Create BioDynaMo singularity image

.github/workflows/singularity-integration.yml

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+name: Singularity Integration
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    name: Build
+    runs-on: ubuntu-latest
+    container:
+      image: quay.io/singularity/singularity:v3.9.0
+      options: "--privileged --workdir /data"
+    steps:
+      - uses: actions/checkout@v2
+      - name: Build singularity image...
+        run: |
+          singularity build Singularity.sif Singularity

Singularity

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+Bootstrap:docker
+From:ubuntu:18.04
+
+%environment
+
+%post -c /bin/bash
+
+  export DEBIAN_FRONTEND=noninteractive 
+  export TZ=Europe/Berlin
+
+  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
+  dpkg-reconfigure locales
+  locale-gen
+
+  wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  bash Miniconda3-latest-Linux-x86_64.sh -b -f -p /miniconda3/
+  rm Miniconda3-latest-Linux-x86_64.sh
+
+  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:$PATH" 
+  curl -L https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer | bash
+  PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.1
+  export PATH="/opt/pyenv/versions/3.9.1/bin:$PATH"
+  export PATH="/opt/pyenv/versions/3.9.1/bin/:$PATH"
+
+  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 clone https://github.com/BioDynaMo/biodynamo.git
+  cd biodynamo 
+  export SILENT_INSTALL=1
+  ./prerequisites.sh all
+
+  cmake -G Ninja \
+  -Dparaview=OFF \
+  -DCMAKE_BUILD_TYPE=Release \
+  -B build
+
+  cmake --build build --parallel 
+
+%runscript

doc/user_guide/Singularity.md

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+---
+title: "Singularity"
+date: "2022-15-02"
+path: "/docs/userguide/singularity/"
+meta_title: "BioDynaMo User Guide"
+meta_description: "This is the singularity page."
+toc: true
+image: ""
+next:
+    url:  "/docs/userguide/singularity/"
+    title: "Singularity"
+    description: "This is the diffusion page."
+sidebar: "userguide"
+keywords:
+  -Singularity
+  -HPC
+  -performance
+---
+In addition to running BioDynaMo on standard computers, users can also utilise the BioDynaMo frame work on high 
+performance computers (HPCs). Due to many HPCs having higher security than standard computers however it is likely
+that a user wishing to do this will need to build BioDynaMo within a container on the chosen HPC.
+
+For this we have chosen to Singularity. Singularity is an open source programme for operating-system-level virtualization. 
+Singularity works simillar to other popular container programmes such as Docker. However, due to its higher level of 
+security it has seen more widespread uptake by HPCs and we thus beleive the best choise for users.
+
+To create our singularity image for BioDynaMo we can use on of two methods.
+
+## Method 1, directly building on the HPC.
+For the first method, we directly import the biodynamo Singularity file from our local PC to the desired HPC as follows.  
+Firstly, we must scp into the desired HPC from our local PC. This can be done directly through the terminal as follows.
+```bash
+ssh -x [HPC.ADDRESS]
+```
+We then must secure copy the BioDynaMo singularity file from the chosen PC to the local HPC.
+```bash
+scp [user@]SRC_LOCALPC/SingularityFileLocation:]Singularity ~/
+```
+From here we can build BioDynaMo utilising the fake root feature of singularity. 
+```bash
+singularity build --fakeroot Singularity.sif Singularity
+```
+Fakeroot is not needed if you have sudo rights on the HPC but this is highly unlikely for most individuals.
+In that case however we simply amend the above to:
+```bash
+sudo singularity build Singularity.sif Singularity
+```
+Then simply run the BioDynaMo singularity container using:
+```bash
+singularity run Singularity.sif
+```
+## Method 2, Export image from local PC to HPC.
+If you cannot utilise either sudo or fakeroot on the HPC, we can isntead build the BioDynaMo image on our local PC and export the image.
+This works simillar to method 1 but with a change in order. Firstly, we must build our image on the local PC with sudo rights:
+```bash
+sudo singularity build Singularity.sif Singularity
+```
+Then ssh into the HPC.
+```bash
+ssh -x [HPC.ADDRESS]
+```
+secure copy the image from our PC to the local HPC.
+```bash
+scp [user@]SRC_LOCALPC/SingularityFileLocation:]Singularity.sif ~/
+```
+Finally we once again run the Singularity image on the HPC:
+```bash
+singularity run Singularity.sif
+```
+
+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.
+