What is the IFB-core Cluster?
The IFB-core Cluster has been in production since November 2018. It is composed of 4300 cores (hyperthreaded) and 2 PB of storage. Its purpose is to provide access to general and specialized bioinformatics resources to users from different fields (biologists and bioinformaticians) and levels of expertise (from novice to expert).
The administration of the IFB-core cluster is done in collaboration. More than six engineers from five IFB platforms build and contribute to the project on a daily basis. In order to manage the multiple contributions, they are managed by CI mechanisms (Ansible + Gitlab runner) connected to a common code repository (Gitlab).
Range of services
User documentation (Do not hesitate to suggest additions or modifications)
- SSH use. An ssh access to the cluster’s login node is provided following an account request. Once logged in, the user can request the infrastructure via the SLURM submission system.
- Open OnDemand. The new portal for accessing Rstudio and JupyterHub applications is located at https://ondemand.cluster.france-bioinformatique.fr. Find the presentation page, the documentation and the dedicated video.
- RStudio. To use R directly in your browser, you need to apply for an account first : https://rstudio.cluster.france-bioinformatique.fr. Attention, this service will no longer be available starting from March 15, 2024.
- JupyterHub. A instance of JupyterHub is available. Attention, this service will no longer be available starting from March 15, 2024.
- Galaxy. The Core Cluster offers a generalist instance such as usegalaxy.org and thematic instances (Métabolomique/Workflow4Metabolomics, Protéomique/Proteor, ...): https://usegalaxy.fr. The provision or distribution of “home-made” tools will be possible but quality requirements will be required.
- Application hosting. The Core Cluster will be able to host on demand perennial applications of Web type.
- Mutual aid and community support. A place to ask for support on the Cluster, but above all to exchange, help each other and discuss about bioinformatics (free registration) https://community.france-bioinformatique.fr
- Contribute. All users can participate in the Cluster’s development effort via Git (install software, set up new services, improve documentation, etc). https://gitlab.com/ifb-elixirfr
- Training. The IFB cluster can host training sessions. Let's see all details on the dedicated page : An infrastructure for your trainings
Contribute to the IFB-core Cluster TaskForce
You have skills in bioinformatics tools or systems administration, join the IFB Cluster TaskForce to deploy your tools or contribute to the management of the IFB infrastructure. Do not hesitate to contact us by sending an email to: contact-nncr-cluster@groupes.france-bioinformatique.fr. Otherwise, if you wish to be trained in the technologies used on the infrastructure, training/tutoring sessions are regularly offered.
> Continuous Integration (CI) & Collaborative work. The administration of resources is done in a collaborative manner. In order to control multiple contributions, these are managed by a continuous integration mechanism connected to a common code repository.
> Traceability. All installation, parameter setting and maintenance actions must be traced as far as possible. This is in order to:
- Debug
- To be able to go back in case of a problem
- Inform other directors of the changes made
We chose to use a Git directory hosted on a GitLab. Git meets all our traceability needs. As for the GitLab interface, it provides us with a place to exchange information and offers the possibility to work with Merge Request (Pull Request). These MRs require us to insert a code review phase before going into production. Each modification or addition is thus validated by a peer to avoid errors and to ensure that at least 2 people are aware of it.
> TaskForce members:
- Gildas LE CORGUILLÉ: : ABiMS, CNRS/Sorbonne Université, FR2424, ROSCOFF (Co-lead)
- Julien SEILER : IGBMC, 1 rue Laurent Fries, 67404, Illkirch (Co-lead)
- David BENABEN : INRAE, UMR 1332 Biologie du Fruit et Pathologie
- Nicole CHARRIERE : IFB/Institut Français de Bioinformatique, CNRS UMS 3601, IFB-core
- Thomas CHAUSSEPIED : IFB/Institut Français de Bioinformatique, CNRS UMS 3601, IFB-core
- Francois GERBES : IFB/Institut Français de Bioinformatique, CNRS UMS 3601, IFB-core
- Didier LABORIE : GenoToul Bioinformatique : Toulouse
- Guillaume SEITH : IGBMC, 1 rue Laurent Fries, 67404, Illkirch,
