Simulation error right after start running
- Jimmy Azarnoosh
- Posts: 25
- Joined: Mon Oct 05, 2020 5:43 pm
Simulation error right after start running
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
i
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
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:
=====================================================================
T
T
T
T
h
h
T
h
h
T
T
e
T
e
h
e
e
h
h
h
e
e
e
p
e
p
p
p
r
r
p
r
r
p
p
o
p
o
r
o
o
r
r
c
r
c
o
c
c
o
o
e
o
e
c
e
e
c
c
s
c
s
e
s
s
e
e
s
e
s
s
s
s
s
s
s
s
s
s
I
s
I
I
I
D
D
I
D
D
I
I
I
D
D
D
f
D
f
f
f
o
o
f
o
o
f
f
r
f
r
o
r
r
o
o
o
r
r
r
m
r
m
m
m
y
y
m
y
y
m
m
r
m
r
y
r
r
y
y
a
y
a
r
a
a
r
r
n
r
n
a
n
n
a
a
k
a
k
n
k
k
n
n
n
k
k
k
(
k
(
(
(
6
7
(
3
2
(
(
)
(
)
1
)
)
5
4
0
)
)
)
i
)
i
i
i
s
s
i
s
s
i
i
i
s
s
s
(
s
(
(
(
3
9
(
1
1
(
(
6
(
1
1
9
9
8
1
6
1
0
1
0
4
9
0
0
5
4
3
5
4
8
2
)
8
)
8
2
4
8
0
.
6
.
0
)
)
)
8
0
)
.
.
.
)
)
.
.
.
The number of processes is 8.
Solver Input Files listed as below:
------------------------------------
Local Config: solver.inp
Default
I
np
ut F
i
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
- Posts: 1677
- Joined: Tue Aug 23, 2005 2:43 pm
Re: Simulation error right after start running
Hi Jimmy,
What platform you are using and OS version ?
What SimVascular version are you using?
Cheers,
Dave
What platform you are using and OS version ?
What SimVascular version are you using?
Cheers,
Dave
- Jimmy Azarnoosh
- Posts: 25
- Joined: Mon Oct 05, 2020 5:43 pm
Re: Simulation error right after start running
Hi Dave,
I'm using Windows 10.
Simvascular is version 2020.09.25
Thanks,
Jimmy
I'm using Windows 10.
Simvascular is version 2020.09.25
Thanks,
Jimmy
- David Parker
- Posts: 1677
- Joined: Tue Aug 23, 2005 2:43 pm
Re: Simulation error right after start running
Hi Jimmy,
The 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
The
Code: Select all
exit code 0xc0000005
Cheers,
Dave
- Jimmy Azarnoosh
- Posts: 25
- Joined: Mon Oct 05, 2020 5:43 pm
Re: Simulation error right after start running
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
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
- Posts: 1677
- Joined: Tue Aug 23, 2005 2:43 pm
Re: Simulation error right after start running
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
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
- Attachments
-
- Screen Shot 2021-03-12 at 12.51.48 PM.png (637.04 KiB) Viewed 1095 times
- Jimmy Azarnoosh
- Posts: 25
- Joined: Mon Oct 05, 2020 5:43 pm
Re: Simulation error right after start running
Hi Dave,
Thanks for your help. I was looking for a way to check out the mesh quality. Thank you for the link.
Jimmy
Thanks for your help. I was looking for a way to check out the mesh quality. Thank you for the link.
Jimmy
- Aloma Blanch
- Posts: 14
- Joined: Mon Jun 17, 2019 8:31 am
Re: Simulation error right after start running
Dear Dave,
I saw this :
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
I saw this :
.davep wrote: ↑Fri Mar 12, 2021 3:19 pmThe 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
- Attachments
-
- cmake_make.PNG (506.37 KiB) Viewed 1051 times
- David Parker
- Posts: 1677
- Joined: Tue Aug 23, 2005 2:43 pm
Re: Simulation error right after start running
Hi Aloma,
There was a problem with vtk headers on Ubuntu, fixed it and now seems to work.
Cheers,
Dave
There was a problem with vtk headers on Ubuntu, fixed it and now seems to work.
Cheers,
Dave
- Aloma Blanch
- Posts: 14
- Joined: Mon Jun 17, 2019 8:31 am
Re: Simulation error right after start running
Hi Dave.
It is working!
Thank you very much.
Aloma
It is working!
Thank you very much.
Aloma