Simulation error right after start running

[Jimmy Azarnoosh]

Hello,

I'm getting an error right after I run a simulation. The error is "Simulation job 'name' has failed with non-zero exit code -3". I know the problem comes from mesh but don't know how to find out the source of issue. I'm using the following setting for mesh:
- Check Boundary Layer Meshing
- Portion of Edge Size: 0.7
- Number of Layers 5
- Layer Decreasing Ration: 0.8
- Check Radius-Based Meshing

Please let me know if there is something wrong.

Here's the details:

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The number of processes is 8.

Solver Input Files listed as below:
------------------------------------
Local Config: solver.inp
Default

I

np

ut F


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le: Not Setup.

Parameter Values setup as below:
----------------------------------------------
Time Varying Boundary Conditions From File: True
BCT File Type: DAT
Number of BCT Files: 1
BCT Matching Type: Global Node ID
BCT Time Scale Factor: 1.0
Equation of State: Incompressible
Time Step Size: 0.0002
Number of Timesteps: 4950
Viscous Control: Viscous
Number of Timesteps between Restarts: 33
Print Average Solution: True
Print Error Indicators: False
Number of Force Surfaces: 1
Surface ID's for Force Calculation: 1
Force Calculation Method: Velocity Based
Apply Wall Deformation: False
Number of Surfaces which Output Pressure and Flow: 0
Density: 1.06
Viscosity: 0.04
Solver Type: svLS
svLS Type: GMRES
Number of Krylov Vectors per GMRES Sweep: 100
Number of Solves per Left-hand-side Formation: 1
Tolerance on Momentum Equations: 0.05
Tolerance on Continuity Equations: 0.05
Tolerance on svLS NS Solver: 0.05
Maximum Number of Iterations for svLS NS Solver: 10
Maximum Number of Iterations for svLS Momentum Loop: 20
Maximum Number of Iterations for svLS Continuity Loop: 400
Time Integration Rule: Second Order
Time Integration Rho Infinity: 0.5
Flow Advection Form: Convective
Quadrature Rule on Interior: 2
Quadrature Rule on Boundary: 3
Number of Elements Per Block: 255
Number of Coupled Surfaces: 5
Pressure Coupling: Implicit
Number of RCR Surfaces: 5
List of RCR Surfaces: 3 4 5 6 7
RCR Values From File: True
Backflow Stabilization Coefficient: 0.2
Deformable Wall: True
Variable Wall Thickness and Young Mod: True
Density of Vessel Wall: 1
Shear Constant of Vessel Wall: 0.833333
Poisson Ratio of Vessel Wall: 0.49
Number of Wall Properties per Node: 10
Wall Mass Matrix for LHS: True
Wall Stiffness Matrix for LHS: True
Residual Control: True
Residual Criteria: 0.0005
Minimum Required Iterations: 3
Step Construction: 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1
Solver Task: Full Simulation

8-procs_case/ does not exist or is unusable
creating a new one
bct.dat
numstart.dat
rcrt.dat
3 file(s) copied.

job aborted:
[ranks] message

[0] process exited without calling finalize

[1-7] terminated

---- error analysis -----

[0] on COE-DSK-2405
C:\Program Files\SimVascular\svSolver\2019-05-28\svsolver-msmpi-bin.exe ended prematurely and may have crashed. exit code 0xc0000005

---- error analysis -----
=====================================================================


Thanks,
Jimmy

[David Parker]

Hi Jimmy,

What platform you are using and OS version ?

What SimVascular version are you using?

Cheers,
Dave

[Jimmy Azarnoosh]

Hi Dave,

I'm using Windows 10.

Simvascular is version 2020.09.25

Thanks,
Jimmy

[David Parker]

Hi Jimmy,

The

Code: Select all

exit code 0xc0000005

is a memory access violation (e.g. accessing an array out of bounds). I guess this might be caused by a bad mesh. Upload you SV Simulations folder someplace I can download it and I'll have a look.

Cheers,
Dave

[Jimmy Azarnoosh]

Hi Dave,

I sent you the simulation folder via email. It was large and I couldn't attach it here.

The way I resolve the issue is I slightly change Global Max Edge Size till it generates a mesh that is good for simulation. I have around 1.5 M elements. By the way, is there any way to check the generated mesh for any possible issues in SImvascualr or Paraview? I checked the mesh in Paraview for negative volume but saw no problem.


Thank you for your help.

Jimmy

[David Parker]

Hi Jimmy,

I had a look at the simulation and reproduced the crash.

Your mesh has elements that are almost flat (volume 1e-8) that are causing numerical problems. i think these flat elements are created when doing boundary layer meshing. Try creating a mesh without a boundary layer and see if that runs OK. If you really want to include a boundary layer then maybe use fewer layers or adjust layer spacing.

SV does not yet have any functionality to check mesh quality. ParaView has a Mesh Quality filter that you could use to identify bad elements. The image I attached was create using a program I wrote using VTK (see https://github.com/ktbolt/vtk/tree/master/mesh-quality).

Cheers,
Dave

[Jimmy Azarnoosh]

Hi Dave,

Thanks for your help. I was looking for a way to check out the mesh quality. Thank you for the link.

Jimmy

[Aloma Blanch]

Dear Dave,
I saw this :

The image I attached was create using a program I wrote using VTK (see https://github.com/ktbolt/vtk/tree/master/mesh-quality).

.
I was curious and I wanted to try it, but I couldn't build the program executable. The following error (attached picture) appeared.
I'm not sure what I'm doing wrong.
I would really appreciate any help.

Thanks

Aloma

[David Parker]

Hi Aloma,

There was a problem with vtk headers on Ubuntu, fixed it and now seems to work.

Cheers,
Dave

[Aloma Blanch]

Hi Dave.
It is working!

Thank you very much.

Aloma