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http://acesgrid.org/http://acesgrid.org/
Overview

Wiki MarkupThe ACES clusters stands for Alliance for Computational Earth Science (ACES) ad I got access from \ [greg\] by emailing him, and he provided access within 24 hours. This came with an email from the grid system itself with a link to their website with lots of useful information. This includes the times for office hours (Tuesdays from 11:30-1:30) and a list of software.

Information

Their website has some useful information, although it's not perfect. If you have any specific questions, you might find it there.

  http://acesgrid.org/getting_started.html

Some of the information might be old. For example, there are not currently office hours and you should just email [greg] if you need help with something specific. If you sign up for the aces-support list, you will get some emails (although I imagine very infrequently) about this.

I'll just summarize a few things I am aware of.

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The website has some examples of how to submit a job. Try to follow their examples.

From the login (head) node, you can find out about the queue system with the command:

qstat -q

And from the login (head) node, you can find out about the qsub command-line options and what they mean with (if you do this from an interactive node you will get a different manual):

man qsub

Note: You can not qsub when you are logged into an interactive node (qubert), it says "qsub: command not found". Instead, qsub from the headnode head node upon logging in.

This script ran on aces by qsubbing the file below like this:
qsub multiple_scripts1-10

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http://acesgrid.org/matlab.html

However, when I tried to log into geojr.acesgrid.org it didn't let me, so I followed the directions from the above web page with login.acesgrid.org and with -X and that worked. I also had to run it without the '-nojvm' flag when calling matlab.

The non-interface version also works as below:

qsub -I -l nodes=1

module add matlab

matlab

if you want run interactively, you reverse a node:

qsub -I -l nodes=1

Then in the next terminal window, you login as you would normally with -X (maybe not as directed on the above webpage):

ssh -X aces

Then you ssh from aces onto the reserved node:

ssh -X reserved.node.name

This should work and bring up X11 (that's what I'm using):

module add matlab

matlabAnd I imagine that if you wanted to do something else interactively, that the qsub command above would also work.

QIIME

You can also get qiime to work, using the qsub command above to get interactive computing and use:

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It's QIIME version 1.6 (I think) so it's got a few quirks that are different from the version 1.3 that was on beagle. You might need to change some variables names etc, but the QIIME documentation should be helpful for this. I still haven't been able to get anything working as a parallel job.

Space

So I was able to make my own directory in /data/ and /scratch/, but it didn't exist before I made it:

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