Segmentation Fault in linux with topologicpy and ifcopenshell

A by agonzalezesteve on 21 Dec 2023, edited 28 Dec 2023 #

Hi @topologic, we are having problems with combining the libraries ifcopenshell and topologicpy (both with the last version available in pip) in a linux system. We are using the build of topologic explained here.

The linuxtest3.py script attached works well in Windows and MacOS but in Ubuntu we get a Segmentation Fault ("Core dumped"). If we change the order of the libraries import (topologicpy before ifcopenshell), the Segmentation Fault appears in a different point of the execution.

@topologic, how we should change the implementation in order to avoid this error?

T by topologic on 21 Dec 2023 #

I’m not a Linux expert sadly. My only suggestion is to check that the software on Linux and Windows are built against the same version of OCCT?

K by knotsruen on 21 Dec 2023, edited 21 Dec 2023 #

@agonzalezesteve what's your python version (python --version)? Is it the same as on Windows/Mac?

A by agonzalezesteve on 22 Dec 2023 #

@topologic @knotsruen in both linux and windows we are using the versions 7.7.2 of occt and 3.10.13 of python.

T by topologic on 22 Dec 2023 # +1 votes

@agonzalezesteve Hi. I did a bit of testing and sadly it seems on linux, the methods dealing with creating a BREP string are not functioning and crashing the whole kernel. This has nothing to do with ifcopenshell. So, as a temporary workaround, please use Topology.ByGeometry and give it a list of vertices, edges, and faces (aka mesh data).

topology = Topology.ByGeometry(vertices=[], edges=[], faces=[], color=[1.0, 1.0, 1.0, 1.0], id=None, name=None, lengthUnit='METERS', outputMode='default', tolerance=0.0001)

Here is an example of a 1x1x1 cell centered around the origin

{'vertices': [[-0.5, -0.5, -0.5], [0.5, -0.5, -0.5], [0.5, 0.5, -0.5], [-0.5, 0.5, -0.5], [0.5, -0.5, 0.5], [-0.5, -0.5, 0.5], [0.5, 0.5, 0.5], [-0.5, 0.5, 0.5]], 'edges': [[1, 0], [2, 1], [3, 2], [0, 3], [1, 4], [4, 5], [5, 0], [2, 6], [6, 4], [3, 7], [7, 6], [5, 7]], 'faces': [[0, 1, 2, 3], [0, 1, 4, 5], [1, 2, 6, 4], [2, 3, 7, 6], [3, 0, 5, 7], [5, 4, 6, 7]]}

T by topologic on 23 Dec 2023 #

@agonzalezesteve Some more testing revelead that this is an issue that happens with jupyter notebook. Running the same script in python directly seems to work. Can you confirm please? Thanks

T by topologic on 23 Dec 2023 #

Here is the smallest script that triggers the bug:

from topologicpy.Vertex import Vertex

 from topologicpy.Topology import Topology

v = Vertex.ByCoordinates(0,0,0)

s = Topology.BREPString(v)

print(s)

T by topologic on 24 Dec 2023 # +1 votes

Dear @agonzalezesteve. I tracked the bug down and sadly, I am now convinced it is a bug with OPENCASCADE and not with topologic. Specifically with this method: BRepTools::Write(GetOcctShape(), oss, false, true, TopTools_FormatVersion_VERSION_3);

This bug is manifesting itself only on Linux and only through Jupyter notebook so it will be difficult to solve without the help of the OPENCASCADE team. The bug will be reported to them in the hope that they can solve it.

A by agonzalezesteve on 27 Dec 2023 #

@topologic said:

@agonzalezesteve Some more testing revelead that this is an issue that happens with jupyter notebook. Running the same script in python directly seems to work. Can you confirm please? Thanks

We don't use jupyter notebook. The script in python directly with linux fails.

A by agonzalezesteve on 27 Dec 2023 #

@topologic we are trying ByGeometry and in the topologicpy version 0.4.39 seems to work but in version 0.4.54 fails.

The error comes from this line of code that was added some motnhs ago. The error is: ValueError: operands could not be broadcast together with shapes (3,) (0,). What about using the length of the array to filter empty values, instead of using the operand ==?

T by topologic on 28 Dec 2023 #

@agonzalezesteve said:

@topologic said:

@agonzalezesteve Some more testing revelead that this is an issue that happens with jupyter notebook. Running the same script in python directly seems to work. Can you confirm please? Thanks

We don't use jupyter notebook. The script in python directly with linux fails.

I am still convinced that this is a bug with OPENCASCADE on Linux as the same code works well on Windows and MacOS.

T by topologic on 28 Dec 2023 #

@agonzalezesteve said:

@topologic we are trying ByGeometry and in the topologicpy version 0.4.39 seems to work but in version 0.4.54 fails.

The error comes from this line of code that was added some motnhs ago. The error is: ValueError: operands could not be broadcast together with shapes (3,) (0,). What about using the length of the array to filter empty values, instead of using the operand ==?

For bugs, it is best if you raise an issue on github? And please point me to the offending file and exact line of code? If you can suggest exact alternative code, that will be very helpful. Thanks.

T by topologic on 28 Dec 2023 #

@agonzalezesteve I just fixed the code for Topology.ByGeometry and uploaded to github. Can you please replace your Topology.py file in your installation with the one from Github to test and let me know if it works better now? If so, this will be included in the next release of topologicpy. Thanks!

A by agonzalezesteve on 28 Dec 2023 #

@topologic said:

For bugs, it is best if you raise an issue on github?

Yes, sure!