Matlab-parallel

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parallel matlab

Parallel matlab comes in two forms.

  • Batch style where many matlab jobs are submitted and run on the Barley cluster. foo is an example of this.
  • Parallelism within matlab by use of matlabpools and parallel matlab constructs such as parfor. See below for an example.

Of course, these two can be combined to run many batch jobs, each with a matlabpool of workers.

batch

example single matlab file run via qsub

Here's our helloworld.m:

disp('Hello World');

Here's a command to run that non-interactively. (note we pass -singleCompThread for best performance):

 matlab -nodesktop -singleCompThread < 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

module load matlab
matlab -nodesktop -singleCompThread < /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
#$ -cwd

module load matlab
matlab -nodesktop -singleCompThread < /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 (Parallel Computing Toolbox aka matlabpool)

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

>> feature('numCores')

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/


batch 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 simultaneously, 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

To see if the matlabpools are running correctly, we will submit some jobs and check the output. In this case, its worth noting that 6 jobs ran at same time on 6 different hosts. They all ran to completion and gave same output.

$ qsub ~/matlabfftparcluster.submit
Your job 1232748 ("matlabfft") has been submitted
$ qsub ~/matlabfftparcluster.submit
Your job 1232749 ("matlabfft") has been submitted
$ qsub ~/matlabfftparcluster.submit
Your job 1232750 ("matlabfft") has been submitted
$ qsub ~/matlabfftparcluster.submit
Your job 1232751 ("matlabfft") has been submitted
$ qsub ~/matlabfftparcluster.submit
Your job 1232752 ("matlabfft") has been submitted
$ qsub ~/matlabfftparcluster.submit
Your job 1232753 ("matlabfft") has been submitted

$ qstat
job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID 
-----------------------------------------------------------------------------------------------------------------
1232748 0.36667 matlabfft  bishopj      r     11/28/2013 09:20:51 raring.q@barley18.Stanford.EDU     4        
1232749 0.36667 matlabfft  bishopj      r     11/28/2013 09:21:06 raring.q@barley01.Stanford.EDU     4        
1232750 0.36667 matlabfft  bishopj      r     11/28/2013 09:21:06 raring.q@barley12.Stanford.EDU     4        
1232751 0.36667 matlabfft  bishopj      r     11/28/2013 09:21:06 raring.q@barley02.Stanford.EDU     4        
1232752 0.36667 matlabfft  bishopj      r     11/28/2013 09:21:06 raring.q@barley07.Stanford.EDU     4        
1232753 0.36667 matlabfft  bishopj      r     11/28/2013 09:21:06 raring.q@barley09.Stanford.EDU     4

barley09.stanford.edu



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

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

 Local Cluster

    Properties: 

                          Profile: local
                         Modified: false
                             Host: barley09.stanford.edu
                       NumWorkers: 12

               JobStorageLocation: /afs/ir/users/b/i/bishopj/.matlab/local_cluster_jobs/R2013a
 RequiresMathWorksHostedLicensing: false

    Associated Jobs: 

                   Number Pending: 0
                    Number Queued: 0
                   Number Running: 0
                  Number Finished: 1

>> 
tmpdirforpool =

/tmp/1232749.1.raring.q/tpdeab63e3_5ca0_46b5_86e0_5df6c5b655de

>> >> 
cluster = 

 Local Cluster

    Properties: 

                          Profile: local
                         Modified: true
                             Host: barley09.stanford.edu
                       NumWorkers: 12

               JobStorageLocation: /tmp/1232749.1.raring.q/tpdeab63e3_5ca0_46b5_86e0_5df6c5b655de
 RequiresMathWorksHostedLicensing: false

    Associated Jobs: 

                   Number Pending: 0
                    Number Queued: 0
                   Number Running: 0
                  Number Finished: 0

>> >> 
msg =

setting matlabpool to 4

>> 
cluster = 

 Local Cluster

    Properties: 

                          Profile: local
                         Modified: true
                             Host: barley09.stanford.edu
                       NumWorkers: 4

               JobStorageLocation: /tmp/1232749.1.raring.q/tpdeab63e3_5ca0_46b5_86e0_5df6c5b655de
 RequiresMathWorksHostedLicensing: false

    Associated Jobs: 

                   Number Pending: 0
                    Number Queued: 0
                   Number Running: 0
                  Number Finished: 0

>> >> Starting matlabpool ... connected to 4 workers.
>> >> 
cluster = 

 Local Cluster

    Properties: 

                          Profile: local
                         Modified: true
                             Host: barley09.stanford.edu
                       NumWorkers: 4

               JobStorageLocation: /tmp/1232749.1.raring.q/tpdeab63e3_5ca0_46b5_86e0_5df6c5b655de
 RequiresMathWorksHostedLicensing: false

    Associated Jobs: 

                   Number Pending: 0
                    Number Queued: 0
                   Number Running: 1
                  Number Finished: 0

>> >> >> 
a =

  Columns 1 through 13

     1     1     1     1     1     1     1     1     1     1     1     1     1
     1     1     1     1     1     1     1     1     1     1     1     1     1
     1     1     1     1     1     1     1     1     1     1     1     1     1
.
.
.

>> >> begin running parfor
>> >> >> done running parfor
>> >> Sending a stop signal to all the workers ... stopped.
>>

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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