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Submitting R2015a Jobs

Ever since Matlab R2008a, I've been copying the “lsf” files forward from release to release to get parallel job submissions working for Lava (v1.x). Every upgrade I ask for Lava integration files instead of having to use generic integration files.

Well, that era came to an end with R2015a. Got it to work but there are some changes.

First the admin side of things: (there has to a better way)

cd /share/apps/CENTOS6/matlab/2015a/toolbox/distcomp/examples/
# read the READMEs on the way down
cd integration/
cd lsf/
cd shared/
cp -p * /share/apps/CENTOS6/matlab/2015a/toolbox/local/

You can of course write a submit script and submit it to the scheduler, but with the Distributed Computational Server (or whatever it is called) you can also do it from within Matlab.

# put this in a script myJob.m, then call it from within Matlab or type it all in,  or set up a profile

% distributed matlab jobs
% start 'matlab -nodisplay', issue the command 'myJob'

% set up the scheduler and matlab worker environment
cluster = parallel.cluster.Generic('JobStorageLocation', '/home/hmeij/matlab');
set(cluster, 'HasSharedFilesystem', true);
set(cluster, 'ClusterMatlabRoot', '/share/apps/CENTOS6/matlab/2015a');
set(cluster, 'OperatingSystem', 'unix');

set(cluster, 'IndependentSubmitFcn', @independentSubmitFcn);
% If you want to run communicating jobs (including parallel pools), you must specify a CommunicatingSubmitFcn
set(cluster, 'CommunicatingSubmitFcn', @communicatingSubmitFcn);
set(cluster, 'GetJobStateFcn', @getJobStateFcn);
set(cluster, 'DeleteJobFcn', @deleteJobFcn);

% create job and assign tasks to be done
j = createJob(cluster);
createTask(j, @tenfunction, 1, {'log.job1',1,2})
createTask(j, @tenfunction, 1, {'log.job2',3,4})
createTask(j, @tenfunction, 1, {'log.job3',5,6})

% submit job and gather scheduled info
submit(j)
get(cluster)

% you can now exit matlab
% at system prompt type 'bjobs'
[hmeij@swallowtail matlab]$ matlab -nodisplay

                                                     < M A T L A B (R) >
                                           Copyright 1984-2015 The MathWorks, Inc.
                                           R2015a (8.5.0.197613) 64-bit (glnxa64) 
                                                      February 12, 2015           

 
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.             
                                                              

        Academic License

>> myJob

ans = 

 Task with properties: 

                   ID: 1
                State: pending
             Function: @tenfunction
               Parent: Job 1       
            StartTime:             
     Running Duration: 0 days 0h 0m 0s

      ErrorIdentifier: 
         ErrorMessage: 


ans = 

 Task with properties: 

                   ID: 2
                State: pending
             Function: @tenfunction
               Parent: Job 1       
            StartTime:             
     Running Duration: 0 days 0h 0m 0s

      ErrorIdentifier: 
         ErrorMessage: 


ans =
...snip...


ans =

                IndependentSubmitFcn: @independentSubmitFcn
              CommunicatingSubmitFcn: @communicatingSubmitFcn
                      GetJobStateFcn: @getJobStateFcn
                        CancelJobFcn: []
                       CancelTaskFcn: []
                        DeleteJobFcn: @deleteJobFcn
                       DeleteTaskFcn: []
                                Host: 'swallowtail'
                 HasSharedFilesystem: 1
    RequiresMathWorksHostedLicensing: 0
                  JobStorageLocation: '/home/hmeij/matlab'
                   ClusterMatlabRoot: '/share/apps/CENTOS6/matlab/2015a'
                       LicenseNumber: ''
                     OperatingSystem: 'unix'
                          NumWorkers: Inf
                                Type: 'Generic'
                             Profile: ''
                            UserData: []
                                Jobs: [1x1 parallel.job.CJSIndependentJob]
                            Modified: 1

>>
>> quit

@swallowtail matlab]$ bjobs
JOBID   USER    STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
352355  hmeij   RUN   bss24      swallowtail b49         Job1.1     Mar 13 15:09
352356  hmeij   RUN   bss24      swallowtail b49         Job1.2     Mar 13 15:09
352357  hmeij   RUN   bss24      swallowtail b48         Job1.3     Mar 13 15:09

Old pages, might be helpful…


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cluster/137.1426275293.txt.gz · Last modified: 2015/03/13 15:34 by hmeij