Dealing with the home directory size limitations

The problem

Our homes are limited to just 10GB! But lots of programs write to home and you will quickly find that you run out of space even if you never put things there. Errors due to running out of space here can be hard to find so I recommend considering this document!

Soft linking common hidden folders

First make a dir for yourself on the lab volume:

mkdir -p /mmfs1/gscratch/stergachislab/${USER}

Then I recommend make these folders within that directory:

.pixi
.apptainer
.local
.conda
.config
.cache
.ipython
.jupyter
.parallel
.vim
.vscode-server
.vscode-R

Once these folders are made you can link them to your home folder e.g.:

ln -s /mmfs1/gscratch/stergachislab/${USER}/.cache ~/.

If these folders already exist in your home first move them to the lab volume then soft link them back as shown above.

To create a quick batch script to automate making these hidden folders, copy the text above and into a file hidden_folders.txt in your lab volume. Then:

sed 's/^/mkdir /' hidden_folders.txt > make_hidden_folders.sh

Execute the batch script in your lab volume:

sh make_hidden_folders.sh

To create a quick batch script to link all these hidden folders to your home directory:

sed 's|^|ln -s /mmfs1/gscratch/stergachislab/${USER}/|; s|$| ~/.|' hidden_folders.txt > link_hidden_folders.sh

Execute the batch script:

sh link_hidden_folders.sh

Double check your home directory to ensure links were created correctly cd ~/. and ls -al.

conda

Just don't install conda in your home. It defaults there, but you will be much happier if you instead install it here:

/mmfs1/gscratch/stergachislab/${USER}

Rust

If you install rust you must first follow the instructions here: https://www.rust-lang.org/tools/install and it will install it in your home dir. If the .cargo or .rustup directories already exit you may get errors and need to remove them first.

However, after it is installed, it is important to move these two directories out of your home because they will become large!

.cargo
.rustup

And then soft link them back into your home.