First steps

Welcome to the DL4MIA 2024 first exercise! In this set of exercises, we will set up the VDI!

DL4MIA 2023: 00 - First steps

The entire DL4MIA course exercises will take place in the VDI virtual machines.

Notes about the exercises

All exercises for the course can be found in the DL4MIA. Each repository has an exercise sheet detailing the instructions for downloading and installing the exercises.

Notes about using the VDI

Here are a few important notes about using the VDI:

• First, how to find it
  

• Log in using your username and password and select EMBO-DL4MIA machine.

• If you have trouble reaching the VDI (black screen then disconnection), let us know.

• Open a terminal
  
  

• Your /home/ (the folder with your name in it) is on the central storage, which is very slow. We have access to a faster storage /localscratch/ that you can use for the exercises!

• We also have a place to share data in /group/dl4miacourse/, be aware that permissions should be set so that other people can access it. Ask the tutors!

Setup

Clone all the course exercises

Open the main DL4MIA repository. Let's follow the instructions there to set up the exercises, open your terminal and type:

cd /localscratch/
git clone --recurse-submodules https://github.com/dl4mia/DL4MIA_2024.git

Install mamba

Then let's run the setup script of the main environment to install mamba on the /localscratch/ folder:

cd DL4MIA_2024
source setup.sh

What's mamba? If you've heard about conda then it is the same, just usually faster. It is a python environment and package manager that will help us install different sets of packages in parallel for each exercise.

Test mamba and install Jupyter Lab

Restart terminal by typing

exec bash

Use the following command to make sure mamba is indeed in localscratch folder

whereis mamba

We'll be doing most of our exercises in Jupyter Lab, so let's install that in our base so it's always available.

mamba install jupyterlab

Important point

Don't try to shut down the machine !