Dell PowerEdge Cluster: ccls.research.sfsu.edu

Dell HPC Cluster

A close-up of the blade servers

The SFSU Center for Computing for Life Sciences (CCLS) Dell PowerEdge Cluster is a high-performance computer cluster designed for general scientific, technical, engineering, and mathematics (STEM) research in the field of life sciences. Its current configuration is particularly suitable for bioinformatics research, as its storage capacity is sufficient to store the complete genomes of a number of species. As CCLS continues to serve the STEM community at SFSU, CCLS Dell PowerEdge cluster shall grow to suit the needs of the community.

The CCLS Dell PowerEdge Cluster is available for student and faculty researchers of CCLS-approved research. CCLS is dedicated to serving the STEM community and has a general policy of installing and supporting Open Source software critical for life science research. Proprietary software may be installed, subject to the Computing Resource Use Policy.

If you are a CCLS researcher and would like access, please read the Computing Resource Use Policy and fill out the HPC account request form. If you have an account and need an application to be installed on the Cluster, fill out the HPC support request form.

For more information, contact Mike Wong at

Important Links

• HPC account request form to get access.
• HPC support request form to request software installation or service.
• Computing Resource Use Policy to see the policies on cluster usage.
• Lava Job Scheduler Information to learn how to submit jobs to the cluster

Documentation and Additional References

• Finding Maximum Likelyhood Bootstrap Trees with PAUP and lavaRepMaker
• Notes on compiling C/C++ code for the cluster
• LAM/MPI website to learn more about LAM/MPI, the message-passing interface
• LAM/MPI User Guide
• Benchmarks techniques
• Platform Lava/LSF documentation
• Technical Specifications

Installed Software Packages for Research and Education

• CARNAC
• ClustalW
• Dynalign
• Emboss
• Exonerate
• Infernal
• InterProScan
• maker
• Matlab Note: This resource is available through Prof. Okada of the CS Dept. Please ask his permission before using.
• miRanda
• MPI-PovRay
• MrBayes , also see Using Mr. Bayes on the CCLS Cluster
• MUSCLE
• PALS
• PAUP , also see Using PAUP on the CCLS Cluster
• PILER
• primer3
• primerD
• R
• RepeatMasker
• SNAP
• UNAFold
• WUBlast

Blast Databases

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