Simulation job has failed with non-zero exit code 139.

Elizabeth Thompson · Post by **Elizabeth Thompson** » Wed May 10, 2023 1:40 pm

Hello,

I have previously successfully run the 3D tutorial simulation on my Windows machine, but am trying to use a mac now so that I can use FSI eventually as well. I am trying to run the aorta tutorial on a mac with os 10.13.6 and 8gb of ram, but when I try to run the solver, I get the following error:

ERROR opening file [geombc.dat.1].
ERROR opening file [restart.0.1].
/usr/local/sv/svsolver/2022-07-22/svsolver-nompi: line 58: 1294 Segmentation fault: 11 $SV_HOME/bin/svsolver-nompi $*

I noticed that the geombc.dat and restart files seemed to have issues, so I also saved the output of the "Create data files for simulation" command (in the latter half of the attached file because I can't seem to add it into the body of this post).

I see a lot of warnings about vtk, and some issues with "symbol not found" which seem like maybe there is an issue with this mac version, but I'm having trouble interpreting all of this to troubleshoot. Any ideas?

Thank you!

Beth

David Parker · Post by **David Parker** » Thu May 11, 2023 12:07 pm

Hi Beth,

This looks like an incompatibility between MacOS 10.13.6 (High Sierra) and 11.1 (Big Sur) which is the OS 2022-07-22 svSolver was built on. High Sierra is end-of-life so you should really upgrade your OS to at least Catalina. Or you could try to install an older version of svSsolver.

Cheers,
Dave

Elizabeth Thompson · Post by **Elizabeth Thompson** » Fri May 12, 2023 11:27 am

Thanks Dave, I was able to upgrade to catalina today and the 3D solver ran fine.

However, I'm now running into an issue with converting results. It seems like the program is looking in the wrong folder for the restart files, despite the fact that I've indicated the correct folder that contains the restart files (folder is /Users/bthompson/Documents/CFD/tutorial and demo from simvascular/ewt_tutorial/aorta_tutorial/Simulations/mactest). Here are the details that come up under the message that says the results were not converted:

Opening /Users/bthompson/Documents/CFD/tutorial/restart.0.1 to scan for number of variables...

ERROR opening file [/Users/bthompson/Documents/CFD/tutorial/restart.0.1].
ERROR: could not open file '/Users/bthompson/Documents/CFD/tutorial/restart.0.1'.

The folder location/file it is trying to open does not exist, but I'm not sure why it's trying to access it when I've indicated it should point to the simulations folder I listed above.

I'm going to try and uninstall/reinstall everything, but if that doesn't work, do you have any ideas what might be causing this / what to try next?

Thank you,

Beth

David Parker · Post by **David Parker** » Fri May 12, 2023 11:45 am

Hi Beth,

The problem is that you are trying to open the directory /Users/bthompson/Documents/CFD/tutorial and demo that has spaces in it (see https://github.com/SimVascular/SimVascular/issues/511).

A workaround is to set the SV Preferences /Simulations to /usr/local/sv/svsolver/2022-02-07/bin/svpost.

: SV Preferences; Screen Shot 2023-05-12 at 11.43.27 AM.png (481.38 KiB) Viewed 206 times

Cheers,
Dave

Elizabeth Thompson · Post by **Elizabeth Thompson** » Fri May 12, 2023 12:09 pm

Thanks so much! My preferences were already set to what you indicated, but I removed the spaces in my directories and it worked!

Best,

Beth

Simulation job has failed with non-zero exit code 139.

Simulation job has failed with non-zero exit code 139.

Re: Simulation job has failed with non-zero exit code 139.

Re: Simulation job has failed with non-zero exit code 139.

Re: Simulation job has failed with non-zero exit code 139.

Re: Simulation job has failed with non-zero exit code 139.