MATLAB: Adapting pattersearch algorithm to use with distributed computing server.

Question

I use a pattern search algorithm in the simulink toolbox to estimate a set of parameters.

Let's say I have a matlab file that opens a matlabpool and calls pattern search algorithm:

– main.m {

   %main calls pattern search
   matlabpool open
   options = psoptimset('UseParallel', 'always')
   X0 = [0.5 0.5];   % Starting point
  [x,fval] = patternsearch(@simple_objective(x),X0)
}

I send it to the hpc cluster using the pbs file as follows:

% PBS file

    #PBS -l nodes=12
    #PBS -l walltime=240:00:00
    #PBS -j oe
    #PBS -l pmem=5gb
    #PBS -q starxf
    cd ..
    matlab -nosplash -nodisplay -r main.m

How can I change this file to use the distributed computing toolbox.

I guess I could not just change the last line to dmatlab ? i.e.

    cd ....
    dmatlab main.m

I understand how simple examples work when a parfor loop is transformed using createTask and then an *.m file is called with dmatlab. But I am new to parallel computing and cannot really wrap my mind about how to do it using the distributed matlab server.

Answer 1

Firstly, you need to set up a parallel configuration to allow Parallel Computing Toolbox to talk to your PBS cluster. You may need to refer to the MATLAB Distributed Computing Engine documentation to do this, http://www.mathworks.com/help/mdce/index.html. Once you've validated you cluster profile, you should be able to simply remove the 'matlabpool open' line from main.m, and then submit a batch job like this:

cluster = parcluster('myPBSProfile');
job = batch(cluster, 'main', 'Pool', 11);
wait(job);
load(job)

See also the documentation for batch.