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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.