Protein Crystallography and Molecular Bioinformatics
University of Konstanz

High Performance Computing

Availability

  • The HPC computers are available to PhD/Master/Diploma students and their supervisors, for scientific work.
  • The idea behind providing access to the hpc computers for members of the University of Konstanz is to provide a platform for computation that goes beyond the ressources of a normal lab.
  • Due to the limited number of computers, this will only work out if the competition for CPU time is overcome by considerateness and mutual respect. E.g. any user is responsible for his/her jobs not consuming more CPU and I/O ressources than appears suitable at the load situation of the cluster. This requires some ressource monitoring, using top and qstat.
  • As a means for communication among users, any user is obliged to subscribe to the "Computing" Mailing List. The HPC Wiki (only accessible from within the 134.34.0.0/16 subnet) is another means of communication.

Hardware

    hpc2, hpc3, hpc4, hpc5

  • purchased 2007
  • Intel S5000PSL motherboard
  • 2 Quadcore X5365 3.00GHz CPUs
  • 16 GB (hpc2, hpc3) or 8 GB (hpc4, hpc5) ECC DDR2-667 memory
  • local scratch space: 300 GB (hpc2, hpc3) or 750 GB (hpc4, hpc5)
  • NFS-mounted scratch space depending on request
  • NFS-mounted software space

    hpc6, hpc7, hpc8, hpc9

  • purchased december 2010
  • Supermicro H8QG6 motherboard
  • 4 12-core AMD Opteron 2.3GHz CPUs
  • 384 GB (hpc6), 128 GB (hpc7) or 64 GB (hpc8, hpc9) ECC DDR3-1333 memory
  • local scratch space: 1.6 TB on each node
  • NFS-mounted scratch space depending on request
  • NFS-mounted software space

    hpc10, hpc11, hpc12, hpc13, hpc14, hpc15, hpc16, hpc17

  • purchased december 2010
  • Supermicro X8DTN+-F motherboard
  • 2 hexa-core Intel Xeon 2.93GHz CPUs
    hpc6-hpc16 have hyperthreading (HT, also "SMT") enabled, and thus appear to have 24 cores.
    hpc17 has HT disabled, to enable users to benchmark with/without HT.
  • 48 GB (hpc10, hpc11) or 24 GB (hpc12 - hpc17) ECC DDR3-1333 memory
  • local scratch space: 1.6 TB on each node
  • NFS-mounted scratch space depending on request
  • NFS-mounted software space

    • all machines coupled with GB ethernet

Software

  • Operating system:
    Scientific Linux 6 (64bit) which is basically Enterprise Linux, recompiled from source (see http://www.scientificlinux.org/).
  • 3rd party repositories:
    epel, rpmforge
  • Queueing system:
    Sun Grid Engine 6.2u5
  • GNU compilers, several MPI implementations
  • Daily backup of home directories

Information exchange


Administration

  • Karsten Schäfer (firstname . lastname at uni-konstanz . de) (request for userid/password)
  • Kay Diederichs (firstname . lastname at uni-konstanz . de)