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Revision as of 18:53, 27 November 2013

getting list of available matlab versions

$ module spider matlab

  --------------------------------------------------------------------------------------------------------------------
  matlab:
  --------------------------------------------------------------------------------------------------------------------
    Description:
      MATLAB and toolboxes

     Versions:
        matlab/r2012b
        matlab/r2013a

  --------------------------------------------------------------------------------------------------------------------
  To find detailed information about matlab please enter the full name.
  For example:

     $ module spider matlab/r2013a
  --------------------------------------------------------------------------------------------------------------------

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 on corn

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

A good way to speed up your matlab code on barley is to submit your matlab job with the shm parallel environment. The parallel environment is specified with -pe shm 4 below. The number you specify after shm will be the number of cores allocated to your job (all from the same host). In this case we are asking for 4 cores, which then become workers in a matlab pool.

There is a problem that frequently occurs with matlab if you run many jobs which all use matlab pools. Matlab is naive and does not handle having multiple instances running at the same time. To allow many matlabpools to be run simulataneously, use the following code to setup your pool. You may substitute any number between 1 and 12 for the number of cores (12 being the max matlab will let us use with current license).

#!/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

example session:

$ module load matlab
$ matlab -nodesktop
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 1984-2013 The MathWorks, Inc.
                                        R2013a (8.1.0.604) 64-bit (glnxa64)
                                                 February 15, 2013

No window system found.  Java option 'MWT' ignored.
 
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
 
>> cd /farmshare/software/non-free/MATLAB-R2013a/tomlab
>> startup
The TOMLAB v7.9 directory is /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab
Found the base path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/base
Found the cgo path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/cgo
Found the testprob path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/testprob
Found the examples path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/examples
Found the optim path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/optim
 
Warning - optimization toolbox drop-in replacements
Remove tomlab\optim from path to disable
 
Found the mex path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/mex
Found the splines path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/splines
Found the quickguide path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/quickguide
Found the MAD path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/mad
Found the lib path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/lib
Found the usersguide path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/usersguide
Found the ampl path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/ampl
Found the common path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/common
Found the finance path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/finance
Found the modellib path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/modellib
MAD successfully installed
Found the PROPT path as /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/propt
Found the TOMSYM path as /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/tomsym
Found the modellib path as  /srv/zfs01/software/non-free/MATLAB-R2013a/tomlab/modellib
 
Run tomlablic to display license information
Done with setting TOMLAB paths
>> cd quickguide
>> nllsQG  
===== * * * =================================================================== * * *
TOMLAB - Stanford University Ac. department  602044. Valid to 2100-01-01
=====================================================================================
Problem: ---  1: Gisela                         f_k     103.648860373704110316
                                              f(x_0)    103.652176276833472457

Solver: clsSolve.  EXIT=0.  INFORM=1.
Fletcher-Xu Hybrid Method. Modified Gauss-Newton - BFGS
Optimal solution found    
Iteration points are close

ResEv   126 JacEv   118 Iter   11 
CPU time: 0.480000 sec. Elapsed time: 0.932415 sec. 
>>

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