[Paraview] Fwd: paraview.simple
Cory Quammen
cory.quammen at kitware.com
Mon Sep 18 10:59:40 EDT 2017
On Sat, Sep 16, 2017 at 7:48 AM, Guillermo <guillermo180395 at gmail.com> wrote:
> Hi Cory,
>
> I am trying again to install paraview 5.3. I have downloaded it from the
> paraview webpage. I am using Ubuntu 16.04 LTS; OS type 64-bit. Then I
> followed these steps:
>
> tar xzvf ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit.tar.gz
>
> sudo mv ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit /opt/
>
> sudo emacs ~/.bashrc # and added the following lines:
>
> export PATH=$PATH:/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/bin/
> export
> PYTHONPATH=$PYTHONPATH:/home/doriad/bin/ParaView/Utilities/VTKPythonWrapping/site-packages
> #fixes "no module named paraview"
> export PYTHONPATH=$PYTHONPATH:/home/doriad/bin/ParaView/bin #fixes
> "ImportError: No module named libvtkCommonPython"
> export
> PYTHONPATH=$PYTHONPATH:/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/python2.7/site-packagesexport
> PYTHONPATH=$PYTHONPATH:/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/paraview-5.3
Setting the PYTHONPATH is not necessary to use pvpython. pvpython sets
up the necessary system paths within the Python executable so you
don't have to.
> Saved and exit
>
> #Created the symbolic links
>
> sudo ln -s /opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/
> /usr/bin/paraview
>
> sudo ln -s /opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/
> /usr/lib/paraview
>
> #Restarted the computer and then executed:
>
> ./paraview
This command means "launch the paraview executable in my current
working directory". To use the paraview executable in your PATH,
remove the ./ and run
paraview
This will make sure the paraview found on your PATH is executed.
> And paraview opens and works fine.
>
> # Execute the script I mentioned in previous emails:
>
> ./<the name of the script>
>
> And the following error message appears:
>
> Error: Could not import vtkCommonComputationalGeometry
> Traceback (most recent call last):
> File "./<name of script>", line 42, in <module>
> from paraview.simple import *
> File
> "/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/python2.7/site-packages/paraview/simple.py",
> line 43, in <module>
> from paraview import servermanager
> File
> "/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/python2.7/site-packages/paraview/servermanager.py",
> line 53, in <module>
> from paraview import vtk
> File
> "/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/python2.7/site-packages/paraview/vtk/__init__.py",
> line 7, in <module>
> from paraview.vtk.vtkCommonCore import *
> File
> "/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/python2.7/site-packages/paraview/vtk/vtkCommonCore.py",
> line 9, in <module>
> from vtkCommonCorePython import *
> ImportError: No module named vtkCommonCorePython
>
> Then I tried running it by using:
>
> ./pvpython <name of script>
>
> And the error message is the following:
>
> bash: ./pvpython: No such file or directory
Again, when you run ./pvpython, it is looking for a pvpython
executable in the present working directory. Drop the ./ and it should
work.
> I have also tried by using:
>
> /opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/bin/pvpython <name of
> script>
>
> And the message is:
>
> /opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/paraview-5.3/libgfortran.so.3:
> version `GFORTRAN_1.4' not found (required by /usr/lib/libarpack.so.2)
> Traceback (most recent call last):
> File <name of script>, line 47, in <module>
> reader = OpenDataFile(prefix+ '.vtu');
> File
> "/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/python2.7/site-packages/paraview/simple.py",
> line 846, in OpenDataFile
> raise RuntimeError (msg)
>
> My python version is (python --version) Python 2.7.12
This is strange. I don't see the same when I download ParaView 5.3 on
Ubuntu 16.04. I wonder if you are pulling in something by setting
PYTHONPATH? Try not setting PYTHONPATH (it isn't needed to use
pvpython) and see if that resolves the error.
HTH,
Cory
> My script starts with:
> #!/usr/bin/python
> import re,sys,os,shutil
> -- and I also use --
> from paraview.simple import *
>
> Sorry for the inconveniences.
>
> Really grateful,
>
> Guillermo S.
>
>
>
> On 07/09/17 18:54, Cory Quammen wrote:
>>>
>>> I usually use:
>>> ./<the name of the script>
>>
>> I think you would be better off running your script with
>>
>> ./pvpython <name of script>
>>
>> pvpython comes with the ParaView binary and is located in the same
>> directory as the 'paraview' executable. pvpython uses the same Python
>> as ParaView is, so compatibility with some local Python on your system
>> is not a problem. Further, pvpython sets up Python environment to
>> provide access to the ParaView and VTK Python modules without having
>> to set up any environment variables.
>>
>>> but I also tried with:
>>> python3 <the name of the script>
>>
>> python3 definitely won't work with the official ParaView binaries,
>> which are built against Python 2.7.
>>
>> HTH,
>> Cory
>>
>>> Guillermo
>>>
>>> P.S: With the version 5.0.1 installed and working fine (the script works)
>>> I
>>> have searched the lib you mentioned to me but I do not have it.
>>>
>>> 2017-08-23 13:15 GMT-01:00 Cory Quammen <cory.quammen at kitware.com>:
>>>>>
>>>>> The problem results when executing the python script from the Ubuntu's
>>>>> terminal.
>>>>
>>>> What command are you using to run the Python script?
>>>>
>>>> Thanks,
>>>> Cory
>>>>
>>>>> Thank you very much.
>>>>>
>>>>> ASAP I will try to install the v5.3 and I will let you know if I
>>>>> encounter
>>>>> any problem.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Guillermo
>>>>>
>>>>>
>>>>> On 23/08/17 12:58, Cory Quammen wrote:
>>>>>
>>>>> Guillermo,
>>>>>
>>>>> I'm sorry that my suggestions didn't work out.
>>>>>
>>>>> Could you try one last thing? Please run the following commands:
>>>>>
>>>>> cd /opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/bin
>>>>> ./paraview
>>>>>
>>>>> That should work without problem. If it doesn't, we definitely have a
>>>>> problem.
>>>>>
>>>>> Cheers,
>>>>> Cory
>>>>>
>>>>> On Wed, Aug 23, 2017 at 7:32 AM, Guillermo <guillermo180395 at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Hi Cory,
>>>>>
>>>>> I have made a purge of paraview, reinstalled the 5.3 version, as I
>>>>> indicated
>>>>> on the first email, but the result is the same, it does not work and
>>>>> the
>>>>> message is the same as in the beginning. Also, the libs you indicated
>>>>> to
>>>>> me
>>>>> are not present.
>>>>>
>>>>> Actually, I really need to use this python script and I do not have too
>>>>> much
>>>>> time to spend on it, so I decided to downgrade to 5.0.1 version.
>>>>>
>>>>> In a near future, 1-1.5 month, I will try it again, as I want to
>>>>> upgrade
>>>>> to
>>>>> a newer version. I will let you know if I experiment any issue.
>>>>>
>>>>> Sorry for the inconveniences,
>>>>>
>>>>> Really grateful,
>>>>>
>>>>> Guillermo S.
>>>>>
>>>>>
>>>>> On 22/08/17 13:46, Cory Quammen wrote:
>>>>>
>>>>> Oops, I failed to change the version number in the line I gave you,
>>>>> but caught that and corrected it, just not quite to the right version
>>>>> number.
>>>>>
>>>>> Try
>>>>>
>>>>> export
>>>>>
>>>>>
>>>>> PYTHONPATH=$PYTHONPATH:/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/paraview-5.3
>>>>>
>>>>> Basically, you have to set the PYTHONPATH to where the lib*Python.so
>>>>> files are located. Make sure
>>>>> /opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/paraview-5.3
>>>>> exists and confirm that a file starting with libvtkCommonCorePython27
>>>>> is there.
>>>>>
>>>>> Stepping back a bit, you wouldn't have to do any of this PYTHONPATH
>>>>> stuff if you just add
>>>>>
>>>>> /opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/bin
>>>>>
>>>>> to your PATH.
>>>>>
>>>>> HTH,
>>>>> Cory
>>>>>
>>>>> On Tue, Aug 22, 2017 at 1:38 PM, Guillermo <guillermo180395 at gmail.com>
>>>>> wrote:
>>>>>
>>>>> I forgot to mention that the error message is the same as before.
>>>>>
>>>>>
>>>>> On 22/08/17 13:24, Cory Quammen wrote:
>>>>>
>>>>> Guillermo,
>>>>>
>>>>> Please CC the mailing list so others can participate and learn from
>>>>> the discussion.
>>>>>
>>>>> That looks like progress. Now try adding to your .bashrc:
>>>>>
>>>>> export
>>>>>
>>>>>
>>>>> PYTHONPATH=$PYTHONPATH:/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/paraview-5.4
>>>>>
>>>>> HTH,
>>>>> Cory
>>>>>
>>>>> On Tue, Aug 22, 2017 at 10:19 AM, Guillermo Suárez
>>>>> <guillermo180395 at gmail.com> wrote:
>>>>>
>>>>> Hi Cory,
>>>>>
>>>>> Thank you very much for your fast response. Unfortunately it didn't
>>>>> work
>>>>> (I
>>>>> just copied and pasted into the .bashrc the sentence you gave to me).
>>>>> However, the new error message is:
>>>>>
>>>>> Error: Could not import vtkCommonComputationalGeometry
>>>>> Traceback (most recent call last):
>>>>> File "./<the name of my file>", line XX, in <module>
>>>>> from paraview.simple import *
>>>>> File
>>>>>
>>>>>
>>>>>
>>>>> "/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/python2.7/site-packages/paraview/simple.py",
>>>>> line 43, in <module>
>>>>> from paraview import servermanager
>>>>> File
>>>>>
>>>>>
>>>>>
>>>>> "/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/python2.7/site-packages/paraview/servermanager.py",
>>>>> line 53, in <module>
>>>>> from paraview import vtk
>>>>> File
>>>>>
>>>>>
>>>>>
>>>>> "/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/python2.7/site-packages/paraview/vtk/__init__.py",
>>>>> line 7, in <module>
>>>>> from paraview.vtk.vtkCommonCore import *
>>>>> File
>>>>>
>>>>>
>>>>>
>>>>> "/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/python2.7/site-packages/paraview/vtk/vtkCommonCore.py",
>>>>> line 9, in <module>
>>>>> from vtkCommonCorePython import *
>>>>> ImportError: No module named vtkCommonCorePython
>>>>>
>>>>> I have searched around the Internet and I found a thread that I though
>>>>> it
>>>>> could help:
>>>>> http://public.kitware.com/pipermail/paraview/2014-February/030506.html
>>>>>
>>>>> The idea is to use this:
>>>>>
>>>>> setenv LD_LIBRARY_PATH
>>>>> your-install/lib/paraview-4.1:${LD_LIBRARY_PATH}
>>>>>
>>>>> setenv PYTHONPATH your-install /lib/paraview-4.1/site-packages:
>>>>> your-install
>>>>> /lib/paraview-4.1: your-install /lib/paraview-4.1/site-packages/vtk
>>>>>
>>>>> I copied and pasted this on my .bashrc file substituting the
>>>>> corresponding
>>>>> names, but it didn't work. :(
>>>>>
>>>>> Any idea?
>>>>>
>>>>> Really grateful,
>>>>>
>>>>> Guillermo S.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> 2017-08-22 12:31 GMT-01:00 Cory Quammen <cory.quammen at kitware.com>:
>>>>>
>>>>> Hi Guillermo,
>>>>>
>>>>> I think the content in that wiki page is outdated.
>>>>>
>>>>> Try setting PYTHONPATH to the following in your .bashrc
>>>>>
>>>>> export
>>>>>
>>>>>
>>>>>
>>>>> PYTHONPATH=$PYTHONPATH:/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/python2.7/site-packages
>>>>>
>>>>> See if that works and let us know,
>>>>> Cory
>>>>>
>>>>> On Tue, Aug 22, 2017 at 6:04 AM, Guillermo Suárez
>>>>> <guillermo180395 at gmail.com> wrote:
>>>>>
>>>>> Dear all,
>>>>>
>>>>> Yesterday I installed paraview v5.3 using the binaries from the website
>>>>> on my Linux (ubuntu) OS. The steps followed are (they my influence on
>>>>> the
>>>>> final result):
>>>>>
>>>>> Download the binaries from http://www.paraview.org. For me this results
>>>>> in: ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit.tar.gz
>>>>> Extract and copy them:
>>>>>
>>>>> tar xzvf -C /opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit.tar.gz
>>>>> sudo emacs ~/.bashrc
>>>>>
>>>>> then insert the following line, save & close
>>>>>
>>>>> export PATH=$PATH:/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/bin/
>>>>>
>>>>> Then I created a symbolic link:
>>>>>
>>>>> sudo ln -s
>>>>> /opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/bin/paraview
>>>>> /usr/bin/paraview
>>>>>
>>>>> sudo ln -s
>>>>> /opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/paraview-5.3/
>>>>> /usr/lib/paraview-5.3
>>>>>
>>>>> Before installing paraview from the binaries files I was using the
>>>>> version from Ubuntu repositories (paraview version 5.0 [I think]). Also
>>>>> I
>>>>> was using a python script which uses paraview to take some snapshoots
>>>>> and it
>>>>> worked really well. The problem is that now, when I want to use this
>>>>> python
>>>>> script, it reports this message:
>>>>>
>>>>> "from paraview.simple import *
>>>>> ImportError: No module named paraview.simple"
>>>>>
>>>>> I have made some searches on the Internet and I found a web page about
>>>>> this problem: https://www.paraview.org/Wiki/ParaView/EnvironmentSetup
>>>>> I have copied and pasted those sentences on my .bashrc file, restarted
>>>>> the computer but it still does not work.
>>>>>
>>>>> Could you please help me?
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Guillermo S.
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Please keep messages on-topic and check the ParaView Wiki at:
>>>>> http://paraview.org/Wiki/ParaView
>>>>>
>>>>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://public.kitware.com/mailman/listinfo/paraview
>>>>>
>>>>>
>>>>> --
>>>>> Cory Quammen
>>>>> Staff R&D Engineer
>>>>> Kitware, Inc.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Cory Quammen
>>>> Staff R&D Engineer
>>>> Kitware, Inc.
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Please keep messages on-topic and check the ParaView Wiki at:
>>> http://paraview.org/Wiki/ParaView
>>>
>>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/paraview
>>>
>>
>>
>
--
Cory Quammen
Staff R&D Engineer
Kitware, Inc.
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