Software repositories
You can make use of git on both clusters. You are free to use public hosting services for git repositories or you can make use of locally available gitlab server:
Leiden University
The Leiden University gitlab server is available here: https://gitlab.services.universiteitleiden.nl/
A ULCN account is required to access the gitlab server and setup a repository.
Note that currently you can only have private and internal repositories and not public repositories.
LUMC
The Leiden University gitlab server is available here: https://git.lumc.nl/
A ULCN account is required to access the gitlab server and setup a repository.
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We strongly recommend using a git repository to host your code and scripts and sync the repository to the cluster. This way, you always have a copy outside of your cluster and you can always go back to previous version of your code. |
Git on ALICE and SHARK
You can make use of git on both clusters.
ALICE
On ALICE, git is not available as system package on the compute nodes. Therefore, it is recommended to use one of the git modules whenever you want to make use of git on ALICE, no matter whether you are on the login nodes or the compute nodes.
Load the default module like this:
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[me@nodelogin02 ~]$ module load git
[me@nodelogin02 ~]$ git version
git version 2.36.0 |
Get an overview of all available git modules like this:
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[me@nodelogin02 ~]$ module -r avail '^git' |
SHARK
On SHARK, git is available directly as a system package without the need to load any modules:
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[me@res-hpc-lo02 ~]$ git version
git version 2.39.0 |
Available compilers
Both clusters have compilers available as well as other frameworks to help you develop and test your code. You can find more information here: Installing your own software
Suitable partitions
While you develop code, you will often need to compile and test what you have written.
If compiling and testing requires a certain amount of resources, you have to make use of a slurm job. We recommend to use a batch job.
The best suitable partitions for this purpose are:
on ALICE: testing
on SHARK: short
Remote access
You can work on your code or git repository directly on the cluster with a suitable. An example is Visual Studio Code for which we have instructions here: Setting up VSCode to work on the cluster