LabIntroduction
Our lab has a computer custer which is accessed by using ssh:
- kim.sas.upenn.edu
- our lab cluster for routine work, this should be where you go first. Our RNA Seq analysis takes place here and is stored on a NAS mounted as /lab/repo
Our lab also has access to other bioinformatics computer clusters:
- consign.pmacs.upenn.edu
- Main HPC system for the med school. Very high capacity, although large jobs may still be queued
- gamma.genomics.upenn.edu
- old PGFI cluster. Unstable and rarely used, we do still have access to it, for instance for jobs that would require majorly changing configurations on kimclust or pmacs
If you need accounts on either computer system, then contact Stephen. An account on the Kim cluster will allow you to access the local file server for backup storage of your desktop computer files, as well as run simulations on the cluster. To connect to the Kim cluster you need to ssh to kim.sas.upenn.edu.
See the following web pages for information on configuring and using the cluster. In short, the cluster computer 'kimclust15' is the ssh/sftp server. When you connect to the computer cluster (via kim.sas.upenn.edu) using ssh or sftp you are connected to kimclust15. The cluster computer 'kimclust15' is also the VNC server. You must run your VNC server on kimclust15 (see below) and when you connect your VNC server (via kim.sas.upenn.edu), your VNC client is connected to kimclust15. So again, all ssh/sftp and vnc clients are automatically directed to kimclust15. In any case, you just connect to kim.sas.upenn.edu and the rest is taken care of for you. When running simulations, you should NOT use any of our servers (eg kimclust15) but rather use one of the cluster nodes (see UsagePolicy).