Getting started on the SAGA cluster

1. Get a SAGA account and ask to have a directory created for you under /mnt/beegfs/users/$USER

2. Install miniconda

   cd /mnt/beegfs/users/$USER
   wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
   sh Miniconda3-latest-Linux-x86_64.sh

   read and accept the license, and install under /mnt/beegfs/users/$USER/miniconda3, answer questions, and restart your shell

3. install mamba for faster package management

   conda install -c conda-forge mamba

4. install jupyterlab

   mamba install -c conda-forge jupyterlab

5. Setup your environment to run CHEASE (optional)

   export PATH=$PATH:/mnt/beegfs/users/meneghini/chease/src-f90

6. Create a symbolic link from /mnt/beegfs/users/$USER/julia/ to ~/.julia

   mkdir -p /mnt/beegfs/users/$USER/julia/dev
   ln -s /mnt/beegfs/users/$USER/julia ~/.julia

   ~/.julia is where the Julia will install itself by default, and this will trick it to install itself in the IR&D folder instead.

   For convenience create also a symbolic link in your $HOME that points to the Julia dev folder:

   ln -s /mnt/beegfs/users/$USER/julia/dev ~/julia_dev

7. Now follow the standard Julia and FUSE installation instructions

Jupyter on SAGA cluster

1. Connect to saga and launch screen

   Note

   You can re-connect to an existing screen session with screen -r

2. Then start the Jupyter lab server from the screen session (screen will keep jupyter running even when you log out)

   jupyter lab --no-browser --port 55667

   Copy the token that you see on this session it should look something like token=1f1e0259cbc1..................

3. On your computer setup your ~/.ssh/config this way (need to do this only once):

   Host cybele cybele.gat.com
   Hostname cybele.gat.com
   User meneghini
   Port 2039
   
   Host sagae saga.gat.com
   Hostname saga.gat.com
   User meneghini
   ProxyCommand ssh -q cybele nc %h %p

4. On your computer start a tunnel going through cybele to saga

   ssh -N -L localhost:33445:localhost:55667 sagae

   Note

   Keep this terminal always open. You may need to re-issue this command whenever you put your laptop to sleep.

5. On your computer open a web browser tab to localhost:33445 to connect to the Jupyter-lab session on saga. Use the token when prompted.