forked from lijiext/lammps
Add Kokkos skip list capability
This commit is contained in:
Stan Moore
parent
1bd9e175e9
commit
45674e6cd3
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@ -151,6 +151,8 @@ action neighbor_kokkos.cpp
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action neighbor_kokkos.h
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action npair_copy_kokkos.cpp
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action npair_copy_kokkos.h
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action npair_skip_kokkos.cpp
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action npair_skip_kokkos.h
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action npair_kokkos.cpp
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action npair_kokkos.h
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action npair_ssa_kokkos.cpp npair_half_bin_newton_ssa.cpp
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@ -0,0 +1,147 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "npair_skip_kokkos.h"
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#include "neighbor.h"
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#include "neigh_list_kokkos.h"
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#include "atom_kokkos.h"
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#include "atom_vec.h"
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#include "molecule.h"
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#include "domain.h"
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#include "my_page.h"
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#include "error.h"
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#include "atom_masks.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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NPairSkipKokkos<DeviceType>::NPairSkipKokkos(LAMMPS *lmp) : NPair(lmp) {
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atomKK = (AtomKokkos *) atom;
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execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
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d_inum = typename AT::t_int_scalar("npair_skip:inum");
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}
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/* ----------------------------------------------------------------------
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build skip list for subset of types from parent list
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works for half and full lists
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works for owned (non-ghost) list, also for ghost list
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iskip and ijskip flag which atom types and type pairs to skip
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if ghost, also store neighbors of ghost atoms & set inum,gnum correctly
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------------------------------------------------------------------------- */
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template<class DeviceType>
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void NPairSkipKokkos<DeviceType>::build(NeighList *list)
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{
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atomKK->sync(execution_space,TYPE_MASK);
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type = atomKK->k_type.view<DeviceType>();
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nlocal = atom->nlocal;
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NeighListKokkos<DeviceType>* k_list_skip = static_cast<NeighListKokkos<DeviceType>*>(list->listskip);
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d_ilist_skip = k_list_skip->d_ilist;
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d_numneigh_skip = k_list_skip->d_numneigh;
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d_neighbors_skip = k_list_skip->d_neighbors;
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int num_skip = list->listskip->inum;
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if (list->ghost) num_skip += list->listskip->gnum;
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NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
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k_list->maxneighs = k_list_skip->maxneighs; // simple, but could be made more memory efficient
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k_list->grow(num_skip);
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d_ilist = k_list->d_ilist;
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d_numneigh = k_list->d_numneigh;
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d_neighbors = k_list->d_neighbors;
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int ntypes = atom->ntypes;
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k_iskip = DAT::tdual_int_1d("npair_skip:iskip",ntypes+1);
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k_ijskip = DAT::tdual_int_2d("npair_skip:ijskip",ntypes+1,ntypes+1);
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d_iskip = k_iskip.view<DeviceType>();
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d_ijskip = k_ijskip.view<DeviceType>();
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for (int itype = 1; itype <= ntypes; itype++) {
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k_iskip.h_view(itype) = list->iskip[itype];
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for (int jtype = 1; jtype <= ntypes; jtype++) {
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k_ijskip.h_view(itype,jtype) = list->ijskip[itype][jtype];
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}
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}
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k_iskip.modify<LMPHostType>();
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k_ijskip.modify<LMPHostType>();
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k_iskip.sync<DeviceType>();
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k_ijskip.sync<DeviceType>();
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Kokkos::deep_copy(d_inum,0);
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// loop over atoms in other list
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// skip I atom entirely if iskip is set for type[I]
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// skip I,J pair if ijskip is set for type[I],type[J]
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Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagNPairSkipCompute>(0,num_skip),*this);
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auto h_inum = Kokkos::create_mirror_view(d_inum);
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Kokkos::deep_copy(h_inum,d_inum);
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const int inum = h_inum();
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list->inum = inum;
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if (list->ghost) {
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int num = 0;
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Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagNPairSkipCountLocal>(0,inum),*this,num);
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list->inum = num;
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list->gnum = inum - num;
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}
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}
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template<class DeviceType>
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KOKKOS_INLINE_FUNCTION
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void NPairSkipKokkos<DeviceType>::operator()(TagNPairSkipCompute, const int &ii) const {
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const int i = d_ilist_skip(ii);
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const int itype = type(i);
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if (d_iskip(itype)) return;
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int n = 0;
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// loop over parent non-skip list
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const int jnum = d_numneigh_skip(i);
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const AtomNeighbors neighbors_i = AtomNeighbors(&d_neighbors(i,0),d_numneigh(i),
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&d_neighbors(i,1)-&d_neighbors(i,0));
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for (int jj = 0; jj < jnum; jj++) {
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const int joriginal = d_neighbors_skip(i,jj);
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int j = joriginal & NEIGHMASK;
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if (d_ijskip(itype,type(j))) continue;
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neighbors_i(n++) = joriginal;
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}
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d_numneigh(i) = n;
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const int inum = Kokkos::atomic_fetch_add(&d_inum(),1);
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d_ilist(inum) = i;
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}
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template<class DeviceType>
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KOKKOS_INLINE_FUNCTION
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void NPairSkipKokkos<DeviceType>::operator()(TagNPairSkipCountLocal, const int &i, int num) const {
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if (d_ilist[i] < nlocal) num++;
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else return;
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}
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namespace LAMMPS_NS {
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template class NPairSkipKokkos<LMPDeviceType>;
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#ifdef KOKKOS_HAVE_CUDA
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template class NPairSkipKokkos<LMPHostType>;
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#endif
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}
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@ -0,0 +1,100 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef NPAIR_CLASS
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typedef NPairSkipKokkos<LMPDeviceType> NPairKokkosSkipDevice;
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NPairStyle(skip/kk/device,
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NPairKokkosSkipDevice,
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NP_SKIP | NP_HALF | NP_FULL |
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NP_NSQ | NP_BIN | NP_MULTI |
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_KOKKOS_DEVICE)
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typedef NPairSkipKokkos<LMPDeviceType> NPairKokkosSkipGhostDevice;
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NPairStyle(skip/ghost/kk/device,
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NPairKokkosSkipGhostDevice,
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NP_SKIP | NP_HALF | NP_FULL |
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NP_NSQ | NP_BIN | NP_MULTI |
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_GHOST | NP_KOKKOS_DEVICE)
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typedef NPairSkipKokkos<LMPHostType> NPairKokkosSkipHost;
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NPairStyle(skip/kk/host,
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NPairKokkosSkipHost,
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NP_SKIP | NP_HALF | NP_FULL |
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NP_NSQ | NP_BIN | NP_MULTI |
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_KOKKOS_HOST)
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typedef NPairSkipKokkos<LMPHostType> NPairKokkosSkipGhostHost;
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NPairStyle(skip/ghost/kk/host,
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NPairKokkosSkipGhostHost,
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NP_SKIP | NP_HALF | NP_FULL |
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NP_NSQ | NP_BIN | NP_MULTI |
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NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_GHOST | NP_KOKKOS_HOST)
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#else
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#ifndef LMP_NPAIR_SKIP_KOKKOS_H
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#define LMP_NPAIR_SKIP_KOKKOS_H
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#include "npair.h"
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#include "kokkos_type.h"
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namespace LAMMPS_NS {
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struct TagNPairSkipCompute{};
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struct TagNPairSkipCountLocal{};
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template<class DeviceType>
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class NPairSkipKokkos : public NPair {
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public:
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typedef DeviceType device_type;
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typedef int value_type;
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typedef ArrayTypes<DeviceType> AT;
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NPairSkipKokkos(class LAMMPS *);
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~NPairSkipKokkos() {}
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void build(class NeighList *);
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KOKKOS_INLINE_FUNCTION
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void operator()(TagNPairSkipCompute, const int&) const;
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KOKKOS_INLINE_FUNCTION
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void operator()(TagNPairSkipCountLocal, const int&, int) const;
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private:
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int nlocal;
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typename AT::t_int_1d_randomread type;
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typename AT::t_int_scalar d_inum;
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typename AT::t_neighbors_2d d_neighbors,d_neighbors_skip;
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typename AT::t_int_1d d_ilist,d_ilist_skip;
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typename AT::t_int_1d d_numneigh,d_numneigh_skip;
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DAT::tdual_int_1d k_iskip;
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DAT::tdual_int_2d k_ijskip;
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typename AT::t_int_1d d_iskip;
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typename AT::t_int_2d d_ijskip;
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ExecutionSpace execution_space;
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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*/
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