Getting access to systems
Given that our class will have students on a variety of operating systems (Windows, OSX, Linux), we will use the HPC (high performance computing) cluster at the University of Arizona for our work. Students using the Windows operating system might find the Cygwin tools useful for getting access to tools like "ssh" and "scp." Students on OSX and Linux machines may choose to install software locally using package management tools like "homebrew" (OSX) or "apt-get" and "yum" (Linux).
University of Arizona HPC
We need to get into a Unix system. If you're on Linux or OSX, open a terminal and type:
ssh <NetID>@hpc.arizona.edu
If all goes well, you should see something like this:
Last login: Thu Aug 24 09:12:07 2017 from dhcp-10-142-130-41.uawifi.arizona.edu
This is a bastion host used to access the rest of the environment.
Shortcut commands to access each resource
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Ocelote: El Gato: Cluster(ICE)/HTC/SMP:
$ ocelote $ elgato $ ice
The name of the machine should be "keymaster.hpc.arizona.edu." Verify this with the command "hostname
===============
HPC.ARIZONA.EDU
===============
Please select a target system to connect to:
(1) Ocelote
(2) El Gato
(3) Cluster/HTC/SMP
(Q) Quit
(D) Disable menu
The menu will be present on your next login session. Make a selection from the menu to login to a head node.
As of 2016, Ocelot is UA's newest cluster. For more information, see https://confluence.arizona.edu/display/UAHPC/Ocelote+Quick+Start.
If you would like to avoid the 2-factor authentication, then read the following:
https://www.protocols.io/view/ssh-to-UA-HPC-fm7bk9n
Stampede (TACC)
The "stampede" cluster is another HPC resource that is freely available to our students. It is located at TACC, the Texas Advanced Computing Center at the University of Texas in Austin. Go to https://portal.tacc.utexas.edu/ to create an account. We recommend our students use the same username at TACC and Cyverse.
Cyverse (UA)
Cyverse is an NSF-funding cyberinfrastructure project headquartered at the University of Arizona. It began life as "iPlant" in 2008. Our students may choose to make use of Cyverse infrastructure, as well, such as "apps" for assemblies, gene calling, protein clustering, and such. Students should go to https://user.cyverse.org/ to create an account. Again, we recommend you use the same username as your TACC account to make communication between the TACC and UA systems easier.
Docker, VirtalBox
If cannot gain access to the UA HPC or TACC, you can follow along at home using a virtual machine such as a Docker (https://www.docker.com/) or VirtualBox (https://www.virtualbox.org/) image installed on your machine.