diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..606e334
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,81 @@
+cmake_minimum_required(VERSION 3.12)
+project(minimd)
+
+add_executable(minimd)
+    # Require C++14
+if (CMAKE_CXX_COMPILER MATCHES ".*nvcc_wrapper" )
+    message("nvcc wrapper requires that CXX standard by set in kokkos build")
+else()
+   target_compile_features(minimd PUBLIC cxx_std_14)
+endif()
+
+# Options
+option(MINIMD_SINGLE_PRECISION, "Use single precision" OFF)
+if (MINIMD_SINGLE_PRECISION)
+  target_compile_definitions(minimd PRIVATE PRECISION=1)
+else()
+  target_compile_definitions(minimd PRIVATE PRECISION=2)
+endif()
+
+option(MINIMD_AUTOMATIC_CHECKPOINT "Use resilience automatic checkpointing" OFF)
+option(MINIMD_MANUAL_CHECKPOINT "Use resilience manual checkpointing" OFF)
+
+target_compile_definitions(minimd PRIVATE PREC_TIMER)
+
+# Dependencies
+if (MINIMD_USE_MPISTUB)
+   find_library( mpi_stub_ NAMES libmpi_stubs.a libmpi_stubs mpi_stubs HINTS ${PROJECT_SOURCE_DIR}/kokkos/MPI-Stubs ) 
+   #add_library(mpi_stubs)
+   #target_link_libraries(minimd PRIVATE mpi_stubs)
+   target_link_libraries(minimd PRIVATE ${mpi_stub_})
+   target_include_directories(minimd PUBLIC
+                           ${PROJECT_SOURCE_DIR}/kokkos/MPI-Stubs
+                           )
+else()
+   find_package(MPI REQUIRED)
+   target_link_libraries(minimd PRIVATE MPI::MPI_CXX)
+endif()
+
+find_package(Kokkos REQUIRED NO_CMAKE_PACKAGE_REGISTRY)
+
+# Optional resilience
+if(MINIMD_AUTOMATIC_CHECKPOINT OR MINIMD_MANUAL_CHECKPOINT OR MINIMD_RESILIENT_EXECUTION)
+  find_package(resilience REQUIRED)
+  target_link_libraries(minimd PRIVATE Kokkos::resilience)
+  target_compile_definitions(minimd PRIVATE MINIMD_RESILIENCE)
+  if(MINIMD_AUTOMATIC_CHECKPOINT)
+     target_compile_definitions(minimd PRIVATE KOKKOS_ENABLE_AUTOMATIC_CHECKPOINT)
+  endif()
+  if(MINIMD_MANUAL_CHECKPOINT)
+     target_compile_definitions(minimd PRIVATE KOKKOS_ENABLE_MANUAL_CHECKPOINT)
+  endif()
+  if(MINIMD_RESILIENT_EXECUTION)
+     target_compile_definitions(minimd PRIVATE KOKKOS_ENABLE_RESILIENT_EXECUTION)
+  endif()
+endif()
+
+TARGET_LINK_KOKKOS(minimd PRIVATE)
+
+target_link_libraries(minimd PRIVATE "-L${resilience_LINK_DIRECTORIES}")
+
+# VeloC config
+add_custom_command(TARGET minimd PRE_BUILD
+                   COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/minimd.cfg ${CMAKE_CURRENT_BINARY_DIR}/minimd.cfg)
+
+# Other inputs
+
+add_custom_command(TARGET minimd PRE_BUILD
+                   COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/kokkos/in.lj.miniMD ${CMAKE_CURRENT_BINARY_DIR}/in.lj.miniMD)
+
+add_custom_command(TARGET minimd PRE_BUILD
+                   COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/kokkos/Cu_u6.eam ${CMAKE_CURRENT_BINARY_DIR}/Cu_u6.eam)
+
+add_subdirectory(kokkos)
+
+
+##get_cmake_property(_variableNames VARIABLES)
+##list (SORT _variableNames)
+##foreach (_variableName ${_variableNames})
+##    message(STATUS "${_variableName}=${${_variableName}}")
+##endforeach()
+
diff --git a/kokkos/CMakeLists.txt b/kokkos/CMakeLists.txt
new file mode 100644
index 0000000..8a753d5
--- /dev/null
+++ b/kokkos/CMakeLists.txt
@@ -0,0 +1,14 @@
+target_sources(minimd PRIVATE
+               ${PROJECT_SOURCE_DIR}/kokkos/atom.cpp
+               ${PROJECT_SOURCE_DIR}/kokkos/comm.cpp
+               ${PROJECT_SOURCE_DIR}/kokkos/force_eam.cpp
+               ${PROJECT_SOURCE_DIR}/kokkos/force_lj.cpp
+               ${PROJECT_SOURCE_DIR}/kokkos/input.cpp
+               ${PROJECT_SOURCE_DIR}/kokkos/integrate.cpp
+               ${PROJECT_SOURCE_DIR}/kokkos/ljs.cpp
+               ${PROJECT_SOURCE_DIR}/kokkos/neighbor.cpp
+               ${PROJECT_SOURCE_DIR}/kokkos/output.cpp
+               ${PROJECT_SOURCE_DIR}/kokkos/setup.cpp
+               ${PROJECT_SOURCE_DIR}/kokkos/thermo.cpp
+               ${PROJECT_SOURCE_DIR}/kokkos/timer.cpp
+               )
diff --git a/kokkos/Makefile b/kokkos/Makefile
index bfa8684..8e57fa9 100644
--- a/kokkos/Makefile
+++ b/kokkos/Makefile
@@ -4,20 +4,36 @@ MPI_PATH =
 HAVE_MPI = yes
 
 #Set the path to Kokkos
-KOKKOS_PATH = /home/crtrott/kokkos
+#KOKKOS_PATH = /home/crtrott/kokkos
 #Set the Devices to compile for
 KOKKOS_DEVICES=OpenMP
 #Set the Architecture to compiler for
-KOKKOS_ARCH=SNB
+KOKKOS_ARCH=
 #Set third party library usage
 KOKKOS_USE_TPL=
+KOKKOS_OPTIONS=enable_hdf5_parallel
 
-CXXFLAGS = -O3 -g 
-LINKFLAGS = 
+CXXFLAGS = -O3 -g
+##LINKFLAGS = -lm -L./ --std=c++11
+LINKFLAGS = -L./ --std=c++11
 LIB =
 
+FILE_EXTENSION=base
+
+ifeq ($(KOKKOS_OPTIONS), enable_stdfile)
+   FILE_EXTENSION=stdfile
+endif
+ifeq ($(KOKKOS_OPTIONS), enable_hdf5)
+   FILE_EXTENSION=hdf5ser
+endif
+ifeq ($(KOKKOS_OPTIONS), enable_hdf5_parallel)
+   FILE_EXTENSION=hdf5par
+endif
+
 ifeq ($(HAVE_MPI), yes)
+##CXX = $(KOKKOS_PATH)/bin/nvcc_wrapper
 CXX = mpicxx
+LIB += -lmpi
 else
 CXX = g++
 override CXXFLAGS += -I./MPI-Stubs
@@ -25,7 +41,7 @@ LIB += MPI-Stubs/libmpi_stubs.a
 endif
 
 LINK = ${CXX}
-EXE = miniMD
+EXE = miniMD.${FILE_EXTENSION}
 
 #CXXFLAGS += -DTEST_LAMBDA_BYCOPY
 #CXXFLAGS += -DTEST_LAMBDA_BYPTR
@@ -75,6 +91,7 @@ default: all
 
 MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
 include $(KOKKOS_PATH)/Makefile.kokkos
+include $(KOKKOS_RESILIENCE_PATH)/Makefile.resilience
 
 SRC = $(wildcard $(MAKEFILE_PATH)*.cpp)
 HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp)
diff --git a/kokkos/atom.cpp b/kokkos/atom.cpp
index f5da0c0..d3181a6 100644
--- a/kokkos/atom.cpp
+++ b/kokkos/atom.cpp
@@ -36,9 +36,14 @@
 #include "atom.h"
 #include "neighbor.h"
 
-#define DELTA 20000
+int Atom::atom_block = 10000;
 
-Atom::Atom(int ntypes_)
+void Atom::set_atom_block_size(int size_)
+{
+   atom_block = size_;
+}
+
+Atom::Atom(int ntypes_) : x("atom",0), v("velocity",0), f("force",0) 
 {
   natoms = 0;
   nlocal = 0;
@@ -61,7 +66,9 @@ Atom::~Atom()
 
 void Atom::growarray()
 {
-  nmax += DELTA;
+//  printf("grow array: %ld\n", nmax);
+//  fflush(stdout);
+  nmax += atom_block;
   Kokkos::resize(x,nmax);
   Kokkos::resize(v,nmax);
   Kokkos::resize(f,nmax);
diff --git a/kokkos/atom.h b/kokkos/atom.h
index ce2d370..b874dda 100644
--- a/kokkos/atom.h
+++ b/kokkos/atom.h
@@ -57,6 +57,9 @@ class Atom
     struct TagAtomUnpackReverse {};
     struct TagAtomSort {};
 
+    static int atom_block;
+    static void set_atom_block_size(int size_);
+
     typedef int value_type;
     int natoms;
     int nlocal, nghost;
@@ -82,7 +85,7 @@ class Atom
 
     Box box;
 
-    Atom() {};
+    Atom() : x("atom",0), v("velocity",0), f("force",0)  {};
     Atom(int ntypes_);
     ~Atom();
 
diff --git a/kokkos/data/hdf5_config.json b/kokkos/data/hdf5_config.json
new file mode 100644
index 0000000..b33bd49
--- /dev/null
+++ b/kokkos/data/hdf5_config.json
@@ -0,0 +1,59 @@
+[
+   {
+      "name":"atom",
+      "Layout_Config":{
+         "data_set":"atom_dataset",
+         "rank":2,
+         "layout":"REGULAR",
+         "data_extents":["{DATA_SIZE}","{MPI_SIZE}"],
+         "local_extents":["{DATA_SIZE}","1"],
+         "offset":["0","{MPI_RANK}"],
+         "stride":["1","{MPI_SIZE}"],
+         "count":["1","1","1","1"],
+         "block":["{DATA_SIZE}","1"],
+         "local_offset":["0","0","0","0"],
+         "local_stride":["1","1","1","1"],
+         "local_count":["1","1","1","1"],
+         "local_block":["{DATA_SIZE}","1","1","1"],
+         "view_offset":["0","0"]
+      }
+   },
+   {
+      "name":"velocity",
+      "Layout_Config":{
+         "data_set":"velocity_dataset",
+         "rank":2,
+         "layout":"REGULAR",
+         "data_extents":["{DATA_SIZE}","{MPI_SIZE}"],
+         "local_extents":["{DATA_SIZE}","1"],
+         "offset":["0","{MPI_RANK}"],
+         "stride":["1","{MPI_SIZE}"],
+         "count":["1","1","1","1"],
+         "block":["{DATA_SIZE}","1"],
+         "local_offset":["0","0","0","0"],
+         "local_stride":["1","1","1","1"],
+         "local_count":["1","1","1","1"],
+         "local_block":["{DATA_SIZE}","1","1","1"],
+         "view_offset":["0","0"]
+      }
+   },
+   {
+      "name":"force",
+      "Layout_Config":{
+         "data_set":"force_dataset",
+         "rank":2,
+         "layout":"REGULAR",
+         "data_extents":["{DATA_SIZE}","{MPI_SIZE}"],
+         "local_extents":["{DATA_SIZE}","1"],
+         "offset":["0","{MPI_RANK}"],
+         "stride":["1","{MPI_SIZE}"],
+         "count":["1","1","1","1"],
+         "block":["{DATA_SIZE}","1"],
+         "local_offset":["0","0","0","0"],
+         "local_stride":["1","1","1","1"],
+         "local_count":["1","1","1","1"],
+         "local_block":["{DATA_SIZE}","1","1","1"],
+         "view_offset":["0","0"]
+      }
+   }
+]
diff --git a/kokkos/integrate.cpp b/kokkos/integrate.cpp
index 8a3aea8..76d48f5 100644
--- a/kokkos/integrate.cpp
+++ b/kokkos/integrate.cpp
@@ -33,6 +33,27 @@
 #include "stdio.h"
 #include "integrate.h"
 #include "math.h"
+#include <cstdlib>
+
+#ifdef KOKKOS_ENABLE_HDF5
+   #define CHECKPOINT_FILESPACE Kokkos::Experimental::HDF5Space
+#else
+   #define CHECKPOINT_FILESPACE Kokkos::Experimental::StdFileSpace
+#endif
+
+#ifdef MINIMD_RESILIENCE
+   #include <Kokkos_Resilience.hpp>
+#endif
+
+#ifdef KOKKOS_ENABLE_RESILIENT_EXECUTION
+   #define DEVICE_EXECUTION_SPACE Kokkos::ResCuda
+#else
+   #ifdef KOKKOS_ENABLE_CUDA
+      #define DEVICE_EXECUTION_SPACE Kokkos::Cuda
+   #else
+      #define DEVICE_EXECUTION_SPACE Kokkos::OpenMP
+   #endif
+#endif
 
 Integrate::Integrate() {sort_every=20;}
 Integrate::~Integrate() {}
@@ -44,7 +65,7 @@ void Integrate::setup()
 
 void Integrate::initialIntegrate()
 {
-  Kokkos::parallel_for(Kokkos::RangePolicy<TagInitialIntegrate>(0,nlocal), *this);
+  Kokkos::parallel_for(Kokkos::RangePolicy<DEVICE_EXECUTION_SPACE, TagInitialIntegrate>(0,nlocal), *this);
 }
 
 KOKKOS_INLINE_FUNCTION
@@ -59,7 +80,7 @@ void Integrate::operator() (TagInitialIntegrate, const int& i) const {
 
 void Integrate::finalIntegrate()
 {
-  Kokkos::parallel_for(Kokkos::RangePolicy<TagFinalIntegrate>(0,nlocal), *this);
+  Kokkos::parallel_for(Kokkos::RangePolicy<DEVICE_EXECUTION_SPACE, TagFinalIntegrate>(0,nlocal), *this);
 }
 
 KOKKOS_INLINE_FUNCTION
@@ -70,7 +91,7 @@ void Integrate::operator() (TagFinalIntegrate, const int& i) const {
 }
 
 void Integrate::run(Atom &atom, Force* force, Neighbor &neighbor,
-                    Comm &comm, Thermo &thermo, Timer &timer)
+                    Comm &comm, Thermo &thermo, Timer &timer, const int restart_)
 {
   int i, n;
 
@@ -83,8 +104,32 @@ void Integrate::run(Atom &atom, Force* force, Neighbor &neighbor,
   dtforce = dtforce / mass;
 
     int next_sort = sort_every>0?sort_every:ntimes+1;
+    int nStart = 0;
+
+#ifdef KOKKOS_ENABLE_MANUAL_CHECKPOINT
+    Kokkos::Experimental::StdFileSpace sfs;
+    auto x_cp = Kokkos::create_chkpt_mirror( sfs, atom.x );
+    auto v_cp = Kokkos::create_chkpt_mirror( sfs, atom.v );
+    auto f_cp = Kokkos::create_chkpt_mirror( sfs, atom.f );
+    nStart = restart_;
+
+// Load from restart ...
+    if (nStart > 0) {
+         if (comm.nprocs > 1)
+            Kokkos::Experimental::DirectoryManager<CHECKPOINT_FILESPACE>::set_checkpoint_directory(comm.me == 0 ? true : false, "./data", (int)((nStart / 10) * 10));
+         else
+            Kokkos::Experimental::DirectoryManager<CHECKPOINT_FILESPACE>::set_checkpoint_directory(comm.me == 0 ? true : false, "./data", (int)((nStart / 10) * 10), comm.me);
+         // need to resize the views to match the checkpoint files ... 
+         Kokkos::Experimental::StdFileSpace::restore_all_views();
+    }
+#endif
 
-    for(n = 0; n < ntimes; n++) {
+    for(n = nStart; n < ntimes; n++) {
+#ifdef KOKKOS_ENABLE_AUTOMATIC_CHECKPOINT
+    #ifdef KR_ENABLE_TRACING
+      auto iter_time = KokkosResilience::Util::begin_trace< KokkosResilience::Util::IterTimingTrace< std::string > >( *resilience_context, "step", n );
+    #endif
+#endif
 
       Kokkos::fence();
 
@@ -94,7 +139,13 @@ void Integrate::run(Atom &atom, Force* force, Neighbor &neighbor,
       xold = atom.xold;
       nlocal = atom.nlocal;
 
+#ifdef KOKKOS_ENABLE_AUTOMATIC_CHECKPOINT
+      KokkosResilience::checkpoint( *resilience_context, "initial", n, [self = *this]() mutable {
+        self.initialIntegrate();
+      }, KokkosResilience::filter::nth_iteration_filter< 10 >{} );
+#else
       initialIntegrate();
+#endif
 
       timer.stamp();
 
@@ -179,8 +230,24 @@ void Integrate::run(Atom &atom, Force* force, Neighbor &neighbor,
 
       Kokkos::fence();
 
+#ifdef KOKKOS_ENABLE_AUTOMATIC_CHECKPOINT
+      KokkosResilience::checkpoint( *resilience_context, "final", n, [self = *this]() mutable {
+        self.finalIntegrate();
+      }, KokkosResilience::filter::nth_iteration_filter< 10 >{} );
+#else
       finalIntegrate();
+#endif
 
       if(thermo.nstat) thermo.compute(n + 1, atom, neighbor, force, timer, comm);
+#ifdef KOKKOS_ENABLE_MANUAL_CHECKPOINT
+      if ( n % 10 == 0 ) {
+         Kokkos::fence();
+         if (comm.nprocs > 1) 
+            Kokkos::Experimental::DirectoryManager<CHECKPOINT_FILESPACE>::set_checkpoint_directory(comm.me == 0 ? true : false, "./data", n);
+         else
+            Kokkos::Experimental::DirectoryManager<CHECKPOINT_FILESPACE>::set_checkpoint_directory(comm.me == 0 ? true : false, "./data", n, comm.me);
+         CHECKPOINT_FILESPACE::checkpoint_views();
+      }
+#endif
     }
 }
diff --git a/kokkos/integrate.h b/kokkos/integrate.h
index 934a5f3..751f063 100644
--- a/kokkos/integrate.h
+++ b/kokkos/integrate.h
@@ -61,5 +61,5 @@ class Integrate
     void finalIntegrate();
     KOKKOS_INLINE_FUNCTION
     void operator() (TagFinalIntegrate, const int& i) const;
-    void run(Atom &, Force*, Neighbor &, Comm &, Thermo &, Timer &);
+    void run(Atom &, Force*, Neighbor &, Comm &, Thermo &, Timer &, const int);
 };
diff --git a/kokkos/ljs.cpp b/kokkos/ljs.cpp
index 3870ae3..b395a83 100644
--- a/kokkos/ljs.cpp
+++ b/kokkos/ljs.cpp
@@ -56,6 +56,14 @@ void output(In &, Atom &, Force*, Neighbor &, Comm &,
             Thermo &, Integrate &, Timer &, int);
 int read_lammps_data(Atom &atom, Comm &comm, Neighbor &neighbor, Integrate &integrate, Thermo &thermo, char* file, int units);
 
+#ifdef KOKKOS_ENABLE_AUTOMATIC_CHECKPOINT
+   #ifdef KOKKOS_ENABLE_VELOC
+      std::unique_ptr< KokkosResilience::Context< KokkosResilience::VeloCCheckpointBackend > > resilience_context;
+   #else
+      std::unique_ptr< KokkosResilience::Context< > > resilience_context;
+   #endif
+#endif
+
 int main(int argc, char** argv)
 {
   In in;
@@ -84,6 +92,7 @@ int main(int argc, char** argv)
   int sort = -1;
   int ntypes = 8;
   int team_neigh = 0;
+  int restart = 0;
 
   for(int i = 0; i < argc; i++) {
     if((strcmp(argv[i], "-i") == 0) || (strcmp(argv[i], "--input_file") == 0)) {
@@ -95,7 +104,15 @@ int main(int argc, char** argv)
   MPI_Init(&argc, &argv);
   MPI_Comm_rank(MPI_COMM_WORLD, &me);
   MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
-
+  
+#ifdef KOKKOS_ENABLE_AUTOMATIC_CHECKPOINT
+   #ifdef KOKKOS_ENABLE_VELOC
+      resilience_context = std::make_unique< KokkosResilience::Context< KokkosResilience::VeloCCheckpointBackend > >(MPI_COMM_WORLD, "minimd.cfg");
+   #else
+      resilience_context = std::make_unique< KokkosResilience::Context< > >();
+   #endif
+#endif
+  
   int error = 0;
 
   if(input_file == NULL)
@@ -136,6 +153,11 @@ int main(int argc, char** argv)
       continue;
     }
 
+    if((strcmp(argv[i], "-r") == 0)) {
+      restart = atoi(argv[++i]);
+      continue;
+    }
+
     if((strcmp(argv[i], "-dm") == 0) || (strcmp(argv[i], "--device_map") == 0)) {
       char* str;
       int local_rank;
@@ -314,6 +336,18 @@ int main(int argc, char** argv)
   // Scope Guard
   {
 
+  if (system_size < 20) {
+     Atom::set_atom_block_size(10000);
+  } else if (system_size < 41) {
+     Atom::set_atom_block_size(100000);
+  } else if (system_size < 61) {
+     Atom::set_atom_block_size(200000);
+  } else if (system_size < 81) {
+     Atom::set_atom_block_size(500000);
+  } else {
+     Atom::set_atom_block_size(1000000);
+  }
+
   Atom atom(ntypes);
   Neighbor neighbor(ntypes);
   Integrate integrate;
@@ -454,21 +488,30 @@ int main(int argc, char** argv)
 
     if(in.forcetype == FORCEEAM) atom.mass = force->mass;
   } else {
+    //printf("creating box\n");
     create_box(atom, in.nx, in.ny, in.nz, in.rho);
 
+    //printf("comm setup\n");
     comm.setup(neighbor.cutneigh, atom);
 
+   // printf("neighbor setup\n");
     neighbor.setup(atom);
 
+   // printf("integration setup\n");
     integrate.setup();
 
+   // printf("force setup\n");
     force->setup();
 
     if(in.forcetype == FORCEEAM) atom.mass = force->mass;
 
+   // printf("atom setup\n");
     create_atoms(atom, in.nx, in.ny, in.nz, in.rho);
+
+   // printf("thermo setup\n");
     thermo.setup(in.rho, integrate, atom, in.units);
 
+   // printf("velocity setup\n");
     create_velocity(in.t_request, atom, thermo);
 
   }
@@ -505,6 +548,7 @@ int main(int argc, char** argv)
     fprintf(stdout, "\t# Use intrinsics: %i\n", force->use_sse);
     fprintf(stdout, "\t# Do safe exchange: %i\n", comm.do_safeexchange);
     fprintf(stdout, "\t# Size of float: %i\n\n", (int) sizeof(MMD_float));
+    fprintf(stdout, "\t# Restart: %i\n\n", restart);
   }
 
   comm.exchange(atom);
@@ -529,7 +573,7 @@ int main(int argc, char** argv)
   }
 
   timer.barrier_start(TIME_TOTAL);
-  integrate.run(atom, force, neighbor, comm, thermo, timer);
+  integrate.run(atom, force, neighbor, comm, thermo, timer, restart);
   timer.barrier_stop(TIME_TOTAL);
 
   int natoms;
@@ -565,6 +609,11 @@ int main(int argc, char** argv)
   }
   // End Scope Guard
 
+
+#ifdef KOKKOS_ENABLE_AUTOMATIC_CHECKPOINT
+   resilience_context.reset();
+#endif
+
   Kokkos::finalize();
   MPI_Finalize();
   return 0;
diff --git a/kokkos/ljs.h b/kokkos/ljs.h
index 47da176..bb82f4c 100644
--- a/kokkos/ljs.h
+++ b/kokkos/ljs.h
@@ -50,4 +50,15 @@ struct In {
   int thermo_nstat;
 };
 
+#ifdef KOKKOS_ENABLE_AUTOMATIC_CHECKPOINT
+   #include <Kokkos_Resilience.hpp>
+   #include <memory>
+   #ifdef KOKKOS_ENABLE_VELOC
+      extern std::unique_ptr< KokkosResilience::Context< KokkosResilience::VeloCCheckpointBackend > > resilience_context;
+   #else
+      // TODO -- need a non-veloc backend before this will compile...
+      extern std::unique_ptr< KokkosResilience::Context< > > resilience_context;
+   #endif
+#endif
+
 #endif
diff --git a/kokkos/neighbor.cpp b/kokkos/neighbor.cpp
index c9c26fe..2939394 100644
--- a/kokkos/neighbor.cpp
+++ b/kokkos/neighbor.cpp
@@ -650,6 +650,7 @@ int Neighbor::setup(Atom &atom)
 
 /* compute closest distance between central bin (0,0,0) and bin (i,j,k) */
 
+KOKKOS_INLINE_FUNCTION
 MMD_float Neighbor::bindist(int i, int j, int k)
 {
   MMD_float delx, dely, delz;
diff --git a/kokkos/neighbor.h b/kokkos/neighbor.h
index 80a58ab..17eb4da 100644
--- a/kokkos/neighbor.h
+++ b/kokkos/neighbor.h
@@ -119,6 +119,7 @@ class Neighbor
 
     KOKKOS_INLINE_FUNCTION
     MMD_float bindist(int, int, int);   // distance between binx
+
     KOKKOS_INLINE_FUNCTION
     int coord2bin(MMD_float, MMD_float, MMD_float) const;   // mapping atom coord to a bin
 
diff --git a/kokkos/setup.cpp b/kokkos/setup.cpp
index 89c9f63..d02aa77 100644
--- a/kokkos/setup.cpp
+++ b/kokkos/setup.cpp
@@ -359,6 +359,7 @@ int create_atoms(Atom &atom, int nx, int ny, int nz, double rho)
 
   int iflag = 0;
 
+  //printf("main atom setup loop \n");
   while(oz * subboxdim <= khi) {
     k = oz * subboxdim + sz;
     j = oy * subboxdim + sy;
diff --git a/minimd.cfg b/minimd.cfg
new file mode 100644
index 0000000..5ae09d5
--- /dev/null
+++ b/minimd.cfg
@@ -0,0 +1,3 @@
+scratch = scratch
+persistent = persistent
+mode = sync
diff --git a/scripts/launch.16.slurm b/scripts/launch.16.slurm
new file mode 100644
index 0000000..a5aa6f6
--- /dev/null
+++ b/scripts/launch.16.slurm
@@ -0,0 +1,44 @@
+#!/bin/bash
+#SBATCH -n 16
+#SBATCH -c 12
+#SBATCH --time=02:00:00
+#SBATCH -o ./benchmark_minimd.out
+export OMP_PROC_BIND=spread
+export OMP_PLACES=threads
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 16 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 12 -i ../kokkos/in.eam.miniMD 
+
diff --git a/scripts/launch.32.slurm b/scripts/launch.32.slurm
new file mode 100644
index 0000000..91add40
--- /dev/null
+++ b/scripts/launch.32.slurm
@@ -0,0 +1,44 @@
+#!/bin/bash
+#SBATCH -n 32
+#SBATCH -c 6
+#SBATCH --time=02:00:00
+#SBATCH -o ./benchmark_minimd.out
+export OMP_PROC_BIND=spread
+export OMP_PLACES=threads
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 32 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 6 -i ../kokkos/in.eam.miniMD 
+
diff --git a/scripts/launch.4.slurm b/scripts/launch.4.slurm
new file mode 100644
index 0000000..7cc2fd0
--- /dev/null
+++ b/scripts/launch.4.slurm
@@ -0,0 +1,44 @@
+#!/bin/bash
+#SBATCH -n 4
+#SBATCH -c 48
+#SBATCH --time=02:00:00
+#SBATCH -o ./benchmark_minimd.out
+export OMP_PROC_BIND=spread
+export OMP_PLACES=threads
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+
diff --git a/scripts/launch.8.slurm b/scripts/launch.8.slurm
new file mode 100644
index 0000000..f7edd3d
--- /dev/null
+++ b/scripts/launch.8.slurm
@@ -0,0 +1,43 @@
+#!/bin/bash
+#SBATCH -n 8
+#SBATCH --time=02:00:00
+#SBATCH -o ./benchmark_minimd.out
+export OMP_PROC_BIND=spread
+export OMP_PLACES=threads
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+rm -r ./data
+mpirun -n 8 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 24 -i ../kokkos/in.eam.miniMD 
+
diff --git a/scripts/launch.slurm b/scripts/launch.slurm
new file mode 100644
index 0000000..a39b16f
--- /dev/null
+++ b/scripts/launch.slurm
@@ -0,0 +1,26 @@
+#!/bin/bash
+#SBATCH -n 4
+#SBATCH -c 48
+#SBATCH --time=02:00:00
+#SBATCH -o ./benchmark_minimd.out
+export OMP_PROC_BIND=spread
+export OMP_PLACES=threads
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+mpirun -n 4 ./miniMD --half_neigh 0 -s 100 --ntypes 1 -t 48 -i ../kokkos/in.eam.miniMD 
+
diff --git a/scripts/process_results.bash b/scripts/process_results.bash
new file mode 100755
index 0000000..070f12d
--- /dev/null
+++ b/scripts/process_results.bash
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+TOT_TIME=0
+
+cat ./benchmark_minimd.out | grep PERF_SUMMARY > benchmark_results.out
+let loop_cnt=0
+while read -r result; do
+
+MD_TIME=`echo $result | awk '{print $5}'`
+TOT_TIME=`echo "${TOT_TIME} + ${MD_TIME}" | bc -l`
+echo $TOT_TIME, $MD_TIME, $result
+
+let loop_cnt+=1
+done < ./benchmark_results.out
+AVG_MD_TIME=`echo "${TOT_TIME} / ${loop_cnt}" | bc -l`
+
+echo "MiniMD: ${AVG_MD_TIME}"