why does my job on cluster stop to produce output

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Patrick Laux 2016-4-12

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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/278594-why-does-my-job-on-cluster-stop-to-produce-output

评论： Simone Stünzi 2021-7-9

Hey, I am using parallel toolbox on a linux cluster (istan nodes and SLURM scheduler). The main routine (the parfor loop section) looks as follows. An 2-d array (MASKE) is used to extract time series which have values, and the function core_eQM is applied on these time series: ...

cd $WORKDIR
pc = parcluster('local')
pc.JobStorageLocation = strcat('$WORKDIR/',getenv('SLURM_JOB_ID'))
% start the matlabpool with maximum available workers
% control how many workers by setting ntasks in your sbatch script
 matlabpool(pc, getenv('SLURM_CPUS_ON_NODE'))
...
pardim=size(MASKE,2);
XX1=NaN(7305,pardim);
parfor ii=1:pardim
     if ~isnan(MASKE(1,ii))
         fprintf('%i \t \n', ii);    %shows me progress of job (creates files, which are empty)
            if meth == 1;
              xx1 = core_eQM(squeeze(VARIABLE_BSE(ii,jj,1:3653)),squeeze(WRF_VARIABLE(ii,jj,1:3653)),squeeze(WRF_VARIABLE(ii,jj,3654:7305)))
              elseif meth == 2
            ...
            end
   end
end

Now, I use the following script to submit it on the cluster:

#!/bin/bash
#SBATCH --job-name=imat_par_test
#SBATCH --output=matlab_parfor.out
#SBATCH --error=matlab_parfor.err
#SBATCH --partition=ivy
#SBATCH --time=72:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=20
source /etc/profile.d/00-modules.sh
module load app/matlab2014b
cd $WORKDIR
# Create a local work directory
mkdir -p $WORKDIR/$SLURM_JOB_ID
#cd $WORKSDIR/$SLURM_JOB_ID
# Kick off matlab
matlab -nodesktop < script_apply_BC.m &
#wait
# Cleanup local work directory
rm -rf $WORKSDIR/$SLURM_JOB_ID

At the beginning (first few hours) the job runs fine. The size of pardim is 420. After pardim reaching approx. 250, the procedure slows down and finally does not "continue", i.e. the job is still running without producing output files. Thus, no problems are reported in the matlab_parfor.err file. I do not know exactly how I can analyse the problems in this case.

Any ideas?