Pre-tutorial materials

If you encounter any questions or issues while going through the pre-tutorial materials, feel free to use the tutorial slack channel (#2024-e3sm-tutorial-workshop) to post your questions.

The tutorial practicums will require participants to ssh onto the perlmutter machine, navigate the code, case, and run directories, and make some small edits to files. The following materials are for participants who are less familiar with working on remote servers and git to learn a bit of the basics, so that they can better follow the practicums.

Skills to know before arriving at the tutorial

Accessing HPC and running basic HPC

https://www.hpc-carpentry.org/hpc-shell/

Set up for performing above tutorial: https://www.hpc-carpentry.org/hpc-shell/setup.html

Intro to shell

https://librarycarpentry.org/lc-shell/

Intro to Git

** Even for those who are familiar with git, section 7 may be useful to review for how to generate ssh-keys on perlmutter**:

Tasks to accomplish before arriving at the tutorial

Using your NERSC account or assigned training account, ssh onto perlmutter

Create a github account and generate ssh keys to connect local git on perlmutter and github. See github ssh instructions.

Clone E3SM model code into a local directory on perlmutter with the following commands.
mkdir ~/E3SM_code
mkdir ~/E3SM_code/master_240430
cd ~/E3SM_code/master_240430
git clone git@github.com:E3SM-Project/E3SM.git ./
git submodule update --init --recursive

**If you encounter the following error message while cloning the the repository:
Cloning into ‘.'...
Warning: Permanently added ‘github.com,140.82.114.4' (ECDSA) to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository
Then you likely haven’t or had issues setting up your ssh-keys. See the instructions above under Intro to Git or the following page:

Explore the NERSC JupyterHub: https://jupyter.nersc.gov/hub/home

The JupyterHub will be used for some of the practicum sessions to work with Jupyter Notebooks
You simply need to login using your NERSC user account, type in your MFA, then click “start” under Login Node. The root directory will be your home directory.
Click Start under Login Node to get started
Official NERSC Jupyter Documentation:

Text editors to make code modifications

On NERSC, the following text editors are available. Quick start, cheat-sheets are also provided below.

emacs ( )

https://ccrma.stanford.edu/guides/package/emacs/emacs.html

https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf

vim ( )

https://www.cs.cmu.edu/~15131/f17/topics/vim/vim-cheatsheet.pdf

nano ( )