HPC @ University of Bern: ubelix – Uni BErn LInuX cluster

See also the original slides of Andres Aeschlimann as pdf »

This Grid HPC infrastructure is primarily designed to support the researchers at the Campus. They should use their time doing research and not be bothered by deploying a Grid HPC infrastructure.

Picture of ubelix

Some facts

  • first Linux Cluster was installed in 2001 (1 master and 32 single core nodes)
  • continuously expanded to ~1000 cores in >200 nodes today
  • Dual- and quadcore worker nodes
  • Mostly Opterons, increasing # of Intels (Nehalem)
  • several suppliers (mostly SUN, but currently also IBM and some Dell)
  • < 100kW
  • Gentoo Linux www.gentoo.org
  • Kernel 2.6.22/2.6.27
  • 2TB memory, 50TB disk
  • Lustre filesystem: 1.8.1
  • Sun Grid Engine 6.2
  • Gb Switch
  • Currently no Infiniband Switch

Internal (private) network

  • TCP/IP
  • Stackable Switches (~40Gbs)
  • „normal“ Gigabit Ethernet on the worker nodes
  • 10GE Ethernet for high throughput servers

Internal Network of ubelix


ubelix Lustre

Application portfolio (local users)

  • HE Physics
  • Astronomy
  • Computational and Molecular Population Genetics Lab
  • Space Research Physics
  • Computer Vision and Artificial Intelligence
  • Chemistry and Biochemistry

Applications from remote (SMSCG)

  • ATLAS: high energy physics application developed for the LHC experiment at CERN
  • RSA768: cryptographic application
  • NAMD and GROMACS: biochemistry applications
  • GAMESS: biochemistry application (work in progress)

Remote access to cluster

Other clusters @ UniBE

  • The LHEP UNIBE Atlas T3 2009 – A ROCKS Cluster with ~200 cores (Sun Fire X2200 IU dual quad cores) and ~50 TB on CentOS. Located in same room as ID UNIBE clusgter. Mainly serves local and remote ATLAS scientists. Backfilled with remote users and applications. Speciality: Access only via ARC clients, i.e. remote and local users habe the same interface. http://ce.lhep.unibe.ch
  • Theoretical Physics (~200 cores, with interconnect)
  • Climate Physics (~100 cores)
  • Space Physics (~100 cores)
  • Chemistry (~100 cores, with interconnect)
  • Computational and Molecular Population Genetics (~60 cores)