Almalinux

.github/workflows/almalinux-ci.yml

@@ -0,0 +1,102 @@
+name: AlmaLinux CI
+
+on:
+  push:
+  pull_request:
+    branches:
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container:
+      image: almalinux:9.5
+
+    steps:
+    - name: Install dependencies
+      run: |
+        dnf -y update
+        dnf -y --enablerepo=crb install epel-release
+        dnf -y --enablerepo=crb install \
+          lsb_release cmake git gcc g++ wget man make ninja-build \
+          bzip2-devel freeglut-devel libXext-devel libXt-devel libXpm-devel \
+          libXft-devel numactl-devel openmpi-devel zlib-devel lapack-devel \
+          blas-devel readline-devel sqlite-devel openssl-devel xz-devel \
+          libffi-devel findutils patch which perl-Digest-SHA \
+          xorg-x11-server-Xvfb fontconfig mesa-dri-drivers
+
+    - name: Start Xvfb
+      run: |
+        set -e
+        XVFBARGS=":99 -ac -screen 0 2560x1440x24"
+        /usr/bin/Xvfb $XVFBARGS >> /tmp/Xvfb.out 2>&1 &
+        disown -ar
+        sleep 3
+
+    - name: Set OSVERS
+      run: |
+        ID=$(grep -oP '(?<=^ID=).+' /etc/os-release | tr -d '"')
+        VERSION=$(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '"')
+        echo "OSVERS=$ID-$VERSION" >> $GITHUB_ENV
+
+    - name: Cache pyenv
+      uses: actions/cache@v4
+      id: pyenv-cache
+      with:
+        path: ~/.pyenv
+        key: ${{ env.OSVERS }}-pyenv-3.9.1
+
+    - name: Install pyenv dependency
+      if: steps.pyenv-cache.outputs.cache-hit != 'true'
+      run: |
+        if [ ! -f "$HOME/.pyenv/bin/pyenv" ]; then
+          curl https://pyenv.run | bash
+        fi
+        export PATH="$HOME/.pyenv/bin:$PATH"
+        eval "$(pyenv init --path)"
+        eval "$(pyenv init -)"
+        PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.1
+        pyenv shell 3.9.1
+
+    - name: Checkout BioDynaMo
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Cache Third Party Packages
+      uses: actions/cache@v4
+      with:
+        path: build/third_party
+        key: ${{ env.OSVERS }}-third-party-${{ hashFiles('cmake/external/SHA256Digests.cmake') }}
+
+    - name: Build BioDynaMo
+      shell: bash
+      run: |
+        export PATH="$HOME/.pyenv/bin:$PATH"
+        eval "$(pyenv init --path)"
+        eval "$(pyenv init -)"
+        pyenv shell 3.9.1
+        . /etc/profile.d/modules.sh || true
+        module load mpi
+        cmake -G Ninja \
+          -Dparaview=OFF \
+          -Dbenchmark=ON \
+          -Dlibgit2=ON \
+          -Dnuma=OFF \
+          -DCMAKE_BUILD_TYPE=Release \
+          -B build
+        cmake --build build --parallel --config Release
+
+    - name: Unit tests BioDynaMo
+      shell: bash
+      working-directory: build
+      run: |
+        . bin/thisbdm.sh
+        bdm config
+        export DISPLAY=:99.0
+        sleep 3
+        ninja run-unit-tests

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

@@ -0,0 +1,161 @@
+# 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: AlmaLinux System CI
+
+on:
+  schedule:
+    # Every day at 3 am
+    - cron: '0 3 * * *'
+  pull_request:
+    # Upon pull requests
+    branches:
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    container:
+      image: almalinux:9.5
+
+    steps:
+    - name: Set GHA_BRANCH_NAME
+      run: |
+        if [ "${{ github.event_name }}" = "pull_request" ]; then
+          echo "GHA_BRANCH_NAME=${{ github.head_ref }}" >> $GITHUB_ENV
+        fi
+        if [ "${{ github.event_name }}" = "schedule" ]; then
+          echo "GHA_BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
+        fi
+
+    - name: Set OSVERS
+      run: |
+        ID=$(grep -oP '(?<=^ID=).+' /etc/os-release | tr -d '"')
+        VERSION=$(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '"')
+        echo "OSVERS=$ID-$VERSION" >> $GITHUB_ENV
+
+      # Do this prior to checkout BioDynaMo, because the AlmaLinux docker
+      # container does not come with git preinstalled. This would mess
+      # up later calls to
+      # `git describe --tags`
+    - name: Install latest version of git
+      shell: bash
+      run: |
+        dnf -y --enablerepo=crb install git
+
+    - name: Start Xvfb
+      run: |
+        set -e
+        dnf -y install xorg-x11-server-Xvfb
+        XVFBARGS=":99 -ac -screen 0 2560x1440x24"
+        /usr/bin/Xvfb $XVFBARGS >> /tmp/Xvfb.out 2>&1 &
+        disown -ar
+        sleep 3
+
+    - name: Install BioDynaMo
+      shell: bash
+      run: |
+        dnf update -y
+        dnf install -y --allowerasing sudo curl
+        curl https://raw.githubusercontent.com/BioDynaMo/biodynamo/${GHA_BRANCH_NAME}/util/install | bash
+        # remove whole BioDynaMo repository to catch errors related to paths pointing into the build dir
+        mktemp -d
+        find /tmp -iname biodynamo -type d || true
+        rm -rf $(find $(mktemp -d)/../* -maxdepth 1 -iname biodynamo -type d 2>/dev/null)
+        echo "Removed"
+        find /tmp -iname biodynamo -type d || true
+
+    - name: Checkout BioDynaMo
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Set INSTALL_DIR
+      run: |
+        if [ "${{ github.event_name }}" = "pull_request" ]; then
+          echo "INSTALL_DIR=${GITHUB_WORKSPACE}/build" >> $GITHUB_ENV
+        fi
+        if [ "${{ github.event_name }}" = "schedule" ]; then
+          echo "INSTALL_DIR=$(echo ${HOME}/biodynamo-*)" >> $GITHUB_ENV
+        fi
+
+    - name: Cache pyenv
+      uses: actions/cache@v4
+      id: pyenv-cache
+      with:
+        path: ~/.pyenv
+        key: ${{ env.OSVERS }}-pyenv-3.9.1
+
+    - name: Install pyenv dependency
+      if: steps.pyenv-cache.outputs.cache-hit != 'true'
+      run: |
+        if [ ! -f "$HOME/.pyenv/bin/pyenv" ]; then
+          curl https://pyenv.run | bash
+        fi
+        export PATH="$HOME/.pyenv/bin:$PATH"
+        eval "$(pyenv init --path)"
+        eval "$(pyenv init -)"
+        if [ ! -f  "$HOME/.pyenv/versions/3.9.1/lib/libpython3.so" ]; then
+          PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.1
+        fi
+        pyenv shell 3.9.1
+
+    - name: Cache Third Party Packages
+      uses: actions/cache@v4
+      with:
+        path: build/third_party
+        key: ${{ env.OSVERS }}-third-party-${{ hashFiles('cmake/external/SHA256Digests.cmake') }}
+
+    - name: Build BioDynaMo
+      shell: bash
+      run: |
+        export PATH="$HOME/.pyenv/bin:$PATH"
+        eval "$(pyenv init --path)"
+        eval "$(pyenv init -)"
+        pyenv shell 3.9.1
+        . /etc/profile.d/modules.sh || true
+        module load mpi
+        cmake \
+          -Dparaview=OFF \
+          -Dbenchmark=ON \
+          -Dsbml=OFF \
+          -Dnuma=OFF \
+          -Dlibgit2=OFF \
+          -DCMAKE_BUILD_TYPE=Release \
+          -B build
+        cmake --build build --config Release
+
+    # # Don't do this in the `Build BioDynaMo step`, because notebooks might time out in GHA
+    # # runners, while waiting for other targets to be compiled
+    # - name: Run notebooks
+    #   shell: bash
+    #   run: |
+    #     export PATH="$HOME/.pyenv/bin:$PATH"
+    #     eval "$(pyenv init --path)"
+    #     eval "$(pyenv init -)"
+    #     pyenv shell 3.9.1
+    #     . /etc/profile.d/modules.sh || true
+    #     module load mpi
+    #     cmake \
+    #       -Dnotebooks=ON \
+    #       -B build
+    #     cmake --build build --config Release --target notebooks -- -j1
+
+    - name: Run system tests
+      shell: bash
+      working-directory: build
+      run: |
+        dnf install -y xorg-x11-server-Xvfb fontconfig mesa-dri-drivers
+        . $INSTALL_DIR/bin/thisbdm.sh
+        git config --system user.name "Test User"
+        git config --system user.email user@test.com
+        export DISPLAY=:99.0
+        biodynamo new test-sim
+        . ../test/util.inc
+        run_cmake_simulation test-sim
+        make run-demos

cmake/external/ROOT.cmake

@@ -58,12 +58,25 @@ if(APPLE)
   elseif("${DETECTED_OS_VERS}" MATCHES "^osx-11")
     message(FATAL_ERROR "We officially only support the latest macOS 11 versions 11.6, 11.7.")
   endif()
-#else()
-  #if("${DETECTED_OS_VERS}" MATCHES "^ubuntu-23" AND
-     #"${DETECTED_ARCH}" STREQUAL "aarch64")
-    #set(ROOT_SHA_KEY ubuntu-23.04-${DETECTED_ARCH}-ROOT)
-    #set(ROOT_TAR_FILE root_v6.30.02_cxx17_python3.9_ubuntu-23.04-${DETECTED_ARCH}.tar.gz)
-#  endif()
+else()
+  if("${DETECTED_OS_VERS}" MATCHES "^ubuntu-24")
+    if("${DETECTED_ARCH}" STREQUAL "aarch64")
+      set(ROOT_SHA_KEY ubuntu-24.04-${DETECTED_ARCH}-ROOT)
+      set(ROOT_TAR_FILE root_v6.32.08_cxx17_python3.12_ubuntu-24.04-${DETECTED_ARCH}.tar.gz)
+    else()
+      set(ROOT_SHA_KEY ubuntu-24.04-ROOT)
+      set(ROOT_TAR_FILE root_v6.32.08_cxx17_python3.12_ubuntu-24.04.tar.gz)
+    endif()
+  endif()
+  if("${DETECTED_OS_VERS}" MATCHES "^almalinux-9")
+    if("${DETECTED_ARCH}" STREQUAL "aarch64")
+      set(ROOT_SHA_KEY almalinux-9-${DETECTED_ARCH}-ROOT)
+      set(ROOT_TAR_FILE root_v6.32.08_cxx17_python3.9_almalinux-9-${DETECTED_ARCH}.tar.gz)
+    else()
+      set(ROOT_SHA_KEY almalinux-9-ROOT)
+      set(ROOT_TAR_FILE root_v6.32.08_cxx17_python3.9_almalinux-9.tar.gz)
+    endif()
+  endif()
 endif()
 set(ROOT_SHA ${${ROOT_SHA_KEY}})
 

cmake/external/SHA256Digests.cmake

@@ -108,11 +108,13 @@ SET(ubuntu-22.04-ParaView afc803835973fdb8b963fe10eaf1103f2e1650e4573141964c1322
 SET(ubuntu-22.04-Qt b2388d1bcca4e3741ab5b2b0fb95395aeb6c448951a0d3cdeb6db33b64a7d41c)
 SET(ubuntu-22.04-ROOT 24921a85b53c5cfbe9f192e523263781d595c59c9c553818349992e61efc64ac)
 
-SET(ubuntu-23.04-aarch64-ROOT 7d2fcaaeb1e452c38c1d8436288e3171d1b6935f5b6f25d5df16b21e00ca45d8)
-SET(ubuntu-23.10-aarch64-ROOT 8f6fa9db579e011ef4ae7e96830d8ab1284b6df95a1b2f46e6a1cea56fd4626f)
+SET(ubuntu-24.04-ROOT xxx)
+SET(ubuntu-24.04-aarch64-ROOT xxx)
 
 SET(centos-7-Libroadrunner a0b49487a28aedc4b909a71c66263d4a388964008e2b23073dd744231251470c)
 SET(centos-7-ParaView 45d545e75baf32c9fe30944781b4f6b172d4efd7d6cd794dcd19ec671cc5ead0)
 SET(centos-7-Qt 4308621ff9ec84585c3aead92a9d2de787b3c700323333b6e78ed45d04a0d2a4)
 SET(centos-7-ROOT 54298aa5f13dc2942925c10d755768f81f53d7135ac1a3e698e9b7ef1a3dfd1e)
 
+SET(almalinux-9-ROOT xxx)
+SET(almalinux-9-aarch64-ROOT xxx)

cmake/utils.cmake

@@ -13,10 +13,11 @@
 # -----------------------------------------------------------------------------
 
 # Detect the system flavour and version. Generate variables
-# called DETECTED_OS (ubuntu-18.04, ubuntu-20.04, centos-7, osx)
-# and DETECTED_OS_VERS (ubuntu-18.04, ubuntu-20.04, centos-7 or osx-11.2-i386).
+# called DETECTED_OS (ubuntu-18.04, ubuntu-20.04, almalinux-9, osx)
+# and DETECTED_OS_VERS (ubuntu-18.04, ubuntu-20.04, almalinux-9 or
+# osx-11.2-i386).
 # In case the Linux arch is aarch64, the DETECTED_OS_VERS ends in -aarch64,
-# like ubuntu-23.10-aarch64. For backward compatibility reasons we don't
+# like ubuntu-24.04-aarch64. For backward compatibility reasons we don't
 # add -x86_64.
 function(detect_os)
     if(APPLE)
@@ -32,12 +33,20 @@ function(detect_os)
     else()
         set(GET_OS_ID "echo $(grep -oP '(?<=^ID=).+' /etc/os-release | tr -d '\"')")
         set(GET_OS_VERSION "echo $(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '\"')")
+        set(GET_ALMA_OS_VERSION "echo $(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '\"' | cut -d . -f 1)")
         execute_process(COMMAND bash -c "${GET_OS_ID}"
                         OUTPUT_VARIABLE DISTRO_NAME
                         OUTPUT_STRIP_TRAILING_WHITESPACE)
-        execute_process(COMMAND bash -c "${GET_OS_VERSION}"
-                        OUTPUT_VARIABLE DISTRO_VERSION
-                        OUTPUT_STRIP_TRAILING_WHITESPACE)
+        if("${DISTRO_NAME}" STREQUAL "almalinux")
+          # strip of minor version number 9.5 -> 9
+          execute_process(COMMAND bash -c "${GET_ALMA_OS_VERSION}"
+                          OUTPUT_VARIABLE DISTRO_VERSION
+                          OUTPUT_STRIP_TRAILING_WHITESPACE)
+        else()
+          execute_process(COMMAND bash -c "${GET_OS_VERSION}"
+                          OUTPUT_VARIABLE DISTRO_VERSION
+                          OUTPUT_STRIP_TRAILING_WHITESPACE)
+        endif()
         execute_process(COMMAND arch
                         OUTPUT_VARIABLE DISTRO_ARCH OUTPUT_STRIP_TRAILING_WHITESPACE)
         set(BDM_OS "${DISTRO_NAME}-${DISTRO_VERSION}")