Merge pull request #35 from lammps/master (482e120a) · Commits · 郑智淋 / lammps

.gitignore

+1 −0

Original line number	Diff line number	Diff line
		@@ -22,6 +22,7 @@ log.cite
		.*.swp
		*.orig
		*.rej
		vgcore.*
		.vagrant
		\#*#
		.#*

cmake/CMakeLists.txt

+100 −52

Original line number	Diff line number	Diff line
		@@ -11,6 +11,10 @@ get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib
		get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
		get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)

		# by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
		if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
		set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
		endif()

		# To avoid conflicts with the conventional Makefile build system, we build everything here
		file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
		@@ -75,6 +79,7 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
		#release comes with -O3 by default
		set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
		endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
		string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)

		# check for files auto-generated by make-based buildsystem
		# this is fast, so check for it all the time
		@@ -422,16 +427,30 @@ if(WITH_FFMPEG)
		add_definitions(-DLAMMPS_FFMPEG)
		endif()

		if(BUILD_SHARED_LIBS)
		set(CONFIGURE_REQUEST_PIC "--with-pic")
		set(CMAKE_REQUEST_PIC "-DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}")
		set(CUDA_REQUEST_PIC "-Xcompiler ${CMAKE_SHARED_LIBRARY_CXX_FLAGS}")
		else()
		set(CONFIGURE_REQUEST_PIC)
		set(CMAKE_REQUEST_PIC)
		set(CUDA_REQUEST_PIC)
		endif()


		if(PKG_VORONOI)
		option(DOWNLOAD_VORO "Download voro++ (instead of using the system's one)" OFF)
		option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" OFF)
		if(DOWNLOAD_VORO)
		message(STATUS "Voro++ download requested - we will build our own")
		include(ExternalProject)

		if(BUILD_SHARED_LIBS)
		set(VORO_BUILD_OPTIONS "CFLAGS=-fPIC")
		set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
		else()
		set(VORO_BUILD_OPTIONS)
		set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
		endif()
		string(APPEND VORO_BUILD_CFLAGS ${CMAKE_CXX_FLAGS})
		set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})

		ExternalProject_Add(voro_build
		URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
		@@ -445,7 +464,7 @@ if(PKG_VORONOI)
		else()
		find_package(VORO)
		if(NOT VORO_FOUND)
		message(FATAL_ERROR "VORO not found, help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
		message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
		endif()
		endif()
		include_directories(${VORO_INCLUDE_DIRS})
		@@ -453,18 +472,18 @@ if(PKG_VORONOI)
		endif()

		if(PKG_LATTE)
		option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF)
		option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" OFF)
		if(DOWNLOAD_LATTE)
		if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
		message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
		endif()
		message(STATUS "LATTE not found - we will build our own")
		message(STATUS "LATTE download requested - we will build our own")
		include(ExternalProject)
		ExternalProject_Add(latte_build
		URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
		URL_MD5 85ac414fdada2d04619c8f936344df14
		SOURCE_SUBDIR cmake
		CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}
		CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
		)
		ExternalProject_get_property(latte_build INSTALL_DIR)
		set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
		@@ -472,7 +491,7 @@ if(PKG_LATTE)
		else()
		find_package(LATTE)
		if(NOT LATTE_FOUND)
		message(FATAL_ERROR "LATTE not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
		message(FATAL_ERROR "LATTE library 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})
		@@ -480,19 +499,17 @@ endif()

		if(PKG_USER-SCAFACOS)
		find_package(GSL REQUIRED)
		option(DOWNLOAD_SCAFACOS "Download ScaFaCoS (instead of using the system's one)" OFF)
		option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" OFF)
		if(DOWNLOAD_SCAFACOS)
		message(STATUS "ScaFaCoS download requested - we will build our own")
		include(ExternalProject)
		ExternalProject_Add(scafacos_build
		URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
		URL_MD5 bd46d74e3296bd8a444d731bb10c1738
		CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
		--disable-doc
		CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
		--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
		--with-internal-fftw
		--with-internal-pfft
		--with-internal-pnfft
		$<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic>
		--with-internal-fftw --with-internal-pfft
		--with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
		FC=${CMAKE_MPI_Fortran_COMPILER}
		CXX=${CMAKE_MPI_CXX_COMPILER}
		CC=${CMAKE_MPI_C_COMPILER}
		@@ -537,15 +554,15 @@ if(PKG_USER-PLUMED)
		validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
		string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)

		option(DOWNLOAD_PLUMED "Download Plumed (instead of using the system's one)" OFF)
		option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF)
		if(DOWNLOAD_PLUMED)
		message(STATUS "PLUMED download requested - we will build our own")
		include(ExternalProject)
		ExternalProject_Add(plumed_build
		URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz
		URL_MD5 b1be7c48971627febc11c61b70767fc5
		BUILD_IN_SOURCE 1
		CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
		$<$<BOOL:${BUILD_SHARED_LIBS}>:--with-pic> )
		CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC})
		ExternalProject_get_property(plumed_build INSTALL_DIR)
		set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
		list(APPEND LAMMPS_DEPS plumed_build)
		@@ -592,8 +609,9 @@ if(PKG_USER-NETCDF)
		endif()

		if(PKG_USER-SMD)
		option(DOWNLOAD_EIGEN3 "Download Eigen3 (instead of using the system's one)" OFF)
		option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
		if(DOWNLOAD_EIGEN3)
		message(STATUS "Eigen3 download requested - we will build our own")
		include(ExternalProject)
		ExternalProject_Add(Eigen3_build
		URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz
		@@ -633,8 +651,9 @@ if(PKG_USER-VTK)
		endif()

		if(PKG_KIM)
		option(DOWNLOAD_KIM "Download kim-api (instead of using the system's one)" OFF)
		option(DOWNLOAD_KIM "Download KIM-API v1 from OpenKIM instead of using an already installed one)" OFF)
		if(DOWNLOAD_KIM)
		message(STATUS "KIM-API v1 download requested - we will build our own")
		include(ExternalProject)
		ExternalProject_Add(kim_build
		URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
		@@ -649,7 +668,7 @@ if(PKG_KIM)
		else()
		find_package(KIM)
		if(NOT KIM_FOUND)
		message(FATAL_ERROR "KIM not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
		message(FATAL_ERROR "KIM-API v1 not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
		endif()
		endif()
		list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
		@@ -662,12 +681,7 @@ if(PKG_MESSAGE)
		${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
		${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)

		if(BUILD_SHARED_LIBS)
		add_library(cslib SHARED ${cslib_SOURCES})
		else()
		add_library(cslib STATIC ${cslib_SOURCES})
		endif()

		if(BUILD_MPI)
		target_compile_definitions(cslib PRIVATE -DMPI_YES)
		set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
		@@ -692,10 +706,10 @@ endif()

		if(PKG_MSCG)
		find_package(GSL REQUIRED)
		option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
		option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" OFF)
		if(DOWNLOAD_MSCG)
		if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
		message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
		message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
		endif()
		include(ExternalProject)
		if(NOT LAPACK_FOUND)
		@@ -705,7 +719,7 @@ if(PKG_MSCG)
		URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
		URL_MD5 8c45e269ee13f60b303edd7823866a91
		SOURCE_SUBDIR src/CMake
		CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ${EXTRA_MSCG_OPTS}
		CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
		BUILD_COMMAND make mscg INSTALL_COMMAND ""
		)
		ExternalProject_get_property(mscg_build BINARY_DIR)
		@@ -753,7 +767,7 @@ set(MATH_LIBRARIES "m" CACHE STRING "math library")
		mark_as_advanced( MATH_LIBRARIES )
		include(CheckLibraryExists)
		if (CMAKE_VERSION VERSION_LESS "3.4")
		enable_language(C) # check_library_exists isn't supported without a c compiler before v3.4
		enable_language(C) # check_library_exists isn't supported without a C compiler before v3.4
		endif()
		# RB: disabled this check because it breaks with KOKKOS CUDA enabled
		#foreach(FUNC sin cos)
		@@ -791,6 +805,13 @@ foreach(PKG ${DEFAULT_PACKAGES})
		endif()
		endforeach()

		# packages that need defines set
		foreach(PKG MPIIO)
		if(PKG_${PKG})
		add_definitions(-DLMP_${PKG})
		endif()
		endforeach()

		# dedicated check for entire contents of accelerator packages
		foreach(PKG ${ACCEL_PACKAGES})
		set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
		@@ -1019,7 +1040,7 @@ if(PKG_USER-INTEL)
		endif()

		if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
		message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
		message(FATAL_ERROR "USER-INTEL needs at least a 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
		endif()

		if(NOT BUILD_OMP)
		@@ -1119,11 +1140,11 @@ if(PKG_GPU)
		find_package(CUDA REQUIRED)
		find_program(BIN2C bin2c)
		if(NOT BIN2C)
		message(FATAL_ERROR "Couldn't find bin2c, use -DBIN2C helping cmake to find it.")
		message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
		endif()
		option(CUDPP_OPT "Enable CUDPP_OPT" ON)

		set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)")
		set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")

		file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.].cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.].cu)
		list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
		@@ -1136,11 +1157,39 @@ if(PKG_GPU)
		file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
		endif()

		cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
		-DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC_SETTING})
		# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
		# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
		set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
		# Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
		if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
		string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
		endif()
		# Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
		if(CUDA_VERSION VERSION_GREATER "4.9")
		string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
		endif()
		# Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
		if(CUDA_VERSION VERSION_GREATER "5.9")
		string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
		endif()
		# Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
		if(CUDA_VERSION VERSION_GREATER "7.9")
		string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
		endif()
		# Volta (GPU Arch 7.0) is supported by CUDA 9 and later
		if(CUDA_VERSION VERSION_GREATER "8.9")
		string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
		endif()
		# Turing (GPU Arch 7.5) is supported by CUDA 10 and later
		if(CUDA_VERSION VERSION_GREATER "9.9")
		string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
		endif()

		cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
		-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})

		cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>
		-DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC_SETTING})
		cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
		-DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})

		foreach(CU_OBJ ${GPU_GEN_OBJS})
		get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
		@@ -1409,7 +1458,6 @@ foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
		endif()
		endforeach()

		string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
		get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
		include(FeatureSummary)
		feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND)

cmake/README.md

+1 −0

Original line number	Diff line number	Diff line
		@@ -195,6 +195,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
		<td><code>CMAKE_INSTALL_PREFIX</code></td>
		<td>Install location where LAMMPS files will be copied to. In the Unix/Linux case with Makefiles this controls what `make install` will do.</td>
		<td>
		Default setting is <code>$HOME/.local</code>.
		</td>
		</tr>
		<tr>

doc/Makefile

+0 −1

Original line number	Diff line number	Diff line
		@@ -176,7 +176,6 @@ $(VENV):
		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
		. $(VENV)/bin/activate; \
		pip install Sphinx; \
		pip install sphinxcontrib-images; \
		deactivate;\
		)

doc/github-development-workflow.md

+8 −3

Original line number	Diff line number	Diff line
		@@ -55,11 +55,11 @@ required changes or ask the submitter of the pull request to implement
		them. Even though, all LAMMPS developers may have write access to pull
		requests (if enabled by the submitter, which is the default), only the
		submitter or the assignee of a pull request may do so. During this
		period the "work_in_progress" label shall be applied to the pull
		period the `work_in_progress` label shall be applied to the pull
		request. The assignee gets to decide what happens to the pull request
		next, e.g. whether it should be assigned to a different developer for
		additional checks and changes, or is recommended to be merged. Removing
		the "work_in_progress" label and assigning the pull request to the
		the `work_in_progress` label and assigning the pull request to the
		developer tasked with merging signals that a pull request is ready to be
		merged.

		@@ -107,7 +107,9 @@ Here are some items to check:
		* new style docs should be added to the "overview" files in
		`doc/src/Commands_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt`
		and `doc/src/lammps.book`
		* new files in packages should be added to `src/.gitignore`
		* check whether manual cleanly translates with `make html` and `make pdf`
		* check spelling of manual with `make spelling` in doc folder
		* new source files in packages should be added to `src/.gitignore`
		* removed or renamed files in packages should be added to `src/Purge.list`
		* C++ source files should use C++ style include files for accessing
		C-library APIs, e.g. `#include <cstdlib>` instead of `#include <stdlib.h>`.
		@@ -143,6 +145,9 @@ Here are some items to check:
		compiling LAMMPS with `-DLAMMPS_BIGBIG`.
		* when including both `lmptype.h` (and using defines or macros from it)
		and `mpi.h`, `lmptype.h` must be included first.
		* when pair styles are added, check if settings for flags like
		`single_enable`, `writedata`, `reinitflag`, `manybody_flag`
		and others are correctly set and supported.

		## GitHub Issues

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