Neovim in Singularity Container

nvim-singularity-demo.md

How to run Neovim/VIM & Jupyter inside a Singularity Container for R Programming

Video tutorial at: https://youtu.be/j63OKiLpUec

Build a Singularity Container

To build a Singularity container copy the lines below to a Singularity.def recipe/definition text file and then execute sudo singularity build container.sif Singularity.def. For more information on how to build a Singularity containers follow the instructions in the README of https://github.com/rohitfarmer/singularity-defs or check out the documentation at https://sylabs.io/.

BootStrap: docker
From: debian:buster

%labels
        APPLICATION_NAME Nvim-R in Singularity Container
        AUTHOR_NAME Rohit Farmer
        AUTHOR_EMAIL rohit.farmer@gmail.com
        YEAR 2020

%help
        This container is based on debian buster and contains R 3.5 and Python 3.6.

%environment
        PATH=/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin
        LANG=C.UTF-8 LC_ALL=C.UTF-8

%post

# Install Development Tools & Essential Packages
        cd /tmp

        apt-get -qq -y update

        export DEBIAN_FRONTEND=noninteractive
        apt-get -qq install -y --no-install-recommends tzdata apt-utils 

        ln -fs /usr/share/zoneinfo/America/New_York /etc/localtime 
        dpkg-reconfigure --frontend noninteractive  tzdata

        apt-get -y update 
        apt-get install -y --no-install-recommends \
                autoconf \
                automake \
                build-essential \
                bzip2 \
                ca-certificates \
                cmake \
                gcc \
                g++ \
                gfortran \
                git \
                graphviz \
                libtool \
                libjpeg-dev \
                libpng-dev \
                libtiff-dev \
                libatlas-base-dev \
                libxml2-dev \
                libcairo2-dev \
                libeigen3-dev \
                libpcre3-dev \
                libssl-dev \
                libcurl4-openssl-dev \
                libboost-all-dev \
                libgtk2.0-dev \
                libreadline-dev \
                libbz2-dev \
                liblzma-dev \
                libzmq3-dev \
                libpcre++-dev \
                libpango1.0-dev \
                libopenblas-base \
                libopenblas-dev \
                liblapack-dev \
                libxt-dev \
                neovim \
                openjdk-11-jdk \
                python3 \
                python3-dev \
                python3-pip \
                python3-setuptools \
                r-base \
                r-base-dev \
                texlive \
                texlive-fonts-extra \
                texinfo \
                vim \
                wget \
                xvfb \
                xauth \
                xfonts-base \
                zip \
                zlib1g-dev


        export LANG=C.UTF-8 LC_ALL=C.UTF-8


# Install Jupyter notebook
        python3 -m pip --no-cache-dir install jupyter

        R --quiet --slave -e 'install.packages(c("IRkernel"), repos="https://cloud.r-project.org/")'

# Install Python client to Neovim
        python3 -m pip --no-cache-dir install pynvim

# Install R packages
        apt-get install -y --no-install-recommends \
            r-cran-tidyverse

# Cleanup
        apt-get -qq clean
        rm -rf /var/lib/apt/lists/* 

Invoke a Shell inside the Container

To invoke a shell inside the container

singularity shell container.sif

Now run nvim as you would normally run in a terminal.

Execute a Jupyter notebook in the Container

To execute a Jupyter notebook inside the container first run

singularity exec container.sif R --quiet --slave -e 'IRkernel::installspec()'

NOTE: You only have to do it once to install kernelspec.

Now execute

singularity exec container.sif jupyter notebook --no-browser --ip=127.0.0.1 --port=8888

Running on an HPC

1. SSH to the HPC.
2. Claim an interactive node.
3. Navigate to your project directory. Singularity container should be in your project directory.
4. Execute singularity exec container.sif jupyter notebook --no-browser --ip='0.0.0.0'
5. Keep the SSH session and Jupyter notebook session running. Copy the URL on your local browser.

NOTE: On some HPCs, you may have to initiate an additional SSH tunnel connecting your local machine to the interactive node on the HPC. In that case, ask your system administrator.

How to use Neovim or VIM Editor as an IDE for R

For a detailed tutorial on how to use Neovim or VIM editor as an IDE for R please watch the video below.