Using git on Pelle

Git is a version control tool made for code but equally useful with other text format files, such as config files, scripts, notes and many input data file formats. Version control is needed for reproducibility when the same files are used in multiple versions, being updated and worked on over time. Therefore you may already be using it for files that you want to use on Pelle.

Using git push and git pull can be a good way to transfer updates to files to/from Pelle.

Caveats

If your files are binary (not in a text format) or if your files are not being updated, this is not the right tool for your file transfer needs.

Due to our storage setup limitations, git on Pelle can only be recommended for relatively small sets of files.

If either of these caveats apply, we advise that you use rsync instead for keeping files on Pelle in sync with files elsewhere.

Other file transfer tools

See the other ways to transfer data to/from Pelle

The risk of a large number of files

Git works by splitting the data into multiple small files and referencing them cleverly. For large repos and deep histories this results in a large number of small files. Our storage setup is not performant for such workloads, wherefore we have a quota not only on storage space but also on number of files.

If git actions are slow it is an indicator that your repository has become too large for our storage system.

No secrets on Pelle

Pelle is not considered a secure system

It is not advisable to store any secrets, such as ssh keys or access tokens, on Pelle.

This means that you cannot push from Pelle to e.g. Github. Instead you can setup Pelle as a remote to push to and pull from with your local computer, with no keys stored on Pelle.

Setting up a git repo on Pelle as a remote

Here is one good way to set up a copy of a git repository you have on your local computer as a remote on Pelle:

1. Start a terminal on your local computer

Start a terminal on your local computer.

2. Connect to Pelle with ssh

In the terminal, run ssh to connect to Pelle by doing:

ssh [username]@pelle.uppmax.uu.se

where [username] is your UPPMAX username, for example:

ssh sven@pelle.uppmax.uu.se

If asked, give your UPPMAX password and your second factor TOTP.

3. Create the folder to hold your repo on Pelle

mkdir myRepo

This example uses ~/myRepo to keep it short. You can use any path in your home folder or project storage. On project storage, you can use git for collaborating.

4. Initialise and configure the git repo on Pelle

cd myRepo
git init
git config receive.denyCurrentBranch updateInstead

The command git init sets up the folder as a git repository.

This git config command sets it up so that you can push to it, but you can also work with the files and git directly in this folder (as opposed to a so-called bare repository, as is used on git servers).

5. Log out from Pelle (or open a second terminal)

Ctrl+D or exit or logout.

6. Set up the path on Pelle as a remote in your local repo

Navigate to the folder that holds the repository on your local computer. In that folder, run:

git remote add pelle [username]@pelle.uppmax.uu.se:~/myRepo

This adds a remote named pelle referring to a URL specifying your user, Pelle's full hostname and your chosen path on Pelle. Git automatically uses ssh to set up the connection when the URL follows this pattern (instead of https if it is an https URL).

Note that the path you give here needs to either start with ~ referring to your home folder or / referring to the root of the system, i.e. it needs to be a full path (there is no current directory on Pelle in this context to start a relative path from).

To check the URL:s of all remotes you have set up (in this repo) use git remote -v.

7. Push the current version of the repo to Pelle

git push pelle

Done! Now you have this repo on Pelle as well.

You cannot push to anywhere from Pelle, but you can push to Pelle and pull from Pelle with your local computer. And you can clone directly from Pelle if you need to work with this repo from more computers, just

git clone [username]@pelle.uppmax.uu.se:~/myRepo

and provide your ssh credentials as needed. That will setup Pelle as the origin remote, no further configuration needed to pull from and push to Pelle.