Merge bence virtonomy2

.gitignore

@@ -1037,4 +1037,8 @@ _deps
 modules.order
 Module.symvers
 Mkfile.old
-dkms.conf
+dkms.conf
+
+# wasm build
+build_wasm_release
+build_wasm_debug

.gitmodules

@@ -1,9 +1,9 @@
-[submodule "oneTBB"]
-	path = oneTBB
-	url = https://github.com/BenceVirtonomy/oneTBB
-[submodule "SPHINXsys/src/shared/clapack_for_SPHinXsys"]
-	path = SPHINXsys/src/shared/clapack_for_SPHinXsys
-	url = https://github.com/BenceVirtonomy/clapack_for_SPHinXsys
-[submodule "SPHINXsys/src/shared/simbody"]
-	path = SPHINXsys/src/shared/simbody
-	url = https://github.com/BenceVirtonomy/simbody
+[submodule "3rd_party/simbody"]
+	path = 3rd_party/simbody
+	url = https://github.com/BenceVirtonomy/simbody.git
+[submodule "3rd_party/eigen"]
+	path = 3rd_party/eigen
+	url = https://gitlab.com/libeigen/eigen.git
+[submodule "3rd_party/wasmtbb"]
+	path = 3rd_party/wasmtbb
+	url = https://github.com/hpcwasm/wasmtbb.git

CMakeLists.txt

@@ -8,8 +8,43 @@ set(SPHINXSYS_PROJECT_DIR ${PROJECT_SOURCE_DIR})
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${SPHINXSYS_PROJECT_DIR}/cmake)
 
 ###### Change settings in this file if you want to build with Simbody and/or oneTBB source code ######
+option(STATIC_BUILD "STATIC_BUILD" 0)
 option(ONLY_3D "ONLY_3D" 0)
-include(Dependency_free_settings)
+option(BUILD_WITH_SIMBODY "BUILD_WITH_SIMBODY" 0)
+option(EMSCRIPTEN "EMSCRIPTEN" 0)
+option(BUILD_TESTS "BUILD_TESTS" 1)
+
+if(EMSCRIPTEN)
+    set(STATIC_BUILD 1)
+    set(BUILD_WITH_SIMBODY 1)
+    set(ONLY_3D 1)
+    set(BUILD_TESTS 1)
+    add_definitions(-D__SIMBODY_WITHOUT_LAPACK__)
+    add_definitions(-D__EIGEN__)
+    add_definitions(-D__EMSCRIPTEN__)
+
+    remove_definitions(-DTBB_2021_2_0)
+    set(TBB_ROOT ${SPHINXSYS_PROJECT_DIR}/3rd_party/wasmtbb)
+    include_directories("${TBB_ROOT}/include")
+    set(OBJDIR "${TBB_ROOT}/build/linux_wasm32_emscripten_emscripten_wasm32_release")
+    file(GLOB TBB_OBJECTS ${OBJDIR}/*.o)
+else()
+    set(BOOST_AVAILABLE 1)
+    add_definitions(-DBOOST_AVAILABLE)
+endif()
+
+if(BUILD_WITH_SIMBODY)
+    add_definitions(-D__SIMBODY_WITHOUT_LAPACK__)
+    add_definitions(-D__EIGEN__)
+    set(EIGEN_ROOT ${SPHINXSYS_PROJECT_DIR}/3rd_party/eigen)
+    message("${EIGEN_ROOT}")
+    include_directories("${EIGEN_ROOT}")
+endif()
+
+if(STATIC_BUILD)
+    set(BUILD_STATIC_LIBRARIES 1) # Simbody
+    set(BUILD_DYNAMIC_LIBRARIES 0) # Simbody
+endif()
 
 if(NOT CMAKE_BUILD_TYPE)
     set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
@@ -39,18 +74,29 @@ if(MSVC)
     SET(CMAKE_CL_64 1)
     SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}" " /MP")
     add_definitions(-D_USE_MATH_DEFINES)
-else(MSVC)
+elseif(EMSCRIPTEN)
+    # set(PRE_POST "")
+    # #set(EM_FLAGS "${PRE_POST} -fPIC -g -O0 --profiling -DUNIX -D__linux__=1 --bind -std=c++11 -s USE_PTHREADS=1 -s DISABLE_EXCEPTION_CATCHING=0")
+    # set(EM_FLAGS "${PRE_POST} -fPIC -g -O3 -DUNIX -D__linux__=1 --bind -std=c++11 -s USE_PTHREADS=1 -s DISABLE_EXCEPTION_CATCHING=0")
+    # set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${EM_FLAGS}")
+    # set(EM_FLAGS " -s INITIAL_MEMORY=536870912 -s ASSERTIONS=1 -s ALLOW_MEMORY_GROWTH=0 -s ERROR_ON_UNDEFINED_SYMBOLS=1")
+    # set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${EM_FLAGS}")
+else()
     add_compile_definitions(__linux__=1)
-    set(CMAKE_CXX_FLAGS "-Wall -Werror -std=c++11 -DUNIX -pthread")
+    set(CMAKE_CXX_FLAGS "-w -std=c++11 -DUNIX -pthread")
     set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
     set(CMAKE_CXX_FLAGS_DEBUG "-g -O0 -ggdb")
     IF(${CMAKE_BUILD_TYPE} MATCHES "Debug")
-        set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS}")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
     ELSE(${CMAKE_BUILD_TYPE} MATCHES "Debug")
         set(CMAKE_CXX_FLAGS "-fPIC ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
     ENDIF(${CMAKE_BUILD_TYPE} MATCHES "Debug")
+endif()
+
+if(NOT BUILD_WITH_SIMBODY)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Werror")
+endif()
 
-endif(MSVC)
 add_compile_definitions(TBB_SUPPRESS_DEPRECATED_MESSAGES=1)
 
 message("===========================================")
@@ -70,23 +116,20 @@ endif()
 
 enable_testing()
 
-if(NOT WASM_BUILD)
-    include(Common)
-    include(Import3rdpartylibs)
+include(Common)
+include(Import3rdpartylibs)
+
+if(BUILD_WITH_SIMBODY)
+    set(simbody_root "${SPHINXSYS_PROJECT_DIR}/3rd_party/simbody")
+    add_subdirectory(${simbody_root})
 endif()
 
-option(BUILD_TESTS "BUILD_TESTS" 1)
 add_subdirectory(SPHINXsys)
-if(BUILD_WITH_ONETBB)
-    add_subdirectory(oneTBB)
-endif()
 
 if(BUILD_TESTS)
     add_subdirectory(tests)
 endif()
 
-add_subdirectory(cases_user)
-
 if(ACTIVATE_CUDA)
     add_subdirectory(cases_test_gpu)
 endif()

Dockerfile

@@ -1,7 +1,7 @@
 FROM ubuntu:20.04
 
 ARG build_with_dependencies_source=0
-ARG sph_only_static_build=0
+ARG STATIC_BUILD=0
 
 ENV TZ=Europe/Berlin
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
@@ -31,4 +31,4 @@ RUN cd /usr/src/gtest
     cd /home/SPHinXsys
 
 RUN rm -rf build
-RUN mkdir build && cd build && cmake .. -DBUILD_WITH_DEPENDENCIES_SOURCE=${build_with_dependencies_source} -DSPH_ONLY_STATIC_BUILD=${sph_only_static_build} && make -j$(nproc)
+RUN mkdir build && cd build && cmake .. -DBUILD_WITH_DEPENDENCIES_SOURCE=${build_with_dependencies_source} -DSTATIC_BUILD=${STATIC_BUILD} && make -j$(nproc)

README.md

@@ -153,7 +153,7 @@ Here, we give the instructions for installing on Ubuntu Linux, Apple OS and Wind
 
 2. Edit the CMake variables to define which dependency to use. Simbody and/or TBB can be built by the project. If one is not built by the project, install that dependency in the usual way as written before.
 
-        Go to SPHinXsys/cmake/Dependency_free_settings.cmake
+        Go to SPHinXsys/cmake/Dependency_settings.cmake
         Set BUILD_WITH_DEPENDENCIES to 1
         Set BUILD_WITH_SIMBODY to 1 if Simbody should be built by the project
         Set BUILD_WITH_ONETBB to 1 if TBB should be built by the project

SPHINXsys/cmake/Dirsearch_shared.cmake

@@ -1,9 +1,6 @@
 if(BUILD_WITH_SIMBODY)
     include(Simbody_header_directories)
 endif()
-if(BUILD_WITH_ONETBB)
-    include(oneTBB_header_directory)
-endif()
 
 MACRO(HEADER_DIRECTORIES_SHARED return_list)
     FILE(GLOB_RECURSE new_list  ${PROJECT_SOURCE_DIR}/src/shared/*.h)
@@ -20,10 +17,6 @@ MACRO(HEADER_DIRECTORIES_SHARED return_list)
             SET(dir_list ${dir_list} ${simbody_header_path})
         ENDFOREACH()
     endif()
-
-    if(BUILD_WITH_ONETBB)
-        SET(dir_list ${dir_list} ${ONETBB_HEADER_DIRECTORY})
-    endif()
 
     SET(${return_list} ${dir_list})
 ENDMACRO()

SPHINXsys/cmake/Simbody_header_directories.cmake

@@ -1,15 +1,21 @@
-set(SHP_SOURCE_DIRECTORY_FOR_INCLUDE_PATHS "")
-set(SHP_SOURCE_DIRECTORY_FOR_INCLUDE_PATHS "${SPHINXSYS_PROJECT_DIR}") #SPHinXsys
+set(simbody_root "${SPHINXSYS_PROJECT_DIR}/3rd_party/simbody")
 
 set(SIMBODY_HEADER_DIRECTORIES
-    "${SHP_SOURCE_DIRECTORY_FOR_INCLUDE_PATHS}/SPHINXsys/src/shared/simbody/SimTKcommon/BigMatrix/include"
-    "${SHP_SOURCE_DIRECTORY_FOR_INCLUDE_PATHS}/SPHINXsys/src/shared/simbody/SimTKcommon/Geometry/include"
-    "${SHP_SOURCE_DIRECTORY_FOR_INCLUDE_PATHS}/SPHINXsys/src/shared/simbody/SimTKcommon/Mechanics/include"
-    "${SHP_SOURCE_DIRECTORY_FOR_INCLUDE_PATHS}/SPHINXsys/src/shared/simbody/SimTKcommon/Polynomial/include"
-    "${SHP_SOURCE_DIRECTORY_FOR_INCLUDE_PATHS}/SPHINXsys/src/shared/simbody/SimTKcommon/Random/include"
-    "${SHP_SOURCE_DIRECTORY_FOR_INCLUDE_PATHS}/SPHINXsys/src/shared/simbody/SimTKcommon/Scalar/include"
-    "${SHP_SOURCE_DIRECTORY_FOR_INCLUDE_PATHS}/SPHINXsys/src/shared/simbody/SimTKcommon/Simulation/include"
-    "${SHP_SOURCE_DIRECTORY_FOR_INCLUDE_PATHS}/SPHINXsys/src/shared/simbody/SimTKcommon/SmallMatrix/include"
-    "${SHP_SOURCE_DIRECTORY_FOR_INCLUDE_PATHS}/SPHINXsys/src/shared/simbody/SimTKmath/Geometry/include"
-    "${SHP_SOURCE_DIRECTORY_FOR_INCLUDE_PATHS}/SPHINXsys/src/shared/simbody/SimTKmath/Integrators/include"
+    "${simbody_root}/SimTKcommon/BigMatrix/include"
+    "${simbody_root}/SimTKcommon/Geometry/include"
+    "${simbody_root}/SimTKcommon/Mechanics/include"
+    "${simbody_root}/SimTKcommon/Polynomial/include"
+    "${simbody_root}/SimTKcommon/Random/include"
+    "${simbody_root}/SimTKcommon/Scalar/include"
+    "${simbody_root}/SimTKcommon/Simulation/include"
+    "${simbody_root}/SimTKcommon/SmallMatrix/include"
+    "${simbody_root}/SimTKcommon/include"
+
+    "${simbody_root}/SimTKmath/Geometry/include"
+    "${simbody_root}/SimTKmath/Integrators/include"
+    "${simbody_root}/SimTKmath/include"
+
+    "${simbody_root}/Simbody/include"
+    "${simbody_root}/Simbody/include/simbody/internal"
+    "${simbody_root}/Simbody/Visualizer/include"
 )

SPHINXsys/src/for_2D_build/CMakeLists.txt

@@ -17,7 +17,6 @@ LIST(REMOVE_ITEM usefulsubdirs ${CMAKE_CURRENT_SOURCE_DIR})
 
 ##Add all useful subdirectories
 FOREACH(subdir_path ${usefulsubdirs})
-	#message(STATUS ${subdir_path})
 	ADD_SUBDIRECTORY(${subdir_path})
 ENDFOREACH()
 
@@ -50,32 +49,66 @@ FOREACH(srcdir_path ${sourcedirs})
 	list(APPEND SCR_FILES ${DIR_scrs})
 ENDFOREACH()
 
-#FOREACH(file1 ${SCR_FILES})
-	#message(STATUS ${file1})
-#ENDFOREACH()
-
-ADD_LIBRARY(sphinxsys_2d SHARED ${SCR_FILES})
-ADD_LIBRARY(sphinxsys_static_2d STATIC ${SCR_FILES})
-
-SET_TARGET_PROPERTIES(sphinxsys_static_2d PROPERTIES OUTPUT_NAME "sphinxsys_2d")
-#SET_TARGET_PROPERTIES(sphinxsys PROPERTIES VERSION 1.0 SOVERSION 0)
-
-SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
-
-if(MSVC)
-    target_link_libraries(sphinxsys_2d ${TBB_LIBRARYS} ${Simbody_LIBRARIES})
-else(MSVC)
-	if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
-    	target_link_libraries(sphinxsys_2d ${TBB_LIBRARYS} ${Simbody_LIBRARIES} ${Boost_LIBRARIES} stdc++)
-	else(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
-		target_link_libraries(sphinxsys_2d ${TBB_LIBRARYS} ${Simbody_LIBRARIES} stdc++ stdc++fs)
-	endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
-endif(MSVC)
-
-INSTALL(TARGETS sphinxsys_2d sphinxsys_static_2d
-RUNTIME DESTINATION 2d_code/bin
-LIBRARY DESTINATION 2d_code/lib
-ARCHIVE DESTINATION 2d_code/lib)
+if(NOT STATIC_BUILD)
+	### SPHinXsys dynamic lib ###
+	ADD_LIBRARY(sphinxsys_2d SHARED ${SCR_FILES})
+
+	if(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+		#target_link_libraries(sphinxsys_3d)
+	else(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+		if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+			target_link_libraries(sphinxsys_2d stdc++)
+		else(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+			target_link_libraries(sphinxsys_2d stdc++ stdc++fs)
+		endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+
+		if(DEFINED BOOST_AVAILABLE) # link Boost if available (not for Windows)
+			target_link_libraries(sphinxsys_2d ${Boost_LIBRARIES})
+		endif()
+	endif(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+
+	if(BUILD_WITH_SIMBODY)
+		target_link_libraries(sphinxsys_2d SimTKcommon SimTKmath SimTKsimbody ${TBB_LIBRARYS})
+	else()
+		target_link_libraries(sphinxsys_2d ${Simbody_LIBRARIES} ${TBB_LIBRARYS})
+	endif()
+	### SPHinXsys dynamic lib ###
+else()
+	### SPHinXsys static lib ###
+	ADD_LIBRARY(sphinxsys_static_2d STATIC ${SCR_FILES})
+	if(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+		#target_link_libraries(sphinxsys_3d)
+	else(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+		if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+			target_link_libraries(sphinxsys_static_2d stdc++)
+		else(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+			target_link_libraries(sphinxsys_static_2d stdc++ stdc++fs)
+		endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+
+		if(DEFINED BOOST_AVAILABLE) # link Boost if available (not for Windows)
+			target_link_libraries(sphinxsys_static_2d ${Boost_LIBRARIES})
+		endif()
+	endif(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+
+	if(BUILD_WITH_SIMBODY)
+		target_link_libraries(sphinxsys_static_2d SimTKcommon_static SimTKmath_static SimTKsimbody_static ${TBB_LIBRARYS})
+	else()
+		target_link_libraries(sphinxsys_static_2d ${Simbody_LIBRARIES} ${TBB_LIBRARYS})
+	endif()
+	### SPHinXsys static lib ###
+endif()
+
+if(NOT STATIC_BUILD)
+	INSTALL(TARGETS sphinxsys_2d
+	RUNTIME DESTINATION 2d_code/bin
+	LIBRARY DESTINATION 2d_code/lib
+	ARCHIVE DESTINATION 2d_code/lib)
+else()
+	INSTALL(TARGETS sphinxsys_static_2d
+	RUNTIME DESTINATION 2d_code/bin
+	LIBRARY DESTINATION 2d_code/lib
+	ARCHIVE DESTINATION 2d_code/lib)
+endif()
 
 FILE(GLOB_RECURSE hpp_headers  ${PROJECT_SOURCE_DIR}/src/shared/*.hpp ${PROJECT_SOURCE_DIR}/src/for_2D_build/*.hpp)
 INSTALL(FILES ${hpp_headers} DESTINATION 2d_code/include)