dolfin-convert fails to convert gmsh mesh Edit

[Fabrice Silva]

I have a3D mesh generated with gmsh

$ gmsh test.geo -3 -format msh

that I convert to xml

$ dolfin-convert -i gmsh test.msh test.xml

The test.msh file contains a mesh with nodes on three parallel disks. The test.xml shows weird cells in a cube! The gmsh file is version 2.2 and dolfin is 1.2.0

(Previously reported in Launchpad )

[Johan Hake]

Looks perfectly fine in development version of dolfin

[Fabrice Silva]

I just installed the whole fenics project using dorsal (no STABLE_BUILD, using SNAPSHOTS). The imported mesh still looks odd!

[Johan Hake]

Could you upload a screenshot or something showing your problem?

[Fabrice Silva]

Views in gmsh and dolfin

[Johan Hake]

How do you visualize the dolfin mesh? Try:

dolfin-plot test.xml

[Fabrice Silva]

It is much nicer! What is the equivalent of the command within a python script? I was using

>>> dolfin.plot(mesh)

[Johan Hake]

from dolfin import *
mesh = Mesh("test.xml")
plot(mesh, interactive=True)

[Fabrice Silva]

Seems matplotlib maybe faulty here. Importing matplotlib (before or after dolfin) leads to weird mesh

import numpy as np
import matplotlib.pyplot as plt
import dolfin as do
mesh = do.Mesh('test.xml')
do.plot(mesh, interactive=True)

[Fabrice Silva]

Further investigation: matplotlib is ok. importing gtk seems to be the problem!

[Johan Hake]

There are no problems with dolfin-convert so this issue is closed. You can open another issue with a proper title and a script that reproduces your error.

The code importing matplotlib above works just fine locally on my computer.

[Fabrice Silva]

Did importing gtk cause any problem ? Importing matplotlib itself may not be a problem if your backend is not one derived from GTK (gtk, gtkagg, gtkcairo for instance).

[Johan Hake]

No, and this has nothing to do with dolfin-convert failing...