MatLab DCS Examples - Revision history

Tanthony@uab.edu: deprecated Banner

2017-03-10T00:38:16Z

deprecated Banner

← Older revision		Revision as of 00:38, 10 March 2017
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			{{Matlab_deprecated}}

	=== Examples ===		=== Examples ===
	Additional examples and submit scripts available in the [[MATLAB_workshop_2011#Workshop_Demo.27s \| Workshop 2011 demo ]] section.		Additional examples and submit scripts available in the [[MATLAB_workshop_2011#Workshop_Demo.27s \| Workshop 2011 demo ]] section.

Tanthony@uab.edu: added the support and category

2012-03-12T14:09:39Z

added the support and category

← Older revision		Revision as of 14:09, 12 March 2012
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	>> job.destroy		>> job.destroy
	</pre>		</pre>


			{{MATLAB Support}}

			[[Category:MATLAB]]

Tanthony@uab.edu at 14:08, 12 March 2012

2012-03-12T14:08:31Z

← Older revision		Revision as of 14:08, 12 March 2012
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	Your job 294773 ("Job1") has been submitted		Your job 294773 ("Job1") has been submitted
	</pre></ul>		</pre></ul>
	<li>Now that the job has been submitted, instruct MATLAB to wait for the job to complete using [http://www.mathworks.com/access/helpdesk/help/toolbox/distcomp/waitforstate.html waitForState]. MATLAB will show as 'Busy' until the job completes, at which time the >> prompt will appear. You can verify that the job is complete by running the job.State function call. (waitForState is not available in R2012a. Use Job Monitor to check ~~fro~~ state of job on the cluster)		<li>Now that the job has been submitted, instruct MATLAB to wait for the job to complete using [http://www.mathworks.com/access/helpdesk/help/toolbox/distcomp/waitforstate.html waitForState]. MATLAB will show as 'Busy' until the job completes, at which time the >> prompt will appear. You can verify that the job is complete by running the job.State function call. (waitForState is not available in R2012a. Use Job Monitor to check for state of job on the cluster)
	<pre>		<pre>
	>> waitForState(job) % not available on R2012a		>> waitForState(job) % not available on R2012a

Tanthony@uab.edu: waitForState not available on R2012a

2012-03-12T14:08:07Z

waitForState not available on R2012a

← Older revision		Revision as of 14:08, 12 March 2012
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	Your job 294773 ("Job1") has been submitted		Your job 294773 ("Job1") has been submitted
	</pre></ul>		</pre></ul>
	<li>Now that the job has been submitted, instruct MATLAB to wait for the job to complete using [http://www.mathworks.com/access/helpdesk/help/toolbox/distcomp/waitforstate.html waitForState]. MATLAB will show as 'Busy' until the job completes, at which time the >> prompt will appear. You can verify that the job is complete by running the job.State function call.		<li>Now that the job has been submitted, instruct MATLAB to wait for the job to complete using [http://www.mathworks.com/access/helpdesk/help/toolbox/distcomp/waitforstate.html waitForState]. MATLAB will show as 'Busy' until the job completes, at which time the >> prompt will appear. You can verify that the job is complete by running the job.State function call. (waitForState is not available in R2012a. Use Job Monitor to check fro state of job on the cluster)
	<pre>		<pre>
	>> waitForState(job)		>> waitForState(job) % not available on R2012a
	>> job.State		>> job.State

Tanthony@uab.edu: added the submit scripts fro R2012a

2012-03-12T14:05:12Z

added the submit scripts fro R2012a

@@ Line 16: / Line 16: @@
 end
 </pre>
-<li>Next create the rParforWave.m script making sure to change the '''YOUREMAIL''' string to a working email address</li>
+<li>Next create the rParforWave.m script making sure to change the '''YOUREMAIL''' string to a working email address. The following submit script is used in case of Matlab R 2011b or older. </li>
 <pre>
 % Always set these variables
 email           = 'YOUREMAIL';
@@ Line 44: / Line 45: @@
 % >> destroy(job)
 </pre>
 <li>Select cheaha as the parallel configuration by clicking '''Parallel -> Select Configuration -> cheaha''' in the main MATLAB window
 <li>Run the rParforWave.m code by opening the script in the MATLAB editor and clicking the green run arrow

Tanthony@uab.edu: /* Examples */

2011-10-13T14:26:37Z

Examples

← Older revision		Revision as of 14:26, 13 October 2011
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	=== Examples ===		=== Examples ===
	Additional examples and submit scripts available in the [[MATLAB_workshop_2011#Workshop_Demo.27s \| ~~workshop~~ demo ]] section.		Additional examples and submit scripts available in the [[MATLAB_workshop_2011#Workshop_Demo.27s \| Workshop 2011 demo ]] section.
	==== Parfor ====		==== Parfor ====
	This example uses two files:		This example uses two files:

Tanthony@uab.edu: /* Examples */ added link to workshop 2011 demo script section

2011-10-13T14:26:09Z

Examples: added link to workshop 2011 demo script section

← Older revision		Revision as of 14:26, 13 October 2011
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	=== Examples ===		=== Examples ===
			Additional examples and submit scripts available in the [[MATLAB_workshop_2011#Workshop_Demo.27s \| workshop demo ]] section.
	==== Parfor ====		==== Parfor ====
	This example uses two files:		This example uses two files:

Jpr@uab.edu: Original content for MatLab DCS

2011-09-06T23:40:24Z

Original content for MatLab DCS

New page

=== Examples ===
==== Parfor ====
This example uses two files:
* myWave.m - a script with a parfor loop generates a wave form
* rParforWave.m - the submission script

The job will use 4 total slots/ MATLAB workers on the cluster (3 workers plus the master worker process).

<ol><li>Create the myWave.m script containing this code
<pre>
parfor i=1:1024

A(i) = sin(i*2*pi/1024);

end
</pre>
<li>Next create the rParforWave.m script making sure to change the '''YOUREMAIL''' string to a working email address</li>
<pre>
% Always set these variables
email = 'YOUREMAIL';
email_opt = 'eas'; % qsub email options
s_rt = '00:05:00'; % soft wall time
h_rt = '00:07:00'; % hard wall time
vf = '1G'; % Amount of memory need per task
min_cpu_slots = 2; % Min number of cpu slots needed for the job
max_cpu_slots = 3; % Max number of cpu slots needed for the job

% Configure the scheduler - Do NOT modify these
sge_options = ['-l vf=', vf, ',h_rt=', h_rt, ',s_rt=', s_rt, ' -m ', email_opt, ' -M ', email];
SGEClusterInfo.setExtraParameter(sge_options);
sched = findResource();
% End of scheduler configuration

% start of user specific commands
job = batch('myWave', 'matlabpool', max_cpu_slots, 'FileDependencies', {'myWave.m'});

% The following commands can be run once the job is submitted to view the results
% >> waitForState(job)
% >> load(job, 'A')
% >> plot(A)

% Once the job is complete, permanently remove its data
% >> destroy(job)
</pre>
<li>Select cheaha as the parallel configuration by clicking '''Parallel -> Select Configuration -> cheaha''' in the main MATLAB window
<li>Run the rParforWave.m code by opening the script in the MATLAB editor and clicking the green run arrow
<li>After several seconds you should see output similar to the following in the MATLAB Command Window
<ul><li>The '''job 294773''' is the job number assigned by the Cheaha scheduler
<li>The '''Job1''' is the job name and number used by MATLAB to reference the job. In most cases, this is the number that you'll use to interact with MATLAB to load the results, clean up the job, etc...
<pre>
Your job 294773 ("Job1") has been submitted
</pre></ul>
<li>Now that the job has been submitted, instruct MATLAB to wait for the job to complete using [http://www.mathworks.com/access/helpdesk/help/toolbox/distcomp/waitforstate.html waitForState]. MATLAB will show as 'Busy' until the job completes, at which time the >> prompt will appear. You can verify that the job is complete by running the job.State function call.
<pre>
>> waitForState(job)
>> job.State

ans =

finished
</pre>
<li>Now that the job has completed, to view the results first use the [http://www.mathworks.com/access/helpdesk/help/toolbox/distcomp/load.html load] function to load the workspace variable '''A''' from our batch job:
<pre>
>> load(job, 'A')
</pre>
<li>Next, display the [http://www.mathworks.com/access/helpdesk/help/techdoc/ref/plot.html plot]
<pre>
>> plot(A)
</pre>
[[Image:RParforWave-plot.png]]
<li>Once you are done with the job, make sure to run the [http://www.mathworks.com/access/helpdesk/help/toolbox/distcomp/destroy.html destroy] the job to clean up the space used on the cluster
<pre>
>> job.destroy
</pre>
</ol>

In the case of longer running jobs, you probably don't want to tie up your MATLAB client by using [http://www.mathworks.com/access/helpdesk/help/toolbox/distcomp/waitforstate.html waitForState].

This will allow you to perform other tasks in MATLAB or exit entirely without having to wait for your job to complete.

MATLAB provides a function to load a previously submitted job back into the workspace, [http://www.mathworks.com/access/helpdesk/help/toolbox/distcomp/findjob.html findJob].

In the example above, our MATLAB job name was '''Job1''' and from that we can deduce that the MATLAB job number was '''1'''. It can be loaded as follows (make sure the correct Parallel configuration is selected):
<pre>
>> sched = findResource();
>> job = findJob(sched, 'ID', 1);
>> job.State

ans =

finished
</pre>

It is important to clean up after the job using [http://www.mathworks.com/access/helpdesk/help/toolbox/distcomp/destroy.html destroy] to free up hard disk space on both your desktop and the cluster. Any output that is to be saved should be copied to another location on your Desktop prior to running [http://www.mathworks.com/access/helpdesk/help/toolbox/distcomp/destroy.html destroy].
<pre>
>> findJob(sched, 'ID', 1)
>> job.destroy
</pre>