Merge pull request #17 from lammps/master

rebase
lammps · Jun 16, 2018 · 40c4461 · 40c4461
2 parents e777380 + fcf9ed0
commit 40c4461
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diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
@@ -2,9 +2,9 @@
 # CMake build system
 # This file is part of LAMMPS
 # Created by Christoph Junghans and Richard Berger
-cmake_minimum_required(VERSION 3.1)
+cmake_minimum_required(VERSION 2.8.12)
 
-project(lammps LANGUAGES CXX)
+project(lammps CXX)
 set(SOVERSION 0)
 set(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src)
 set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib)
@@ -129,31 +129,35 @@ foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
 endforeach()
 
 macro(pkg_depends PKG1 PKG2)
-  if(PKG_${PKG1} AND NOT PKG_${PKG2})
+  if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
     message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
   endif()
 endmacro()
 
 pkg_depends(MPIIO MPI)
 pkg_depends(QEQ MANYBODY)
 pkg_depends(USER-ATC MANYBODY)
-pkg_depends(USER-H5MD MPI)
 pkg_depends(USER-LB MPI)
 pkg_depends(USER-MISC MANYBODY)
 pkg_depends(USER-PHONON KSPACE)
+pkg_depends(CORESHELL KSPACE)
 
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
 if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE)
   enable_language(Fortran)
+  list(APPEND LAMMPS_LINK_LIBS ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
 
-if(PKG_MEAM)
+if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM)
   enable_language(C)
 endif()
 
-if(PKG_KOKKOS OR PKG_MSCG)
+if(PKG_MSCG)
+  if (CMAKE_VERSION VERSION_LESS "3.1") 
+    message(FATAL_ERROR "For the MSCG package you need at least cmake-3.1")
+  endif()
   # starting with CMake 3.1 this is all you have to do to enforce C++11
   set(CMAKE_CXX_STANDARD 11) # C++11...
   set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required...
@@ -312,7 +316,7 @@ if(PKG_LATTE)
       message(FATAL_ERROR "LATTE not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
     endif()
   endif()
-  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
 endif()
 
 if(PKG_USER-MOLFILE)
@@ -355,14 +359,14 @@ endif()
 
 if(PKG_USER-QUIP)
   find_package(QUIP REQUIRED)
-  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES})
 endif()
 
 if(PKG_USER-QMMM)
   message(WARNING "Building QMMM with CMake is still experimental")
   find_package(QE REQUIRED)
   include_directories(${QE_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES})
 endif()
 
 if(PKG_USER-VTK)
@@ -657,6 +661,9 @@ if(PKG_USER-INTEL)
 endif()
 
 if(PKG_GPU)
+    if (CMAKE_VERSION VERSION_LESS "3.1") 
+      message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
+    endif()
     set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
     set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
                     ${GPU_SOURCES_DIR}/fix_gpu.h
@@ -753,7 +760,7 @@ if(PKG_GPU)
       add_library(gpu STATIC ${GPU_LIB_SOURCES})
       target_link_libraries(gpu ${OpenCL_LIBRARIES})
       target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
-      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
       target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
 
       list(APPEND LAMMPS_LINK_LIBS gpu)

diff --git a/cmake/README.md b/cmake/README.md
@@ -9,7 +9,7 @@ cmake /path/to/lammps/source/cmake
 
 To enable package, e.g. GPU do
 ```
-cmake /path/to/lammps/source/cmake -DENABLE_GPU=ON
+cmake /path/to/lammps/source/cmake -DPKG_GPU=ON
 ```
 
 cmake has many many options, do get an overview use the curses-based cmake interface, ccmake:

diff --git a/lib/gpu/Makefile.linux_multi b/lib/gpu/Makefile.linux_multi
@@ -0,0 +1,53 @@
+# /* ----------------------------------------------------------------------   
+#  Generic Linux Makefile for CUDA 
+#     - Change CUDA_ARCH for your GPU
+# ------------------------------------------------------------------------- */
+
+# which file will be copied to Makefile.lammps
+
+EXTRAMAKE = Makefile.lammps.standard
+
+ifeq ($(CUDA_HOME),)
+CUDA_HOME = /usr/local/cuda
+endif
+
+NVCC = nvcc
+
+# Kepler CUDA
+#CUDA_ARCH = -arch=sm_35
+# newer CUDA
+#CUDA_ARCH = -arch=sm_13
+# older CUDA
+#CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
+
+CUDA_ARCH = -gencode arch=compute_60,code=sm_60 -gencode arch=compute_61,code=sm_61
+
+# this setting should match LAMMPS Makefile
+# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
+
+LMP_INC = -DLAMMPS_SMALLBIG
+
+# precision for GPU calculations
+# -D_SINGLE_SINGLE  # Single precision for all calculations
+# -D_DOUBLE_DOUBLE  # Double precision for all calculations
+# -D_SINGLE_DOUBLE  # Accumulation of forces, etc. in double
+
+CUDA_PRECISION = -D_SINGLE_DOUBLE
+
+CUDA_INCLUDE = -I$(CUDA_HOME)/include
+CUDA_LIB = -L$(CUDA_HOME)/lib64
+CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) -Xcompiler "-fPIC -std=c++98"
+
+CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
+CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
+
+BIN_DIR = ./
+OBJ_DIR = ./
+LIB_DIR = ./
+AR = ar
+BSH = /bin/sh
+
+CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
+
+include Nvidia.makefile_multi
+
diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile
@@ -77,7 +77,9 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \
        $(OBJ_DIR)/lal_coul_debye.o $(OBJ_DIR)/lal_coul_debye_ext.o \
        $(OBJ_DIR)/lal_zbl.o $(OBJ_DIR)/lal_zbl_ext.o \
        $(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \
-       $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o 
+       $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \
+       $(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \
+       $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o
 
 CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
        $(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \
@@ -133,7 +135,9 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
        $(OBJ_DIR)/coul_debye.cubin $(OBJ_DIR)/coul_debye_cubin.h \
        $(OBJ_DIR)/zbl.cubin $(OBJ_DIR)/zbl_cubin.h \
        $(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic_cubin.h \
-       $(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm_cubin.h
+       $(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm_cubin.h \
+       $(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj_cubin.h \
+       $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h
 
 all: $(OBJ_DIR) $(GPU_LIB) $(EXECS)
 
@@ -809,6 +813,30 @@ $(OBJ_DIR)/lal_lj_cubic.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic.cpp $(OBJ_DIR)/l
 $(OBJ_DIR)/lal_lj_cubic_ext.o: $(ALL_H) lal_lj_cubic.h lal_lj_cubic_ext.cpp lal_base_atomic.h
 	$(CUDR) -o $@ -c lal_lj_cubic_ext.cpp -I$(OBJ_DIR)
 
+$(OBJ_DIR)/dipole_long_lj.cubin: lal_dipole_long_lj.cu lal_precision.h lal_preprocessor.h
+	$(CUDA) --cubin -DNV_KERNEL -o $@ lal_dipole_long_lj.cu
+
+$(OBJ_DIR)/dipole_long_lj_cubin.h: $(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj.cubin
+	$(BIN2C) -c -n dipole_long_lj $(OBJ_DIR)/dipole_long_lj.cubin > $(OBJ_DIR)/dipole_long_lj_cubin.h
+
+$(OBJ_DIR)/lal_dipole_long_lj.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj.cpp $(OBJ_DIR)/dipole_long_lj_cubin.h $(OBJ_DIR)/lal_base_dipole.o
+	$(CUDR) -o $@ -c lal_dipole_long_lj.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_dipole_long_lj_ext.o: $(ALL_H) lal_dipole_long_lj.h lal_dipole_long_lj_ext.cpp lal_base_dipole.h
+	$(CUDR) -o $@ -c lal_dipole_long_lj_ext.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lj_expand_coul_long.cubin: lal_lj_expand_coul_long.cu lal_precision.h lal_preprocessor.h
+	$(CUDA) --cubin -DNV_KERNEL -o $@ lal_lj_expand_coul_long.cu
+
+$(OBJ_DIR)/lj_expand_coul_long_cubin.h: $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long.cubin
+	$(BIN2C) -c -n lj_expand_coul_long $(OBJ_DIR)/lj_expand_coul_long.cubin > $(OBJ_DIR)/lj_expand_coul_long_cubin.h
+
+$(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long.cpp $(OBJ_DIR)/lj_expand_coul_long_cubin.h $(OBJ_DIR)/lal_base_charge.o
+	$(CUDR) -o $@ -c lal_lj_expand_coul_long.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h
+	$(CUDR) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR)
+
 $(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
 	$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda