Merge branch 'master' into fix-active (97ab08d7) · Commits · 郑智淋 / lammps

cmake/Modules/FindKIM-API.cmake

+27 −1

Original line number	Diff line number	Diff line
		@@ -37,6 +37,26 @@
		# KIM-API-CMAKE_Fortran_COMPILER
		#

		function(_KIMAPI_GET_VERSION _OUT_ver _version_hdr)
		if(NOT EXISTS ${_version_hdr})
		message(FATAL_ERROR "Header file ${_version_hdr} not found (check value of KIM-API_INCLUDE_DIR)")
		endif()
		foreach(_var KIM_VERSION_MAJOR KIM_VERSION_MINOR KIM_VERSION_PATCH)
		file(STRINGS ${_version_hdr} _contents REGEX "#define ${_var}[ \t]+")
		if(_contents)
		string(REGEX REPLACE ".#define ${_var}[ \t]+([0-9]+)." "\\1" _${_var} "${_contents}")
		if(${_${_var}} STREQUAL "")
		message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, got empty return!")
		elseif(NOT ${_${_var}} MATCHES "^[0-9]+$")
		message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, excepted a number but got ${_${_var}}!")
		endif()
		else()
		message(FATAL_ERROR "No ${_var} line found in include file ${_version_hdr}")
		endif()
		endforeach()
		set(${_OUT_ver} ${_KIM_VERSION_MAJOR}.${_KIM_VERSION_MINOR}.${_KIM_VERSION_PATCH} PARENT_SCOPE)
		endfunction()

		if(KIM-API_FIND_QUIETLY)
		set(REQ_OR_QUI "QUIET")
		else()
		@@ -54,6 +74,12 @@ if(KIM-API_FOUND)
		pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
		endif()

		if(KIM-API_INCLUDEDIR)
		_KIMAPI_GET_VERSION(KIM-API_VERSION ${KIM-API_INCLUDEDIR}/KIM_Version.h)
		else()
		set(KIM-API_VERSION 0)
		endif()

		# handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
		# if all listed variables are TRUE
		find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES)
		find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES VERSION_VAR KIM-API_VERSION)

cmake/Modules/Packages/KIM.cmake

+12 −4

Original line number	Diff line number	Diff line
		if(PKG_KIM)
		set(KIM-API_MIN_VERSION 2.1)
		find_package(CURL)
		if(CURL_FOUND)
		include_directories(${CURL_INCLUDE_DIRS})
		@@ -7,10 +8,17 @@ if(PKG_KIM)
		endif()
		find_package(KIM-API QUIET)
		if(KIM-API_FOUND)
		if (KIM-API_VERSION VERSION_LESS ${KIM-API_MIN_VERSION})
		if ("${DOWNLOAD_KIM}" STREQUAL "")
		message(WARNING "Unsuitable KIM-API version \"${KIM-API_VERSION}\" found, but required is at least \"${KIM-API_MIN_VERSION}\". Default behavior set to download and build our own.")
		endif()
		set(DOWNLOAD_KIM_DEFAULT ON)
		else()
		set(DOWNLOAD_KIM_DEFAULT OFF)
		endif()
		else()
		if (NOT DOWNLOAD_KIM)
		message(WARNING "KIM-API package not found. We will download and build our own")
		if ("${DOWNLOAD_KIM}" STREQUAL "")
		message(WARNING "KIM-API package not found. Default behavior set to download and build our own")
		endif()
		set(DOWNLOAD_KIM_DEFAULT ON)
		endif()
		@@ -42,7 +50,7 @@ if(PKG_KIM)
		set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
		list(APPEND LAMMPS_DEPS kim_build)
		else()
		find_package(KIM-API REQUIRED)
		find_package(KIM-API ${KIM-API_MIN_VERSION} REQUIRED)
		endif()
		list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
		include_directories(${KIM-API_INCLUDE_DIRS})

src/MAKE/MACHINES/Makefile.astra_arm

0 → 100644

+119 −0

Original line number	Diff line number	Diff line
		# astra_arm - ThunderX2 ARM/OpenMPI Based, use Arm-PL for FFTW

		# need to load the following modules:
		# 1) arm-based developer pack

		SHELL = /bin/sh

		# ---------------------------------------------------------------------
		# compiler/linker settings
		# specify flags and libraries needed for your compiler

		CC = mpicxx
		CCFLAGS = -O3 -funroll-loops -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
		DEPFLAGS = -M
		LINK = mpicxx
		LINKFLAGS = -O3 -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
		LIB = -lstdc++
		ARCHIVE = ar
		ARFLAGS = -rcsv
		SIZE = size

		# ---------------------------------------------------------------------
		# LAMMPS-specific settings, all OPTIONAL
		# specify settings for LAMMPS features you will use
		# if you change any -D setting, do full re-compile after "make clean"

		# LAMMPS ifdef settings
		# see possible settings in Section 2.2 (step 4) of manual

		LMP_INC = -DLAMMPS_GZIP

		# MPI library
		# see discussion in Section 2.2 (step 5) of manual
		# MPI wrapper compiler/linker can provide this info
		# can point to dummy MPI library in src/STUBS as in Makefile.serial
		# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
		# INC = path for mpi.h, MPI compiler settings
		# PATH = path for MPI library
		# LIB = name of MPI library

		MPI_INC =
		MPI_PATH =
		MPI_LIB =

		# FFT library
		# see discussion in Section 2.2 (step 6) of manaul
		# can be left blank to use provided KISS FFT library
		# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
		# PATH = path for FFT library
		# LIB = name of FFT library

		FFT_INC = -DFFT_FFTW2 -armpl
		FFT_PATH =
		FFT_LIB =

		# JPEG and/or PNG library
		# see discussion in Section 2.2 (step 7) of manual
		# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
		# INC = path(s) for jpeglib.h and/or png.h
		# PATH = path(s) for JPEG library and/or PNG library
		# LIB = name(s) of JPEG library and/or PNG library

		JPG_INC =
		JPG_PATH =
		JPG_LIB =

		# ---------------------------------------------------------------------
		# build rules and dependencies
		# do not edit this section

		include Makefile.package.settings
		include Makefile.package

		EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
		EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
		EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
		EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
		EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

		# Path to src files

		vpath %.cpp ..
		vpath %.h ..

		# Link target

		$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS)
		$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
		$(SIZE) $(EXE)

		# Library targets

		lib: $(OBJ) $(EXTRA_LINK_DEPENDS)
		$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)

		shlib: $(OBJ) $(EXTRA_LINK_DEPENDS)
		$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
		$(OBJ) $(EXTRA_LIB) $(LIB)

		# Compilation rules

		%.o:%.cpp $(EXTRA_CPP_DEPENDS)
		$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<

		%.d:%.cpp $(EXTRA_CPP_DEPENDS)
		$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@

		%.o:%.cu $(EXTRA_CPP_DEPENDS)
		$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<

		# Individual dependencies

		depend : fastdep.exe $(SRC)
		@./fastdep.exe $(EXTRA_INC) -- $^ > .depend \|\| exit 1

		fastdep.exe: ../DEPEND/fastdep.c
		cc -O -o $@ $<

		sinclude .depend

src/MAKE/MACHINES/Makefile.astra_gcc

0 → 100644

+119 −0

Original line number	Diff line number	Diff line
		# astra-gcc - ThunderX2 GCC/OpenMPI Based, FFTW

		# need to load the following modules:
		# 1) arm-based developer pack

		SHELL = /bin/sh

		# ---------------------------------------------------------------------
		# compiler/linker settings
		# specify flags and libraries needed for your compiler

		CC = mpicxx
		CCFLAGS = -O3 -funroll-loops -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
		DEPFLAGS = -M
		LINK = mpicxx
		LINKFLAGS = -O3 -fopenmp -mcpu=thunderx2t99 -mtune=thunderx2t99
		LIB = -lstdc++
		ARCHIVE = ar
		ARFLAGS = -rcsv
		SIZE = size

		# ---------------------------------------------------------------------
		# LAMMPS-specific settings, all OPTIONAL
		# specify settings for LAMMPS features you will use
		# if you change any -D setting, do full re-compile after "make clean"

		# LAMMPS ifdef settings
		# see possible settings in Section 2.2 (step 4) of manual

		LMP_INC = -DLAMMPS_GZIP

		# MPI library
		# see discussion in Section 2.2 (step 5) of manual
		# MPI wrapper compiler/linker can provide this info
		# can point to dummy MPI library in src/STUBS as in Makefile.serial
		# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
		# INC = path for mpi.h, MPI compiler settings
		# PATH = path for MPI library
		# LIB = name of MPI library

		MPI_INC =
		MPI_PATH =
		MPI_LIB =

		# FFT library
		# see discussion in Section 2.2 (step 6) of manaul
		# can be left blank to use provided KISS FFT library
		# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
		# PATH = path for FFT library
		# LIB = name of FFT library

		FFT_INC = -DFFT_FFTW2 -I${FFTW_INC}
		FFT_PATH = -I${FFTW_INC}
		FFT_LIB = -L${FFTW_LIB} -lfftw3

		# JPEG and/or PNG library
		# see discussion in Section 2.2 (step 7) of manual
		# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
		# INC = path(s) for jpeglib.h and/or png.h
		# PATH = path(s) for JPEG library and/or PNG library
		# LIB = name(s) of JPEG library and/or PNG library

		JPG_INC =
		JPG_PATH =
		JPG_LIB =

		# ---------------------------------------------------------------------
		# build rules and dependencies
		# do not edit this section

		include Makefile.package.settings
		include Makefile.package

		EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
		EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
		EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
		EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
		EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)

		# Path to src files

		vpath %.cpp ..
		vpath %.h ..

		# Link target

		$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS)
		$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
		$(SIZE) $(EXE)

		# Library targets

		lib: $(OBJ) $(EXTRA_LINK_DEPENDS)
		$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)

		shlib: $(OBJ) $(EXTRA_LINK_DEPENDS)
		$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
		$(OBJ) $(EXTRA_LIB) $(LIB)

		# Compilation rules

		%.o:%.cpp $(EXTRA_CPP_DEPENDS)
		$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<

		%.d:%.cpp $(EXTRA_CPP_DEPENDS)
		$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@

		%.o:%.cu $(EXTRA_CPP_DEPENDS)
		$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<

		# Individual dependencies

		depend : fastdep.exe $(SRC)
		@./fastdep.exe $(EXTRA_INC) -- $^ > .depend \|\| exit 1

		fastdep.exe: ../DEPEND/fastdep.c
		cc -O -o $@ $<

		sinclude .depend

src/MAKE/MACHINES/Makefile.theta

+15 −25

Original line number	Diff line number	Diff line
		# knl = Flags for Knights Landing Xeon Phi Processor,Intel Compiler/MPI,MKL FFT
		# module load perftools-base perftools
		# theta = Flags for Knights Landing Xeon Phi Processor, Intel Compiler, Cray MPI, MKL FFT
		# make theta -j 8
		# pat_build -g mpi -u ./lmp_theta

		SHELL = /bin/sh

		@@ -10,24 +8,16 @@ SHELL = /bin/sh
		# specify flags and libraries needed for your compiler

		CC = CC -mkl
		#OPTFLAGS = -O0
		OPTFLAGS = -xMIC-AVX512 -O3 -fp-model fast=2 -no-prec-div -qoverride-limits
		CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -qno-offload \
		-fno-alias -ansi-alias -restrict $(OPTFLAGS)
		#CCFLAGS += -DLMP_INTEL_NO_TBB
		#CCFLAGS += -DLAMMPS_BIGBIG
		#CCFLAGS += -D_USE_PAPI
		#CCFLAGS += -D_USE_CRAYPAT_API
		CCFLAGS += -std=c++11
		SHFLAGS = -fPIC
		DEPFLAGS = -M

		LINK = $(CC)
		LINKFLAGS = -g -qopenmp $(OPTFLAGS)
		LINKFLAGS += -dynamic
		LIB =
		#LIB += -L${TBBROOT}/lib/intel64/gcc4.7 -ltbbmalloc
		LIB += -ltbbmalloc
		#LIB += /soft/debuggers/forge-7.0-2017-02-16/lib/64/libdmallocthcxx.a -zmuldefs
		LINKFLAGS = -g -qopenmp $(OPTFLAGS) -dynamic
		LIB = -ltbbmalloc
		SIZE = size

		ARCHIVE = ar

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