From FarmShare

Revision as of 14:17, 27 November 2013 (view source) Bishopj (Talk | contribs) ← Older edit		Revision as of 14:27, 27 November 2013 (view source) Bishopj (Talk | contribs) Newer edit →
Line 165:		Line 165:
	hostname		hostname
-
-	grep Cpu /proc/self/status
	echo ""		echo ""

---

Revision as of 14:27, 27 November 2013

Contents 1 first steps 2 interactive MATLAB 3 example single matlab file run via qsub 4 example second matlab file run via qsub 5 PCT 5.1 simple PCT run 5.2 matlab with matlabpools on the barley 6 tomlab

first steps

Per FarmShare software try something like:

module avail
module load matlab

If you're running MATLAB for the first time, it'll try to write some stuff into $HOME/.matlab so make sure you have your AFS tokens or else MATLAB will crash with an undecipherable error message.

As of 9/22/2013 this works on the corn.stanford.edu cluster but NOT on the myth.stanford.edu cluster.

interactive MATLAB

This is the "regular" way to use it, it pops up a GUI.

ssh -X corn.stanford.edu
module load matlab
matlab

If your X11 forwarding is configured correctly, it will pop up the MATLAB gui on your display.

If you don't have X11 forwarding enabled, you'll get an error message like this:

 Warning: No display specified.  You will not be able to display graphics on the screen.

and then you get the cli interface.

If you want the cli interface, just use 'matlab -nodesktop'.

If you want a single-threaded matlab, use something like

 matlab -nosplash -nodesktop -nodisplay -singleCompThread

example single matlab file run via qsub

Here's our helloworld.m:

disp('Hello World');

Here's a command to run that non-interactively:

 matlab -nodesktop < helloworld.m

We want to run this same command via the job scheduling system. Let's write a job script (save this as matlab_example.script)

#!/bin/bash

#$ -N matlab_example
#$ -m bes
#$ -M chekh@stanford.edu
#$ -V

module load matlab
matlab -nodesktop < /farmshare/software/examples/matlab/helloworld.m

Submit the script:

 qsub matlab_example.script

Look at the job status:

 qstat

You should get output file like matlab_example.oXXXXX

Warning: No display specified.  You will not be able to display graphics on the screen.
Warning: No window system found.  Java option 'MWT' ignored

                            < M A T L A B (R) >
                  Copyright 1984-2011 The MathWorks, Inc.
                    R2011b (7.13.0.564) 64-bit (glnxa64)
                              August 13, 2011

 
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
 
> > Hello World

example second matlab file run via qsub

Now we want to make sure we avoid AFS.

Here's our helloworld.m:

disp('Hello World');

Here's a command to run that non-interactively:

 matlab -nodesktop < helloworld.m

We want to run this same command via the job scheduling system. Let's write a job script.

#!/bin/bash

#$ -N matlab_example
#$ -m bes
#$ -M chekh@stanford.edu

module load matlab
matlab -nodesktop < /farmshare/software/examples/matlab/helloworld.m

Submit the script:

 cd /farmshare/user_data/$USER
 qsub -cwd matlab_example.script

Look at the job status:

 qstat

You should get output file like matlab_example.oXXXXX in your current directory

Warning: No display specified.  You will not be able to display graphics on the screen.
Warning: No window system found.  Java option 'MWT' ignored

                            < M A T L A B (R) >
                  Copyright 1984-2011 The MathWorks, Inc.
                    R2011b (7.13.0.564) 64-bit (glnxa64)
                              August 13, 2011

 
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
 
>> Hello World

PCT

We have the Parallel Computing Toolbox, you can use that to parallelize your job across multiple cores in a single machine.

Here's how to write a job using MDCS: http://docs.uabgrid.uab.edu/wiki/MatLab_CLI#Parallel_MATLAB

You can use the "maxNumCompThreads" command (deprecated) to see how many parallel threads you can run. I get "24" on barley, or "8" on corn.

simple PCT run

matlab -nodesktop -r 'maxNumCompThreads'

>> matlabpool ( 'open', 'local', 8)
Starting matlabpool using the 'local' configuration ... connected to 8 labs.
>> 
>> matlabpool size

ans =

     8

Then use 'parfor' instead of 'for'.

matlabpool of size 0 and size 1 are effectively the same, except the latter uses a PCT toolbox license.

Here are some training slides and example code that I copied from http://www.osc.edu/~samsi/sc11edu/

• http://stanford.edu/~chekh/matlab.tar

matlab with matlabpools on the barley

#!/bin/bash

#$ -N matlabfft
#$ -S /bin/bash
#$ -pe shm 4
#$ -l mem_free=500M
#$ -cwd

hostname

echo ""
echo ""
echo ""

module load matlab

matlab -nodesktop <<EOF
cluster = parcluster('local')
tmpdirforpool = tempname
mkdir(tmpdirforpool)
cluster.JobStorageLocation = tmpdirforpool

msg = sprintf('setting matlabpool to %s', getenv('NSLOTS'))
cluster.NumWorkers = str2num(getenv('NSLOTS'))

matlabpool(cluster)

cluster

a = ones(1000,1000)

disp('begin running parfor')
parfor i = 1:10000
  b=ones./a
end

disp('done running parfor')

matlabpool close
EOF

tomlab

We have a TOMLAB license. To start it up:

1. launch matlab r2013a
2. cd to /farmshare/software/non-free/MATLAB-R2013a/tomlab
3. startup

---

Search the farmshare-discuss archives for posts about Matlab.