Difference: MatLab (5 vs. 6)

Revision 62015-09-09 - dpane

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Matlab

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Running Matlab on the headnode

Matlab Distributed Computing toolbox/server is installed on psych-o and this requires running Matlab on the head node due to how it integrates with PBS. Otherwise, users should avoid running Matlab on the head node for processing.

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Interactive Matlab Sessions

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When running Matlab interactive, users should avoid running it on the head node. Instead, they should request an interactive session through the PBS job scheduler.
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When running Matlab interactively, users should avoid running it on the head node. Instead, they should request an interactive session through the PBS job scheduler. Since running Matlab on Psycho using an interactive session has been painfully sluggish and unusable, (Apparently there is a bug or problem using PBS job scheduler and Matlab, we have a method you can follow to work around this problem.

Note: Users are not permitted to log onto a cluster backend node from the psych-o head node without having a PBS job on that particular node. Users would get this response similar to this:
[dpane@psych-o ~]$ ssh -Y compute-0-15 
Connection closed by 10.1.1.246

 
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[<username@headnode> ~]$ qsub -I -X -l nodes=1:ppn=1 
qsub: waiting for job <some job name> to start qsub: job <some job name> ready   
[<username@compute node> ~]$

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But, if a user initiates a pbs session using qsub to receive an interactive session (NOTE: Keep in mind that walltime remains important. Once your PBS Interactive session ends, your ssh session along with any other processes will be killed automatically.):

[dpane@psych-o ~]$ qsub -I -X
qsub: waiting for job 2462.psych-o.hpc1.cs.cmu.edu to start
qsub: job 2462.psych-o.hpc1.cs.cmu.edu ready

 
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You can then run Matlab and any other interactive commands you would like:
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The can the You can then use another psych-o shell to ssh to the node that you have that interactive session or PBS job:
[dpane@psych-o ~]$ ssh -Y compute-0-15 
Last login: Wed Sep 9 15:40:53 2015 from psych-o.local
Rocks Compute Node
Rocks 6.0 (Mamba)
Profile built 18:20 17-Jun-2015

Kickstarted 18:47 17-Jun-2015
[dpane@compute-0-15 ~]$

 
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[username@<compute node> ~]$ pwd
/home/<username>
[username@<compute node> ~]$ module avail

----------------------------------------------------- /usr/share/Modules/modulefiles ----------------------------------------------------------
dot                 glx-indirect        matlab-8.1          module-info         python27            rocks-openmpi
freesurfer          matlab-7.13         matlab-8.1-toolbox  modules             qt-4.8.2            use.own
fsl-5               matlab-7.13-toolbox module-cvs          null                qt-4.8.5

----------------------------------------------------- /etc/modulefiles ---------------------------------------------------------------------
openmpi-x86_64

[username@<compute node> ~]$ module load matlab-7.13
[username@<compute node> ~]$ matlab
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Users can then use that session to proceed to run Matlab in an interactive way:
[dpane@compute-0-15 ~]$ pwd
/home/<username>
[dpane@compute-0-15 ~]$ module avail

----------------------------------------------------- /usr/share/Modules/modulefiles ----------------------------------------------------------
dot                 glx-indirect        matlab-8.1          module-info         python27            rocks-openmpi
freesurfer          matlab-7.13         matlab-8.1-toolbox  modules             qt-4.8.2            use.own
fsl-5               matlab-7.13-toolbox module-cvs          null                qt-4.8.5

----------------------------------------------------- /etc/modulefiles ---------------------------------------------------------------------
openmpi-x86_64

[dpane@compute-0-15 ~]$ module load matlab-7.13
[dpane@compute-0-15 ~]$ matlab &
  When you are done with your interactive commands, you can use the exit command to end the job:
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[username@<compute node> ~]$ exit

Non-interactive Matlab Sessions

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[dpane@compute-0-15 ~]$ exit


Non-interactive Matlab Sessions

  Matlab interactive mode can be used to take advantage of the integrated environment. But, it can also be run in a non-interactive mode for "batch processing" and to take advantage of cluster computing resources. If fact, the preferred mode of operation for Matlab on our cluster is non-interactive.
 
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