Guides for High Performance Computing

Here are some information that i have gathered or written with respect to High Performance Computing. Some information on these topics should be available through searching this site.

Software and Tools in High Performance Computing

Some of the common tools required in High Performance Computing includes things like Schedulers and Parallel libraries.

Schedulers/Workload Management Systems

Some common schedulers includes

  • LSF by Platform Computing
  • Sun Grid Engine
  • Load Leveler by IBM
  • PBSPro by Altair
  • OpenPBS
  • Torque
  • XGrid

Parallel Libraries

Some common parallel libraries includes

Openmpi –
MPICH version 1 –
MPICH version 2 –
Parallel Virtual Machines (PVM) –


Some software that i have investigated before includes but not limited to the following

  • VMD and NAMD – Visual Molecular Dynamics and NAMD Scalable Molecular Dynamics
  • d2_cluster – White paper i wrote on my parallization work of d2_cluster when i was in IBM
    POVRay for Beowulf
  • Molecular modelling with PyMOL – Data files available from
  • OSIRIX for Medical Visulization – Data files available from
  • Tetruss for CFD on Macs
  • NWChem
  • SAGE Graphics Environment
  • Chromium Graphics Environment

Monitoring, Management and Benchmark Tools

Some tools to use for management and benchmarking

  • BProc for cluster process management
  • NetPipe for network measurement
  • xCAT Cluster Management Tools
  • OSCAR – Open Source Cluster Application Resources
  • HPL – High Performance Linpack
  • Ganglia – Cluster/Grid monitoring tool

Papers and Publications

A list of my papers and publications is available in the section Papers and Publications.