Getting started with image analysis on LUNARC

The essentials

This is a very quick guide to getting started with the LUNARC system. A more detailed version is found below.

Connect to Aurora

Either connect to the HPC desktop as described here or ssh to aurora.lunarc.lu.se

Enable the QIM software environment

Enable the QIM virtual environment

source /lunarc/nobackup/projects/qim/load_qim_env.sh

Running code

Python scripts

python script.py arguments -keywords

Jupyter notebooks

jupyter lab notebook.ipynb

open the link printed in the terminal with a browser (e.g. Firefox) to access the notebook.

Transfer data from your local computer

scp file your_username@aurora.lunarc.lu.se:/home/your_username/

More details

QIM software environment

A description will be here soon.

Cloning the git repository

The code developed in the QIM project is hosted on GitHub here. To get the code you can either download a snapshot of the repository, or clone it. To clone the repository run

git clone https://github.com/jhektor/qim.git

in a terminal. This will create a local copy of the repository in a folder called qim in the current directory. To sync your local copy with the GitHub repository run

git pull

inside the qim directory. If you have modified any files in your local repository the git pull command will likely give a bunch of error messages. A better approach in case you want to modify the code is to fork the GitHub repository. To set-up the forked repository you can follow this tutorial. If you have improved on the code or implemented a new feature you are very welcome to create a pull request to add your code to the qim repository. You can read about how to do that here.

Transferring data to LUNARC

At the moment the most convenient way to transfer data to and from LUNARC is to use ´scp´ in a terminal. To transfer a file from your local computer to your /home directory on Aurora the syntax is

scp file your_username@aurora.lunarc.lu.se:/home/your_username/

You'll then need to input your password and a Pocket Pass OTP in the terminal. You can find more examples on how to use scp here. The path to the folder for the QIM storage project on Aurora is /lunarc/nobackup/projects/qim. There should also be a soft-link to the folder in your home directory. Each of the projects in QIM are given a separate folder within the storage folder.