Fix thread safety issue in fused forward comm (d1e751d7) · Commits · 郑智淋 / lammps

src/KOKKOS/atom_vec_kokkos.cpp

+22 −16

Original line number	Diff line number	Diff line
		@@ -281,6 +281,7 @@ struct AtomVecKokkos_PackCommSelfFused {
		typename ArrayTypes<DeviceType>::t_int_1d_const _pbc_flag;
		typename ArrayTypes<DeviceType>::t_int_1d_const _firstrecv;
		typename ArrayTypes<DeviceType>::t_int_1d_const _sendnum_scan;
		typename ArrayTypes<DeviceType>::t_int_1d_const _g2l;
		X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;

		AtomVecKokkos_PackCommSelfFused(
		@@ -290,6 +291,7 @@ struct AtomVecKokkos_PackCommSelfFused {
		const typename DAT::tdual_int_1d &pbc_flag,
		const typename DAT::tdual_int_1d &firstrecv,
		const typename DAT::tdual_int_1d &sendnum_scan,
		const typename DAT::tdual_int_1d &g2l,
		const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
		const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz):
		_x(x.view<DeviceType>()),_xw(x.view<DeviceType>()),
		@@ -298,6 +300,7 @@ struct AtomVecKokkos_PackCommSelfFused {
		_pbc_flag(pbc_flag.view<DeviceType>()),
		_firstrecv(firstrecv.view<DeviceType>()),
		_sendnum_scan(sendnum_scan.view<DeviceType>()),
		_g2l(g2l.view<DeviceType>()),
		_xprd(xprd),_yprd(yprd),_zprd(zprd),
		_xy(xy),_xz(xz),_yz(yz) {};

		@@ -310,42 +313,45 @@ struct AtomVecKokkos_PackCommSelfFused {
		if (iswap > 0)
		i = ii - _sendnum_scan[iswap-1];
		const int _nfirst = _firstrecv[iswap];
		const int nlocal = _firstrecv[0];

		int j = _list(iswap,i);
		if (j >= nlocal)
		j = _g2l(j-nlocal);

		const int j = _list(iswap,i);
		if (_pbc_flag(iswap) == 0) {
		if (_pbc_flag(ii) == 0) {
		_xw(i+_nfirst,0) = _x(j,0);
		_xw(i+_nfirst,1) = _x(j,1);
		_xw(i+_nfirst,2) = _x(j,2);
		} else {
		if (TRICLINIC == 0) {
		_xw(i+_nfirst,0) = _x(j,0) + _pbc(iswap,0)*_xprd;
		_xw(i+_nfirst,1) = _x(j,1) + _pbc(iswap,1)*_yprd;
		_xw(i+_nfirst,2) = _x(j,2) + _pbc(iswap,2)*_zprd;
		_xw(i+_nfirst,0) = _x(j,0) + _pbc(ii,0)*_xprd;
		_xw(i+_nfirst,1) = _x(j,1) + _pbc(ii,1)*_yprd;
		_xw(i+_nfirst,2) = _x(j,2) + _pbc(ii,2)*_zprd;
		} else {
		_xw(i+_nfirst,0) = _x(j,0) + _pbc(iswap,0)_xprd + _pbc(iswap,5)_xy + _pbc(iswap,4)*_xz;
		_xw(i+_nfirst,1) = _x(j,1) + _pbc(iswap,1)_yprd + _pbc(iswap,3)_yz;
		_xw(i+_nfirst,2) = _x(j,2) + _pbc(iswap,2)*_zprd;
		_xw(i+_nfirst,0) = _x(j,0) + _pbc(ii,0)_xprd + _pbc(ii,5)_xy + _pbc(ii,4)*_xz;
		_xw(i+_nfirst,1) = _x(j,1) + _pbc(ii,1)_yprd + _pbc(ii,3)_yz;
		_xw(i+_nfirst,2) = _x(j,2) + _pbc(ii,2)*_zprd;
		}
		}

		}
		};

		/* ---------------------------------------------------------------------- */

		int AtomVecKokkos::pack_comm_self_fused(const int &n, const DAT::tdual_int_2d &list, const DAT::tdual_int_1d &sendnum_scan,
		const DAT::tdual_int_1d &firstrecv, const DAT::tdual_int_1d &pbc_flag, const DAT::tdual_int_2d &pbc) {
		const DAT::tdual_int_1d &firstrecv, const DAT::tdual_int_1d &pbc_flag, const DAT::tdual_int_2d &pbc,
		const DAT::tdual_int_1d &g2l) {
		if(commKK->forward_comm_on_host) {
		sync(Host,X_MASK);
		modified(Host,X_MASK);
		if(domain->triclinic) {
		struct AtomVecKokkos_PackCommSelfFused<LMPHostType,1> f(atomKK->k_x,list,pbc,pbc_flag,firstrecv,sendnum_scan,
		struct AtomVecKokkos_PackCommSelfFused<LMPHostType,1> f(atomKK->k_x,list,pbc,pbc_flag,firstrecv,sendnum_scan,g2l,
		domain->xprd,domain->yprd,domain->zprd,
		domain->xy,domain->xz,domain->yz);
		Kokkos::parallel_for(n,f);
		} else {
		struct AtomVecKokkos_PackCommSelfFused<LMPHostType,0> f(atomKK->k_x,list,pbc,pbc_flag,firstrecv,sendnum_scan,
		struct AtomVecKokkos_PackCommSelfFused<LMPHostType,0> f(atomKK->k_x,list,pbc,pbc_flag,firstrecv,sendnum_scan,g2l,
		domain->xprd,domain->yprd,domain->zprd,
		domain->xy,domain->xz,domain->yz);
		Kokkos::parallel_for(n,f);
		@@ -354,12 +360,12 @@ int AtomVecKokkos::pack_comm_self_fused(const int &n, const DAT::tdual_int_2d &l
		sync(Device,X_MASK);
		modified(Device,X_MASK);
		if(domain->triclinic) {
		struct AtomVecKokkos_PackCommSelfFused<LMPDeviceType,1> f(atomKK->k_x,list,pbc,pbc_flag,firstrecv,sendnum_scan,
		struct AtomVecKokkos_PackCommSelfFused<LMPDeviceType,1> f(atomKK->k_x,list,pbc,pbc_flag,firstrecv,sendnum_scan,g2l,
		domain->xprd,domain->yprd,domain->zprd,
		domain->xy,domain->xz,domain->yz);
		Kokkos::parallel_for(n,f);
		} else {
		struct AtomVecKokkos_PackCommSelfFused<LMPDeviceType,0> f(atomKK->k_x,list,pbc,pbc_flag,firstrecv,sendnum_scan,
		struct AtomVecKokkos_PackCommSelfFused<LMPDeviceType,0> f(atomKK->k_x,list,pbc,pbc_flag,firstrecv,sendnum_scan,g2l,
		domain->xprd,domain->yprd,domain->zprd,
		domain->xy,domain->xz,domain->yz);
		Kokkos::parallel_for(n,f);

src/KOKKOS/atom_vec_kokkos.h

+2 −1

Original line number	Diff line number	Diff line
		@@ -56,7 +56,8 @@ class AtomVecKokkos : public AtomVec {
		const DAT::tdual_int_1d &sendnum_scan,
		const DAT::tdual_int_1d &firstrecv,
		const DAT::tdual_int_1d &pbc_flag,
		const DAT::tdual_int_2d &pbc);
		const DAT::tdual_int_2d &pbc,
		const DAT::tdual_int_1d &g2l);

		virtual int
		pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &list,

src/KOKKOS/comm_kokkos.cpp

+46 −28

Original line number	Diff line number	Diff line
		@@ -140,31 +140,6 @@ void CommKokkos::init()
		forward_comm_classic = true;
		}

		/* ---------------------------------------------------------------------- */

		void CommKokkos::setup()
		{
		CommBrick::setup();

		k_pbc_flag = DAT::tdual_int_1d("comm:pbc_flag",nswap);
		k_pbc = DAT::tdual_int_2d("comm:pbc",nswap,6);

		for (int iswap = 0; iswap < nswap; iswap++) {
		k_pbc_flag.h_view[iswap] = pbc_flag[iswap];
		k_pbc.h_view(iswap,0) = pbc[iswap][0];
		k_pbc.h_view(iswap,1) = pbc[iswap][1];
		k_pbc.h_view(iswap,2) = pbc[iswap][2];
		k_pbc.h_view(iswap,3) = pbc[iswap][3];
		k_pbc.h_view(iswap,4) = pbc[iswap][4];
		k_pbc.h_view(iswap,5) = pbc[iswap][5];
		}
		k_pbc_flag.modify<LMPHostType>();
		k_pbc.modify<LMPHostType>();

		k_pbc_flag.sync<LMPDeviceType>();
		k_pbc.sync<LMPDeviceType>();
		}

		/* ----------------------------------------------------------------------
		forward communication of atom coords every timestep
		other per-atom attributes may also be sent via pack/unpack routines
		@@ -211,11 +186,12 @@ void CommKokkos::forward_comm_device(int dummy)
		k_sendlist.sync<DeviceType>();
		atomKK->sync(ExecutionSpaceFromDevice<DeviceType>::space,X_MASK);

		if (comm->nprocs == 1) {
		if (comm->nprocs == 1 && !ghost_velocity) {
		k_swap.sync<DeviceType>();
		k_swap2.sync<DeviceType>();
		k_pbc.sync<DeviceType>();
		n = avec->pack_comm_self_fused(totalsend,k_sendlist,k_sendnum_scan,
		k_firstrecv,k_pbc_flag,k_pbc);
		k_firstrecv,k_pbc_flag,k_pbc,k_g2l);
		} else {

		for (int iswap = 0; iswap < nswap; iswap++) {
		@@ -783,7 +759,7 @@ void CommKokkos::borders()
		atomKK->modified(Host,ALL_MASK);
		}

		if (comm->nprocs == 1 && !forward_comm_classic)
		if (comm->nprocs == 1 && !ghost_velocity && !forward_comm_classic)
		copy_swap_info();
		}

		@@ -1092,7 +1068,49 @@ void CommKokkos::copy_swap_info()
		}
		totalsend = scan;

		int* list = NULL;
		memory->create(list,totalsend,"comm:list");
		if (totalsend > k_pbc.extent(0)) {
		k_pbc = DAT::tdual_int_2d("comm:pbc",totalsend,6);
		k_swap2 = DAT::tdual_int_2d("comm:swap2",2,totalsend);
		k_pbc_flag = Kokkos::subview(k_swap2,0,Kokkos::ALL);
		k_g2l = Kokkos::subview(k_swap2,1,Kokkos::ALL);
		}

		// create map of ghost atoms to local atoms
		// store periodic boundary transform from local to ghost

		for (int iswap = 0; iswap < nswap; iswap++) {
		for (int i = 0; i < sendnum[iswap]; i++) {
		int source = sendlist[iswap][i] - atom->nlocal;
		int dest = firstrecv[iswap] + i - atom->nlocal;
		k_pbc_flag.h_view(dest) = pbc_flag[iswap];
		k_pbc.h_view(dest,0) = pbc[iswap][0];
		k_pbc.h_view(dest,1) = pbc[iswap][1];
		k_pbc.h_view(dest,2) = pbc[iswap][2];
		k_pbc.h_view(dest,3) = pbc[iswap][3];
		k_pbc.h_view(dest,4) = pbc[iswap][4];
		k_pbc.h_view(dest,5) = pbc[iswap][5];
		k_g2l.h_view(dest) = atom->nlocal + source;

		if (source >= 0) {
		k_pbc_flag.h_view(dest) = k_pbc_flag.h_view(dest) \|\| k_pbc_flag.h_view(source);
		k_pbc.h_view(dest,0) += k_pbc.h_view(source,0);
		k_pbc.h_view(dest,1) += k_pbc.h_view(source,1);
		k_pbc.h_view(dest,2) += k_pbc.h_view(source,2);
		k_pbc.h_view(dest,3) += k_pbc.h_view(source,3);
		k_pbc.h_view(dest,4) += k_pbc.h_view(source,4);
		k_pbc.h_view(dest,5) += k_pbc.h_view(source,5);
		k_g2l.h_view(dest) = k_g2l.h_view(source);
		}
		}
		}

		k_swap.modify<LMPHostType>();
		k_swap2.modify<LMPHostType>();
		k_pbc.modify<LMPHostType>();

		memory->destroy(list);
		}

		/* ----------------------------------------------------------------------

src/KOKKOS/comm_kokkos.h

+2 −1

Original line number	Diff line number	Diff line
		@@ -33,7 +33,6 @@ class CommKokkos : public CommBrick {
		CommKokkos(class LAMMPS *);
		~CommKokkos();
		void init();
		void setup();

		void forward_comm(int dummy = 0); // forward comm of atom coords
		void reverse_comm(); // reverse comm of atom coords
		@@ -66,8 +65,10 @@ class CommKokkos : public CommBrick {
		//double *buf_recv; // recv buffer for all comm

		DAT::tdual_int_2d k_swap;
		DAT::tdual_int_2d k_swap2;
		DAT::tdual_int_2d k_pbc;
		DAT::tdual_int_1d k_pbc_flag;
		DAT::tdual_int_1d k_g2l;
		DAT::tdual_int_1d k_firstrecv;
		DAT::tdual_int_1d k_sendnum_scan;
		int totalsend;

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