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.dur...@enpc.fr – 01 64 15 37 21 ( 06 58 88 05 41 ) –
linkedin.com/in/baptistedurand
# This file reimplements gmsh/tutorial/t1.geo in Python.
# For all the elementary explanations about the general philosphy of entities in
# Gmsh, see the comments in the .geo file. Comments here focus on the specifics
# of the Python API.
# The API is entirely defined in the gmsh module
# import matplotlib.pyplot as plt # ! ERROR : Segmentation fault.
import gmsh
# import matplotlib.pyplot as plt
# Before using any functions in the Python API, Gmsh must be initialized.
gmsh.initialize()
# By default Gmsh will not print out any messages: in order to output messages
# on the terminal, just set the standard Gmsh option "General.Terminal" (same
# format and meaning as in .geo files):
gmsh.option.setNumber("General.Terminal", 1)
# Next we add a new model named "t1" (if gmsh.model.add() is not called a new
# unnamed model will be created on the fly, if necessary):
gmsh.model.add("t1")
# The Python API provides direct access to the internal CAD kernels. The
# built-in CAD kernel was used in t1.geo: the corresponding API functions have
# the "gmsh.model.geo" prefix. To create geometrical points with the built-in
# CAD kernel, one thus uses gmsh.model.geo.addPoint():
#
# - the first 3 arguments are the point coordinates (x, y, z)
#
# - the next (optional) argument is the target mesh size close to the point
#
# - the last (optional) argument is the point tag
lc = 1e-2
gmsh.model.geo.addPoint(0, 0, 0, lc, 1)
gmsh.model.geo.addPoint(.1, 0, 0, lc, 2)
gmsh.model.geo.addPoint(.1, .3, 0, lc, 3)
gmsh.model.geo.addPoint(0, .3, 0, lc, 4)
# The API to create lines with the built-in kernel follows the same
# conventions: the first 2 arguments are point tags, the last (optional one)
# is the line tag.
gmsh.model.geo.addLine(1, 2, 1)
gmsh.model.geo.addLine(3, 2, 2)
gmsh.model.geo.addLine(3, 4, 3)
gmsh.model.geo.addLine(4, 1, 4)
# The philosophy to construct curve loops and surfaces is similar: the first
# argument is now a vector of integers.
gmsh.model.geo.addCurveLoop([4, 1, -2, 3], 1)
gmsh.model.geo.addPlaneSurface([1], 1)
# Physical groups are defined by providing the dimension of the group (0 for
# physical points, 1 for physical curves, 2 for physical surfaces and 3 for
# phsyical volumes) followed by a vector of entity tags. The last (optional)
# argument is the tag of the new group to create.
gmsh.model.addPhysicalGroup(0, [1, 2], 1)
gmsh.model.addPhysicalGroup(1, [1, 2], 2)
gmsh.model.addPhysicalGroup(2, [1], 6)
# Physical names are also defined by providing the dimension and tag of the
# entity.
gmsh.model.setPhysicalName(2, 6, "My surface")
# Before it can be meshed, the internal CAD representation must be synchronized
# with the Gmsh model, which will create the relevant Gmsh data structures. This
# is achieved by the gmsh.model.geo.synchronize() API call for the built-in CAD
# kernel. Synchronizations can be called at any time, but they involve a non
# trivial amount of processing; so while you could synchronize the internal CAD
# data after every CAD command, it is usually better to minimize the number of
# synchronization points.
gmsh.model.geo.synchronize()
# We can then generate a 2D mesh...
gmsh.model.mesh.generate(2)
# ... and save it to disk
gmsh.write("t1_msh2.msh")
gmsh.option.setNumber("Mesh.MshFileVersion",4.1)
gmsh.write("t1_msh4.msh")
# Remember that by default, if physical groups are defined, Gmsh will export in
# the output mesh file only those elements that belong to at least one physical
# group. To force Gmsh to save all elements, you can use
#
# gmsh.option.setNumber("Mesh.SaveAll", 1)
# This should be called at the end:
gmsh.finalize()
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