So, you have been given an account on the University of Florida HPC Center's cluster. Now what? Well, hopefully we can answer some of those questions here...
To login to the cluster, you need an SSH client of some sort. If you are using a linux or unix based system, there is most likely one already available to you in a shell, and you can get to your account very quickly...
Linux / Unix
So, here is how you would go about logging in via a linux or unix account:
test@puppy:~$ ssh email@example.com firstname.lastname@example.org's password: Last login: Fri Feb 9 00:03:38 2007 from wsip-70-168-187-166.ga.at.cox.net [test@submit ~]$
ssh email@example.com is what you would type in at a command prompt on your system. After this, it asks you for a password, which you type in. After that, you are logged in and ready to work.
For Microsoft Windows, things are a bit trickier. Windows does not come with a built-in SSH client, and this makes things difficult. What you have to do is download a client from the Internet and install it, then use that client. We recommend the following:
Both of the above clients have documentation at their websites, so I will not go into it here. Once you are logged in and have a prompt that resembles that in the Unix / Linux section above, you can continue with this tutorial.
We expect the users of the HPC Center cluster to already have a working knowledge of the linux operating system, so we are not going to go into detail here on using the operating system. Below are some links to webpages that describe a lot of this, however:
We have a structured file system that is important to know about. Please read about it here: HPC File System
Editing files on the cluster can be done through a couple of different methods...
- vi - vi is the basic editor for a number of people. Using the editor is not necessarily intuitive, so we have provided a link to a tutorial.
- emacs - emacs is a much heavier duty editor, but again has the problem of having commands that are non-intuitive. Again, we have provided a link to a tutorial for this editor.
You can also use your favorite editor on your local machine and then transfer the files over to the HPC Cluster afterwards. One caveat to this is that with files created on Windows machines, very often extra characters get injected into text files which can cause major problems when it comes time to interpret the files. If this happens, there is a utility called
dos2unix that you can use to remove the extra characters.
PBS Pro Scheduler
The Torque Resource Manager has been installed on the HPC cluster, and is slowly being switched over to from the PBS Pro scheduler as time goes on. The Maui scheduler is also running in this environment.
The Torque scheduler is installed on [code]iogw2.hpc.ufl.edu[/code], and accepts the same commands as the PBS Pro scheduler with a couple of exceptions. Currently we are experimenting with these packages so that we can provide improved scheduling to HPC users. While we are still learning about Torque and Maui, our experiences so far have been good and we are guardedly optimistic that Torque and Maui will end up being the resource manager and scheduler for the HPC Center sometime in the not-too-distant future.
The Altix is known to the Torque batch system, but not to PBSPro. To submit jobs to the Altix via the batch system, you will have to log into the host 'iogw2' and submit your jobs from there.