View source for How to access the public servers

== How to Gain Access to the Public Genomics Institute Compute Servers ==

If you need access to the Genomics Institute compute servers, please ask your PI or sponsor to email 'cluster-admin@soe.ucsc.edu' requesting that you be granted access.  Then we can set up a quick meeting to create your account and go over the details.

== Server Types and Management==

You can ssh into our public compute servers via SSH:

 '''courtyard.gi.ucsc.edu''': 1TB RAM, 64 cores, 672GB local scratch space
 '''plaza.gi.ucsc.edu''': 1TB RAM, 64 cores, 672GB local scratch space

These servers are running CentOS 7.5 Linux.  They are managed by the Genomics Institute Cluster Admin group.  If you need software installed on them, please make your request by emailing cluster-admin@soe.ucsc.edu.

== Storage ==

These servers mount two types of storage; home directories and group storage directories.  Your home directory will be located as "/public/home/username" and has a 30GB quota.  The group storage directories are created per PI, and each group directory has a 15TB quota.  For example, if David Haussler is the PI that you report to directly, then the directory would exist as /public/groups/hausslerlab.  Request access to that group directory and you will then be able to write to it.  Each of those group directories are shared by the lab it belongs to, so you must be wary of everyone's data usage and share the 15TB available per group accordingly.

On the compute servers you can check your group's current quota usage by using the '/usr/bin/viewquota' command.  You can only check the quota of a group you are part of (you would be a member of the UNIX group of the same name).  If you wanted to check the quota usage of /public/groups/hausslerlab for example, you would do:

 $ viewquota hausslerlab
 
 Project quota on /export (/dev/mapper/export)
 Project ID   Used   Soft   Hard Warn/Grace   
 ---------- --------------------------------- 
 hausslerlab   1.8T    15T    16T  00 [------]

== Actually Doing Work and Computing ==

When doing research, running jobs and the like, please be careful of your resource consumption on the server you are on.  Don't run too many threads or cores at once if such a thing overruns the RAM available or the disk IO available.  If you are not sure of your potential RAM, CPU or disk impact, start small with one or two processes and work your way up from there.  Also, before running your stuff, check what else is already happening on the server by using the 'top' command to see who else and what else is running and what kind of resources are already being consumed.  If, after starting a process, you realize that the server slows down considerably or becomes unusable, kill your processes and re-evaluate what you need to make things work.  These servers are shared resources - be a good neighbor!

== Serving Files to the Public via the Web ==

If you want to setup a web page on courtyard, or serve files over HTTP from there, do this:

  mkdir /public/home/''your_username''/public_html
  chmod 755 /public/home/''your_username''/public_html

Put data in the public_html directory. The URL will be:

  http://public.gi.ucsc.edu/''~username''/

== /scratch Space on the Servers ==

Each server will generally have a local /scratch filesystem that you can use to store temporary files.  '''BE ADVISED''' that /scratch is not backed up, and the data there could disappear in the event of a disk failure or anything else.  Do not store important data there.  If it is important, it should be moved somewhere else very soon after creation.