Computing power

Bioinformatics description facility:
We manage a dedicated cluster – located in a air-cooled datacentre – to carry out our projects.

schem56t

The resources of the Bioinformatics unit consist of a frontend (head) server and 10 worker nodes fully dedicated to NGS analysis. These are complemented by additional storage (56TB), giving a total of 192 CPU cores and 2.5TB RAM. The backup is linked to central IT facilities of University of St Andrews. It includes many commonly used bioinformatics packages and programs, which are both extended and updated on a continual basis.

Total CPU cores:

  • 192

Storage:

  • 56TB with full backup
  • 20TB without backup

Head node:

  • Quad AMD Opteron 6320 (4 x 8 cores at 2.8GHz)
  • 512GB DDR3-1600 ECC Registered Memory
  • 2 x 300GB 15Krpm 6Gb/s SAS Hard Disk Drive

8 standard memory nodes:

  • Dual AMD Opteron 6320 (2 x 8 cores at 2.8GHz)
  • 128GB DDR3-1600 ECC Registered Memory
  • 1 x 300GB SSD Hard Disk

2 high memory nodes:

  • Dual AMD Opteron 6320 (2 x 8 cores at 2.8GHz)
  • 512GB DDR3-1600 ECC Registered Memory
  • 1 x 300GB SSD Hard Disk – SATA

Software

  • The cluster system software is Red Hat Enterprise Linux, version 6.8
  • A C++11 standard software compiler is available via Red Hat’s Developer Toolset
  • The MPI version used is OpenMPI, version 2.0.0
  • Inter-node network speed of up to 20Gbit/s possible through bonded ethernet interfaces
  • User software is NGS and bioinformatics oriented such as sequence aligners, genome and transcriptome annotators, de-novo and referenced bases assemblers and full and updated BioPerl, Biopython and R Bioconductor analysis software