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Old   June 25, 2011, 20:46
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  #221
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Bernhard Gschaider
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Quote:
Originally Posted by Aurel View Post
Hi,

the installation of the current pyFOAM version (0.5.5) as a regular user worked fine. I followed the Wiki (http://openfoamwiki.net/index.php/Co...m#Installation).

With the new OF version 2.0.x I've got problems. SimpleFoam doesn't work at all with pitzDaily tutorial.
I receive following message:

"aurel@aurel-desktop:~/OpenFOAM/aurel-2.0.x/run/pitzDaily$ simpleFoam > log & pyFoamPlotWatcher.py log
[1] 5283
Traceback (most recent call last):
File "/home/aurel/OpenFOAM/PyFOAM/bin/pyFoamPlotWatcher.py", line 3, in <module>
from PyFoam.Applications.PlotWatcher import PlotWatcher
ImportError: No module named PyFoam.Applications.PlotWatcher
aurel@aurel-desktop:~/OpenFOAM/aurel-2.0.x/run/pitzDaily$ "

For assistance to find the error I would be very grateful.

Best regards

Marc
At a first glance I'd say that the PyFoam-Library is not in your PYTHONPATH. Test this with

python -c "import PyFoam"

If nothing happens your installation is OK
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Old   June 26, 2011, 04:01
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Hi Bernhard,

thank you for your prompt help.
I got my error:
Wiki gives following path:
export PYTHONPATH=/home/nonroot/my_python/lib/python-2.3/site-packages:$PYTHONPATHAccording to my directories I changed the path.
But in the lib-directory the sub directory was "python2.6" and not "python-2.6".
So the error was just the "-" character.

Best regards

Marc
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Old   July 15, 2011, 08:28
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Tibor Nyers
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Hi,

I can't resolve how to specify the case/logfile name in PlotWatcher.

In my script casePath variable holds the (absolute) path for the directory which should be analyzed.
Decomposer have no complaints with:
Code:
Decomposer(args=["--progress","--method=simple","--n=2,1,1","--delta=1e-4",casePath,2])
With PlotWatcher it gives me SyntaxError:
Code:
PlotWatcher(args=["--solver-not-running-anymore",casePath)
or
Code:
logfile = path.join(casePath,"PyFoamRunner.icoFoam.logfile")
PlotWatcher(args=["--solver-not-running-anymore",logfile)
Thx!
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Old   July 18, 2011, 06:53
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My bad, it was a typo - the ending square bracket of args was missing.
Code:
from PyFoam.Applications.PlotWatcher import PlotWatcher
logfile = path.join(casePath,"PyFoamRunner.icoFoam.logfile")
if (path.isfile(logfile)):
    PlotWatcher(args=["--silent","--solver-not-running-anymore","--hardcopy","--format-of-hardcopy=pdf",logfile])
Another small thing, how can one specify the destination directory where the plots actually lands?
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Old   July 18, 2011, 09:47
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Quote:
Originally Posted by Toorop View Post
Another small thing, how can one specify the destination directory where the plots actually lands?
Currently there is not option for that (main reason: I never needed it ) Your options are:

- have a look wheter the --prefix-hardcopy-option can be abused for that

- write an enhancement bug report and hope for the best

- implement it yourself and submit a patch

Last edited by gschaider; July 18, 2011 at 10:21. Reason: Insert Newlines that were swallowed from the original
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Old   July 19, 2011, 05:30
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Thank you, so I guess it's about time I delve into python coding.
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Old   July 28, 2011, 09:57
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Can someone give me a hint how to use ParsedParameterFile with controlDict. I have checked the "Automatization with pyFoam" pdf, but couldn't deduce the solution.
Code:
controlFile = ParsedParameterFile( path.join(work.initialDir(),"system","controlDict") )

#set a new solver (application) here

conrolFile.writeFile()
PS: I'm creating a script for scalarTransportFoam so it can use precomputed U values from a solved case, not just an initial one from 0. If there's an off-the-shelf solution for this issue, let me know.

Thx!

OMG, I really need a sleep!
Code:
controlFilePath = path.abspath(path.join(casePath,"system","controlDict"))
controlFile = ParsedParameterFile(controlFilePath)
controlFile["application"] = "myFoam"
controlFile.writeFile()

Last edited by Toorop; July 28, 2011 at 11:32. Reason: Solution
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Old   August 4, 2011, 08:45
Default Convergence Problems - pyFoamPlotRunner "--steady-run"
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Hi Foamers

I am really hoping someone can help me with this problem.
I'm using the pyFoamPlotRunner module of PyFoam with the "--steady-run" option (i.e. steady-state problem).

From the attached plot and the output from the solver you can see that the residuals are below the specified tolerances in the fvSolution file:
T: 1e-04
U: 1e-03
pd: 1e-04

The problem is that the pyFoamPlotRunner didn't terminate the simulation.

I get the following msg in the terminal:
"PyFoam WARNING on line 320 of file /usr/local/lib/python2.7/dist-packages/PyFoam/Execution/BasicRunner.py : Stopping run at next write "
But it the continues to run the simulation to the endTime in the controlDict file.

Any possible reason for this ???


Code:
Time = 5995

DILUPBiCG:  Solving for T, Initial residual = 9.96799e-05, Final residual = 9.96799e-05, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1.20307e-05, Final residual = 1.20307e-05, No Iterations 0
DILUPBiCG:  Solving for Uy, Initial residual = 1.1291e-05, Final residual = 1.1291e-05, No Iterations 0
DICPCG:  Solving for pd, Initial residual = 0.000109391, Final residual = 9.08461e-05, No Iterations 3
time step continuity errors : sum local = 3.94991e-05, global = 5.374e-06, cumulative = 0.00253859
ExecutionTime = 109.27 s  ClockTime = 110 s

Time = 5996

DILUPBiCG:  Solving for T, Initial residual = 9.96901e-05, Final residual = 9.96901e-05, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1.26358e-05, Final residual = 1.26358e-05, No Iterations 0
DILUPBiCG:  Solving for Uy, Initial residual = 1.11147e-05, Final residual = 1.11147e-05, No Iterations 0
DICPCG:  Solving for pd, Initial residual = 9.33589e-05, Final residual = 9.33589e-05, No Iterations 0
time step continuity errors : sum local = 4.05917e-05, global = 4.34201e-06, cumulative = 0.00254293
ExecutionTime = 109.28 s  ClockTime = 110 s

Time = 5997

DILUPBiCG:  Solving for T, Initial residual = 9.96888e-05, Final residual = 9.96888e-05, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1.25973e-05, Final residual = 1.25973e-05, No Iterations 0
DILUPBiCG:  Solving for Uy, Initial residual = 1.10894e-05, Final residual = 1.10894e-05, No Iterations 0
DICPCG:  Solving for pd, Initial residual = 9.54102e-05, Final residual = 9.54102e-05, No Iterations 0
time step continuity errors : sum local = 4.14834e-05, global = 2.98703e-06, cumulative = 0.00254592
ExecutionTime = 109.29 s  ClockTime = 110 s

Time = 5998

DILUPBiCG:  Solving for T, Initial residual = 9.96934e-05, Final residual = 9.96934e-05, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1.25635e-05, Final residual = 1.25635e-05, No Iterations 0
DILUPBiCG:  Solving for Uy, Initial residual = 1.10723e-05, Final residual = 1.10723e-05, No Iterations 0
DICPCG:  Solving for pd, Initial residual = 0.000100084, Final residual = 8.60074e-05, No Iterations 3
time step continuity errors : sum local = 3.7395e-05, global = 1.43804e-06, cumulative = 0.00254735
ExecutionTime = 109.31 s  ClockTime = 110 s

Time = 5999

DILUPBiCG:  Solving for T, Initial residual = 9.97056e-05, Final residual = 9.97056e-05, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1.28526e-05, Final residual = 1.28526e-05, No Iterations 0
DILUPBiCG:  Solving for Uy, Initial residual = 1.10423e-05, Final residual = 1.10423e-05, No Iterations 0
DICPCG:  Solving for pd, Initial residual = 8.5294e-05, Final residual = 8.5294e-05, No Iterations 0
time step continuity errors : sum local = 3.70849e-05, global = 2.18425e-07, cumulative = 0.00254757
ExecutionTime = 109.32 s  ClockTime = 110 s

Time = 6000

DILUPBiCG:  Solving for T, Initial residual = 9.97047e-05, Final residual = 9.97047e-05, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1.27986e-05, Final residual = 1.27986e-05, No Iterations 0
DILUPBiCG:  Solving for Uy, Initial residual = 1.10194e-05, Final residual = 1.10194e-05, No Iterations 0
DICPCG:  Solving for pd, Initial residual = 8.84995e-05, Final residual = 8.84995e-05, No Iterations 0
time step continuity errors : sum local = 3.84785e-05, global = -1.15081e-06, cumulative = 0.00254642
ExecutionTime = 109.33 s  ClockTime = 110 s

End
Attached Images
File Type: png Screenshot.png (17.1 KB, 29 views)

Last edited by Logan Page; August 4, 2011 at 09:30. Reason: more info
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Old   August 4, 2011, 09:45
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  #229
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Bernhard Gschaider
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Quote:
Originally Posted by Logan Page View Post
Hi Foamers

I am really hoping someone can help me with this problem.
I'm using the pyFoamPlotRunner module of PyFoam with the "--steady-run" option (i.e. steady-state problem).

From the attached plot and the output from the solver you can see that the residuals are below the specified tolerances in the fvSolution file:
T: 1e-04
U: 1e-03
pd: 1e-04

The problem is that the pyFoamPlotRunner didn't terminate the simulation.
Any possible reason for this ???


Code:
Time = 5995

DILUPBiCG:  Solving for T, Initial residual = 9.96799e-05, Final residual = 9.96799e-05, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1.20307e-05, Final residual = 1.20307e-05, No Iterations 0
DILUPBiCG:  Solving for Uy, Initial residual = 1.1291e-05, Final residual = 1.1291e-05, No Iterations 0
DICPCG:  Solving for pd, Initial residual = 0.000109391, Final residual = 9.08461e-05, No Iterations 3
time step continuity errors : sum local = 3.94991e-05, global = 5.374e-06, cumulative = 0.00253859
ExecutionTime = 109.27 s  ClockTime = 110 s

Time = 5996

DILUPBiCG:  Solving for T, Initial residual = 9.96901e-05, Final residual = 9.96901e-05, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1.26358e-05, Final residual = 1.26358e-05, No Iterations 0
DILUPBiCG:  Solving for Uy, Initial residual = 1.11147e-05, Final residual = 1.11147e-05, No Iterations 0
DICPCG:  Solving for pd, Initial residual = 9.33589e-05, Final residual = 9.33589e-05, No Iterations 0
time step continuity errors : sum local = 4.05917e-05, global = 4.34201e-06, cumulative = 0.00254293
ExecutionTime = 109.28 s  ClockTime = 110 s

Time = 5997

DILUPBiCG:  Solving for T, Initial residual = 9.96888e-05, Final residual = 9.96888e-05, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1.25973e-05, Final residual = 1.25973e-05, No Iterations 0
DILUPBiCG:  Solving for Uy, Initial residual = 1.10894e-05, Final residual = 1.10894e-05, No Iterations 0
DICPCG:  Solving for pd, Initial residual = 9.54102e-05, Final residual = 9.54102e-05, No Iterations 0
time step continuity errors : sum local = 4.14834e-05, global = 2.98703e-06, cumulative = 0.00254592
ExecutionTime = 109.29 s  ClockTime = 110 s

Time = 5998

DILUPBiCG:  Solving for T, Initial residual = 9.96934e-05, Final residual = 9.96934e-05, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1.25635e-05, Final residual = 1.25635e-05, No Iterations 0
DILUPBiCG:  Solving for Uy, Initial residual = 1.10723e-05, Final residual = 1.10723e-05, No Iterations 0
DICPCG:  Solving for pd, Initial residual = 0.000100084, Final residual = 8.60074e-05, No Iterations 3
time step continuity errors : sum local = 3.7395e-05, global = 1.43804e-06, cumulative = 0.00254735
ExecutionTime = 109.31 s  ClockTime = 110 s

Time = 5999

DILUPBiCG:  Solving for T, Initial residual = 9.97056e-05, Final residual = 9.97056e-05, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1.28526e-05, Final residual = 1.28526e-05, No Iterations 0
DILUPBiCG:  Solving for Uy, Initial residual = 1.10423e-05, Final residual = 1.10423e-05, No Iterations 0
DICPCG:  Solving for pd, Initial residual = 8.5294e-05, Final residual = 8.5294e-05, No Iterations 0
time step continuity errors : sum local = 3.70849e-05, global = 2.18425e-07, cumulative = 0.00254757
ExecutionTime = 109.32 s  ClockTime = 110 s

Time = 6000

DILUPBiCG:  Solving for T, Initial residual = 9.97047e-05, Final residual = 9.97047e-05, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1.27986e-05, Final residual = 1.27986e-05, No Iterations 0
DILUPBiCG:  Solving for Uy, Initial residual = 1.10194e-05, Final residual = 1.10194e-05, No Iterations 0
DICPCG:  Solving for pd, Initial residual = 8.84995e-05, Final residual = 8.84995e-05, No Iterations 0
time step continuity errors : sum local = 3.84785e-05, global = -1.15081e-06, cumulative = 0.00254642
ExecutionTime = 109.33 s  ClockTime = 110 s

End
Am staring at the doAnalysis-method of the SteadyConvergedLineAnalyzer-class (that is where the action isa) and not 100% sure whether I did something so brilliant that I now don't understand it or whether it is plain wrong.

Am a bit busy at the moment, but a bug-report would remind me to have a look at it
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Old   August 4, 2011, 10:02
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Thanks Bernhard

I'll add a bug report.

I tried the running the pyFoamSteadyRunner directly from the terminate for my case and i got the same issue.
Terminal msg:
"t = 2880 PyFoam WARNING on line 320 of file /usr/local/lib/python2.7/dist-packages/PyFoam/Execution/BasicRunner.py : Stopping run at next write"
next write time would be t = 3000, but it continued to endTime in controlDict file.

Not sure if its a bug or if its something I havn't setup properly.
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Old   August 4, 2011, 10:54
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I just ran both pyFoamSteadyRunner and pyFoamPlotRunner["--steady-run"] for the icoFoam/cavityGrade tutorial problem and they both worked perfectly, as expected.

I cant figure out why, for my case, the simulation is not stopped.
Would a erratic behaviour of one of residuals affect it ????
In other words a few iterations its below the tolerance then a few iterations afterwards its above the tolerance.
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Old   August 4, 2011, 12:50
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Quote:
Originally Posted by Logan Page View Post
Thanks Bernhard

I'll add a bug report.

I tried the running the pyFoamSteadyRunner directly from the terminate for my case and i got the same issue.
Terminal msg:
"t = 2880 PyFoam WARNING on line 320 of file /usr/local/lib/python2.7/dist-packages/PyFoam/Execution/BasicRunner.py : Stopping run at next write"
next write time would be t = 3000, but it continued to endTime in controlDict file.

Not sure if its a bug or if its something I havn't setup properly.
It should stop the simulation by modifying the controlDict (by setting stopAt to atNextWrite -that is called differently but I can't be bothered to look it up- and writeIntervall to 1) and restoring it after the solver terminated. Check whether the controlDict was modified and also whether runTimeModifialble ist true (because false won't work)
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Old   August 5, 2011, 04:36
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Quote:
Originally Posted by Logan Page View Post
Thanks Bernhard

I'll add a bug report.

I tried the running the pyFoamSteadyRunner directly from the terminate for my case and i got the same issue.
Terminal msg:
"t = 2880 PyFoam WARNING on line 320 of file /usr/local/lib/python2.7/dist-packages/PyFoam/Execution/BasicRunner.py : Stopping run at next write"
next write time would be t = 3000, but it continued to endTime in controlDict file.

Not sure if its a bug or if its something I havn't setup properly.

Hi Bernhard

I tracked down what was wrong.
It was a set-up issue on my part with the controlDict file.

In short:
I copied any old controlDict from a previous case of mine.
I then formatted it neatly, aligning columns etc. Unfortunetly I ended up both tabs and spaces separating the parameters and values in the controlDict file, i.e. [parameter]\t\t\t____[value]
This was causing that PyFoam wasn't updating the controlDict file at all.

It now works 100% with that corrected.
Two thumbs up for this awesome set of tools.

I apologise if I wasted any of your time.
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Old   August 5, 2011, 05:13
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Quote:
Originally Posted by Logan Page View Post
Hi Bernhard

I tracked down what was wrong.
It was a set-up issue on my part with the controlDict file.

In short:
I copied any old controlDict from a previous case of mine.
I then formatted it neatly, aligning columns etc. Unfortunetly I ended up both tabs and spaces separating the parameters and values in the controlDict file, i.e. [parameter]\t\t\t____[value]
This was causing that PyFoam wasn't updating the controlDict file at all.

It now works 100% with that corrected.
Two thumbs up for this awesome set of tools.

I apologise if I wasted any of your time.
I'd have to have a look, because that kind of separation shouldn't matter if the controlDict is modified with the ParsedParameterFile (but I'm not 100% which mechanism is used to modify the file). Could you attach the faulty controlDict to the case so that I can have a look at it?
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Old   August 5, 2011, 05:14
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Quote:
Originally Posted by gschaider View Post
Could you attach the faulty controlDict to the case so that I can have a look at it?
I meant bug-report. Not case
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Old   August 5, 2011, 05:29
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Quote:
Originally Posted by gschaider View Post
I meant bug-report. Not case
Thanks.
Added files to bug report.
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Old   August 8, 2011, 05:18
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Originally Posted by Logan Page View Post
Thanks.
Added files to bug report.
Thanks. Also thanks for suggesting a fix (everybody interested myay have a look at http://sourceforge.net/apps/mantisbt...view.php?id=86)
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Old   November 8, 2011, 10:04
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Hi All,

Sorry for the newbie question.

I got a very similar error to the post #1 trying to run
Code:
roberto@roberto:~/Desktop/mesh_test1$ pyFoamDisplayBlockMesh.py constant/polyMesh/blockMeshDict
It gives me
Code:
Traceback (most recent call last):
  File "/home/roberto/OpenFOAM/PyFoam-0.5.6/bin/pyFoamDisplayBlockMesh.py", line 7, in <module>
    from PyFoam.Error import warning
ImportError: No module named PyFoam.Error
Thanks and regards,
Robert
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Old   November 8, 2011, 17:02
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Quote:
Originally Posted by rob3rt 0ng View Post
Hi All,

Sorry for the newbie question.

I got a very similar error to the post #1 trying to run
Code:
roberto@roberto:~/Desktop/mesh_test1$ pyFoamDisplayBlockMesh.py constant/polyMesh/blockMeshDict
It gives me
Code:
Traceback (most recent call last):
  File "/home/roberto/OpenFOAM/PyFoam-0.5.6/bin/pyFoamDisplayBlockMesh.py", line 7, in <module>
    from PyFoam.Error import warning
ImportError: No module named PyFoam.Error
Thanks and regards,
Robert
Other PyFoam-Utilities work?

I don't think so. Seems to me that PyFoam is not in the PYTHONPATH

Could you please check your installation with pyFoamVersion.py and report what you see?
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Old   November 9, 2011, 03:41
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Hi Bernhard,

I've set the PyFOam in the right PYTHONPATH

Now, when I tried pyFoamDisplayBlockMesh.py constant/polyMesh/blockMeshDict

It gives me
Code:
Error in /home/roberto/OpenFOAM/PyFoam-0.5.6/bin/pyFoamDisplayBlockMesh.py : PyFoam FATAL ERROR on line 26 of file /home/roberto/OpenFOAM/PyFoam-0.5.6/PyFoam/Applications/DisplayBlockMesh.py: Error while importing modules: No module named libvtkCommonPython
I couldn't find the libvtkCommonPython anywhere in my computer...

The pyFaomVersion.py gives me
Code:
PYTHONPATH: //home/roberto/OpenFOAM/PyFoam-0.5.6/lib/python-2.7/site-packages:
OpenFOAM (1, 7, 'x') of the installed versions ['2.0.x', '1.7.x']
pyFoam-Version: 0.5.6
Configuration search path: [('file', '/etc/pyFoam/pyfoamrc'), ('directory', '/etc/pyFoam/pyfoamrc.d'), ('file', '/home/roberto/.pyFoam/pyfoamrc'), ('directory', '/home/roberto/.pyFoam/pyfoamrc.d')]
Configuration files (used): []

Installed libraries:
Gnuplot              :  No     Not a problem. Version from ThirdParty is used
ply                  :  No     Not a problem. Version from ThirdParty is used
Numeric              :  No     Not a problem if numpy is present
numpy                :  Yes
matplotlib           :  Yes
psyco                :  No     Not a problem. Acceleration not possible
hotshot              :  Yes
profile              :  No     Not a problem. Can't profile using this library
cProfile             :  Yes
PyQt4                :  No     Only some experimental GUI-stuff relies on this
PyQt4.Qwt5           :  No     Only an alternate plotting back-end
vtk                  :  No     Not a problem. Only used for some utilities
Tkinter              :  Yes
mercurial            :  No     Not a problem. Used for experimental case handling
Thanks for your help.

Have a nice day

Regards,
Robert
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PyFoam library seb62 OpenFOAM Post-Processing 52 September 30, 2011 08:28


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