Kokkos neighbor refactor (8318c678) · Commits · 郑智淋 / lammps

src/KOKKOS/Install.sh

+4 −3

Original line number	Diff line number	Diff line
		@@ -105,11 +105,14 @@ action modify_kokkos.cpp
		action modify_kokkos.h
		action neigh_bond_kokkos.cpp
		action neigh_bond_kokkos.h
		action neigh_full_kokkos.h
		action neigh_list_kokkos.cpp
		action neigh_list_kokkos.h
		action neighbor_kokkos.cpp
		action neighbor_kokkos.h
		action npair_kokkos.cpp
		action npair_kokkos.h
		action nbin_kokkos.cpp
		action nbin_kokkos.h
		action math_special_kokkos.cpp
		action math_special_kokkos.h
		action pair_buck_coul_cut_kokkos.cpp
		@@ -169,8 +172,6 @@ action pair_reax_c_kokkos.cpp pair_reax_c.cpp
		action pair_reax_c_kokkos.h pair_reax_c.h
		action pair_sw_kokkos.cpp pair_sw.cpp
		action pair_sw_kokkos.h pair_sw.h
		action pair_vashishta_kokkos.cpp pair_vashishta.cpp
		action pair_vashishta_kokkos.h pair_vashishta.h
		action pair_table_kokkos.cpp
		action pair_table_kokkos.h
		action pair_tersoff_kokkos.cpp pair_tersoff.cpp

src/KOKKOS/atom_vec_kokkos.h

+2 −12

Original line number	Diff line number	Diff line
		@@ -83,13 +83,8 @@ class AtomVecKokkos : public AtomVec {
		std::is_same<typename ViewType::execution_space,LMPDeviceType>::value,
		Kokkos::CudaHostPinnedSpace,typename ViewType::memory_space>::type,
		Kokkos::MemoryTraits<Kokkos::Unmanaged> > mirror_type;
		if (buffer_size == 0) {
		buffer = Kokkos::kokkos_malloc<Kokkos::CudaHostPinnedSpace>(src.capacity());
		buffer_size = src.capacity();
		} else if (buffer_size < src.capacity()) {
		if(buffer_size < src.capacity())
		buffer = Kokkos::kokkos_realloc<Kokkos::CudaHostPinnedSpace>(buffer,src.capacity());
		buffer_size = src.capacity();
		}
		return mirror_type( buffer ,
		src.dimension_0() ,
		src.dimension_1() ,
		@@ -109,13 +104,8 @@ class AtomVecKokkos : public AtomVec {
		std::is_same<typename ViewType::execution_space,LMPDeviceType>::value,
		Kokkos::CudaHostPinnedSpace,typename ViewType::memory_space>::type,
		Kokkos::MemoryTraits<Kokkos::Unmanaged> > mirror_type;
		if (buffer_size == 0) {
		buffer = Kokkos::kokkos_malloc<Kokkos::CudaHostPinnedSpace>(src.capacity()*sizeof(typename ViewType::value_type));
		buffer_size = src.capacity();
		} else if (buffer_size < src.capacity()) {
		if(buffer_size < src.capacity())
		buffer = Kokkos::kokkos_realloc<Kokkos::CudaHostPinnedSpace>(buffer,src.capacity()*sizeof(typename ViewType::value_type));
		buffer_size = src.capacity();
		}
		mirror_type tmp_view( (typename ViewType::value_type*)buffer ,
		src.dimension_0() ,
		src.dimension_1() ,

src/KOKKOS/fix_qeq_reax_kokkos.cpp

+0 −2

Original line number	Diff line number	Diff line
		@@ -125,12 +125,10 @@ void FixQEqReaxKokkos<DeviceType>::init()
		neighbor->requests[irequest]->pair = 0;
		neighbor->requests[irequest]->full = 1;
		neighbor->requests[irequest]->half = 0;
		neighbor->requests[irequest]->full_cluster = 0;
		} else { //if (neighflag == HALF \|\| neighflag == HALFTHREAD)
		neighbor->requests[irequest]->fix = 1;
		neighbor->requests[irequest]->full = 0;
		neighbor->requests[irequest]->half = 1;
		neighbor->requests[irequest]->full_cluster = 0;
		neighbor->requests[irequest]->ghost = 1;
		}
		}

src/KOKKOS/kokkos.cpp

+18 −31

Original line number	Diff line number	Diff line
		@@ -168,7 +168,6 @@ void KokkosLMP::accelerator(int narg, char **arg)
		else
		neighflag = HALF;
		} else if (strcmp(arg[iarg+1],"n2") == 0) neighflag = N2;
		else if (strcmp(arg[iarg+1],"full/cluster") == 0) neighflag = FULLCLUSTER;
		else error->all(FLERR,"Illegal package kokkos command");
		iarg += 2;
		} else if (strcmp(arg[iarg],"binsize") == 0) {
		@@ -232,20 +231,6 @@ void KokkosLMP::accelerator(int narg, char **arg)
		called by Finish
		------------------------------------------------------------------------- */

		int KokkosLMP::neigh_list_kokkos(int m)
		{
		NeighborKokkos nk = (NeighborKokkos ) neighbor;
		if (nk->lists_host[m] && nk->lists_host[m]->d_numneigh.dimension_0())
		return 1;
		if (nk->lists_device[m] && nk->lists_device[m]->d_numneigh.dimension_0())
		return 1;
		return 0;
		}

		/* ----------------------------------------------------------------------
		called by Finish
		------------------------------------------------------------------------- */

		int KokkosLMP::neigh_count(int m)
		{
		int inum;
		@@ -255,28 +240,30 @@ int KokkosLMP::neigh_count(int m)
		ArrayTypes<LMPHostType>::t_int_1d h_numneigh;

		NeighborKokkos nk = (NeighborKokkos ) neighbor;
		if (nk->lists_host[m]) {
		inum = nk->lists_host[m]->inum;
		if (nk->lists[m]->execution_space == Host) {
		NeighListKokkos<LMPHostType>* nlistKK = (NeighListKokkos<LMPHostType>*) nk->lists[m];
		inum = nlistKK->inum;
		#ifndef KOKKOS_USE_CUDA_UVM
		h_ilist = Kokkos::create_mirror_view(nk->lists_host[m]->d_ilist);
		h_numneigh = Kokkos::create_mirror_view(nk->lists_host[m]->d_numneigh);
		h_ilist = Kokkos::create_mirror_view(nlistKK->d_ilist);
		h_numneigh = Kokkos::create_mirror_view(nlistKK->d_numneigh);
		#else
		h_ilist = nk->lists_host[m]->d_ilist;
		h_numneigh = nk->lists_host[m]->d_numneigh;
		h_ilist = nlistKK->d_ilist;
		h_numneigh = nlistKK->d_numneigh;
		#endif
		Kokkos::deep_copy(h_ilist,nk->lists_host[m]->d_ilist);
		Kokkos::deep_copy(h_numneigh,nk->lists_host[m]->d_numneigh);
		} else if (nk->lists_device[m]) {
		inum = nk->lists_device[m]->inum;
		Kokkos::deep_copy(h_ilist,nlistKK->d_ilist);
		Kokkos::deep_copy(h_numneigh,nlistKK->d_numneigh);
		} else if (nk->lists[m]->execution_space == Device) {
		NeighListKokkos<LMPDeviceType>* nlistKK = (NeighListKokkos<LMPDeviceType>*) nk->lists[m];
		inum = nlistKK->inum;
		#ifndef KOKKOS_USE_CUDA_UVM
		h_ilist = Kokkos::create_mirror_view(nk->lists_device[m]->d_ilist);
		h_numneigh = Kokkos::create_mirror_view(nk->lists_device[m]->d_numneigh);
		h_ilist = Kokkos::create_mirror_view(nlistKK->d_ilist);
		h_numneigh = Kokkos::create_mirror_view(nlistKK->d_numneigh);
		#else
		h_ilist = nk->lists_device[m]->d_ilist;
		h_numneigh = nk->lists_device[m]->d_numneigh;
		h_ilist = nlistKK->d_ilist;
		h_numneigh = nlistKK->d_numneigh;
		#endif
		Kokkos::deep_copy(h_ilist,nk->lists_device[m]->d_ilist);
		Kokkos::deep_copy(h_numneigh,nk->lists_device[m]->d_numneigh);
		Kokkos::deep_copy(h_ilist,nlistKK->d_ilist);
		Kokkos::deep_copy(h_numneigh,nlistKK->d_numneigh);
		}

		for (int i = 0; i < inum; i++) nneigh += h_numneigh[h_ilist[i]];

src/KOKKOS/kokkos.h

+0 −1

Original line number	Diff line number	Diff line
		@@ -34,7 +34,6 @@ class KokkosLMP : protected Pointers {
		KokkosLMP(class LAMMPS , int, char *);
		~KokkosLMP();
		void accelerator(int, char **);
		int neigh_list_kokkos(int);
		int neigh_count(int);
		private:
		static void my_signal_handler(int);

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