More changes for Kokkos neighbor

src/KOKKOS/Install.sh

@@ -109,6 +109,8 @@ action neigh_list_kokkos.cpp
 action neigh_list_kokkos.h
 action neighbor_kokkos.cpp
 action neighbor_kokkos.h
+action npair_copy_kokkos.cpp
+action npair_copy_kokkos.h
 action npair_kokkos.cpp
 action npair_kokkos.h
 action nbin_kokkos.cpp

src/KOKKOS/nbin_kokkos.cpp

@@ -116,6 +116,7 @@ void NBinKokkos<DeviceType>::bin_atoms()
       k_bins = DAT::tdual_int_2d("bins", mbins, atoms_per_bin);
       bins = k_bins.view<DeviceType>();
       c_bins = bins;
+      last_bin_memory = update->ntimestep;
     }
   }
 }

src/KOKKOS/npair_copy_kokkos.cpp

@@ -0,0 +1,62 @@
+/* ----------------------------------------------------------------------
+   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 "npair_copy_kokkos.h"
+#include "neighbor.h"
+#include "neigh_list_kokkos.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "molecule.h"
+#include "domain.h"
+#include "my_page.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+NPairCopyKokkos<DeviceType>::NPairCopyKokkos(LAMMPS *lmp) : NPair(lmp) {}
+
+/* ----------------------------------------------------------------------
+   create list which is simply a copy of parent list
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void NPairCopyKokkos<DeviceType>::build(NeighList *list)
+{
+  NeighList *listcopy = list->listcopy;
+
+  list->inum = listcopy->inum;
+  list->gnum = listcopy->gnum;
+  list->ilist = listcopy->ilist;
+  list->numneigh = listcopy->numneigh;
+  list->firstneigh = listcopy->firstneigh;
+  list->firstdouble = listcopy->firstdouble;
+  list->ipage = listcopy->ipage;
+  list->dpage = listcopy->dpage;
+
+  NeighListKokkos<DeviceType>* list_kk = (NeighListKokkos<DeviceType>*) list;
+  NeighListKokkos<DeviceType>* listcopy_kk = (NeighListKokkos<DeviceType>*) list->listcopy;
+
+  list_kk->d_ilist = listcopy_kk->d_ilist;
+  list_kk->d_numneigh = listcopy_kk->d_numneigh;
+  list_kk->d_neighbors = listcopy_kk->d_neighbors;
+}
+
+namespace LAMMPS_NS {
+template class NPairCopyKokkos<LMPDeviceType>;
+#ifdef KOKKOS_HAVE_CUDA
+template class NPairCopyKokkos<LMPHostType>;
+#endif
+}

src/KOKKOS/npair_copy_kokkos.h

@@ -0,0 +1,48 @@
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#ifdef NPAIR_CLASS
+
+NPairStyle(copy/kk/device,
+           NPairCopyKokkos<LMPDeviceType>,
+           NP_COPY | NP_KOKKOS_DEVICE)
+
+NPairStyle(copy/kk/host,
+           NPairCopyKokkos<LMPHostType>,
+           NP_COPY | NP_KOKKOS_HOST)
+
+#else
+
+#ifndef LMP_NPAIR_COPY_KOKKOS_H
+#define LMP_NPAIR_COPY_KOKKOS_H
+
+#include "npair.h"
+
+namespace LAMMPS_NS {
+
+template<class DeviceType>
+class NPairCopyKokkos : public NPair {
+ public:
+  NPairCopyKokkos(class LAMMPS *);
+  ~NPairCopyKokkos() {}
+  void build(class NeighList *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/

src/KOKKOS/npair_kokkos.cpp

@@ -51,9 +51,9 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST>::copy_neighbor_info()
   k_ex2_type = neighborKK->k_ex2_type;
   k_ex_type = neighborKK->k_ex_type;
   k_ex1_group = neighborKK->k_ex1_group;
-  k_ex2_group = neighborKK->k_ex1_group;
+  k_ex2_group = neighborKK->k_ex2_group;
-  k_ex1_bit = neighborKK->k_ex1_group;
+  k_ex1_bit = neighborKK->k_ex1_bit;
-  k_ex2_bit = neighborKK->k_ex1_group;
+  k_ex2_bit = neighborKK->k_ex2_bit;
   k_ex_mol_group = neighborKK->k_ex_mol_group;
   k_ex_mol_bit = neighborKK->k_ex_mol_bit;
 }
@@ -135,16 +135,16 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST>::build(NeighList *list_)
          atomKK->molecular,
          nbinx,nbiny,nbinz,mbinx,mbiny,mbinz,mbinxlo,mbinylo,mbinzlo,
          bininvx,bininvy,bininvz,
-         exclude, nex_type,maxex_type,
+         exclude, nex_type,
          k_ex1_type.view<DeviceType>(),
          k_ex2_type.view<DeviceType>(),
          k_ex_type.view<DeviceType>(),
-         nex_group,maxex_group,
+         nex_group,
          k_ex1_group.view<DeviceType>(),
          k_ex2_group.view<DeviceType>(),
          k_ex1_bit.view<DeviceType>(),
          k_ex2_bit.view<DeviceType>(),
-         nex_mol, maxex_mol,
+         nex_mol,
          k_ex_mol_group.view<DeviceType>(),
          k_ex_mol_bit.view<DeviceType>(),
          bboxhi,bboxlo,
@@ -161,6 +161,8 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST>::build(NeighList *list_)
   k_ex2_bit.sync<DeviceType>();
   k_ex_mol_group.sync<DeviceType>();
   k_ex_mol_bit.sync<DeviceType>();
+  k_bincount.sync<DeviceType>(),
+  k_bins.sync<DeviceType>(),
   atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK);
 
   data.special_flag[0] = special_flag[0];
@@ -415,6 +417,7 @@ void NeighborKokkosExecute<DeviceType>::
 
     if(n >= new_maxneighs()) new_maxneighs() = n;
   }
+
   neigh_list.d_ilist(i) = i;
 }
 

src/KOKKOS/npair_kokkos.h

@@ -75,14 +75,6 @@ class NPairKokkos : public NPair {
 
  private:
   int newton_pair;
-  int nex_type;
-  int maxex_type;
-
-  int nex_group;
-  int maxex_group;
-
-  int nex_mol;
-  int maxex_mol;
 
   // data from Neighbor class
 
@@ -127,17 +119,14 @@ class NeighborKokkosExecute
   const int exclude;
 
   const int nex_type;
-  const int maxex_type;
   const typename AT::t_int_1d_const ex1_type,ex2_type;
   const typename AT::t_int_2d_const ex_type;
 
   const int nex_group;
-  const int maxex_group;
   const typename AT::t_int_1d_const ex1_group,ex2_group;
   const typename AT::t_int_1d_const ex1_bit,ex2_bit;
 
   const int nex_mol;
-  const int maxex_mol;
   const typename AT::t_int_1d_const ex_mol_group;
   const typename AT::t_int_1d_const ex_mol_bit;
 
@@ -204,16 +193,16 @@ class NeighborKokkosExecute
                         const int & _mbinx,const int & _mbiny,const int & _mbinz,
                         const int & _mbinxlo,const int & _mbinylo,const int & _mbinzlo,
                         const X_FLOAT &_bininvx,const X_FLOAT &_bininvy,const X_FLOAT &_bininvz,
-                        const int & _exclude,const int & _nex_type,const int & _maxex_type,
+                        const int & _exclude,const int & _nex_type,
                         const typename AT::t_int_1d_const & _ex1_type,
                         const typename AT::t_int_1d_const & _ex2_type,
                         const typename AT::t_int_2d_const & _ex_type,
-                        const int & _nex_group,const int & _maxex_group,
+                        const int & _nex_group,
                         const typename AT::t_int_1d_const & _ex1_group,
                         const typename AT::t_int_1d_const & _ex2_group,
                         const typename AT::t_int_1d_const & _ex1_bit,
                         const typename AT::t_int_1d_const & _ex2_bit,
-                        const int & _nex_mol,const int & _maxex_mol,
+                        const int & _nex_mol,
                         const typename AT::t_int_1d_const & _ex_mol_group,
                         const typename AT::t_int_1d_const & _ex_mol_bit,
                         const X_FLOAT *_bboxhi, const X_FLOAT* _bboxlo,
@@ -229,11 +218,11 @@ class NeighborKokkosExecute
     mbinx(_mbinx),mbiny(_mbiny),mbinz(_mbinz),
     mbinxlo(_mbinxlo),mbinylo(_mbinylo),mbinzlo(_mbinzlo),
     bininvx(_bininvx),bininvy(_bininvy),bininvz(_bininvz),
-    exclude(_exclude),nex_type(_nex_type),maxex_type(_maxex_type),
+    exclude(_exclude),nex_type(_nex_type),
     ex1_type(_ex1_type),ex2_type(_ex2_type),ex_type(_ex_type),
-    nex_group(_nex_group),maxex_group(_maxex_group),
+    nex_group(_nex_group),
     ex1_group(_ex1_group),ex2_group(_ex2_group),
-    ex1_bit(_ex1_bit),ex2_bit(_ex2_bit),nex_mol(_nex_mol),maxex_mol(_maxex_mol),
+    ex1_bit(_ex1_bit),ex2_bit(_ex2_bit),nex_mol(_nex_mol),
     ex_mol_group(_ex_mol_group),ex_mol_bit(_ex_mol_bit),
     xperiodic(_xperiodic),yperiodic(_yperiodic),zperiodic(_zperiodic),
     xprd_half(_xprd_half),yprd_half(_yprd_half),zprd_half(_zprd_half) {

src/neighbor.cpp

@@ -660,10 +660,8 @@ void Neighbor::init_pair()
   // processes copy,skip,half_from_full,granhistory,respaouter lists
   // error checks and resets internal ptrs to other lists that now exist
 
-  for (i = 0; i < nrequest; i++) {
+  for (i = 0; i < nrequest; i++)
-    if (!lists[i]) continue;
     lists[i]->post_constructor(requests[i]);
-  }
   
   // (B) rule:
   // if request = pair, half, newton != 2
@@ -680,6 +678,10 @@ void Neighbor::init_pair()
   for (i = 0; i < nrequest; i++) {
     if (requests[i]->pair && requests[i]->half && requests[i]->newton != 2) {
       for (j = 0; j < nrequest; j++) {
+        // Kokkos doesn't yet support half from full
+        if (requests[i]->kokkos_device || requests[j]->kokkos_device) continue;
+        if (requests[i]->kokkos_host || requests[j]->kokkos_host) continue;
+
         if (requests[j]->full && requests[j]->occasional == 0 &&
             !requests[j]->skip && !requests[j]->copy) break;
       }
@@ -706,6 +708,10 @@ void Neighbor::init_pair()
   for (i = 0; i < nrequest; i++) {
     if (!requests[i]->fix && !requests[i]->compute) continue;
     for (j = 0; j < nrequest; j++) {
+      // Kokkos flags must match
+      if (requests[i]->kokkos_device != requests[j]->kokkos_device) continue;
+      if (requests[i]->kokkos_host != requests[j]->kokkos_host) continue;
+
       if (requests[i]->half && requests[j]->pair && 
           !requests[j]->skip && requests[j]->half && !requests[j]->copy)
         break;
@@ -727,6 +733,10 @@ void Neighbor::init_pair()
       continue;
     }
     for (j = 0; j < nrequest; j++) {
+      // Kokkos doesn't yet support half from full
+      if (requests[i]->kokkos_device || requests[j]->kokkos_device) continue;
+      if (requests[i]->kokkos_host || requests[j]->kokkos_host) continue;
+
       if (requests[i]->half && requests[j]->pair &&
           !requests[j]->skip && requests[j]->full && !requests[j]->copy)
         break;
@@ -1434,7 +1444,11 @@ int Neighbor::choose_pair(NeighRequest *rq)
   for (int i = 0; i < npclass; i++) {
     mask = pairmasks[i];
 
-    if (copyflag && (mask & NP_COPY)) return i+1;
+    if (copyflag && (mask & NP_COPY)) {
+      if (kokkos_device_flag != (mask & NP_KOKKOS_DEVICE)) continue;
+      if (kokkos_host_flag != (mask & NP_KOKKOS_HOST)) continue;
+      return i+1;
+    }
     if (skipflag != (mask & NP_SKIP)) continue;
 
     if (halfflag) {