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Kokkos neighbor refactor

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This commit is contained in:
Stan Moore
2016-12-07 13:00:27 -07:00
parent 7c61dbf5e2
commit 8318c67816
60 changed files with 1742 additions and 1279 deletions
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62
src/neighbor.cpp
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@ -621,8 +621,7 @@ void Neighbor::init_pair()
delete [] neigh_stencil;
delete [] neigh_pair;
if (lmp->kokkos) nlist = init_lists_kokkos();
else nlist = nrequest;
nlist = nrequest;
lists = new NeighList*[nrequest];
neigh_bin = new NBin*[nrequest];
@ -634,11 +633,10 @@ void Neighbor::init_pair()
// wait to allocate initial pages until copy lists are detected
for (i = 0; i < nrequest; i++) {
if (requests[i]->kokkos_host || requests[i]->kokkos_device) {
lists[i] = NULL;
continue;
}
lists[i] = new NeighList(lmp);
if (requests[i]->kokkos_host || requests[i]->kokkos_device)
create_kokkos_list(i);
else
lists[i] = new NeighList(lmp);
lists[i]->index = i;
if (requests[i]->pair) {
@ -680,10 +678,8 @@ void Neighbor::init_pair()
// would be useful when reax/c used in hybrid mode, e.g. with airebo
for (i = 0; i < nrequest; i++) {
if (lists[i] == NULL) continue; // Kokkos
if (requests[i]->pair && requests[i]->half && requests[i]->newton != 2) {
for (j = 0; j < nrequest; j++) {
if (lists[j] == NULL) continue; // Kokkos
if (requests[j]->full && requests[j]->occasional == 0 &&
!requests[j]->skip && !requests[j]->copy) break;
}
@ -708,10 +704,8 @@ void Neighbor::init_pair()
// for 1st or 2nd check, parent can be copy list or pair or fix
for (i = 0; i < nrequest; i++) {
if (lists[i] == NULL) continue; // Kokkos
if (!requests[i]->fix && !requests[i]->compute) continue;
for (j = 0; j < nrequest; j++) {
if (lists[j] == NULL) continue; // Kokkos
if (requests[i]->half && requests[j]->pair &&
!requests[j]->skip && requests[j]->half && !requests[j]->copy)
break;
@ -733,7 +727,6 @@ void Neighbor::init_pair()
continue;
}
for (j = 0; j < nrequest; j++) {
if (lists[j] == NULL) continue; // Kokkos
if (requests[i]->half && requests[j]->pair &&
!requests[j]->skip && requests[j]->full && !requests[j]->copy)
break;
@ -844,7 +837,6 @@ void Neighbor::init_pair()
int dnummax = 0;
for (i = 0; i < nlist; i++) {
if (lists[i] == NULL) continue; // Kokkos
if (lists[i]->copy) continue;
lists[i]->setup_pages(pgsize,oneatom);
dnummax = MAX(dnummax,lists[i]->dnum);
@ -864,14 +856,8 @@ void Neighbor::init_pair()
// also Kokkos list initialization
int maxatom = atom->nmax;
for (i = 0; i < nlist; i++) {
if (lists[i]) {
if (neigh_pair[i] && !lists[i]->copy) lists[i]->grow(maxatom,maxatom);
} else {
init_list_flags1_kokkos(i);
init_list_grow_kokkos(i);
}
}
for (i = 0; i < nlist; i++)
if (neigh_pair[i] && !lists[i]->copy) lists[i]->grow(maxatom,maxatom);
// plist = indices of perpetual NPair classes
// perpetual = non-occasional, re-built at every reneighboring
@ -885,10 +871,8 @@ void Neighbor::init_pair()
plist = new int[nlist];
for (i = 0; i < nlist; i++) {
if (lists[i]) {
if (lists[i]->occasional == 0 && lists[i]->pair_method)
plist[npair_perpetual++] = i;
} else init_list_flags2_kokkos(i);
if (lists[i]->occasional == 0 && lists[i]->pair_method)
plist[npair_perpetual++] = i;
}
for (i = 0; i < nstencil; i++) {
@ -910,7 +894,6 @@ void Neighbor::init_pair()
while (!done) {
done = 1;
for (i = 0; i < npair_perpetual; i++) {
if (!lists[plist[i]]) continue; // Kokkos check
ptr = NULL;
if (lists[plist[i]]->listcopy) ptr = lists[plist[i]]->listcopy;
if (lists[plist[i]]->listskip) ptr = lists[plist[i]]->listskip;
@ -1154,15 +1137,14 @@ void Neighbor::print_pairwise_info()
else if (requests[i]->respamiddle) kind = "respa/middle";
else if (requests[i]->respaouter) kind = "respa/outer";
else if (requests[i]->half_from_full) kind = "half/from/full";
else if (requests[i]->full_cluster) kind = "full/cluster"; // Kokkos
fprintf(out," kind: %s",kind);
if (requests[i]->occasional) fprintf(out,", occasional");
else fprintf(out,", perpetual");
if (requests[i]->ghost) fprintf(out,", ghost");
if (requests[i]->ssa) fprintf(out,", ssa");
if (requests[i]->omp) fprintf(out,", omp");
if (requests[i]->intel) fprintf(out,", intel");
if (requests[i]->kokkos_device) fprintf(out,", kokkos_device");
if (requests[i]->kokkos_host) fprintf(out,", kokkos_host");
if (requests[i]->copy)
fprintf(out,", copy from (%d)",requests[i]->otherlist+1);
if (requests[i]->skip)
@ -1237,13 +1219,17 @@ int Neighbor::choose_bin(NeighRequest *rq)
// flags for settings the request + system requires of NBin class
// ssaflag = no/yes ssa request
// intelflag = no/yes intel request
// kokkos_device_flag = no/yes kokkos device request
// kokkos_host_flag = no/yes kokkos host request
int ssaflag,intelflag;
int ssaflag,intelflag,kokkos_device_flag,kokkos_host_flag;
ssaflag = intelflag = 0;
ssaflag = intelflag = kokkos_device_flag = kokkos_host_flag = 0;
if (rq->ssa) ssaflag = NB_SSA;
if (rq->intel) intelflag = NB_INTEL;
if (rq->kokkos_device) kokkos_device_flag = NB_KOKKOS_DEVICE;
if (rq->kokkos_host) kokkos_host_flag = NB_KOKKOS_HOST;
// use flags to match exactly one of NBin class masks, bit by bit
@ -1254,6 +1240,8 @@ int Neighbor::choose_bin(NeighRequest *rq)
if (ssaflag != (mask & NB_SSA)) continue;
if (intelflag != (mask & NB_INTEL)) continue;
if (kokkos_device_flag != (mask & NB_KOKKOS_DEVICE)) continue;
if (kokkos_host_flag != (mask & NB_KOKKOS_HOST)) continue;
return i+1;
}
@ -1308,6 +1296,7 @@ int Neighbor::choose_stencil(NeighRequest *rq)
else if (rq->newton == 1) newtflag = 1;
else if (rq->newton == 2) newtflag = 0;
// use flags to match exactly one of NStencil class masks, bit by bit
// exactly one of halfflag,fullflag is set and thus must match
@ -1381,16 +1370,18 @@ int Neighbor::choose_pair(NeighRequest *rq)
// ssaflag = no/yes request
// ompflag = no/yes omp request
// intelflag = no/yes intel request
// kokkos_device_flag = no/yes Kokkos device request
// kokkos_host_flag = no/yes Kokkos host request
// newtflag = newton off/on request
// style = NSQ/BIN/MULTI neighbor style
// triclinic = orthgonal/triclinic box
int copyflag,skipflag,halfflag,fullflag,halffullflag,sizeflag,respaflag,
ghostflag,off2onflag,onesideflag,ssaflag,ompflag,intelflag;
ghostflag,off2onflag,onesideflag,ssaflag,ompflag,intelflag,kokkos_device_flag,kokkos_host_flag;
copyflag = skipflag = halfflag = fullflag = halffullflag = sizeflag =
ghostflag = respaflag = off2onflag = onesideflag = ssaflag =
ompflag = intelflag = 0;
ompflag = intelflag = kokkos_device_flag = kokkos_host_flag = 0;
if (rq->copy) copyflag = NP_COPY;
if (rq->skip) skipflag = NP_SKIP;
@ -1420,6 +1411,8 @@ int Neighbor::choose_pair(NeighRequest *rq)
if (rq->ssa) ssaflag = NP_SSA;
if (rq->omp) ompflag = NP_OMP;
if (rq->intel) intelflag = NP_INTEL;
if (rq->kokkos_device) kokkos_device_flag = NP_KOKKOS_DEVICE;
if (rq->kokkos_host) kokkos_host_flag = NP_KOKKOS_HOST;
int newtflag;
if (rq->newton == 0 && newton_pair) newtflag = 1;
@ -1460,6 +1453,8 @@ int Neighbor::choose_pair(NeighRequest *rq)
if (ssaflag != (mask & NP_SSA)) continue;
if (ompflag != (mask & NP_OMP)) continue;
if (intelflag != (mask & NP_INTEL)) continue;
if (kokkos_device_flag != (mask & NP_KOKKOS_DEVICE)) continue;
if (kokkos_host_flag != (mask & NP_KOKKOS_HOST)) continue;
if (style == NSQ && !(mask & NP_NSQ)) continue;
if (style == BIN && !(mask & NP_BIN)) continue;
@ -1802,6 +1797,7 @@ void Neighbor::build_one(class NeighList *mylist, int preflag)
ns->create();
}
// build the list
np->build_setup();