User Tools

Site Tools


wiki:documentation:computing

Computing resources

Lab github

All your code should be committed in a repository on our github. As per the lab manual, on Fridays your code should be pushed to the repository and up to date. Talk to me about how to organize your code.

Contributing to code

After getting access to github, here are the steps to follow to start developing:

  1. Getting anaconda Most of our code is in python and to make development easier, it is tyically developed in a so-called anaconda environment. Install anaconda for your computer. The code you will work on either has a requirements.txt or environment.yml file in it. These files say which python packages need to be installed for the code to run.
  2. Cloning a repository Read up online on how to clone a github repository and do so.
  3. Anaconda environment
    • Create the suitable anaconda environment using the environment.yml or the requirements.txt file.
    • Learn how to create and activate environments here: conda environments
    • activate your new environment.
  4. working with git So you have a copy of the code on your computer - what now? Let's say you want to play around and familiarize yourself with it. Do the following:
    • Create a git branch with an easy identifiable name eg monika_testing
    • go on your branch
    • Do some coding, exploration, plotting
    • Once you are happy with the state of your work, or it is Friday (as per lab manual): commit your changes to the code to your branch
    • push your changes to the online copy of the repository.

(the underlined terms are git commands. You will find a lot of literature about what they do. Git is very powerful, but also infinitely complex from the outside. Try focusing on the three commands here and you should be fine!)

Coding tips

general coding advice can be found under Coding Tips.

NAS Storage system

We now have a new NAS storage system with 60 TB capacity, single backed up. 8 TB are earmarked for the uncorrupted soma files, the rest is for our primary data. Please use this as you would use soma: As storage for large datasets, ideally curated and compressed before upload.

  • Create a folder with your name in the main directory
  • you can access on windows on a caesar computer \\nif9202\nif-data on a different computer \\nif9202.ad01.caesar.de\nif-data as address and your ad01 (caesar) credentials
  • if this doesn't work see if the name resolution works: nslookup nif9202
    IP adress should be 10.40.100.202
  • if this still does not work, open a ticket with IT
  • a permanent mounting is already created on nif3011/nif3004

Lab email address

scholzlabcaesar@gmail.com Password is our standard lab password. Ask me if you don't know it.

Remote computing

caesar HPC

NIF computers

Axon (garching)

wiki/documentation/computing.txt · Last modified: 2021/12/21 03:29 by bschloegl

Bitnami