[Paraview] Fwd: paraview.simple

Sat Oct 21 14:01:13 EDT 2017

Hi Cory,

Sorry for the delayed response. I have been trying to understand and 
learn to use the gdb, but I could not accomplish the task you mentioned. 
I am sorry :(.

When ever it is possible I will give it another try.

Cheers,

Guillermo

On 26/09/17 14:16, Cory Quammen wrote:
> Hmm, this is very odd. I don't know why libarpack would be loaded. It
> looks like something is loading it and libarpack does not like the
> libgfortran that ships with ParaView.
>
> If you are familiar with gdb, could you run pvpython through gdb and
> get a stack trace where libarpack is being loaded?
>
> Thanks,
> Cory
>
>
>
> On Mon, Sep 18, 2017 at 2:48 PM, Guillermo <guillermo180395 at gmail.com> wrote:
>> Sorry but I could not fix it.
>>
>> I removed the ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit from /opt/
>> directory
>>
>> Reinstalled paraview following the steps I have indicated on the previous
>> email.
>>
>> I have deleted all sentences from ~/.bashrc except the first one: "export
>> PATH=$PATH:/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/bin/"
>>
>> Run paraview as:
>>
>> paraview
>>
>> And worked fine.
>> However I executed the script as you indicated:
>>
>> pvpython <name of script>
>>
>> And the error message is:
>>
>> /opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/paraview-5.3/libgfortran.so.3:
>> version `GFORTRAN_1.4' not found (required by /usr/lib/libarpack.so.2)
>> Traceback (most recent call last):
>>    File <name of script>, line 47, in <module>
>>      reader = OpenDataFile(prefix+ '.vtu'); #This is sentence from my script
>>    File
>> "/opt/ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit/lib/python2.7/site-packages/paraview/simple.py",
>> line 846, in OpenDataFile
>>      raise RuntimeError (msg)
>>
>> I am really sorry for the inconveniences.
>>
>> Guillermo
>>
>>
>> On 18/09/17 13:59, Cory Quammen wrote:
>>
>> On Sat, Sep 16, 2017 at 7:48 AM, Guillermo <guillermo180395 at gmail.com>
>> wrote:
>>
>> Hi Cory,
>>
>> I am trying again to install paraview 5.3. I have downloaded it from the
>> paraview webpage. I am using Ubuntu 16.04 LTS; OS type 64-bit. Then I
>> followed these steps:
>>
>> tar xzvf ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit.tar.gz
>>
>> sudo mv ParaView-5.3.0-Qt5-OpenGL2-MPI-Linux-64bit /opt/
>>
>> sudo emacs ~/.bashrc # and added the following lines:
>>
>> export PATH=$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.
>>
>>
>>
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>>
>> --
>> 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
>>
>>
>>
>>
>>
>
>