ValueError: invalid literal for int() with base 10 when using meshconvert.py

1

Hi, I get the following error when I run the command:

dolfin-convert mymesh.msh mymesh.xml

Traceback (most recent call last):
  File "/usr/bin/dolfin-convert", line 132, in <module>
    main(sys.argv[1:])
  File "/usr/bin/dolfin-convert", line 79, in main
    meshconvert.convert2xml(ifilename, ofilename, iformat=iformat)
  File "/usr/lib/python3/dist-packages/dolfin_utils/meshconvert/meshconvert.py", line 1301, in convert2xml
    convert(ifilename, XmlHandler(ofilename), iformat=iformat)
  File "/usr/lib/python3/dist-packages/dolfin_utils/meshconvert/meshconvert.py", line 1322, in convert
    gmsh2xml(ifilename, handler)
  File "/usr/lib/python3/dist-packages/dolfin_utils/meshconvert/meshconvert.py", line 271, in gmsh2xml
    num_elements = int(line)
ValueError: invalid literal for int() with base 10: '7 5905 1 5905\n'

I am using ubuntu 18.04 and installed FEniCS by the command

sudo apt-get install --no-install-recommends fenics

My fenics version is (1:2019.1.0.1~ppa1~bionic1).

I am using a geometry and a mesh that was taken from tutorial on the web and was converted succesfully to dolphin .xml format so I do not have made any mistake when creating the geo files.

2

I have solved this problem by installing Gmsh using apt-get in Ubuntu instead of using the binaries downloaded from the Gmsh page, and generating the mesh this way.

3

The error message invalid literal for int() with base 10 would seem to indicate that you are passing a string that’s not an integer to the int() function . In other words it’s either empty, or has a character in it other than a digit.

You can solve this error by using Python isdigit() method to check whether the value is number or not. The returns True if all the characters are digits, otherwise False .

if val.isdigit():

The other way to overcome this issue is to wrap your code inside a Python try…except block to handle this error.

Python2.x and Python3.x

Sometimes the difference between Python2.x and Python3.x that leads to this ValueError: invalid literal for int() with base 10 .

With Python2.x , int(str(3/2)) gives you “1”. With Python3.x , the same gives you (“1.5”): ValueError: invalid literal for int() with base 10: “1.5”.

4

I had the same problem and solved it by downloading an earlier version of gmsh (3.0.6) and produced the mesh that way. Then dolfin-convert can handle it.

5

Instead of installing an older version of Gmsh, you may save your mesh as Gmsh MSH (.msh) file with Version 2 ASCII format option (it appears as you are saving the file in Gmsh). Then, you can use “dolfin-convert themesh.msh themesh.xml”. It worked for me.

1 Like
6

@scengizci Thank you! Saving in Version 2 ASCII format works for me, too.

7

This resolved my issue as well. I will just state the command line option for building the .msh file from the .geo geometry file in the format you have specified.

gmsh -3 my3dmesh.geo -format msh2