MATLAB Parallel Computing Toolbox (PCT)
Alternative to dfeval
This page demonstrates an effective alternative to the MATLAB Parallel Computing
Toolbox's dfeval method for distributed parallel computing.
Distributed parallel computing, or task-parallel computing, is a special type
of parallel computing in which the tasks are independent of each other and
hence can be processed individually.
The
alternative method is described in the Katana's multiple_matlab_tasks webpage.
Its advantages are: 1) no learning of MATLAB PCT is required; 2) No PCT or worker licenses are required.
Included below are the specifics of applying that to the example
of solving multiple linear algebraic systems.
There are three scripts required to accomplish the goal:
- The first is a matlab function that solves a linear system
function myfunc(M, C, i)
% Solves a linear system of Ax = b
% Multiple systems are solved in parallel; each on a separate worker.
% Companion scripts used: submitmjobs and run_matlab_job
% This demonstrates the use of SCV's parallel method in place of
% MATLAB Parallel Computing Toolbox's dfeval
[A, x, b] = linearSystem(M, C, i) % compute coefficient matrices
y = A\b % solves Ay = b; y should equal x
- Next, a run_matlab_job shell script is needed to run the myfunc m-file
defined above
#!/bin/csh
# this script is a companion script for submitmjobs for MATLAB apps
unsetenv DISPLAY
@ rank = $MATLAB_RANK
@ size = $MATLAB_N
# IMPORTANT: DONOT indent any of the below statements
matlab -nojvm >! myoutput_$rank << MATLAB_ENV
% The below works like a script m-file between MATLAB_ENVs
i = $rank + 1 % define index i
n = $size; % matrix size
M = rand(n); % n x n random number matrix
C = ones(n, 1); % define array c
myfunc(M, C, i) % how to handle a function m-file
exit % don't forget to exit
MATLAB_ENV
- Finally, a submitmjobs shell script is responsible for submitting
jobs to the batch queue
#!/bin/csh
#
#Usage: submitmjobs ntasks batch_script "SGE options such as wallclock limit"
# ntasks -- the number of tasks
# batch_script -- batch script, see run_matlab_job for MATLAB app
# The OPTIONAL input (in red) must be valid SGE batch parameters.
# Example: To submit 4 tasks with run_matlab_job and 9-hour wallclock limit
# katana% submitmjobs 4 run_matlab_job "-l h_rt=09:00:00"
#
# The Sun Grid Engine batch preserves the current dir in batch.
# A different dir may also be used
# cd my_dir
@ ntasks = $1
set batch_script = $2
set options = "$3"
@ size = 3
@ rank = 0
while ($rank < $ntasks)
setenv MATLAB_RANK $rank
setenv MATLAB_N $size
qsub $options -V $batch_script
@ rank++
end
- Example.
katana% submitmjobs 4 run_matlab_job
Your job 62446 ("run_matlab_job") has been submitted
Your job 62447 ("run_matlab_job") has been submitted
Your job 62448 ("run_matlab_job") has been submitted
Your job 62449 ("run_matlab_job") has been submitted
The four independent tasks are submitted as four single processor jobs. The
output, as specified in run_matlab_job, go to myoutput_1,
myoutput_2, myoutput_3, myoutput_4, respectively.
- The m-file linearSystem, defined in the Katana PCT page, is
included below for your convenience
function [A, x, b] = linearSystem(M, C, i)
%function [A, x, b] = linearSystem(M, C, i)
% Returns matrices of a linear algebraic system Ax=b
% M -- matrix
% C -- a vector used to generate the solution
% i -- number used to generate solution x;
% in this example, pass in the for-loop index
A = M + M'; % A is real and symmetric
x = i*C; % define solution
b = A * x; % Ax = b is the RHS of linear system
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