Prblems with pyFoamPVSnapshot-PATHS in OF-2.0.1
 

Hi!!

I'd like to do a snapshot with pyFoamPVSnapshot! I set the paths as its said in README of ThirdParty-2.0.x/ParaView-3.10.1/VTK/Wrapping/Python/README.txt

But it even caused following Error:

pyFoamPVSnapshot.py --state-file=state.pvsm --latest-time state1
Traceback (most recent call last):
File "/usr/local/bin/pyFoamPVSnapshot.py", line 3, in <module>
from PyFoam.Applications.PVSnapshot import PVSnapshot
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Applications/PVSnapshot.py", line 13, in <module>
from PyFoam.Paraview.ServermanagerWrapper import ServermanagerWrapper as SM
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Paraview/__init__.py", line 15, in <module>
from paraview import servermanager
File "/usr/lib/pymodules/python2.6/paraview/servermanager.py", line 43, in <module>
import paraview, re, os, new, sys, vtk
File "/usr/lib/pymodules/python2.6/paraview/vtk/__init__.py", line 4, in <module>
from libvtkCommonPython import *
ImportError: No module named libvtkCommonPython

may it is an important information that i have installed OF as discribed on this WebPage:
http://www.tfd.chalmers.se/~hani/kur...OwnLaptop.html

I don't know what to do ....

The problem seems to be that python can't find the dynamic library libvtkCommonPython.so which implements the python-module libvtkCommonPython. pyFoamPVSnapshot.py uses pvpython as an interpreter. pvpython is a special python version that should set the paths appropriately so that these module is found. So it seems that there is a problem with the paraview-installation.

On the OS-shell type

pvpython

A python-shell should appear. There you type

import paraview

Should one of these steps fail then the installation of paraview is the problem

Thank you!

But it didn't work! (I was able to folow your setps without failures but NO)

I also tried to add the path where the libvtk... .so File is to the PYTHONPATH!
I have installed python-vtk.

Nothing worked!

I don't quite get what didn't work. Please remember: it is your problem. So what "it" means is clear to you but not necessarily to anyone else (and not many people care about it as much as you do). So try to be short, but precise. "But NO" is what I say to putting further effort into this problem if I have to ask for clarification what "but NO" means

As I understand it the VTK that comes with Paraview is not exactly compatible to the "normal" VTK. So maybe your problem is that they're mixed.

If "normal" pvpython works (but you're terribly unclear there) try calling the script with

pvpython <fullPathToScript>/pyFoamPVSnapShot.py <your parameters>

Hello!
Thanks for your efforts!

I ment it as you understood it. pvpython is working. I seemed like pvpython has imported the paraview library but when I type in the pyFoamPVSnapshot command with or without pvpython I get the same error again.

Maybe paraview python support is not enabled and that is the problem ... !

Greatings klio

I think in that case pvpython shouldn't even exist (and should be unable to import paraview). But check that: the Tools-menu in Paraview should have an entry "Python Shell". If not then it seems like your paraview is without Python-support (the "official" OF-Paraview usually is without Python)

I have no PythonSell and with the command paraview --script=sript.py it opens paraview but says "no python support" in the output message.

Also when i type paraview in a schell where pyFoam and OpenFoam is activated It opens another version than in an other shell.

I tried to confugure paraView (which OF uses) with ccmake to enable python. Now in the configfile the PARAVIEW_ENABLE_PYTHON is ON and also in the other files but I stil get the same output message from paraview. (I also compiled it agian but nothing changed).

I think maybe the pvpython command works because of the other paraview which is installed on the system and has nothing to do with the OF and pyFoam installation. but also the config there has the PYTHON variable ON.

Yes, you have python shell. Just enter "python" and you will end up in a command line where you can enter stuff like

import paraview

BTW: afterwards try

print paraview

to see which library is actually used (same applies for pvpython)

But it seems that you have no python-support in Paraview

Sounds like the paraview-variant of DLL-hell: when two versions of paraview are installed (usually one by the package-manager, one by whatever way you installed OF)

Have no idea except to check the environmentvariables PATH, LD_LIBRARY_PATH, PYTHONPATH and make sure that the "pythony" paraview comes first. Also check the environment variable starting with PV and PARA (there may not necessarily be some). The most radical method may be to get rid of one of the Paraview-versions and trying to get the other one to work

Dear gschaider

I am facing the same problems as Klio.

I have read and followed all the procedure here and other place for installing/Compiling Paraview with Python.
1. I had able to load a python file from my paraview and get a output.
2. I am not able to use the Python ( pypython ) to create snapshots using pyFoamPVSnapShot.py

atmoun@balder:/mnt/N/_AUTOMATISATION/Unni_save_dir/atmoun/Particle_image_velocimetry/PIV_Modell_Zylinder_perpendicularCylinders$ pvpython
Python 2.6.5 (r265:79063, Oct 1 2012, 22:16:31)
[GCC 4.4.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import paraview
>>> pvpython /home/atmoun/OpenFOAM/linuxSrc/PyFoam-0.5.7/build/scripts-2.6/pyFoamPVSnapShot.py --state-file="Measurements.pvsm" --latest-time
File "<stdin>", line 1
pvpython /home/atmoun/OpenFOAM/linuxSrc/PyFoam-0.5.7/build/scripts-2.6/pyFoamPVSnapShot.py --state-file="Measurements.pvsm" --latest-time
^
SyntaxError: invalid syntax
>>> pvpython /home/atmoun/OpenFOAM/linuxSrc/PyFoam-0.5.7/build/scripts-2.6/pyFoamPVSnapShot.py
File "<stdin>", line 1
pvpython /home/atmoun/OpenFOAM/linuxSrc/PyFoam-0.5.7/build/scripts-2.6/pyFoamPVSnapShot.py
^
SyntaxError: invalid syntax
>>> print paraview
<module 'paraview' from '/home/atmoun/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/paraview-3.12.0/lib/paraview-3.12/site-packages/paraview/__init__.pyc'>
>>>

Kindly help me.

Thanks & Regards
Unnikrishnan.

I don't think it as the same problem as Klios. There the problem is that paraview is not correctly imported. In your case this works. What you do on the next line ("pvpython ...") can not be done on the python-shell. Try it on the regular shell and report what the error message is then

Dear gschaider,

Thanks for the reply,

Also I would like to inform, after the previous messages, i changed the OpenFoam version and a installation procedure a couple of times.. Just trying to find a solution by trial and error.

Checking pvpython is not working now.

atmoun@balder:~/Documents/Particle_image_velocimetry/ZKW_Multiregion-simpleFoam_cavity_PIV_Zylinder_Model_1$ pypython
No command 'pypython' found, did you mean:
Command 'pvpython' from package 'paraview' (universe)
Command 'cypython' from package 'cyphesis-cpp-clients' (universe)
pypython: command not found
atmoun@balder:~/Documents/Particle_image_velocimetry/ZKW_Multiregion-simpleFoam_cavity_PIV_Zylinder_Model_1$


Also i wanted to say:

1. Installation of OpenFOAM 2.1.1 as User(Non-root in my home directory)
As I have a version of OpenFOAM 2.0.1 already installed in my system by system admin.

I had to install a version of OpenFOAM 2.1.1 in my home directory.
/home/atmoun/OpenFOAM/OpenFOAM-2.1.x


2. Installation of python 2.7.3
Installed python 2.7.3 in my home directory at the following location.
/home/atmoun/OpenFOAM/Python-2.7.3

atmoun@balder:~/OpenFOAM$cd Python-2.7.3
atmoun@balder:~/OpenFOAM/Python-2.7.3$make clean
atmoun@balder:~/OpenFOAM/Python-2.7.3$./configure --prefix=/home/atmoun/OpenFOAM/Python-2.7.3
atmoun@balder:~/OpenFOAM/Python-2.7.3$make
atmoun@balder:~/OpenFOAM/Python-2.7.3$make install

Then run using:
/home/atmoun/OpenFOAM/Python-2.7.3 /bin/python

3. Compiling Paraview with Python
While Compiling paraview i had a problem

/home/atmoun/OpenFOAM/ThirdParty-2.1.x
./makeParaView
# Python support:
# note: script will try to determine the appropriate python library.
#
If it fails, specify the path using the PYTHON_LIBRARY variable
withPYTHON=true
PYTHON_LIBRARY="/usr/lib64/libpython2.6.so.1.0"
# PYTHON_LIBRARY="/usr/lib64/libpython2.6.so.1.0"

I cannot Find the libpython2.7.so.1.0 in my installation directory or in /opt/ or in /usr/lib*/, I think this is the root cause for all the problem.
But i am not sure. if someone can help me.. where i can find the above file.

I dont want to use PYTHON_LIBRARY="/usr/lib64/libpython2.6.so.1.0" due to the admin rights. but still i am using the same to compile paraview.

4. Installing pyFoam
(as in http://www.tfd.chalmers.se/~hani/kur...OwnLaptop.html )
/home/atmoun/OpenFOAM/linuxSrc/PyFoam-0.5.7
atmoun@balder:~/OpenFOAM/linuxSrc/PyFoam-0.5.7$ python setup.py install --prefix=$HOME/OpenFOAM/PyFoam-0.5.7

atmoun@balder:~/OpenFOAM/linuxSrc/PyFoam-0.5.7$ echo "alias PF='export PYTHONPATH=/$HOME/OpenFOAM/Python-2.7.3/lib/python2.7/site-packages:$PYTHONPATH; export PATH=$HOME/OpenFOAM/Python-2.7.3/bin:$PATH'" >> $HOME/.bashrc

Also i am really confused in the above 2 lines..
when installing pyFoam
I get the following
Neither numpy nor Numeric python-package installed. Plotting won't work

export pythonpath to /home/atmoun/OpenFOAM/my_python

Results : If you or anyone can check and tell me, if i am doing some thing wrong with the procedure, Kindly please explain in detail.

Attached: Picture of my User directory with Installation location of OpenFOAM-2.1.1, Paraview3.12 in thirdParty

Thanks in advance for the help.

Thanks & Regards
Unnikrishnan.

Dear All,
I experience similar problems with OpenFOAM2.2.x on Ubuntu13.04 (64bit) an I hope someone knows a solution because I want to print a lot of snapshots and I hoped pyFoam could help me.
I folowed this thread and collected all the data asked for. Please feel free to ask for additional information

best regards
wouter

starting ParaFoam->tools-Python Shell

That's strange because pvpython knew the paraview module (thanks for the diagnosis output BTW). Now I have a big suspicion. Check how the file /usr/local/bin/pyFoamPVSnapshot.py looks like. At my machine it looks like this
You installed with setup.py right? I think it may be possible that this replaces the pvpython in the first line with python. If that is the case replace it with pvpython and retry. If that fixes it I'd be grateful for a bug-report on the Mantis (so that I get around to fixing it. My problem is that I rarely install with setup.py so I stumbled onto this problem some time ago and forgot to fix it permanently)

Dear gschaider,
Thank you for responding. You were right with your assumption. I changed the header and I got a different error
There was no core dump. As far as I know I downloaded the latest version of pyFoam so I have to make two bug reports?
one for the header and one for the older version. I will look up how to make a bugreport.
Thanks again.

Best regards
Wouter

I found that this is already in a bugreport of 2009

... and one for the misspelling of utility in the warning ;)

I just tried PVSnapshot on my machine and it works. I use a Kitware-Binary PV 3.98.1 (so it is unlikely that your 3.12 broke i) with a state-file that has a file for the built-in reader (.foam). Are you by any chance using the PV3Reader (.OpenFOAM)? If yes: could you try a simple state file using a .foam-file?

For a bug report I'll need the state-file and a case (preferably small) to reproduce the error

Dear gschaider,
Thank you for responding. Attached a casefile for testing. I tried with paraFoam -builtin to make the .pvsm file but this does not change anything.
Is this what you meant with with simple state. I had .Openfoam and I got .foam but after pyFoamPVSnapshot.py I had Openfoam also.
hope this helps
Regards
Wouter

Thanks for the test case and bad news (see below; just building up the suspense):
The Bad News is that it works for me without problems (see attached image as proof). The image was done with a precompiled ParaView3.98.1 on a Mac (so that is as different from your configuration as it could get). I'm pretty sure that I didn't change anything to the Paraview-code since the last release of PyFoam (and my logs support me in that)
Attachment 25268
So I'm afraid this is a problem with Paraview. Try the following:
- Try loading the state file with "Load state" from the menue
- Try a different version binary of Paraview from KitWare
and see if you get a similar error message

Dear gschaider,
Thank you for the information. I will try to install paraview but I have some bad experiences with that on an other computer.
It will take a will
I wil get back with the results
Regards
Wouter

Good. I'm afraid the issue is outside of my control but I'm willing to find a workaround. One last thing: try the "official" way to load a state-file in pvpython http://paraview.org/Wiki/ParaView/Py...anipulating_It
If that fails then there is a problem with your paraview I'd say

Dear gschaider,
Thank you for the persistance. This evening I certainly will try this. I can load the statefile with paraview --state=testje.pvsm. but I did not try it with pvpython. Thanks for the link.

Best regards
Wouter

Dear gschaider,

Yesterday I tried things and tonight I continued.
first test
The picture was visible in paraview as it was when making the .pvsm file. So no problem with paraview 3.12 only warnings.

Second test with OF221 debian binary and paraviewopenfoam debian binary
not compiled with python support so no go.

Back to OF22x
from paraView see picture (it works)
I got a picture Visualization Toolkit OpenGL

The next core dump I missed the cause of and I cannot reproduce it, but maybe it helps
to be sure I tried pyFoamPVSnapshot.py again:
maybe this caused the previous coredump, but it is before the command.

Is there an easy way to use the system paraview3.98-python with openfoam 2.2.x? My attempt to build paraview3.98 and use it in openfoam failed because of missing headerfiles or headerfiles in the wrong places.
any help is appreciated.
best regards
wouter

Pitty. That would have solved the problem ... for meOr the library files in the PYTHONPATH. Only good way to check for Python-support is in the GUI: if no Python-Shell or Programmable-Filter in the menus then there is no Python-supportI'm afraid without intimate knowledge of the VTK/Paraview sources this is quite hard to interpret. But would be good to know which command caused itUsing it with the built-in reader is always possible. I' only had a quick look at compiling the OF-Reader. I'm afraid fixing it won't be trivial because 3.98 is practically the Beta for 4.0 where parts of the API are changing

If you still want to find the problem in pyFoam then the next thing would be to sprinkle the code with print-statements to see which call breaks everything (as the PV-libraries cause a core-dump there is no stack-trace).

One candidate would be before and after
in PVSnapshot.py to see if this is the problem

Hello gschaider,
Thanks again for your commitment to pyFoam. I will try to follow the program and see where the interface has problems. It will take a while because my python knowledge is minimal.
Best regards
wouter

Just add something like
before ReadState (and similar after). The only important thing is that the number of spaces before the print has to be the same as the command (indentation is Pyhons {} )

Sorry to offload debugging to you but it'd take me to long to reproduce the environment you have

Hello gschaider,
As I wrote, my knoledge of Python is minimal. Can you tell me where I can find the module PVSnapshot.py that is called, or do I have to "compile" with setup.py
best regards
wouter
edit:
I found it in usr/local/lib/python2.7/dist-packages/PyFoam/Applications.
I also found that it goes wrong at calling SM(PV3FoamReader)

That would be the ServerManagerWrapper.py (that file is used to work around different versions of Paraview. I was hoping that the problem is not there). Anyway. Discovered that in fact I worked on that file recently to make it work with 3.98 (probably I forgot it because I was just fixing it to get the real work done). Anyway. Could you use the uploaded version (had to zip it because the Forum doesn't accept Python-files) and the one you have with it. If that doesn't fix it (and I'm afraid it won't) I'll have to ask you to put in prints again to find out which command triggers the problem

Attachment 25324

Hello gschaider,
what do I do with this file? I cannot find this file on my system and I do know to little of python to know where to put this file.
Regards
Wouter
Edit: found it (typo in find). It is the same as you sent me (diff gave only header difference) so I go on with print and report back, but not tonight anymore.

Hello gschaider,
succes.
Gives me the nice picture attached.
Thank you for the patience

This is not of consequence? The program generates the picture.

edit2:
in ServermanagerWrapper.py I replaced libPV3FoamReader.so into libvtkPV3Reader.so and the error message disappeared except for the Inconsistency. Still I get the pictures I want. I get the last error or warning also if I use paraview.

Best regards
wouter

So the failure happened exactly at the connect line? Which is a bummer. Because that is exactly what the try should work around: "If it fails on Python-level set to None and continue". But if it fails one level deeper it is har to do anything.
But that is still with you fix above (comment out Connect) in place?

Hello gschaider,
The 'fix' was still in place. Because of the fix the program worked but there was still an error. I looked for it and found that the library called was not available and I replaced it with one that was available in PV3FoamReader directory.
The last error has something to do with my Thirdparty paraview, because if I only use paraview this error occures, not with paraFoam and not with /usr/bin/paraview. I tried to rebuild it but the error remained.

Best Regards
Wouter

Thanks for the clarification. I'll have to see what to do about he fix. Because leaving out the Connect (or removing the whole try/except-business) will disable old versions of Paraview while it seems to crash new ones.