Gaia
HPC Cluster
About Gaia
The Gaia High-Performance Computing (HPC) cluster is a resource provided by BIOPOLIS to support our researchers' advanced computational needs and enable users to perform complex simulations, data analysis, modelling, and other computationally intensive tasks. An HPC cluster is composed of many servers (computers) called nodes. Nodes are typically connected to a fast network. The HPC cluster has many computer cores with large amounts of memory, scratch (temporary) storage volumes suitable for computation and data processing, and access to BIOPOLIS archive storage.
The BIOPOLIS HPC cluster is based on a "co-op" model: researchers can contribute to this existing cluster instead of setting up and managing their private servers. In turn, contributing researchers receive higher priority time allocations on the cluster proportional to the amount of CPU time they contribute to the cluster.
Status
The Gaia cluster is currently in testing.
Testing Limitations:
Group archive storage is still unavailable (it should be active in the coming weeks).
Only a subset of the compute nodes are available (approximately four nodes active).
Limitations
Network scratch storage is not available.
Before you start
Requirements before using and requesting an HPC account:
Linux familiarity: You should be comfortable using the Linux operating system. This is because the HPC environment is Linux-based.
Document review: You should carefully read and understand the information in the following documents:
Getting an Account
Before using the Gaia cluster, you must request HPC access.
The process starts with your sponsor (group leader) submitting a ticket through the IT Support webpage (link here) to request access:
Topic: Gaia HPC
Message: should state the "request to access the Gaia cluster" and include your BIOPOLIS institutional email address.
Once your group leader request is processed, you'll receive an email with a link. This link will lead you to a form where you will:
Acknowledge reading the HPC policy (here) and
Get your Gaia driver's licence by answering a few questions to ensure your understanding of the policy and usage of the cluster.
Once granted HPC access, you can use your standard CIBIO/BIOPOLIS login credentials to connect to the cluster. It may take up to three working days for access to be enabled. You need to be listed in at least one research group (https://itu.biopolis.pt/research/research-groups) for the access to be enabled.
Optional Mailing List
You can subscribe to the optional mailing list (hpc_announce@biopolis.pt) to stay updated on the latest information about the Gaia cluster, including testing updates, bug fixes, and announcements. Note that @cibio.up.pt or @biopolis.pt emails are required to join the mailing list. To join follow the following link: https://groups.google.com/u/2/a/biopolis.pt/g/hpc_announce/
Questions/Issues
The faster approach is to check if your question is already answered in the mailing list (check the link above).
Alternatively, submit a ticket through the IT Support webpage (link here) with the topic "Gaia HPC" and describe your question or issue in the message.
Acknowledgement
When presenting or publishing research findings relating to the Gaia Cluster, please acknowledge and cite the following DOI: https://doi.org/10.5281/zenodo.12587844.
APA: BIOPOLIS IT Unit. (2024). GAIA HPC Cluster (Version 1). Zenodo. https://doi.org/10.5281/zenodo.12587844
MLA: BIOPOLIS IT Unit. GAIA HPC Cluster. 1, Zenodo, 28 June 2024, doi:10.5281/zenodo.12587844.
Can my research group purchase dedicated resources for the HPC?
Yes, the Gaia cluster has the concept of reserved/dedicated nodes, as outlined in the HPC policy (available here). These nodes are dedicated resources purchased by specific research groups for their exclusive use—more detailed information in Quick introduction to the Gaia HPC cluster.
