Merge pull request #30 from streeve/split_aosoa

Flexible number of AoSoA and vector lengths

CMakeLists.txt

@@ -32,18 +32,16 @@ foreach(_device ${CABANAMD_SUPPORTED_DEVICES})
   endif()
 endforeach()
 
-
 ##---------------------------------------------------------------------------##
-# Set up optional libraries
+# Set up neural network options
 ##---------------------------------------------------------------------------##
-
 option(CabanaMD_ENABLE_NNP "Build CabanaMD with neural network potential (and n2p2 libnnp)" OFF)
 if(NOT DEFINED N2P2_DIR)
   set(N2P2_DIR ~/n2p2/)
 endif()
 
 ##---------------------------------------------------------------------------##
-## Print the revision number to stdout
+## Print the Git revision number to stdout
 ##---------------------------------------------------------------------------##
 FIND_PACKAGE(Git)
 IF(GIT_FOUND AND IS_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/.git)
@@ -60,26 +58,24 @@ MESSAGE(STATUS "CabanaMD Revision = '${CabanaMD_GIT_COMMIT_HASH}'")
 ##---------------------------------------------------------------------------##
 ## Build CabanaMD
 ##---------------------------------------------------------------------------##
-
 add_subdirectory(src)
 add_subdirectory(bin)
 
 ##---------------------------------------------------------------------------##
 ## Enable Tests?
 ##---------------------------------------------------------------------------##
-
 option(CabanaMD_ENABLE_TESTING "Build tests" OFF)
 if(CabanaMD_ENABLE_TESTING)
   enable_testing()
   add_subdirectory(unit_test)
 endif()
 
 ##---------------------------------------------------------------------------##
-## Pretty-printing wizardry:
+## Clang format
 ##---------------------------------------------------------------------------##
 find_package(CLANG_FORMAT)
 if(CLANG_FORMAT_FOUND)
-  file(GLOB_RECURSE FORMAT_SOURCES src/*.cpp src/*.h)
+  file(GLOB_RECURSE FORMAT_SOURCES src/*.cpp src/*.h bin/*.cpp)
   add_custom_target(format
     COMMAND ${CLANG_FORMAT_EXECUTABLE} -i -style=file ${FORMAT_SOURCES}
     DEPENDS ${FORMAT_SOURCES})

README.md

@@ -49,6 +49,7 @@ cmake \
     -D CabanaMD_ENABLE_Serial=OFF \
     -D CabanaMD_ENABLE_OpenMP=ON \
     -D CabanaMD_ENABLE_Cuda=OFF \
+    -D CabanaMD_VECTORLENGTH=1 \
     \
     .. ;
 make install
@@ -67,15 +68,17 @@ cmake \
     -D CabanaMD_ENABLE_Serial=OFF \
     -D CabanaMD_ENABLE_OpenMP=OFF \
     -D CabanaMD_ENABLE_Cuda=ON \
+    -D CabanaMD_VECTORLENGTH=32 \
     \
     .. ;
 ```
 
 ## Neural network potential build
-If using the optional neural network potential, additional flags for the
+If using the optional neural network potential, additional CMake flags for the
 location of the libnnp library (https://github.com/CompPhysVienna/n2p2)
-and enabling the potential are needed for CMake:
+and enabling the potential are needed (with one additional optional setting):
 ```
     -D N2P2_DIR=$N2P2_INSTALL_DIR \
     -D CabanaMD_ENABLE_NNP=ON \
+    -D CabanaMD_VECTORLENGTH_NNP=1 \
 ```

bin/main.cpp

@@ -47,29 +47,29 @@
 //************************************************************************
 
 #include <cabanamd.h>
-
-// CabanaMD can be used as a library
-// This main file is simply a driver
+#include <mdfactory.h>
+#include <types.h>
 
 #include "mpi.h"
 
+// CabanaMD can be used as a library
+// This main file is simply a driver
 int main( int argc, char *argv[] )
 {
 
     MPI_Init( &argc, &argv );
 
     Kokkos::ScopeGuard scope_guard( argc, argv );
 
-    CabanaMD cabanamd;
-    cabanamd.init( argc, argv );
-
-    cabanamd.run( cabanamd.input->nsteps );
+    InputCL commandline;
+    commandline.read_args( argc, argv );
 
-    //   cabanamd.check_correctness();
+    CabanaMD *cabanamd = MDfactory::create( commandline );
 
-    cabanamd.print_performance();
+    cabanamd->init( commandline );
+    cabanamd->run();
 
-    cabanamd.shutdown();
+    //   cabanamd.check_correctness();
 
     MPI_Finalize();
 }

src/CMakeLists.txt

@@ -1,9 +1,34 @@
-configure_file(CabanaMD_config.hpp.cmakein CabanaMD_config.hpp)
+#------------------------------------------------------------
+# Set up vector length options
+#------------------------------------------------------------
+if(NOT CabanaMD_VECTORLENGTH)
+  if(Kokkos_ENABLE_CUDA)
+    set(CabanaMD_VECTORLENGTH 32)
+  else()
+    set(CabanaMD_VECTORLENGTH 1)
+  endif()
+endif()
+message( STATUS "Using vector length: ${CabanaMD_VECTORLENGTH}" )
+
+if(CabanaMD_ENABLE_NNP)
+  if(NOT CabanaMD_VECTORLENGTH_NNP)
+    if(Kokkos_ENABLE_CUDA)
+      set(CabanaMD_VECTORLENGTH_NNP 32)
+    else()
+      set(CabanaMD_VECTORLENGTH_NNP 1)
+    endif()
+  endif()
+  message( STATUS "Using vector length: ${CabanaMD_VECTORLENGTH_NNP} (NNP)" )
+endif()
+
+#------------------------------------------------------------
+
+configure_file(CabanaMD_config.hpp.cmakein CabanaMD_config.hpp @ONLY)
 
 #------------------------------------------------------------
 
 file(GLOB HEADERS_PUBLIC
-     GLOB *.h force_types/*.h
+     GLOB *.h force_types/*.h system_types/*.h
     )
 
 file(GLOB SOURCES
@@ -15,7 +40,8 @@ if(CabanaMD_ENABLE_NNP)
 else()
   file(GLOB FORCE_TYPES force_types/force_lj*.cpp)
 endif()
-list(APPEND SOURCES ${FORCE_TYPES})
+
+list(APPEND SOURCES ${FORCE_TYPES} ${SYSTEM_TYPES} ${SYSNNP_TYPES})
 
 install(FILES ${HEADERS_PUBLIC} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 install(FILES ${CMAKE_CURRENT_BINARY_DIR}/CabanaMD_config.hpp DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
@@ -27,6 +53,7 @@ add_library(CabanaMD ${SOURCES})
 # Sources linking against CabanaMD will implicitly include these directories:
 target_include_directories(CabanaMD PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}
                                     ${CMAKE_CURRENT_SOURCE_DIR}/force_types
+                                    ${CMAKE_CURRENT_SOURCE_DIR}/system_types
                                     $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
                                     $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>)
 

src/CabanaMD_config.hpp.cmakein

@@ -8,6 +8,16 @@
 #cmakedefine CabanaMD_ENABLE_Threads
 #cmakedefine CabanaMD_ENABLE_OpenMP
 #cmakedefine CabanaMD_ENABLE_Cuda
+
 #cmakedefine CabanaMD_ENABLE_NNP
 
+#cmakedefine CabanaMD_LAYOUT_1AoSoA
+#cmakedefine CabanaMD_LAYOUT_2AoSoA
+#cmakedefine CabanaMD_LAYOUT_6AoSoA
+#cmakedefine CabanaMD_VECTORLENGTH @CabanaMD_VECTORLENGTH@
+
+#cmakedefine CabanaMD_LAYOUT_NNP_1AoSoA
+#cmakedefine CabanaMD_LAYOUT_NNP_3AoSoA
+#cmakedefine CabanaMD_VECTORLENGTH_NNP @CabanaMD_VECTORLENGTH_NNP@
+
 #endif

src/binning_cabana.h

@@ -54,19 +54,21 @@
 
 #include <Cabana_Core.hpp>
 
+template <class t_System>
 class Binning
 {
-    System *system;
+    t_System *system;
 
   public:
     T_INT nbinx, nbiny, nbinz, nhalo;
     T_X_FLOAT minx, maxx, miny, maxy, minz, maxz;
-    typename AoSoA::member_slice_type<Positions> x;
 
-    Binning( System *s );
+    Binning( t_System *s );
     void create_binning( T_X_FLOAT dx, T_X_FLOAT dy, T_X_FLOAT dz,
                          int halo_depth, bool do_local, bool do_ghost,
                          bool sort );
     const char *name();
 };
+
+#include <binning_cabana_impl.h>
 #endif

src/binning_cabana.cpp → src/binning_cabana_impl.h

@@ -46,16 +46,17 @@
 //
 //************************************************************************
 
-#include <binning_cabana.h>
-
-Binning::Binning( System *s )
+template <class t_System>
+Binning<t_System>::Binning( t_System *s )
     : system( s )
 {
 }
 
-void Binning::create_binning( T_X_FLOAT dx_in, T_X_FLOAT dy_in, T_X_FLOAT dz_in,
-                              int halo_depth, bool do_local, bool do_ghost,
-                              bool sort )
+template <class t_System>
+void Binning<t_System>::create_binning( T_X_FLOAT dx_in, T_X_FLOAT dy_in,
+                                        T_X_FLOAT dz_in, int halo_depth,
+                                        bool do_local, bool do_ghost,
+                                        bool sort )
 {
     if ( do_local || do_ghost )
     {
@@ -91,15 +92,20 @@ void Binning::create_binning( T_X_FLOAT dx_in, T_X_FLOAT dy_in, T_X_FLOAT dz_in,
         T_X_FLOAT min[3] = {minx, miny, minz};
         T_X_FLOAT max[3] = {maxx, maxy, maxz};
 
-        x = Cabana::slice<Positions>( system->xvf );
+        system->slice_x();
+        auto x = system->x;
 
         t_linkedcell cell_list( x, begin, end, delta, min, max );
 
         if ( sort )
         {
-            Cabana::permute( cell_list, system->xvf );
+            system->permute( cell_list );
         }
     }
 }
 
-const char *Binning::name() { return "Binning:CabanaLinkedCell"; }
+template <class t_System>
+const char *Binning<t_System>::name()
+{
+    return "Binning:CabanaLinkedCell";
+}

src/cabanamd.h

@@ -46,10 +46,14 @@
 //
 //************************************************************************
 
+#ifndef CABANAMD_H
+#define CABANAMD_H
+
 #include <binning_cabana.h>
 #include <comm_mpi.h>
 #include <force.h>
-#include <input.h>
+#include <inputCL.h>
+#include <inputFile.h>
 #include <integrator_nve.h>
 #include <system.h>
 #include <types.h>
@@ -62,23 +66,32 @@
 class CabanaMD
 {
   public:
-    System *system;
-    Integrator *integrator;
-    Force *force;
-    Comm *comm;
-    Input *input;
-    Binning *binning;
-
-    CabanaMD();
+    int nsteps;
 
-    void init( int argc, char *argv[] );
+    virtual void init( InputCL cl ) = 0;
+    virtual void run() = 0;
 
-    void run( int nsteps );
+    virtual void dump_binary( int ) = 0;
+    virtual void check_correctness( int ) = 0;
+};
 
-    void dump_binary( int );
-    void check_correctness( int );
+template <class t_System>
+class CbnMD : public CabanaMD
+{
+  public:
+    t_System *system;
+    Integrator<t_System> *integrator;
+    Force<t_System> *force;
+    Comm<t_System> *comm;
+    InputFile<t_System> *input;
+    Binning<t_System> *binning;
 
-    void print_performance();
+    void init( InputCL cl ) override;
+    void run() override;
 
-    void shutdown();
+    void dump_binary( int ) override;
+    void check_correctness( int ) override;
 };
+
+#include <cabanamd_impl.h>
+#endif