Troubleshooting¶
This page addresses some problems that may be encountered with MicroStructPy. If this page does not address your problem, please submit an issue through the package GitHub page.
Installation¶
These are problems encountered when installing MicroStructPy.
Missing library for pygmsh on Linux¶
Problem Description
When running MicroStructPy for the first time on a Linux operating system, there is an error message like:
...
src/microstructpy/meshing/trimesh.py:19: in <module>
import pygmsh as pg
/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/pygmsh/__init__.py:1: in <module>
from . import geo, occ
/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/pygmsh/geo/__init__.py:1: in <module>
from .geometry import Geometry
/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/pygmsh/geo/geometry.py:1: in <module>
import gmsh
/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/site-packages/gmsh-4.6.0-Linux64-sdk/lib/gmsh.py:39: in <module>
lib = CDLL(libpath)
/opt/hostedtoolcache/Python/3.7.9/x64/lib/python3.7/ctypes/__init__.py:364: in __init__
self._handle = _dlopen(self._name, mode)
E OSError: libGLU.so.1: cannot open shared object file: No such file or directory
Problem Solution
The libGLU library is misssing from the computer. To add it, run:
sudo apt-get install libglu1
MeshPy fails to install¶
Problem Description
When installing the package, either through PyPI as
pip install microstructpy
or from the source as pip install -e .
in
the top-level directory, an error message appears during the meshpy install.
The error message indicates that Visual Studio cannot find the pybind11
headers.
Problem Solution
Install pybind11 first by running pip install pybind11
, then try to
install MicroStructPy.
Command Line Interface¶
These are problems encountered when running microstructpy input_file.xml
.
Command not found on Linux¶
Problem Description
The MicroStructPy package installs without a problem, however on running
microstructpy example_file.xml
the following message appears:
microstructpy: command not found
Problem Solution
The command line interface (CLI) is install to a directory that is not in
the PATH variable. Check for the CLI in ~/.local/bin
and if it is there,
add the following to your ~/.bash_profile
file:
export PATH=$PATH:~/.local/bin
then source the .bash_profile file by running source ~/.bash_profile
.
‘tkinter’ not found on Linux¶
Problem Description
The MicroStructPy package installs without a problem, however on running
microstructpy example_file.xml
the following error is raised:
ModuleNotFoundError: No module named 'tkinter'
Problem Solution
To install tkinter
for Python 3 on Linux, run the following command:
sudo apt-get install python3-tk
For Python 2, run the following instead:
sudo apt-get install python-tk
Program quits/segfaults while calculating Voronoi diagram¶
Problem Description
During the calculating Voronoi diagram step, the program either quits or segfaults.
Problem Solution
This issue was experienced while running 32-bit Python with a large number of seeds. Python ran out of memory addresses and segfaulted. Switching from 32-bit to 64-bit Python solved the problem.