How to run a job on a remote cluster?

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Ryan
Ryan 2014-10-4
评论： Aleksander Lidtke 2015-8-24
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.
  1 个评论
Aleksander Lidtke
Aleksander Lidtke 2015-8-24
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.

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回答（1 个）

Edric Ellis
Edric Ellis 2014-10-6
Parallel Computing Toolbox relies on Java, so you should omit the -nojvm flag from your matlab command-line.
  2 个评论
Ryan
Ryan 2014-10-6
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
Edric Ellis 2014-10-6
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.

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