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cluster:137 [2015/03/13 19:35]
hmeij [Submitting R2015a Jobs] 		cluster:137 [2019/06/12 17:00] (current)
hmeij07 [Submitting R2017+ Jobs]
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 \\ \\
 **[[cluster:0|Back]]** **[[cluster:0|Back]]**
 +
 +
 +==== 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
 +
 +<code>
 +#!/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
 +
 +</code>
 +
  
  
 ==== Submitting R2015a Jobs ==== ==== 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.+2015 Matlab DCE has been uninstalled 
 + --- //[[hmeij@wesleyan.edu|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. Well, that era came to an end with R2015a. Got it to work but there are some changes.
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 </code> </code>
  
-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.+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 ===
  
 <code> <code>
Line 145: Line 180:
 </code> </code>
  
 +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''
 +
 +<code>
 +
 +#!/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
 +
 +</code>
 +
 +
 +
 +<code>
 +
 +# 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
 +
 +</code>
  
 Old pages, might be helpful... Old pages, might be helpful...
  
   * [[cluster:96|the Matlab 2010b scripts page 02/09/2011]]   * [[cluster:96|the Matlab 2010b scripts page 02/09/2011]]
-  * [[cluster:36|the Running Matlab Jobs page 07/16/2007]] 2007a+  * [[cluster:39|the Running Matlab Jobs page 07/16/2007]] 2007a
  
  
cluster/137.1426275352.txt.gz · Last modified: 2015/03/13 19:35 by hmeij

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