MATLAB

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(New page: We have a trial version of MATLAB Distributed Compute Server until 2011-12-25. It is installed in /mnt/glusterfs/apps/MATLAB/R2011b/bin/matlab Very soon the standard MATLAB install in AF...)
 
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We have a trial version of MATLAB Distributed Compute Server until 2011-12-25.  It is installed in /mnt/glusterfs/apps/MATLAB/R2011b/bin/matlab
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[https://www.mathworks.com/products/matlab.html MATLAB] is a multi-paradigm numerical computing environment and programming language.
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Very soon the standard MATLAB install in AFS will also be R2011b instead of R2011b.
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== Getting Started  ==
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You will need to write your MATLAB code to use the Parallel Computing Toolbox before using the Distributed Computing Server.
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Run <code>module avail</code> to get a list of all software modules, or <code>module spider</code> to get a list of available versions of MATLAB.
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Here's how to write a job using MDCS: http://docs.uabgrid.uab.edu/wiki/MatLab_CLI#Parallel_MATLAB
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<source lang="sh">
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module spider matlab     
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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.
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--------------------------------------------------------------------------------------------------------------------------------
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  matlab:
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--------------------------------------------------------------------------------------------------------------------------------
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    Description:
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      A multi-paradigm numerical computing environment and programming language.
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==simple PCT run==
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    Versions:
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<pre>
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        matlab/r2016b
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/afs/ir.stanford.edu/software/matlab-2011b/bin/matlab -nodesktop -r 'maxNumCompThreads'
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        matlab/r2017a
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>> matlabpool ( 'open', 'local', 8)
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--------------------------------------------------------------------------------------------------------------------------------
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Starting matlabpool using the 'local' configuration ... connected to 8 labs.
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</source>
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>>
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>> matlabpool size
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ans =
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Use <code>module load</code> to set up your environment, and then run <code>matlab</code> to start an interactive session.
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    8
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<source lang="sh">
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module load matlab
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matlab
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</source>
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Then use 'parfor' instead of 'for'.
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If you have not configured a [https://srcc.stanford.edu/farmshare2/connecting remote display] MATLAB will start in text-mode, but the MATLAB desktop is also supported.
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</pre>
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matlabpool of size 0 and size 1 are effectively the same, except the latter uses a PCT toolbox license.
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<source lang="sh">
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ssh -X sunetid@rice.stanford.edu
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module load matlab
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matlab &
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</source>
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== Running MATLAB in Batch Mode ==
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If you have prepared MATLAB code as a program (<code>.m</code>) file you can run it non-interactively.
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<source lang="sh">matlab -nodesktop < program.m</source>
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You can use this method to submit a MATLAB job to a compute node, and you can even include MATLAB code in-line in an <code>sbatch</code> script.
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<source lang=sh>
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#!/bin/bash
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module load matlab
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matlab -nodesktop << EOF
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  % MATLAB code
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EOF
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</source>
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== Using MDCS ==
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MATLAB Distributed Computing Server is supported, and you can submit jobs using up to 127 workers. To set up the cluster, load the <code>matlab</code> module, start MATLAB, and run <code>configCluster</code>. This only needs to be done once.
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Once the cluster has been configured, commands like <code>parcluster</code> should use cluster (rather than local) workers by default. You can get a handle to the cluster using the <code>parcluster</code> command, submit jobs using <code>batch</code> (which returns a handle to the job), and query job state and results using <code>State</code> and <code>fetchOuputs</code>.
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<source lang="matlab">
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c = parcluster;
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j = c.batch(@pwd, 1, {}, 'Pool', 4);
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j.State
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j.fetchOutputs{:}
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</source>
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For a more detailed walkthrough see [[Media:Getting_Started_with_Serial_and_Parallel_MATLAB.pdf|Getting Started with Serial and Parallel MATLAB]].
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Please note that, while multi-node jobs are supported, FarmShare does not have a fast interconnect, so code that requires a lot of communication or synchronization between workers may not fully realize any expected improvement in performance. You may want to restrict your MDCS jobs to a single node, or to 15 (or fewer) workers, when possible.

Latest revision as of 16:46, 15 February 2018

MATLAB is a multi-paradigm numerical computing environment and programming language.

Getting Started

Run module avail to get a list of all software modules, or module spider to get a list of available versions of MATLAB. 

module spider matlab       

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  matlab:
--------------------------------------------------------------------------------------------------------------------------------
    Description:
      A multi-paradigm numerical computing environment and programming language.

     Versions:
        matlab/r2016b
        matlab/r2017a

--------------------------------------------------------------------------------------------------------------------------------

Use module load to set up your environment, and then run matlab to start an interactive session. 

module load matlab
matlab

If you have not configured a remote display MATLAB will start in text-mode, but the MATLAB desktop is also supported. 

ssh -X sunetid@rice.stanford.edu
module load matlab
matlab &

Running MATLAB in Batch Mode

If you have prepared MATLAB code as a program (.m) file you can run it non-interactively. 

matlab -nodesktop < program.m

You can use this method to submit a MATLAB job to a compute node, and you can even include MATLAB code in-line in an sbatch script. 

#!/bin/bash

module load matlab
matlab -nodesktop << EOF
  % MATLAB code
EOF

Using MDCS

MATLAB Distributed Computing Server is supported, and you can submit jobs using up to 127 workers. To set up the cluster, load the matlab module, start MATLAB, and run configCluster. This only needs to be done once.

Once the cluster has been configured, commands like parcluster should use cluster (rather than local) workers by default. You can get a handle to the cluster using the parcluster command, submit jobs using batch (which returns a handle to the job), and query job state and results using State and fetchOuputs. 

c = parcluster;
j = c.batch(@pwd, 1, {}, 'Pool', 4);
j.State
j.fetchOutputs{:}

For a more detailed walkthrough see Getting Started with Serial and Parallel MATLAB.

Please note that, while multi-node jobs are supported, FarmShare does not have a fast interconnect, so code that requires a lot of communication or synchronization between workers may not fully realize any expected improvement in performance. You may want to restrict your MDCS jobs to a single node, or to 15 (or fewer) workers, when possible.

Retrieved from "http://stanford.edu/group/farmshare/cgi-bin/wiki/index.php/MATLAB"
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