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September 9, 2010 1:26pm UTC

Tip: Batch calculations with Matlab + Comsol 4.0a

Hi,

I just wanted to share my experience regarding batch-type (i.e., non-interactive) calculations using comsol 4.0a and the matlab livelink. I lost quite some time trying to run a comsol matlab script (.m file) on a linux cluster, and I thought some people might be interested in hearing the workaround I found.

When working with the cluster, I have two major constraints:
1. I do not have any kind of display (X) support,
2. I have to submit the calculation via a simple bash script.


In 3.5a, running a .m file in batch mode was very easy (At the very least, it was nicely documented : http://www.comsol.com/support/knowledgebase/980/), One would use:

comsol matlab -ml -nodesktop -ml -nosplash -mlr "myscript, exit"

In comsol 4.0a, using something along the lines of

comsol server matlab -nodesktop -nosplash -r myfile

does not lead to similar behavior. First, an xterm is spawned, and the 'nodesktop' matlab runs in this new terminal. The '-r myfile' option is ignored, and matlab does not run my .m file on startup.

To work around the fact that 'comsol server matlab' spawns an xterm, I was told by comsol support to do the following:

1. Start the comsol server
2. Start matlab, and connect to the server using mphstart



To be able to do this within one bash script, I basically had to launch the server in the background. However, I could not use

comsol server &
matlab -nodesktop -nosplash -r myfile

as the server process would stop before matlab could connect to it whenever it was launched as a background process. By using instead

comsol server </dev/null > /dev/null &
matlab -nodesktop -nosplash -r myfile

instead of simply "comsol server &" then the server process is not stopped and you can run matlab, connect to comsol server, and run your .m script, without any user-intervention nor need for X support. Also, the comsol server exits when running ModelUtil.disconnect in Matlab, so I don't leave any process on the compute node..

Hoping this might be useful for someone ;)
By the way, if anyone has a better (cleaner?) way of achieving the same thing, I'd be happy to hear it!

Charles

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September 14, 2010 10:18am UTC in response to Charles Doiron

Re: Tip: Batch calculations with Matlab + Comsol 4.0a

This is a very good tip, i just need it to solve my problem, but as i tried as you suggested.

the command
$comsol server < /dev/null > /dev/null &
does work, while after running this command, you can see there is a 'comsollauncher' process
running in the background, also consuming quite a lot of cpu, though nothing is running at all.
then i run the command
$matlab -nodesktop -nosplash -r file
it gives me an error like
'??? Undefined function or variable 'ModelUtil'.'

Do you guys know what's wrong with it?

Thanks in advance.

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December 7, 2010 2:14am UTC in response to Charles Doiron

Re: Tip: Batch calculations with Matlab + Comsol 4.0a

This is a great tip!

Perhaps one step better, for people running OSX - I've saved the whole thing into it's own symbolic link.

Navigate to /usr/bin, create a file with the text editor of your choice (I used nano, for simplicity's sake). In the file, put in:

#!/bin/bash
comsol server </dev/null> /dev/null &
matlab -nodesktop -nosplash -r 'mphstart'

If it gives you trouble, you might have to use a sudo command to get it to create (as in sudo nano shortcutname).

Finally, you need to give everyone access to run this program, so back in the /usr/bin directory,

chmod +x /usr/bin/shortcutname

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April 6, 2011 12:39pm UTC in response to Shakeeb Bin Hasan

Re: Tip: Batch calculations with Matlab + Comsol 4.0a

Good tip, that also works for Comsol 4.1

But nevertheless: very inconvenient to be honest..
Hopefully there is a better solution in the next version.

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October 26, 2011 3:29am UTC in response to Charles Doiron

Re: Tip: Batch calculations with Matlab + Comsol 4.0a

Hi Charles,

Do you have any idea of running batch process on windows?
I have two files and I want to run them one by one in the way that results of one should be used as initial conditions for the other, is there any way of doing it?

Thanks in advance for any of your help!

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October 26, 2011 1:19pm UTC in response to Charles Doiron

Re: Tip: Batch calculations with Matlab + Comsol 4.0a

Thanks a lot Charles for your feedback!

I have defined the second study step in the same file but could not find any option in the second study to set the results of first study as initial values.(Please see the attached image for the options)

Do you mean that I need to define the whole model again?

Can you please elaborate what do you mean by setting the second file as second study step?

Thanks in advance!

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