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

[Christophe Geuzaine]

> On 28 Oct 2019, at 18:28, Baptiste DURAND <baptiste.durand at enpc.fr> wrote:
> 
> 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!
> 

Ok, great.

> 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.
> 

Ok.

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

Correct !

Christophe


> 
> 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 :
> 
> 
> 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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— 
Prof. Christophe Geuzaine
University of Liege, Electrical Engineering and Computer Science 
http://www.montefiore.ulg.ac.be/~geuzaine