[Gmsh] Gmsh Pyhon API + matplotlib cause unreadable msh files and Segmentation fault

[Baptiste DURAND]

Dear Christophe, 

Thank you for your assistance. 

I have downloaded the last snapshot of the SDK from http://gmsh.info/ (downloaded file : http://gmsh.info/bin/Linux/gmsh-git-Linux64-sdk.tgz ), extracted the files from the archive and copy the folder gmsh-git-Linux64-sdk to the python3.6/site-package repository. 
The segmentation fault no longer occurs when the demo script t1.py is running. Good news! 

Regarding the second mistake, I think I have gotten rid of it after an extra operation. 
In the Ubuntu settings, I set the regional format to "English (United Kingdom)" ("Display numbers, dates and currency amounts in the usual format for: " in the package Language Support). 
Previously, the choice was "Français". I thought I had already deleted this trace of French settings. 

To conclude, I should use this snapshot of the SDK and then version 4.5 when it will be released, is that correct? 


Best regards, 

Baptiste Durand 

--- 
Baptiste Durand 
Doctorant – Laboratoire Navier 
baptiste.durand at enpc.fr – 01 64 15 37 21 ( 06 58 88 05 41 ) – linkedin.com/in/baptistedurand 


De: cgeuzaine at uliege.be 
À: "Baptiste DURAND" <baptiste.durand at enpc.fr> 
Cc: gmsh at onelab.info 
Envoyé: Vendredi 25 Octobre 2019 13:33:46 
Objet: Re: [Gmsh] Gmsh Pyhon API + matplotlib cause unreadable msh files and Segmentation fault 

Can you try a recent snapshot of the SDK and let us know if it fixes the issue (which IIRC was due to statically linking the standard C++ lib)? 

Thanks, 

Christophe 




Le 25 oct. 2019 à 12:30, Baptiste DURAND <baptiste.durand at enpc.fr> a écrit : 





BQ_BEGIN

Dear all, 

I'm used to using gmsh through the python API, on Ubuntu 18.04. 
With the version 4.4 of gmsh , I am faced with an unwanted behaviour when I try to import both gmsh and matplotlib into the same script. 

Firstly, if matplotlib is imported before gmsh , a Segmentation fault error occurs. 
Steps to reproduce this : 


    * Create a new virtual environment : 
    * Activate this environment : 
    * Install wheels : pip3 install wheels 
    * Install gmsh python API using the gmsh -sdk package on pypi.org : pip3 install gmsh -sdk 
    * Install the matplotlib package : pip3 install matplotlib 
    * Add the line "import matplotlib" before "import gmsh " in the demo script t1.py 
    * Run this demo script in the virtual environment : python3 t1.py 

This results in : Segmentation fault (core dumped) 
If matplotlib is not imported or is imported after gmsh this segmentation fault doesn't occur. 


In addition, if include-system-site-packages is set to true in the configuration file of the virtual environment (pyvenv.cfg) another problem appears. 
I need this setting because I would like to use the FEniCS finite element code and it cannot be installed inside a virtual environment. 
Even if matplotlib is imported after gmsh , the resulting mesh file is unreadable because the decimal separator is a comma. 


Has anyone faced a similar issue ? 


Best regards, 

Baptiste Durand 

--- 
Baptiste Durand 
Doctorant – Laboratoire Navier 
baptiste.durand at enpc.fr – 01 64 15 37 21 ( 06 58 88 05 41 ) – linkedin.com/in/baptistedurand 
<t1_with_matplotlib.py> 
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BQ_END

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