Running Multiple MATLAB Tasks

Described in the following is a procedure to run multiple independent MATLAB tasks in a single batch job. Typically, users who want to run MATLAB jobs in this mode do so for parametric studies of the same code under different conditions. These conditions are often controlled by an index or an input file. Since multiple copies of MATLAB are processed concurrently, the computed results from each must be saved in a distinct file. Shown below is a sample batch script that is sufficiently general to accomodate a great variety of situations. This method supercedes an earlier method for the same onjective. It is still available.

1. This new batch script is called mplbatch ("l" stands for Linux to distincguish it from the Katana Cluster version, mpkbatch).

   #!/bin/csh
   # All PBS batch scheduler (on Linux Cluster) commands start with #PBS
   # The following requests 4 processors (see scv.bu.edu for details)
   # It can be overridden, for example, with "qsub mplbatch -l nodes=4:ppn=2"
   #PBS -l nodes=2:ppn=2
   # IMPORTANT: DONOT precede the above with any non-PBS statements
   unsetenv DISPLAY
   echo CWD is $PBS_O_WORKDIR
   echo Nodes assigned are :
   cat $PBS_NODEFILE
   # cd to the dir from which this script is launched; or provide your own
   cd $PBS_O_WORKDIR
   set nproc = `wc -l $PBS_NODEFILE |  awk '{print $1}'`
   echo number of procs is $nproc
   @ rank = 0
   # IMPORTANT: DONOT indent any of the below statements
   foreach node (`cat $PBS_NODEFILE`)
   matlab -nojvm  >! myoutput_$rank << MATLAB_ENV &
   myrank = $rank              % Between MATLAB_ENVs, carry on any MATLAB ops
   outname = ['output.' num2str(myrank)]; % output file name for current proc
   myfunc(myrank,outname)      % a function
   myscript                    % a script
   exit                        % don't forget to exit
   MATLAB_ENV
   @ rank++
   end
   wait
   

   myfunc.m:

   function myfunc(myrank, outname)
   %function myfunc(myrank, outname)
   disp('This is a MATLAB function')
   if myrank == 0
     disp('Perform a task')
   else
     disp('Perform a different task')
   end
   %  can also construct outname here with myrank
   save(outname);   % save data
   

   myscript.m:

   disp('This is a MATLAB script')

   In the above example, four instances of MATLAB (resulting from #PBS -l nodes=2:ppn=2) are launched. The myoutput_* files trap any output sent to the screen by each MATLAB instant.

   Please avoid combining tasks that vary significantly in compute time as the tasks that finish first will wait for the longest task to complete and therefore waste computing resources. Please call or email Kadin Tseng (kadin@bu.edu) if you'd like to explore other possibilities of multiprocessing with MATLAB.

2. Give mplbatch execute attribute

   cootie:~ % chmod +x mplbatch 

3. Submit batch job to the batch queue requesting four processors and a (default) two hours wallclock time.

   cootie:~ % qsub mplbatch

4. You can override the pre-defined PBS parameters such as walltime and processor count with the following, optional, input.

   cootie:~ % qsub mplbatch -l nodes=4:ppn=2 -l walltime=24:00:00