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Problem with parallel pool

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Francesco Terribile
Francesco Terribile on 8 Oct 2019
Commented: Jason Ross on 9 Oct 2019
I am trying to run from Linux a simple parallel Matlab code :
parfor i=1:10
and I'm doing that with the sh file:
#PBS -S /bin/bash
#PBS -l nodes=1:ppn=2,walltime=24:00:00
#PBS -N parallel_trial.m
#PBS -o out-hostname-XyZ-N1x1-qsub.txt
#PBS -j oe
#PBS -e out-hostname-XyZ-N1x1.txt
/opt/bin/matlab -nosplash -nodisplay < parallel_trial.m > parallel_output.txt 2>&1
The problem is that I get the message 'Starting parallel pool (parpool) using the 'local' profile ...' for minutes, and nothing happens.
If I try to use the command -nojvm, I get the error: Undefined variable "com" or class
Can someone help to fix this problem?


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Answers (1)

Edric Ellis
Edric Ellis on 9 Oct 2019
Don't use -nojvm, Java is required for Parallel Computing Toolbox functionality.
It looks like you're trying to start 4 workers, having already launched a "client" under PBS (or Torque?). Perhaps the scheduler is limiting the resources you're allowed to use - does it work to use parpool(1) instead?


Francesco Terribile
Francesco Terribile on 9 Oct 2019
It works both with 4 and 1 workers, without -nojvm, but it takes almost one hour to start the parallel profile
Jason Ross
Jason Ross on 9 Oct 2019
In your PBS/Torque resource selection, you are asking for 2 processors (ppn="processors per node") on 1 node:
In your code you are trying to start a MATLAB and then four addtitional MATLAB processes with the parpool. So depending on how strict your scheduler is enforcing job limits, you are trying to use five cores when you have asked for two. Are you able to ask for five cores?
I'll also note that there are ways to submit a job to a PBS/Torque cluster if it's been set up to integrate with Parallel Server.

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