| layout | title | nav_order | description | permalink |
|---|---|---|---|---|
default |
Welcome |
1 |
Home |
/ |
This is the index page for the Penn Brain Science Center cluster computing documentation.
The BSC computing cluster is hosted by DART (formerly PMACS) in their "Limited Performance Computing" (LPC) environment.
The LPC is distinct from the PMACS High Performance Computing (HPC) service. The HPC is better suited for large-scale data processing beyond the capabilities of the LPC.
The LPC serves multiple different labs and centers. Some groups affiliated with the BSC also have independent LPC resources outside of the BSC cluster, which are generally similar, but not identical to the BSC. Therefor the LPC documentation provided by other LPC users can be a useful source of information to BSC users, but some details may differ.
- TOC {:toc}
The LPC is a shared resource for cluster computing, supported by DART and the BSC. The LPC provides a substantial upgrade in hardware and software performance compared to the previous CFN cluster. Like the old CFN cluster, the LPC is a Linux computing environment with multiple compute nodes, a grid engine job scheduler, and backed-up network storage.
Please see the article on accessing the PMACS cluster about how to access the BSC PMACS cluster.
All data on the cluster should be de-identified. Contact PMACS if you have specific requirements
How to get an LPC account.
Main article: LSF for CFN users
The LPC cluster uses the IBM LSF system for parallel computing, while the CFN cluster used the Sun Grid Engine. While many of the same concepts apply, there are several differences in how jobs are submitted and run.
BSC LPC Access
Using the cluster effectively requires familiarity with the Linux command line and basic scripting. There are many resources online for this. Penn personnel can access LinkedIn Learning (formerly Lynda), by signing in with their PennKey at
http://linkedinlearning.upenn.edu/
Some courses of interest:
Learning Linux Command Line this course gives an introduction to using the Linux command line.
Learning Linux Shell Scripting this course covers basic shell scripting.
Linux: Bash Shell and Scripts this is a longer course on shell scripting that covers the basics but also gets into more advanced topics. Shell scripting is powerful and convenient to run basic tasks quickly, but users should consider another language such as Python for complex systems.