Differences

This shows you the differences between two versions of the page.

--- cluster:96 [2011/02/09 19:53] – created hmeij
+++ cluster:96 [2015/03/13 17:52] (current) – [Note] hmeij
@@ Line 1: / Line 1: @@
 \\
 **[[cluster:0|Home]]**
+==== Note ====
+You can also run matlab jobs via scripts like other software.
+Create a file with the matlab commands and then create a shell script to submit the job.
+It would look like
+<code>
+#!/bin/bash
+# submit via 'bsub < run.serial'
+#BSUB -q matlab
+#BSUB -J test
+#BSUB -o test.stdout
+#BSUB -e test.stderr
+matlab -no display < my_code.m > /dev/null
+</code>
+==== Matlab 2013a ====
+Is now the default matlab version, just change the paths in scripts below
+ --- //[[hmeij@wesleyan.edu|Meij, Henk]] 2013/03/14 14:57//
 ==== Matlab 2010b ====
@@ Line 11: / Line 41: @@
   * [[http://www.mathworks.com/help/toolbox/distcomp/bqxceii-1.html|Part2]]
-In the examples below the code waits for the results.  Don't do that when submitting jobs, it is just for debug purposes. Change the last 3 lines with this 'get(sched)' and then you exit Matlab interactive session.
+=== Serial 1 ===
+In the example below, the code waits for the results.  Don't do that when submitting jobs, it is just for debugging purposes.
+This old way still works for distributed jobs:
-This old way still works:
 <code>
 % distributed matlab jobs
-% start 'matlab -nodisplay', issue the command 'newSimple'
+% start 'matlab -nodisplay', issue the command 'Simple'
 % set up the scheduler and matlab worker environment
@@ Line 23: / Line 56: @@
 set(sched, 'HasSharedFilesystem', true);
 set(sched, 'ClusterMatlabRoot', '/share/apps/matlab/2010b')
-set(sched, 'SubmitFcn', @distributedSubmitFcn)
+set(sched, 'SubmitFcn', @lsfSimpleSubmitFcn)
 % specify location for worker output
@@ Line 34: / Line 67: @@
 % submit job, wait for jobs to finish, fetch output
 submit(j)
 % WARNING: this may hang if the workers are busy!
 waitForState(j)
 results = getAllOutputArguments(j);
 results{1:5}
+% better to do it like Simple2.m
 </code>
+=== Serial 2 ===
+After you submit the job, you can exit matlab.
+<code>
+% distributed matlab jobs
+% start 'matlab -nodisplay', issue the command 'Simple2'
+% set up the scheduler and matlab worker environment
+sched = findResource('scheduler', 'type', 'generic');
+set(sched, 'HasSharedFilesystem', true);
+set(sched, 'ClusterMatlabRoot', '/share/apps/matlab/2010b')
+set(sched, 'SubmitFcn', @lsfSimpleSubmitFcn)
+% specify location for worker output
+set(sched, 'DataLocation', '/home/hmeij/hp/matlab')
+% create job and assign tasks to be done
+j = createJob(sched);
+T = createTask(j, @rand, 1, {{3,3} {3,3} {3,3} {3,3} {3,3}});
+% submit job, then exit matlab interactive session
+submit(j)
+get(sched)
+</code>
+=== Parallel ===
+Slightly different syntax.  Adjust your number of workers values based on some benchmarking, not always do the most workers finish a job in the shortest amount of time.
+<code>
+% parallel matlab jobs
+% start 'matlab -nodisplay', issue the command 'Simplep'
+% set up the scheduler and matlab worker environment
+sched = findResource('scheduler', 'type', 'generic')
+set(sched, 'HasSharedFilesystem', true);
+set(sched, 'ClusterMatlabRoot', '/share/apps/matlab/2010b')
+set(sched, 'ParallelSubmitFcn', @lsfParallelSubmitFcn)
+% specify location for worker output
+set(sched, 'DataLocation', '/home/hmeij/hp/matlab')
+pj = createParallelJob(sched);
+set(pj, 'MaximumNumberOfWorkers', 8)
+set(pj, 'MinimumNumberOfWorkers', 8)
+T = createTask(pj, @rand, 1, {{300,300}});
+% submit job, wait to finish, get status jobs, gather results
+submit(pj)
+get(sched)
+% you can now exit matlab
+% at system prompt type 'bjobs'
+</code>
 \\
 **[[cluster:0|Home]]**