Related Web Sites

Parallel Computing Resources

• Cluster Hardware and Design
• Beowulf.org has an extensive list of cluster resources, as well as a guide to building your own Beowulf cluster.
• Engineering a Beowulf-style Compute Cluster is an online book with good information on cluster design.
• InfiniBand is an emerging set of network standards for high-performance computing.
• Parallel Programming Libraries and Other Resources
• MPI is a robust, open interface specification for parallel computing.
• The Extreme Linux section of Linux Magazine has many excellent articles about cluster programming.
• An MPI tutorial hosted at Lawrence-Livermore National Laboratory.
• The Web page for a course on Parallel Computing taught by Dr. Chen Yu Zong at the University of Singapore has several MPI tutorials.

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.