Bioinformatics and Computational Biology

The Bioinformatics and Computational Biology Unit has a data processing centre (DPC), which houses a High Performance Computing Server (HPC cluster), in which to carry out the execution and analysis of computationally intensive tasks.

The cluster was implemented in 2014 and extended in 2021. It is composed of the following nodes:

• Management and storage node: it has 2 Intel XEON Cascadelake Silver 42100R processors (2.4 Ghz, 8.5 MB cache), 1 Mellanox Infiniband network card (56Gb/s FDR, 384 GB DDR4 RAM, 2 SSD disks of 960GB and 26 HDD hard disks of 16TB each.
•  Accessory management node: 2 Xeon Ivy Bridge E5-2630 V2 processors (2.6 GHz, 20 MB cache, 7.2 GT/s), 1 Mellanox Infiniband network card (FDR 56Gb/s) and 1 SSD disk of 120 GB.
•  Backup node: 2 Intel XEON Cascadelake Silver 42100R processors (2.4 Ghz, 28.5 MB cache), 1 Mellanox Infiniband network card (FDR 56Gb/s, 192 GB of DDR4 RAM, 2 SSD 512GB disks and 14 HDD hard disks of 16 TB each.
•  Compute nodes:
•  4 nodes of with 2 AMD ROME EPYC 7742 processors (2.25 Ghz, 256 MB cache), 1 Mellanox Infiniband network card (FDR 56GB/s), 1024 GB DDR4 RAM and 1 SSD disk of 1TB each.
•  4 nodes with 8 cores per processor (16 per node) and 64 GB RAM, and 4 additional nodes with 10 cores per processor (20 per node) and 128 GB RAM each.
• GPU compute node: 2 Intel XEON Cascadelake Silver 42100R processors (2.4 Ghz, 28.5 MB cache), 1 Mellanox Infiniband network card (56Gb/s FDR, 192 GB of DDR4 RAM, 1 x 2TB SSD and 5 Nvidia Tesla A 100 cards each with 40GB of dedicated RAM.

The DPC also contains a Web Server and a Database Server, where web services (the unit's website, courses) and database replicas (Uniprot, PDB, GenBank, EnsEMBL) are stored respectively:

• Web server: 2 Intel E5-2620 V2 processors (six cores, 2.1 GHz, 12 MB cache, 5 GT/s), 2 network cards as RAID1 and 2 Seagate Constellation disks (2 TB, 7200 rpm, 6 GB/s, 64M cache).
• Database server: 2 Intel Ivy Bridge E5-2640 V2 processors (eight cores, 2 GHz, 20 MB cache, 7.2 GT/s, 1 Infiniband network card (FDR 56 GB/s), 64 GB RAM, 2 SSDs (120 GB) as RAID1 and 4 Seagate Constellation Enterprise Server disks (3 TB, 7200 rpm, 6 GB/s, 64M cache).

In addition, the bioinformatics service has a workstation in its laboratory with a lonux operating system (Debian 8), i7-5820K processor (6 cores, 2 threads per core, 3.30 GHz, 15M cache) and 16 GB RAM.

The centre also has an ISILON storage server with 300 TB of space, to be used by the bioinformatics service for backups.

The cluster has an extensive list of software related to Bioinformatics and Machine Learning, as well as a licence to use Matlab and a queue manager (SLURM) for job submission.