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lammps
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Merge branch 'master' into restrain_lbound

This commit is contained in:
Axel Kohlmeyer 2020-04-15 14:24:47 -04:00
parent 0796a7032e 80311891f1
commit 01f97f1936
No known key found for this signature in database
GPG Key ID: D9B44E93BF0C375A
2974 changed files with 166511 additions and 137505 deletions
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1
.gitignore vendored
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@ -9,6 +9,7 @@
*.d
*.x
*.exe
*.sif
*.dll
*.pyc
__pycache__

495
cmake/CMakeLists.txt
View File

@ -21,17 +21,12 @@ 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)
file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
include(LAMMPSUtils)
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h PROJECT_VERSION)
include(PreventInSourceBuilds)
@ -69,9 +64,10 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
set(CMAKE_TUNE_DEFAULT "-ffast-math -march=native")
endif()
# we require C++11
# we require C++11 without extensions
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
# GNU compiler specific features for testing
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
@ -85,43 +81,33 @@ endif()
########################################################################
# User input options #
########################################################################
option(BUILD_EXE "Build lmp binary" ON)
if(BUILD_EXE)
set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
mark_as_advanced(LAMMPS_MACHINE)
if(LAMMPS_MACHINE)
set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
endif()
set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
mark_as_advanced(LAMMPS_MACHINE)
if(LAMMPS_MACHINE)
set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
endif()
set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
option(BUILD_LIB "Build LAMMPS library" OFF)
if(BUILD_LIB)
option(BUILD_SHARED_LIBS "Build shared library" OFF)
if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
set(LAMMPS_LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file")
mark_as_advanced(LAMMPS_LIB_SUFFIX)
if(LAMMPS_LIB_SUFFIX)
set(LAMMPS_LIB_SUFFIX "_${LAMMPS_LIB_SUFFIX}")
endif()
option(BUILD_SHARED_LIBS "Build shared library" OFF)
if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
if(NOT BUILD_EXE AND NOT BUILD_LIB)
message(FATAL_ERROR "You need to at least enable one of two following options: BUILD_LIB or BUILD_EXE")
endif()
include(GNUInstallDirs)
file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
add_library(lammps ${ALL_SOURCES})
add_executable(lmp ${MAIN_SOURCES})
target_link_libraries(lmp PRIVATE lammps)
set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
include(GNUInstallDirs)
set(LAMMPS_LINK_LIBS)
set(LAMMPS_DEPS)
set(LAMMPS_API_DEFINES)
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MOLECULE PERI POEMS QEQ
REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS
@ -130,33 +116,15 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU)
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
######################################################
# download and unpack support binaries for compilation
# of windows binaries.
######################################################
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
endif()
set(OpenCL_INCLUDE_DIR "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
endif()
######################################################
######################################################
# packages with special compiler needs or external libs
######################################################
include_directories(${LAMMPS_SOURCE_DIR})
target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}>)
if(PKG_USER-ADIOS)
# The search for ADIOS2 must come before MPI because
@ -164,35 +132,50 @@ if(PKG_USER-ADIOS)
# script that defines the MPI::MPI_C target
enable_language(C)
find_package(ADIOS2 REQUIRED)
list(APPEND LAMMPS_LINK_LIBS adios2::adios2)
target_link_libraries(lammps PRIVATE adios2::adios2)
endif()
# do MPI detection after language activation,
# in case MPI for these languages is required
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
if (CMAKE_SYSTEM_NAME STREQUAL Windows)
option(BUILD_MPI "Build MPI version" OFF)
else()
# do MPI detection after language activation,
# in case MPI for these languages is required
set(MPI_CXX_SKIP_MPICXX TRUE)
find_package(MPI QUIET)
option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
endif()
if(BUILD_MPI)
# We use a non-standard procedure to compile with MPI on windows
if (CMAKE_SYSTEM_NAME STREQUAL Windows)
include(MPI4WIN)
target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
else()
set(MPI_CXX_SKIP_MPICXX ON)
find_package(MPI REQUIRED)
include_directories(${MPI_CXX_INCLUDE_PATH})
add_definitions(-DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1)
list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG)
add_definitions(-DLAMMPS_LONGLONG_TO_LONG)
target_compile_definitions(lammps PRIVATE -DLAMMPS_LONGLONG_TO_LONG)
endif()
endif()
else()
enable_language(C)
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
add_library(mpi_stubs STATIC ${MPI_SOURCES})
include_directories(${LAMMPS_SOURCE_DIR}/STUBS)
list(APPEND LAMMPS_LINK_LIBS mpi_stubs)
if(NOT BUILD_SHARED_LIBS)
install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS> $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi>)
install(FILES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi)
if(BUILD_SHARED_LIBS)
target_link_libraries(lammps PRIVATE mpi_stubs)
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS> $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps/mpi>)
else()
target_link_libraries(lammps PUBLIC mpi_stubs)
endif()
add_library(MPI::MPI_CXX ALIAS mpi_stubs)
endif()
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
@ -200,8 +183,7 @@ set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
add_definitions(-DLAMMPS_${LAMMPS_SIZES})
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_${LAMMPS_SIZES}")
target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES})
# posix_memalign is not available on Windows
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
@ -210,13 +192,12 @@ else()
set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")
endif()
if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
endif()
option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
if(LAMMPS_EXCEPTIONS)
add_definitions(-DLAMMPS_EXCEPTIONS)
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS")
target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
endif()
# "hard" dependencies between packages resulting
@ -227,27 +208,36 @@ pkg_depends(USER-LB MPI)
pkg_depends(USER-PHONON KSPACE)
pkg_depends(USER-SCAFACOS MPI)
# detect if we may enable OpenMP support by default
set(BUILD_OMP_DEFAULT OFF)
find_package(OpenMP QUIET)
# TODO: this is a temporary workaround until a better solution is found. AK 2019-05-30
# GNU GCC 9.x uses settings incompatible with our use of 'default(none)' in OpenMP pragmas
# where we assume older GCC semantics. For the time being, we disable OpenMP by default
# for GCC 9.x and beyond. People may manually turn it on, but need to run the script
# src/USER-OMP/hack_openmp_for_pgi_gcc9.sh on all sources to make it compatible with gcc 9.
if ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.99.9))
option(BUILD_OMP "Build with OpenMP support" OFF)
else()
option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
if(OpenMP_FOUND)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
if(HAVE_OMP_H_INCLUDE)
set(BUILD_OMP_DEFAULT ON)
endif()
endif()
option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
if(BUILD_OMP)
find_package(OpenMP REQUIRED)
check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
if(NOT HAVE_OMP_H_INCLUDE)
message(FATAL_ERROR "Cannot find required 'omp.h' header file")
message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
endif()
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.99.9)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 9.99.9)) OR
((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 18.99.9))
)
# GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
# Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=4)
else()
target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=3)
endif()
target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
endif()
if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
@ -262,6 +252,10 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
add_library(linalg STATIC ${LAPACK_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS linalg EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
else()
@ -274,9 +268,13 @@ find_package(JPEG QUIET)
option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
if(WITH_JPEG)
find_package(JPEG REQUIRED)
add_definitions(-DLAMMPS_JPEG)
include_directories(${JPEG_INCLUDE_DIR})
list(APPEND LAMMPS_LINK_LIBS ${JPEG_LIBRARIES})
target_compile_definitions(lammps PRIVATE -DLAMMPS_JPEG)
if(CMAKE_VERSION VERSION_LESS 3.12)
target_include_directories(lammps PRIVATE ${JPEG_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE ${JPEG_LIBRARIES})
else()
target_link_libraries(lammps PRIVATE JPEG::JPEG)
endif()
endif()
find_package(PNG QUIET)
@ -289,9 +287,8 @@ endif()
if(WITH_PNG)
find_package(PNG REQUIRED)
find_package(ZLIB REQUIRED)
include_directories(${PNG_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${PNG_LIBRARIES} ${ZLIB_LIBRARIES})
add_definitions(-DLAMMPS_PNG)
target_link_libraries(lammps PRIVATE PNG::PNG ZLIB::ZLIB)
target_compile_definitions(lammps PRIVATE -DLAMMPS_PNG)
endif()
find_program(GZIP_EXECUTABLE gzip)
@ -301,7 +298,7 @@ if(WITH_GZIP)
if(NOT GZIP_FOUND)
message(FATAL_ERROR "gzip executable not found")
endif()
add_definitions(-DLAMMPS_GZIP)
target_compile_definitions(lammps PRIVATE -DLAMMPS_GZIP)
endif()
find_program(FFMPEG_EXECUTABLE ffmpeg)
@ -311,7 +308,7 @@ if(WITH_FFMPEG)
if(NOT FFMPEG_FOUND)
message(FATAL_ERROR "ffmpeg executable not found")
endif()
add_definitions(-DLAMMPS_FFMPEG)
target_compile_definitions(lammps PRIVATE -DLAMMPS_FFMPEG)
endif()
if(BUILD_SHARED_LIBS)
@ -324,29 +321,24 @@ else()
set(CUDA_REQUEST_PIC)
endif()
include(Packages/KSPACE)
include(Packages/PYTHON)
include(Packages/VORONOI)
include(Packages/USER-COLVARS)
include(Packages/USER-MOLFILE)
include(Packages/USER-NETCDF)
include(Packages/USER-PLUMED)
include(Packages/USER-QMMM)
include(Packages/USER-QUIP)
include(Packages/USER-SCAFACOS)
include(Packages/USER-SMD)
include(Packages/USER-VTK)
include(Packages/KIM)
include(Packages/LATTE)
include(Packages/MESSAGE)
include(Packages/MSCG)
include(Packages/COMPRESS)
foreach(PKG_WITH_INCL KSPACE PYTHON VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
endforeach()
set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific optimization or instrumentation")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_TUNE_FLAGS}")
if(CMAKE_Fortran_COMPILER)
set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${CMAKE_TUNE_FLAGS}")
endif()
separate_arguments(CMAKE_TUNE_FLAGS)
include(CheckCXXCompilerFlag)
foreach(_FLAG ${CMAKE_TUNE_FLAGS})
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
if(COMPILER_SUPPORTS${_FLAG})
target_compile_options(lammps PRIVATE ${_FLAG})
else()
message(WARNING "${_FLAG} found in CMAKE_TUNE_FLAGS, but not supported by the compiler, skipping")
endif()
endforeach()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
@ -359,15 +351,7 @@ endforeach(HEADER)
set(MATH_LIBRARIES "m" CACHE STRING "math library")
mark_as_advanced( MATH_LIBRARIES )
include(CheckLibraryExists)
# RB: disabled this check because it breaks with KOKKOS CUDA enabled
#foreach(FUNC sin cos)
# check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
# if(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
# message(FATAL_ERROR "Could not find needed math function - ${FUNC}")
# endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
#endforeach(FUNC)
list(APPEND LAMMPS_LINK_LIBS ${MATH_LIBRARIES})
target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
######################################
# Generate Basic Style files
@ -378,7 +362,7 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
##############################################
# add sources of enabled packages
############################################
foreach(PKG ${DEFAULT_PACKAGES})
foreach(PKG ${STANDARD_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
@ -391,8 +375,8 @@ foreach(PKG ${DEFAULT_PACKAGES})
# detects styles in package and adds them to global list
RegisterStyles(${${PKG}_SOURCES_DIR})
list(APPEND LIB_SOURCES ${${PKG}_SOURCES})
include_directories(${${PKG}_SOURCES_DIR})
target_sources(lammps PRIVATE ${${PKG}_SOURCES})
target_include_directories(lammps PRIVATE ${${PKG}_SOURCES_DIR})
endif()
RegisterPackages(${${PKG}_SOURCES_DIR})
@ -401,12 +385,12 @@ endforeach()
# packages that need defines set
foreach(PKG MPIIO)
if(PKG_${PKG})
add_definitions(-DLMP_${PKG})
target_compile_definitions(lammps PRIVATE -DLMP_${PKG})
endif()
endforeach()
# dedicated check for entire contents of accelerator packages
foreach(PKG ${ACCEL_PACKAGES})
foreach(PKG ${SUFFIX_PACKAGES})
set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
@ -426,14 +410,14 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.F
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
if(LAMMPS_USE_MPI4WIN)
add_dependencies(${PKG_LIB} mpi4win_build)
if(NOT BUILD_SHARED_LIBS)
install(TARGETS ${PKG_LIB} EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
target_link_libraries(lammps PRIVATE ${PKG_LIB})
if(PKG_LIB STREQUAL awpmd)
target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
elseif(PKG_LIB STREQUAL h5md)
@ -445,30 +429,31 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD)
endforeach()
if(PKG_USER-AWPMD)
target_link_libraries(awpmd ${LAPACK_LIBRARIES})
target_link_libraries(awpmd PRIVATE ${LAPACK_LIBRARIES})
endif()
if(PKG_USER-ATC)
if(LAMMPS_SIZES STREQUAL BIGBIG)
message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
endif()
target_link_libraries(atc ${LAPACK_LIBRARIES})
target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES} MPI::MPI_CXX)
target_include_directories(atc PRIVATE ${LAMMPS_SOURCE_DIR})
target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
endif()
include(Packages/USER-H5MD)
if(PKG_USER-H5MD)
include(Packages/USER-H5MD)
endif()
######################################################################
# packages which selectively include variants based on enabled styles
# e.g. accelerator packages
######################################################################
include(Packages/CORESHELL)
include(Packages/QEQ)
include(Packages/USER-OMP)
include(Packages/USER-SDPD)
include(Packages/KOKKOS)
include(Packages/OPT)
include(Packages/USER-INTEL)
include(Packages/GPU)
foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU)
if(PKG_${PKG_WITH_INCL})
include(Packages/${PKG_WITH_INCL})
endif()
endforeach()
######################################################################
# the windows version of LAMMPS requires a couple extra libraries
@ -476,10 +461,7 @@ include(Packages/GPU)
# and after everything else that is compiled locally
######################################################################
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
if(LAMMPS_USE_MPI4WIN)
list(APPEND LAMMPS_LINK_LIBS ${MPI4WIN_LIBRARIES})
endif()
list(APPEND LAMMPS_LINK_LIBS -lwsock32 -lpsapi)
target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi)
endif()
######################################################
@ -492,14 +474,14 @@ set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR})
GeneratePackagesHeaders(${LAMMPS_STYLE_HEADERS_DIR})
include_directories(${LAMMPS_STYLE_HEADERS_DIR})
target_include_directories(lammps PRIVATE ${LAMMPS_STYLE_HEADERS_DIR})
######################################
# Generate lmpinstalledpkgs.h
######################################
set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")
set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] = {\n")
set(temp_PKG_LIST ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
set(temp_PKG_LIST ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
list(SORT temp_PKG_LIST)
foreach(PKG ${temp_PKG_LIST})
if(PKG_${PKG})
@ -521,7 +503,7 @@ add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
-DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
-P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/generate_lmpgitversion.cmake)
set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${LAMMPS_STYLE_HEADERS_DIR}/gitversion.h)
list(APPEND LAMMPS_DEPS gitversion)
add_dependencies(lammps gitversion)
###########################################
# Actually add executable and lib to build
@ -529,85 +511,54 @@ list(APPEND LAMMPS_DEPS gitversion)
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
list (FIND LANGUAGES "Fortran" _index)
if (${_index} GREATER -1)
list(APPEND LAMMPS_LINK_LIBS ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif()
list(REMOVE_DUPLICATES LAMMPS_LINK_LIBS)
if(BUILD_LIB)
add_library(lammps ${LIB_SOURCES})
target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
if(LAMMPS_DEPS)
add_dependencies(lammps ${LAMMPS_DEPS})
endif()
set(LAMMPS_CXX_HEADERS
${LAMMPS_SOURCE_DIR}/angle.h
${LAMMPS_SOURCE_DIR}/atom.h
${LAMMPS_SOURCE_DIR}/bond.h
${LAMMPS_SOURCE_DIR}/citeme.h
${LAMMPS_SOURCE_DIR}/comm.h
${LAMMPS_SOURCE_DIR}/compute.h
${LAMMPS_SOURCE_DIR}/dihedral.h
${LAMMPS_SOURCE_DIR}/domain.h
${LAMMPS_SOURCE_DIR}/error.h
${LAMMPS_SOURCE_DIR}/fix.h
${LAMMPS_SOURCE_DIR}/force.h
${LAMMPS_SOURCE_DIR}/group.h
${LAMMPS_SOURCE_DIR}/improper.h
${LAMMPS_SOURCE_DIR}/input.h
${LAMMPS_SOURCE_DIR}/kspace.h
${LAMMPS_SOURCE_DIR}/lammps.h
${LAMMPS_SOURCE_DIR}/lattice.h
${LAMMPS_SOURCE_DIR}/lmppython.h
${LAMMPS_SOURCE_DIR}/memory.h
${LAMMPS_SOURCE_DIR}/modify.h
${LAMMPS_SOURCE_DIR}/neighbor.h
${LAMMPS_SOURCE_DIR}/neigh_list.h
${LAMMPS_SOURCE_DIR}/output.h
${LAMMPS_SOURCE_DIR}/pair.h
${LAMMPS_SOURCE_DIR}/pointers.h
${LAMMPS_SOURCE_DIR}/region.h
${LAMMPS_SOURCE_DIR}/timer.h
${LAMMPS_SOURCE_DIR}/universe.h
${LAMMPS_SOURCE_DIR}/update.h
${LAMMPS_SOURCE_DIR}/variable.h)
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
install(FILES ${LAMMPS_CXX_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Modules)
else()
list(APPEND LMP_SOURCES ${LIB_SOURCES})
set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
input.h info.h kspace.h lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h
pair.h pointers.h region.h timer.h universe.h update.h variable.h)
if(LAMMPS_EXCEPTIONS)
list(APPEND LAMMPS_CXX_HEADERS exceptions.h)
endif()
if(BUILD_EXE)
add_executable(lmp ${LMP_SOURCES})
if(BUILD_LIB)
target_link_libraries(lmp lammps)
else()
target_link_libraries(lmp ${LAMMPS_LINK_LIBS})
if(LAMMPS_DEPS)
add_dependencies(lmp ${LAMMPS_DEPS})
endif()
endif()
set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
endif()
set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
foreach(_HEADER ${LAMMPS_CXX_HEADERS})
add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
add_dependencies(lammps ${_HEADER})
install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
endforeach()
target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
add_library(LAMMPS::lammps ALIAS lammps)
get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS)
set(LAMMPS_API_DEFINES)
foreach(_DEF ${LAMMPS_DEFINES})
set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
endforeach()
configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
file(GLOB MODULE_FILES ${CMAKE_CURRENT_SOURCE_DIR}/Modules/Find*.cmake)
install(FILES ${MODULE_FILES} DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
include(CMakePackageConfigHelpers)
configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
if(BUILD_TOOLS)
add_executable(binary2txt ${LAMMPS_TOOLS_DIR}/binary2txt.cpp)
target_compile_definitions(binary2txt PRIVATE -DLAMMPS_${LAMMPS_SIZES})
install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
include(CheckGeneratorSupport)
if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
enable_language(Fortran)
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
else()
message(WARNING "CMake build doesn't support fortran, skipping building 'chain.x'")
@ -617,7 +568,7 @@ if(BUILD_TOOLS)
get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
add_executable(msi2lmp ${MSI2LMP_SOURCES})
target_link_libraries(msi2lmp m)
target_link_libraries(msi2lmp PRIVATE ${MATH_LIBRARIES})
install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
endif()
@ -647,12 +598,19 @@ install(
# conventional build. Only available, if a shared library is built.
# This is primarily for people that only want to use the Python wrapper.
###############################################################################
if(BUILD_LIB AND BUILD_SHARED_LIBS)
find_package(PythonInterp)
if (PYTHONINTERP_FOUND)
if(BUILD_SHARED_LIBS)
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
find_package(Python COMPONENTS Interpreter)
endif()
if (Python_EXECUTABLE)
add_custom_target(
install-python
${PYTHON_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
-m ${LAMMPS_PYTHON_DIR}/lammps.py
-l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR}
@ -673,10 +631,17 @@ endif()
# LAMMPS for package managers and with different prefix settings.
# This requires either a shared library or that the PYTHON package is included.
###############################################################################
if((BUILD_LIB AND BUILD_SHARED_LIBS) OR (PKG_PYTHON))
find_package(PythonInterp)
if (PYTHONINTERP_FOUND)
execute_process(COMMAND ${PYTHON_EXECUTABLE}
if(BUILD_SHARED_LIBS OR PKG_PYTHON)
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
find_package(Python COMPONENTS Interpreter)
endif()
if (Python_EXECUTABLE)
execute_process(COMMAND ${Python_EXECUTABLE}
-c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")
@ -690,67 +655,83 @@ include(CodeCoverage)
###############################################################################
# Print package summary
###############################################################################
foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
if(PKG_${PKG})
message(STATUS "Building package: ${PKG}")
endif()
endforeach()
get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
include(FeatureSummary)
feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
message(STATUS "<<< Build configuration >>>
Build type ${CMAKE_BUILD_TYPE}
Install path ${CMAKE_INSTALL_PREFIX}
Generator ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}
Compilers and Flags:
C++ Compiler ${CMAKE_CXX_COMPILER}
Type ${CMAKE_CXX_COMPILER_ID}
Version ${CMAKE_CXX_COMPILER_VERSION}
C++ Flags ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
Defines ${CPPFLAGS}")
Build type: ${CMAKE_BUILD_TYPE}
Install path: ${CMAKE_INSTALL_PREFIX}
Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}
-- <<< Compilers and Flags: >>>
-- C++ Compiler: ${CMAKE_CXX_COMPILER}
Type: ${CMAKE_CXX_COMPILER_ID}
Version: ${CMAKE_CXX_COMPILER_VERSION}
C++ Flags: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
Defines: ${DEFINES}")
get_target_property(OPTIONS lammps COMPILE_OPTIONS)
if(OPTIONS)
message(" Options: ${OPTIONS}")
endif()
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
list (FIND LANGUAGES "Fortran" _index)
if (${_index} GREATER -1)
message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER}
Type ${CMAKE_Fortran_COMPILER_ID}
Version ${CMAKE_Fortran_COMPILER_VERSION}
Fortran Flags ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}
Type: ${CMAKE_Fortran_COMPILER_ID}
Version: ${CMAKE_Fortran_COMPILER_VERSION}
Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
endif()
list (FIND LANGUAGES "C" _index)
if (${_index} GREATER -1)
message(STATUS "C compiler ${CMAKE_C_COMPILER}
Type ${CMAKE_C_COMPILER_ID}
Version ${CMAKE_C_COMPILER_VERSION}
C Flags ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
message(STATUS "C compiler: ${CMAKE_C_COMPILER}
Type: ${CMAKE_C_COMPILER_ID}
Version: ${CMAKE_C_COMPILER_VERSION}
C Flags: ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
endif()
message(STATUS "<<< Linker flags: >>>")
message(STATUS "Executable name: ${LAMMPS_BINARY}")
if(CMAKE_EXE_LINKER_FLAGS)
message(STATUS "Linker flags:
Executable ${CMAKE_EXE_LINKER_FLAGS}")
message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")
endif()
if(BUILD_SHARED_LIBS)
message(STATUS "Shared library flags: ${CMAKE_SHARED_LINKER_FLAGS}")
message(STATUS "Shared library flags: ${CMAKE_SHARED_LINKER_FLAGS}")
else()
message(STATUS "Static library flags: ${CMAKE_STATIC_LINKER_FLAGS}")
message(STATUS "Static library flags: ${CMAKE_STATIC_LINKER_FLAGS}")
endif()
message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
if(BUILD_MPI)
message(STATUS "Using MPI with headers in ${MPI_CXX_INCLUDE_PATH} and these libraries: ${MPI_CXX_LIBRARIES};${MPI_Fortran_LIBRARIES}")
message(STATUS "<<< MPI flags >>>
-- MPI includes: ${MPI_CXX_INCLUDE_PATH}
-- MPI libraries: ${MPI_CXX_LIBRARIES};${MPI_Fortran_LIBRARIES}")
endif()
if(PKG_GPU)
message(STATUS "GPU API: ${GPU_API}")
message(STATUS "<<< GPU package settings >>>
-- GPU API: ${GPU_API}")
if(GPU_API STREQUAL "CUDA")
message(STATUS "GPU architecture: ${GPU_ARCH}")
elseif(GPU_API STREQUAL "OPENCL")
message(STATUS "OpenCL parameter tuning: ${OCL_TUNE}")
message(STATUS "OpenCL tuning: ${OCL_TUNE}")
elseif(GPU_API STREQUAL "HIP")
message(STATUS "HIP platform: ${HIP_PLATFORM}")
message(STATUS "HIP architecture: ${HIP_ARCH}")
if(HIP_USE_DEVICE_SORT)
message(STATUS "HIP GPU sorting: on")
else()
message(STATUS "HIP GPU sorting: off")
endif()
endif()
message(STATUS "GPU precision: ${GPU_PREC}")
message(STATUS "GPU precision: ${GPU_PREC}")
endif()
if(PKG_KOKKOS)
message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
endif()
if(PKG_KSPACE)
message(STATUS "Using ${FFT} as primary FFT library")
message(STATUS "<<< FFT settings >>>
-- Primary FFT lib: ${FFT}")
if(FFT_SINGLE)
message(STATUS "Using single precision FFTs")
else()
@ -762,7 +743,7 @@ if(PKG_KSPACE)
message(STATUS "Using non-threaded FFTs")
endif()
if(PKG_KOKKOS)
if(KOKKOS_ENABLE_CUDA)
if(Kokkos_ENABLE_CUDA)
if (${FFT} STREQUAL "KISS")
message(STATUS "Kokkos FFT: KISS")
else()

48
cmake/FindLAMMPS.cmake.in
View File

@ -1,48 +0,0 @@
# - Find liblammps
# Find the native liblammps headers and libraries.
#
# The following variables will set:
# LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc.
# LAMMPS_LIBRARIES - List of libraries when using lammps.
# LAMMPS_API_DEFINES - lammps library api defines
# LAMMPS_VERSION - lammps library version
# LAMMPS_FOUND - True if liblammps found.
#
# In addition a LAMMPS::LAMMPS imported target is getting created.
#
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# the GNU General Public License.
#
# See the README file in the top-level LAMMPS directory.
#
find_package(PkgConfig)
pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)
find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)
set(LAMMPS_VERSION @LAMMPS_VERSION@)
set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@)
find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}")
set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}")
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION)
mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY)
if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS)
add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED)
set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}")
endif()

87
cmake/LAMMPSConfig.cmake.in Normal file
View File

@ -0,0 +1,87 @@
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
include(CMakeFindDependencyMacro)
if(@BUILD_MPI@)
find_dependency(MPI REQUIRED CXX)
endif()
if(@PKG_KSPACE@)
if(@FFT@ STREQUAL "FFTW3")
find_dependency(@FFTW@ REQUIRED MODULE)
endif()
endif()
if(NOT @BUILD_SHARED_LIBS@)
if(@BUILD_OMP@)
find_dependency(OpenMP REQUIRED)
endif()
if(@WITH_JPEG@)
find_dependency(JPEG REQUIRED)
endif()
if(@WITH_PNG@)
find_dependency(PNG REQUIRED)
find_dependency(ZLIB REQUIRED)
endif()
if(@PKG_KIM@)
find_dependency(PkgConfig REQUIRED)
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=@KIM-API_MIN_VERSION@)
if(@CURL_FOUND@)
find_dependency(CURL REQUIRED)
endif()
endif()
if(@PKG_USER-SMD@)
find_dependency(Eigen3 NO_MODULE REQUIRED)
endif()
if(@PKG_USER-SCAFACOS@)
find_dependency(PkgConfig REQUIRED)
find_ependency(GSL REQUIRED)
find_dependency(MPI REQUIRED C Fortran)
pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)
endif()
if(@PKG_PYTHON@ AND NOT CMAKE_VERSION VERSION_LESS 3.12)
find_package(Python REQUIRED COMPONENTS Development)
endif()
if(@PKG_COMPRESS@)
find_dependency(ZLIB REQUIRED)
endif()
if(@PKG_KOKKOS@)
if(@EXTERNAL_KOKKOS@)
find_dependency(Kokkos 3 REQUIRED)
endif()
endif()
if(@PKG_VORONOI@)
find_dependency(VORO REQUIRED)
endif()
if(@PKG_USER-INTEL@)
if(@INTEL_LRT_MODE@ STREQUAL "THREADS")
find_dependency(Threads REQUIRED)
endif()
if(@TBB_MALLOC_FOUND@)
find_ependency(TBB_MALLOC REQUIRED)
endif()
endif()
if(@PKG_USER-ADIOS@)
find_ependency(ADIOS2 REQUIRED)
endif()
if(@PKG_LATTE@)
find_ependency(LATTE REQUIRED)
endif()
if(@PKG_MESSAGE@)
if(@MESSAGE_ZMQ@)
find_ependency(ZMQ REQUIRED)
endif()
endif()
if(@PKG_MSCG@)
find_ependency(GSL REQUIRED)
find_ependency(MSCG REQUIRED)
endif()
if(@USER-NETCDF@)
if(@NETCDF_FOUND@)
find_ependency(NetCDF REQUIRED)
endif()
if(@PNETCDF_FOUND@)
find_ependency(PNetCDF REQUIRED)
endif()
endif()
if(@PKG_QUIP@)
find_ependency(QUIP REQUIRED)
endif()
endif()
include("${CMAKE_CURRENT_LIST_DIR}/LAMMPS_Targets.cmake")

42
cmake/Modules/Documentation.cmake
View File

@ -1,10 +1,8 @@
###############################################################################
# Build documentation
###############################################################################
option(BUILD_DOC "Build LAMMPS documentation" OFF)
option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
if(BUILD_DOC)
include(ProcessorCount)
ProcessorCount(NPROCS)
find_package(PythonInterp 3 REQUIRED)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
@ -26,15 +24,49 @@ if(BUILD_DOC)
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
)
# download mathjax distribution and unpack to folder "mathjax"
file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
"${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
if(NOT EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${CMAKE_CURRENT_BINARY_DIR}/mathjax)
endif()
file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax)
file(COPY ${CMAKE_CURRENT_BINARY_DIR}/mathjax/es5 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/html/_static/mathjax/)
# note, this may run in parallel with other tasks, so we must not use multiple processes here
add_custom_command(
OUTPUT html
DEPENDS ${DOC_SOURCES} docenv requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
)
# copy selected image files to html output tree
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/html/JPG)
set(HTML_EXTRA_IMAGES balance_nonuniform.jpg balance_rcb.jpg
balance_uniform.jpg bow_tutorial_01.png bow_tutorial_02.png
bow_tutorial_03.png bow_tutorial_04.png bow_tutorial_05.png
dump1.jpg dump2.jpg examples_mdpd.gif gran_funnel.png gran_mixer.png
hop1.jpg hop2.jpg saed_ewald_intersect.jpg saed_mesh.jpg
screenshot_atomeye.jpg screenshot_gl.jpg screenshot_pymol.jpg
screenshot_vmd.jpg sinusoid.jpg xrd_mesh.jpg)
set(HTML_IMAGE_TARGETS "")
foreach(_IMG ${HTML_EXTRA_IMAGES})
string(PREPEND _IMG JPG/)
list(APPEND HTML_IMAGE_TARGETS "html/${_IMG}")
add_custom_command(
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/html/${_IMG}
DEPENDS ${LAMMPS_DOC_DIR}/src/${_IMG} html/JPG
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/src/${_IMG} ${CMAKE_BINARY_DIR}/html/${_IMG}
)
endforeach()
add_custom_target(
doc ALL
DEPENDS html
DEPENDS html html/_static/mathjax/es5 ${HTML_IMAGE_TARGETS}
SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
)

16
cmake/Modules/FindCUB.cmake Normal file
View File

@ -0,0 +1,16 @@
# - Find CUB
# Find the CUB header library
#
# CUB_INCLUDE_DIRS - where to find cub/cub.cuh
# CUB_FOUND - True if CUB found.
#
find_path(CUB_INCLUDE_DIR cub.cuh PATH_SUFFIXES cub)
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set CUB_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(CUB DEFAULT_MSG CUB_INCLUDE_DIR)
mark_as_advanced(CUB_INCLUDE_DIR)

28
cmake/Modules/FindFFTW3.cmake
View File

@ -14,14 +14,34 @@ find_path(FFTW3_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3_INCLUDE_DIRS})
find_library(FFTW3_LIBRARY NAMES fftw3 HINTS ${PC_FFTW3_LIBRARY_DIRS})
find_library(FFTW3_OMP_LIBRARY NAMES fftw3_omp HINTS ${PC_FFTW3_LIBRARY_DIRS})
set(FFTW3_INCLUDE_DIRS ${FFTW3_INCLUDE_DIR})
set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
set(FFTW3_OMP_LIBRARIES ${FFTW3_OMP_LIBRARY})
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set FFTW3_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(FFTW3 DEFAULT_MSG FFTW3_LIBRARY FFTW3_INCLUDE_DIR)
# Copy the results to the output variables and target.
if(FFTW3_FOUND)
set(FFTW3_LIBRARIES ${FFTW3_LIBRARY} )
set(FFTW3_INCLUDE_DIRS ${FFTW3_INCLUDE_DIR} )
if(NOT TARGET FFTW3::FFTW3)
add_library(FFTW3::FFTW3 UNKNOWN IMPORTED)
set_target_properties(FFTW3::FFTW3 PROPERTIES
IMPORTED_LINK_INTERFACE_LANGUAGES "C"
IMPORTED_LOCATION "${FFTW3_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${FFTW3_INCLUDE_DIRS}")
endif()
if(FFTW3_OMP_LIBRARY)
set(FFTW3_OMP_LIBRARIES ${FFTW3_OMP_LIBRARY})
if(NOT TARGET FFTW3::FFTW3_OMP)
add_library(FFTW3::FFTW3_OMP UNKNOWN IMPORTED)
set_target_properties(FFTW3::FFTW3_OMP PROPERTIES
IMPORTED_LINK_INTERFACE_LANGUAGES "C"
IMPORTED_LOCATION "${FFTW3_OMP_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${FFTW3_INCLUDE_DIRS}")
endif()
endif()
endif()
mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY FFTW3_OMP_LIBRARY)

30
cmake/Modules/FindFFTW3F.cmake
View File

@ -13,14 +13,34 @@ find_path(FFTW3F_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3F_INCLUDE_DIRS})
find_library(FFTW3F_LIBRARY NAMES fftw3f HINTS ${PC_FFTW3F_LIBRARY_DIRS})
find_library(FFTW3F_OMP_LIBRARY NAMES fftw3f_omp HINTS ${PC_FFTW3F_LIBRARY_DIRS})
set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR})
set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY})
set(FFTW3F_OMP_LIBRARIES ${FFTW3F_OMP_LIBRARY})
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set FFTW3F_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(FFTW3F DEFAULT_MSG FFTW3F_LIBRARY FFTW3F_INCLUDE_DIR)
mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY)
# Copy the results to the output variables and target.
if(FFTW3F_FOUND)
set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY} )
set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR} )
if(NOT TARGET FFTW3F::FFTW3F)
add_library(FFTW3F::FFTW3F UNKNOWN IMPORTED)
set_target_properties(FFTW3F::FFTW3F PROPERTIES
IMPORTED_LINK_INTERFACE_LANGUAGES "C"
IMPORTED_LOCATION "${FFTW3F_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${FFTW3F_INCLUDE_DIRS}")
endif()
if(FFTW3F_OMP_LIBRARY)
set(FFTW3F_OMP_LIBRARIES ${FFTW3F_OMP_LIBRARY})
if(NOT TARGET FFTW3F::FFTW3F_OMP)
add_library(FFTW3F::FFTW3F_OMP UNKNOWN IMPORTED)
set_target_properties(FFTW3F::FFTW3F_OMP PROPERTIES
IMPORTED_LINK_INTERFACE_LANGUAGES "C"
IMPORTED_LOCATION "${FFTW3F_OMP_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${FFTW3F_INCLUDE_DIRS}")
endif()
endif()
endif()
mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY FFTW3F_OMP_LIBRARY)

85
cmake/Modules/FindKIM-API.cmake
View File

@ -1,85 +0,0 @@
#
# CDDL HEADER START
#
# The contents of this file are subject to the terms of the Common Development
# and Distribution License Version 1.0 (the "License").
#
# You can obtain a copy of the license at
# http://www.opensource.org/licenses/CDDL-1.0. See the License for the
# specific language governing permissions and limitations under the License.
#
# When distributing Covered Code, include this CDDL HEADER in each file and
# include the License file in a prominent location with the name LICENSE.CDDL.
# If applicable, add the following below this CDDL HEADER, with the fields
# enclosed by brackets "[]" replaced with your own identifying information:
#
# Portions Copyright (c) [yyyy] [name of copyright owner]. All rights reserved.
#
# CDDL HEADER END
#
#
# Copyright (c) 2013--2019, Regents of the University of Minnesota.
# All rights reserved.
#
# Contributors:
# Richard Berger
# Christoph Junghans
# Ryan S. Elliott
#
# - Find KIM-API
#
# sets standard pkg_check_modules variables plus:
#
# KIM-API-CMAKE_C_COMPILER
# KIM-API-CMAKE_CXX_COMPILER
# 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()
set(REQ_OR_QUI "REQUIRED")
endif()
find_package(PkgConfig ${REQ_OR_QUI})
include(FindPackageHandleStandardArgs)
pkg_check_modules(KIM-API ${REQ_OR_QUI} libkim-api>=2.0)
if(KIM-API_FOUND)
pkg_get_variable(KIM-API-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)
pkg_get_variable(KIM-API-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)
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 VERSION_VAR KIM-API_VERSION)

13
cmake/Modules/FindLATTE.cmake
View File

@ -7,12 +7,21 @@
find_library(LATTE_LIBRARY NAMES latte)
set(LATTE_LIBRARIES ${LATTE_LIBRARY})
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set LATTE_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(LATTE DEFAULT_MSG LATTE_LIBRARY)
# Copy the results to the output variables and target.
if(LATTE_FOUND)
set(LATTE_LIBRARIES ${LATTE_LIBRARY})
if(NOT TARGET LATTE::latte)
add_library(LATTE::latte UNKNOWN IMPORTED)
set_target_properties(LATTE::latte PROPERTIES
IMPORTED_LOCATION "${LATTE_LIBRARY}")
endif()
endif()
mark_as_advanced(LATTE_LIBRARY)

15
cmake/Modules/FindMKL.cmake
View File

@ -10,13 +10,22 @@ find_path(MKL_INCLUDE_DIR mkl_dfti.h HINTS $ENV{MKLROOT}/include)
find_library(MKL_LIBRARY NAMES mkl_rt HINTS $ENV{MKLROOT}/lib $ENV{MKLROOT}/lib/intel64)
set(MKL_LIBRARIES ${MKL_LIBRARY})
set(MKL_INCLUDE_DIRS ${MKL_INCLUDE_DIR})
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set MKL_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(MKL DEFAULT_MSG MKL_LIBRARY MKL_INCLUDE_DIR)
if(MKL_FOUND)
set(MKL_LIBRARIES ${MKL_LIBRARY})
set(MKL_INCLUDE_DIRS ${MKL_INCLUDE_DIR})
if(NOT TARGET MKL::MKL)
add_library(MKL::MKL UNKNOWN IMPORTED)
set_target_properties(MKL::MKL PROPERTIES
IMPORTED_LOCATION "${MKL_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${MKL_INCLUDE_DIR}")
endif()
endif()
mark_as_advanced(MKL_INCLUDE_DIR MKL_LIBRARY )

16
cmake/Modules/FindMSCG.cmake
View File

@ -10,13 +10,23 @@ find_path(MSCG_INCLUDE_DIR mscg.h PATH_SUFFIXES mscg)
find_library(MSCG_LIBRARY NAMES mscg)
set(MSCG_LIBRARIES ${MSCG_LIBRARY})
set(MSCG_INCLUDE_DIRS ${MSCG_INCLUDE_DIR})
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set MSCG_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(MSCG DEFAULT_MSG MSCG_LIBRARY MSCG_INCLUDE_DIR)
# Copy the results to the output variables and target.
if(MSCG_FOUND)
set(MSCG_LIBRARIES ${MSCG_LIBRARY})
set(MSCG_INCLUDE_DIRS ${MSCG_INCLUDE_DIR})
if(NOT TARGET MSCG::MSCG)
add_library(MSCG::MSCG UNKNOWN IMPORTED)
set_target_properties(MSCG::MSCG PROPERTIES
IMPORTED_LOCATION "${MSCG_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${MSCG_INCLUDE_DIR}")
endif()
endif()
mark_as_advanced(MSCG_INCLUDE_DIR MSCG_LIBRARY )

11
cmake/Modules/FindNetCDF.cmake
View File

@ -120,3 +120,14 @@ set (NETCDF_INCLUDE_DIRS ${NetCDF_includes})
include (FindPackageHandleStandardArgs)
find_package_handle_standard_args (NetCDF
DEFAULT_MSG NETCDF_LIBRARIES NETCDF_INCLUDE_DIRS NETCDF_HAS_INTERFACES)
# Copy the results to the output variables and target.
if(NetCDF_FOUND)
if(NOT TARGET NetCDF::NetCDF)
add_library(NetCDF::NetCDF UNKNOWN IMPORTED)
set_target_properties(NetCDF::NetCDF PROPERTIES
IMPORTED_LOCATION "${NETCDF_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${NETCDF_INCLUDE_DIRS}"
INTERFACE_LINK_LIBRARIES "${NETCDF_LIBRARIES}")
endif()
endif()

9
cmake/Modules/FindPNetCDF.cmake
View File

@ -53,3 +53,12 @@ include (FindPackageHandleStandardArgs)
find_package_handle_standard_args (PNetCDF DEFAULT_MSG PNETCDF_LIBRARIES PNETCDF_INCLUDES)
mark_as_advanced (PNETCDF_LIBRARIES PNETCDF_INCLUDES)
if(PNetCDF_FOUND)
if(NOT TARGET PNetCDF::PNetCDF)
add_library(PNetCDF::PNetCDF UNKNOWN IMPORTED)
set_target_properties(PNetCDF::PNetCDF PROPERTIES
IMPORTED_LOCATION "${PNETCDF_LIBRARIES}"
INTERFACE_INCLUDE_DIRECTORIES "${PNETCDF_INCLUDES}")
endif()
endif()

13
cmake/Modules/FindQUIP.cmake
View File

@ -7,12 +7,21 @@
find_library(QUIP_LIBRARY NAMES quip)
set(QUIP_LIBRARIES ${QUIP_LIBRARY})
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set QUIP_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(QUIP DEFAULT_MSG QUIP_LIBRARY)
# Copy the results to the output variables and target.
if(QUIP_FOUND)
set(QUIP_LIBRARIES ${QUIP_LIBRARY})
if(NOT TARGET QUIP::QUIP)
add_library(QUIP::QUIP UNKNOWN IMPORTED)
set_target_properties(QUIP::QUIP PROPERTIES
IMPORTED_LOCATION "${QUIP_LIBRARY}")
endif()
endif()
mark_as_advanced(QUIP_LIBRARY)

46
cmake/Modules/FindTBB.cmake
View File

@ -1,46 +0,0 @@
# - Find parts of TBB
# Find the native TBB headers and libraries.
#
# TBB_INCLUDE_DIRS - where to find tbb.h, etc.
# TBB_LIBRARIES - List of libraries when using tbb.
# TBB_FOUND - True if tbb found.
#
########################################################
# TBB
# TODO use more generic FindTBB
find_path(TBB_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
find_library(TBB_LIBRARY NAMES tbb PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
$ENV{TBBROOT}/lib/intel64/gcc4.4
$ENV{TBBROOT}/lib/intel64/gcc4.1)
set(TBB_LIBRARIES ${TBB_LIBRARY})
set(TBB_INCLUDE_DIRS ${TBB_INCLUDE_DIR})
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set TBB_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(TBB DEFAULT_MSG TBB_LIBRARY TBB_INCLUDE_DIR)
mark_as_advanced(TBB_INCLUDE_DIR TBB_LIBRARY )
########################################################
# TBB Malloc
find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
$ENV{TBBROOT}/lib/intel64/gcc4.4
$ENV{TBBROOT}/lib/intel64/gcc4.1)
set(TBB_MALLOC_LIBRARIES ${TBB_MALLOC_LIBRARY})
set(TBB_MALLOC_INCLUDE_DIRS ${TBB_MALLOC_INCLUDE_DIR})
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set TBB_MALLOC_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(TBB_MALLOC DEFAULT_MSG TBB_MALLOC_LIBRARY TBB_MALLOC_INCLUDE_DIR)
mark_as_advanced(TBB_MALLOC_INCLUDE_DIR TBB_MALLOC_LIBRARY )

36
cmake/Modules/FindTBB_MALLOC.cmake Normal file
View File

@ -0,0 +1,36 @@
# - Find parts of TBB_MALLOC
# Find the native TBB_MALLOC headers and libraries.
#
# TBB_MALLOC_INCLUDE_DIRS - where to find tbb.h, etc.
# TBB_MALLOC_LIBRARIES - List of libraries when using tbb.
# TBB_MALLOC_FOUND - True if tbb found.
#
########################################################
# TBB Malloc
find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
$ENV{TBBROOT}/lib/intel64/gcc4.4
$ENV{TBBROOT}/lib/intel64/gcc4.1)
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set TBB_MALLOC_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(TBB_MALLOC DEFAULT_MSG TBB_MALLOC_LIBRARY TBB_MALLOC_INCLUDE_DIR)
if(TBB_MALLOC_FOUND)
set(TBB_MALLOC_LIBRARIES ${TBB_MALLOC_LIBRARY})
set(TBB_MALLOC_INCLUDE_DIRS ${TBB_MALLOC_INCLUDE_DIR})
if(NOT TARGET TBB::TBB_MALLOC)
add_library(TBB::TBB_MALLOC UNKNOWN IMPORTED)
set_target_properties(TBB::TBB_MALLOC PROPERTIES
IMPORTED_LOCATION "${TBB_MALLOC_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${TBB_MALLOC_INCLUDE_DIR}")
endif()
endif()
mark_as_advanced(TBB_MALLOC_INCLUDE_DIR TBB_MALLOC_LIBRARY )

16
cmake/Modules/FindVORO.cmake
View File

@ -10,13 +10,23 @@ find_path(VORO_INCLUDE_DIR voro++.hh PATH_SUFFIXES voro++)
find_library(VORO_LIBRARY NAMES voro++)
set(VORO_LIBRARIES ${VORO_LIBRARY})
set(VORO_INCLUDE_DIRS ${VORO_INCLUDE_DIR})
include(FindPackageHandleStandardArgs)
# handle the QUIETLY and REQUIRED arguments and set VORO_FOUND to TRUE
# if all listed variables are TRUE
find_package_handle_standard_args(VORO DEFAULT_MSG VORO_LIBRARY VORO_INCLUDE_DIR)
# Copy the results to the output variables and target.
if(VORO_FOUND)
set(VORO_LIBRARIES ${VORO_LIBRARY})
set(VORO_INCLUDE_DIRS ${VORO_INCLUDE_DIR})
if(NOT TARGET VORO::VORO)
add_library(VORO::VORO UNKNOWN IMPORTED)
set_target_properties(VORO::VORO PROPERTIES
IMPORTED_LOCATION "${VORO_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${VORO_INCLUDE_DIR}")
endif()
endif()
mark_as_advanced(VORO_INCLUDE_DIR VORO_LIBRARY )

17
cmake/Modules/FindZMQ.cmake
View File

@ -1,8 +1,19 @@
find_path(ZMQ_INCLUDE_DIR zmq.h)
find_library(ZMQ_LIBRARY NAMES zmq)
set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)
# Copy the results to the output variables and target.
if(ZMQ_FOUND)
set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
if(NOT TARGET ZMQ::ZMQ)
add_library(ZMQ::ZMQ UNKNOWN IMPORTED)
set_target_properties(ZMQ::ZMQ PROPERTIES
IMPORTED_LINK_INTERFACE_LANGUAGES "C"
IMPORTED_LOCATION "${ZMQ_LIBRARY}"
INTERFACE_INCLUDE_DIRECTORIES "${ZMQ_INCLUDE_DIR}")
endif()
endif()

3
cmake/Modules/GenerateBinaryHeader.cmake Normal file
View File

@ -0,0 +1,3 @@
# utility script to call GenerateBinaryHeader function
include(${SOURCE_DIR}/Modules/LAMMPSUtils.cmake)
GenerateBinaryHeader(${VARNAME} ${HEADER_FILE} ${SOURCE_FILES})

16
cmake/Modules/LAMMPSUtils.cmake
View File

@ -69,3 +69,19 @@ macro(pkg_depends PKG1 PKG2)
message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
endif()
endmacro()
# CMake-only replacement for bin2c and xxd
function(GenerateBinaryHeader varname outfile files)
message("Creating ${outfile}...")
file(WRITE ${outfile} "// CMake generated file\n")
math(EXPR ARG_END "${ARGC}-1")
foreach(IDX RANGE 2 ${ARG_END})
list(GET ARGV ${IDX} filename)
file(READ ${filename} content HEX)
string(REGEX REPLACE "([0-9a-f][0-9a-f])" "0x\\1," content "${content}")
string(REGEX REPLACE ",$" "" content "${content}")
file(APPEND ${outfile} "const unsigned char ${varname}[] = { ${content} };\n")
file(APPEND ${outfile} "const unsigned int ${varname}_size = sizeof(${varname});\n")
endforeach()
endfunction(GenerateBinaryHeader)

12
cmake/Modules/MPI4WIN.cmake
View File

@ -16,8 +16,10 @@ else()
endif()
ExternalProject_get_property(mpi4win_build SOURCE_DIR)
add_definitions(-DMPICH_SKIP_MPICXX)
include_directories("${SOURCE_DIR}/include")
set(MPI4WIN_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
list(APPEND LAMMPS_DEPS mpi4win_build)
set(LAMMPS_USE_MPI4WIN ON)
file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
set_target_properties(MPI::MPI_CXX PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
add_dependencies(MPI::MPI_CXX mpi4win_build)

7
cmake/Modules/Packages/COMPRESS.cmake
View File

@ -1,5 +1,2 @@
if(PKG_COMPRESS)
find_package(ZLIB REQUIRED)
include_directories(${ZLIB_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
endif()
find_package(ZLIB REQUIRED)
target_link_libraries(lammps PRIVATE ZLIB::ZLIB)

18
cmake/Modules/Packages/CORESHELL.cmake
View File

@ -1,13 +1,11 @@
if(PKG_CORESHELL)
set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL)
set(CORESHELL_SOURCES)
set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}")
set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL)
set(CORESHELL_SOURCES)
set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}")
# detects styles which have a CORESHELL version
RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES)
# detects styles which have a CORESHELL version
RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES)
get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES)
get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES)
list(APPEND LIB_SOURCES ${CORESHELL_SOURCES})
include_directories(${CORESHELL_SOURCES_DIR})
endif()
target_sources(lammps PRIVATE ${CORESHELL_SOURCES})
target_include_directories(lammps PRIVATE ${CORESHELL_SOURCES_DIR})

552
cmake/Modules/Packages/GPU.cmake
View File

@ -1,197 +1,363 @@
if(PKG_GPU)
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
${GPU_SOURCES_DIR}/fix_gpu.h
${GPU_SOURCES_DIR}/fix_gpu.cpp)
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
${GPU_SOURCES_DIR}/fix_gpu.h
${GPU_SOURCES_DIR}/fix_gpu.cpp)
set(GPU_API "opencl" CACHE STRING "API used by GPU package")
set(GPU_API_VALUES opencl cuda)
set_property(CACHE GPU_API PROPERTY STRINGS ${GPU_API_VALUES})
validate_option(GPU_API GPU_API_VALUES)
string(TOUPPER ${GPU_API} GPU_API)
set(GPU_API "opencl" CACHE STRING "API used by GPU package")
set(GPU_API_VALUES opencl cuda hip)
set_property(CACHE GPU_API PROPERTY STRINGS ${GPU_API_VALUES})
validate_option(GPU_API GPU_API_VALUES)
string(TOUPPER ${GPU_API} GPU_API)
set(GPU_PREC "mixed" CACHE STRING "LAMMPS GPU precision")
set(GPU_PREC_VALUES double mixed single)
set_property(CACHE GPU_PREC PROPERTY STRINGS ${GPU_PREC_VALUES})
validate_option(GPU_PREC GPU_PREC_VALUES)
string(TOUPPER ${GPU_PREC} GPU_PREC)
set(GPU_PREC "mixed" CACHE STRING "LAMMPS GPU precision")
set(GPU_PREC_VALUES double mixed single)
set_property(CACHE GPU_PREC PROPERTY STRINGS ${GPU_PREC_VALUES})
validate_option(GPU_PREC GPU_PREC_VALUES)
string(TOUPPER ${GPU_PREC} GPU_PREC)
if(GPU_PREC STREQUAL "DOUBLE")
set(GPU_PREC_SETTING "DOUBLE_DOUBLE")
elseif(GPU_PREC STREQUAL "MIXED")
set(GPU_PREC_SETTING "SINGLE_DOUBLE")
elseif(GPU_PREC STREQUAL "SINGLE")
set(GPU_PREC_SETTING "SINGLE_SINGLE")
endif()
file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(GPU_API STREQUAL "CUDA")
find_package(CUDA REQUIRED)
find_program(BIN2C bin2c)
if(NOT BIN2C)
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)
option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
if(CUDA_MPS_SUPPORT)
set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
endif()
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 ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(CUDPP_OPT)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
endif()
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${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 ${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 ${CU_OBJ} NAME_WE)
string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
DEPENDS ${CU_OBJ}
COMMENT "Generating ${CU_NAME}_cubin.h")
list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
endforeach()
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
if(CUDPP_OPT)
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
endif()
list(APPEND LAMMPS_LINK_LIBS gpu)
if(LAMMPS_USE_MPI4WIN)
add_dependencies(gpu mpi4win_build)
endif()
add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
elseif(GPU_API STREQUAL "OPENCL")
find_package(OpenCL REQUIRED)
set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
validate_option(OCL_TUNE OCL_TUNE_VALUES)
string(TOUPPER ${OCL_TUNE} OCL_TUNE)
include(OpenCLUtils)
set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
)
foreach(GPU_KERNEL ${GPU_LIB_CU})
get_filename_component(basename ${GPU_KERNEL} NAME_WE)
string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
endforeach()
GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu)
GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu)
GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
list(APPEND GPU_LIB_SOURCES
${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
)
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_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
list(APPEND LAMMPS_LINK_LIBS gpu)
if(LAMMPS_USE_MPI4WIN)
add_dependencies(gpu mpi4win_build)
endif()
add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
target_link_libraries(ocl_get_devices PRIVATE ${OpenCL_LIBRARIES})
target_include_directories(ocl_get_devices PRIVATE ${OpenCL_INCLUDE_DIRS})
endif()
# GPU package
FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
# detects styles which have GPU version
RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
list(APPEND LIB_SOURCES ${GPU_SOURCES})
include_directories(${GPU_SOURCES_DIR})
if(GPU_PREC STREQUAL "DOUBLE")
set(GPU_PREC_SETTING "DOUBLE_DOUBLE")
elseif(GPU_PREC STREQUAL "MIXED")
set(GPU_PREC_SETTING "SINGLE_DOUBLE")
elseif(GPU_PREC STREQUAL "SINGLE")
set(GPU_PREC_SETTING "SINGLE_SINGLE")
endif()
file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(GPU_API STREQUAL "CUDA")
find_package(CUDA REQUIRED)
find_program(BIN2C bin2c)
if(NOT BIN2C)
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)
option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
if(CUDA_MPS_SUPPORT)
set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
endif()
set(GPU_ARCH "sm_50" 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 ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(CUDPP_OPT)
cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
endif()
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(GPU_CUDA_GENCODE "-arch=${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 ${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 ${CU_OBJ} NAME_WE)
string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
DEPENDS ${CU_OBJ}
COMMENT "Generating ${CU_NAME}_cubin.h")
list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
endforeach()
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
if(CUDPP_OPT)
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
endif()
target_link_libraries(lammps PRIVATE gpu)
add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
elseif(GPU_API STREQUAL "OPENCL")
if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
# download and unpack support binaries for compilation of windows binaries.
set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
endif()
set_target_properties(OpenCL::OpenCL PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
else()
find_package(OpenCL REQUIRED)
endif()
set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
validate_option(OCL_TUNE OCL_TUNE_VALUES)
string(TOUPPER ${OCL_TUNE} OCL_TUNE)
include(OpenCLUtils)
set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
list(REMOVE_ITEM GPU_LIB_CU
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
)
foreach(GPU_KERNEL ${GPU_LIB_CU})
get_filename_component(basename ${GPU_KERNEL} NAME_WE)
string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
endforeach()
GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu)
GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu)
GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
list(APPEND GPU_LIB_SOURCES
${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
)
add_library(gpu STATIC ${GPU_LIB_SOURCES})
target_link_libraries(gpu PRIVATE OpenCL::OpenCL)
target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu)
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
target_link_libraries(lammps PRIVATE gpu)
add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
elseif(GPU_API STREQUAL "HIP")
if(NOT DEFINED HIP_PATH)
if(NOT DEFINED ENV{HIP_PATH})
set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to which HIP has been installed")
else()
set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to which HIP has been installed")
endif()
endif()
set(CMAKE_MODULE_PATH "${HIP_PATH}/cmake" ${CMAKE_MODULE_PATH})
find_package(HIP REQUIRED)
option(HIP_USE_DEVICE_SORT "Use GPU sorting" ON)
if(NOT DEFINED HIP_PLATFORM)
if(NOT DEFINED ENV{HIP_PLATFORM})
set(HIP_PLATFORM "hcc" CACHE PATH "HIP Platform to be used during compilation")
else()
set(HIP_PLATFORM $ENV{HIP_PLATFORM} CACHE PATH "HIP Platform used during compilation")
endif()
endif()
set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
if(HIP_PLATFORM STREQUAL "hcc")
set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
elseif(HIP_PLATFORM STREQUAL "nvcc")
find_package(CUDA REQUIRED)
set(HIP_ARCH "sm_50" CACHE STRING "HIP primary CUDA architecture (e.g. sm_60)")
# build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
# --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
set(HIP_CUDA_GENCODE "-arch=${HIP_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 HIP_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 HIP_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 HIP_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 HIP_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 HIP_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 HIP_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
endif()
endif()
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)
set(GPU_LIB_CU_HIP "")
foreach(CU_FILE ${GPU_LIB_CU})
get_filename_component(CU_NAME ${CU_FILE} NAME_WE)
string(REGEX REPLACE "^.*lal_" "" CU_NAME "${CU_NAME}")
set(CU_CPP_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cu.cpp")
set(CUBIN_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
if(HIP_PLATFORM STREQUAL "hcc")
configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
DEPENDS ${CU_CPP_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
elseif(HIP_PLATFORM STREQUAL "nvcc")
add_custom_command(OUTPUT ${CUBIN_FILE}
VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
DEPENDS ${CU_FILE}
COMMENT "Generating ${CU_NAME}.cubin")
endif()
add_custom_command(OUTPUT ${CUBIN_H_FILE}
COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR} -D VARNAME=${CU_NAME} -D HEADER_FILE=${CUBIN_H_FILE} -D SOURCE_FILES=${CUBIN_FILE} -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateBinaryHeader.cmake
DEPENDS ${CUBIN_FILE}
COMMENT "Generating ${CU_NAME}_cubin.h")
list(APPEND GPU_LIB_SOURCES ${CUBIN_H_FILE})
endforeach()
set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h ${LAMMPS_LIB_BINARY_DIR}/gpu/*.cu.cpp")
hip_add_library(gpu STATIC ${GPU_LIB_SOURCES})
target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu)
target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
target_compile_definitions(gpu PRIVATE -DUSE_HIP)
if(HIP_USE_DEVICE_SORT)
# add hipCUB
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
target_compile_definitions(gpu PRIVATE -DUSE_HIP_DEVICE_SORT)
if(HIP_PLATFORM STREQUAL "nvcc")
find_package(CUB)
if(CUB_FOUND)
set(DOWNLOAD_CUB_DEFAULT OFF)
else()
set(DOWNLOAD_CUB_DEFAULT ON)
endif()
option(DOWNLOAD_CUB "Download and compile the CUB library instead of using an already installed one" ${DOWNLOAD_CUB_DEFAULT})
if(DOWNLOAD_CUB)
message(STATUS "CUB download requested")
include(ExternalProject)
ExternalProject_Add(CUB
GIT_REPOSITORY https://github.com/NVlabs/cub
TIMEOUT 5
PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
CONFIGURE_COMMAND ""
BUILD_COMMAND ""
INSTALL_COMMAND ""
UPDATE_COMMAND ""
)
ExternalProject_get_property(CUB SOURCE_DIR)
set(CUB_INCLUDE_DIR ${SOURCE_DIR})
else()
find_package(CUB)
if(NOT CUB_FOUND)
message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
endif()
endif()
target_include_directories(gpu PRIVATE ${CUB_INCLUDE_DIR})
endif()
endif()
hip_add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
target_compile_definitions(hip_get_devices PRIVATE -DUCL_HIP)
if(HIP_PLATFORM STREQUAL "nvcc")
target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)
target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/include)
target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS})
target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_NVCC__)
target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/include)
target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
endif()
target_link_libraries(lammps PRIVATE gpu)
endif()
# GPU package
FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
# detects styles which have GPU version
RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
target_link_libraries(gpu PRIVATE MPI::MPI_CXX)
if(NOT BUILD_SHARED_LIBS)
install(TARGETS gpu EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
target_sources(lammps PRIVATE ${GPU_SOURCES})
target_include_directories(lammps PRIVATE ${GPU_SOURCES_DIR})

122
cmake/Modules/Packages/KIM.cmake
View File

@ -1,67 +1,61 @@
if(PKG_KIM)
set(KIM-API_MIN_VERSION 2.1)
find_package(CURL)
if(CURL_FOUND)
include_directories(${CURL_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
add_definitions(-DLMP_KIM_CURL)
set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
mark_as_advanced(LMP_DEBUG_CURL)
if(LMP_DEBUG_CURL)
add_definitions(-DLMP_DEBUG_CURL)
endif()
set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
mark_as_advanced(LMP_NO_SSL_CHECK)
if(LMP_NO_SSL_CHECK)
add_definitions(-DLMP_NO_SSL_CHECK)
endif()
set(KIM-API_MIN_VERSION 2.1.3)
find_package(CURL)
if(CURL_FOUND)
target_link_libraries(lammps PRIVATE CURL::libcurl)
target_compile_definitions(lammps PRIVATE -DLMP_KIM_CURL)
set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
mark_as_advanced(LMP_DEBUG_CURL)
if(LMP_DEBUG_CURL)
target_compile_definitions(lammps PRIVATE -DLMP_DEBUG_CURL)
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 ("${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)
set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
mark_as_advanced(LMP_NO_SSL_CHECK)
if(LMP_NO_SSL_CHECK)
target_compile_definitions(lammps PRIVATE -DLMP_NO_SSL_CHECK)
endif()
option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
if(DOWNLOAD_KIM)
message(STATUS "KIM-API download requested - we will build our own")
# Workaround for cross compilation with MinGW where ${CMAKE_INSTALL_LIBDIR}
# is a full path, so we need to remove the prefix
string(REPLACE ${CMAKE_INSTALL_PREFIX} "" _KIM_LIBDIR ${CMAKE_INSTALL_LIBDIR})
include(ExternalProject)
enable_language(C)
enable_language(Fortran)
ExternalProject_Add(kim_build
URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
BINARY_DIR build
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <INSTALL_DIR>/${_KIM_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX}
)
ExternalProject_get_property(kim_build INSTALL_DIR)
set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)
set(KIM-API_LDFLAGS ${INSTALL_DIR}/${_KIM_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
list(APPEND LAMMPS_DEPS kim_build)
else()
find_package(KIM-API ${KIM-API_MIN_VERSION} REQUIRED)
endif()
list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
include_directories(${KIM-API_INCLUDE_DIRS})
endif()
find_package(PkgConfig QUIET)
set(DOWNLOAD_KIM_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(KIM-API QUIET libkim-api>=${KIM-API_MIN_VERSION})
if(KIM-API_FOUND)
set(DOWNLOAD_KIM_DEFAULT OFF)
endif()
endif()
option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
if(DOWNLOAD_KIM)
message(STATUS "KIM-API download requested - we will build our own")
include(ExternalProject)
enable_language(C)
enable_language(Fortran)
ExternalProject_Add(kim_build
URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
BINARY_DIR build
CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
-DCMAKE_INSTALL_LIBDIR=lib
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX}
)
ExternalProject_get_property(kim_build INSTALL_DIR)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include/kim-api)
add_library(LAMMPS::KIM UNKNOWN IMPORTED)
set_target_properties(LAMMPS::KIM PROPERTIES
IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX}"
INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api")
target_link_libraries(lammps PRIVATE LAMMPS::KIM)
add_dependencies(LAMMPS::KIM kim_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})
target_link_libraries(lammps PRIVATE PkgConfig::KIM-API)
endif()

171
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -1,74 +1,111 @@
if(PKG_KOKKOS)
# TODO: this option needs to be documented when this works with a
# regular release version of KOKKOS, and a version compatibility check
# of external KOKKOS lib versus what the KOKKOS package needs is required.
option(EXTERNAL_KOKKOS "Build against external kokkos library")
if(EXTERNAL_KOKKOS)
find_package(Kokkos REQUIRED)
list(APPEND LAMMPS_LINK_LIBS Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
########################################################################
# consistency checks and Kokkos options/settings required by LAMMPS
if(Kokkos_ENABLE_CUDA)
message(STATUS "KOKKOS: Enabling CUDA LAMBDA function support")
set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "" FORCE)
endif()
# Adding OpenMP compiler flags without the checks done for
# BUILD_OMP can result in compile failures. Enforce consistency.
if(Kokkos_ENABLE_OPENMP AND NOT BUILD_OMP)
message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
endif()
########################################################################
set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
${LAMMPS_LIB_KOKKOS_BIN_DIR})
include_directories(${Kokkos_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS kokkos)
option(EXTERNAL_KOKKOS "Build against external kokkos library" OFF)
option(DOWNLOAD_KOKKOS "Download the KOKKOS library instead of using the bundled one" OFF)
if(DOWNLOAD_KOKKOS)
message(STATUS "KOKKOS download requested - we will build our own")
file(DOWNLOAD https://github.com/kokkos/kokkos/compare/3.0.00...stanmoore1:lammps.diff ${CMAKE_CURRENT_BINARY_DIR}/kokkos-lammps.patch)
include(ExternalProject)
ExternalProject_Add(kokkos_build
URL https://github.com/kokkos/kokkos/archive/3.0.00.tar.gz
URL_MD5 281c7093aa3a603276e93abdf4be23b9
PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/kokkos-lammps.patch
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_INSTALL_LIBDIR=lib
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
)
ExternalProject_get_property(kokkos_build INSTALL_DIR)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
add_library(LAMMPS::KOKKOS UNKNOWN IMPORTED)
set_target_properties(LAMMPS::KOKKOS PROPERTIES
IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscore.a"
INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include"
INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
add_dependencies(LAMMPS::KOKKOS kokkos_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
add_definitions(-DLMP_KOKKOS)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3)
if(NOT Kokkos_FOUND)
message(FATAL_ERROR "KOKKOS library not found, help CMake to find it by setting KOKKOS_LIBRARY, or set DOWNLOAD_KOKKOS=ON to download it")
endif()
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
${LAMMPS_LIB_KOKKOS_BIN_DIR})
target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
target_link_libraries(lammps PRIVATE kokkos)
endif()
target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS)
if(PKG_KSPACE)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
if(KOKKOS_ENABLE_CUDA)
if(NOT ${FFT} STREQUAL "KISS")
add_definitions(-DFFT_CUFFT)
list(APPEND LAMMPS_LINK_LIBS cufft)
endif()
set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
if(PKG_KSPACE)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
if(Kokkos_ENABLE_CUDA)
if(NOT ${FFT} STREQUAL "KISS")
target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
target_link_libraries(lammps PRIVATE cufft)
endif()
endif()
set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
# detects styles which have KOKKOS version
RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
# register kokkos-only styles
RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h)
if(PKG_USER-DPD)
get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
endif()
get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})
include_directories(${KOKKOS_PKG_SOURCES_DIR})
endif()
set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
# detects styles which have KOKKOS version
RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
# register kokkos-only styles
RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h)
if(PKG_USER-DPD)
get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
endif()
get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
target_sources(lammps PRIVATE ${KOKKOS_PKG_SOURCES})
target_include_directories(lammps PRIVATE ${KOKKOS_PKG_SOURCES_DIR})

114
cmake/Modules/Packages/KSPACE.cmake
View File

@ -1,60 +1,56 @@
if(PKG_KSPACE)
option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)
set(FFTW "FFTW3")
if(FFT_SINGLE)
set(FFTW "FFTW3F")
add_definitions(-DFFT_SINGLE)
endif()
find_package(${FFTW} QUIET)
if(${FFTW}_FOUND)
set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
else()
set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
endif()
set(FFT_VALUES KISS FFTW3 MKL)
set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
validate_option(FFT FFT_VALUES)
string(TOUPPER ${FFT} FFT)
if(FFT STREQUAL "FFTW3")
find_package(${FFTW} REQUIRED)
add_definitions(-DFFT_FFTW3)
include_directories(${${FFTW}_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
else()
option(FFT_FFTW_THREADS "Use threaded FFT library" OFF)
endif()
if(FFT_FFTW_THREADS)
if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
add_definitions(-DFFT_FFTW_THREADS)
list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_OMP_LIBRARIES})
else()
message(FATAL_ERROR "Need OpenMP enabled FFTW3 library for FFT_THREADS")
endif()
endif()
elseif(FFT STREQUAL "MKL")
find_package(MKL REQUIRED)
add_definitions(-DFFT_MKL)
option(FFT_MKL_THREADS "Use threaded MKL FFT" ON)
if(FFT_MKL_THREADS)
add_definitions(-DFFT_MKL_THREADS)
endif()
include_directories(${MKL_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
else()
# last option is KISSFFT
add_definitions(-DFFT_KISS)
endif()
set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
set(FFT_PACK_VALUES array pointer memcpy)
set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
validate_option(FFT_PACK FFT_PACK_VALUES)
if(NOT FFT_PACK STREQUAL "array")
string(TOUPPER ${FFT_PACK} FFT_PACK)
add_definitions(-DFFT_PACK_${FFT_PACK})
endif()
option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)
set(FFTW "FFTW3")
if(FFT_SINGLE)
set(FFTW "FFTW3F")
target_compile_definitions(lammps PUBLIC -DFFT_SINGLE)
endif()
find_package(${FFTW} QUIET)
if(${FFTW}_FOUND)
set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
else()
set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
endif()
set(FFT_VALUES KISS FFTW3 MKL)
set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
validate_option(FFT FFT_VALUES)
string(TOUPPER ${FFT} FFT)
if(FFT STREQUAL "FFTW3")
find_package(${FFTW} REQUIRED)
target_compile_definitions(lammps PUBLIC -DFFT_FFTW3)
target_link_libraries(lammps PUBLIC ${FFTW}::${FFTW})
if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
else()
option(FFT_FFTW_THREADS "Use threaded FFT library" OFF)
endif()
if(FFT_FFTW_THREADS)
if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
target_compile_definitions(lammps PRIVATE -DFFT_FFTW_THREADS)
target_link_libraries(lammps PRIVATE ${FFTW}::${FFTW}_OMP)
else()
message(FATAL_ERROR "Need OpenMP enabled FFTW3 library for FFT_THREADS")
endif()
endif()
elseif(FFT STREQUAL "MKL")
find_package(MKL REQUIRED)
target_compile_definitions(lammps PRIVATE -DFFT_MKL)
option(FFT_MKL_THREADS "Use threaded MKL FFT" ON)
if(FFT_MKL_THREADS)
target_compile_definitions(lammps PRIVATE -DFFT_MKL_THREADS)
endif()
target_link_libraries(lammps PRIVATE MKL::MKL)
else()
# last option is KISSFFT
target_compile_definitions(lammps PRIVATE -DFFT_KISS)
endif()
set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
set(FFT_PACK_VALUES array pointer memcpy)
set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
validate_option(FFT_PACK FFT_PACK_VALUES)
if(NOT FFT_PACK STREQUAL "array")
string(TOUPPER ${FFT_PACK} FFT_PACK)
target_compile_definitions(lammps PRIVATE -DFFT_PACK_${FFT_PACK})
endif()

77
cmake/Modules/Packages/LATTE.cmake
View File

@ -1,40 +1,39 @@
if(PKG_LATTE)
enable_language(Fortran)
find_package(LATTE)
if(LATTE_FOUND)
set(DOWNLOAD_LATTE_DEFAULT OFF)
else()
set(DOWNLOAD_LATTE_DEFAULT ON)
endif()
option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
if(DOWNLOAD_LATTE)
message(STATUS "LATTE download requested - we will build our own")
# Workaround for cross compilation with MinGW where ${CMAKE_INSTALL_LIBDIR}
# is a full path, so we need to remove the prefix
string(REPLACE ${CMAKE_INSTALL_PREFIX} "" _LATTE_LIBDIR ${CMAKE_INSTALL_LIBDIR})
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> ${CMAKE_REQUEST_PIC}
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
-DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <INSTALL_DIR>/${_LATTE_LIBDIR}/liblatte.a
)
list(APPEND LAMMPS_DEPS latte_build)
ExternalProject_get_property(latte_build INSTALL_DIR)
set(LATTE_LIBRARIES ${INSTALL_DIR}/${_LATTE_LIBDIR}/liblatte.a)
else()
find_package(LATTE)
if(NOT LATTE_FOUND)
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()
if(NOT LAPACK_FOUND)
add_dependencies(latte_build linalg)
endif()
list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
enable_language(Fortran)
find_package(LATTE)
if(LATTE_FOUND)
set(DOWNLOAD_LATTE_DEFAULT OFF)
else()
set(DOWNLOAD_LATTE_DEFAULT ON)
endif()
option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
if(DOWNLOAD_LATTE)
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> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
-DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/liblatte.a
)
ExternalProject_get_property(latte_build INSTALL_DIR)
add_library(LAMMPS::LATTE UNKNOWN IMPORTED)
set_target_properties(LAMMPS::LATTE PROPERTIES
IMPORTED_LOCATION "${INSTALL_DIR}/lib/liblatte.a"
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
add_dependencies(LAMMPS::LATTE latte_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(LATTE)
if(NOT LATTE_FOUND)
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()
target_link_libraries(lammps PRIVATE LATTE::latte)
endif()

65
cmake/Modules/Packages/MESSAGE.cmake
View File

@ -1,32 +1,35 @@
if(PKG_MESSAGE)
if(LAMMPS_SIZES STREQUAL BIGBIG)
message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
endif()
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
add_library(cslib STATIC ${cslib_SOURCES})
if(BUILD_MPI)
target_compile_definitions(cslib PRIVATE -DMPI_YES)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
else()
target_compile_definitions(cslib PRIVATE -DMPI_NO)
target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
endif()
if(MESSAGE_ZMQ)
target_compile_definitions(cslib PRIVATE -DZMQ_YES)
find_package(ZMQ REQUIRED)
target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
else()
target_compile_definitions(cslib PRIVATE -DZMQ_NO)
target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
endif()
list(APPEND LAMMPS_LINK_LIBS cslib)
include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
if(LAMMPS_SIZES STREQUAL BIGBIG)
message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
endif()
option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
add_library(cslib STATIC ${cslib_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS cslib EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
target_compile_definitions(cslib PRIVATE -DLAMMPS_${LAMMPS_SIZES})
set_target_properties(cslib PROPERTIES OUTPUT_NAME lammps_cslib${LAMMPS_MACHINE})
if(BUILD_MPI)
target_compile_definitions(cslib PRIVATE -DMPI_YES)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
target_link_libraries(cslib PRIVATE MPI::MPI_CXX)
else()
target_compile_definitions(cslib PRIVATE -DMPI_NO)
target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
endif()
if(MESSAGE_ZMQ)
target_compile_definitions(cslib PRIVATE -DZMQ_YES)
find_package(ZMQ REQUIRED)
target_link_libraries(cslib PUBLIC ZMQ::ZMQ)
else()
target_compile_definitions(cslib PRIVATE -DZMQ_NO)
target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
endif()
target_link_libraries(lammps PRIVATE cslib)
target_include_directories(lammps PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)

94
cmake/Modules/Packages/MSCG.cmake
View File

@ -1,48 +1,48 @@
if(PKG_MSCG)
find_package(GSL REQUIRED)
find_package(MSCG QUIET)
if(MSGC_FOUND)
set(DOWNLOAD_MSCG_DEFAULT OFF)
else()
set(DOWNLOAD_MSCG_DEFAULT ON)
endif()
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
if(DOWNLOAD_MSCG)
include(ExternalProject)
if(NOT LAPACK_FOUND)
set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
endif()
ExternalProject_Add(mscg_build
URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
URL_MD5 8c45e269ee13f60b303edd7823866a91
SOURCE_SUBDIR src/CMake
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_COMMAND ${CMAKE_COMMAND} --build . --target mscg
INSTALL_COMMAND ""
BUILD_BYPRODUCTS <BINARY_DIR>/libmscg.a
)
ExternalProject_get_property(mscg_build BINARY_DIR)
set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)
ExternalProject_get_property(mscg_build SOURCE_DIR)
set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src)
list(APPEND LAMMPS_DEPS mscg_build)
if(NOT LAPACK_FOUND)
file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS})
add_dependencies(mscg_build linalg)
endif()
else()
find_package(MSCG)
if(NOT MSCG_FOUND)
message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
endif()
endif()
list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
include_directories(${MSCG_INCLUDE_DIRS})
find_package(GSL REQUIRED)
find_package(MSCG QUIET)
if(MSGC_FOUND)
set(DOWNLOAD_MSCG_DEFAULT OFF)
else()
set(DOWNLOAD_MSCG_DEFAULT ON)
endif()
option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
if(DOWNLOAD_MSCG)
include(ExternalProject)
ExternalProject_Add(mscg_build
URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
URL_MD5 8c45e269ee13f60b303edd7823866a91
SOURCE_SUBDIR src/CMake
CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
-DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
BUILD_COMMAND ${CMAKE_COMMAND} --build . --target mscg
INSTALL_COMMAND ""
BUILD_BYPRODUCTS <BINARY_DIR>/libmscg.a
)
ExternalProject_get_property(mscg_build BINARY_DIR)
ExternalProject_get_property(mscg_build SOURCE_DIR)
file(MAKE_DIRECTORY ${SOURCE_DIR}/src)
add_library(LAMMPS::MSCG UNKNOWN IMPORTED)
set_target_properties(LAMMPS::MSCG PROPERTIES
IMPORTED_LOCATION "${BINARY_DIR}/libmscg.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src"
INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
target_link_libraries(lammps PRIVATE LAMMPS::MSCG)
add_dependencies(LAMMPS::MSCG mscg_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(MSCG)
if(NOT MSCG_FOUND)
message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
endif()
target_link_libraries(lammps PRIVATE MSCG::MSCG)
endif()
target_link_libraries(lammps PRIVATE GSL::gsl ${LAPACK_LIBRARIES})

18
cmake/Modules/Packages/OPT.cmake
View File

@ -1,13 +1,11 @@
if(PKG_OPT)
set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
set(OPT_SOURCES)
set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
set(OPT_SOURCES)
set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
# detects styles which have OPT version
RegisterStylesExt(${OPT_SOURCES_DIR} opt OPT_SOURCES)
# detects styles which have OPT version
RegisterStylesExt(${OPT_SOURCES_DIR} opt OPT_SOURCES)
get_property(OPT_SOURCES GLOBAL PROPERTY OPT_SOURCES)
get_property(OPT_SOURCES GLOBAL PROPERTY OPT_SOURCES)
list(APPEND LIB_SOURCES ${OPT_SOURCES})
include_directories(${OPT_SOURCES_DIR})
endif()
target_sources(lammps PRIVATE ${OPT_SOURCES})
target_include_directories(lammps PRIVATE ${OPT_SOURCES_DIR})

13
cmake/Modules/Packages/PYTHON.cmake
View File

@ -1,6 +1,9 @@
if(PKG_PYTHON)
find_package(PythonLibs REQUIRED)
add_definitions(-DLMP_PYTHON)
include_directories(${PYTHON_INCLUDE_DIR})
list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
if(CMAKE_VERSION VERSION_LESS 3.12)
find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIR})
target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARY})
else()
find_package(Python REQUIRED COMPONENTS Development)
target_link_libraries(lammps PRIVATE Python::Python)
endif()
target_compile_definitions(lammps PRIVATE -DLMP_PYTHON)

32
cmake/Modules/Packages/QEQ.cmake
View File

@ -1,20 +1,18 @@
# Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed
if(PKG_QEQ)
set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
if(NOT PKG_MANYBODY)
list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
endif()
set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
foreach(MY_HEADER ${QEQ_HEADERS})
AddStyleHeader(${MY_HEADER} FIX)
endforeach()
get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
list(APPEND LIB_SOURCES ${QEQ_SOURCES})
include_directories(${QEQ_SOURCES_DIR})
if(NOT PKG_MANYBODY)
list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
endif()
set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
foreach(MY_HEADER ${QEQ_HEADERS})
AddStyleHeader(${MY_HEADER} FIX)
endforeach()
get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
target_sources(lammps PRIVATE ${QEQ_SOURCES})
target_include_directories(lammps PRIVATE ${QEQ_SOURCES_DIR})

49
cmake/Modules/Packages/USER-COLVARS.cmake
View File

@ -1,27 +1,32 @@
if(PKG_USER-COLVARS)
set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
# Build Lepton by default
option(COLVARS_LEPTON "Build and link the Lepton library" ON)
# Build Lepton by default
option(COLVARS_LEPTON "Build and link the Lepton library" ON)
if(COLVARS_LEPTON)
set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
add_library(lepton STATIC ${LEPTON_SOURCES})
target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
if(COLVARS_LEPTON)
set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
add_library(lepton STATIC ${LEPTON_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS lepton EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
add_library(colvars STATIC ${COLVARS_SOURCES})
target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
list(APPEND LAMMPS_LINK_LIBS colvars)
if(COLVARS_LEPTON)
list(APPEND LAMMPS_LINK_LIBS lepton)
target_compile_options(colvars PRIVATE -DLEPTON)
target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
endif()
set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
endif()
add_library(colvars STATIC ${COLVARS_SOURCES})
if(NOT BUILD_SHARED_LIBS)
install(TARGETS colvars EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
target_compile_definitions(colvars PRIVATE -DLAMMPS_${LAMMPS_SIZES})
set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
target_link_libraries(lammps PRIVATE colvars)
if(COLVARS_LEPTON)
target_link_libraries(lammps PRIVATE lepton)
target_compile_options(colvars PRIVATE -DLEPTON)
target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
endif()

11
cmake/Modules/Packages/USER-H5MD.cmake
View File

@ -1,8 +1,5 @@
if(PKG_USER-H5MD)
enable_language(C)
enable_language(C)
find_package(HDF5 REQUIRED)
target_link_libraries(h5md ${HDF5_LIBRARIES})
target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
include_directories(${HDF5_INCLUDE_DIRS})
endif()
find_package(HDF5 REQUIRED)
target_link_libraries(h5md PRIVATE ${HDF5_LIBRARIES})
target_include_directories(h5md PUBLIC ${HDF5_INCLUDE_DIRS})

220
cmake/Modules/Packages/USER-INTEL.cmake
View File

@ -1,113 +1,109 @@
if(PKG_USER-INTEL)
check_include_file_cxx(immintrin.h FOUND_IMMINTRIN)
if(NOT FOUND_IMMINTRIN)
message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it")
endif()
add_definitions(-DLMP_USER_INTEL)
set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
set(INTEL_ARCH_VALUES cpu knl)
set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
find_package(Threads QUIET)
if(Threads_FOUND)
set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
else()
set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
endif()
set(INTEL_LRT_VALUES none threads c++11)
set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES})
validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES)
string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE)
if(INTEL_LRT_MODE STREQUAL "THREADS")
if(Threads_FOUND)
add_definitions(-DLMP_INTEL_USELRT)
list(APPEND LAMMPS_LINK_LIBS ${CMAKE_THREAD_LIBS_INIT})
else()
message(FATAL_ERROR "Must have working threads library for Long-range thread support")
endif()
endif()
if(INTEL_LRT_MODE STREQUAL "C++11")
add_definitions(-DLMP_INTEL_USERLRT -DLMP_INTEL_LRT11)
endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
endif()
else()
message(WARNING "USER-INTEL gives best performance with Intel compilers")
endif()
find_package(TBB QUIET)
if(TBB_FOUND)
list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES})
else()
add_definitions(-DLMP_INTEL_NO_TBB)
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
endif()
endif()
find_package(MKL QUIET)
if(MKL_FOUND)
add_definitions(-DLMP_USE_MKL_RNG)
list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
else()
message(STATUS "Pair style dpd/intel will be faster with MKL libraries")
endif()
if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
endif()
if(INTEL_ARCH STREQUAL "KNL")
if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
endif()
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
add_definitions(-DLMP_INTEL_OFFLOAD)
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
include(CheckCXXCompilerFlag)
foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG})
if(COMPILER_SUPPORTS${_FLAG})
add_compile_options(${_FLAG})
endif()
endforeach()
else()
add_compile_options(-O3 -ffast-math)
endif()
endif()
# collect sources
set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
# detect styles which have a USER-INTEL version
RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
if(PKG_KSPACE)
list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
endif()
list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
include_directories(${USER-INTEL_SOURCES_DIR})
check_include_file_cxx(immintrin.h FOUND_IMMINTRIN)
if(NOT FOUND_IMMINTRIN)
message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it")
endif()
target_compile_definitions(lammps PRIVATE -DLMP_USER_INTEL)
set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
set(INTEL_ARCH_VALUES cpu knl)
set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
find_package(Threads QUIET)
if(Threads_FOUND)
set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
else()
set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
endif()
set(INTEL_LRT_VALUES none threads c++11)
set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES})
validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES)
string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE)
if(INTEL_LRT_MODE STREQUAL "THREADS")
if(Threads_FOUND)
target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT)
target_link_libraries(lammps PRIVATE Threads::Threads)
else()
message(FATAL_ERROR "Must have working threads library for Long-range thread support")
endif()
endif()
if(INTEL_LRT_MODE STREQUAL "C++11")
target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
endif()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
endif()
else()
message(WARNING "USER-INTEL gives best performance with Intel compilers")
endif()
find_package(TBB_MALLOC QUIET)
if(TBB_MALLOC_FOUND)
target_link_libraries(lammps PRIVATE TBB::TBB_MALLOC)
else()
target_compile_definitions(lammps PRIVATE -DLMP_INTEL_NO_TBB)
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
endif()
endif()
find_package(MKL QUIET)
if(MKL_FOUND)
target_compile_definitions(lammps PRIVATE -DLMP_USE_MKL_RNG)
target_link_libraries(lammps PRIVATE MKL::MKL)
else()
message(STATUS "Pair style dpd/intel will be faster with MKL libraries")
endif()
if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
endif()
if(INTEL_ARCH STREQUAL "KNL")
if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
endif()
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
target_compile_options(lammps PRIVATE -xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
target_compile_definitions(lammps PRIVATE -DLMP_INTEL_OFFLOAD)
else()
if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
include(CheckCXXCompilerFlag)
foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
if(COMPILER_SUPPORTS${_FLAG})
target_compile_options(lammps PRIVATE ${_FLAG})
endif()
endforeach()
endif()
endif()
# collect sources
set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
# detect styles which have a USER-INTEL version
RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
if(PKG_KSPACE)
list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
endif()
target_sources(lammps PRIVATE ${USER-INTEL_SOURCES})
target_include_directories(lammps PRIVATE ${USER-INTEL_SOURCES_DIR})

19
cmake/Modules/Packages/USER-MOLFILE.cmake
View File

@ -1,10 +1,11 @@
if(PKG_USER-MOLFILE)
set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
add_library(molfile INTERFACE)
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
# no need to link with -ldl on windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
endif()
list(APPEND LAMMPS_LINK_LIBS molfile)
set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
add_library(molfile INTERFACE)
if(NOT BUILD_SHARED_LIBS)
install(TARGETS molfile EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
# no need to link with -ldl on windows
if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
endif()
target_link_libraries(lammps PRIVATE molfile)

38
cmake/Modules/Packages/USER-NETCDF.cmake
View File

@ -1,24 +1,20 @@
if(PKG_USER-NETCDF)
# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
# NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
find_package(NetCDF)
if(NETCDF_FOUND)
find_package(PNetCDF)
else(NETCDF_FOUND)
find_package(PNetCDF REQUIRED)
endif(NETCDF_FOUND)
# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
# NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
find_package(NetCDF)
if(NETCDF_FOUND)
find_package(PNetCDF)
else(NETCDF_FOUND)
find_package(PNetCDF REQUIRED)
endif(NETCDF_FOUND)
if(NETCDF_FOUND)
include_directories(${NETCDF_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
add_definitions(-DLMP_HAS_NETCDF)
endif(NETCDF_FOUND)
if(NETCDF_FOUND)
target_link_libraries(lammps PRIVATE NetCDF::NetCDF)
target_compile_definitions(lammps PRIVATE -DLMP_HAS_NETCDF)
endif(NETCDF_FOUND)
if(PNETCDF_FOUND)
include_directories(${PNETCDF_INCLUDES})
list(APPEND LAMMPS_LINK_LIBS ${PNETCDF_LIBRARIES})
add_definitions(-DLMP_HAS_PNETCDF)
endif(PNETCDF_FOUND)
if(PNETCDF_FOUND)
target_link_libraries(lammps PRIVATE PNetCDF::PNetCDF)
target_compile_definitions(lammps PRIVATE -DLMP_HAS_PNETCDF)
endif(PNETCDF_FOUND)
add_definitions(-DNC_64BIT_DATA=0x0020)
endif()
target_compile_definitions(lammps PRIVATE -DNC_64BIT_DATA=0x0020)

68
cmake/Modules/Packages/USER-OMP.cmake
View File

@ -1,42 +1,40 @@
if(PKG_USER-OMP)
set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
${USER-OMP_SOURCES_DIR}/thr_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
add_definitions(-DLMP_USER_OMP)
set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
${USER-OMP_SOURCES_DIR}/thr_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
target_compile_definitions(lammps PRIVATE -DLMP_USER_OMP)
set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
# detects styles which have USER-OMP version
RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
# detects styles which have USER-OMP version
RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
# manually add package dependent source files from USER-OMP that do not provide styles
# manually add package dependent source files from USER-OMP that do not provide styles
if(PKG_ASPHERE)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
endif()
if(PKG_ASPHERE)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
endif()
if(PKG_RIGID)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
endif()
if(PKG_RIGID)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
endif()
if(PKG_USER-REAXC)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
endif()
if(PKG_USER-REAXC)
list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
endif()
list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
include_directories(${USER-OMP_SOURCES_DIR})
endif()
target_sources(lammps PRIVATE ${USER-OMP_SOURCES})
target_include_directories(lammps PRIVATE ${USER-OMP_SOURCES_DIR})

191
cmake/Modules/Packages/USER-PLUMED.cmake
View File

@ -1,96 +1,103 @@
if(PKG_USER-PLUMED)
set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
set(PLUMED_MODE_VALUES static shared runtime)
set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
set(PLUMED_MODE_VALUES static shared runtime)
set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
set(PLUMED_LINK_LIBS "")
if(PLUMED_MODE STREQUAL "STATIC")
find_package(LAPACK REQUIRED)
find_package(BLAS REQUIRED)
find_package(GSL REQUIRED)
list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${GSL_LIBRARIES})
find_package(ZLIB QUIET)
if(ZLIB_FOUND)
list(APPEND PLUMED_LINK_LIBS ${ZLIB_LIBRARIES})
endif()
set(PLUMED_LINK_LIBS)
if(PLUMED_MODE STREQUAL "STATIC")
find_package(LAPACK REQUIRED)
find_package(BLAS REQUIRED)
find_package(GSL REQUIRED)
list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)
find_package(ZLIB QUIET)
if(ZLIB_FOUND)
list(APPEND PLUMED_LINK_LIBS ZLIB::ZLIB)
endif()
find_package(PkgConfig QUIET)
set(DOWNLOAD_PLUMED_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(PLUMED QUIET plumed)
if(PLUMED_FOUND)
set(DOWNLOAD_PLUMED_DEFAULT OFF)
endif()
find_package(FFTW3 QUIET)
if(FFTW3_FOUND)
list(APPEND PLUMED_LINK_LIBS FFTW3::FFTW3)
endif()
option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
if(DOWNLOAD_PLUMED)
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_MPI_CXX_COMPILER})
else()
set(PLUMED_CONFIG_MPI "--disable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_CXX_COMPILER})
endif()
if(BUILD_OMP)
set(PLUMED_CONFIG_OMP "--enable-openmp")
else()
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
message(STATUS "PLUMED download requested - we will build our own")
if(PLUMED_MODE STREQUAL "STATIC")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed.a")
elseif(PLUMED_MODE STREQUAL "SHARED")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
endif()
include(ExternalProject)
ExternalProject_Add(plumed_build
URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz
URL_MD5 204d2edae58d9b10ba3ad460cad64191
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
${CONFIGURE_REQUEST_PIC}
--enable-modules=all
${PLUMED_CONFIG_MPI}
${PLUMED_CONFIG_OMP}
CXX=${PLUMED_CONFIG_CXX}
CC=${PLUMED_CONFIG_CC}
BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
)
ExternalProject_get_property(plumed_build INSTALL_DIR)
set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
list(APPEND LAMMPS_DEPS plumed_build)
if(PLUMED_MODE STREQUAL "STATIC")
add_definitions(-D__PLUMED_WRAPPER_CXX=1)
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${PLUMED_LINK_LIBS} ${CMAKE_DL_LIBS})
elseif(PLUMED_MODE STREQUAL "SHARED")
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} ${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_DL_LIBS})
elseif(PLUMED_MODE STREQUAL "RUNTIME")
add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
endif()
set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed)
if(PLUMED_MODE STREQUAL "STATIC")
add_definitions(-D__PLUMED_WRAPPER_CXX=1)
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
elseif(PLUMED_MODE STREQUAL "SHARED")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
elseif(PLUMED_MODE STREQUAL "RUNTIME")
add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
endif()
list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})
endif()
include_directories(${PLUMED_INCLUDE_DIRS})
endif()
find_package(PkgConfig QUIET)
set(DOWNLOAD_PLUMED_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(PLUMED QUIET plumed)
if(PLUMED_FOUND)
set(DOWNLOAD_PLUMED_DEFAULT OFF)
endif()
endif()
option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
if(DOWNLOAD_PLUMED)
if(BUILD_MPI)
set(PLUMED_CONFIG_MPI "--enable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_MPI_CXX_COMPILER})
else()
set(PLUMED_CONFIG_MPI "--disable-mpi")
set(PLUMED_CONFIG_CC ${CMAKE_C_COMPILER})
set(PLUMED_CONFIG_CXX ${CMAKE_CXX_COMPILER})
endif()
if(BUILD_OMP)
set(PLUMED_CONFIG_OMP "--enable-openmp")
else()
set(PLUMED_CONFIG_OMP "--disable-openmp")
endif()
message(STATUS "PLUMED download requested - we will build our own")
if(PLUMED_MODE STREQUAL "STATIC")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed.a")
elseif(PLUMED_MODE STREQUAL "SHARED")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
endif()
include(ExternalProject)
ExternalProject_Add(plumed_build
URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz
URL_MD5 204d2edae58d9b10ba3ad460cad64191
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
${CONFIGURE_REQUEST_PIC}
--enable-modules=all
${PLUMED_CONFIG_MPI}
${PLUMED_CONFIG_OMP}
CXX=${PLUMED_CONFIG_CXX}
CC=${PLUMED_CONFIG_CC}
BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
)
ExternalProject_get_property(plumed_build INSTALL_DIR)
add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
add_dependencies(LAMMPS::PLUMED plumed_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
if(PLUMED_MODE STREQUAL "STATIC")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_WRAPPER_CXX=1")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "SHARED")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_HAS_DLOPEN=1;__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumedWrapper.a INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed)
add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
if(PLUMED_MODE STREQUAL "STATIC")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_WRAPPER_CXX=1")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
elseif(PLUMED_MODE STREQUAL "SHARED")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
elseif(PLUMED_MODE STREQUAL "RUNTIME")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_HAS_DLOPEN=1;__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
endif()
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

21
cmake/Modules/Packages/USER-QMMM.cmake
View File

@ -1,13 +1,12 @@
if(PKG_USER-QMMM)
enable_language(C)
enable_language(C)
if(NOT BUILD_LIB)
message(FATAL_ERROR "Building a QM/MM executable with USER-QMMM requires BUILD_LIB=yes")
endif()
if(NOT BUILD_SHARED_LIBS)
message(WARNING "It is recommended to use BUILD_SHARED_LIBS=yes with USER-QMMM")
endif()
add_library(qmmm STATIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm/libqmmm.c)
list(APPEND LAMMPS_LINK_LIBS qmmm)
target_include_directories(qmmm PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm)
if(NOT BUILD_SHARED_LIBS)
message(WARNING "It is recommended to use BUILD_SHARED_LIBS=yes with USER-QMMM")
endif()
add_library(qmmm STATIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm/libqmmm.c)
if(NOT BUILD_SHARED_LIBS)
install(TARGETS qmmm EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
endif()
set_target_properties(qmmm PROPERTIES OUTPUT_NAME lammps_qmmm${LAMMPS_MACHINE})
target_link_libraries(lammps PRIVATE qmmm)
target_include_directories(qmmm PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm)

8
cmake/Modules/Packages/USER-QUIP.cmake
View File

@ -1,5 +1,3 @@
if(PKG_USER-QUIP)
enable_language(Fortran)
find_package(QUIP REQUIRED)
list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES})
endif()
enable_language(Fortran)
find_package(QUIP REQUIRED)
target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})

132
cmake/Modules/Packages/USER-SCAFACOS.cmake
View File

@ -1,76 +1,62 @@
if(PKG_USER-SCAFACOS)
enable_language(Fortran)
enable_language(C)
enable_language(Fortran)
enable_language(C)
find_package(GSL REQUIRED)
find_package(PkgConfig QUIET)
find_package(MPI REQUIRED)
set(DOWNLOAD_SCAFACOS_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(SCAFACOS QUIET scafacos)
if(SCAFACOS_FOUND)
set(DOWNLOAD_SCAFACOS_DEFAULT OFF)
endif()
find_package(GSL REQUIRED)
find_package(PkgConfig QUIET)
find_package(MPI REQUIRED)
set(DOWNLOAD_SCAFACOS_DEFAULT ON)
if(PKG_CONFIG_FOUND)
pkg_check_modules(SCAFACOS QUIET scafacos)
if(SCAFACOS_FOUND)
set(DOWNLOAD_SCAFACOS_DEFAULT OFF)
endif()
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
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
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
--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}
F77=
BUILD_BYPRODUCTS
<INSTALL_DIR>/lib/libfcs.a
<INSTALL_DIR>/lib/libfcs_direct.a
<INSTALL_DIR>/lib/libfcs_ewald.a
<INSTALL_DIR>/lib/libfcs_fmm.a
<INSTALL_DIR>/lib/libfcs_p2nfft.a
<INSTALL_DIR>/lib/libfcs_p3m.a
<INSTALL_DIR>/lib/libfcs_near.a
<INSTALL_DIR>/lib/libfcs_gridsort.a
<INSTALL_DIR>/lib/libfcs_resort.a
<INSTALL_DIR>/lib/libfcs_redist.a
<INSTALL_DIR>/lib/libfcs_common.a
<INSTALL_DIR>/lib/libfcs_pnfft.a
<INSTALL_DIR>/lib/libfcs_pfft.a
<INSTALL_DIR>/lib/libfcs_fftw3_mpi.a
<INSTALL_DIR>/lib/libfcs_fftw3.a
)
ExternalProject_get_property(scafacos_build INSTALL_DIR)
set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})
set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include)
list(APPEND LAMMPS_DEPS scafacos_build)
# list and order from pkg_config file of ScaFaCoS build
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a)
list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a)
list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(SCAFACOS REQUIRED scafacos)
list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
endif()
include_directories(${SCAFACOS_INCLUDE_DIRS})
endif()
option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
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
--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
--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}
F77=
BUILD_BYPRODUCTS
<INSTALL_DIR>/lib/libfcs.a
<INSTALL_DIR>/lib/libfcs_direct.a
<INSTALL_DIR>/lib/libfcs_ewald.a
<INSTALL_DIR>/lib/libfcs_fmm.a
<INSTALL_DIR>/lib/libfcs_p2nfft.a
<INSTALL_DIR>/lib/libfcs_p3m.a
<INSTALL_DIR>/lib/libfcs_near.a
<INSTALL_DIR>/lib/libfcs_gridsort.a
<INSTALL_DIR>/lib/libfcs_resort.a
<INSTALL_DIR>/lib/libfcs_redist.a
<INSTALL_DIR>/lib/libfcs_common.a
<INSTALL_DIR>/lib/libfcs_pnfft.a
<INSTALL_DIR>/lib/libfcs_pfft.a
<INSTALL_DIR>/lib/libfcs_fftw3_mpi.a
<INSTALL_DIR>/lib/libfcs_fftw3.a
)
ExternalProject_get_property(scafacos_build INSTALL_DIR)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
add_library(LAMMPS::SCAFACOS UNKNOWN IMPORTED)
set_target_properties(LAMMPS::SCAFACOS PROPERTIES
IMPORTED_LOCATION "${INSTALL_DIR}/lib/libfcs.a"
INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include"
INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libfcs.a;${INSTALL_DIR}/lib/libfcs_direct.a;${INSTALL_DIR}/lib/libfcs_ewald.a;${INSTALL_DIR}/lib/libfcs_fmm.a;${INSTALL_DIR}/lib/libfcs_p2nfft.a;${INSTALL_DIR}/lib/libfcs_p3m.a;GSL::gsl;${INSTALL_DIR}/lib/libfcs_near.a;${INSTALL_DIR}/lib/libfcs_gridsort.a;${INSTALL_DIR}/lib/libfcs_resort.a;${INSTALL_DIR}/lib/libfcs_redist.a;${INSTALL_DIR}/lib/libfcs_common.a;${INSTALL_DIR}/lib/libfcs_pnfft.a;${INSTALL_DIR}/lib/libfcs_pfft.a;${INSTALL_DIR}/lib/libfcs_fftw3_mpi.a;${INSTALL_DIR}/lib/libfcs_fftw3.a;MPI::MPI_Fortran;MPI::MPI_C")
target_link_libraries(lammps PRIVATE LAMMPS::SCAFACOS)
add_dependencies(LAMMPS::SCAFACOS scafacos_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(SCAFACOS REQUIRED IMPORTED_TARGET scafacos)
target_link_libraries(lammps PRIVATE PkgConfig::SCAFACOS)
endif()

20
cmake/Modules/Packages/USER-SDPD.cmake
View File

@ -1,13 +1,13 @@
# Fix rigid/meso requires RIGID to be installed
if(PKG_USER-SDPD)
set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)
set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)
get_property(hlist GLOBAL PROPERTY FIX)
if(NOT PKG_RIGID)
list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
list(REMOVE_ITEM LIB_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
endif()
set_property(GLOBAL PROPERTY FIX "${hlist}")
include_directories(${USER-SDPD_SOURCES_DIR})
get_property(hlist GLOBAL PROPERTY FIX)
if(NOT PKG_RIGID)
list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
get_target_property(LAMMPS_SOURCES lammps SOURCES)
list(REMOVE_ITEM LAMMPS_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
set_property(TARGET lammps PROPERTY SOURCES ${LAMMPS_SOURCES})
endif()
set_property(GLOBAL PROPERTY FIX "${hlist}")
target_include_directories(lammps PRIVATE ${USER-SDPD_SOURCES_DIR})

57
cmake/Modules/Packages/USER-SMD.cmake
View File

@ -1,28 +1,31 @@
if(PKG_USER-SMD)
find_package(Eigen3 NO_MODULE)
if(EIGEN3_FOUND)
set(DOWNLOAD_EIGEN3_DEFAULT OFF)
else()
set(DOWNLOAD_EIGEN3_DEFAULT ON)
endif()
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
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/3.3.7.tar.gz
URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
)
ExternalProject_get_property(Eigen3_build SOURCE_DIR)
set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
list(APPEND LAMMPS_DEPS Eigen3_build)
else()
find_package(Eigen3 NO_MODULE)
mark_as_advanced(Eigen3_DIR)
if(NOT EIGEN3_FOUND)
message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
endif()
endif()
include_directories(${EIGEN3_INCLUDE_DIR})
find_package(Eigen3 NO_MODULE)
if(EIGEN3_FOUND)
set(DOWNLOAD_EIGEN3_DEFAULT OFF)
else()
set(DOWNLOAD_EIGEN3_DEFAULT ON)
endif()
option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
if(DOWNLOAD_EIGEN3)
message(STATUS "Eigen3 download requested - we will build our own")
include(ExternalProject)
ExternalProject_Add(Eigen3_build
URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
)
ExternalProject_get_property(Eigen3_build SOURCE_DIR)
add_library(LAMMPS::EIGEN3 INTERFACE IMPORTED)
set_target_properties(LAMMPS::EIGEN3 PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}")
target_link_libraries(lammps PRIVATE LAMMPS::EIGEN3)
add_dependencies(LAMMPS::EIGEN3 Eigen3_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(Eigen3 NO_MODULE)
mark_as_advanced(Eigen3_DIR)
if(NOT EIGEN3_FOUND)
message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
endif()
target_link_libraries(lammps PRIVATE Eigen3::Eigen)
endif()

10
cmake/Modules/Packages/USER-VTK.cmake
View File

@ -1,6 +1,4 @@
if(PKG_USER-VTK)
find_package(VTK REQUIRED NO_MODULE)
include(${VTK_USE_FILE})
add_definitions(-DLAMMPS_VTK)
list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
endif()
find_package(VTK REQUIRED NO_MODULE)
include(${VTK_USE_FILE})
target_compile_definitions(lammps PRIVATE -DLAMMPS_VTK)
target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES})

88
cmake/Modules/Packages/VORONOI.cmake
View File

@ -1,43 +1,47 @@
if(PKG_VORONOI)
find_package(VORO)
if(VORO_FOUND)
set(DOWNLOAD_VORO_DEFAULT OFF)
else()
set(DOWNLOAD_VORO_DEFAULT ON)
endif()
option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
if(DOWNLOAD_VORO)
message(STATUS "Voro++ download requested - we will build our own")
include(ExternalProject)
if(BUILD_SHARED_LIBS)
set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
else()
set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
endif()
if(APPLE)
get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
else()
set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
endif()
ExternalProject_Add(voro_build
URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
URL_MD5 2338b824c3b7b25590e18e8df5d68af9
CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/src/libvoro++.a
)
ExternalProject_get_property(voro_build SOURCE_DIR)
set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a)
set(VORO_INCLUDE_DIRS ${SOURCE_DIR}/src)
list(APPEND LAMMPS_DEPS voro_build)
else()
find_package(VORO)
if(NOT VORO_FOUND)
message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
endif()
endif()
include_directories(${VORO_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
find_package(VORO)
if(VORO_FOUND)
set(DOWNLOAD_VORO_DEFAULT OFF)
else()
set(DOWNLOAD_VORO_DEFAULT ON)
endif()
option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
if(DOWNLOAD_VORO)
message(STATUS "Voro++ download requested - we will build our own")
include(ExternalProject)
if(BUILD_SHARED_LIBS)
set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
else()
set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
endif()
if(APPLE)
get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
else()
set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
endif()
ExternalProject_Add(voro_build
URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
URL_MD5 2338b824c3b7b25590e18e8df5d68af9
CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
BUILD_BYPRODUCTS <SOURCE_DIR>/src/libvoro++.a
)
ExternalProject_get_property(voro_build SOURCE_DIR)
file(MAKE_DIRECTORY ${SOURCE_DIR}/src)
add_library(LAMMPS::VORO UNKNOWN IMPORTED)
set_target_properties(LAMMPS::VORO PROPERTIES
IMPORTED_LOCATION "${SOURCE_DIR}/src/libvoro++.a"
INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/src")
target_link_libraries(lammps PRIVATE LAMMPS::VORO)
add_dependencies(LAMMPS::VORO voro_build)
if(NOT BUILD_SHARED_LIBS)
install(CODE "MESSAGE(FATAL_ERROR \"Installing liblammps with downloaded libraries is currently not supported.\")")
endif()
else()
find_package(VORO)
if(NOT VORO_FOUND)
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()
target_link_libraries(lammps PRIVATE VORO::VORO)
endif()

7
cmake/Modules/Testing.cmake
View File

@ -2,7 +2,7 @@
# Testing
###############################################################################
option(ENABLE_TESTING "Enable testing" OFF)
if(ENABLE_TESTING AND BUILD_EXE)
if(ENABLE_TESTING)
enable_testing()
option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master")
@ -28,7 +28,7 @@ if(ENABLE_TESTING AND BUILD_EXE)
"https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
endif()
add_test(ShowHelp ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -help)
add_test(NAME ShowHelp COMMAND $<TARGET_FILE:lmp> -help)
if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
message(STATUS "Running test discovery...")
@ -42,8 +42,7 @@ if(ENABLE_TESTING AND BUILD_EXE)
string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
set(TEST_NAME "test_core_${TEST_NAME}_serial")
add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})
set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})
add_test(NAME ${TEST_NAME} COMMAND $<TARGET_FILE:lmp> -in ${SCRIPT_NAME} WORKING_DIRECTORY ${PARENT_DIR})
endforeach()
list(LENGTH TEST_SCRIPTS NUM_TESTS)

2320
cmake/README.md
View File

File diff suppressed because it is too large Load Diff

10
cmake/pkgconfig/liblammps.pc.in
View File

@ -18,12 +18,6 @@
# myapp_CFLAGS = $(LAMMPS_CFLAGS)
# myapp_LDADD = $(LAMMPS_LIBS)
# Use this in CMake:
# CMakeLists.txt:
# find_package(PkgConfig)
# pkg_check_modules(LAMMPS IMPORTED_TARGET lammps)
# target_link_libraries(<lib> PkgConfig::LAMMPS)
prefix=@CMAKE_INSTALL_PREFIX@
libdir=@CMAKE_INSTALL_FULL_LIBDIR@
includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
@ -31,8 +25,8 @@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
Name: liblammps@LAMMPS_MACHINE@
Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
URL: http://lammps.sandia.gov
Version: @LAMMPS_VERSION@
Version: @PROJECT_VERSION@
Requires:
Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
Libs: -L${libdir} -llammps@LAMMPS_MACHINE@
Libs.private: -lm
Cflags: -I${includedir} @LAMMPS_API_DEFINES@

1
cmake/presets/intel.cmake
View File

@ -2,7 +2,6 @@
set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS "-O3 -DNDEBG" CACHE STRING "" FORCE)
set(MPI_CXX "icpc" CACHE STRING "" FORCE)
set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)

11
cmake/presets/kokkos-cuda.cmake Normal file
View File

@ -0,0 +1,11 @@
# preset that enables KOKKOS and selects CUDA compilation with OpenMP
# enabled as well. This preselects CC 5.0 as default GPU arch, since
# that is compatible with all higher CC, but not the default CC 3.5
set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA ON CACHE BOOL "" FORCE)
set(Kokkos_ARCH_MAXWELL50 on CACHE BOOL "" FORCE)
set(BUILD_OMP ON CACHE BOOL "" FORCE)
get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)

6
cmake/presets/kokkos-openmp.cmake Normal file
View File

@ -0,0 +1,6 @@
# preset that enables KOKKOS and selects OpenMP (only) compilation
set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA OFF CACHE BOOL "" FORCE)
set(BUILD_OMP ON CACHE BOOL "" FORCE)

5
cmake/presets/kokkos-serial.cmake Normal file
View File

@ -0,0 +1,5 @@
# preset that enables KOKKOS and selects serial compilation only
set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_OPENMP OFF CACHE BOOL "" FORCE)
set(Kokkos_ENABLE_CUDA OFF CACHE BOOL "" FORCE)

3
cmake/presets/mingw-cross.cmake
View File

@ -23,6 +23,7 @@ set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
set(CMAKE_TUNE_FLAGS "-Wno-missing-include-dirs" CACHE STRING "" FORCE)
set(CMAKE_EXE_LINKER_FLAGS "--enable-stdcall-fixup" CACHE STRING "" FORCE)
set(CMAKE_EXE_LINKER_FLAGS "-Wl,--enable-stdcall-fixup" CACHE STRING "" FORCE)
set(CMAKE_SHARED_LINKER_FLAGS "-Wl,--enable-stdcall-fixup" CACHE STRING "" FORCE)
set(BUILD_TOOLS ON CACHE BOOL "" FORCE)
set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")

17
doc/Makefile
View File

@ -12,6 +12,7 @@ PYTHON = $(shell which python3)
VIRTUALENV = virtualenv
HAS_PYTHON3 = NO
HAS_VIRTUALENV = NO
HAS_PDFLATEX = NO
ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
HAS_PYTHON3 = YES
@ -27,6 +28,11 @@ VIRTUALENV = virtualenv
HAS_VIRTUALENV = YES
endif
ifeq ($(shell which pdflatex >/dev/null 2>&1; echo $$?), 0)
HAS_PDFLATEX = YES
endif
SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check
@ -51,7 +57,7 @@ help:
# ------------------------------------------
clean-all: clean
rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees $(BUILDDIR)/mathjax
rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees $(BUILDDIR)/mathjax Manual.pdf Developer.pdf
clean: clean-spelling
rm -rf html epub latex
@ -77,7 +83,7 @@ html: $(ANCHORCHECK) $(MATHJAX)
@rm -rf html/JPG
@cp -r src/PDF html/PDF
@mkdir -p html/JPG
@cp `grep -A2 '\.\. .*image::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
@rm -rf html/PDF/.[sg]*
@mkdir -p html/_static/mathjax
@cp -r $(MATHJAX)/es5 html/_static/mathjax/
@ -86,8 +92,7 @@ html: $(ANCHORCHECK) $(MATHJAX)
spelling: $(VENV) utils/sphinx-config/false_positives.txt
@(\
. $(VENV)/bin/activate ;\
pip install sphinxcontrib-spelling ;\
cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ; env PYTHONWARNINGS= \
sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
deactivate ;\
)
@ -113,6 +118,7 @@ mobi: epub
@echo "Conversion finished. The MOBI manual file is created."
pdf: $(ANCHORCHECK)
@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
@(\
cd src/Developer; \
pdflatex developer; \
@ -187,7 +193,10 @@ $(VENV):
@( \
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
. $(VENV)/bin/activate; \
pip install --upgrade pip; \
pip install Sphinx; \
pip install sphinxcontrib-spelling ;\
pip install breathe; \
deactivate;\
)

6
doc/README
View File

@ -93,12 +93,18 @@ support for PDFLaTeX. Also the following LaTeX packages need
to be installed (e.g. from texlive):
- amsmath
- babel
- capt-of
- cmap
- fncychap
- framed
- geometry
- hyperref
- hypcap
- needspace
- times
- tabulary
- upquote
- wrapfig
----------------
Installing prerequisites for epub build

2
doc/src/.gitignore vendored
View File

@ -1,3 +1 @@
/Eqs
/JPG
/false_positives.txt

14
doc/src/Build.rst
View File

@ -1,12 +1,14 @@
Build LAMMPS
************
LAMMPS can be built as an executable or library from source code via
either traditional makefiles (which may require manual editing)
for use with GNU make or gmake, or a build environment generated by CMake
(Unix Makefiles, Xcode, Visual Studio, KDevelop or more). As an
alternative you can download a package with pre-built executables
as described on the :doc:`Install <Install>` doc page.
LAMMPS is built as a library and an executable from source code using
either traditional makefiles for use with GNU make (which may require
manual editing), or using a build environment generated by CMake (Unix
Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
As an alternative you can download a package with pre-built executables
or automated build trees as described on the :doc:`Install <Install>`
doc page.
.. toctree::
:maxdepth: 1

323
doc/src/Build_basics.rst
View File

@ -6,7 +6,8 @@ CMake and make:
* :ref:`Serial vs parallel build <serial>`
* :ref:`Choice of compiler and compile/link options <compile>`
* :ref:`Build LAMMPS as an executable or a library <exe>`
* :ref:`Build the LAMMPS executable and library <exe>`
* :ref:`Including and removing debug support <debug>`
* :ref:`Build the LAMMPS documentation <doc>`
* :ref:`Install LAMMPS after a build <install>`
@ -15,7 +16,7 @@ CMake and make:
.. _serial:
Serial vs parallel build
-------------------------------------
------------------------
LAMMPS is written to use the ubiquitous `MPI (Message Passing Interface)
<https://en.wikipedia.org/wiki/Message_Passing_Interface>`_ library API
@ -28,8 +29,8 @@ MPI STUBS library.
Independent of the distributed memory MPI parallelization, parts of
LAMMPS are also written with support for shared memory parallelization
using the OpenMP threading standard. A more detailed discussion of that
is below.
using the `OpenMP <https://en.wikipedia.org/wiki/OpenMP>`_ threading
standard. A more detailed discussion of that is below.
**CMake build**\ :
@ -41,7 +42,7 @@ is below.
# no default value
The executable created by CMake (after running make) is named ``lmp`` unless
the LAMMPS_MACHINE option is set. When setting ``LAMMPS_MACHINE=name``
the ``LAMMPS_MACHINE`` option is set. When setting ``LAMMPS_MACHINE=name``
the executable will be called ``lmp_name``. Using ``BUILD_MPI=no`` will
enforce building a serial executable using the MPI STUBS library.
@ -55,18 +56,20 @@ The build with traditional makefiles has to be done inside the source folder ``s
make serial # serial build, produces lmp_serial using Makefile/serial
make mybox # uses Makefile.mybox to produce lmp_mybox
Any "make machine" command will look up the make settings from a file
Makefile.machine, create a folder Obj_machine with all objects and
generated files and an executable called ``lmp_machine``\ . The standard
parallel build with ``make mpi`` assumes a standard MPI installation with
MPI compiler wrappers where all necessary compiler and linker flags to
get access and link with the suitable MPI headers and libraries are set
by the wrapper programs. For other cases or the serial build, you have
to adjust the make file variables ``MPI_INC``, ``MPI_PATH``, ``MPI_LIB``
as well as ``CC`` and ``LINK``\ . To enable OpenMP threading usually
a compiler specific flag needs to be added to the compile and link
commands. For the GNU compilers, this is ``-fopenmp``\ , which can be
added to the ``CC`` and ``LINK`` makefile variables.
Any ``make machine`` command will look up the make settings from a file
``Makefile.machine`` in the folder ``src/MAKE`` or one of its
sub-directories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a folder
``Obj_machine`` with all objects and generated files and an executable
called ``lmp_machine``\ . The standard parallel build with ``make mpi``
assumes a standard MPI installation with MPI compiler wrappers where all
necessary compiler and linker flags to get access and link with the
suitable MPI headers and libraries are set by the wrapper programs. For
other cases or the serial build, you have to adjust the make file
variables ``MPI_INC``, ``MPI_PATH``, ``MPI_LIB`` as well as ``CC`` and
``LINK``\ . To enable OpenMP threading usually a compiler specific flag
needs to be added to the compile and link commands. For the GNU
compilers, this is ``-fopenmp``\ , which can be added to the ``CC`` and
``LINK`` makefile variables.
For the serial build the following make variables are set (see src/MAKE/Makefile.serial):
@ -80,18 +83,19 @@ For the serial build the following make variables are set (see src/MAKE/Makefile
You also need to build the STUBS library for your platform before making
LAMMPS itself. A ``make serial`` build does this for you automatically,
otherwise, type ``make mpi-stubs`` from the src directory, or ``make`` from
the src/STUBS dir. If the build fails, you will need to edit the
STUBS/Makefile for your platform. The stubs library does not provide
MPI/IO functions required by some LAMMPS packages, e.g. MPIIO or USER-LB,
and thus is not compatible with those packages.
otherwise, type ``make mpi-stubs`` from the src directory, or ``make``
from the ``src/STUBS`` dir. If the build fails, you may need to edit
the ``STUBS/Makefile`` for your platform. The stubs library does not
provide MPI/IO functions required by some LAMMPS packages,
e.g. ``MPIIO`` or ``USER-LB``, and thus is not compatible with those
packages.
.. note::
The file ``src/STUBS/mpi.c`` provides a CPU timer function called
MPI_Wtime() that calls gettimeofday() . If your operating system
does not support gettimeofday() , you will need to insert code to
call another timer. Note that the ANSI-standard function clock()
``MPI_Wtime()`` that calls ``gettimeofday()``. If your operating system
does not support ``gettimeofday()``, you will need to insert code to
call another timer. Note that the ANSI-standard function ``clock()``
rolls over after an hour or so, and is therefore insufficient for
timing long LAMMPS simulations.
@ -111,20 +115,22 @@ self-installed MPICH or OpenMPI, so you should study the provided
documentation to find out how to build and link with it.
The majority of OpenMP (threading) support in LAMMPS is provided by the
USER-OMP package; see the :doc:`Speed omp <Speed_omp>` doc page for
details. The USER-INTEL package also includes OpenMP threading (it is
compatible with USER-OMP) and adds vectorization support when compiled
with compatible compilers, in particular the Intel compilers on top of
OpenMP. Also, the KOKKOS package can be compiled to include OpenMP
threading.
``USER-OMP`` package; see the :doc:`Speed omp <Speed_omp>` doc page for
details. The ``USER-INTEL`` package also includes OpenMP threading (it
is compatible with ``USER-OMP`` and will usually fall back on styles
from that package, if a ``USER-INTEL`` does not exist) and adds
vectorization support when compiled with compatible compilers, in
particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
package can be compiled to include OpenMP threading.
In addition, there are a few commands in LAMMPS that have native OpenMP
support included as well. These are commands in the MPIIO, SNAP,
USER-DIFFRACTION, and USER-DPD packages. In addition some packages
support OpenMP threading indirectly through the libraries they interface
to: e.g. LATTE and USER-COLVARS. See the :doc:`Packages details
<Packages_details>` doc page for more info on these packages and the doc
pages for their respective commands for OpenMP threading info.
support included as well. These are commands in the ``MPIIO``,
``SNAP``, ``USER-DIFFRACTION``, and ``USER-DPD`` packages. In addition
some packages support OpenMP threading indirectly through the libraries
they interface to: e.g. ``LATTE``, ``KSPACE``, and ``USER-COLVARS``.
See the :doc:`Packages details <Packages_details>` doc page for more
info on these packages and the doc pages for their respective commands
for OpenMP threading info.
For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
and turn on their native OpenMP support and turn on their native OpenMP
@ -142,14 +148,15 @@ please refer to its documentation.
**OpenMP Compiler compatibility info**\ :
Some compilers do not fully support the ``default(none)`` directive
and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
semantics, which are incompatible with the OpenMP 3.1 semantics used
in LAMMPS (for maximal compatibility with compiler versions in use).
In those case, all ``default(none)`` directives (which aid in detecting
incorrect and unwanted sharing) can be replaced with ``default(shared)``
while dropping all ``shared()`` directives. The script
'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate
this conversion.
and others (e.g. GCC version 9 and beyond, Clang version 10 and later)
may implement strict OpenMP 4.0 and later semantics, which are incompatible
with the OpenMP 3.1 semantics used in LAMMPS for maximal compatibility
with compiler versions in use. If compilation with OpenMP enabled fails
because of your compiler requiring strict OpenMP 4.0 semantic, you can
change the behavior by adding ``-D LAMMPS_OMP_COMPAT=4`` to the ``LMP_INC``
variable in your makefile, or add it to the command line while configuring
with CMake. CMake will detect the suitable setting for the GNU, Clang,
and Intel compilers.
----------
@ -158,15 +165,18 @@ this conversion.
Choice of compiler and compile/link options
---------------------------------------------------------
The choice of compiler and compiler flags can be important for
The choice of compiler and compiler flags can be important for maximum
performance. Vendor provided compilers for a specific hardware can
produce faster code than open-source compilers like the GNU compilers.
On x86 hardware most popular compilers are quite similar in performance
of C/C++ code at high optimization levels. When using the USER-INTEL
package, there is a distinct advantage in using the `Intel C++ compiler
<intel_>`_ due to much improved vectorization through SSE and AVX
instructions on compatible hardware as the source code includes changes
and compiler directives to enable high degrees of vectorization.
On the most common x86 hardware most popular C++ compilers are quite
similar in performance of C/C++ code at high optimization levels. When
using the ``USER-INTEL`` package, there is a distinct advantage in using
the `Intel C++ compiler <intel_>`_ due to much improved vectorization
through SSE and AVX instructions on compatible hardware as the source
code includes changes and Intel compiler specific directives to enable
high degrees of vectorization. This may change over time as equivalent
vectorization directives are included into OpenMP standard revisions and
other compilers adopt them.
.. _intel: https://software.intel.com/en-us/intel-compilers
@ -177,17 +187,20 @@ LAMMPS.
**CMake build**\ :
By default CMake will use a compiler it finds and it will add
optimization flags appropriate to that compiler and any
:doc:`accelerator packages <Speed_packages>` you have included in the
build.
By default CMake will use a compiler it finds according to internal
preferences and it will add optimization flags appropriate to that
compiler and any :doc:`accelerator packages <Speed_packages>` you have
included in the build.
You can tell CMake to look for a specific compiler with these variable
settings. Likewise you can specify the corresponding ``CMAKE_*_FLAGS``
variables if you want to experiment with alternate optimization flags.
You should specify all 3 compilers, so that the small number of LAMMPS
source files written in C or Fortran are built with a compiler consistent
with the one used for all the C++ files:
You can tell CMake to look for a specific compiler with setting CMake
variable during configuration. For a few common choices, there are also
presets in the ``cmake/presets`` folder. For convenience, there is a
``CMAKE_TUNE_FLAGS`` variable that can be set to apply global compiler
options. More on that below, but you can also specify the corresponding
``CMAKE_*_FLAGS`` variables individually if you want to experiment with
alternate optimization flags. You should specify all 3 compilers, so
that the (few) LAMMPS source files written in C or Fortran are built
with a compiler consistent with the one used for the C++ files:
.. code-block:: bash
@ -210,16 +223,17 @@ A few example command lines are:
# Building with LLVM/Clang Compilers:
cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
For compiling with the Clang/LLVM compilers a special CMake preset is
included that can be loaded with `-C ../cmake/presets/clang.cmake`.
For compiling with the Clang/LLVM compilers a CMake preset is provided that
can be loaded with `-C ../cmake/presets/clang.cmake`. Similarly,
`-C ../cmake/presets/intel.cmake` should switch the
In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add compiler
flags to tune for optimal performance on given hosts. By default these are
initialized to some compiler specific flags, where known, to optimize the
LAMMPS executable with optimizations and instructions available on the host
where LAMMPS is compiled. For example, for Intel compilers this would be
``-xHost`` and for GNU compilers this would be ``-march=native``. To turn
these flags off, set ``-D CMAKE_TUNE_FLAGS=``.
In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
compiler flags to tune for optimal performance on given hosts. By
default these are initialized to some compiler specific flags, to
optimize the LAMMPS executable with optimizations and instructions
available on the host where LAMMPS is compiled. For example, for Intel
compilers this would be ``-xHost`` and for GNU compilers this would be
``-march=native``. To turn these flags off, do ``-D CMAKE_TUNE_FLAGS=``.
.. note::
@ -235,11 +249,11 @@ these flags off, set ``-D CMAKE_TUNE_FLAGS=``.
The "compiler/linker settings" section of a Makefile.machine lists
compiler and linker settings for your C++ compiler, including
optimization flags. For a parallel build it is recommended to use
mpicxx or mpiCC, since these compiler wrappers will include a variety of
settings appropriate for your MPI installation and thus avoiding the
guesswork of finding the right flags.
``mpicxx`` or ``mpiCC``, since these compiler wrappers will include a
variety of settings appropriate for your MPI installation and thus
avoiding the guesswork of finding the right flags.
Parallel build (see src/MAKE/Makefile.mpi):
Parallel build (see ``src/MAKE/Makefile.mpi``):
.. code-block:: bash
@ -248,7 +262,7 @@ Parallel build (see src/MAKE/Makefile.mpi):
LINK = mpicxx
LINKFLAGS = -g -O
Serial build (see src/MAKE/Makefile.serial):
Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``):
.. code-block:: make
@ -257,17 +271,35 @@ Serial build (see src/MAKE/Makefile.serial):
LINK = g++
LINKFLAGS = -g -O
.. note::
If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>`
included, there may be specific optimization flags that are either
required or recommended to enable required features and to achieve
optimal performance. You need to include these in the CCFLAGS and
LINKFLAGS settings above. For details, see the individual package
doc pages listed on the :doc:`Speed packages <Speed_packages>` doc
page. Or examine these files in the src/MAKE/OPTIONS directory.
They correspond to each of the 5 accelerator packages and their
hardware variants:
If compilation stops with a message like the following:
.. code-block::
g++ -g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I../STUBS -c ../main.cpp
In file included from ../pointers.h:24:0,
from ../input.h:17,
from ../main.cpp:16:
../lmptype.h:34:2: error: #error LAMMPS requires a C++11 (or later) compliant compiler. Enable C++11 compatibility or upgrade the compiler.
then you have either an unsupported (old) compiler or you have to
turn on C++11 mode. The latter applies to GCC 4.8.x shipped with
RHEL 7.x and CentOS 7.x. For those compilers, you need to add the
``-std=c++11`` flag. Otherwise, you would have to install a newer
compiler that supports C++11; either as a binary package or through
compiling from source.
If you build LAMMPS with any :doc:`accelerator packages
<Speed_packages>` included, there may be specific optimization flags
that are either required or recommended to enable required features and
to achieve optimal performance. You need to include these in the
CCFLAGS and LINKFLAGS settings above. For details, see the individual
package doc pages listed on the :doc:`Speed packages <Speed_packages>`
doc page. Or examine these files in the src/MAKE/OPTIONS directory.
They correspond to each of the 5 accelerator packages and their hardware
variants:
.. code-block:: bash
@ -284,69 +316,74 @@ Serial build (see src/MAKE/Makefile.serial):
.. _exe:
Build LAMMPS as an executable or a library
----------------------------------------------------
Build the LAMMPS executable and library
---------------------------------------
LAMMPS can be built as either an executable or as a static or shared
library. The LAMMPS library can be called from another application or
a scripting language. See the :doc:`Howto couple <Howto_couple>` doc
LAMMPS is always built as a library of C++ classes plus an executable.
The executable is a simple ``main()`` function that sets up MPI and then
creates a LAMMPS class instance from the LAMMPS library, which
will then process commands provided via a file or from the console
input. The LAMMPS library can also be called from another application
or a scripting language. See the :doc:`Howto couple <Howto_couple>` doc
page for more info on coupling LAMMPS to other codes. See the
:doc:`Python <Python_head>` doc page for more info on wrapping and
running LAMMPS from Python via its library interface.
**CMake build**\ :
For CMake builds, you can select through setting CMake variables which
files the compilation produces during the configuration step. If none
are set, defaults are applied.
For CMake builds, you can select through setting CMake variables between
building a shared or a static LAMMPS library and what kind of suffix is
added to them (in case you want to concurrently install multiple variants
of binaries with different settings). If none are set, defaults are applied.
.. code-block:: bash
-D BUILD_EXE=value # yes (default) or no
-D BUILD_LIB=value # yes or no (default)
-D BUILD_SHARED_LIBS=value # yes or no (default)
-D LAMMPS_LIB_SUFFIX=name # name = mpi, serial, mybox, titan, laptop, etc
-D LAMMPS_MACHINE=name # name = mpi, serial, mybox, titan, laptop, etc
# no default value
Setting ``BUILD_EXE=no`` will not produce an executable. Setting
``BUILD_LIB=yes`` will produce a static library named ``liblammps.a``\ .
Setting both ``BUILD_LIB=yes`` and ``BUILD_SHARED_LIBS=yes`` will produce a
shared library named ``liblammps.so`` instead. If ``LAMMPS_LIB_SUFFIX=name``
is set in addition, the name of the generated libraries will be changed to
either ``liblammps_name.a`` or ``liblammps_name.so``\ , respectively.
The compilation will always produce a LAMMPS library and an executable
linked to it. By default this will be a static library named
``liblammps.a`` and an executable named ``lmp`` Setting
``BUILD_SHARED_LIBS=yes`` will instead produce a shared library called
``liblammps.so`` (or ``liblammps.dylib`` or ``liblammps.dll`` depending
on the platform) If ``LAMMPS_MACHINE=name`` is set in addition, the name
of the generated libraries will be changed to either
``liblammps_name.a`` or ``liblammps_name.so``\ , respectively and the
executable will be called ``lmp_name``.
**Traditional make**\ :
With the traditional makefile based build process, the choice of
the generated executable or library depends on the "mode" setting.
Several options are available and ``mode=exe`` is the default.
Several options are available and ``mode=static`` is the default.
.. code-block:: bash
make machine # build LAMMPS executable lmp_machine
make mode=exe machine # same as "make machine"
make mode=lib machine # build LAMMPS static lib liblammps_machine.a
make mode=shlib machine # build LAMMPS shared lib liblammps_machine.so
make mode=shexe machine # same as "mode=exe" but uses objects from "mode=shlib"
make mode=static machine # same as "make machine"
make mode=shared machine # build LAMMPS shared lib liblammps_machine.so instead
The two "exe" builds will generate and executable ``lmp_machine``\ ,
while the two library builds will create a file ``liblammps_machine.a``
or ``liblammps_machine.so``\ . They will also create generic soft links,
named ``liblammps.a`` and ``liblammps.so``\ , which point to the specific
The "static" build will generate a static library called
``liblammps_machine.a`` and an executable named ``lmp_machine``\ , while
the "shared" build will generate a shared library
``liblammps_machine.so`` instead and ``lmp_machine`` will be linked to
it. The build step will also create generic soft links, named
``liblammps.a`` and ``liblammps.so``\ , which point to the specific
``liblammps_machine.a/so`` files.
**CMake and make info**\ :
Note that for a shared library to be usable by a calling program, all
the auxiliary libraries it depends on must also exist as shared
libraries. This will be the case for libraries included with LAMMPS,
such as the dummy MPI library in src/STUBS or any package libraries in
the lib/packages directory, since they are always built in a shared
library compatible way using the ``-fPIC`` switch. However, if a library
like MPI or FFTW does not exist as a shared library, the shared library
build may generate an error. This means you will need to install a
shared library version of the auxiliary library. The build instructions
for the library should tell you how to do this.
Note that for creating a shared library, all the libraries it depends on
must be compiled to be compatible with shared libraries. This should be
the case for libraries included with LAMMPS, such as the dummy MPI
library in ``src/STUBS`` or any package libraries in the ``lib``
directory, since they are always built in a shared library compatible
way using the ``-fPIC`` compiler switch. However, if an auxiliary
library (like MPI or FFTW) does not exist as a compatible format, the
shared library linking step may generate an error. This means you will
need to install a compatible version of the auxiliary library. The
build instructions for that library should tell you how to do this.
As an example, here is how to build and install the `MPICH library
<mpich_>`_, a popular open-source version of MPI, as a shared library
@ -360,10 +397,12 @@ in the default /usr/local/lib location:
make
make install
You may need to use ``sudo make install`` in place of the last line if you
do not have write privileges for ``/usr/local/lib``. The end result should
be the file ``/usr/local/lib/libmpich.so``. On many Linux installations the
folder ``${HOME}/.local`` is an alternative to using ``/usr/local`` and does
You may need to use ``sudo make install`` in place of the last line if
you do not have write privileges for ``/usr/local/lib`` or use the
``--prefix`` configuration option to select an installation folder,
where you do have write access. The end result should be the file
``/usr/local/lib/libmpich.so``. On many Linux installations the folder
``${HOME}/.local`` is an alternative to using ``/usr/local`` and does
not require superuser or sudo access. In that case the configuration
step becomes:
@ -371,12 +410,41 @@ step becomes:
./configure --enable-shared --prefix=${HOME}/.local
Avoiding using "sudo" for custom software installation (i.e. from source
Avoiding to use "sudo" for custom software installation (i.e. from source
and not through a package manager tool provided by the OS) is generally
recommended to ensure the integrity of the system software installation.
----------
.. _debug:
Excluding or removing debug support
-----------------------------------
By default the compilation settings will include the *-g* flag which
instructs the compiler to include debug information (e.g. which line of
source code a particular instruction correspond to). This can be
extremely useful in case LAMMPS crashes and can help to provide crucial
information in :doc:`tracking down the origin of a crash <Errors_debug>`
and help the LAMMPS developers fix bugs in the source code. However,
this increases the storage requirements for object files, libraries, and
the executable 3-5 fold.
If this is a concern, you can change the compilation settings or remove
the debug information from the LAMMPS executable:
- **Traditional make**: edit your ``Makefile.<machine>`` to remove the
*-g* flag from the ``CCFLAGS`` and ``LINKFLAGS`` definitions
- **CMake**: use ``-D CMAKE_BUILD_TYPE=Release`` or explicitly reset
the applicable compiler flags (best done using the text mode or
graphical user interface).
- **Remove debug info**: If you are only concerned about the executable
being too large, you can use the ``strip`` tool (e.g. ``strip
lmp_serial``) to remove the debug information from the executable file.
Do not strip libraries or object files, as that will render them unusable.
----------
.. _doc:
Build the LAMMPS documentation
@ -427,7 +495,8 @@ It is also possible to create the HTML version of the manual within
the :doc:`CMake build directory <Build_cmake>`. The reason for this
option is to include the installation of the HTML manual pages into
the "install" step when installing LAMMPS after the CMake build via
``make install``.
``make install``. The documentation build is included in the default
build target, but can also be requested independently with ``make doc``.
.. code-block:: bash

316
doc/src/Build_cmake.rst
View File

@ -1,205 +1,158 @@
Build LAMMPS with CMake
=======================
This page is a short summary of how to use CMake to build LAMMPS.
Details on CMake variables that enable specific LAMMPS build options
are given on the pages linked to from the :doc:`Build <Build>` doc page.
This page describes how to use `CMake <https://cmake.org>`_ in general
to build LAMMPS. Details for specific compile time settings and options
to enable and configure add-on packages are discussed with those
packages. Links to those pages on the :doc:`Build overview <Build>`
page.
Richard Berger (Temple U) has also written a `more comprehensive guide <https://github.com/lammps/lammps/blob/master/cmake/README.md>`_
for how to use CMake to build LAMMPS. If you are new to CMake it is a
good place to start.
The following text assumes some familiarity with CMake and focuses on
using the command line tool ``cmake`` and what settings are supported
for building LAMMPS. A more detailed tutorial on how to use ``cmake``
itself, the text mode or graphical user interface, change the generated
output files for different build tools and development environments is
on a :doc:`separate page <Howto_cmake>`.
----------
.. note::
LAMMPS currently requires that CMake version 3.10 or later is available;
version 3.12 or later is preferred.
.. warning::
You must not mix the :doc:`traditional make based <Build_make>`
LAMMPS build procedure with using CMake. Thus no packages may be
installed or a build been previously attempted in the LAMMPS source
directory by using ``make <machine>``. CMake will detect if this is
the case and generate an error. To remove conflicting files from the
``src`` you can use the command ``make no-all purge`` which will
un-install all packages and delete all auto-generated files.
Advantages of using CMake
^^^^^^^^^^^^^^^^^^^^^^^^^
CMake is an alternative to compiling LAMMPS in the traditional way
through :doc:`(manually customized) makefiles <Build_make>` and a recent
addition to LAMMPS thanks to the efforts of Christoph Junghans (LANL)
and Richard Berger (Temple U). Using CMake has multiple advantages that
are specifically helpful for people with limited experience in compiling
software or for people that want to modify or extend LAMMPS.
- CMake can detect available hardware, tools, features, and libraries
and adapt the LAMMPS default build configuration accordingly.
- CMake can generate files for different build tools and integrated
development environments (IDE).
- CMake supports customization of settings with a text mode or graphical
user interface. No knowledge of file formats or and complex command
line syntax required.
- All enabled components are compiled in a single build operation.
- Automated dependency tracking for all files and configuration options.
- Support for true out-of-source compilation. Multiple configurations
and settings with different choices of LAMMPS packages, settings, or
compilers can be configured and built concurrently from the same
source tree.
- Simplified packaging of LAMMPS for Linux distributions, environment
modules, or automated build tools like `Homebrew <https://brew.sh/>`_.
- Integration of automated regression testing (the LAMMPS side for that
is still under development).
.. _cmake_build:
Getting started
^^^^^^^^^^^^^^^
Building LAMMPS with CMake is a two-step process. First you use CMake
to create a build environment in a new directory. On Linux systems,
this will be by default based on Unix-style makefiles for use with make.
Then you use the *make* command to build LAMMPS, which uses the created
Makefile(s). Example:
to generate a build environment in a new directory. For that purpose
you can use either the command-line utility ``cmake`` (or ``cmake3``),
the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the graphical
utility ``cmake-gui``, or use them interchangeably. The second step is
then the compilation and linking of all objects, libraries, and
executables. Here is a minimal example using the command line version of
CMake to build LAMMPS with no add-on packages enabled and no
customization:
.. code-block:: bash
cd lammps # change to the LAMMPS distribution directory
mkdir build; cd build # create a new directory (folder) for build
cmake [options ...] ../cmake # configuration with (command-line) cmake
cmake --build . # compilation (or type "make")
cd lammps # change to the LAMMPS distribution directory
mkdir build; cd build # create and use a build directory
cmake ../cmake # configuration reading CMake scripts from ../cmake
cmake --build . # compilation (or type "make")
The ``cmake`` command will detect available features, enable selected
packages and options, and will generate the build environment. By default
this build environment will be created for "Unix Makefiles" on most
platforms and particularly on Linux. However, alternate build tools
(e.g. Ninja) and project files for Integrated Development Environments
(IDEs) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
selected via the ``-G`` command line flag. Further details about features
and settings for CMake are in the `CMake online documentation <cmake_doc_>`_
This will create and change into a folder called ``build``, then run the
configuration step to generate build files for the default build command
and then launch that build command to compile LAMMPS. During the
configuration step CMake will try to detect whether support for MPI,
OpenMP, FFTW, gzip, JPEG, PNG, and ffmpeg are available and enable the
corresponding configuration settings. The progress of this
configuration can be followed on the screen and a summary of selected
options and settings will be printed at the end. The ``cmake --build
.`` command will launch the compilation, which, if successful, will
ultimately produce a library ``liblammps.a`` and the LAMMPS executable
``lmp`` inside the ``build`` folder.
.. _cmake_doc: https://cmake.org/documentation/
Compilation can take a long time, since LAMMPS is a large project with
many features. If your machine has multiple CPU cores (most do these
days), you can speed this up by compiling sources in parallel with
``make -j N`` (with N being the maximum number of concurrently executed
tasks). Also installation of the `ccache <https://ccache.dev/>`_ (=
Compiler Cache) software may speed up repeated compilation even more,
e.g. during code development.
For the rest of the documentation
we will assume that the build environment is generated for "Unix Makefiles"
and thus the ``make`` command will be used to compile and link LAMMPS as
indicated above, producing (by default) an executable called ``lmp`` and
a library called ``liblammps.a`` in the ``build`` folder.
If your machine has multiple CPU cores (most do these days), you can
compile sources in parallel with a command like ``make -j N`` (with N
being the maximum number of concurrently executed tasks). Also
installation of the ``ccache`` (= Compiler Cache) software may speed
up repeated compilation, e.g. during code development, significantly.
After the initial build, whenever you edit LAMMPS source files, enable
or disable packages, change compiler flags or build options, you must
re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
``make``). If the compilation fails for some reason, try running
``cmake .`` and then compile again. The included dependency tracking
should make certain that only the necessary subset of files are
re-compiled. You can also delete compiled objects, libraries and
executables with ``cmake --build . clean`` (or ``make clean``).
After compilation, you may optionally install the LAMMPS executable into
your system with:
.. code-block:: bash
make install # optional, copy LAMMPS executable & library elsewhere
make install # optional, copy compiled files into installation location
This will install the lammps executable and library (if requested), some
tools (if configured) and additional files like library API headers,
manpages, potential and force field files. The location of the installation
tree is set by the CMake variable "CMAKE_INSTALL_PREFIX" which defaults
to ${HOME}/.local
This will install the LAMMPS executable and library, some tools (if
configured) and additional files like LAMMPS API headers, manpages,
potential and force field files. The location of the installation tree
defaults to ``${HOME}/.local``.
----------
.. _cmake_options:
.. _cmake_build:
Configuration and build options
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
There are 3 variants of the CMake command itself: a command-line version
(``cmake`` or ``cmake3``), a text mode UI version (``ccmake`` or ``ccmake3``),
and a graphical GUI version (``cmake-gui``). You can use any of them
interchangeably to configure and create the LAMMPS build environment.
On Linux all the versions produce a Makefile as their output by default.
See more details on each below.
The CMake commands have one mandatory argument: a folder containing a
file called ``CMakeLists.txt`` (for LAMMPS it is located in the
``cmake`` folder) or a build folder containing a file called
``CMakeCache.txt``, which is generated at the end of the CMake
configuration step. The cache file contains all current CMake settings.
You can specify a variety of options with any of the 3 versions, which
affect how the build is performed and what is included in the LAMMPS
executable. Links to pages explaining all the options are listed on
the :doc:`Build <Build>` doc page.
To modify settings, enable or disable features, you need to set *variables*
with either the *-D* command line flag (``-D VARIABLE1_NAME=value``) or
change them in the text mode of graphical user interface. The *-D* flag
can be used several times in one command.
You must perform the CMake build system generation and compilation in
a new directory you create. It can be anywhere on your local machine.
In these Build pages we assume that you are building in a directory
called ``lammps/build``. You can perform separate builds independently
with different options, so long as you perform each of them in a
separate directory you create. All the auxiliary files created by one
build process (executable, object files, log files, etc) are stored in
this directory or sub-directories within it that CMake creates.
For your convenience we provide :ref:`CMake presets <cmake_presets>`
that combine multiple settings to enable optional LAMMPS packages or use
a different compiler tool chain. Those are loaded with the *-C* flag
(``-C ../cmake/presets/minimal.cmake``). This step would only be needed
once, as the settings from the preset files are stored in the
``CMakeCache.txt`` file. It is also possible to customize the build
by adding one or more *-D* flags to the CMake command line.
.. note::
Generating files for alternate build tools (e.g. Ninja) and project files
for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the *-G*
command line flag. A list of available generator settings for your
specific CMake version is given when running ``cmake --help``.
To perform a CMake build, no packages can be installed or a build
been previously attempted in the LAMMPS src directory by using ``make``
commands to :doc:`perform a conventional LAMMPS build <Build_make>`.
CMake detects if this is the case and generates an error, telling you
to type ``make no-all purge`` in the src directory to un-install all
packages. The purge removes all the \*.h files auto-generated by
make.
You must have CMake version 3.10 or later on your system to build
LAMMPS. Installation instructions for CMake are below.
After the initial build, if you edit LAMMPS source files, or add your
own new files to the source directory, you can just re-type make from
your build directory and it will re-compile only the files that have
changed. If you want to change CMake options you can run cmake (or
ccmake or cmake-gui) again from the same build directory and alter
various options; see details below. Or you can remove the entire build
folder, recreate the directory and start over.
----------
**Command-line version of CMake**\ :
.. code-block:: bash
cmake [options ...] /path/to/lammps/cmake # build from any dir
cmake [options ...] ../cmake # build from lammps/build
cmake3 [options ...] ../cmake # build from lammps/build
The cmake command takes one required argument, which is the LAMMPS
cmake directory which contains the CMakeLists.txt file.
The argument can be prefixed or followed by various CMake
command-line options. Several useful ones are:
.. code-block:: bash
-D CMAKE_INSTALL_PREFIX=path # where to install LAMMPS executable/lib if desired
-D CMAKE_BUILD_TYPE=type # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
-G output # style of output CMake generates (e.g. "Unix Makefiles" or "Ninja")
-D CMAKE_MAKE_PROGRAM=builder # name of the builder executable (e.g. when using "gmake" instead of "make")
-DVARIABLE=value # setting for a LAMMPS feature to enable
-D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir
-C path/to/preset/file # load some CMake settings before configuring
All the LAMMPS-specific -D variables that a LAMMPS build supports are
described on the pages linked to from the :doc:`Build <Build>` doc page.
All of these variable names are upper-case and their values are
lower-case, e.g. -D LAMMPS_SIZES=smallbig. For boolean values, any of
these forms can be used: yes/no, on/off, 1/0.
On Unix/Linux machines, CMake generates a Makefile by default to
perform the LAMMPS build. Alternate forms of build info can be
generated via the -G switch, e.g. Visual Studio on a Windows machine,
Xcode on MacOS, or KDevelop on Linux. Type ``cmake --help`` to see the
"Generator" styles of output your system supports.
.. note::
When CMake runs, it prints configuration info to the screen.
You should review this to verify all the features you requested were
enabled, including packages. You can also see what compilers and
compile options will be used for the build. Any errors in CMake
variable syntax will also be flagged, e.g. mis-typed variable names or
variable values.
CMake creates a CMakeCache.txt file when it runs. This stores all the
settings, so that when running CMake again you can use the current
folder '.' instead of the path to the LAMMPS cmake folder as the
required argument to the CMake command. Either way the existing
settings will be inherited unless the CMakeCache.txt file is removed.
If you later want to change a setting you can rerun cmake in the build
directory with different setting. Please note that some automatically
detected variables will not change their value when you rerun cmake.
In these cases it is usually better to first remove all the
files/directories in the build directory, or start with a fresh build
directory.
----------
**Curses version (terminal-style menu) of CMake**\ :
.. code-block:: bash
ccmake ../cmake
You initiate the configuration and build environment generation steps
separately. For the first you have to type **c**\ , for the second you
have to type **g**\ . You may need to type **c** multiple times, and may be
required to edit some of the entries of CMake configuration variables
in between. Please see the `ccmake manual <https://cmake.org/cmake/help/latest/manual/ccmake.1.html>`_ for
more information.
----------
**GUI version of CMake**\ :
.. code-block:: bash
cmake-gui ../cmake
You initiate the configuration and build environment generation steps
separately. For the first you have to click on the **Configure** button,
for the second you have to click on the **Generate** button. You may
need to click on **Configure** multiple times, and may be required to
edit some of the entries of CMake configuration variables in between.
Please see the `cmake-gui manual <https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html>`_
for more information.
----------
**Installing CMake**
Installing CMake
^^^^^^^^^^^^^^^^
Check if your machine already has CMake installed:
@ -216,11 +169,12 @@ software packages, do this:
module list # is a module for cmake already loaded?
module avail # is a module for cmake available?
module load cmake3 # load cmake module with appropriate name
module load cmake # load cmake module with appropriate name
Most Linux distributions offer pre-compiled cmake packages through
their package management system. If you do not have CMake or a new
enough version, you can download the latest version at
`https://cmake.org/download/ <https://cmake.org/download/>`_.
Instructions on how to install it on various platforms can be found
`on this page <https://cmake.org/install/>`_.
Most Linux distributions offer pre-compiled cmake packages through their
package management system. If you do not have CMake or a recent enough
version (Note: for CentOS 7.x you need to enable the EPEL repository),
you can download the latest version from `https://cmake.org/download/
<https://cmake.org/download/>`_. Instructions on how to install it on
various platforms can be found `on this page
<https://cmake.org/install/>`_.

38
doc/src/Build_development.rst
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@ -1,15 +1,15 @@
Development build options (CMake only)
======================================
The CMake build of LAMMPS has a few extra options which are useful during
development, testing or debugging.
The CMake build procedure of LAMMPS offers a few extra options which are
useful during development, testing or debugging.
----------
.. _compilation:
Verify compilation flags
------------------------------------------
------------------------
Sometimes it is necessary to verify the complete sequence of compilation flags
generated by the CMake build. To enable a more verbose output during
@ -30,7 +30,7 @@ Another way of doing this without reconfiguration is calling make with variable
.. _sanitizer:
Address, Undefined Behavior, and Thread Sanitizer Support
-------------------------------------------------------------------------
---------------------------------------------------------
Compilers such as GCC and Clang support generating instrumented binaries
which use different sanitizer libraries to detect problems in code
@ -41,10 +41,11 @@ during run-time. They can detect issues like:
- `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_
Please note that this kind of instrumentation usually comes with a small
performance hit (much less than using tools like `Valgrind <valgrind_>`_).
The to enable these features additional compiler flags need to be added
to the compilation and linking stages. This is most easily done through
setting the ``CMAKE_TUNE_FLAGS`` variable during configuration. Examples:
performance hit (much less than using tools like `Valgrind
<https://valgrind.org>`_). The to enable these features additional
compiler flags need to be added to the compilation and linking stages.
This is most easily done through setting the ``CMAKE_TUNE_FLAGS``
variable during configuration. Examples:
.. code-block:: bash
@ -52,8 +53,6 @@ setting the ``CMAKE_TUNE_FLAGS`` variable during configuration. Examples:
-D CMAKE_TUNE_FLAGS=-fsanitize=undefined # enable undefined behavior sanitizer
-D CMAKE_TUNE_FLAGS=-fsanitize=thread # enable thread sanitizer
.. _valgrind: https://valgrind.org
----------
.. _testing:
@ -75,24 +74,26 @@ developers can run the tests directly on their workstation.
-D LAMMPS_TESTING_SOURCE_DIR=path # path to lammps-testing repository (option if in custom location)
-D LAMMPS_TESTING_GIT_TAG=value # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
If you enable testing in the CMake build it will create an additional
target called "test". You can run them with:
.. code-block:: bash
make test
cmake --build . test
The test cases used come from the lammps-testing repository. They are
derivatives of the examples folder with some modifications to make the run
faster.
derivatives of the examples folder with some modifications to make the
run faster.
You can also collect code coverage metrics while running the tests by enabling
coverage support during building.
You can also collect code coverage metrics while running the tests by
enabling coverage support during building.
.. code-block:: bash
-D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes
This will also add the following targets to generate coverage reports after running the LAMMPS executable:
This will also add the following targets to generate coverage reports
after running the LAMMPS executable:
.. code-block:: bash
@ -100,7 +101,8 @@ This will also add the following targets to generate coverage reports after runn
make gen_coverage_html # generate coverage report in HTML format
make gen_coverage_xml # generate coverage report in XML format
These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
These reports require GCOVR to be installed. The easiest way to do this
to install it via pip:
.. code-block:: bash

290
doc/src/Build_extras.rst
View File

@ -87,27 +87,33 @@ GPU package
---------------------
To build with this package, you must choose options for precision and
which GPU hardware to build for.
which GPU hardware to build for. The GPU package currently supports
three different types of backends: OpenCL, CUDA and HIP.
**CMake build**\ :
.. code-block:: bash
-D GPU_API=value # value = opencl (default) or cuda
-D GPU_PREC=value # precision setting
# value = double or mixed (default) or single
-D OCL_TUNE=value # hardware choice for GPU_API=opencl
# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX, see below
# default is sm_30
-D CUDPP_OPT=value # optimization setting for GPU_API=cuda
# enables CUDA Performance Primitives Optimizations
# value = yes (default) or no
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
# value = yes or no (default)
-D GPU_API=value # value = opencl (default) or cuda or hip
-D GPU_PREC=value # precision setting
# value = double or mixed (default) or single
-D OCL_TUNE=value # hardware choice for GPU_API=opencl
# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
# value = sm_XX, see below
# default is sm_30
-D HIP_ARCH=value # primary GPU hardware choice for GPU_API=hip
# value depends on selected HIP_PLATFORM
# default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_30' for HIP_PLATFORM=nvcc
-D HIP_USE_DEVICE_SORT=value # enables GPU sorting
# value = yes (default) or no
-D CUDPP_OPT=value # optimization setting for GPU_API=cuda
# enables CUDA Performance Primitives Optimizations
# value = yes (default) or no
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
# value = yes or no (default)
GPU_ARCH settings for different GPU hardware is as follows:
:code:`GPU_ARCH` settings for different GPU hardware is as follows:
* sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5)
* sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5)
@ -126,6 +132,28 @@ Thus the GPU_ARCH setting is merely an optimization, to have code for
the preferred GPU architecture directly included rather than having to wait
for the JIT compiler of the CUDA driver to translate it.
If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
and the linker to work correctly.
.. code:: bash
# AMDGPU target
export HIP_PLATFORM=hcc
export HCC_AMDGPU_TARGET=gfx906
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
make -j 4
.. code:: bash
# CUDA target
# !!! DO NOT set CMAKE_CXX_COMPILER !!!
export HIP_PLATFORM=nvcc
export CUDA_PATH=/usr/local/cuda
cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 ..
make -j 4
**Traditional make**\ :
Before building LAMMPS, you must build the GPU library in ``lib/gpu``\ .
@ -189,13 +217,27 @@ KIM package
---------------------
To build with this package, the KIM library with API v2 must be downloaded
and built on your system. It must include the KIM models that you want to
use with LAMMPS. If you want to use the :doc:`kim_query <kim_commands>`
and built on your system. It must include the KIM models that you want to
use with LAMMPS.
If you would like to use the :doc:`kim_query <kim_commands>`
command, you also need to have libcurl installed with the matching
development headers and the curl-config tool.
See the `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
web page to
If you would like to use the :doc:`kim_property <kim_commands>`
command, you need to build LAMMPS with the Python 3.6 or later package
installed. See the :doc:`Python <python>` doc page for more info on building
LAMMPS with the version of Python on your system.
After successfully building LAMMPS with Python, you need to
install the kim-property Python package, which can be easily done using
*pip* as ``pip install kim-property``, or from the *conda-forge* channel as
``conda install kim-property`` if LAMMPS is built in Conda. More detailed
information is available at:
`kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
In addition to installing the KIM API, it is also necessary to install the
library of KIM models (interatomic potentials).
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
learn how to install a pre-build binary of the OpenKIM Repository of Models.
See the list of all KIM models here: https://openkim.org/browse/models
@ -265,74 +307,131 @@ using. For example:
.. _kokkos:
KOKKOS package
---------------------------
--------------
To build with this package, you must choose which hardware you want to
build for, either CPUs (multi-threading via OpenMP) or KNLs (OpenMP)
or GPUs (NVIDIA Cuda).
Using the KOKKOS package requires choosing several settings. You have
to select whether you want to compile with parallelization on the host
and whether you want to include offloading of calculations to a device
(e.g. a GPU). The default setting is to have no host parallelization
and no device offloading. In addition, you can select the hardware
architecture to select the instruction set. Since most hardware is
backward compatible, you may choose settings for an older architecture
to have an executable that will run on this and newer architectures.
For a CMake or make build, these are the possible choices for the
``KOKKOS_ARCH`` settings described below. Note that for CMake, these are
really Kokkos variables, not LAMMPS variables. Hence you must use
case-sensitive values, e.g. BDW, not bdw.
.. note::
* AMDAVX = AMD 64-bit x86 CPUs
* EPYC = AMD EPYC Zen class CPUs
* ARMv80 = ARMv8.0 Compatible CPU
* ARMv81 = ARMv8.1 Compatible CPU
* ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU
* ARMv8-TX2 = ARMv8 Cavium ThunderX2 CPU
* WSM = Intel Westmere CPUs
* SNB = Intel Sandy/Ivy Bridge CPUs
* HSW = Intel Haswell CPUs
* BDW = Intel Broadwell Xeon E-class CPUs
* SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512)
* KNC = Intel Knights Corner Xeon Phi
* KNL = Intel Knights Landing Xeon Phi
* BGQ = IBM Blue Gene/Q CPUs
* Power7 = IBM POWER8 CPUs
* Power8 = IBM POWER8 CPUs
* Power9 = IBM POWER9 CPUs
* Kepler = NVIDIA Kepler default (generation CC 3.5)
* Kepler30 = NVIDIA Kepler generation CC 3.0
* Kepler32 = NVIDIA Kepler generation CC 3.2
* Kepler35 = NVIDIA Kepler generation CC 3.5
* Kepler37 = NVIDIA Kepler generation CC 3.7
* Maxwell = NVIDIA Maxwell default (generation CC 5.0)
* Maxwell50 = NVIDIA Maxwell generation CC 5.0
* Maxwell52 = NVIDIA Maxwell generation CC 5.2
* Maxwell53 = NVIDIA Maxwell generation CC 5.3
* Pascal60 = NVIDIA Pascal generation CC 6.0
* Pascal61 = NVIDIA Pascal generation CC 6.1
* Volta70 = NVIDIA Volta generation CC 7.0
* Volta72 = NVIDIA Volta generation CC 7.2
* Turing75 = NVIDIA Turing generation CC 7.5
NVIDIA GPUs with CC 5.0 (Maxwell) and newer are not compatible with
CC 3.x (Kepler). If you run Kokkos on a newer architecture than what
LAMMPS was compiled with, there will be a significant delay during
device initialization since the just-in-time compiler has to
recompile the GPU kernel code for the new hardware.
**CMake build**\ :
The settings discussed below have been tested with LAMMPS and are
confirmed to work. Kokkos is an active project with ongoing improvements
and projects working on including support for additional architectures.
More information on Kokkos can be found on the
`Kokkos GitHub project <https://github.com/kokkos>`_.
Available Architecture settings
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
These are the possible choices for the Kokkos architecture ID. They must
be specified in uppercase.
.. list-table::
:header-rows: 0
:widths: auto
* - **Arch-ID**
- **Description**
* - AMDAVX
- AMD 64-bit x86 CPU (AVX 1)
* - EPYC
- AMD EPYC Zen class CPU (AVX 2)
* - ARMV80
- ARMv8.0 Compatible CPU
* - ARMV81
- ARMv8.1 Compatible CPU
* - ARMV8_THUNDERX
- ARMv8 Cavium ThunderX CPU
* - ARMV8_THUNDERX2
- ARMv8 Cavium ThunderX2 CPU
* - WSM
- Intel Westmere CPU (SSE 4.2)
* - SNB
- Intel Sandy/Ivy Bridge CPU (AVX 1)
* - HSW
- Intel Haswell CPU (AVX 2)
* - BDW
- Intel Broadwell Xeon E-class CPU (AVX 2 + transactional mem)
* - SKX
- Intel Sky Lake Xeon E-class HPC CPU (AVX512 + transactional mem)
* - KNC
- Intel Knights Corner Xeon Phi
* - KNL
- Intel Knights Landing Xeon Phi
* - BGQ
- IBM Blue Gene/Q CPU
* - POWER7
- IBM POWER8 CPU
* - POWER8
- IBM POWER8 CPU
* - POWER9
- IBM POWER9 CPU
* - KEPLER30
- NVIDIA Kepler generation CC 3.0 GPU
* - KEPLER32
- NVIDIA Kepler generation CC 3.2 GPU
* - KEPLER35
- NVIDIA Kepler generation CC 3.5 GPU
* - KEPLER37
- NVIDIA Kepler generation CC 3.7 GPU
* - MAXWELL50
- NVIDIA Maxwell generation CC 5.0 GPU
* - MAXWELL52
- NVIDIA Maxwell generation CC 5.2 GPU
* - MAXWELL53
- NVIDIA Maxwell generation CC 5.3 GPU
* - PASCAL60
- NVIDIA Pascal generation CC 6.0 GPU
* - PASCAL61
- NVIDIA Pascal generation CC 6.1 GPU
* - VOLTA70
- NVIDIA Volta generation CC 7.0 GPU
* - VOLTA72
- NVIDIA Volta generation CC 7.2 GPU
* - TURING75
- NVIDIA Turing generation CC 7.5 GPU
CMake build settings:
^^^^^^^^^^^^^^^^^^^^^
For multicore CPUs using OpenMP, set these 2 variables.
.. code-block:: bash
-D KOKKOS_ARCH=archCPU # archCPU = CPU from list above
-D KOKKOS_ENABLE_OPENMP=yes
-D Kokkos_ARCH_CPUARCH=yes # CPUARCH = CPU from list above
-D Kokkos_ENABLE_OPENMP=yes
-D BUILD_OMP=yes
For Intel KNLs using OpenMP, set these 2 variables:
Please note that enabling OpenMP for KOKKOS requires that OpenMP is
also :ref:`enabled for the rest of LAMMPS <serial>`.
For Intel KNLs using OpenMP, set these variables:
.. code-block:: bash
-D KOKKOS_ARCH=KNL
-D KOKKOS_ENABLE_OPENMP=yes
-D Kokkos_ARCH_KNL=yes
-D Kokkos_ENABLE_OPENMP=yes
For NVIDIA GPUs using CUDA, set these 4 variables:
For NVIDIA GPUs using CUDA, set these variables:
.. code-block:: bash
-D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU
# archGPU = GPU from list above
-D KOKKOS_ENABLE_CUDA=yes
-D KOKKOS_ENABLE_OPENMP=yes
-D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper
-D Kokkos_ARCH_CPUARCH=yes # CPUARCH = CPU from list above
-D Kokkos_ARCH_GPUARCH=yes # GPUARCH = GPU from list above
-D Kokkos_ENABLE_CUDA=yes
-D Kokkos_ENABLE_OPENMP=yes
-D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper
The wrapper value is the Cuda nvcc compiler wrapper provided in the
Kokkos library: ``lib/kokkos/bin/nvcc_wrapper``\ . The setting should
@ -340,20 +439,35 @@ include the full path name to the wrapper, e.g.
.. code-block:: bash
-D CMAKE_CXX_COMPILER=/home/username/lammps/lib/kokkos/bin/nvcc_wrapper
-D CMAKE_CXX_COMPILER=${HOME}/lammps/lib/kokkos/bin/nvcc_wrapper
**Traditional make**\ :
To simplify the compilation, three preset files are included in the
``cmake/presets`` folder, ``kokkos-serial.cmake``, ``kokkos-openmp.cmake``,
and ``kokkos-cuda.cmake``. They will enable the KOKKOS package and
enable some hardware choice. So to compile with OpenMP host parallelization,
CUDA device parallelization (for GPUs with CC 5.0 and up) with some
common packages enabled, you can do the following:
.. code-block:: bash
mkdir build-kokkos-cuda
cd build-kokkos-cuda
cmake -C ../cmake/presets/minimal.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake
cmake --build .
Traditional make settings:
^^^^^^^^^^^^^^^^^^^^^^^^^^
Choose which hardware to support in ``Makefile.machine`` via
``KOKKOS_DEVICES`` and ``KOKKOS_ARCH`` settings. See the
``src/MAKE/OPTIONS/Makefile.kokkos\*`` files for examples.
``src/MAKE/OPTIONS/Makefile.kokkos*`` files for examples.
For multicore CPUs using OpenMP:
.. code-block:: make
KOKKOS_DEVICES = OpenMP
KOKKOS_ARCH = archCPU # archCPU = CPU from list above
KOKKOS_ARCH = CPUARCH # CPUARCH = CPU from list above
For Intel KNLs using OpenMP:
@ -367,22 +481,28 @@ For NVIDIA GPUs using CUDA:
.. code-block:: make
KOKKOS_DEVICES = Cuda
KOKKOS_ARCH = archCPU,archGPU # archCPU = CPU from list above that is hosting the GPU
# archGPU = GPU from list above
FFT_INC = -DFFT_CUFFT # enable use of cuFFT (optional)
FFT_LIB = -lcufft # link to cuFFT library
KOKKOS_ARCH = CPUARCH,GPUARCH # CPUARCH = CPU from list above that is hosting the GPU
# GPUARCH = GPU from list above
FFT_INC = -DFFT_CUFFT # enable use of cuFFT (optional)
FFT_LIB = -lcufft # link to cuFFT library
For GPUs, you also need the following 2 lines in your Makefile.machine
before the CC line is defined, in this case for use with OpenMPI mpicxx.
The 2 lines define a nvcc wrapper compiler, which will use nvcc for
compiling CUDA files and use a C++ compiler for non-Kokkos, non-CUDA
files.
For GPUs, you also need the following lines in your ``Makefile.machine``
before the CC line is defined. They tell ``mpicxx`` to use an ``nvcc``
compiler wrapper, which will use ``nvcc`` for compiling CUDA files and a
C++ compiler for non-Kokkos, non-CUDA files.
.. code-block:: make
# For OpenMPI
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
CC = mpicxx
CC = mpicxx
.. code-block:: make
# For MPICH and derivatives
KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
CC = mpicxx -cxx=$(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
----------
@ -421,7 +541,7 @@ args:
$ make lib-latte args="-b" # download and build in lib/latte/LATTE-master
$ make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte
$ make lib-latte args="-b -m gfortran" # download and build in lib/latte and
# copy Makefile.lammps.gfortran to Makefile.lammps
# copy Makefile.lammps.gfortran to Makefile.lammps
Note that 3 symbolic (soft) links, "includelink" and "liblink" and
"filelink.o", are created in lib/latte to point into the LATTE home

147
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@ -1,33 +1,35 @@
Link LAMMPS as a library to another code
========================================
LAMMPS can be used as a library by another application, including
Python scripts. The files src/library.cpp and library.h define the
LAMMPS is designed as a library of C++ objects and can thus be
integrated into other applications including Python scripts.
The files ``src/library.cpp`` and ``src/library.h`` define a
C-style API for using LAMMPS as a library. See the :doc:`Howto
library <Howto_library>` doc page for a description of the interface
and how to extend it for your needs.
The :doc:`Build basics <Build_basics>` doc page explains how to build
LAMMPS as either a shared or static library. This results in one of
these 2 files:
.. code-block:: bash
liblammps.so # shared library
liblammps.a # static library
LAMMPS as either a shared or static library. This results in a file
in the compilation folder called ``liblammps.a`` or ``liblammps_<name>.a``
in case of building a static library. In case of a shared library
the name is the same only that the suffix is going to be either ``.so``
or ``.dylib`` or ``.dll`` instead of ``.a`` depending on the OS.
In some cases the ``.so`` file may be a symbolic link to a file with
the suffix ``.so.0`` (or some other number).
.. note::
Care should be taken to use the same MPI library for the calling
code and the LAMMPS library. The library.h file includes mpi.h and
uses definitions from it so those need to be available and
consistent. When LAMMPS is compiled with the MPI STUBS library,
then its mpi.h file needs to be included. While it is technically
possible to use a full MPI library in the calling code and link to
a serial LAMMPS library compiled with MPI STUBS, it is recommended
to use the *same* MPI library for both, and then use MPI_Comm_split()
in the calling code to pass a suitable communicator with a subset
of MPI ranks to the function creating the LAMMPS instance.
Care should be taken to use the same MPI library for the calling code
and the LAMMPS library. The ``library.h`` file includes ``mpi.h``
and uses definitions from it so those need to be available and
consistent. When LAMMPS is compiled with the included STUBS MPI
library, then its ``mpi.h`` file needs to be included. While it is
technically possible to use a full MPI library in the calling code
and link to a serial LAMMPS library compiled with MPI STUBS, it is
recommended to use the *same* MPI library for both, and then use
``MPI_Comm_split()`` in the calling code to pass a suitable
communicator with a subset of MPI ranks to the function creating the
LAMMPS instance.
----------
@ -42,11 +44,11 @@ executable code from the library is copied into the calling executable.
*CMake build*\ :
This assumes that LAMMPS has been configured with "-D BUILD_LIB=yes"
and installed with "make install" and the PKG_CONFIG_PATH environment
variable updated to include the *liblammps.pc* file installed into the
configured destination folder, if needed. The commands to compile and
link the coupled executable are then:
This assumes that LAMMPS has been configured without setting a
``LAMMPS_MACHINE`` name, installed with "make install", and the
``PKG_CONFIG_PATH`` environment variable has been updated to include the
``liblammps.pc`` file installed into the configured destination folder.
The commands to compile and link a coupled executable are then:
.. code-block:: bash
@ -56,30 +58,35 @@ link the coupled executable are then:
*Traditional make*\ :
This assumes that LAMMPS has been compiled in the folder
"${HOME}/lammps/src" with "make mode=lib mpi". The commands to compile
and link the coupled executable are then:
``${HOME}/lammps/src`` with "make mpi". The commands to compile and link
a coupled executable are then:
.. code-block:: bash
mpicc -c -O -I${HOME}/lammps/src caller.c
mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps
mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps_mpi
The *-I* argument is the path to the location of the *library.h*
The *-I* argument is the path to the location of the ``library.h``
header file containing the interface to the LAMMPS C-style library
interface. The *-L* argument is the path to where the *liblammps.a*
file is located. The *-llammps* argument is shorthand for telling the
compiler to link the file *liblammps.a*\ .
interface. The *-L* argument is the path to where the ``liblammps_mpi.a``
file is located. The *-llammps_mpi* argument is shorthand for telling the
compiler to link the file ``liblammps_mpi.a``. If LAMMPS has been
built as a shared library, then the linker will use ``liblammps_mpi.so``
instead. If both files are available, the linker will usually prefer
the shared library. In case of a shared library, you may need to update
the ``LD_LIBRARY_PATH`` environment variable or running the ``caller``
executable will fail since it cannot find the shared library at runtime.
However, it is only as simple as shown above for the case of a plain
LAMMPS library without any optional packages that depend on libraries
(bundled or external). Otherwise, you need to include all flags,
libraries, and paths for the coupled executable, that are also
required to link the LAMMPS executable.
(bundled or external) or when using a shared library. Otherwise, you
need to include all flags, libraries, and paths for the coupled
executable, that are also required to link the LAMMPS executable.
*CMake build*\ :
When using CMake, additional libraries with sources in the lib folder
are built, but not included in liblammps.a and (currently) not
are built, but not included in ``liblammps.a`` and (currently) not
installed with "make install" and not included in the *pkgconfig*
configuration file. They can be found in the top level build folder,
but you have to determine the necessary link flags manually. It is
@ -87,23 +94,26 @@ therefore recommended to either use the traditional make procedure to
build and link with a static library or build and link with a shared
library instead.
.. TODO: this needs to be updated to reflect that latest CMake changes after they are complete.
*Traditional make*\ :
After you have compiled a static LAMMPS library using the conventional
build system for example with "make mode=lib serial". And you also
have installed the POEMS package after building its bundled library in
lib/poems. Then the commands to build and link the coupled executable
build system for example with "make mode=static serial". And you also
have installed the ``POEMS`` package after building its bundled library
in ``lib/poems``. Then the commands to build and link the coupled executable
change to:
.. code-block:: bash
gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
-L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps -lpoems -lmpi_stubs
-L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps_serial -lpoems -lmpi_stubs
Note, that you need to link with "g++" instead of "gcc", since LAMMPS
is C++ code. You can display the currently applied settings for building
LAMMPS for the "serial" machine target by using the command:
Note, that you need to link with "g++" instead of "gcc", since the
LAMMPS library is C++ code. You can display the currently applied
settings for building LAMMPS for the "serial" machine target by using
the command:
.. code-block:: bash
@ -113,16 +123,16 @@ Which should output something like:
.. code-block:: bash
# Compiler:
# Compiler:
CXX=g++
# Linker:
# Linker:
LD=g++
# Compilation:
CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/lammps/lib/poems -I${HOME}/lammps/src/STUBS
# Linking:
# Compilation:
CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/compile/lammps/lib/poems -I${HOME}/compile/lammps/src/STUBS
# Linking:
LDFLAGS=-g -O
# Libraries:
LDLIBS=-L${HOME}/lammps/lib/poems -L${HOME}/lammps/src/STUBS -lpoems -lmpi_stubs
# Libraries:
LDLIBS=-L${HOME}/compile/lammps/src -llammps_serial -L${HOME}/compile/lammps/lib/poems -L${HOME}/compile/lammps/src/STUBS -lpoems -lmpi_stubs
From this you can gather the necessary paths and flags. With
makefiles for other *machine* configurations you need to do the
@ -133,14 +143,13 @@ of the makefile.
**Link with LAMMPS as a shared library**\ :
When linking to LAMMPS built as a shared library, the situation
becomes much simpler, as all dependent libraries and objects are
included in the shared library, which is - technically speaking -
effectively a regular LAMMPS executable that is missing the `main()`
function. Thus those libraries need not to be specified when linking
the calling executable. Only the *-I* flags are needed. So the
example case from above of the serial version static LAMMPS library
with the POEMS package installed becomes:
When linking to LAMMPS built as a shared library, the situation becomes
much simpler, as all dependent libraries and objects are either included
in the shared library or registered as a dependent library in the shared
library file. Thus those libraries need not to be specified when
linking the calling executable. Only the *-I* flags are needed. So the
example case from above of the serial version static LAMMPS library with
the POEMS package installed becomes:
*CMake build*\ :
@ -155,19 +164,19 @@ build process are the same as for the static library.
*Traditional make*\ :
The commands with a shared LAMMPS library compiled with the
traditional make build using "make mode=shlib serial" becomes:
traditional make build using "make mode=shared serial" becomes:
.. code-block:: bash
gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
g++ -o caller caller.o -L${HOME}/lammps/src -llammps
g++ -o caller caller.o -L${HOME}/lammps/src -llammps_serial
*Locating liblammps.so at runtime*\ :
However, now the `liblammps.so` file is required at runtime and needs
However, now the ``liblammps.so`` file is required at runtime and needs
to be in a folder, where the shared linker program of the operating
system can find it. This would be either a folder like "/usr/local/lib64"
or "${HOME}/.local/lib64" or a folder pointed to by the LD_LIBRARY_PATH
system can find it. This would be either a folder like ``/usr/local/lib64``
or ``${HOME}/.local/lib64`` or a folder pointed to by the ``LD_LIBRARY_PATH``
environment variable. You can type
.. code-block:: bash
@ -177,11 +186,11 @@ environment variable. You can type
to see what directories are in that list.
Or you can add the LAMMPS src directory (or the directory you performed
a CMake style build in) to your LD_LIBRARY_PATH, so that the current
a CMake style build in) to your ``LD_LIBRARY_PATH``, so that the current
version of the shared library is always available to programs that use it.
For the Bourne or Korn shells (/bin/sh, /bin/ksh, /bin/bash etc.), you
would add something like this to your ~/.profile file:
would add something like this to your ``${HOME}/.profile`` file:
.. code-block:: bash
@ -189,14 +198,14 @@ would add something like this to your ~/.profile file:
export LD_LIBRARY_PATH
For the csh or tcsh shells, you would equivalently add something like this
to your ~/.cshrc file:
to your ``${HOME}/.cshrc`` file:
.. code-block:: csh
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HOME}/lammps/src
You can verify whether all required shared libraries are found with the
`ldd` tool. Example:
``ldd`` tool. Example:
.. code-block:: bash
@ -229,20 +238,20 @@ If a required library is missing, you would get a 'not found' entry:
Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program. When used from a
C++ program, most of the symbols and functions in LAMMPS are wrapped
in a LAMMPS_NS namespace; you can safely use any of its classes and
in a ``LAMMPS_NS`` namespace; you can safely use any of its classes and
methods from within the calling code, as needed, and you will not incur
conflicts with functions and variables in your code that share the name.
This, however, does not extend to all additional libraries bundled with
LAMMPS in the lib folder and some of the low-level code of some packages.
To be compatible with C, Fortran, Python programs, the library has a simple
C-style interface, provided in src/library.cpp and src/library.h.
C-style interface, provided in ``src/library.cpp`` and ``src/library.h``.
See the :doc:`Python library <Python_library>` doc page for a
description of the Python interface to LAMMPS, which wraps the C-style
interface from a shared library through the `ctypes python module <ctypes_>`_.
See the sample codes in examples/COUPLE/simple for examples of C++ and
See the sample codes in ``examples/COUPLE/simple`` for examples of C++ and
C and Fortran codes that invoke LAMMPS through its library interface.
Other examples in the COUPLE directory use coupling ideas discussed on
the :doc:`Howto couple <Howto_couple>` doc page.

93
doc/src/Build_make.rst
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@ -2,10 +2,14 @@ Build LAMMPS with make
======================
Building LAMMPS with traditional makefiles requires that you have a
Makefile."machine" file appropriate for your system in the src/MAKE,
src/MAKE/MACHINES, src/MAKE/OPTIONS, or src/MAKE/MINE directory (see
below). It can include various options for customizing your LAMMPS
build with a number of global compilation options and features.
``Makefile.<machine>`` file appropriate for your system in either the
``src/MAKE``, ``src/MAKE/MACHINES``, ``src/MAKE/OPTIONS``, or
``src/MAKE/MINE`` directory (see below). It can include various options
for customizing your LAMMPS build with a number of global compilation
options and features.
Requirements
^^^^^^^^^^^^
Those makefiles are written for and tested with GNU make and may not
be compatible with other make programs. In most cases, if the "make"
@ -16,44 +20,54 @@ with :doc:`CMake <Build_cmake>`. The makefiles of the traditional
make based build process and the scripts they are calling expect a few
additional tools to be available and functioning.
* a Bourne shell compatible "Unix" shell program (often this is bash)
* a few shell utilities: ls, mv, ln, rm, grep, sed, tr, cat, touch, diff, dirname
* python (optional, required for "make lib-XXX" in the src folder)
* a working C/C++ compiler toolchain supporting the C++11 standard; on
Linux these are often the GNU compilers. Some older compilers
require adding flags like ``-std=c++11`` to enable the C++11 mode.
* a Bourne shell compatible "Unix" shell program (often this is ``bash``)
* a few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
* python (optional, required for ``make lib-<pkg>`` in the src folder).
python scripts are currently tested with python 2.7 and 3.6. The procedure
for :doc:`building the documentation <Manual_build>` requires python 3.
To include LAMMPS packages (i.e. optional commands and styles) you
must enable them first, as discussed on the :doc:`Build package
<Build_package>` doc page. If a packages requires (provided or
Getting started
^^^^^^^^^^^^^^^
To include LAMMPS packages (i.e. optional commands and styles) you must
enable (or "install") them first, as discussed on the :doc:`Build
package <Build_package>` doc page. If a packages requires (provided or
external) libraries, you must configure and build those libraries
**before** building LAMMPS itself and especially **before** enabling
such a package with "make yes-<package>". Building :doc:`LAMMPS
with CMake <Build_cmake>` can automate much of this for many types of
such a package with ``make yes-<package>``. Building :doc:`LAMMPS with
CMake <Build_cmake>` can automate much of this for many types of
machines, especially workstations, desktops, and laptops, so we suggest
you try it first when building LAMMPS in those cases.
The commands below perform a default LAMMPS build, producing the LAMMPS
executable lmp_serial and lmp_mpi in lammps/src:
executable ``lmp_serial`` and ``lmp_mpi`` in ``lammps/src``:
.. code-block:: bash
cd lammps/src
make serial # build a serial LAMMPS executable
cd lammps/src # change to main LAMMPS source folder
make serial # build a serial LAMMPS executable using GNU g++
make mpi # build a parallel LAMMPS executable with MPI
make # see a variety of make options
This initial compilation can take a long time, since LAMMPS is a large
project with many features. If your machine has multiple CPU cores
(most do these days), using a command like "make -jN mpi" (with N =
the number of available CPU cores) can be much faster. If you plan to
do development on LAMMPS or need to re-compile LAMMPS repeatedly, the
installation of the ccache (= Compiler Cache) software may speed up
compilation even more.
Compilation can take a long time, since LAMMPS is a large project with
many features. If your machine has multiple CPU cores (most do these
days), you can speed this up by compiling sources in parallel with
``make -j N`` (with N being the maximum number of concurrently executed
tasks). Also installation of the `ccache <https://ccache.dev/>`_ (=
Compiler Cache) software may speed up repeated compilation even more,
e.g. during code development.
After the initial build, whenever you edit LAMMPS source files, or add
or remove new files to the source directory (e.g. by installing or
uninstalling packages), you must re-compile and relink the LAMMPS
executable with the same "make" command. This makefiles dependencies
should insure that only the subset of files that need to be are
re-compiled.
executable with the same ``make <machine>`` command. The makefile's
dependency tracking should insure that only the necessary subset of
files are re-compiled. If you change settings in the makefile, you have
to recompile *everything*. To delete all objects you can use ``make
clean-<machine>``.
.. note::
@ -65,13 +79,15 @@ re-compiled.
correctly detect which parts need to be recompiled after changes
were made to the sources.
----------
Customized builds and alternate makefiles
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The lammps/src/MAKE tree contains the Makefile.machine files included
in the LAMMPS distribution. Typing "make machine" uses
*Makefile.machine*\ . Thus the "make serial" or "make mpi" lines above
use Makefile.serial and Makefile.mpi, respectively. Other makefiles
are in these directories:
The ``src/MAKE`` directory tree contains the ``Makefile.<machine>``
files included in the LAMMPS distribution. Typing ``make example`` uses
``Makefile.example`` from one of those folders, if available. Thus the
``make serial`` and ``make mpi`` lines above use
``src/MAKE/Makefile.serial`` and ``src/MAKE/Makefile.mpi``,
respectively. Other makefiles are in these directories:
.. code-block:: bash
@ -79,11 +95,16 @@ are in these directories:
MACHINES # Makefiles for specific machines
MINE # customized Makefiles you create (you may need to create this folder)
Typing "make" lists all the available Makefile.machine files. A file
with the same name can appear in multiple folders (not a good idea).
The order the directories are searched is as follows: src/MAKE/MINE,
src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES. This gives preference
to a customized file you put in src/MAKE/MINE.
Simply typing ``make`` lists all the available ``Makefile.<machine>``
files with a single line description toward the end of the output. A
file with the same name can appear in multiple folders (not a good
idea). The order the directories are searched is as follows:
``src/MAKE/MINE``, ``src/MAKE``, ``src/MAKE/OPTIONS``,
``src/MAKE/MACHINES``. This gives preference to a customized file you
put in ``src/MAKE/MINE``. If you create your own custom makefile under
a new name, please edit the first line with the description and machine
name, so you will not confuse yourself, when looking at the machine
summary.
Makefiles you may wish to try include these (some require a package
first be installed). Many of these include specific compiler flags

2
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@ -130,6 +130,8 @@ src directory.
----------
.. _cmake_presets:
**CMake shortcuts for installing many packages**\ :
Instead of specifying all the CMake options via the command-line,

1
doc/src/Commands_all.rst
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@ -70,6 +70,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`kim_init <kim_commands>`
* :doc:`kim_interactions <kim_commands>`
* :doc:`kim_param <kim_commands>`
* :doc:`kim_property <kim_commands>`
* :doc:`kim_query <kim_commands>`
* :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>`

1
doc/src/Commands_pair.rst
View File

@ -131,6 +131,7 @@ OPT.
* :doc:`lj/class2/coul/cut (ko) <pair_class2>`
* :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`
* :doc:`lj/class2/coul/long (gko) <pair_class2>`
* :doc:`lj/class2/coul/long/cs <pair_cs>`
* :doc:`lj/class2/coul/long/soft <pair_fep_soft>`
* :doc:`lj/class2/soft <pair_fep_soft>`
* :doc:`lj/cubic (go) <pair_lj_cubic>`

2
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View File

@ -48,7 +48,7 @@ The USER-CUDA package had been removed, since it had been unmaintained
for a long time and had known bugs and problems. Significant parts of
the design were transferred to the
:ref:`KOKKOS package <PKG-KOKKOS>`, which has similar
performance characteristics on Nvidia GPUs. Both, the KOKKOS
performance characteristics on NVIDIA GPUs. Both, the KOKKOS
and the :ref:`GPU package <PKG-GPU>` are maintained
and allow running LAMMPS with GPU acceleration.

1
doc/src/Errors.rst
View File

@ -12,5 +12,6 @@ additional details for many of them.
Errors_common
Errors_bugs
Errors_debug
Errors_messages
Errors_warnings

24
doc/src/Errors_bugs.rst
View File

@ -1,7 +1,8 @@
Reporting bugs
==============
If you are confident that you have found a bug in LAMMPS, please follow the steps outlined below:
If you are confident that you have found a bug in LAMMPS, please follow
the steps outlined below:
* Check the `New features and bug fixes
<https://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site
@ -17,20 +18,22 @@ If you are confident that you have found a bug in LAMMPS, please follow the step
* Check the `mailing list archives <https://lammps.sandia.gov/mail.html>`_
to see if the issue has been discussed before.
If none of these steps yields any useful information, please file
a new bug report on the `GitHub Issue page <gip_>`_\ .
The website will offer you to select a suitable template with explanations
and then you should replace those explanations with the information
that you can provide to reproduce your issue.
If none of these steps yields any useful information, please file a new
bug report on the `GitHub Issue page <gip_>`_. The website will offer
you to select a suitable template with explanations and then you should
replace those explanations with the information that you can provide to
reproduce your issue.
The most useful thing you can do to help us verify and fix a bug is to
isolate the problem. Run it on the smallest number of atoms and fewest
number of processors with the simplest input script that reproduces the
bug. Try to identify what command or combination of commands is
causing the problem and upload the complete input deck as a tar or zip
archive. Please avoid using binary restart files unless the issue requires
it. In the latter case you should also include an input deck to quickly
bug. Try to identify what command or combination of commands is causing
the problem and upload the complete input deck as a tar or zip archive.
Please avoid using binary restart files unless the issue requires it.
In the latter case you should also include an input deck to quickly
generate this restart from a data file or a simple additional input.
This input deck can be used with tools like a debugger or `valgrind
<valgrind_>`_ to further :doc:`debug the crash <Errors_debug>`.
You may also send an email to the LAMMPS mailing list at
"lammps-users at lists.sourceforge.net" describing the problem with the
@ -43,3 +46,4 @@ have looked at it.
.. _lws: https://lammps.sandia.gov
.. _gip: https://github.com/lammps/issues
.. _valgrind: https://valgrind.org

237
doc/src/Errors_debug.rst Normal file
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@ -0,0 +1,237 @@
Debugging crashes
=================
If LAMMPS crashes with a "segmentation fault" or a "bus error" or
similar message, then you can use the following two methods to further
narrow down the origin of the issue. This will help the LAMMPS
developers (or yourself) to understand the reason for the crash and
apply a fix (either to the input script or the source code).
This requires that your LAMMPS executable includes the required
:ref:`debug information <debug>`. Otherwise it is not possible to
look up the names of functions or variables.
The following patch will introduce a bug into the code for pair style
:doc:`lj/cut <pair_lj>` when using the ``examples/melt/in.melt`` input.
We use it to show how to identify the origin of a segmentation fault.
.. code-block:: diff
--- a/src/pair_lj_cut.cpp
+++ b/src/pair_lj_cut.cpp
@@ -81,6 +81,7 @@ void PairLJCut::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
+ double comx = 0.0;
inum = list->inum;
ilist = list->ilist;
@@ -134,8 +135,10 @@ void PairLJCut::compute(int eflag, int vflag)
evdwl,0.0,fpair,delx,dely,delz);
}
}
- }
+ comx += atom->rmass[i]*x[i][0]; /* BUG */
+ }
+ printf("comx = %g\n",comx);
if (vflag_fdotr) virial_fdotr_compute();
}
After recompiling LAMMPS and running the input you should get something like this:
.. code-block:
$ ./lmp -in in.melt
LAMMPS (19 Mar 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
Created 4000 atoms
create_atoms CPU = 0.000432253 secs
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
Segmentation fault (core dumped)
Using the GDB debugger to get a stack trace
-------------------------------------------
There are two options to use the GDB debugger for identifying the origin
of the segmentation fault or similar crash. The GDB debugger has many
more features and options, as can be seen for example its `online
documentation <http://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
Run LAMMPS from within the debugger
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Running LAMMPS under the control of the debugger as shown below only
works for a single MPI rank (for debugging a program running in parallel
you usually need a parallel debugger program). A simple way to launch
GDB is to prefix the LAMMPS command line with ``gdb --args`` and then
type the command "run" at the GDB prompt. This will launch the
debugger, load the LAMMPS executable and its debug info, and then run
it. When it reaches the code causing the segmentation fault, it will
stop with a message why it stopped, print the current line of code, and
drop back to the GDB prompt.
.. code-block::
[...]
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
Program received signal SIGSEGV, Segmentation fault.
0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x829740, eflag=1, vflag=<optimized out>) at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139
139 comx += atom->rmass[i]*x[i][0]; /* BUG */
(gdb)
Now typing the command "where" will show the stack of functions starting from
the current function back to "main()".
.. code-block::
(gdb) where
#0 0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x829740, eflag=1, vflag=<optimized out>) at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139
#1 0x00000000004cf0a2 in LAMMPS_NS::Verlet::setup (this=0x7e6c90, flag=1) at /home/akohlmey/compile/lammps/src/verlet.cpp:131
#2 0x000000000049db42 in LAMMPS_NS::Run::command (this=this@entry=0x7fffffffcca0, narg=narg@entry=1, arg=arg@entry=0x7e8750)
at /home/akohlmey/compile/lammps/src/run.cpp:177
#3 0x000000000041258a in LAMMPS_NS::Input::command_creator<LAMMPS_NS::Run> (lmp=<optimized out>, narg=1, arg=0x7e8750)
at /home/akohlmey/compile/lammps/src/input.cpp:878
#4 0x0000000000410ad3 in LAMMPS_NS::Input::execute_command (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:864
#5 0x00000000004111fb in LAMMPS_NS::Input::file (this=0x7d1410) at /home/akohlmey/compile/lammps/src/input.cpp:229
#6 0x000000000040933a in main (argc=<optimized out>, argv=<optimized out>) at /home/akohlmey/compile/lammps/src/main.cpp:65
(gdb)
You can also print the value of variables and see if there is anything
unexpected. Segmentation faults, for example, commonly happen when a
pointer variable is not assigned and still initialized to NULL.
.. code-block::
(gdb) print x
$1 = (double **) 0x7ffff7ca1010
(gdb) print i
$2 = 0
(gdb) print x[0]
$3 = (double *) 0x7ffff6d80010
(gdb) print x[0][0]
$4 = 0
(gdb) print x[1][0]
$5 = 0.83979809569125363
(gdb) print atom->rmass
$6 = (double *) 0x0
(gdb)
Inspect a core dump file with the debugger
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
When an executable crashes with a "core dumped" message, it creates a
file "core" or "core.<PID#>" which contains the information about the
current state. This file may be located in the folder where you ran
LAMMPS or in some hidden folder managed by the systemd daemon. In the
latter case, you need to "extract" the core file with the ``coredumpctl``
utility to the current folder. Example: ``coredumpctl -o core dump lmp``.
Now you can launch the debugger to load the executable, its debug info
and the core dump and drop you to a prompt like before.
.. code-block::
$ gdb lmp core
Reading symbols from lmp...
[New LWP 1928535]
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Core was generated by `./lmp -in in.melt'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0 0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x1b10740, eflag=1, vflag=<optimized out>)
at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139
139 comx += atom->rmass[i]*x[i][0]; /* BUG */
(gdb)
From here on, you use the same commands as shown before to get a stack
trace and print current values of (pointer) variables.
Using valgrind to get a stack trace
-----------------------------------
The `valgrind <https://valgrind.org>`_ suite of tools allows to closely
inspect the behavior of a compiled program by essentially emulating a
CPU and instrumenting the program while running. This slows down
execution quite significantly, but can also report issues that are not
resulting in a crash. The default valgrind tool is a memory checker and
you can use it by prefixing the normal command line with ``valgrind``.
Unlike GDB, this will also work for parallel execution, but it is
recommended to redirect the valgrind output to a file (e.g. with
``--log-file=crash-%p.txt``, the %p will be substituted with the
process ID) so that the messages of the multiple valgrind instances to
the console are not mixed.
.. code-block::
$ valgrind ./lmp -in in.melt
==1933642== Memcheck, a memory error detector
==1933642== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==1933642== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info
==1933642== Command: ./lmp -in in.melt
==1933642==
LAMMPS (19 Mar 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
Created 4000 atoms
create_atoms CPU = 0.032964 secs
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
==1933642== Invalid read of size 8
==1933642== at 0x6653AB: LAMMPS_NS::PairLJCut::compute(int, int) (pair_lj_cut.cpp:139)
==1933642== by 0x4CF0A1: LAMMPS_NS::Verlet::setup(int) (verlet.cpp:131)
==1933642== by 0x49DB41: LAMMPS_NS::Run::command(int, char**) (run.cpp:177)
==1933642== by 0x412589: void LAMMPS_NS::Input::command_creator<LAMMPS_NS::Run>(LAMMPS_NS::LAMMPS*, int, char**) (input.cpp:881)
==1933642== by 0x410AD2: LAMMPS_NS::Input::execute_command() (input.cpp:864)
==1933642== by 0x4111FA: LAMMPS_NS::Input::file() (input.cpp:229)
==1933642== by 0x409339: main (main.cpp:65)
==1933642== Address 0x0 is not stack'd, malloc'd or (recently) free'd
==1933642==
As you can see, the stack trace information is similar to that obtained
from GDB. In addition you get a more specific hint about what cause the
segmentation fault, i.e. that it is a NULL pointer dereference. To find
out which pointer exactly was NULL, you need to use the debugger, though.

23
doc/src/Errors_messages.rst
View File

@ -2783,7 +2783,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
if this helps.
*Did not find all elements in MEAM library file*
The requested elements were not found in the MEAM file.
Some requested elements were not found in the MEAM file. Check spelling etc.
*Did not find fix shake partner info*
Could not find bond partners implied by fix shake command. This error
@ -3135,6 +3135,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Epsilon or sigma reference not set by pair style in ewald/n*
The pair style is not providing the needed epsilon or sigma values.
*Error in MEAM parameter file: keyword %s (further information)*
Self-explanatory. Check the parameter file.
*Error in vdw spline: inner radius > outer radius*
A pre-tabulated spline is invalid. Likely a problem with the
potential parameters.
@ -4611,7 +4614,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Incorrect format in COMB3 potential file*
Incorrect number of words per line in the potential file.
*Incorrect format in MEAM potential file*
*Incorrect format in MEAM library file*
Incorrect number of words per line in the potential file.
*Incorrect format in SNAP coefficient file*
@ -5669,6 +5672,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
A fix is referenced incorrectly or a fix that produces per-atom
values is used in an equal-style variable formula.
*Mismatched parameter in MEAM library file: z!=lat*
The coordination number and lattice do not match, check that consistent values are given.
*Mismatched variable in variable formula*
A variable is referenced incorrectly or an atom-style variable that
produces per-atom values is used in an equal-style variable
@ -5845,6 +5851,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Cannot use the temper command with only one processor partition. Use
the -partition command-line option.
*Must not have multiple fixes change box parameter ...*
Self-explanatory.
*Must read Atoms before Angles*
The Atoms section of a data file must come before an Angles section.
@ -7764,6 +7773,9 @@ keyword to allow for additional bonds to be formed
*Too many atoms to dump sort*
Cannot sort when running with more than 2\^31 atoms.
*Too many elements extracted from MEAM library.*
Increase 'maxelt' in meam.h and recompile.
*Too many exponent bits for lookup table*
Table size specified via pair_modify command does not work with your
machine's floating point representation.
@ -7997,11 +8009,11 @@ keyword to allow for additional bonds to be formed
*Unknown unit_style*
Self-explanatory. Check the input script or data file.
*Unrecognized lattice type in MEAM file 1*
*Unrecognized lattice type in MEAM library file*
The lattice type in an entry of the MEAM library file is not
valid.
*Unrecognized lattice type in MEAM file 2*
*Unrecognized lattice type in MEAM parameter file*
The lattice type in an entry of the MEAM parameter file is not
valid.
@ -8017,6 +8029,9 @@ keyword to allow for additional bonds to be formed
*Unsupported order in kspace_style pppm/disp, pair_style %s*
Only pair styles with 1/r and 1/r\^6 dependence are currently supported.
*Unsupported parameter in MEAM library file*
Self-explanatory.
*Use cutoff keyword to set cutoff in single mode*
Mode is single so cutoff/multi keyword cannot be used.

1
doc/src/Howto.rst
View File

@ -16,6 +16,7 @@ Tutorials howto
:name: tutorials
:maxdepth: 1
Howto_cmake
Howto_github
Howto_pylammps
Howto_bash

6
doc/src/Howto_bash.rst
View File

@ -12,6 +12,10 @@ via apt-get and all files are accessible in both the Windows Explorer and your
Linux shell (bash). This avoids switching to a different operating system or
installing a virtual machine. Everything runs on Windows.
.. seealso::
You can find more detailed information at the `Windows Subsystem for Linux Installation Guide for Windows 10 <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_.
Installing Bash on Windows
--------------------------
@ -103,7 +107,7 @@ needed for various LAMMPS features:
.. code-block:: bash
sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng12-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools
sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools
Files in Ubuntu on Windows
^^^^^^^^^^^^^^^^^^^^^^^^^^

483
doc/src/Howto_cmake.rst Normal file
View File

@ -0,0 +1,483 @@
Using CMake with LAMMPS tutorial
================================
The support for building LAMMPS with CMake is a recent addition to
LAMMPS thanks to the efforts of Christoph Junghans (LANL) and Richard
Berger (Temple U). One of the key strengths of CMake is that it is not
tied to a specific platform or build system and thus generate the files
necessary to build and develop for different build systems and on
different platforms. Note, that this applies to the build system itself
not the LAMMPS code. In other words, without additional porting effort,
it is not possible - for example - to compile LAMMPS with Visual C++ on
Windows. The build system output can also include support files
necessary to program LAMMPS as a project in integrated development
environments (IDE) like Eclipse, Visual Studio, QtCreator, Xcode,
CodeBlocks, Kate and others.
A second important feature of CMake is, that it can detect and validate
available libraries, optimal settings, available support tools and so
on, so that by default LAMMPS will take advantage of available tools
without requiring to provide the details about how to enable/integrate
them.
The downside of this approach is, that there is some complexity
associated with running CMake itself and how to customize the building
of LAMMPS. This tutorial will show how to manage this through some
selected examples. Please see the chapter about :doc:`building LAMMPS
<Build>` for descriptions of specific flags and options for LAMMPS in
general and for specific packages.
CMake can be used through either the command-line interface (CLI)
program ``cmake`` (or ``cmake3``), a text mode interactive user
interface (TUI) program ``ccmake`` (or ``ccmake3``), or a graphical user
interface (GUI) program ``cmake-gui``. All of them are portable
software available on all supported platforms and can be used
interchangeably. The minimum supported CMake version is 3.10 (3.12 or
later is recommended).
All details about features and settings for CMake are in the `CMake
online documentation <https://cmake.org/documentation/>`_. We focus
below on the most important aspects with respect to compiling LAMMPS.
Prerequisites
-------------
This tutorial assumes that you are operating in a command-line environment
using a shell like Bash.
- Linux: any Terminal window will work
- MacOS X: launch the Terminal application.
- Windows 10: install and run the :doc:`Windows subsystem for Linux <Howto_bash>`
We also assume that you have downloaded and unpacked a recent LAMMPS source code package
or used Git to create a clone of the LAMMPS sources on your compilation machine.
You should change into the top level directory of the LAMMPS source tree all
paths mentioned in the tutorial are relative to that. Immediately after downloading
it should look like this:
.. code-block:: bash
$ ls
bench doc lib potentials README tools
cmake examples LICENSE python src
Build versus source directory
-----------------------------
When using CMake the build procedure is separated into multiple distinct phases:
#. **Configuration:** detect or define which features and settings
should be enable and used and how LAMMPS should be compiled
#. **Compilation:** generate and compile all necessary source files
and build libraries and executables.
#. **Installation:** copy selected files from the compilation into
your file system, so they can be used without having to keep the
source and build tree around.
The configuration and compilation of LAMMPS has to happen in a dedicated
*build directory* which must be different from the source directory.
Also the source directory (``src``) must remain pristine, so it is not
allowed to "install" packages using the traditional make process and
after an compilation attempt all created source files must be removed.
This can be achieved with ``make no-all purge``.
You can pick **any** folder outside the source tree. We recommend to
create a folder ``build`` in the top-level directory, or multiple
folders in case you want to have separate builds of LAMMPS with
different options (``build-parallel``, ``build-serial``) or with
different compilers (``build-gnu``, ``build-clang``, ``build-intel``)
and so on. All the auxiliary files created by one build process
(executable, object files, log files, etc) are stored in this directory
or sub-directories within it that CMake creates.
Running CMake
-------------
CLI version
^^^^^^^^^^^
In the (empty) ``build`` directory, we now run the command ``cmake
../cmake``, which will start the configuration phase and you will see
the progress of the configuration printed to the screen followed by a
summary of the enabled features, options and compiler settings. A typical
summary screen will look like this:
.. code-block::
$ cmake ../cmake/
-- The CXX compiler identification is GNU 8.2.0
-- Check for working CXX compiler: /opt/tools/gcc-8.2.0/bin/c++
-- Check for working CXX compiler: /opt/tools/gcc-8.2.0/bin/c++ - works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /usr/bin/git (found version "2.25.2")
-- Running check for auto-generated files from make-based build system
-- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Looking for C++ include omp.h
-- Looking for C++ include omp.h - found
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found JPEG: /usr/lib64/libjpeg.so (found version "62")
-- Found PNG: /usr/lib64/libpng.so (found version "1.6.37")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Found GZIP: /usr/bin/gzip
-- Found FFMPEG: /usr/bin/ffmpeg
-- Performing Test COMPILER_SUPPORTS-ffast-math
-- Performing Test COMPILER_SUPPORTS-ffast-math - Success
-- Performing Test COMPILER_SUPPORTS-march=native
-- Performing Test COMPILER_SUPPORTS-march=native - Success
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Generating style_angle.h...
[...]
-- Generating lmpinstalledpkgs.h...
-- The following tools and libraries have been found and configured:
* Git
* MPI
* OpenMP
* JPEG
* PNG
* ZLIB
-- <<< Build configuration >>>
Build type: RelWithDebInfo
Install path: /home/akohlmey/.local
Generator: Unix Makefiles using /usr/bin/gmake
-- <<< Compilers and Flags: >>>
-- C++ Compiler: /opt/tools/gcc-8.2.0/bin/c++
Type: GNU
Version: 8.2.0
C++ Flags: -O2 -g -DNDEBUG
Defines: LAMMPS_SMALLBIG;LAMMPS_MEMALIGN=64;LAMMPS_JPEG;LAMMPS_PNG;LAMMPS_GZIP;LAMMPS_FFMPEG
Options: -ffast-math;-march=native
-- <<< Linker flags: >>>
-- Executable name: lmp
-- Static library flags:
-- <<< MPI flags >>>
-- MPI includes: /usr/include/mpich-x86_64
-- MPI libraries: /usr/lib64/mpich/lib/libmpicxx.so;/usr/lib64/mpich/lib/libmpi.so;
-- Configuring done
-- Generating done
-- Build files have been written to: /home/akohlmey/compile/lammps/build
The ``cmake`` command has one mandatory argument, and that is a folder
with either the file ``CMakeLists.txt`` or ``CMakeCache.txt``. The
``CMakeCache.txt`` file is created during the CMake configuration run
and contains all active settings, thus after a first run of CMake
all future runs in the build folder can use the folder ``.`` and CMake
will know where to find the CMake scripts and reload the settings
from the previous step. This means, that one can modify an existing
configuration by re-running CMake, but only needs to provide flags
indicating the desired change, everything else will be retained. One
can also mix compilation and configuration, i.e. start with a minimal
configuration and then, if needed, enable additional features and
recompile.
The steps above **will NOT compile the code**\ . The compilation can be
started in a portable fashion with ``cmake --build .``, or you use the
selected built tool, e.g. ``make``.
TUI version
^^^^^^^^^^^
For the text mode UI CMake program the basic principle is the same.
You start the command ``ccmake ../cmake`` in the ``build`` folder.
.. list-table::
* - .. figure:: JPG/ccmake-initial.png
:target: JPG/ccmake-initial.png
:align: center
Initial ``ccmake`` screen
- .. figure:: JPG/ccmake-config.png
:target: JPG/ccmake-config.png
:align: center
Configure output of ``ccmake``
- .. figure:: JPG/ccmake-options.png
:target: JPG/ccmake-options.png
:align: center
Options screen of ``ccmake``
This will show you the initial screen (left image) with the empty
configuration cache. Now you type the 'c' key to run the configuration
step. That will do a first configuration run and show the summary
(center image). You exit the summary screen with 'e' and see now the
main screen with detected options and settings. You can now make changes
by moving and down with the arrow keys of the keyboard and modify
entries. For on/off settings, the enter key will toggle the state.
For others, hitting enter will allow you to modify the value and
you commit the change by hitting the enter key again or cancel using
the escape key. All "new" settings will be marked with a star '\*'
and for as long as one setting is marked like this, you have to
re-run the configuration by hitting the 'c' key again, sometimes
multiple times unless the TUI shows the word "generate" next to the
letter 'g' and by hitting the 'g' key the build files will be written
to the folder and the TUI exits. You can quit without generating
build files by hitting 'q'.
GUI version
^^^^^^^^^^^
For the graphical CMake program the steps are similar to the TUI
version. You can type the command ``cmake-gui ../cmake`` in the
``build`` folder. In this case the path to the CMake script folder is
not required, it can also be entered from the GUI.
.. list-table::
* - .. figure:: JPG/cmake-gui-initial.png
:target: JPG/cmake-gui-initial.png
:align: center
Initial ``cmake-gui`` screen
- .. figure:: JPG/cmake-gui-popup.png
:target: JPG/cmake-gui-popup.png
:align: center
Generator selection in ``cmake-gui``
- .. figure:: JPG/cmake-gui-options.png
:target: JPG/cmake-gui-options.png
:align: center
Options screen of ``cmake-gui``
Again, you start with an empty configuration cache (left image) and need
to start the configuration step. For the very first configuration in a
folder, you will have a pop-up dialog (center image) asking to select
the desired build tool and some configuration settings (stick with the
default) and then you get the option screen with all new settings
highlighted in red. You can modify them (or not) and click on the
"configure" button again until satisfied and click on the "generate"
button to write out the build files. You can exit the GUI from the
"File" menu or hit "ctrl-q".
Setting options
---------------
Options that enable, disable or modify settings are modified by setting
the value of CMake variables. This is done on the command line with the
*-D* flag in the format ``-D VARIABLE=value``, e.g. ``-D
CMAKE_BUILD_TYPE=Release`` or ``-D BUILD_MPI=on``. There is one quirk:
when used before the CMake directory, there may be a space between the
*-D* flag and the variable, after it must not be. Such CMake variables
can have boolean values (on/off, yes/no, or 1/0 are all valid) or are
strings representing a choice, or a path, or are free format. If the
string would contain whitespace, it must be put in quotes, for example
``-D CMAKE_TUNE_FLAGS="-ftree-vectorize -ffast-math"``.
CMake variables fall into two categories: 1) common CMake variables that
are used by default for any CMake configuration setup and 2) project
specific variables, i.e. settings that are specific for LAMMPS.
Also CMake variables can be flagged as *advanced*, which means they are
not shown in the text mode or graphical CMake program in the overview
of all settings by default, but only when explicitly requested (by hitting
the 't' key or clicking on the 'Advanced' check-box).
Some common CMake variables
^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. list-table::
:header-rows: 1
* - Variable
- Description
* - ``CMAKE_INSTALL_PREFIX``
- root directory of install location for ``make install`` (default: ``$HOME/.local``)
* - ``CMAKE_BUILD_TYPE``
- controls compilation options:
one of ``RelWithDebInfo`` (default), ``Release``, ``Debug``, ``MinSizeRel``
* - ``BUILD_SHARED_LIBS``
- if set to ``on`` build the LAMMPS library as shared library (default: ``off``)
* - ``CMAKE_MAKE_PROGRAM``
- name/path of the compilation command (default depends on *-G* option, usually ``make``)
* - ``CMAKE_VERBOSE_MAKEFILE``
- if set to ``on`` echo commands while executing during build (default: ``off``)
* - ``CMAKE_C_COMPILER``
- C compiler to be used for compilation (default: system specific, ``gcc`` on Linux)
* - ``CMAKE_CXX_COMPILER``
- C++ compiler to be used for compilation (default: system specific, ``g++`` on Linux)
* - ``CMAKE_Fortran_COMPILER``
- Fortran compiler to be used for compilation (default: system specific, ``gfortran`` on Linux)
* - ``CXX_COMPILER_LAUNCHER``
- tool to launch the C++ compiler, e.g. ``ccache`` or ``distcc`` for faster compilation (default: empty)
Some common LAMMPS specific variables
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. list-table::
:header-rows: 1
* - Variable
- Description
* - ``BUILD_MPI``
- build LAMMPS with MPI support (default: ``on`` if a working MPI available, else ``off``)
* - ``BUILD_OMP``
- build LAMMPS with OpenMP support (default: ``on`` if compiler supports OpenMP fully, else ``off``)
* - ``BUILD_TOOLS``
- compile some additional executables from the ``tools`` folder (default: ``off``)
* - ``BUILD_DOC``
- include building the HTML format documentation for packaging/installing (default: ``off``)
* - ``CMAKE_TUNE_FLAGS``
- common compiler flags, for optimization or instrumentation (default: compiler specific)
* - ``LAMMPS_MACHINE``
- when set to ``name`` the LAMMPS executable and library will be called ``lmp_name`` and ``liblammps_name.a``
* - ``LAMMPS_EXCEPTIONS``
- when set to ``on`` errors will throw a C++ exception instead of aborting (default: ``off``)
* - ``FFT``
- select which FFT library to use: ``FFTW3``, ``MKL``, ``KISS`` (default, unless FFTW3 is found)
* - ``FFT_SINGLE``
- select whether to use single precision FFTs (default: ``off``)
* - ``WITH_JPEG``
- whether to support JPEG format in :doc:`dump image <dump_image>` (default: ``on`` if found)
* - ``WITH_PNG``
- whether to support PNG format in :doc:`dump image <dump_image>` (default: ``on`` if found)
* - ``WITH_GZIP``
- whether to support reading and writing compressed files (default: ``on`` if found)
* - ``WITH_FFMPEG``
- whether to support generating movies with :doc:`dump movie <dump_image>` (default: ``on`` if found)
Enabling or disabling LAMMPS packages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The LAMMPS software is organized into a common core that is always
included and a large number of :doc:`add-on packages <Packages>` that
have to be enabled to be included into a LAMMPS executable. Packages
are enabled through setting variables of the kind ``PKG_<NAME>`` to
``on`` and disabled by setting them to ``off`` (or using ``yes``,
``no``, ``1``, ``0`` correspondingly). ``<NAME>`` has to be replaced by
the name of the package, e.g. ``MOLECULE`` or ``USER-MISC``.
Using presets
-------------
Since LAMMPS has a lot of optional features and packages, specifying
them all on the command line can be tedious. Or when selecting a
different compiler toolchain, multiple options have to be changed
consistently and that is rather error prone. Or when enabling certain
packages, they require consistent settings to be operated in a
particular mode. For this purpose, we are providing a selection of
"preset files" for CMake in the folder ``cmake/presets``. They
represent a way to pre-load or override the CMake configuration cache by
setting or changing CMake variables. Preset files are loaded using the
*-C* command line flag. You can combine loading multiple preset files or
change some variables later with additional *-D* flags. A few examples:
.. code-block:: bash
cmake -C ../cmake/preset/minimal.cmake -D PKG_MISC=on ../cmake
cmake -C ../cmake/preset/clang.cmake -C ../cmake/preset/most.cmake ../cmake
cmake -C ../cmake/preset/minimal.cmake -D BUILD_MPI=off ../cmake
The first command will install the packages ``KSPACE``, ``MANYBODY``,
``MOLECULE``, ``RIGID`` and ``MISC``; the first four from the preset
file and the fifth from the explicit variable definition. The second
command will first switch the compiler toolchain to use the Clang
compilers and install a large number of packages that are not depending
on any special external libraries or tools and are not very unusual.
The third command will enable the first four packages like above and
then enforce compiling LAMMPS as a serial program (using the MPI STUBS
library).
It is also possible to do this incrementally.
.. code-block:: bash
cmake -C ../cmake/preset/minimal.cmake ../cmake
cmake -D PKG_MISC=on .
will achieve the same configuration like in the first example above. In
this scenario it is particularly convenient to do the second
configuration step using either the text mode or graphical user
interface (``ccmake`` or ``cmake-gui``).
Compilation and build targets
-----------------------------
The actual compilation will be started by running the selected build
command (on Linux this is by default ``make``, see below how to select
alternatives). You can also use the portable command ``cmake --build .``
which will adapt to whatever the selected build command is.
This is particularly convenient, if you have set a custom build command
via the ``CMAKE_MAKE_PROGRAM`` variable.
When calling the build program, you can also select which "target" is to
be build through appending the name of the target to the build command.
Example: ``cmake --build . all``. The following abstract targets are available:
.. list-table::
:header-rows: 1
* - Target
- Description
* - ``all``
- build "everything" (default)
* - ``lammps``
- build the LAMMPS library and executable
* - ``doc``
- build the HTML documentation (if configured)
* - ``install``
- install all target files into folders in ``CMAKE_INSTALL_PREFIX``
* - ``test``
- run some simple tests (if configured with ``-D ENABLE_TESTING=on``)
* - ``clean``
- remove all generated files
Choosing generators
-------------------
While CMake usually defaults to creating makefiles to compile software
with the ``make`` program, it supports multiple alternate build tools
(e.g. ``ninja-build`` which tends to be faster and more efficient in
parallelizing builds than ``make``) and can generate project files for
integrated development environments (IDEs) like VisualStudio, Eclipse or
CodeBlocks. This is specific to how the local CMake version was
configured and compiled. The list of available options can be seen at
the end of the output of ``cmake --help``. Example on Fedora 31 this is:
.. code-block::
Generators
The following generators are available on this platform (* marks default):
* Unix Makefiles = Generates standard UNIX makefiles.
Green Hills MULTI = Generates Green Hills MULTI files
(experimental, work-in-progress).
Ninja = Generates build.ninja files.
Ninja Multi-Config = Generates build-<Config>.ninja files.
Watcom WMake = Generates Watcom WMake makefiles.
CodeBlocks - Ninja = Generates CodeBlocks project files.
CodeBlocks - Unix Makefiles = Generates CodeBlocks project files.
CodeLite - Ninja = Generates CodeLite project files.
CodeLite - Unix Makefiles = Generates CodeLite project files.
Sublime Text 2 - Ninja = Generates Sublime Text 2 project files.
Sublime Text 2 - Unix Makefiles
= Generates Sublime Text 2 project files.
Kate - Ninja = Generates Kate project files.
Kate - Unix Makefiles = Generates Kate project files.
Eclipse CDT4 - Ninja = Generates Eclipse CDT 4.0 project files.
Eclipse CDT4 - Unix Makefiles= Generates Eclipse CDT 4.0 project files.
Below is a screenshot of using the CodeBlocks IDE with the ninja build tool
after running CMake as follows:
.. code-block:: bash
cmake -G 'CodeBlocks - Ninja' ../cmake/presets/most.cmake ../cmake/
.. image:: JPG/cmake-codeblocks.png
:align: center

4
doc/src/Install_mac.rst
View File

@ -34,9 +34,9 @@ install the `openkim-models` package
% brew install openkim-models
If you have problems with the installation you can post issues to
`this link <homebrew_>`_.
`this link <https://github.com/Homebrew/homebrew-core/issues>`_.
.. _homebrew: https://github.com/Homebrew/homebrew-core/issues
.. _homebrew: https://brew.sh
Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
up the Homebrew capability.

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