Run matlabpool and parfor with qsub on torque

I am not able to create a matlabpool on a cluster. I hope somebody can help me.

This is my code...

clear all
close all
clc

fid = fopen('output.txt','wt');
fprintf(fid,'output \n');
fprintf(fid,'###')
fprintf(fid,strcat(pwd,'\n'));
fprintf(fid,'###')

p = rand(1,10);
q = ones(10);
save('pqfile.mat','p','q')

W = [.41 .99 .51 .32 .15 .45 .38 .32 .36 .29 .21];
DG = sparse([6 1 2 2 3 4 4 5 5 6 1],[2 6 3 5 4 1 6 3 4 3 5],W)
[dist,path,pred] = graphshortestpath(DG,1,6)

fprintf(fid,strcat(num2str(dist),'\n'))
fprintf(fid,'###')
fprintf(fid,strcat(num2str(path),'\n'))
fprintf(fid,'###')
fprintf(fid,strcat(num2str(pred),'\n'))
fprintf(fid,'###')

tic
for i=1:10
    i
    eig(rand(1000));
end
a = toc

if matlabpool('size') == 0 %%%%%THIS IS LINE 35 %%%%
    matlabpool open 2
end
tic
parfor i=1:10
    i
    eig(rand(1000));
end
b = toc
matlabpool close

fprintf(fid,strcat(num2str(a),'\n'))
fprintf(fid,'###')
fprintf(fid,strcat(num2str(b),'\n'))
fprintf(fid,'###')
fclose(fid);

I have written this code on an Ubuntu-machine in Matlab 2013b. I used the Application Compiler to create a standalone program in which all required toolboxes are present.

I use qsub to launch the next bit of code.

#!/bin/bash
#PBS -m a
#PBS -l nodes=1:ppn=2
echo "Hello world!"
for_testing/run_main01parfor.sh /tools/matlab/2013b/x86_64 > for_testing/log.txt 2>&1

The log-file contains the information below...

Error using matlabpool (line 151)
Undefined variable "com" or class "com.mathworks.toolbox.distcomp.pmode.SessionFactory.getCurrentSession".

Error in main01 (line 35)

MATLAB:undefinedVarOrClass

Is this related to a missing toolbox on the server or is it something else? Can this be solved on my side or is this problem related to the way the cluster has been designed?

[Harsheel]

Usually this error occurs if the application is executed against MATLAB that does not have the Parallel computing toolbox (PCT) installed. Does the installation at '/tools/matlab/2013b/x86_64' have PCT? If you've MATLAB installed there then, you can open it and check the output of typing:

    ver

[Lu Maz]

ver when I run Matlab on the cluster...

----------------------------------------------------------------------------------------------------
MATLAB Version: 8.2.0.701 (R2013b)
MATLAB License Number: ••••••
Operating System: Linux 3.2.0-4-amd64 #1 SMP Debian 3.2.54-2 x86_64
Java Version: Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
----------------------------------------------------------------------------------------------------
MATLAB                                                Version 8.2        (R2013b)
Simulink                                              Version 8.2        (R2013b)
Control System Toolbox                                Version 9.6        (R2013b)
Database Toolbox                                      Version 5.0        (R2013b)
MATLAB Builder JA                                     Version 2.3        (R2013b)
MATLAB Coder                                          Version 2.5        (R2013b)
MATLAB Compiler                                       Version 5.0        (R2013b)
Neural Network Toolbox                                Version 8.1        (R2013b)
Optimization Toolbox                                  Version 6.4        (R2013b)
Signal Processing Toolbox                             Version 6.20       (R2013b)
Simulink Coder                                        Version 8.5        (R2013b)
Statistics Toolbox                                    Version 8.3        (R2013b)
Symbolic Math Toolbox                                 Version 5.11       (R2013b)

No PCT! However no bioinformatics toolbox either and the graphshortestpath still works. I compiled the script in the startpost and I always believed all required toolboxes were added to the compiled, standalone program.

So, how is it possible that "graphshortestpath" works and that "matlabpool" does not work? Both related toolboxes are not availabe on the cluster. I used the "which" command to check if a function is present on the cluster. Below is the reuslt.

>> which clear
built-in (/tools/matlab/2013b/x86_64/toolbox/matlab/general/clear)
>> which rand
built-in (/tools/matlab/2013b/x86_64/toolbox/matlab/randfun/rand)
>> which graphshortestpath
'graphshortestpath' not found.
>> which matlabpool
'matlabpool' not found.

[Lu Maz]

I added the "ver" function to the start of the script, which I showed you in the first post.

The output is below. You can see that PCT and bioinformatics toolboxes are present. Both these toolboxes are not installed on the cluster. I guess these toolboxes were added to the standalone program during compilation.

So, it looks like PCT is present, so, why do I get the error I described in my first post?

------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/tools/matlab/2013b/x86_64/runtime/glnxa64:/tools/matlab/2013b/x86_64/bin/glnxa64:/tools/matlab/2013b/x86_64/sys/os/glnxa64
[H[2J----------------------------------------------------------------------------------------------------
MATLAB Version: 8.2.0.701 (R2013b)
MATLAB License Number: unknown
Operating System: Linux 3.2.0-4-amd64 #1 SMP Debian 3.2.54-2 x86_64
Java Version: Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
----------------------------------------------------------------------------------------------------
MATLAB                                                Version 8.2        (R2013b)
Bioinformatics Toolbox                                Version 4.3.1      (R2013b)
Control System Toolbox                                Version 9.6        (R2013b)
Database Toolbox                                      Version 5.0        (R2013b)
Global Optimization Toolbox                           Version 3.2.4      (R2013b)
Image Processing Toolbox                              Version 8.3        (R2013b)
MATLAB                                                Version 8.2        (R2013b)
MATLAB Compiler                                       Version 5.0        (R2013b)
Mapping Toolbox                                       Version 4.0        (R2013b)
Neural Network Toolbox                                Version 8.1        (R2013b)
Optimization Toolbox                                  Version 6.4        (R2013b)
Parallel Computing Toolbox                            Version 6.3        (R2013b)
Signal Processing Toolbox                             Version 6.20       (R2013b)
Statistics Toolbox                                    Version 8.3        (R2013b)
System Identification Toolbox                         Version 8.3        (R2013b)