Problems with PyFoam

gschaider · May 8, 2013, 16:46

Quote:

Originally Posted by simone.rowing

dear geschaider, after a bit of fiddling with the folders, we have the PyQt4 installed and able to import it in python. the vtk package must also be installed, however it shows the following erro after runnung the code "pyFoamVersion.py"

Code:

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 supported anymore. No need to install it
/Applications/Paraview_3.98.1.app/Contents/Python/numpy/random/__init__.py:87: RuntimeWarning: compiletime version 2.6 of module 'mtrand' does not match runtime version 2.7
  from mtrand import *
numpy                :  Yes      version: 1.6.2
matplotlib           :  Yes      version: 1.1.1
psyco                :  No      Not a problem. Acceleration not possible
hotshot              :  Yes
profile              :  Yes
cProfile             :  Yes
PyQt4                :  Yes
PyQt4.Qwt5           :  No      Only an alternate plotting back-end
vtk                  :  Error: Could not import vtkCommonComputationalGeometryPython
No      Not a problem. Only used for some utilities
Tkinter              :  Yes      version: $Revision: 81008 $
mercurial            :  No      Not a problem. Used for experimental case handling
nose                 :  No      Only needed for running the unit-tests (developers only)
twisted              :  Yes      version: 11.0.0
pandas               :  No      Not yet used. Maybe handling of timelines will be reimplemented with it
scipy                :  No      Not yet used. Possibly use signal-fitting etc

not entirely sure what to do next, many thanks for the help so far.

Please always poste the complete output of the utility and let me judge what is needed. As far as I can see you still got the Paraview-binaries in the PYTHONPATH. At the very least this breaks numpy (because you use Python 2.7, Paraview 2.6). Not sure, but this probably also breaks VTK.

So remove all parts pointing to the Paraview-installation from the PYTHONPATH and retry

simone.rowing · May 8, 2013, 17:13

Ok, I do in this way:
run Python
import sys
print sys.path
import paraview
import vtk

Code:

MacBook-di-Simone:~ simomartini$ python
Python 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> print sis
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
NameError: name 'sis' is not defined
>>> quit()
MacBook-di-Simone:~ simomartini$ python
Python 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> print sys.path
['', '/Users/simomartini', '/Applications/Paraview_3.98.1.app/Contents/Python', '/Applications/Paraview_3.98.1.app/Contents/Python/paraview', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages', '/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old', '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload', '/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyObjC', '/Library/Python/2.7/site-packages']
>>> import paraview
>>> import vtk
Error: Could not import vtkCommonComputationalGeometryPython
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Applications/Paraview_3.98.1.app/Contents/Python/paraview/vtk/__init__.py", line 7, in <module>
    from vtkCommonCorePython import *
ImportError: No module named vtkCommonCorePython
>>>

and this in my pyFoamVersion.py

Code:

MacBook-di-Simone:~ simomartini$ pyFoamVersion.py
Machine info: Darwin | MacBook-di-Simone.local | 11.4.2 | Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 | x86_64 | i386

Python version: 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]

PYTHONPATH: :/Applications/Paraview_3.98.1.app/Contents/Python:/Applications/Paraview_3.98.1.app/Contents/Python/paraview

Location of this utility: /usr/local/bin/pyFoamVersion.py

OpenFOAM () of the installed versions ['2.2.0']
  This version of OpenFOAM uses the old calling convention

pyFoam-Version: 0.6.0

Path where PyFoam was found (PyFoam.__path__) is ['/Library/Python/2.7/site-packages/PyFoam']

Configuration search path: [('file', '/etc/pyFoam/pyfoamrc'), ('directory', '/etc/pyFoam/pyfoamrc.d'), ('file', '/Users/simomartini/.pyFoam/pyfoamrc'), ('directory', '/Users/simomartini/.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 supported anymore. No need to install it
/Applications/Paraview_3.98.1.app/Contents/Python/numpy/random/__init__.py:87: RuntimeWarning: compiletime version 2.6 of module 'mtrand' does not match runtime version 2.7
  from mtrand import *
numpy                :  Yes      version: 1.6.2
matplotlib           :  Yes      version: 1.1.1
psyco                :  No      Not a problem. Acceleration not possible
hotshot              :  Yes
profile              :  Yes
cProfile             :  Yes
PyQt4                :  Yes
PyQt4.Qwt5           :  No      Only an alternate plotting back-end
vtk                  :  Error: Could not import vtkCommonComputationalGeometryPython
No      Not a problem. Only used for some utilities
Tkinter              :  Yes      version: $Revision: 81008 $
mercurial            :  No      Not a problem. Used for experimental case handling
nose                 :  No      Only needed for running the unit-tests (developers only)
twisted              :  Yes      version: 11.0.0
pandas               :  No      Not yet used. Maybe handling of timelines will be reimplemented with it
scipy                :  No      Not yet used. Possibly use signal-fitting etc
MacBook-di-Simone:~ simomartini$

gschaider · May 8, 2013, 17:32

Quote:

Originally Posted by simone.rowing

and this in my pyFoamVersion.py

Code:

MacBook-di-Simone:~ simomartini$ pyFoamVersion.py
Machine info: Darwin | MacBook-di-Simone.local | 11.4.2 | Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 | x86_64 | i386

Python version: 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]

PYTHONPATH: :/Applications/Paraview_3.98.1.app/Contents/Python:/Applications/Paraview_3.98.1.app/Contents/Python/paraview

As I suspected: Paraview is in the PYTHONPATH. Completely erase the path with 'unset PYTHONPATH' and retry

The VTK-version that comes with Paraview is NO help. For some technical reason (you'll have to research that yourself) the version of VTK that comes with Paraview is modified and in parts behaves differently. Make sure you use the version from MacPorts (I think I described that before)

simone.rowing · May 8, 2013, 18:25

this is my version of ports

Code:

MacBook-di-Simone:~ simomartini$ port
MacPorts 2.1.3
Entering interactive mode... ("help" for help, "quit" to quit)
[Users/simomartini] >

the pyFoam doesn't recognize the vtk and the installation with port that you already suggested didn't work with python. Do you know another way to install vtk to work with pyFoam. I tried to use Homebrew but I have not had any success.

Code:

MacBook-di-Simone:~ simomartini$ pyFoamVersion.py
Machine info: Darwin | MacBook-di-Simone.local | 11.4.2 | Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 | x86_64 | i386

Python version: 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]

PYTHONPATH: :/Users/simomartini/projects/ParaView-bin/lib/site-packages/

Location of this utility: /usr/local/bin/pyFoamVersion.py

OpenFOAM () of the installed versions ['2.2.0']
  This version of OpenFOAM uses the old calling convention

pyFoam-Version: 0.6.0

Path where PyFoam was found (PyFoam.__path__) is ['/Library/Python/2.7/site-packages/PyFoam']

Configuration search path: [('file', '/etc/pyFoam/pyfoamrc'), ('directory', '/etc/pyFoam/pyfoamrc.d'), ('file', '/Users/simomartini/.pyFoam/pyfoamrc'), ('directory', '/Users/simomartini/.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 supported anymore. No need to install it
numpy                :  Yes      version: 1.5.1
matplotlib           :  No      Only Gnuplot-plotting possible
psyco                :  No      Not a problem. Acceleration not possible
hotshot              :  Yes
profile              :  Yes
cProfile             :  Yes
PyQt4                :  Yes
PyQt4.Qwt5           :  No      Only an alternate plotting back-end
vtk                  :  No      Not a problem. Only used for some utilities
Tkinter              :  Yes      version: $Revision: 81008 $
mercurial            :  No      Not a problem. Used for experimental case handling
nose                 :  No      Only needed for running the unit-tests (developers only)
twisted              :  Yes      version: 12.3.0
pandas               :  No      Not yet used. Maybe handling of timelines will be reimplemented with it
scipy                :  No      Not yet used. Possibly use signal-fitting etc

gschaider · May 8, 2013, 18:44

Quote:

Originally Posted by simone.rowing

this is my version of ports

Code:

MacBook-di-Simone:~ simomartini$ port
MacPorts 2.1.3
Entering interactive mode... ("help" for help, "quit" to quit)
[Users/simomartini] >

the pyFoam doesn't recognize the vtk and the installation with port that you already suggested didn't work with python. Do you know another way to install vtk to work with pyFoam. I tried to use Homebrew but I have not had any success.

I already explained it to you in a previous post (Problems with PyFoam install the vtk from MacPorts! I assumed you've already done that and the library was "shadowed" by the paraview-version

simone.rowing · May 10, 2013, 05:35

I already install the vtk5! but I really don't know why this doesn't work.

Code:

MacBook-di-Simone:~ simomartini$ sudo port install vtk5 +python27 +qt4_mac
Password:
--->  Computing dependencies for vtk5
--->  Deactivating vtk5 @5.10.1_0+tcltk+x11
--->  Cleaning vtk5
--->  Activating vtk5 @5.10.1_0+python27+qt4_mac
--->  Cleaning vtk5
--->  Scanning binaries for linking errors: 100.0%
--->  No broken files found.
MacBook-di-Simone:~ simomartini$ pyFoamVersion.py
Machine info: Darwin | dhcp-201-211.wireless.soton.ac.uk | 11.4.2 | Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 | x86_64 | i386

Python version: 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]

PYTHONPATH: :/Users/simomartini/projects/ParaView-bin/lib/site-packages/

Location of this utility: /usr/local/bin/pyFoamVersion.py

OpenFOAM () of the installed versions ['2.2.0']
  This version of OpenFOAM uses the old calling convention

pyFoam-Version: 0.6.0

Path where PyFoam was found (PyFoam.__path__) is ['/Library/Python/2.7/site-packages/PyFoam']

Configuration search path: [('file', '/etc/pyFoam/pyfoamrc'), ('directory', '/etc/pyFoam/pyfoamrc.d'), ('file', '/Users/simomartini/.pyFoam/pyfoamrc'), ('directory', '/Users/simomartini/.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 supported anymore. No need to install it
numpy                :  Yes      version: 1.5.1
matplotlib           :  No      Only Gnuplot-plotting possible
psyco                :  No      Not a problem. Acceleration not possible
hotshot              :  Yes
profile              :  Yes
cProfile             :  Yes
PyQt4                :  Yes
PyQt4.Qwt5           :  No      Only an alternate plotting back-end
vtk                  :  No      Not a problem. Only used for some utilities
Tkinter              :  Yes      version: $Revision: 81008 $
mercurial            :  No      Not a problem. Used for experimental case handling
nose                 :  No      Only needed for running the unit-tests (developers only)
twisted              :  Yes      version: 12.3.0
pandas               :  No      Not yet used. Maybe handling of timelines will be reimplemented with it
scipy                :  No      Not yet used. Possibly use signal-fitting etc
MacBook-di-Simone:~ simomartini$

gschaider · May 11, 2013, 06:17

Quote:

Originally Posted by simone.rowing

I already install the vtk5! but I really don't know why this doesn't work.

Code:

MacBook-di-Simone:~ simomartini$ sudo port install vtk5 +python27 +qt4_mac
Password:
--->  Computing dependencies for vtk5
--->  Deactivating vtk5 @5.10.1_0+tcltk+x11
--->  Cleaning vtk5
--->  Activating vtk5 @5.10.1_0+python27+qt4_mac
--->  Cleaning vtk5
--->  Scanning binaries for linking errors: 100.0%
--->  No broken files found.
MacBook-di-Simone:~ simomartini$ pyFoamVersion.py
Machine info: Darwin | dhcp-201-211.wireless.soton.ac.uk | 11.4.2 | Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 | x86_64 | i386

Python version: 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]

PYTHONPATH: :/Users/simomartini/projects/ParaView-bin/lib/site-packages/

Location of this utility: /usr/local/bin/pyFoamVersion.py

OpenFOAM () of the installed versions ['2.2.0']
  This version of OpenFOAM uses the old calling convention

pyFoam-Version: 0.6.0

Path where PyFoam was found (PyFoam.__path__) is ['/Library/Python/2.7/site-packages/PyFoam']

Configuration search path: [('file', '/etc/pyFoam/pyfoamrc'), ('directory', '/etc/pyFoam/pyfoamrc.d'), ('file', '/Users/simomartini/.pyFoam/pyfoamrc'), ('directory', '/Users/simomartini/.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 supported anymore. No need to install it
numpy                :  Yes      version: 1.5.1
matplotlib           :  No      Only Gnuplot-plotting possible
psyco                :  No      Not a problem. Acceleration not possible
hotshot              :  Yes
profile              :  Yes
cProfile             :  Yes
PyQt4                :  Yes
PyQt4.Qwt5           :  No      Only an alternate plotting back-end
vtk                  :  No      Not a problem. Only used for some utilities
Tkinter              :  Yes      version: $Revision: 81008 $
mercurial            :  No      Not a problem. Used for experimental case handling
nose                 :  No      Only needed for running the unit-tests (developers only)
twisted              :  Yes      version: 12.3.0
pandas               :  No      Not yet used. Maybe handling of timelines will be reimplemented with it
scipy                :  No      Not yet used. Possibly use signal-fitting etc
MacBook-di-Simone:~ simomartini$

Which python-version are you using? From the version reported I guess the apple-version in /usr/bin/python (but please verify with "which"). I use the MacPorts-version and the variant +python27 of vtk5 assumes that. Either select the MacPorts-version with "port select python python27" or reinstall vtk5 without that option (but I haven't tested that)

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