OpenFoam snappyHexMesh killed

Alminnawi · October 25, 2023, 06:37

Hi,

I am creating stl models from CT scans then running CFD simulations on them.

I split the mesh into sections per CPU "decomposePar" then I run the analysis using "mpirun -np 8 snappyHexMesh -overwrite -parallel"

at one point it gives me the following issue and I am not sure if it is related to memory or an actual problem and I would appreciate your input:

Surface refinement iteration 1
------------------------------

Marked for refinement due to surface intersection : 737438 cells.
Determined cells to refine in = 0.9 s
Selected for refinement : 805539 cells (out of 1806561)
Edge intersection testing:
Number of edges : 24387267
Number of edges to retest : 23405550
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node MED81341 exited on signal 9 (Killed).

thanks you

LuckyTran · October 27, 2023, 09:20

Nothing you write makes sense.

snappyHexMesh is the meshing utility, not the analysis.

Alminnawi · October 30, 2023, 06:37

I write a bash code for the entire thing, the analysis is preceded by meshing using snappyHexMesh, and since the issue occurred at snappyHexMesh level, I mentioned it specifically. I guess that confused you so much so maybe this is better for you to understand:

Before running the analysis I used "mpirun -np 8 snappyHexMesh -overwrite -parallel" to mesh it

AtoHM · October 30, 2023, 08:33

Lucky knows very well what you meant, I think between the lines he/she is telling you, that this is very little information to go with.

If you suspect it to be a memory issue, why don't you run again and monitor your memory load? If it is anything else, there is very little information to make an educated guess. It could be a lot of things ...

Alminnawi · October 30, 2023, 09:26

it was indeed a memory issue. I reduced the stl file and then it worked fine.
thank you.

October 25, 2023, 06:37	OpenFoam snappyHexMesh killed	#1
Alminnawi New Member A. Alminnawi Join Date: Jul 2023 Posts: 9 Rep Power: 3	Hi, I am creating stl models from CT scans then running CFD simulations on them. I split the mesh into sections per CPU "decomposePar" then I run the analysis using "mpirun -np 8 snappyHexMesh -overwrite -parallel" at one point it gives me the following issue and I am not sure if it is related to memory or an actual problem and I would appreciate your input: Surface refinement iteration 1 ------------------------------ Marked for refinement due to surface intersection : 737438 cells. Determined cells to refine in = 0.9 s Selected for refinement : 805539 cells (out of 1806561) Edge intersection testing: Number of edges : 24387267 Number of edges to retest : 23405550 -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun noticed that process rank 0 with PID 0 on node MED81341 exited on signal 9 (Killed). thanks you

October 30, 2023, 08:33		#4
AtoHM Senior Member M Join Date: Dec 2017 Posts: 703 Rep Power: 13	Lucky knows very well what you meant, I think between the lines he/she is telling you, that this is very little information to go with. If you suspect it to be a memory issue, why don't you run again and monitor your memory load? If it is anything else, there is very little information to make an educated guess. It could be a lot of things ... Alminnawi likes this.

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October 27, 2023, 09:20		#2
LuckyTran Senior Member Lucky Join Date: Apr 2011 Location: Orlando, FL USA Posts: 5,764 Rep Power: 66	Nothing you write makes sense. snappyHexMesh is the meshing utility, not the analysis.

October 30, 2023, 06:37		#3
Alminnawi New Member A. Alminnawi Join Date: Jul 2023 Posts: 9 Rep Power: 3	I write a bash code for the entire thing, the analysis is preceded by meshing using snappyHexMesh, and since the issue occurred at snappyHexMesh level, I mentioned it specifically. I guess that confused you so much so maybe this is better for you to understand: Before running the analysis I used "mpirun -np 8 snappyHexMesh -overwrite -parallel" to mesh it

October 30, 2023, 09:26		#5
Alminnawi New Member A. Alminnawi Join Date: Jul 2023 Posts: 9 Rep Power: 3	it was indeed a memory issue. I reduced the stl file and then it worked fine. thank you.