Improve Singularity image (#330)

Fixes shortcomings in singularity image (pyenv and paraview related). See PR for details.

Co-authored-by: Umar <[email protected]>
Co-authored-by: Ahmad Hesam <[email protected]>

.github/workflows/singularity-integration.yml

@@ -16,6 +16,23 @@ jobs:
       options: "--privileged --workdir /data"
     steps:
       - uses: actions/checkout@v3
+
+      - name: Add root user to subuid and subgid...
+        run: |
+          echo root:100000:65536 >> /etc/subuid
+          echo root:100000:65536 >> /etc/subgid
+
+      - name: Set correct branch...
+        run: |
+          export GITHUB_BRANCH_NAME=${{ github.head_ref || github.ref_name }}
+          sed -i "s|BDM_BRANCH=\"master\"|BDM_BRANCH=\"$GITHUB_BRANCH_NAME\"|" Singularity
+
       - name: Build singularity image...
         run: |
-          singularity build Singularity.sif Singularity
+          chmod 777 .
+          singularity build --fakeroot Singularity.sif Singularity
+          
+      - name: Source Biodynamo and run demo...
+        run: |
+          singularity exec --cleanenv -i Singularity.sif bash -c "source /biodynamo/build/third_party/root/bin/thisroot.sh && source /biodynamo/build/bin/thisbdm.sh && \
+            export DISPLAY=:99.0 && /biodynamo/util/xvfb-initd.sh start && cd $(mktemp -d) && bdm demo tumor_concept && cd tumor_concept && bdm clean && bdm run"

Singularity

@@ -1,71 +1,30 @@
 Bootstrap:docker
-From:ubuntu:18.04
+From:ubuntu:20.04
 
 %environment
 
 %post -c /bin/bash
 
   export DEBIAN_FRONTEND=noninteractive 
   export TZ=Europe/Berlin
+  unset Qt5_DIR
+  unset ParaView_DIR
+  unset ROOT_INCLUDE_PATH
+  unset CMAKE_PREFIX_PATH
+  unset PYENV_ROOT
+  unset BDMSYS
+  unset CC
+  unset CXX
 
-  apt-get -y update &&
-  apt-get -y install python &&
-  apt-get -y install python3 &&
-  apt-get -y install git &&
-  apt-get -y install curl &&
-  apt-get -y install make &&
-  apt-get -y install gcc &&
-  apt-get -y install g++ &&
-  apt-get -y install wget &&
-  apt-get -y install wamerican && 
-  apt-get -y install libffi-dev &&
-  apt-get -y install libncurses5-dev &&
-  apt-get -y install zlib1g &&
-  apt-get -y install zlib1g-dev &&
-  apt-get -y install bzip2 &&
-  apt-get -y install zlib1g-dev && 
-  apt-get -y install aptitude &&
-  aptitude -y install libreadline-dev &&
-  apt-get -y install libssl-dev &&
-  apt-get -y install libsqlite3-dev &&
-  apt-get -y install apt-utils &&
-  apt-get -y install openmpi-bin &&
-  apt-get -y install libopenmpi-dev &&
-  apt-get -y install libxkbcommon-x11-dev &&
-  apt-get -y install bsdmainutils &&
-  apt-get -y install clang &&
-  apt-get -y install clang-format &&
-  apt-get -y install clang-tidy &&
-  apt-get -y install doxygen &&
-  apt-get -y install graphviz &&
-  apt-get -y install libxml2-dev &&
-  apt-get -y install llvm-7 &&
-  apt-get -y install llvm-7-dev &&
-  apt-get -y install llvm-7-runtime &&
-  apt-get -y install valgrind &&
-  apt-get -y install libgsl-dev &&
-  apt-get -y install freeglut3-dev &&
-  apt-get -y install libbz2-dev &&
-  apt-get -y install libnuma-dev &&
-  apt-get -y install libomp5 &&
-  apt-get -y install libomp-dev &&
-  apt-get -y install libopenmpi-dev &&
-  apt-get -y install libpthread-stubs0-dev &&
-  apt-get -y install zlib1g-dev &&
-  apt-get -y install libbz2-dev &&
-  apt-get -y install libffi-dev &&
-  apt-get -y install liblzma-dev &&
-  apt-get -y install libreadline-dev &&
-  apt-get -y install libsqlite3-dev &&
-  apt-get -y install libssl-dev &&
-  apt-get -y install python-openssl &&
-  apt-get -y install tk-dev &&
-  apt-get -y install xz-utils &&
-  apt-get -y install zlib1g-dev &&
-  apt-get -y install sudo &&
-  apt-get -y install software-properties-common
 
-  apt-get -y install locales locales-all
+  apt-get -y update
+  apt-get -y install apt-utils
+  apt-get -y install software-properties-common
+  apt-get -y install python python3 git curl make gcc g++ wget wamerican wget wamerican libffi-dev libncurses5-dev zlib1g zlib1g-dev bzip2 aptitude libreadline-dev libssl-dev libsqlite3-dev \
+    openmpi-bin libopenmpi-dev libxkbcommon-x11-dev bsdmainutils clang clang-format clang-tidy doxygen graphviz libxml2-dev llvm-7 llvm-7-dev llvm-7-runtime valgrind libgsl-dev freeglut3-dev \
+    libbz2-dev libnuma-dev libomp5 libomp-dev libopenmpi-dev libpthread-stubs0-dev zlib1g-dev libbz2-dev libffi-dev liblzma-dev libreadline-dev libsqlite3-dev libssl-dev python-openssl tk-dev \
+    xz-utils zlib1g-dev sudo libblas-dev liblapack-dev nano locales locales-all ninja-build python3-pip freeglut3-dev valgrind xvfb
+
   dpkg-reconfigure locales
   locale-gen
 
@@ -76,46 +35,41 @@ From:ubuntu:18.04
   export PATH="/miniconda3/bin:$PATH"
   conda install -y -c conda-forge pip numpy 
   conda update -y --all
-  apt -y install git
-  apt -y install curl
-  sudo  rm -rf ~/.pyenv
-  curl https://pyenv.run | bash
-  export PATH="$HOME/.pyenv/bin:$PATH"
-  eval "$(pyenv init --path)"
-  eval "$(pyenv virtualenv-init -)"
-  eval "$(pyenv init -)"
 
-  export PYENV_ROOT="/opt/pyenv"
-  export PATH="/opt/pyenv/bin:$PATH" 
+  export PYENV_ROOT="/opt/.pyenv"
+  export PATH="$PYENV_ROOT/bin:$PATH" 
   curl -L https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer | bash
+  eval "$(pyenv init --path)"
+  eval "$(pyenv init -)"
   PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.1
-  export PATH="/opt/pyenv/versions/3.9.1/bin:$PATH"
-  export PATH="/opt/pyenv/versions/3.9.1/bin/:$PATH"
+  echo 'export PATH="/opt/.pyenv/versions/3.9.1/bin/:$PATH"' >> $SINGULARITY_ENVIRONMENT
+  export PATH="/opt/.pyenv/versions/3.9.1/bin/:$PATH"
+
+  pyenv shell 3.9.1
 
   wget https://bootstrap.pypa.io/get-pip.py
   python3 get-pip.py
   python3 -m pip install -U pip
   python3 -m pip install --upgrade pip
   python3 -m pip install numpy
-  apt-get install -y python3-pip
-  apt-get install -y freeglut3-dev valgrind
 
   pip install cmake --upgrade
   pyenv global 3.9.1
 
-  apt-get -y dist-upgrade   
-  sudo apt-get -y install ninja-build
+  git config --system user.name "Test User"
+  git config --system user.email [email protected]
 
+  export BDM_BRANCH="master"
   git clone https://github.com/BioDynaMo/biodynamo.git
-  cd biodynamo 
-  export SILENT_INSTALL=1
-  ./prerequisites.sh all
+  cd biodynamo
+  git checkout $BDM_BRANCH
 
-  cmake -G Ninja \
-  -Dparaview=OFF \
-  -DCMAKE_BUILD_TYPE=Release \
-  -B build
+  mkdir build
+  cd build
+
+  cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ..
+
+  ninja -j $(($(nproc) - 1)) 
 
-  cmake --build build --parallel 
 
 %runscript

cmake/env/thisbdm.fish

@@ -245,8 +245,14 @@ function source_thisbdm
 
         set -pgx PATH "$PYENV_ROOT/bin"
 
-        pyenv init --path | source; or return 1
-        pyenv init - | source; or return 1
+        # Rehashing is not possible within a read-only Singularity container
+        # and will cause sourcing of thisbdm to get stuck
+        if test -n "$SINGULARITY_CONTAINER"
+            set PYENV_NO_REHASH "--no-rehash"
+        end
+
+        pyenv init --path $PYENV_NO_REHASH | source; or return 1
+        pyenv init - $PYENV_NO_REHASH | source; or return 1        
         pyenv shell @pythonvers@; or return 1
 
         # Location of jupyter executable (installed with `pip install` command)

cmake/env/thisbdm.sh

@@ -361,8 +361,14 @@ _source_thisbdm()
     fi
     export PATH="$PYENV_ROOT/bin:$PATH"
 
-    eval "$(pyenv init --path)" || return 1
-    eval "$(pyenv init -)" || return 1
+    # Rehashing is not possible within a read-only Singularity container
+    # and will cause sourcing of thisbdm to get stuck
+    if [ -n "$SINGULARITY_CONTAINER" ]; then
+      PYENV_NO_REHASH="--no-rehash"
+    fi
+
+    eval "$(pyenv init --path $PYENV_NO_REHASH)" || return 1
+    eval "$(pyenv init - $PYENV_NO_REHASH)" || return 1
     pyenv shell @pythonvers@ || return 1
 
     # Location of jupyter executable (installed with `pip install` command)

doc/user_guide/Singularity.md

@@ -48,7 +48,16 @@ sudo singularity build Singularity.sif Singularity
 ```
 Then simply run the BioDynaMo singularity container using:
 ```bash
-singularity run Singularity.sif
+singularity run --cleanenv Singularity.sif
+```
+where the ``--cleanenv`` option clears out all the environment variables set in the host machine to avoid conflicts.
+
+Once the container is running we can source Root and the BioDynaMo environment:
+```bash
+source /biodynamo/build/third_party/root/bin/thisroot.sh
+```
+```bash
+source /biodynamo/build/bin/thisbdm.sh
 ```
 ## Method 2, Export image from local PC to HPC.
 If you cannot utilise either sudo or fakeroot on the HPC, we can instead build the BioDynaMo image on our local PC and export the image.
@@ -66,9 +75,17 @@ scp [user@]SRC_LOCALPC/SingularityFileLocation:]Singularity.sif ~/
 ```
 Finally we once again run the Singularity image on the HPC:
 ```bash
-singularity run Singularity.sif
+singularity run --cleanenv Singularity.sif
 ```
+where the ``--cleanenv`` option clears out all the environment variables set in the host machine to avoid conflicts.
 
+Once the container is running we can source Root and the BioDynaMo environment:
+```bash
+source /biodynamo/build/third_party/root/bin/thisroot.sh
+```
+```bash
+source /biodynamo/build/bin/thisbdm.sh
+```
 If you wish to read further about Singularity, you can find a substantial amount of information on the 
 singularity home website: https://sylabs.io/guides/3.5/user-guide/introduction.html. Including many tutorials and more 
 complex use cases.