Submitting R2017+ Jobs
Wesleyan has obtained a campus wide site license for Matlab since version 2017. Hence there is no need to check out a license and the queue matlab has been removed. You can use version 2017 and onward on all queues in unlimited number off jobs. Your submit script should do something simple like
#!/bin/bash # create this file then submit # submit via 'bsub < run.sh' #BSUB -q tinymem #BSUB -J test #BSUB -o out #BSUB -e err # match maxNumCompThreads(8); in matlab code #BSUB -n 8 # all cores on single host #BSUB -R "span[hosts=1]" export PATH=/share/apps/CENTOS6/matlab/R2019a/bin:$PATH matlab -nodisplay < myJob.m > myJob.log
Submitting R2015a Jobs
2015 Matlab DCE has been uninstalled — Henk 2018/08/30 08:01
MATLAB's Distributed Computing Server R2015a requires CentOS6 so launch on swallowtail or petaltail and use all queues but not hp12.
Ever since Matlab R2008a, I've been copying the “lsf” integration files forward from release to release to get parallel job submissions working for Lava (v1.x). Every upgrade I ask for Lava integration support 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 (see below) and submit it to the scheduler, but with the Distributed Computing Server you can also do it from within Matlab.
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
Integrated with OpenLava 2.2
Using bsub
Once this is working you can also do it via a script ofcourse. Build a simple script run.serial
#!/bin/bash # submit via 'bsub < run.serial' #BSUB -q matlab #BSUB -J test #BSUB -o out #BSUB -e err /home/apps/CENTOS6/matlab/2015a/bin/matlab -nodisplay < ./myJob2015.m > /dev/null
# this is the main matlab invocation which will launch the workers JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME 353128 hmeij RUN matlab swallowtail n33 test Mar 18 14:57 [hmeij@swallowtail matlab]$ ssh n33 top -u hmeij -b -n 1 unloading gcc module top - 14:58:20 up 75 days, 2:29, 1 user, load average: 23.44, 23.27, 23.56 Tasks: 816 total, 17 running, 799 sleeping, 0 stopped, 0 zombie Cpu(s): 59.7%us, 2.3%sy, 0.0%ni, 38.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 264635888k total, 156440960k used, 108194928k free, 221504k buffers Swap: 31999992k total, 24716k used, 31975276k free, 152396920k cached PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 18809 hmeij 20 0 2844m 270m 99m S 112.6 0.1 0:11.76 MATLAB 19021 hmeij 20 0 15560 1700 832 R 5.6 0.0 0:00.08 top 18798 hmeij 20 0 20596 2132 1020 S 0.0 0.0 0:00.01 res 18805 hmeij 20 0 103m 1280 1092 S 0.0 0.0 0:00.00 1426705068.3531 18808 hmeij 20 0 103m 1180 1004 S 0.0 0.0 0:00.00 1426705068.3531 19020 hmeij 20 0 107m 1872 868 S 0.0 0.0 0:00.00 sshd # and the workers appear, note the FROM_HOST [hmeij@swallowtail matlab]$ bjobs JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME 353129 hmeij RUN bss24 n33 b49 Job2.1 Mar 18 14:58 353130 hmeij RUN bss24 n33 b49 Job2.2 Mar 18 14:58 353131 hmeij RUN bss24 n33 b48 Job2.3 Mar 18 14:58
Old pages, might be helpful…
