Hoffman2

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A compilation of lab know-how regarding the Hoffman2 Computing Cluster.

Anyone new to the lab and using Hoffman2 NEEDS to read the first section to have adequate working knowledge of the system.


Getting Started

Introduction

Hoffman2 is a Computing Cluster at UCLA, find out how it generally works so you know how to use it.

Hoffman2:Introduction

Getting an Account

You know what it is, now you want to use it. First you need an account.

Hoffman2:Getting an Account

Accessing the Cluster

Now how do you use that account to access the cluster?

Hoffman2:Accessing the Cluster

Working in a UNIX Environment

Never heard of a command line before? Vaguely know what "permissions" are and have no idea how to navigate a filesystem? This page is meant to take the scare out of the words "command line" so you can actually use Hoffman2, because no matter how many GUIs there are, command line is king.

Hoffman2:UNIX Tutorial

Quotas

Resources are not infinite, and disk space is a resource. Find out how to manage your disk space usage to stay under quota.

Hoffman2:Quotas

Profile

You have an account, know how to get there, and now you need to make one last step for you account to be fully usable. Time to get access to all the fun computation tools.

Hoffman2:Profile


Computing

You can find your way through Hoffman2, now it is time to start making things happen.

Software Tools

You've got your account, you are logged on, now how do you get to using a real software tool?

Hoffman2:Software Tools

Submitting Jobs

Now you have the tools, but how do you ask Hoffman2 to run them for you as a job? Since you aren't supposed to be running them on a login node...

Hoffman2:Submitting Jobs

Monitoring Jobs

Right after they zap their robot monster to life, every mad scientist wishes they had the tools to check on or stop their creation. Now that you can submit jobs, you need to be able to check on them and stop them if they start terrorizing downtown Tokyo.

Hoffman2:Monitoring Jobs

Interactive Sessions

Some software tools need you to interact with them while they work. Other times you just need to be able to run your script over and over while you work to eradicate all of its bugs. Enter Interactive Sessions.

Hoffman2:Interactive Sessions


Software

MATLAB

How to use MATLAB on the cluster. It is easier than you think. (Well, maybe...)

Hoffman2:MATLAB

Compiling MATLAB

So you have a MATLAB script, but you don't need to GUI open all night to have it process your data. How to submit MATLAB jobs to Hoffman2.

Hoffman2:Compiling MATLAB

EEGLAB

We try to maintain the three most recent versions of EEGLAB for your convenience. Make sure to add it to your MATLAB path.

Hoffman2:MATLAB:EEGLAB
EEGLAB Jobs

Processing multiple subjects through EEGLAB can be tiring and inconvenient if you do it by hand. Learn how to make scripts that run as jobs leveraging the power of Hoffman2.

Hoffman2:MATLAB:EEGLAB:Jobs

SPM Compiled (Batch)

Maybe FSL isn't your cup of tea for neuroimaging work. SPM is a capable alternative and, even though it is MATLAB based, it has a compiled version that will let you leverage the power of the cluster.

Hoffman2:MATLAB:SPM

R

You are probably a statistician, or you just prefer open source software. Here's how to run R on Hoffman2.

Hoffman2:R

WEKA

If machine learning is your thing, maybe you've heard of WEKA. If not, maybe it will be your new best friend.

Hoffman2:WEKA

FSL

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Hoffman2:FSL


Productivity

How about streamlining some of those tasks, or getting more things done.

Scripts

All of the difficulties you are experiencing now have probably been experienced before by someone else. And for that reason we already have scripts to simplify your life.

Hoffman2:Scripts

Data Transfer

All dressed up with no where to go? That's how Hoffman2 feels if you don't give it any data to work with. Find out how to avoid hurting the Cluster's feelings.

Hoffman2:Data Transfer

Sharing Filesystems

All you want to do is be able to look at your precious data. But it is locked up on Hoffman2 and you want to use tools on your computer to look at it. There's an app for that.

Hoffman2:Sharing Filesystems

Tools

Simple tools that will help your productivity.

Hoffman2:Tools

Mailing List

Information about the the CCN-Hoffman mailing list, including how to join the list.

Hoffman2:Mailing List

FAQ

Wesley's Usage, so you can plan around it and ask him to stop beating the cluster up.

Hoffman2:WTK Usage

Delete/Old Hoffman2 Pages

Hoffman2:Archive