Fixing Kokkos bug and adding host version of CommTiled (d7bb53e4) · Commits · 郑智淋 / lammps

src/KOKKOS/comm_tiled_kokkos.cpp

0 → 100644

+266 −0

Original line number	Diff line number	Diff line
		/* ----------------------------------------------------------------------
		LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
		http://lammps.sandia.gov, Sandia National Laboratories
		Steve Plimpton, sjplimp@sandia.gov

		Copyright (2003) Sandia Corporation. Under the terms of Contract
		DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		certain rights in this software. This software is distributed under
		the GNU General Public License.

		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		#include <string.h>
		#include "comm_tiled_kokkos.h"
		#include "comm_brick.h"
		#include "atom_kokkos.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"
		#include "atom_masks.h"

		using namespace LAMMPS_NS;

		#define BUFFACTOR 1.5
		#define BUFFACTOR 1.5
		#define BUFMIN 1000
		#define BUFEXTRA 1000
		#define EPSILON 1.0e-6

		#define DELTA_PROCS 16

		enum{SINGLE,MULTI}; // same as in Comm
		enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files

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

		CommTiledKokkos::CommTiledKokkos(LAMMPS *lmp) : CommTiled(lmp)
		{

		}

		/* ---------------------------------------------------------------------- */
		//IMPORTANT: we MUST pass "*oldcomm" to the Comm initializer here, as
		// the code below requires that the (implicit) copy constructor
		// for Comm is run and thus creating a shallow copy of "oldcomm".
		// The call to Comm::copy_arrays() then converts the shallow copy
		// into a deep copy of the class with the new layout.

		CommTiledKokkos::CommTiledKokkos(LAMMPS lmp, Comm oldcomm) : CommTiled(lmp,oldcomm)
		{

		}

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

		CommTiledKokkos::~CommTiledKokkos()
		{

		}

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


		/* ----------------------------------------------------------------------
		forward communication of atom coords every timestep
		other per-atom attributes may also be sent via pack/unpack routines
		------------------------------------------------------------------------- */

		void CommTiledKokkos::forward_comm(int dummy)
		{
		if (comm_x_only) {
		atomKK->sync(Host,X_MASK);
		atomKK->modified(Host,X_MASK);
		} else if (ghost_velocity) {
		atomKK->sync(Host,X_MASK \| V_MASK);
		atomKK->modified(Host,X_MASK \| V_MASK);
		} else {
		atomKK->sync(Host,ALL_MASK);
		atomKK->modified(Host,ALL_MASK);
		}

		CommTiled::forward_comm(dummy);
		}

		/* ----------------------------------------------------------------------
		reverse communication of forces on atoms every timestep
		other per-atom attributes may also be sent via pack/unpack routines
		------------------------------------------------------------------------- */

		void CommTiledKokkos::reverse_comm()
		{
		if (comm_f_only)
		atomKK->sync(Host,F_MASK);
		else
		atomKK->sync(Host,ALL_MASK);
		CommTiled::reverse_comm();
		if (comm_f_only)
		atomKK->modified(Host,F_MASK);
		else
		atomKK->modified(Host,ALL_MASK);
		atomKK->sync(Device,ALL_MASK);
		}

		/* ----------------------------------------------------------------------
		exchange: move atoms to correct processors
		atoms exchanged with procs that touch sub-box in each of 3 dims
		send out atoms that have left my box, receive ones entering my box
		atoms will be lost if not inside a touching proc's box
		can happen if atom moves outside of non-periodic bounary
		or if atom moves more than one proc away
		this routine called before every reneighboring
		for triclinic, atoms must be in lamda coords (0-1) before exchange is called
		------------------------------------------------------------------------- */

		void CommTiledKokkos::exchange()
		{
		atomKK->sync(Host,ALL_MASK);
		CommTiled::exchange();
		atomKK->modified(Host,ALL_MASK);
		}

		/* ----------------------------------------------------------------------
		borders: list nearby atoms to send to neighboring procs at every timestep
		one list is created per swap/proc that will be made
		as list is made, actually do communication
		this does equivalent of a forward_comm(), so don't need to explicitly
		call forward_comm() on reneighboring timestep
		this routine is called before every reneighboring
		for triclinic, atoms must be in lamda coords (0-1) before borders is called
		------------------------------------------------------------------------- */

		void CommTiledKokkos::borders()
		{
		atomKK->sync(Host,ALL_MASK);
		CommTiled::borders();
		atomKK->modified(Host,ALL_MASK);
		}

		/* ----------------------------------------------------------------------
		forward communication invoked by a Pair
		nsize used only to set recv buffer limit
		------------------------------------------------------------------------- */

		void CommTiledKokkos::forward_comm_pair(Pair *pair)
		{
		CommTiled::forward_comm_pair(pair);
		}

		/* ----------------------------------------------------------------------
		reverse communication invoked by a Pair
		nsize used only to set recv buffer limit
		------------------------------------------------------------------------- */

		void CommTiledKokkos::reverse_comm_pair(Pair *pair)
		{
		CommTiled::reverse_comm_pair(pair);
		}

		/* ----------------------------------------------------------------------
		forward communication invoked by a Fix
		size/nsize used only to set recv buffer limit
		size = 0 (default) -> use comm_forward from Fix
		size > 0 -> Fix passes max size per atom
		the latter is only useful if Fix does several comm modes,
		some are smaller than max stored in its comm_forward
		------------------------------------------------------------------------- */

		void CommTiledKokkos::forward_comm_fix(Fix *fix, int size)
		{
		CommTiled::forward_comm_fix(fix,size);
		}

		/* ----------------------------------------------------------------------
		reverse communication invoked by a Fix
		size/nsize used only to set recv buffer limit
		size = 0 (default) -> use comm_forward from Fix
		size > 0 -> Fix passes max size per atom
		the latter is only useful if Fix does several comm modes,
		some are smaller than max stored in its comm_forward
		------------------------------------------------------------------------- */

		void CommTiledKokkos::reverse_comm_fix(Fix *fix, int size)
		{
		CommTiled::reverse_comm_fix(fix,size);
		}

		/* ----------------------------------------------------------------------
		reverse communication invoked by a Fix with variable size data
		query fix for all pack sizes to insure buf_send is big enough
		handshake sizes before irregular comm to insure buf_recv is big enough
		NOTE: how to setup one big buf recv with correct offsets ??
		------------------------------------------------------------------------- */

		void CommTiledKokkos::reverse_comm_fix_variable(Fix *fix)
		{
		CommTiled::reverse_comm_fix_variable(fix);
		}

		/* ----------------------------------------------------------------------
		forward communication invoked by a Compute
		nsize used only to set recv buffer limit
		------------------------------------------------------------------------- */

		void CommTiledKokkos::forward_comm_compute(Compute *compute)
		{
		CommTiled::forward_comm_compute(compute);
		}

		/* ----------------------------------------------------------------------
		reverse communication invoked by a Compute
		nsize used only to set recv buffer limit
		------------------------------------------------------------------------- */

		void CommTiledKokkos::reverse_comm_compute(Compute *compute)
		{
		CommTiled::reverse_comm_compute(compute);
		}

		/* ----------------------------------------------------------------------
		forward communication invoked by a Dump
		nsize used only to set recv buffer limit
		------------------------------------------------------------------------- */

		void CommTiledKokkos::forward_comm_dump(Dump *dump)
		{
		CommTiled::forward_comm_dump(dump);
		}

		/* ----------------------------------------------------------------------
		reverse communication invoked by a Dump
		nsize used only to set recv buffer limit
		------------------------------------------------------------------------- */

		void CommTiledKokkos::reverse_comm_dump(Dump *dump)
		{
		CommTiled::reverse_comm_dump(dump);
		}

		/* ----------------------------------------------------------------------
		forward communication of Nsize values in per-atom array
		------------------------------------------------------------------------- */

		void CommTiledKokkos::forward_comm_array(int nsize, double **array)
		{
		CommTiled::forward_comm_array(nsize,array);
		}

		/* ----------------------------------------------------------------------
		exchange info provided with all 6 stencil neighbors
		NOTE: this method is currently not used
		------------------------------------------------------------------------- */

		int CommTiledKokkos::exchange_variable(int n, double inbuf, double &outbuf)
		{
		CommTiled::exchange_variable(n,inbuf,outbuf);
		}
		No newline at end of file

src/KOKKOS/comm_tiled_kokkos.h

0 → 100644

+59 −0

Original line number	Diff line number	Diff line
		/* -- c++ -- ----------------------------------------------------------
		LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
		http://lammps.sandia.gov, Sandia National Laboratories
		Steve Plimpton, sjplimp@sandia.gov

		Copyright (2003) Sandia Corporation. Under the terms of Contract
		DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
		certain rights in this software. This software is distributed under
		the GNU General Public License.

		See the README file in the top-level LAMMPS directory.
		------------------------------------------------------------------------- */

		#ifndef LMP_COMM_TILED_KOKKOS_H
		#define LMP_COMM_TILED_KOKKOS_H

		#include "comm_tiled.h"
		#include "kokkos_type.h"

		namespace LAMMPS_NS {

		class CommTiledKokkos : public CommTiled {
		public:
		CommTiledKokkos(class LAMMPS *);
		CommTiledKokkos(class LAMMPS , class Comm );
		virtual ~CommTiledKokkos();

		void forward_comm(int dummy = 0); // forward comm of atom coords
		void reverse_comm(); // reverse comm of forces
		void exchange(); // move atoms to new procs
		void borders(); // setup list of atoms to comm

		void forward_comm_pair(class Pair *); // forward comm from a Pair
		void reverse_comm_pair(class Pair *); // reverse comm from a Pair
		void forward_comm_fix(class Fix *, int size=0);
		// forward comm from a Fix
		void reverse_comm_fix(class Fix *, int size=0);
		// reverse comm from a Fix
		void reverse_comm_fix_variable(class Fix *);
		// variable size reverse comm from a Fix
		void forward_comm_compute(class Compute *); // forward from a Compute
		void reverse_comm_compute(class Compute *); // reverse from a Compute
		void forward_comm_dump(class Dump *); // forward comm from a Dump
		void reverse_comm_dump(class Dump *); // reverse comm from a Dump

		void forward_comm_array(int, double **); // forward comm of array
		int exchange_variable(int, double , double &); // exchange on neigh stencil

		private:

		};

		}

		#endif

		/* ERROR/WARNING messages:

		*/

src/KOKKOS/neighbor_kokkos.cpp

+10 −6

Original line number	Diff line number	Diff line
		@@ -280,15 +280,19 @@ void NeighborKokkos::choose_build(int index, NeighRequest *rq)
		if (rq->kokkos_host != 0) {
		PairPtrHost pb = NULL;
		if (rq->ghost) {
		if (rq->full) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,1>;
		else if (rq->half) &NeighborKokkos::full_bin_kokkos<LMPHostType,1,1>;
		pair_build_host[index] = pb;
		if (rq->full) {
		if (rq->full_cluster) pb = &NeighborKokkos::full_bin_cluster_kokkos<LMPHostType>;
		else pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,1>;
		}
		else if (rq->half) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,1,1>;
		} else {
		if (rq->full) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,0>;
		if (rq->full) {
		if (rq->full_cluster) pb = &NeighborKokkos::full_bin_cluster_kokkos<LMPHostType>;
		else pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,0>;
		}
		else if (rq->half) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,1,0>;
		pair_build_host[index] = pb;
		}
		return;
		pair_build_host[index] = pb;
		}
		if (rq->kokkos_device != 0) {
		PairPtrDevice pb = NULL;

src/USER-REAXC/pair_reax_c.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -348,7 +348,7 @@ void PairReaxC::init_style( )

		int iqeq;
		for (iqeq = 0; iqeq < modify->nfix; iqeq++)
		if (strcmp(modify->fix[iqeq]->style,"qeq/reax") == 0) break;
		if (strstr(modify->fix[iqeq]->style,"qeq/reax")) break;
		if (iqeq == modify->nfix && qeqflag == 1)
		error->all(FLERR,"Pair reax/c requires use of fix qeq/reax");

src/comm_tiled.cpp

+0 −6

Original line number	Diff line number	Diff line
		@@ -45,9 +45,6 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files

		CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
		{
		if (lmp->kokkos)
		error->all(FLERR,"KOKKOS package does not yet support comm_style tiled");

		style = 1;
		layout = LAYOUT_UNIFORM;
		pbc_flag = NULL;
		@@ -63,9 +60,6 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)

		CommTiled::CommTiled(LAMMPS lmp, Comm oldcomm) : Comm(*oldcomm)
		{
		if (lmp->kokkos)
		error->all(FLERR,"KOKKOS package does not yet support comm_style tiled");

		style = 1;
		layout = oldcomm->layout;
		Comm::copy_arrays(oldcomm);

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