How to access the public servers: Difference between revisions

Revision as of 01:25, 13 July 2018

Server Types and Management

You can ssh into our public computer server via SSH:

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

This server is running CentOS 7.5 Linux. It is managed by the Genomics Institute Cluster Admin group. If you need software installed on it, 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.

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/

@@ Line 1: / Line 1: @@
-The Genomic Institute public server is courtyard.gi.ucsc.edu
+== Server Types and Management==
-To access the server, first request an account by emailing cluster-admin@soe.ucsc.edu. If you already have an account on kolossus, please provide your full name, your username on the server kolossus and the name of your PI and the lab or project you are working with. If you are affiliated with Genomic Institute, but do not have an account on kolossus, please make an appointment with the SysAdmin to setup your account in person.
+You can ssh into our public computer server via SSH:
-You can also request to be added to a group. A group for a PI is named as ''PI's_lastname_lab'' or the name of a project such as ''treehouse''.
+'''courtyard.gi.ucsc.edu''': 1TB RAM, 64 cores, 672GBTB local scratch space
-After you get the account, you can login by typing:
+This server is running CentOS 7.5 Linux.  It is managed by the Genomics Institute Cluster Admin group.  If you need software installed on it, please make your request by emailing cluster-admin@soe.ucsc.edu.
-  ssh ''your_username''@courtyard.gi.ucsc.edu
-Your home directory path is /public/home/''your_username''. Your home directory quota is 30GB.
+== Storage ==
-A group's directory's path is /public/groups/''name_of_the_group'' You can create your directory under there. You share the disk space with your group mates. The quota for your group is 15TB.
+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.
-You can use '''''rsync''''' to copy files from kolossus.sdsc.edu to courtyard.gi.ucsc.edu. If needed, you can read about '''''rsync''''' [https://linux.die.net/man/1/rsync  here].
+== 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:
-If you want to setup a web page on courtyard, 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:
+Put data in the public_html directory. The URL will be:
    http://public.gi.ucsc.edu/''~username''/