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Pre-requirements for virtualization using Brainvisa - Linux

With Linux, Singularity seems to work perfectly well.

Given the characteristics of the 2 proposed technologies (singularity container or virtual machine) it is clear that it is better to use a container for performance reasons.

In the following we propose exclusively for Linux the use of a Singularity container.

Install Singularity

Fedora

Singularity is available in the Fedora repositories.

% dnf info singularity
Last metadata expiration check: 0:01:58 ago on Tue 05 Jul 2022 01:41:01 PM CEST.
Installed Packages
Name         : singularity
Version      : 3.8.4
Release      : 1.fc33
Architecture : x86_64
Size         : 123 M
Source       : singularity-3.8.4-1.fc33.src.rpm
Repository   : @System
From repo    : updates
Summary      : Application and environment virtualization
URL          : https://singularity.hpcng.org
License      : BSD-3-Clause-LBNL
Description  : Singularity provides functionality to make portable
             : containers that can be used across host environments.

Check that Singularity is already installed in your station:

% singularity version
3.8.4-1.fc33

If Singularity is not already installed:

% sudo dnf install singularity  # sudo dnf install singularity-ce, for recent versions of singularity

Ubuntu

To date, no suitable version of Singularity is available as system package for Ubuntu.

You can install it yourself.

However, we advise you to use the package provided by BrainVisa, corresponding to your OS. For example download singularity-ce_3.8.3~ubuntu-20.04_amd64.deb then :

% sudo dpkg -i singularity-ce_3.8.3~ubuntu-20.04_amd64.deb

Then, check that Singularity is well installed on your station:

% singularity -- version

After installing singularity in your station

Reminder: Two software must be installed: Python (version >= 3.7) and Singularity (version > 3.6).

Open a shell, then:

mkdir -p $HOME/brainvisa-5 # create an installation directory

Download the latest BrainVISA image found in brainvisa site into this new directory (ex. brainvisa-5.0.4.sif).

In the opened shell:

singularity run -B $HOME/brainvisa-5:/casa/setup $HOME/brainvisa-5/brainvisa-5.0.4.sif # Run Singularity using the downloaded image
echo 'export PATH=${HOME}/brainvisa-5/bin:${PATH}' >> $HOME/.bashrc # set the bin/ directory of the installation directory in the PATH environment variable

Optionally, you can launch the graphical configuration interface, e.g. to define mounting points, etc:

bv

Build from the container terminal (after bv bash) or outside the container:

bv_maker

Then open an interactive shell in the container:

bv bash

And continue with the Installation part …