Using Agustina

Using Agustina

Agustina is a High Performance Computing (HPC) center. There are many such centers in the world (a list of the most powerful supercomputers is available in the Top500, in case you are curious).

The main documentation of Agustina is here, which includes account creation and basic usage. Remember that any changes you do to your .bashrc will be applied once you create a new terminal or run source .bashrc.

• Like most HPC centers, Agustina requires users to connect from a local network for security reasons. In other centers you must use a VPN. In Agustina, you can ssh to the login node (agustina.bifi.unizar.es) through a bridge node (bridge.bifi.unizar.es). Setting up these aliases in your .bashrc file will be useful:

alias tob='ssh -X username@bridge.bifi.unizar.es'
alias toa='ssh -J username@bridge.bifi.unizar.es username@agustina.bifi.unizar.es'

That way you can jump over bridge to access Agustina using simply toa.

• Once in Agustina, you will notice that the command line interface is very plain. To improve it, you can set up a few extras in your .bashrc file (in your Agustina user home!):

export PS1="\[\e[31m\][\[\e[m\]\[\e[33m\]\u\[\e[m\]@\[\e[36m\]\h\[\e[m\]\[\e[31m\]]\[\e[m\]:\[\e[33;40m\]\w\[\e[m\]\[\e[40m\] \[\e[m\]\[\e[32;40m\]\\$\[\e[m\] "
alias wqm="watch squeue --format=\'%.18i %.9P %.30j %.8u %.8T %.10M %.9l %.6D %R\' -u username"

• Next step is setting up github and git. To start, go to your github keys setting and then generate a new ssh key in Agustina and add it to your account following the instructions.

Once that is done, you can get the lab’s utility scripts from the group organization page, assuming you have asked for permissions. Clone this directory to a directory (I put it in /home/username/Software/) and add the directory to your path in .bashrc :

export PATH="/home/username/Software/utility_scripts:$PATH"

Now you can use the scripts from this directory in your command line. You can check usage by reading the scripts or, in general, using the help flag, e.g.:

subconda.sh -h

• The next step is setting up conda or some other package manager.

You can follow the instructions in the documentation here.

Personally, I added these to my .bashrc as well:

module load anaconda/2025 > /dev/null # This avoids errors with scp and rsync with host jumping
export CONDA_PKGS_DIRS=/fs/agustina/$(whoami)/.conda-pkgs
mkdir -p /fs/agustina/$(whoami)/conda-env
# To activate or create envs, we now need --prefix=/fs/agustina/$(whoami)/conda-env/my-conda-env-name
# ... other lines you may need
export TERMINFO=/usr/share/terminfo # This makes sure that clear command works

The space you have in your /home in Agustina is small, so your conda envs should be stored in /fs/agustina/username/conda-env/ (some packages are very big!). Since typing the full path to activate an env is a pain in the derriere, you can add that location to let conda figure out aliases.

conda config --append envs_dirs /fs/agustina/username/conda-env/

You can now activate envs using their names directly.