Error or crashing when creating data files for simulation with repository models

[Jason Voorneveld]

Hi, sorry for posting on the github issues page first, I only found the forum afterwards - reposting here in case this is a better place:

I am trying to perform flow simulations with the aorto-femoral models supplied in the SV model repository. However I always encounter errors or crashes when I click "Create Data Files for Simulation". The error I receive is "Failed to finish creating data files" with no details provided. In the bottom left corner of the GUI it says "Creating Data files: bct, restart, geombc, etc."

I am running on windows 10 x64 with the latest binaries of SV and also the latest july version of SVSolver.
I tried running on a ubuntu virtual machine and get the same issues.

To Reproduce
Download model 0006_0001 from the repository
Press "Create Data Files for Simulation"
-> GUI will either crash or an error will be returned.

Desktop:

OS: Windows 10 x64
SimVascular Version 2022.02.09
SVSolver 2022-07-21
File 0006_0001

[David Parker]

Hi Jason,

I just tried creating the simulation files for 0006_0001 and SV crashes for me too. The problem is that the format of some of the mesh data (e.g. GlobalNodeID) in the Model Repository is incorrect. I will talk with the maintainers of the Model Repository.

As a work-around I've written a Python script here https://github.com/ktbolt/cardiovascula ... ays/python that can be used to modify the .vtp file in the SV Meshes directory. It will create a -modified.vtp file that you can copy to the original .vtp file.

Cheers,
Dave

[Luca Pegolotti]

Hi Jason,

Thank you for posting about this issue. We updated the problematic meshes in the repository. Please let us know if you have other problems.

Best,
Luca

[Jason Voorneveld]

Hi David/Luca,

Thanks for your help. I downloaded the files again from the repository but I am still unable to create the data files for simulation. It still says "Failed to finish creating data files" with no details .I also tried the script that David sent but it looks like the node IDs are already Int32 (note I had to modify the script to get it to run for .vtu files - see attached).

Note that this occurs even if I create a new mesh.

Jason

[David Parker]

Hi Jason,

I just downloaded 0006_0001 and created the solver data files no problem. What platform are you running on? Which version of SV and svSolver are you using?

Cheers,
Dave

[Jason Voorneveld]

I am using:
SimVascular 2022.07.20 (MITK 2018.4.2, VTK 8.1.1, ITK 4.13.2, Qt 5.11.3)
SvSolver 2022.07.21
Window 10 - 64 bit

Just uninstalled SimVascular and SvSolver and reinstalled but that did not help. I still get the error "Failed to finish creating data files".
Is there a way to get an error log?

Edit: I just tried on my Ubuntu virtual machine and was able to create data files for simulation, however I cannot run the simulation because I get an error: "/usr/local/sv/svsolver/2022-07-22/bin/svsolver-nompi: error while loading shared libraries: libvtkIOXML-7.1.so.7.1p: cannot open shared object file: No such file or directory"

So the data file creation issue seems to be linked to my windows installation but something is also wrong with my ubuntu installation? Am I supposed to build VTK separately if I installed the prebuilt simvascular? (same version as mentioned above except for Ubuntu-20

Jason

[Jason Voorneveld]

Update- for the Ubuntu installation I managed to solve the issue by installing "libvtk7.1p"
So I am now able to create the data files for simulation and can run a simulation without errors (still in progress though).

My windows installation still does not work though, and I don't get any errors to help figure out what the problem is.

Jason

[David Parker]

Hi Jason,

To run svSolver on Ubuntu 20 you need to install OpenMPI and VTK.

I just tested on 0006_0001 Windows and was able to create the solver data files. The data files are created by the svpre-bin.exe program. If this fails then a log should be printed and viewed in the Details button on the error popup window. Make sure that the location of the svpre-bin.exe program is set in the SV Preferences panel. You may also want to remove the directories under your C:\Users\NAME\AppData\Local\SimVascular directory.

If the 0006_0001.svpre file is created OK then you can run the svpre-bin.exe command from a Power Shell window like this (DIR is the path to where the 0006_0001 SV project was downloaded to)

Code: Select all

cd DIR\0006_0001\Simulations\0006_0001

Start-Process -FilePath "C:\Program Files\SimVascular\svSolver\2022-07-19\svpre-bin.exe" -WorkingDirectory "DIR\0006_0001\Simulations\0006_0001" -ArgumentList "0006_0001.svpre"

You can then see what svpre-bin.exe is doing.

Cheers,
Dave

[Jason Voorneveld]

Hi Dave,

My simulation completed successfully on my virtual machine, so I can run the sim. However, getting this running on Windows would be great because I lose a lot of performance running a virtual machine.

For windows:

I cleared the files in the AppData directory you mentioned but that didn't help. I also made sure that simvascular has the correct location of the presolver bins, this also did not help (they were correct to start with).
I ran the .svpre file you specified with power shell and received the following error:
"The procedure entry point for_stop_core_quiet could not be located in the dynamic link library C:\Program Files\SimVascular\svSolver\2022-07-21\svpre-bin.exe."

I looked up the error and it looks like I did not have a Fortran compiler installed, so I installed one from here: https://www.intel.com/content/www/us/en ... ents.html and now I can create the data files for simulation.

However, when I actually run the simulation I get an error with exit code -3. The details box is blank.
Any ideas?

Thanks for your help so far, I really appreciate it.

Jason

[David Parker]

Hi Jason,

I think the exit code -3 means that something can't be found, maybe mpiexec.

You need to install the Intel Fortran compiler and Microsoft MPI to run svSolver. Do you have MPI installed?

Cheers,
Dave