Running Matlab on Legion

Matlab on Legion Overview

• Only works within one node so no MPI on Legion.
  • Largest nodes on Legion have 32 cores, but typically 12 or 16 cores.
• Matlab requires exclusive access to the node unless it's running in single threaded mode
  • Use #$ -ac exclusive to request this in your submission script.
• Multi-threading is built in to some Matlab functions
  • Parallel Computing Toolbox is available on Legion for more control of threading
• Speed-up relative to desktop will not always be that great...
  • ...but, array jobs can increase throughput
• Dont't forget to load the matlab module!
  • module load matlab/full/r2015a/8.5

Headless Matlab

Matlab tries by default to open a GUI when you start it, but we don't want this when a job is running on a compute node.

So, instead of typing matlab, we need to supress the GUI like this:

matlab -nodesktop -nodisplay -nosplash

Headless Matlab

We also need to pass a Matlab script file to matlab since we can't use it interactively

Either:

matlab < my_script.m

Or:

matlab -r "run('my_script.m');quit;"

Headless Matlab

So altogether:

matlab -nodesktop -nodisplay -nosplash < my_script.m

Or

matlab -nodesktop -nodisplay -nosplash -r "run('my_script.m');quit;"

Exercise

wget https://raw.githubusercontent.com/UCL-RITS/pi_examples/master/matlab_pi_dir/calcpi.m

1. Download the matlab pi example using the above command and try running it from the command line without the GUI
2. Have a look at the script to see how it works. Can you set an alternative value for n to change the number of slices?

Simple Matlab Submission Script

Job Script:

#!/bin/bash -l
#$ -l h_rt=0:01:00
#$ -l mem=1G
#$ -pe smp 12
#$ -l matlab=1
#$ -ac exclusive
#$ -N My_Job_Name
#$ -wd /home/<your_UCL_id>/Scratch/<job_directory>

module load matlab/full/r2015a/8.5
matlab -nodisplay -nodesktop -nosplash -r "run('my_script.m');quit;"

Important settings for Matlab

Exercise

1. Write a submission script and submit a job to run the calcpi.m script
2. Edit your script to submit an array of four jobs. Use $SGE_TASK_ID to change the number of slices run by calcpi.m

Single thread mode

An alternative to requesting exclusive access to a whole node is to run Matlab in single thread mode:

matlab -nodisplay -nodesktop -nosplash -nojvm -singleCompThread

• nojvm suppresses java virtual machine and is worth considering if you want to optimise Matlab on Legion in general.

Interactive Matlab on Legion

Do not use login nodes for production work

It is actually possible to view the GUI from Matlab running on a login node, but you need an X server.

An X server runs on your local PC and takes care of displaying the GUI, handling mouse and keyboard interaction, and communicating these to the remote server.

We'll be using Exceed because UCL have a licence, but Xming (windows) or XQuartz (Mac) are alternatives.

Setup

We need to set up the X server before logging in to Legion.

1. Find Exceed under programs and start it.
2. Open PuTTY and enter the Legion host name as usual, but also...
3. Go to Connection>SSH>X11 and enable X11 forwarding
4. Click Open, and login to Legion as normal

Interactive Matlab on Legion

On a login node, load a Matlab module and run Matlab without any options.

The Matlab GUI should launch.

Useful for visualising results.

Do not use login nodes for production work