How to run a job on a remote cluster?

I created a bash script that I have uploaded to a remote cluster via scp. In this script I load a Matlab module (version R2014a) which I use to run some Matlab code.

    #$ -pe smp 4  //tells the cluster to provide 4 cores local to a single node
    module load matlab14/R2014a
    matlab -nosplash -nodisplay -r "code I want to run"

Within my Matlab code I am creating a parallel object and running the following (I'm trying to learn how to run a job in parallel on the cluster before writing the real code).

    pool = parpool('local',4);
    parfor k = 1 : 10000
        disp(k); //console input saved is to file to demonstrate I have the general syntax right
    end
    delete(pool);

When I run my code I get the following error

    {^HUndefined variable "com" or class
    "com.mathworks.toolbox.distcomp.pmode.SessionInfo.NULL_SESSION_INFO".

    Error in parpool (line 96)
        sessionInfo =
        com.mathworks.toolbox.distcomp.pmode.SessionInfo.NULL_SESSION_INFO;

    Error in main (line 4)
    pool = parpool('local',4);

    Error in run (line 63)
    evalin('caller', [script ';']);
    }^H
    ^G{^HError: File: /Users/name/scripts/main.m Line: 4 Column: 1
    The input character is not valid in MATLAB statements or expressions.

    Error in run (line 63)
    evalin('caller', [script ';']);
    }^H
    ^G{^HUndefined variable "com" or class
    "com.mathworks.toolbox.distcomp.pmode.SessionInfo.NULL_SESSION_INFO".

    Error in parpool (line 96)
        sessionInfo =
        com.mathworks.toolbox.distcomp.pmode.SessionInfo.NULL_SESSION_INFO;

    Error in main (line 4)
    pool = parpool('local',4);

    Error in run (line 63)
    evalin('caller', [script ';']);
    }^H
    ^G

What might I be doing wrong and how might I fix it? I have been able to run other Matlab scripts but I have not been able to run any that implement parallelization. I checked the cluster and the Parallel Computing Toolbox is present.

[Aleksander Lidtke]

Hi, I just ran into the same issue. My supercomputer help page suggests starting Matlab with -nodisplay -nojvm -nosplash options. It turns out that -nojvm causes this error. The variable com the error message mentions is, in fact, some Java module, so it won't work without the Jave Virtual Machine.

Answer 1

[Edric Ellis]

Parallel Computing Toolbox relies on Java, so you should omit the -nojvm flag from your matlab command-line.

[Ryan]

Yes, you are correct. I had already removed it and forgot to remove it for this post. It did not change the results I was getting though. I have updated my post.

[Edric Ellis]

Hm, the error message that you get (unhelpful though it is) is precisely the error that you see when specifying -nojvm, and I know of no other way to get that error. Perhaps you could try adding

error(javachk('jvm'))

to the start of your script - that will error out if Java is not enabled before you get any further.