From b8897765572e454ace662b80e1e87d115a244579 Mon Sep 17 00:00:00 2001
From: Stan Moore <stamoor@sandia.gov>
Date: Mon, 26 Jun 2017 10:51:26 -0600
Subject: [PATCH] Fixing memory leak in Kokkos neighborlist
---
src/KOKKOS/fix_qeq_reax_kokkos.cpp | 2 --
src/KOKKOS/neigh_list_kokkos.cpp | 19 ++++++-------------
src/KOKKOS/neigh_list_kokkos.h | 7 +------
src/KOKKOS/npair_kokkos.h | 2 +-
src/KOKKOS/pair_coul_dsf_kokkos.cpp | 3 ---
src/KOKKOS/pair_coul_wolf_kokkos.cpp | 3 ---
src/KOKKOS/pair_eam_alloy_kokkos.cpp | 3 ---
src/KOKKOS/pair_eam_fs_kokkos.cpp | 3 ---
src/KOKKOS/pair_eam_kokkos.cpp | 5 +----
src/KOKKOS/pair_kokkos.h | 4 ++--
src/KOKKOS/pair_reaxc_kokkos.cpp | 3 ---
src/KOKKOS/pair_sw_kokkos.cpp | 1 -
src/KOKKOS/pair_tersoff_kokkos.cpp | 1 -
src/KOKKOS/pair_tersoff_mod_kokkos.cpp | 1 -
src/KOKKOS/pair_tersoff_zbl_kokkos.cpp | 1 -
src/neigh_list.cpp | 2 ++
src/neigh_list.h | 3 ++-
17 files changed, 15 insertions(+), 48 deletions(-)
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index 5cafbd2ef3..cef003222a 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -218,8 +218,6 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag)
d_ilist = k_list->d_ilist;
inum = list->inum;
- k_list->clean_copy();
- //cleanup_copy();
copymode = 1;
int teamsize = TEAMSIZE;
diff --git a/src/KOKKOS/neigh_list_kokkos.cpp b/src/KOKKOS/neigh_list_kokkos.cpp
index b1b4e4467a..caf2dfee56 100644
--- a/src/KOKKOS/neigh_list_kokkos.cpp
+++ b/src/KOKKOS/neigh_list_kokkos.cpp
@@ -22,21 +22,14 @@ enum{NSQ,BIN,MULTI};
/* ---------------------------------------------------------------------- */
template<class Device>
-void NeighListKokkos<Device>::clean_copy()
+NeighListKokkos<Device>::NeighListKokkos(class LAMMPS *lmp):NeighList(lmp)
{
- ilist = NULL;
- numneigh = NULL;
- firstneigh = NULL;
- firstdouble = NULL;
- dnum = 0;
- iskip = NULL;
- ijskip = NULL;
-
- ipage = NULL;
- dpage = NULL;
-
+ _stride = 1;
+ maxneighs = 16;
+ kokkos = 1;
maxatoms = 0;
-}
+ execution_space = ExecutionSpaceFromDevice<Device>::space;
+};
/* ---------------------------------------------------------------------- */
diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h
index 45e768927c..c887bd13b7 100644
--- a/src/KOKKOS/neigh_list_kokkos.h
+++ b/src/KOKKOS/neigh_list_kokkos.h
@@ -68,18 +68,13 @@ class NeighListKokkos: public NeighList {
public:
int maxneighs;
- void clean_copy();
void grow(int nmax);
typename ArrayTypes<Device>::t_neighbors_2d d_neighbors;
typename DAT::tdual_int_1d k_ilist; // local indices of I atoms
typename ArrayTypes<Device>::t_int_1d d_ilist;
typename ArrayTypes<Device>::t_int_1d d_numneigh; // # of J neighs for each I
- NeighListKokkos(class LAMMPS *lmp):
- NeighList(lmp) {_stride = 1; maxneighs = 16; kokkos = 1; maxatoms = 0;
- execution_space = ExecutionSpaceFromDevice<Device>::space;
- };
- ~NeighListKokkos() {numneigh = NULL; ilist = NULL;};
+ NeighListKokkos(class LAMMPS *lmp);
KOKKOS_INLINE_FUNCTION
AtomNeighbors get_neighbors(const int &i) const {
diff --git a/src/KOKKOS/npair_kokkos.h b/src/KOKKOS/npair_kokkos.h
index 8e81c57618..53183114d3 100644
--- a/src/KOKKOS/npair_kokkos.h
+++ b/src/KOKKOS/npair_kokkos.h
@@ -265,7 +265,7 @@ class NeighborKokkosExecute
h_new_maxneighs() = neigh_list.maxneighs;
};
- ~NeighborKokkosExecute() {neigh_list.clean_copy();};
+ ~NeighborKokkosExecute() {neigh_list.copymode = 1;};
template<int HalfNeigh, int Newton, int Tri>
KOKKOS_FUNCTION
diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
index f2063bdc08..e6f5407f2d 100644
--- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
@@ -120,9 +120,6 @@ void PairCoulDSFKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
int inum = list->inum;
- // Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
-
- k_list->clean_copy();
copymode = 1;
// loop over neighbors of my atoms
diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
index 8049ba0031..75177e2d81 100644
--- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
@@ -121,9 +121,6 @@ void PairCoulWolfKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
int inum = list->inum;
- // Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
-
- k_list->clean_copy();
copymode = 1;
// loop over neighbors of my atoms
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index 76c701213d..f8b7a69d60 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -122,9 +122,6 @@ void PairEAMAlloyKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_ilist = k_list->d_ilist;
int inum = list->inum;
- // Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
-
- k_list->clean_copy();
copymode = 1;
// zero out density
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index 9b565f8ede..57820afb26 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -122,9 +122,6 @@ void PairEAMFSKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_ilist = k_list->d_ilist;
int inum = list->inum;
- // Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
-
- k_list->clean_copy();
copymode = 1;
// zero out density
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index 7be8e54605..e848669947 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -117,9 +117,6 @@ void PairEAMKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_ilist = k_list->d_ilist;
int inum = list->inum;
- // Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
-
- k_list->clean_copy();
copymode = 1;
// zero out density
@@ -868,4 +865,4 @@ template class PairEAMKokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class PairEAMKokkos<LMPHostType>;
#endif
-}
\ No newline at end of file
+}
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index 1e01b3df15..b0614a934b 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -87,7 +87,7 @@ struct PairComputeFunctor {
vatom(c.d_vatom),list(*list_ptr) {};
// Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
- ~PairComputeFunctor() {c.cleanup_copy();list.clean_copy();};
+ ~PairComputeFunctor() {c.cleanup_copy();list.copymode = 1;};
KOKKOS_INLINE_FUNCTION int sbmask(const int& j) const {
return j >> SBBITS & 3;
@@ -344,7 +344,7 @@ struct PairComputeFunctor<PairStyle,N2,STACKPARAMS,Specialisation> {
PairComputeFunctor(PairStyle* c_ptr,
NeighListKokkos<device_type>* list_ptr):
c(*c_ptr),list(*list_ptr) {};
- ~PairComputeFunctor() {c.cleanup_copy();list.clean_copy();};
+ ~PairComputeFunctor() {c.cleanup_copy();list.copymode = 1;};
KOKKOS_INLINE_FUNCTION int sbmask(const int& j) const {
return j >> SBBITS & 3;
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 6082c93287..6be09548da 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -709,8 +709,6 @@ void PairReaxCKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
- k_list->clean_copy();
-
if (eflag_global) {
for (int i = 0; i < 14; i++)
pvector[i] = 0.0;
@@ -3985,7 +3983,6 @@ void PairReaxCKokkos<DeviceType>::FindBond(int &numbonds)
const int inum = list->inum;
NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
d_ilist = k_list->d_ilist;
- k_list->clean_copy();
numbonds = 0;
PairReaxCKokkosFindBondFunctor<DeviceType> find_bond_functor(this);
diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp
index a8950a0c79..e5c947cc8e 100644
--- a/src/KOKKOS/pair_sw_kokkos.cpp
+++ b/src/KOKKOS/pair_sw_kokkos.cpp
@@ -115,7 +115,6 @@ void PairSWKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_numneigh = k_list->d_numneigh;
d_neighbors = k_list->d_neighbors;
- k_list->clean_copy();
copymode = 1;
EV_FLOAT ev;
diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp
index 75280c8f7c..833c815ad9 100644
--- a/src/KOKKOS/pair_tersoff_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_kokkos.cpp
@@ -200,7 +200,6 @@ void PairTersoffKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
- k_list->clean_copy();
copymode = 1;
EV_FLOAT ev;
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
index d16a7fc4d7..d77ba2f141 100644
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
@@ -200,7 +200,6 @@ void PairTersoffMODKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
- k_list->clean_copy();
copymode = 1;
EV_FLOAT ev;
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
index e9bae49fb7..040d8c5230 100644
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
@@ -214,7 +214,6 @@ void PairTersoffZBLKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
d_neighbors = k_list->d_neighbors;
d_ilist = k_list->d_ilist;
- k_list->clean_copy();
copymode = 1;
EV_FLOAT ev;
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index edc8634373..a5ca7a5366 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -48,6 +48,7 @@ NeighList::NeighList(LAMMPS *lmp) : Pointers(lmp)
ghost = 0;
ssa = 0;
copy = 0;
+ copymode = 0;
dnum = 0;
// ptrs
@@ -85,6 +86,7 @@ NeighList::NeighList(LAMMPS *lmp) : Pointers(lmp)
NeighList::~NeighList()
{
+ if (copymode) return;
if (!copy) {
memory->destroy(ilist);
memory->destroy(numneigh);
diff --git a/src/neigh_list.h b/src/neigh_list.h
index 9a77a0311d..3fb3868114 100644
--- a/src/neigh_list.h
+++ b/src/neigh_list.h
@@ -34,7 +34,8 @@ class NeighList : protected Pointers {
int occasional; // 0 if build every reneighbor, 1 if not
int ghost; // 1 if list stores neighbors of ghosts
int ssa; // 1 if list stores Shardlow data
- int copy; // 1 if this list copied from another list
+ int copy; // 1 if this list is (host) copied from another list
+ int copymode; // 1 if this is a Kokkos on-device copy
int dnum; // # of doubles per neighbor, 0 if none
// data structs to store neighbor pairs I,J and associated values
--
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