Prerequisities

13.1. Prerequisities#

13.1.1. Recommendations#

  • VSCode does a good job with ssh and opening remote servers. Hence, working with VSCode is highly recommended. Mainly to visualize root files one can simply download them from VS Code.

  • Secondly, the software required to use the containers singularity works best for linux systems. So if in windows, having WSL2 is highly recommended and is assumed in here. Instructions on how to install WSL2 in windows is shown here. If in macOS having a Virtual machines and have singularity installed. The instructions on how to install singularity in macOS is shown here.

  • You can start either by using the HPC account at W&M or have a local installation. The HPC account is recommended.

13.1.1.1. Project Directory#

The entire tutorial section is going to have the project directory defined in the variable $EIC_PROJECT_DIR

export EIC_PROJECT_DIR="/path/to/ProjectDir"

setenv EIC_PROJECT_DIR "/path/to/ProjectDir"

13.1.2. Installing Singularity (locally assuming linux)#

13.1.2.1. Update your installed packages#

sudo apt-get update && sudo apt-get install -y \
    build-essential \
    uuid-dev \
    libgpgme-dev \
    squashfs-tools \
    libseccomp-dev \
    wget \
    pkg-config \
    git \
    cryptsetup-bin

sudo yum update -y && \
     sudo yum groupinstall -y 'Development Tools' && \
     sudo yum install -y \
     openssl-devel \
     libuuid-devel \
     libseccomp-devel \
     wget \
     squashfs-tools \
     cryptsetup

13.1.2.2. Install go#

  • download compiled version of go

export VERSION=1.13.5 OS=linux ARCH=amd64 && \
    wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
    sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
    rm go$VERSION.$OS-$ARCH.tar.gz

echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \
echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \
source ~/.bashrc

13.1.2.3. Install singularity#

  • download singularity

export VERSION=3.5.3 && # adjust this as necessary \
    wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \
    tar -xzf singularity-${VERSION}.tar.gz && \
    cd singularity

  • Check out a version of singularity

 git clone https://github.com/sylabs/singularity.git && \
    cd singularity && \
    git checkout v3.5.3

  • compile singularity. if needed can give --prefix=/path/to/install for install in custom directory else, it will get installed in /usr/local/

./mconfig && \
    make -C ./builddir && \
    sudo make -C ./builddir install

  • check your installation as singularity --version

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