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Commit 5d42663

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WeinaJipramodk
WeinaJi
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pramodk
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Add travis CI configuration (#205)
 - test multiple cmake options - test ISPC backend - test NMODL backend Fixes #41
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‎.travis.yml‎

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#=============================================================================
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# Travis CoreNeuron settings
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#=============================================================================
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#=============================================================================
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# Environment
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#=============================================================================
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language: cpp
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#=============================================================================
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# Build matrix
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#=============================================================================
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matrix:
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fast_finish: true
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include:
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- os: linux
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dist: xenial
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env:
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- cmake_option="-DCORENRN_ENABLE_MPI=ON"
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- os: linux
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dist: xenial
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env:
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- cmake_option="-DCORENRN_ENABLE_MPI=OFF"
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- os: linux
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dist: xenial
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env:
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- cmake_option="-DCORENRN_ENABLE_SOA=ON"
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- os: linux
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dist: xenial
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env:
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- cmake_option="-DCORENRN_ENABLE_SOA=OFF"
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- os: linux
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dist: xenial
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env:
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- cmake_option="-DCORENRN_ENABLE_NMODL=ON"
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- PYTHON_VERSION=3.6.7 # for nmodl pip3 install
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- USE_NMODL=ON
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- os: osx
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osx_image: xcode10.2
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env:
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- cmake_option="-DCORENRN_ENABLE_MPI=ON"
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- os: osx
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osx_image: xcode10.2
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env:
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- cmake_option="-DCORENRN_ENABLE_MPI=OFF"
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- os: osx
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osx_image: xcode10.2
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env:
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- cmake_option="-DCORENRN_ENABLE_SOA=ON"
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- os: osx
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osx_image: xcode10.2
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env:
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- cmake_option="-DCORENRN_ENABLE_SOA=OFF"
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- os: osx
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osx_image: xcode10.2
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env:
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- cmake_option="-DCORENRN_ENABLE_NMODL=ON"
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- USE_NMODL=ON
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- os: linux
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dist: xenial
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addons:
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apt:
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sources:
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- ubuntu-toolchain-r-test
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packages:
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- bison
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- flex
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- g++-9
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- libboost-all-dev
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- libopenmpi-dev
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- openmpi-bin
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env:
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- GCC_VERSION=9
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- os: linux
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dist: xenial
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env:
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- USE_ISPC=ON
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- PYTHON_VERSION=3.6.7
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#=============================================================================
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# Common Packages
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#=============================================================================
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addons:
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# for Linux builds, we use APT
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apt:
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sources:
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- ubuntu-toolchain-r-test
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packages:
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- bison
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- flex
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- libboost-all-dev
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- libopenmpi-dev
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- openmpi-bin
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# for Mac builds, we use Homebrew
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homebrew:
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packages:
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- bison
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- flex
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- openmpi
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- boost
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#=============================================================================
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# Set up environments
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#=============================================================================
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before_install:
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# brew installed flex and bison is not in $PATH
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- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
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export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH;
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fi
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# when python 3.6.7 is required, ex. NMODL in linux
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- if [ -n "$PYTHON_VERSION" ]; then
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pyenv global $PYTHON_VERSION;
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fi
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# install NMODL dependencies
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- if [[ "$USE_NMODL" == "ON" || "$USE_ISPC" == "ON" ]]; then
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pip3 install jinja2 pyyaml pytest sympy;
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fi
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- if [ -n "$GCC_VERSION" ]; then
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export CXX="g++-${GCC_VERSION}" CC="gcc-${GCC_VERSION}";
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$CXX --version;
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fi
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# install ISPC compiler (only for mac or linux build for now)
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- if [[ "$USE_ISPC" == "ON" ]]; then
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if [ "$TRAVIS_OS_NAME" == "linux" ]; then
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url_os="linux";
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else
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url_os="macOS";
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fi;
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url="https://sourceforge.net/projects/ispcmirror/files/v1.12.0/ispc-v1.12.0-${url_os}.tar.gz";
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wget -O ispc.tar.gz $url;
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mkdir ispc && tar -xvzf ispc.tar.gz -C ispc --strip 1;
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fi
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#=============================================================================
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# Build, test and install
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#=============================================================================
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script:
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- echo "------- Build, Test and Install -------"
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- mkdir build && cd build
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- if [[ "$USE_ISPC" == "ON" ]]; then
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cmake -DCORENRN_ENABLE_ISPC=ON -DCMAKE_ISPC_COMPILER=../ispc/bin/ispc
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-DCMAKE_INSTALL_PREFIX=$HOME/CoreNeuron ..;
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else
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cmake ${cmake_option} -DCMAKE_INSTALL_PREFIX=$HOME/CoreNeuron ..;
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fi
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- cmake --build .
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- ctest --output-on-failure
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- make install

‎coreneuron/CMakeLists.txt‎

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@@ -56,6 +56,13 @@ else()
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set(NMODL_CODEGEN_TARGET serial)
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endif()
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# configure every mod file to configure with mod2c/nmodl
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foreach(MOD ${INBUILT_MOD_FILES})
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nmodl_to_cpp_target(KEY INBUILT_MOD MODFILE "${INBUILT_MOD_PATH}/${MOD}" TARGET ${NMODL_CODEGEN_TARGET})
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endforeach()
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set_source_files_properties(${NMODL_INBUILT_MOD_OUTPUTS} PROPERTIES GENERATED TRUE)
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# for ispc generated files, we need add extra compilation flags
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if(CORENRN_ENABLE_ISPC)
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set(NMODL_ISPC_INBUILT_MOD_OUTPUTS ${NMODL_INBUILT_MOD_OUTPUTS})
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set_source_files_properties(${NMODL_ISPC_INBUILT_MOD_OUTPUTS}
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PROPERTIES
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COMPILE_FLAGS
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"-I${nmodl_INCLUDE}")
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"-I${CORENRN_NMODL_INCLUDE} --pic")
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endif()
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# configure every mod file to configure with mod2c/nmodl
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foreach(MOD ${INBUILT_MOD_FILES})
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nmodl_to_cpp_target(KEY INBUILT_MOD MODFILE "${INBUILT_MOD_PATH}/${MOD}" TARGET ${NMODL_CODEGEN_TARGET})
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endforeach()
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set_source_files_properties(${NMODL_INBUILT_MOD_OUTPUTS} PROPERTIES GENERATED TRUE)
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# =============================================================================
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# coreneuron GPU library
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# =============================================================================

‎coreneuron/nrnoc/nrnoc_ml.ispc‎

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};
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struct NrnFastImem {
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double* uniform nrn_sav_rhs;
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double* uniform nrn_sav_d;
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};
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struct NrnThread {
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uniform double _t;
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uniform double _dt;
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double* uniform _actual_diam;
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double* uniform _shadow_rhs;
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double* uniform _shadow_d;
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NrnFastImem* uniform nrn_fast_imem;
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int* uniform _v_parent_index;
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int* uniform _permute;
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int8* uniform _sp13mat;

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