NAMD Wiki: LinuxClusters

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Linux clusters are a cost-effective and versatile way to get your jobs run.

See also:

A good mailing list for life science oriented clusters is the bioclusters mailing list. Archives and subscription information can be found online at

A good book on running a Linux machine is Running Linux,

A good book on building a Linux cluster is the online and under-construction Engineering a Beowulf-Style Compute Cluster by Robert G. Brown,

A free and reasonably simple to install queueing system is Sun's Grid Engine, (see NamdOnGridEngine)

Useful testing tools are cpuburn and netperf

There are several cluster-oriented distributions of Linux:

Scyld (see NamdOnScyld) and Clustermatic (see NamdOnClustermatic) use Bproc ( to provide a unified process space and eliminate installing Linux on the slaves completely. These are good for running a single NAMD job on the entire cluster and in some other circumstances, but programs expecting a full Linux environment will be disappointed.

NPACI Rocks ( maintains node consistency by using RPM to completely reinstall the slaves to propagate any minor change.

OSCAR ( takes a less radical approach, bundling tools for configuring and maintaining a traditional cluster.