MATLAB: How to create a cluster profile without GUI

Question

I'm trying to run matlab codes on a HPC cluster with MATLAB Distributed Computing Server (Version 6.11 R2017b) installed using PBS Pro.

I can only submit non-interactive jobs, which can lunch matlab and execute codes automatically, so I created a PBS Pro cluster profile without validation (all properties are default) on my NB, with Parallel Computing Toolbox (Version 6.12 R2018a) installed only, then I uploaded the exported setting file, and added the importing command into codes.

this is an example I submit.

the .sh file submiting job:

#!/bin/bash
#PBS -P TRI107382
#PBS -N 0
#PBS -l select=2:ncpus=2
#PBS -l walltime=00:30:00
#PBS -q ctest
cd $PBS_O_WORKDIR
/pkg/matlab/bin/matlab  -nodisplay -r test

test.m:

parallel.importProfile('PBSProProfile')
parallel.defaultClusterProfile('PBSProProfile1');
c = parcluster
c.ResourceTemplate='-l select=2:ncpus=2 -P TRI107382'; %I use two nodes with two cpu cores in each.
set(c, 'NumWorkers', 4);
j = createJob(c);
for i = 1:3
  createTask(j,@test_f,1,{i});
end
submit(j);
wait(j);
j.State
out = fetchOutputs(j)

test_f.m:

function y=test_f(x)
y=x;
end

Then, I got output messages and error messages as follows:

output:

ans =
  'PBSProProfile1_Import_10'
[Warning: The PBSPro cluster type is being used with a possibly incompatible
version of PBS. The use of job arrays has been disabled. The version of PBS
detected was: "14.2.4.20171012010902".] 
[> In parallel.cluster.PBSPro>iCheckPBSProVersion (line 114)
In parallel.cluster.PBSPro (line 63)
In parcluster (line 54)
In test (line 3)] 
c = 
PBSPro Cluster
    Properties: 
                          Profile: PBSProProfile1
                         Modified: false
                             Host: srvc1
                       NumWorkers: Inf
                       NumThreads: 1
               JobStorageLocation: /home/u7/gsblovedyt0
                ClusterMatlabRoot: /pkg/matlab
                  OperatingSystem: unix
                  SubmitArguments: 
                 ResourceTemplate: -l select=^N^
                       RcpCommand: rcp
                       RshCommand: pbs_remsh
          CommunicatingJobWrapper: unix
 RequiresMathWorksHostedLicensing: false
    Associated Jobs: 
                   Number Pending: 3
                    Number Queued: 2
                   Number Running: 0
                  Number Finished: 4
ans =
    'failed'

error:

Error using parallel.Job/fetchOutputs (line 1087)
Outputs can only be fetched if the job is in State 'finished'.
Error in test (line 16)
out = fetchOutputs(j)

I think the reason is that because of the difference of PBS Pro's version, the job array is disable, so the job is failed. Therefore I'm seeking a way of creating a PBS Pro cluster profile on the HPC with command-line interface so that the version may be correct. At the login node of HPC, for trial running, I can launch matlab in command-line mode, so I can interactively execute matlab commands, but I don't know how to generate cluster profiles in this way.

Answer 1

Have you tried using the PBS Pro Support Package? You can get it through the Add Ons menu -- just search on "pbs". After you install it, there's a wizard that will help you build the profile. It will take care of connecting to the submit node and submitting the job.