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Question :
How do I setup and run a parallel Matlab batch job on the HPCVL clusters?
Category Matlab Interview Questions
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Added on 4/28/2009
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Answers:

In most cases, you will run Matlab in parallel "Batch" mode on our clusters. Since you have to have access to Matlab outside of the HPCVL license, most interactive work could be done elsewhere, whereas the computationally intensive runs can be executed on HPCVL clusters.

Production jobs on HPCVL clusters are submitted via the GridEngine, which is a load-balancing software. To obtain details, read our Gridengine FAQ . For a Matlab batch job, this means that you have to prepare your Matlab setup to interface with GridEngine.

To setup running parallel jobs, you need to create a "Parallel Configuration" in Matlab. This needs to be done only once. First, you call a Configuration Manager by selecting the Parallel tab and the Manage Configurations sub-tab in the Matlab GUI. In the Configuration Manager Window, select File -> New -> generic to add a new configuration. Youu will be given a Generic Scheduler Configuration Properties window, and need to fill in the following items:

* Choose a Configuration name (for instance SGE), and enter it in the corresponding text box.
* Into the (ClusterMatlabRoot) box, enter /opt/matlab/R2008b/64bit.
* Into the (ClusterSize) box, enter 16.
* Into the (ParallelSubmitFunction) box, enter {@sgeParallelSubmitFcn,'sfnode0.hpcvl.queensu.ca','/scatch'}.
* Into the (SubmitFunction) box, enter {@sgeSubmitFcn,'sfnode0.hpcvl.queensu.ca','/scatch'}.
* In the (ClusterOsType) tab, select unix.
* In the (HasSharedFileSystem) tab, select True if you are setting up Matlab on an HPCVL node, and False if you are setting up on a remote system.

After making these entries, you select from the main Matlab window Parallel -> Select Configuration -> SGE (assuming you called the new configuration SGE. You should also go back ionto the Configuration Manager by selecting Parallel -> Manage Configurations and select SGE as a default. The Configuration Manager also lets you validate your new configuration by highlighting it and press the Start Validation button.

Once your parallel configuration is properly set up to enable job submission to the HPCVL production clusters, you can create a so-called Matlab Pool by typeing the following command in the main Matlab window or command line:

matlabpool open SGE 8

where we are assuming that you called the configuration SGE and want to run you Matlab program with 8 processors. Note that you should not select more than 16 processes because that was the ClusterSize limit defined in the configuration SGE.

At this point Matlab will submit a reservation of 8 processors to the Grid Engine, and SGE will schedule it when the requested resources (i.e. enough processors and licenses) are available. Of course, you have not yet defined what you want to run with these 8 processors. Let us assume you have a parallel Matlab program, for instance the following simple mywave.m:

parfor i=1:1024
A(i) = sin(i*2*pi/1024);
end

which computes 1024 points in a sinewave and stores the result in a vector called "A". You can submit this program by typing

mywave

and it will use the Matlab pool of processes that you just started for execution. Once the program returns from its run (i.e. the prompt re-appears) you don't need the pool anymore and can close it with

matlabpool close

All of these command can be included in a single file, for instance the mywave.m file, and the quence reduces to simply typing



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