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Old   April 27, 2009, 10:47
Default OpenFOAM command from inside MATLAB
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Hello World.

I'm doing some post-processing with MATLAB and need to run the OpenFOAM 'sample' command from within MATLAB.

Unfortunately the MATLAB unix command used like
Code:
unix('sample -time 8');
does not work out, but produced this error:

Code:
>> [s,w]=unix('sample')

s =

     1


w =

sample: /usr/local/matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by sample)
sample: /usr/local/matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /home/gatzka/OpenFOAM/OpenFOAM-1.5.x/lib/linux64GccDPOpt/libfiniteVolume.so)
sample: /usr/local/matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /home/gatzka/OpenFOAM/OpenFOAM-1.5.x/lib/linux64GccDPOpt/libmeshTools.so)
sample: /usr/local/matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /home/gatzka/OpenFOAM/OpenFOAM-1.5.x/lib/linux64GccDPOpt/libsampling.so)
sample: /usr/local/matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /home/gatzka/OpenFOAM/OpenFOAM-1.5.x/lib/linux64GccDPOpt/libtriSurface.so)
sample: /usr/local/matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /home/gatzka/OpenFOAM/OpenFOAM-1.5.x/lib/linux64GccDPOpt/liblagrangian.so)
sample: /usr/local/matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /home/gatzka/OpenFOAM/OpenFOAM-1.5.x/lib/linux64GccDPOpt/libOpenFOAM.so)
sample: /usr/local/matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /home/gatzka/OpenFOAM/OpenFOAM-1.5.x/lib/linux64GccDPOpt/openmpi-1.2.6/libPstream.so)
Do you have any ideas how I can fix this?
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Old   April 29, 2009, 12:31
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As I have found out through the MATLAB Newsgroup this is a problem due to a wrong pointer to GLIB.

I will have to change a setting so MATLAB will not use its own GLIB, but the one needed by OpenFOAM.

To do this I will have to know, where OpenFOAM's GLIB is located!
Can anybody tell me, so I can set the right path?
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Old   April 30, 2009, 02:24
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Hi Sebastian

I believe that you should target the following file:

~/OpenFOAM/ThirdParty/gcc-4.3.1/platforms/linux/lib/libstdc++.so.6

Best regards,

Niels
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Old   June 30, 2010, 10:55
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Hi
I must use Openfoam in a matlab routine. OpenFoam run correcty but when I use this matlab command, unix('simpleFoam'), I have this error message:

/bin/bash: simpleFoam: command not found.

Why?

Thanks
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Old   December 29, 2010, 10:15
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Hello

Please, could you explain how i must change the settings so MATLAB will not use its own GLIB and use ~/OpenFOAM/ThirdParty/gcc-4.3.1/platforms/linux/lib/libstdc++.so.6
Because I would like to launch OF from matlab but i obtain the following error.
interDyMFoam: /MATHWORKS_R2008A/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by interDyMFoam)

Best regards
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Old   December 30, 2010, 10:16
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Greetings to all!

Interesting, I thought this was something that was already solved and well documented... I guess not.

Well, it's somewhat easy, but a bit annoying to use:
Code:
unix('export LD_LIBRARY_PATH=""; $HOME/OpenFOAM/OpenFOAM-1.7.x/bin/foamExec foamInfoExec')
Let me explain:
  1. the first export command will reset the Library search path list. This way, MATLAB's libraries won't get in the way
  2. the long path to foamExec will make it possible to execute the desired solver/utility, in this case foamInfoExec. In other words, it will take care of the bureaucracy needed for run OpenFOAM executables.
In case you don't want to use foamExec (some-rare-times it doesn't work very well ), then you can do it like this as well:
Code:
unix('export LD_LIBRARY_PATH=""; . $HOME/OpenFOAM/OpenFOAM-1.7.x/etc/bashrc; foamInfoExec')
If this feels too cumbersome to go around launching utilities like this, then wrap this command in a function... something like this:
Code:
function result=goGoOpenFOAM(command)
result=unix(['export LD_LIBRARY_PATH=""; . $HOME/OpenFOAM/OpenFOAM-1.7.x/etc/bashrc; ' command])
(Ironically, Inspector Gadget's famous "Go-Go-Gadget" command line came to mind, when I tried to come up with the name for the function )
Then simply use:
Code:
goGoOpenFOAM('foamInfoExec')
Best regards,
Bruno
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Old   December 30, 2010, 14:46
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Many Thanks,

With your explanations it looks like easy, but without them I had not been able to solve.

It works for me,

Best regards and happy new year

Best regards and happy new year
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Old   April 13, 2011, 11:39
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Hi,

I want to use matlab to call openfoam and its solvers. I am using openfoam17x.

I have done the mentioned things in this topic but it did not help. when I just type unix('pisoFoam'). I get messages like:

Quote:
/opt/apps/matlab-R2008b/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by pisoFoam)
when i type this:

Quote:
unix('export LD_LIBRARY_PATH=""; $HOME/OpenFOAM/OpenFOAM-1.7.x/bin/foamExec pisoFoam')
I get:

Quote:
home/OpenFOAM/OpenFOAM-1.7.x/etc/bashrc: line 90: /opt/apps/openfoam//OpenFOAM-1.7.x/bin/foamEtcFile: No such file or directory
what should I do ?
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Old   April 13, 2011, 11:46
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Quote:
home/OpenFOAM/OpenFOAM-1.7.x/etc/bashrc: line 90: /opt/apps/openfoam//OpenFOAM-1.7.x/bin/foamEtcFile: No such file or directory
Read the error message: There is an extra '/' in an environment variable.
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Old   April 13, 2011, 12:06
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Quote:
Originally Posted by l_r_mcglashan View Post
Read the error message: There is an extra '/' in an environment variable.


I do not know where the extra / came from. I have checked the path, that should be correct. but I see that program does not search on the directory where Openfoam is installed, but it searches on other directory where normally applications are installed.
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Old   April 13, 2011, 18:04
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Greetings to all!

The extra slash (usually) doesn't hurt in Linux. The main concern is "/opt/apps/openfoam/" being picked up at "bashrc: line 90".
The question is how did it get there, when you called the version installed at the "$HOME" folder? It seems to me that you have more than one version of OpenFOAM installed in your system. Somehow environment variables from another OpenFOAM installation have contaminated the environment used by MATLAB.

Try the other possibility I listed on the other post, the one that uses bashrc directly. It should give you the exact same error. In case you don't see the elusive dot-space, here's another way to use it:
Code:
unix('export LD_LIBRARY_PATH=""; source $HOME/OpenFOAM/OpenFOAM-1.7.x/etc/bashrc; foamInfoExec')
If this doesn't work either, here is the flame-thrower way to do it:
Code:
unix('env -i HOME=~ $HOME/OpenFOAM/OpenFOAM-1.7.x/bin/foamExec foamInfoExec')
The break down of this command line is as follows:
  • "env -i" will make create new pseudo-shell to use a seriously clean environment;
  • "HOME=~" will jump-start the new environment to include the variable "$HOME" properly defined, which is required by the OpenFOAM scripts.
  • The rest is business as usual

Best regards,
Bruno
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Old   April 14, 2011, 04:28
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Quote:
The extra slash (usually) doesn't hurt in Linux.
I recently had to install OF, and the OF environment variables weren't set due to the HOME env variable having an extra slash at the end.

On another note, interesting that people are running foam through matlab. Why not just do it with a shell script? Is there an advantage to doing it this way?
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Old   April 14, 2011, 06:22
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Quote:
Originally Posted by wyldckat View Post
the flame-thrower way to do it

Bruno
Thank you very much Bruno . Indeed, the flame-thrower did the job .

I will sequentially run openfoam and hereby with matlab I will change some input values for each run. I am not familiar with shell scripting, matlab looks easier for this kind of operations for me.
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Old   October 3, 2011, 06:20
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Quote:
Originally Posted by Daniele111 View Post
Hi
I must use Openfoam in a matlab routine. OpenFoam run correcty but when I use this matlab command, unix('simpleFoam'), I have this error message:

/bin/bash: simpleFoam: command not found.

Why?

Thanks

Dear Daniele,

have you solved your problem?

I have the same your problem and I cannot succeed in solving it.

Your sincerely,

Claudio
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Old   October 3, 2011, 10:59
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Greetings Claudio,

Quote:
Originally Posted by claco View Post
Dear Daniele,

have you solved your problem?

I have the same your problem and I cannot succeed in solving it.
Why did you stop reading at post #4? There are multiple solutions after that post! Did none of them work?

If none of them work, then what errors occur after each possible solution?

Best regards,
Bruno
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Old   September 20, 2012, 14:42
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I tried writing Bruno's "flame thrower" command, with the following result

Code:
unix('env -i HOME=/opt/openfoam211/bin/foamExec foamInfoExec')

fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by fluent3DMeshToFoam)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by fluent3DMeshToFoam)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libmeshTools.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libmeshTools.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libdynamicMesh.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libdynamicMesh.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libtriSurface.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libtriSurface.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libfiniteVolume.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libfiniteVolume.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libfileFormats.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libfileFormats.so)
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Old   September 22, 2012, 17:04
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Greetings Robert,

Apparently something got lost along the way... After all of the details I wrote down, you still didn't notice the discrepancy between the command you posted and the one I wrote months ago?

Mine was:
Code:
unix('env -i HOME=~ $HOME/OpenFOAM/OpenFOAM-1.7.x/bin/foamExec foamInfoExec')
Your command line was:
Code:
unix('env -i HOME=/opt/openfoam211/bin/foamExec foamInfoExec')
Comparing the two, it should be very easy to notice that you're missing a tilde and a space
Code:
unix('env -i HOME=~ /opt/openfoam211/bin/foamExec foamInfoExec')
Best regards,
Bruno
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Old   September 24, 2012, 13:58
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Having corrected the error I am still not having success:

Code:
 >> unix('env -i HOME=~ /opt/openfoam211/bin/foamExec foamInfoExec')
ans =
     0
>> unix('fluent3DMeshToFoam')
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by fluent3DMeshToFoam)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by fluent3DMeshToFoam)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libmeshTools.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libmeshTools.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libdynamicMesh.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libdynamicMesh.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libtriSurface.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libtriSurface.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libfiniteVolume.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libfiniteVolume.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libfileFormats.so)
fluent3DMeshToFoam: /usr/local/Matlab/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /opt/openfoam211/platforms/linux64GccDPOpt/lib/libfileFormats.so)
ans =
     1
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Old   September 25, 2012, 07:35
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Hi Robert,

I guess you didn't read post #6 :
Quote:
Originally Posted by wyldckat View Post
Let me explain:
  1. the first export command will reset the Library search path list. This way, MATLAB's libraries won't get in the way
  2. the long path to foamExec will make it possible to execute the desired solver/utility, in this case foamInfoExec. In other words, it will take care of the bureaucracy needed for run OpenFOAM executables.
In other words: foamInfoExec is an OpenFOAM application that you're meant to replace for the desired solver or utility! It does not prepare the shell environment in MATLAB

As a side note: foamInfoExec use to provide the standard run-time OpenFOAM header, including version number and so on. But since OpenFOAM 2.0, it changed and it will only show the header if the proper arguments are given...

Have fun!
Bruno
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