[Paraview] Fwd: paraview.simple
Cory Quammen
cory.quammen at kitware.com
Tue Sep 26 11:16:09 EDT 2017
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
>
>
>
>
>
--
Cory Quammen
Staff R&D Engineer
Kitware, Inc.
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