Parallel computing not working on remote cluster

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John Doe
John Doe 2013-10-28
评论： John Doe 2013-11-1
Hello I have access to a cluster computer located in London and am having trouble getting the program running in parallel. I can get it to run a non-parallel matlab program fine. I submit the code as an SMP job using the documentation provided here:
https://www.hpc.qmul.ac.uk/twiki/bin/view/HPC/SubmittingJobs
I tried using the answer given to a similar question http://www.mathworks.com/matlabcentral/answers/45438-how-to-use-parfor-loop-or-parallel-computation-on-a-cluster
but as well as having the problem of not being able to find my saved files or view the matlab outputs of the batch script (I'm trying to time it using tictoc) it gives this error:
OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors.
OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled".
OMP: Warning #72: KMP_AFFINITY: affinity only supported for Intel(R) processors.
OMP: Warning #71: KMP_AFFINITY: affinity not supported, using "disabled".
Obviously a cluster computer with matlab installed on it must be able to make use of parallel processing but I don't know how. All helplines for this cluster are non-responsive.
  2 个评论
Edric Ellis
Edric Ellis 2013-10-30
It looks like you're not using PCT from your MATLAB client, in which case using the "batch" command wont help you, and you're on your own in terms of staging code and data, and then retrieving it.
Secondly, those warnings appear to be just that - warnings. Are you observing problems from some functions that are backed by OMP?
John Doe
John Doe 2013-11-1
Yes, this was sort of a long shot as the solution will be heavily dependent on the Cluster setup. The way this cluster works is that we log in remotely to an SSH shell via Putty. We then have to submit jobs that will execute the programs we want on the cores we have requested, e.g.
#!/bin/sh
#$ -cwd
#$ -V
#$ -pe smp 5 # Request 5 CPU cores
#$ -l h_rt=0:1:0 # Request 1 hour runtime
#$ -l h_vmem=4G # Request 4GB RAM / core
module load matlab/2012b
matlab -nodisplay < test42.m
where test42's content is:
job = batch('testScript', 'Matlabpool', 4);
% Wait for the job to complete execution.
wait(job);
where testScript is a matlab program that runs fine on Apocrita in single-core mode and runs on my desktop fine in multi-core mode.

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