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Getting started

First Steps

You can log in to Genepool using SSH (Secure Shell) with the following command from any UNIX, Linux, FreeBSD, etc. command shell or terminal:

ssh -l username

There are several SSH-capable clients available for Windows, Mac, and UNIX/Linux machines. NERSC does not support or recommend any particular client.

By ssh'ing to, you will access one of the seven genepool login nodes.  These login nodes are situated behind a load balancer, so you may reach a different login node on different days.  If you make use of a tool like "screen" or "tmux", make sure to take note of which login node you started it on.

In addition to the genepool login nodes, the "gpint" systems are available for direct-ssh access.  The gpints differ from the login nodes in that login nodes are intended purely for file management, batch job submission, software compilation, and other "light" use; whereas the gpints can be used for heavier-weight interactive processing.  If you want to run a short (and small) alignment or other calculation without using the batch system, use a gpint.  Some gpints are available for all genepool users, while others are intended for group-specific work.  Please visit page to identify which gpints you may access.

Once you have logged into the login nodes or gpint systems, you should take a look at the list of installed software on genepool, and then familiarize yourself with the modules system and the user environment on genepool.  To try out some of the software, it is recommended to interactively use a compute node, using the "qlogin" command.

To begin running jobs on genepool in earnest, you should begin learning about the genepool batch scheduler system, and look at the example batch scripts before submitting your first job.