Software Development
You are free to use the cluster to develop and test your code during development.
Of course, you can also do the development on your local workstation and use the cluster only for testing or when your local workstation does not have sufficient resources for testing any more.
Or you might do your development and testing entirely on your local workstation and use the cluster only for your production jobs. In this case, you probably can skip this section and proceed right to running jobs on the cluster.
Software repositories
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.
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, the git version directly available is rather old because this depends on what is available for CentOS7
Therefore, we strongly recommend 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.
You can load the default module like this for example:
[me@nodelogin02 ~]$ module load git
[me@nodelogin02 ~]$ git version
git version 2.36.0Get an overview of all available git modules like this:
[me@nodelogin02 ~]$ module -r avail '^git'SHARK
On SHARK, git is available directly as a system package without the need to load any modules:
[me@res-hpc-lo02 ~]$ git version
git version 2.39.0Available 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: https://pubappslu.atlassian.net/wiki/spaces/HPCWIKI/pages/37749364
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: https://pubappslu.atlassian.net/wiki/spaces/HPCWIKI/pages/37028145