[Mark JIN]

p { margin-bottom: 0.25cm; line-height: 120%; } Hi friends,


I ran my snappyHexMesh but it ended halfway. Not sure whether its mesh number went out of limit. Could anyone help check my case? And what processes should I go through to solve this error?



Thanks a lot!!!





markjin@markjin-VirtualBox:~/OpenFOAM/markjin-4.0/run/Building_NV$ mpirun -np 8 snappyHexMesh -overwrite -parallel
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 4.0 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 4.0-665f1db4c1f1
Exec : snappyHexMesh -overwrite -parallel
Date : Oct 03 2016
Time : 00:30:08
Host : "markjin-VirtualBox"
PID : 3300
Case : /home/markjin/OpenFOAM/markjin-4.0/run/Building_NV
nProcs : 8
Slaves :
7
(
"markjin-VirtualBox.3301"
"markjin-VirtualBox.3302"
"markjin-VirtualBox.3303"
"markjin-VirtualBox.3304"
"markjin-VirtualBox.3305"
"markjin-VirtualBox.3306"
"markjin-VirtualBox.3307"
)

Pstream initialized with:
floatTransfer : 0
nProcsSimpleSum : 0
commsType : nonBlocking
polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Read mesh in = 0.04 s

Overall mesh bounding box : (-0.125 -0.125 -0.001) (0.125 0.125 0.125)
Relative tolerance : 1e-06
Absolute matching distance : 3.75335e-07

Reading refinement surfaces.
Read refinement surfaces in = 0.03 s

Reading refinement shells.
Refinement level 4 for all cells inside refinementBox
Read refinement shells in = 0 s

Setting refinement level of surface to be consistent with shells.
Checked shell refinement in = 0 s

Reading features.
Read edgeMesh buildings_NV.eMesh
points : 296
edges : 308
boundingBox : (-0.0242074 -0.0072614 0) (0.024024 0.0249582 0.00830749)

Refinement level according to distance to "buildings_NV.eMesh" (296 points, 308 edges).
level 3 for all cells within 0 metre.
Read features in = 0 s


Determining initial surface intersections
-----------------------------------------

Edge intersection testing:
Number of edges : 382500
Number of edges to retest : 382500
Number of intersected edges : 76
Calculated surface intersections in = 0.18 s

Initial mesh : cells:125000 faces:382500 points:132651
Cells per refinement level:
0 125000

Adding patches for surface regions
----------------------------------

Patch Type Region
----- ---- ------
buildings_NV:

6 wall buildings_NV

Added patches in = 0.03 s

Selecting decompositionMethod simple
Layer thickness specified as final layer and expansion ratio.

Refinement phase
----------------

Found point (0.1 0.1 0.1) in cell 9895 on processor 7

Feature refinement iteration 0
------------------------------

Marked for refinement due to explicit features : 60 cells.
Determined cells to refine in = 0.25 s
Selected for feature refinement : 60 cells (out of 125000)
Edge intersection testing:
Number of edges : 384072
Number of edges to retest : 2387
Number of intersected edges : 368
Refined mesh in = 0.18 s
After refinement feature refinement iteration 0 : cells:125420 faces:384072 points:133422
Cells per refinement level:
0 124940
1 480
Skipping balancing since max unbalance 0.00918543 is less than allowable 0.1

Feature refinement iteration 1
------------------------------

Marked for refinement due to explicit features : 136 cells.
Determined cells to refine in = 0.23 s
Selected for feature refinement : 212 cells (out of 125420)
Edge intersection testing:
Number of edges : 389427
Number of edges to retest : 7866
Number of intersected edges : 1019
Refined mesh in = 0.18 s
After refinement feature refinement iteration 1 : cells:126904 faces:389427 points:135901
Cells per refinement level:
0 124864
1 952
2 1088
Skipping balancing since max unbalance 0.0401563 is less than allowable 0.1

Feature refinement iteration 2
------------------------------

Marked for refinement due to explicit features : 292 cells.
Determined cells to refine in = 0.28 s
Selected for feature refinement : 623 cells (out of 126904)
Edge intersection testing:
Number of edges : 405033
Number of edges to retest : 22738
Number of intersected edges : 2936
Refined mesh in = 0.2 s
After refinement feature refinement iteration 2 : cells:131265 faces:405033 points:143023
Cells per refinement level:
0 124793
1 1260
2 2876
3 2336
Balanced mesh in = 0.37 s
After balancing feature refinement iteration 2 : cells:131265 faces:405033 points:143023
Cells per refinement level:
0 124793
1 1260
2 2876
3 2336

Feature refinement iteration 3
------------------------------

Marked for refinement due to explicit features : 0 cells.
Determined cells to refine in = 0.28 s
Selected for feature refinement : 0 cells (out of 131265)
Stopping refining since too few cells selected.


Surface refinement iteration 0
------------------------------

Marked for refinement due to surface intersection : 245 cells.
Marked for refinement due to curvature/regions : 386 cells.
Determined cells to refine in = 0.03 s
Selected for refinement : 679 cells (out of 131265)
Edge intersection testing:
Number of edges : 420105
Number of edges to retest : 28830
Number of intersected edges : 4068
Refined mesh in = 0.19 s
After refinement surface refinement iteration 0 : cells:136018 faces:420105 points:148500
Cells per refinement level:
0 124774
1 1138
2 4682
3 5424
Balanced mesh in = 0.51 s
After balancing surface refinement iteration 0 : cells:136018 faces:420105 points:148500
Cells per refinement level:
0 124774
1 1138
2 4682
3 5424

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

Marked for refinement due to surface intersection : 0 cells.
Marked for refinement due to curvature/regions : 0 cells.
Determined cells to refine in = 0.08 s
Selected for refinement : 0 cells (out of 136018)
Stopping refining since too few cells selected.


Removing mesh beyond surface intersections
------------------------------------------

Found point (0.1 0.1 0.1) in global region 0 out of 4 regions.
Keeping all cells in region 0 containing point (0.1 0.1 0.1)
Selected for keeping : 134616 cells.
Edge intersection testing:
Number of edges : 416905
Number of edges to retest : 2696
Number of intersected edges : 4068

Shell refinement iteration 0
----------------------------

Marked for refinement due to distance to explicit features : 0 cells.
Marked for refinement due to refinement shells : 133404 cells.
Determined cells to refine in = 0.39 s
Selected for internal refinement : 133778 cells (out of 134616)
Edge intersection testing:
Number of edges : 3262987
Number of edges to retest : 3262721
Number of intersected edges : 13382
Refined mesh in = 1.43 s
After refinement shell refinement iteration 0 : cells:1071062 faces:3262987 points:1121496
Cells per refinement level:
0 0
1 998289
2 8386
3 29979
4 34408
Skipping balancing since max unbalance 0.0770081 is less than allowable 0.1

Shell refinement iteration 1
----------------------------

Marked for refinement due to distance to explicit features : 0 cells.
Marked for refinement due to refinement shells : 1024312 cells.
Determined cells to refine in = 0.17 s
Selected for internal refinement : 1024725 cells (out of 1071062)
Balanced mesh in = 3.65 s
After balancing shell refinement iteration 1 : cells:1071062 faces:3262987 points:1121496
Cells per refinement level:
0 0
1 998289
2 8386
3 29979
4 34408
Edge intersection testing:
Number of edges : 24886768
Number of edges to retest : 24841470
Number of intersected edges : 21256
Refined mesh in = 10.48 s
After refinement shell refinement iteration 1 : cells:8244137 faces:24886768 points:8398857
Cells per refinement level:
0 0
1 9784
2 7908302
3 66875
4 259176

Shell refinement iteration 2
----------------------------

No cells marked for refinement since reached limit 2000000.
Determined cells to refine in = 0.7 s
Selected for internal refinement : 13 cells (out of 8244137)
Skipping balancing since max unbalance 0.0586432 is less than allowable 0.1
After balancing shell refinement iteration 2 : cells:8244137 faces:24886768 points:8398857
Cells per refinement level:
0 0
1 9784
2 7908302
3 66875
4 259176
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 3302 on node markjin-VirtualBox exited on signal 9 (Killed).
--------------------------------------------------------------------------

[danielbanos10]

You have reached your pc limits, try selecting less cpu's. I recomend you to leave 1-2 cpu's for the Op. system.
In additnion, it seems that your are using a virtual box, take a look into it's configurations and adding more ram will be usefull too.

[Mark JIN]

Originally Posted by danielbanos10

You have reached your pc limits, try selecting less cpu's. I recomend you to leave 1-2 cpu's for the Op. system.
In additnion, it seems that your are using a virtual box, take a look into it's configurations and adding more ram will be usefull too.

Thanks Daniel, I have solved the issue!

[Mondal131211]

Originally Posted by Mark JIN

Thanks Daniel, I have solved the issue!

Hi Mark,


Though it is a old thread, it could be beneficial for me as I am encountered the same problem.

Marked for refinement due to surface intersection : 276480 cells.
Determined cells to refine in = 0.47 s
Selected for refinement : 289408 cells (out of 4788114)
Killed

Can you please share how you solved this issue? I am still not sure whether this problem arise because of wrong set up of snappyHexMesh or for PC configuration? My PC config...core i7 with 16 GB ram.


I appreciate any help from anyone in this community. If you know the issue who is seeing my post please comment..


Cheers
Razon

[sancho78rus]

Better late than never.

I confirm that this is due to computing resources.
I run mpirun snappyHexMesh -overwrite in a virtual machine on xeon silver (6 cores, 16GB of memory).
With complex models, I got the same errors almost immediately.
Added 2 more cores and 16GB of memory - errors appear, but now not immediately, but after 20-30 minutes of work.
I have no more resources.
What to do in such a situation? How can you limit snappyHexMesh in resources?

[sancho78rus]

It looks like I managed to find a solution. I removed 2 processor cores and now everything works fine. It looks like it takes less memory to compute on fewer cores. Therefore, free memory does not end and mpirun does not crash.

[Mojtaba.a]

Originally Posted by sancho78rus

It looks like I managed to find a solution. I removed 2 processor cores and now everything works fine. It looks like it takes less memory to compute on fewer cores. Therefore, free memory does not end and mpirun does not crash.

Unfortunately, this didn't work for me. Even with single-core it still crashes. It should be around ~20M cells and I have a 32Gb RAM. I don't think that would be a problem. I wonder if there is an option to restrict SHM uses more RAM.

[sancho78rus]

Originally Posted by Mojtaba.a

Unfortunately, this didn't work for me. Even with single-core it still crashes. It should be around ~20M cells and I have a 32Gb RAM. I don't think that would be a problem. I wonder if there is an option to restrict SHM uses more RAM.

Try to increase swap.