General Preparations

Welcome to our Applied Atmospheric Modelling Seminar.

This is a collection of all preparations which need to be done prior to the exercises. We will remind you about these preparations at the begin of the different exercises.

• Grouping (especially for ICON exercises):

  • Do you already have an account for the DKRZ HPC platform “Levante”? If not, ask you supervisor!

  • Please gather together and build groups with two persons per group. Decide only for one account, the other account remains unused - only for backup purposes.

  • for onsite:

    • we sit together in one room and also work together as group

    • please find a good compromise between working for your own and asking for help

  • for online only:

    • Each group will have a dedicated breakout room in our zoom session. Please check if you know which group you belong to and also check if it works to enter the breakout room.

    • General workflow for each group of two people:

      • One is typing and sharing the screen.

      • The otherone is talking and gives advices.

      • Please change roles between morning and afternoon sessions.

• Learn vim

  • https://www.openvim.com

  • https://vim-adventures.com

  • http://www.vimgenius.com/lessons/vim-intro/levels/level-1

• Test (or install) panoply

  • https://www.giss.nasa.gov/tools/panoply/download/

• Learn to work with the High-Performance Computing (HPC) platform “Levante”

  • “Levante” is the supercomputer at German Climate Computing Center DKRZ (see https://docs.dkrz.de/doc/levante/index.html). It is a Linux server.

  • You will mainly work on Levante in a “Terminal”. (https://www.giga.de/extra/linux/specials/linux-befehle/)

  • Please make familiar with standard bash commands. (https://www.educative.io/blog/bash-shell-command-cheat-sheet)

  • Login to “Levante” via ssh. Test (or prepare) your machine for remote connections with ssh and sshfs: https://www.digitalocean.com/community/tutorials/how-to-use-sshfs-to-mount-remote-file-systems-over-ssh. If <MyUser> stands for your account (or the account you selected in your group as main account), than login works as follows:

    ssh <MyUser>@levante.dkrz.de
    

    You will be asked for your password. Please enter it and proceed! You will end in your home directory.

  • In a “Terminal”, editing a file is a little bit less intuitive than in a GUI. We will use vim as editor. Please make yourself familiar with basic commands (see links above or e.g. https://opensource.com/article/19/3/getting-started-vim )

  • Special commands (e.g. sbatch, scancel, squeue) exist to submit or cancel simulation jobs on Levante. The job scheduler is called slurm. Please read through this page (https://docs.dkrz.de/doc/levante/running-jobs/index.html) before you start your first job!

• JupyterHub can be used for data analysis with Python. A dedicated tutorial exists to help you to get started.