Add Github Actions cron jobs for system and valgrind tests

.github/workflows/centos-ci.yml

@@ -82,7 +82,8 @@ jobs:
         . bin/thisbdm.sh
         export DISPLAY=:99.0
         ../util/xvfb-initd.sh start
-        bin/biodynamo-unit-tests
+        sleep 3
+        ninja run-unit-tests
         ../util/xvfb-initd.sh stop
 
     - name: Notify Slack

.github/workflows/centos-system-ci.yml

@@ -0,0 +1,121 @@
+# Runs the installation tests and valgrind tests in the following cases:
+#   1) every day at 3 am
+#   2) a pull request to the master branch
+
+name: CentOS System CI
+
+on:
+  schedule:
+    # Every day at 3 am
+    - cron: '0 3 * * *'
+  pull_request:
+    # Upon pull requests
+    branches:
+      - master
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container:
+      image: centos:7
+
+    steps:
+    - name: Install dependencies
+      run: |
+        yum -y update
+        yum -y install centos-release-scl epel-release
+        yum -y install man wget environment-modules libXt-devel libXext-devel ninja-build make \
+          devtoolset-7-gcc* numactl-devel openmpi3-devel freeglut-devel redhat-lsb-core \
+          scl-utils which xorg-x11-server-Xvfb fontconfig mesa-dri-drivers valgrind
+        yum -y install @development zlib-devel bzip2 bzip2-devel readline-devel sqlite \
+          sqlite-devel openssl-devel xz xz-devel libffi-devel findutils
+        yum -y remove git*
+        yum -y install https://packages.endpoint.com/rhel/7/os/x86_64/endpoint-repo-1.7-1.x86_64.rpm
+        yum -y install git
+        curl -L -O https://github.com/Kitware/CMake/releases/download/v3.17.3/cmake-3.17.3-Linux-x86_64.sh
+        chmod +x cmake-3.17.3-Linux-x86_64.sh
+        ./cmake-3.17.3-Linux-x86_64.sh --skip-license --prefix=/usr/local
+
+    - name: Set OSVERS
+      run: echo "::set-env name=OSVERS::$(lsb_release -si)-$(lsb_release -sr)"
+
+    - name: Cache pyenv
+      uses: actions/cache@v2
+      id: pyenv-cache
+      with:
+        path: ~/.pyenv
+        key: ${{ env.OSVERS }}-pyenv-3.6.9
+
+    - name: Install pyenv dependency
+      if: steps.pyenv-cache.outputs.cache-hit != 'true'
+      run: |
+        curl https://pyenv.run | bash
+        export PATH="$HOME/.pyenv/bin:$PATH"
+        eval "$(pyenv init -)"
+        PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.6.9
+        pyenv shell 3.6.9
+
+    - name: Checkout BioDynaMo
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Cache Third Party Packages
+      uses: actions/cache@v2
+      with:
+        path: build/third_party
+        key: ${{ env.OSVERS }}-third-party-${{ hashFiles('cmake/external/SHA256Digests.cmake') }}
+
+    - name: Build BioDynaMo
+      shell: bash
+      run: |
+        . scl_source enable devtoolset-7 || true
+        . /etc/profile.d/modules.sh || true
+        module load mpi
+        cmake -G Ninja \
+          -Dparaview=ON \
+          -Dnuma=OFF \
+          -DCMAKE_BUILD_TYPE=Release \
+          -B build
+        cmake --build build --parallel --config Release
+
+    - name: Valgrind tests BioDynaMo
+      shell: bash
+      working-directory: build
+      run: |
+        . scl_source enable devtoolset-7 || true
+        . /etc/profile.d/modules.sh || true
+        module load mpi
+        . bin/thisbdm.sh
+        export DISPLAY=:99.0
+        ../util/xvfb-initd.sh start
+        sleep 3
+        ninja run-valgrind
+        ../util/xvfb-initd.sh stop
+
+    - name: System tests BioDynaMo
+      shell: bash
+      working-directory: build
+      run: |
+        . scl_source enable devtoolset-7 || true
+        . /etc/profile.d/modules.sh || true
+        module load mpi
+        . bin/thisbdm.sh
+        git config --system user.name "Test User"	
+        git config --system user.email user@test.com
+        export DISPLAY=:99.0
+        ../util/xvfb-initd.sh start
+        sleep 3
+        ninja run-demos
+        ../util/xvfb-initd.sh stop
+
+    - name: Notify Slack
+      uses: 8398a7/action-slack@v3
+      with:
+        status: ${{ job.status }}
+        author_name: Integration Test
+        fields: repo,ref,message,author,action,workflow # default: repo,commit
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # optional
+        SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} # required
+      if: always() # Pick up events even if the job fails or is canceled.

.github/workflows/macos-ci.yml

@@ -61,7 +61,7 @@ jobs:
       working-directory: build
       run: |
         . bin/thisbdm.sh
-        bin/biodynamo-unit-tests
+        ninja run-unit-tests
 
     - name: Notify Slack
       uses: 8398a7/action-slack@v3

.github/workflows/macos-system-ci.yml

@@ -0,0 +1,87 @@
+# Runs the installation tests in the following cases:
+#   1) every day at 3 am
+#   2) a pull request to the master branch
+
+name: macOS System CI
+
+on:
+  schedule:
+    # Every day at 3 am
+    - cron: '0 3 * * *'
+  pull_request:
+    # Upon pull requests
+    branches:
+      - master
+
+jobs:
+  build:
+    runs-on: macos-latest
+
+    steps:
+    - name: Install dependencies
+      run: |
+        brew install libomp open-mpi git pyenv llvm wget cmake ninja
+
+    - name: Cache pyenv
+      uses: actions/cache@v2
+      id: pyenv-cache
+      with:
+        path: ~/.pyenv
+        key: ${{ runner.os }}-pyenv-3.6.9
+
+    - name: Install pyenv dependency
+      if: steps.pyenv-cache.outputs.cache-hit != 'true'
+      run: |
+        eval "$(pyenv init -)"
+        PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.6.9
+        pyenv shell 3.6.9
+
+    - name: Checkout BioDynaMo
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Cache Third Party Packages
+      uses: actions/cache@v2
+      with:
+        path: build/third_party
+        key: ${{ runner.os }}-third-party-${{ hashFiles('cmake/external/SHA256Digests.cmake') }}
+
+    - name: Build BioDynaMo
+      shell: bash
+      run: |
+        cmake -G Ninja \
+          -Dopencl=OFF \
+          -Dparaview=OFF \
+          -DCMAKE_BUILD_TYPE=Release \
+          -DCMAKE_CXX_COMPILER=/usr/local/opt/llvm/bin/clang++ \
+          -DCMAKE_CXX_FLAGS="-isysroot `xcrun --show-sdk-path`" \
+          -DCMAKE_C_COMPILER=/usr/local/opt/llvm/bin/clang \
+          -DCMAKE_EXPORT_COMPILE_COMMANDS=TRUE \
+          -DCMAKE_EXE_LINKER_FLAGS_INIT=-L/usr/local/opt/llvm/lib \
+          -DCMAKE_SHARED_LINKER_FLAGS_INIT=-L/usr/local/opt/llvm/lib \
+          -B build
+        cmake --build build --parallel --config Release
+
+    - name: System tests BioDynaMo
+      shell: bash
+      working-directory: build
+      run: |
+        . bin/thisbdm.sh
+        git config --system user.name "Test User"	
+        git config --system user.email user@test.com
+        export DISPLAY=:99.0
+        ../util/xvfb-initd.sh start
+        ninja run-demos
+        ../util/xvfb-initd.sh stop
+
+    - name: Notify Slack
+      uses: 8398a7/action-slack@v3
+      with:
+        status: ${{ job.status }}
+        author_name: Integration Test
+        fields: repo,ref,message,author,action,workflow # default: repo,commit
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # optional
+        SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} # required
+      if: always() # Pick up events even if the job fails or is canceled.

.github/workflows/ubuntu-ci.yml

@@ -18,8 +18,7 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get install -y libopenmpi-dev libomp5 libomp-dev libnuma-dev freeglut3-dev \
-          libreadline-dev libsqlite3-dev tk-dev python-openssl ninja-build \
-          valgrind
+          libreadline-dev libsqlite3-dev tk-dev python-openssl ninja-build
         curl -L -O https://github.com/Kitware/CMake/releases/download/v3.17.3/cmake-3.17.3-Linux-x86_64.sh
         chmod +x cmake-3.17.3-Linux-x86_64.sh
         sudo ./cmake-3.17.3-Linux-x86_64.sh --skip-license --prefix=/usr/local
@@ -70,7 +69,8 @@ jobs:
         . bin/thisbdm.sh
         export DISPLAY=:99.0
         ../util/xvfb-initd.sh start
-        bin/biodynamo-unit-tests
+        sleep 3
+        ninja run-unit-tests
         ../util/xvfb-initd.sh stop
 
     - name: Notify Slack

.github/workflows/ubuntu-system-ci.yml

@@ -0,0 +1,106 @@
+# Runs the installation tests and valgrind tests in the following cases:
+#   1) every day at 3 am
+#   2) a pull request to the master branch
+
+name: Ubuntu System CI
+
+on:
+  schedule:
+    # Every day at 3 am
+    - cron: '0 3 * * *'
+  pull_request:
+    # Upon pull requests
+    branches:
+      - master
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-18.04, ubuntu-20.04]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libopenmpi-dev libomp5 libomp-dev libnuma-dev freeglut3-dev \
+          libreadline-dev libsqlite3-dev tk-dev python-openssl ninja-build \
+          valgrind
+        curl -L -O https://github.com/Kitware/CMake/releases/download/v3.17.3/cmake-3.17.3-Linux-x86_64.sh
+        chmod +x cmake-3.17.3-Linux-x86_64.sh
+        sudo ./cmake-3.17.3-Linux-x86_64.sh --skip-license --prefix=/usr/local
+
+    - name: Set OSVERS
+      run: echo "::set-env name=OSVERS::$(lsb_release -si)-$(lsb_release -sr)"
+
+    - name: Cache pyenv
+      uses: actions/cache@v2
+      id: pyenv-cache
+      with:
+        path: ~/.pyenv
+        key: ${{ env.OSVERS }}-pyenv-3.6.9
+
+    - name: Install pyenv dependency
+      if: steps.pyenv-cache.outputs.cache-hit != 'true'
+      run: |
+        curl https://pyenv.run | bash
+        export PATH="$HOME/.pyenv/bin:$PATH"
+        eval "$(pyenv init -)"
+        PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.6.9
+        pyenv shell 3.6.9
+
+    - name: Checkout BioDynaMo
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+    - name: Cache Third Party Packages
+      uses: actions/cache@v2
+      with:
+        path: build/third_party
+        key: ${{ env.OSVERS }}-third-party-${{ hashFiles('cmake/external/SHA256Digests.cmake') }}
+
+    - name: Build BioDynaMo
+      shell: bash
+      run: |
+        cmake -G Ninja \
+          -Dparaview=ON \
+          -DCMAKE_BUILD_TYPE=Release \
+          -B build
+        cmake --build build --parallel --config Release
+
+    - name: Valgrind tests BioDynaMo
+      shell: bash
+      working-directory: build
+      run: |
+        . bin/thisbdm.sh
+        export DISPLAY=:99.0
+        ../util/xvfb-initd.sh start
+        sleep 3
+        ninja run-valgrind
+        ../util/xvfb-initd.sh stop
+
+    - name: System tests BioDynaMo
+      shell: bash
+      working-directory: build
+      run: |
+        . bin/thisbdm.sh
+        sudo git config --system user.name "Test User"	
+        sudo git config --system user.email user@test.com
+        export DISPLAY=:99.0
+        ../util/xvfb-initd.sh start
+        sleep 3
+        ninja run-demos
+        ../util/xvfb-initd.sh stop
+
+    - name: Notify Slack
+      uses: 8398a7/action-slack@v3
+      with:
+        status: ${{ job.status }}
+        author_name: Integration Test
+        fields: repo,ref,message,author,action,workflow # default: repo,commit
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # optional
+        SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }} # required
+      if: always() # Pick up events even if the job fails or is canceled.

CMakeLists.txt

@@ -113,6 +113,7 @@ option(tcmalloc  "Use tcmalloc for memory allocations." OFF)
 option(jemalloc  "Use jemalloc for memory allocations." OFF)
 option(website   "Enable website generation (make website<-live>)." OFF)
 option(valgrind  "Enable valgrind tests and make build compatible with valgrind tool." ON)
+option(rpath     "Link libraries with built-in RPATH (run-time search path)." OFF)
 
 if(APPLE)
   find_program(BREW_BIN brew)
@@ -394,16 +395,22 @@ endif()
 include(SetCompilerFlags)
 
 # -------------------- set rpath options ---------------------------------------
-# When building, use the RPATH
-set(CMAKE_INSTALL_RPATH "")
-set(CMAKE_BUILD_RPATH "")
-set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
-set(CMAKE_SKIP_BUILD_RPATH TRUE) # skip the full RPATH for the build tree
-set(CMAKE_INSTALL_RPATH_USE_LINK_PATH FALSE)
-set(CMAKE_MACOSX_RPATH TRUE) # use @rpath keyword for the MacOS rpath
-# Sets @rpath for libbiodynamo.dylib on Mac OS in the build directory
-if (APPLE)
-  SET(CMAKE_BUILD_WITH_INSTALL_RPATH ON)
+#  When building, don't use the install RPATH already (but later on when installing)
+set(CMAKE_SKIP_BUILD_RPATH FALSE)         # don't skip the full RPATH for the build tree
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) # use always the build RPATH for the build tree
+set(CMAKE_MACOSX_RPATH TRUE)              # use RPATH for MacOSX
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) # point to directories outside the build tree to the install RPATH
+
+# Check whether to add RPATH to the installation (the build tree always has the RPATH enabled)
+if(rpath)
+  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR}) # install LIBDIR
+  set(CMAKE_SKIP_INSTALL_RPATH FALSE)          # don't skip the full RPATH for the install tree
+elseif(APPLE)
+  set(CMAKE_INSTALL_NAME_DIR "@rpath")
+  set(CMAKE_INSTALL_RPATH "@loader_path/../lib")    # self relative LIBDIR
+  set(CMAKE_SKIP_INSTALL_RPATH FALSE)          # don't skip the full RPATH for the install tree
+else()
+  set(CMAKE_SKIP_INSTALL_RPATH TRUE)           # skip the full RPATH for the install tree
 endif()
 
 # -------------------- extract third party libraries ---------------------------