Merge pull request #204 from BioDataAnalysis/bda_several_build_improv…

…ements

Several build improvements

CMakeLists.txt

@@ -11,7 +11,6 @@ endif()
 
 option(BUILD_SHARED_LIBS "Build as a shared library" ON)
 option(USE_CUDA "Compile with CUDA" ON)
-option(USE_EIGEN "Compile with Eigen" OFF)
 option(BUILD_TESTS "Build Tests" OFF)
 option(USE_DOUBLE "Use double as kernel_type" OFF)
 
@@ -21,14 +20,14 @@ endif()
 if (NOT CMAKE_BUILD_TYPE)
     set(CMAKE_BUILD_TYPE Release)
 endif ()
+if (MSVC AND BUILD_SHARED_LIBS)
+    set (CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
+endif ()
+
 find_package(Threads)
 find_package(OpenMP REQUIRED)
 add_definitions("-DELPP_NO_LOG_TO_FILE")
 
-if (USE_CUDA AND USE_EIGEN)
-    message (FATAL_ERROR "CUDA and Eigen are mutually exclusive. Please specify either USE_CUDA or USE_EIGEN, not both.")
-endif ()
-
 if (USE_CUDA)
     message("Compile with CUDA")
     find_package(CUDA REQUIRED QUIET)
@@ -39,9 +38,6 @@ if (USE_CUDA)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_MWAITXINTRIN_H_INCLUDED -D_FORCE_INLINES")
 else ()
     message("Compile without CUDA")
-endif ()
-
-if (USE_EIGEN)
     find_package (Eigen3 3.3 NO_MODULE)
     if (Eigen3_FOUND)
         message("using external Eigen3 for acceleration")
@@ -51,7 +47,9 @@ if (USE_EIGEN)
         message("using internal Eigen3 for acceleration")
         include_directories(${PROJECT_SOURCE_DIR}/eigen)
     endif ()
-    add_compile_options("-march=native")
+    if (NOT CMAKE_CXX_FLAGS MATCHES "-march")
+        add_compile_options("-march=native")
+    endif ()
 endif ()
 
 if (CMAKE_VERSION VERSION_LESS "3.1")

README.md

@@ -85,7 +85,7 @@ cmake -DCMAKE_C_COMPILER=gcc-6 -DCMAKE_CXX_COMPILER=g++-6 ..
 ```bash
 # in thundersvm root directory
 git submodule init eigen && git submodule update
-mkdir build && cd build && cmake -DUSE_CUDA=OFF -DUSE_EIGEN=ON .. && make -j
+mkdir build && cd build && cmake -DUSE_CUDA=OFF .. && make -j
 ```
 If ```make -j``` doesn't work, please simply use ```make```. The number of CPU cores to use can be specified by the ```-o``` option (e.g., ```-o 10```), and refer to [Parameters](docs/parameters.md) for more information.
 

appveyor.yml

@@ -12,7 +12,7 @@ before_build:
 
     cd build
 
-    cmake .. -DCMAKE_WINDOWS_EXPORT_ALL_SYMBOLS=TRUE -DBUILD_SHARED_LIBS=TRUE -DUSE_CUDA=OFF -DUSE_EIGEN=ON -DBUILD_TESTS=ON -G "Visual Studio 14 2015 Win64"
+    cmake .. -DBUILD_SHARED_LIBS=TRUE -DUSE_CUDA=OFF -DBUILD_TESTS=ON -G "Visual Studio 14 2015 Win64"
 build:
   project: build/thundersvm.sln
   parallel: true

cmake/thundersvmConfig.cmake.in

@@ -2,7 +2,7 @@
 
 find_dependency(OpenMP)
 
-if (@USE_EIGEN@)
+if (NOT @USE_CUDA@)
     if (@Eigen3_FOUND@)
         find_dependency(Eigen3)
     endif ()

docs/get-started.md

@@ -45,7 +45,7 @@ mkdir build
 cd build
 cmake \
   -DUSE_CUDA=OFF \
-  -DUSE_EIGEN=ON \
+  \
   -DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" \
   -DOpenMP_C_LIB_NAMES=omp \
   -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" \
@@ -65,11 +65,11 @@ git clone https://github.com/Xtra-Computing/thundersvm.git
 ```bash
 mkdir build
 cd build
-cmake .. -DCMAKE_WINDOWS_EXPORT_ALL_SYMBOLS=TRUE -DBUILD_SHARED_LIBS=TRUE -G "Visual Studio 14 2015 Win64"
+cmake .. -DBUILD_SHARED_LIBS=TRUE -G "Visual Studio 14 2015 Win64"
 ```
 You need to change the Visual Studio version if you are using a different version of Visual Studio. Visual Studio can be downloaded from [this link](https://www.visualstudio.com/vs/). The above commands generate some Visual Studio project files, open the Visual Studio project to build ThunderSVM. Please note that CMake should be 3.4 or above for Windows.
 
-After you execute `cmake .. -DCMAKE_WINDOWS_EXPORT_ALL_SYMBOLS=TRUE -DBUILD_SHARED_LIBS=TRUE -G "Visual Studio 14 2015 Win64"`, you can find a project "thundersvm.sln" under build directory. You can double click it to open it with Visual Studio. Then you should build the solution inside Visual Studio. You can refer to this [this link](https://docs.microsoft.com/en-us/visualstudio/ide/building-and-cleaning-projects-and-solutions-in-visual-studio?view=vs-2019). After you build the project, you should be able to use the python interface.
+After you execute `cmake .. -DBUILD_SHARED_LIBS=TRUE -G "Visual Studio 14 2015 Win64"`, you can find a project "thundersvm.sln" under build directory. You can double click it to open it with Visual Studio. Then you should build the solution inside Visual Studio. You can refer to this [this link](https://docs.microsoft.com/en-us/visualstudio/ide/building-and-cleaning-projects-and-solutions-in-visual-studio?view=vs-2019). After you build the project, you should be able to use the python interface.
 
 #### Working without GPUs<a name="withoutGPU"></a>
 If you don't have GPUs, ThunderSVM can run purely on CPUs. The number of CPU cores to use can be specified by the ```-o``` option (e.g., ```-o 10```), and refer to [Parameters](http://thundersvm.readthedocs.io/en/latest/parameters.html) for more information.
@@ -88,21 +88,21 @@ git submodule init eigen && git submodule update
 * Build without GPUs for Linux
 ```bash
 # in thundersvm root directory
-mkdir build && cd build && cmake -DUSE_CUDA=OFF -DUSE_EIGEN=ON .. && make -j
+mkdir build && cd build && cmake -DUSE_CUDA=OFF .. && make -j
 ```
 If ```make -j``` doesn't work, please simply use ```make```. Now ThunderSVM will work solely on CPUs and does not rely on CUDA.
 
 * Build without GPUs for MacOS
 ```bash
 # in thundersvm root directory
-mkdir build && cd build && cmake -DCMAKE_CXX_COMPILER=[path_to_g++] -DCMAKE_C_COMPILER=[path_to_gcc] -DUSE_CUDA=OFF -DUSE_EIGEN=ON .. && make -j
+mkdir build && cd build && cmake -DCMAKE_CXX_COMPILER=[path_to_g++] -DCMAKE_C_COMPILER=[path_to_gcc] -DUSE_CUDA=OFF .. && make -j
 ```
 
 * Build without GPUs for Windows
 ```bash
 mkdir build
 cd build
-cmake .. -DCMAKE_WINDOWS_EXPORT_ALL_SYMBOLS=TRUE -DBUILD_SHARED_LIBS=TRUE -DUSE_CUDA=OFF -DUSE_EIGEN=ON -G "Visual Studio 14 2015 Win64"
+cmake .. -DBUILD_SHARED_LIBS=TRUE -DUSE_CUDA=OFF -G "Visual Studio 14 2015 Win64"
 ```
 Then, you can open the generated the Visual Studio project file to build ThunderSVM.
 

docs/how-to.md

@@ -89,7 +89,7 @@ git submodule update --init src/test/googletest
 ```bash
 mkdir build
 cd build
-cmake .. -DCMAKE_CXX_COMPILER=[path_to_g++]/usr/local/bin/g++-7 -DCMAKE_C_COMPILER=[path_to_gcc] -DUSE_CUDA=OFF -DUSE_EIGEN=ON -DBUILD_TESTS=ON
+cmake .. -DCMAKE_CXX_COMPILER=[path_to_g++]/usr/local/bin/g++-7 -DCMAKE_C_COMPILER=[path_to_gcc] -DUSE_CUDA=OFF -DBUILD_TESTS=ON
 make -j runtest
 ```
 Where ```[path_to_g++]``` and ```[path_to_gcc]``` typically look like ```/usr/local/bin/g++-7``` and ```/usr/local/bin/gcc-7```, respectively.
@@ -105,7 +105,7 @@ git submodule update --init src/test/googletest
 ```bash
 mkdir build
 cd build
-cmake .. -DCMAKE_WINDOWS_EXPORT_ALL_SYMBOLS=TRUE -DBUILD_SHARED_LIBS=TRUE -DBUILD_TESTS=ON -G "Visual Studio 14 2015 Win64"
+cmake .. -DBUILD_SHARED_LIBS=TRUE -DBUILD_TESTS=ON -G "Visual Studio 14 2015 Win64"
 cmake --build . --target runtest
 ```
 You need to change the Visual Studio version if you are using a different version of Visual Studio. Visual Studio can be downloaded from [this link](https://www.visualstudio.com/vs/). The above commands generate some Visual Studio project files, open the Visual Studio project to build ThunderSVM. Please note that CMake should be 3.4 or above for Windows.

include/thundersvm/config.h.in

@@ -1,4 +1,3 @@
 #cmakedefine DATASET_DIR "@DATASET_DIR@"
 #cmakedefine USE_CUDA
-#cmakedefine USE_EIGEN
 #cmakedefine USE_DOUBLE

scripts/build_cpu_wheel.sh

@@ -7,13 +7,12 @@ cd build
 
 case ${TRAVIS_OS_NAME} in
 linux)
-    cmake -DUSE_CUDA=OFF -DUSE_EIGEN=ON ..
+    cmake -DUSE_CUDA=OFF ..
     ;;
 osx)
     brew install cmake libomp
     cmake \
     -DUSE_CUDA=OFF \
-    -DUSE_EIGEN=ON \
     -DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" \
     -DOpenMP_C_LIB_NAMES=omp \
     -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" \
@@ -23,7 +22,7 @@ osx)
    ;;
 windows)
     export PATH=${MSBUILD_PATH}:$PATH
-    cmake -DCMAKE_WINDOWS_EXPORT_ALL_SYMBOLS=TRUE -DBUILD_SHARED_LIBS=TRUE  -DUSE_CUDA=OFF -DUSE_EIGEN=ON -G "Visual Studio 14 2015 Win64" ..
+    cmake -DBUILD_SHARED_LIBS=TRUE  -DUSE_CUDA=OFF -G "Visual Studio 14 2015 Win64" ..
     choco install python --version=3.6.3
     python -m pip install --upgrade pip
     pip install wheel

scripts/build_cputest.sh

@@ -7,13 +7,13 @@ cd build_cputest
 
 case ${TRAVIS_OS_NAME} in
 linux)
-    cmake -DBUILD_TESTS=ON -DUSE_CUDA=OFF -DUSE_EIGEN=ON ..
+    cmake -DBUILD_TESTS=ON -DUSE_CUDA=OFF ..
     ;;
 osx)
     brew install cmake libomp
     cmake \
     -DUSE_CUDA=OFF \
-    -DUSE_EIGEN=ON \
+    \
     -DOpenMP_C_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" \
     -DOpenMP_C_LIB_NAMES=omp \
     -DOpenMP_CXX_FLAGS="-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include" \
@@ -24,7 +24,7 @@ osx)
    ;;
 windows)
     export PATH=${MSBUILD_PATH}:$PATH
-    cmake -DCMAKE_WINDOWS_EXPORT_ALL_SYMBOLS=TRUE -DBUILD_SHARED_LIBS=TRUE -DUSE_CUDA=OFF -DUSE_EIGEN=ON -DBUILD_TESTS=ON -G "Visual Studio 14 2015 Win64" ..
+    cmake -DBUILD_SHARED_LIBS=TRUE -DUSE_CUDA=OFF -DBUILD_TESTS=ON -G "Visual Studio 14 2015 Win64" ..
     ;;
 esac
 

scripts/build_gpu_wheel.sh

@@ -26,7 +26,7 @@ windows)
     wget -q http://developer.download.nvidia.com/compute/cuda/10.1/Prod/local_installers/cuda_10.1.243_426.00_win10.exe
     ./cuda_10.1.243_426.00_win10.exe -s nvcc_10.1 cusparse_dev_10.1
     export PATH=${MSBUILD_PATH}:$PATH
-    cmake -DCMAKE_WINDOWS_EXPORT_ALL_SYMBOLS=TRUE -DBUILD_SHARED_LIBS=TRUE -DCUDA_TOOLKIT_ROOT_DIR="/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v10.1" -G "Visual Studio 14 2015 Win64" ..
+    cmake -DBUILD_SHARED_LIBS=TRUE -DCUDA_TOOLKIT_ROOT_DIR="/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v10.1" -G "Visual Studio 14 2015 Win64" ..
     choco install python --version=3.6.3
     python -m pip install --upgrade pip
     pip install wheel