Fixing Kokkos bug and adding host version of CommTiled

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15676 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/KOKKOS/comm_tiled_kokkos.cpp

@@ -0,0 +1,266 @@
+/* ----------------------------------------------------------------------
+   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);
+}

src/KOKKOS/comm_tiled_kokkos.h

@@ -0,0 +1,59 @@
+/* -*- 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

@@ -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

@@ -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

@@ -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);

src/comm_tiled.h

@@ -26,26 +26,26 @@ class CommTiled : public Comm {
 
   void init();
   void setup();                        // setup comm pattern
-  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
+  virtual void forward_comm(int dummy = 0);    // forward comm of atom coords
+  virtual void reverse_comm();                 // reverse comm of forces
+  virtual void exchange();                     // move atoms to new procs
+  virtual 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
+  virtual void forward_comm_pair(class Pair *);    // forward comm from a Pair
+  virtual void reverse_comm_pair(class Pair *);    // reverse comm from a Pair
   virtual void forward_comm_fix(class Fix *, int size=0);
                                                    // forward comm from a Fix
   virtual void reverse_comm_fix(class Fix *, int size=0);
                                                    // reverse comm from a Fix
   virtual 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
+  virtual void forward_comm_compute(class Compute *);  // forward from a Compute
+  virtual void reverse_comm_compute(class Compute *);  // reverse from a Compute
+  virtual void forward_comm_dump(class Dump *);    // forward comm from a Dump
+  virtual 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
+  virtual void forward_comm_array(int, double **);          // forward comm of array
+  virtual int exchange_variable(int, double *, double *&);  // exchange on neigh stencil
 
   void coord2proc_setup();
   int coord2proc(double *, int &, int &, int &);