Related Web Sites

Parallel Computing Resources

Cluster Software

  • Application Software
    • CHARMM is a customizable, parallelized, multi-platform molecular modelling program.
    • A Tutorial for CHARMM by Laboratory of Computational Biology staff.
    • A Web-portal for CHARMM also by Laboratory of Computational Biology staff.
    • NAMD is a parallel molecular dynamics code designed for high performance simulations.
    • MPICH is an open-source implementation of MPI for Unix and Windows systems.
    • PVM is another set of parallel communications libraries, similar to MPI.
    • For benchmarking, HPL is a freely-available implementation of Linpack.
  • Administration and Monitoring Software
    • LoBoS uses Torque, an extension of OpenPBS, as its batch processing system.
    • NAGIOS is a flexible, extensible distributed monitoring tool.
    • Ganglia is a distributed monitoring tool designed specifically for clusters.

Other Clusters of Note

  • Biowulf is another cluster at NIH.
  • Vrana at the Slovenian National Institute of Chemistry, which is run by Milan Hodoscek, who did early work on LoBoS.

Links compiled by Tim Miller, with the assistance of the Computational Biophysics Section staff.