Hoffman2: Difference between revisions
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<!-- Anyone new to the lab and using Hoffman2 NEEDS to read the first section to have adequate working knowledge of the system. --> | <!-- Anyone new to the lab and using Hoffman2 NEEDS to read the first section to have adequate working knowledge of the system. --> | ||
== Getting Started == | == Getting Started == | ||
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=== Getting an Account === | === Getting an Account === | ||
You know what it is, now you want to use it. First you need an account. | You know what it is, now you want to use it. First, you need an account. | ||
: [[Hoffman2:Getting an Account]] | : [[Hoffman2:Getting an Account]] | ||
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=== Password-less Logins === | === Password-less Logins === | ||
Log in to Hoffman2 without typing your password every time. | Log in to Hoffman2 without typing your password every time. | ||
: [https://www.hoffman2.idre.ucla.edu/ | : [https://www.hoffman2.idre.ucla.edu/About/FAQ/FAQ.html#set-up-ssh-public-key-authentication Password-less ssh] | ||
== Computing == | == Computing == | ||
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=== Run Your Jobs === | === Run Your Jobs === | ||
You can run your job by starting an interactive session or submitting it with batch mode. | |||
: [[Hoffman2:Submitting Jobs]] | <!--: [[Hoffman2:Submitting Jobs]]--> | ||
<!--: [[Hoffman2:Interactive Mode]]--> | |||
:[[Hoffman2:Interactive_Sessions]] | |||
:[[Hoffman2:Batch Mode]] | |||
:[[Hoffman2:Job Array]] | |||
=== Monitoring Jobs === | === Monitoring Jobs === | ||
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: [[Hoffman2:Monitoring Jobs]] | : [[Hoffman2:Monitoring Jobs]] | ||
=== Interactive Sessions === | <!--=== 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. | 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]] | : [[Hoffman2:Interactive Sessions]]--> | ||
== Software == | == Software == | ||
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How to use MATLAB on the cluster. It is easier than you think. (Well, maybe...) | How to use MATLAB on the cluster. It is easier than you think. (Well, maybe...) | ||
: [[Hoffman2:MATLAB]] | : [[Hoffman2:MATLAB]] | ||
: [[Hoffman2:parpoolexample.m]] | |||
==== Compiling MATLAB ==== | ==== Compiling MATLAB ==== | ||
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=== R === | === R === | ||
You are probably a statistician, or you just prefer open source software. Here's how to run R on Hoffman2. | You are probably a statistician, or you just prefer open-source software. Here's how to run R on Hoffman2. | ||
: [[Hoffman2:R]] | : [[Hoffman2:R]] | ||
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=== FSL === | === FSL === | ||
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. | FSL is a comprehensive library of analysis tools for FMRI, MRI, and DTI brain imaging data. | ||
: [[Hoffman2:FSL]] | : [[Hoffman2:FSL]] | ||
=== Python === | |||
: [[Hoffman2:Python]] | |||
=== Jupyter Notebook === | === Jupyter Notebook === | ||
: [[Hoffman2:JupyterNotebook]] | : [[Hoffman2:JupyterNotebook]] | ||
=== Singularity === | |||
: [[Hoffman2:Singularity]] | |||
=== Git === | |||
: [[Hoffman2:Git]] | |||
== Productivity == | == Productivity == |
Revision as of 21:11, 11 February 2022
A compilation of lab know-how regarding the Hoffman2 Computing Cluster.
Getting Started
Introduction
Hoffman2 is a Computing Cluster at UCLA, find out how it generally works so you know how to use it.
Getting an Account
You know what it is, now you want to use it. First, you need an account.
Accessing the Cluster
Now how do you use that account to access the cluster?
Working in a Linux 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.
Quotas
Resources are not infinite, and disk space is a resource. Find out how to manage your disk space usage to stay under quota.
Environmental Modules
How to get access to CCN-supported software.
Changing Passwords
How to change your Hoffman2 password.
Password-less Logins
Log in to Hoffman2 without typing your password every time.
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?
Run Your Jobs
You can run your job by starting an interactive session or submitting it with batch mode.
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.
Software
MATLAB
How to use MATLAB on the cluster. It is easier than you think. (Well, maybe...)
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.
EEGLAB
We try to maintain the three most recent versions of EEGLAB for your convenience. Make sure to add it to your MATLAB path.
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.
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.
R
You are probably a statistician, or you just prefer open-source software. Here's how to run R on Hoffman2.
WEKA
If machine learning is your thing, maybe you've heard of WEKA. If not, maybe it will be your new best friend.
FSL
FSL is a comprehensive library of analysis tools for FMRI, MRI, and DTI brain imaging data.
Python
Jupyter Notebook
Singularity
Git
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.
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.
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.
Tools
Simple tools that will help your productivity.
Mailing List
Information about the the CCN-Hoffman mailing list, including how to join the list.