and 342247 deletions
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92
src/comm_tiled.cpp
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@ -15,19 +15,17 @@
Contributing author (multi) : Adrian Diaz (University of Florida)
------------------------------------------------------------------------- */
#include <cstring>
#include "comm_tiled.h"
#include "comm_brick.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
#include "neighbor.h"
#include "modify.h"
#include "fix.h"
#include "compute.h"
#include "output.h"
#include "dump.h"
#include "memory.h"
#include "error.h"
@ -36,8 +34,7 @@ using namespace LAMMPS_NS;
#define BUFFACTOR 1.5
#define BUFFACTOR 1.5
#define BUFMIN 1000
#define BUFEXTRA 1000
#define BUFMIN 1024
#define EPSILON 1.0e-6
#define DELTA_PROCS 16
@ -89,17 +86,9 @@ void CommTiled::init_buffers()
{
sendbox_multi = NULL;
cutghostmulti = NULL;
// bufextra = max size of one exchanged atom
// = allowed overflow of sendbuf in exchange()
// atomvec, fix reset these 2 maxexchange values if needed
// only necessary if their size > BUFEXTRA
maxexchange = maxexchange_atom + maxexchange_fix;
bufextra = maxexchange + BUFEXTRA;
maxsend = BUFMIN;
memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
maxrecv = BUFMIN;
buf_send = buf_recv = NULL;
maxsend = maxrecv = BUFMIN;
grow_send(maxsend,2);
memory->create(buf_recv,maxrecv,"comm:buf_recv");
maxoverlap = 0;
@ -118,7 +107,6 @@ void CommTiled::init()
Comm::init();
// memory for multi-style communication
int maxswap = 6;
if (mode == Comm::MULTI) {
memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti");
}
@ -126,6 +114,10 @@ void CommTiled::init()
memory->destroy(cutghostmulti);
}
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
// temporary restrictions
if (triclinic)
@ -174,19 +166,23 @@ void CommTiled::setup()
// set cutoff for comm forward and comm reverse
// check that cutoff < any periodic box length
double cut;
if (mode == Comm::MULTI) {
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++) {
cut = 0.0;
if (cutusermulti) cut = cutusermulti[i];
cutghostmulti[i][0] = MAX(cut,cuttype[i]);
cutghostmulti[i][1] = MAX(cut,cuttype[i]);
cutghostmulti[i][2] = MAX(cut,cuttype[i]);
}
if (mode == Comm::MULTI) {
double *cuttype = neighbor->cuttype;
double cut;
for (i = 1; i <= ntypes; i++) {
cut = 0.0;
if (cutusermulti) cut = cutusermulti[i];
cutghostmulti[i][0] = MAX(cut,cuttype[i]);
cutghostmulti[i][1] = MAX(cut,cuttype[i]);
cutghostmulti[i][2] = MAX(cut,cuttype[i]);
}
cut = MAX(neighbor->cutneighmax,cutghostuser);
}
double cut = get_comm_cutoff();
if ((cut == 0.0) && (me == 0))
error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms "
"will be generated. Atoms may get lost.");
cutghost[0] = cutghost[1] = cutghost[2] = cut;
@ -601,7 +597,7 @@ void CommTiled::forward_comm(int /*dummy*/)
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 = 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);
@ -733,15 +729,14 @@ void CommTiled::exchange()
atom->nghost = 0;
atom->avec->clear_bonus();
// insure send buf is large enough for single atom
// bufextra = max size of one atom = allowed overflow of sendbuf
// fixes can change per-atom size requirement on-the-fly
// insure send buf has extra space for a single atom
// only need to reset if a fix can dynamically add to size of single atom
int bufextra_old = bufextra;
maxexchange = maxexchange_atom + maxexchange_fix;
bufextra = maxexchange + BUFEXTRA;
if (bufextra > bufextra_old)
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
if (maxexchange_fix_dynamic) {
int bufextra_old = bufextra;
init_exchange();
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
}
// domain properties used in exchange method and methods it calls
// subbox bounds for orthogonal or triclinic
@ -1953,18 +1948,23 @@ int CommTiled::coord2proc(double *x, int &igx, int &igy, int &igz)
/* ----------------------------------------------------------------------
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
flag = 0, don't need to realloc with copy, just free/malloc w/ BUFFACTOR
flag = 1, realloc with BUFFACTOR
flag = 2, free/malloc w/out BUFFACTOR
------------------------------------------------------------------------- */
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 {
if (flag == 0) {
maxsend = static_cast<int> (BUFFACTOR * n);
memory->destroy(buf_send);
memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
} else if (flag == 1) {
maxsend = static_cast<int> (BUFFACTOR * n);
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
} else {
memory->destroy(buf_send);
memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
}
}