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[snappyHexMesh] SnappyHexMesh running killed!

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Old   October 2, 2016, 10:54
Default SnappyHexMesh running killed!
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JIN WEIGUO
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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).
--------------------------------------------------------------------------
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Old   October 3, 2016, 11:13
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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.
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Old   October 4, 2016, 01:19
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Quote:
Originally Posted by danielbanos10 View Post
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!
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Old   March 12, 2020, 18:50
Default SnappyHexMesh Killed
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Quote:
Originally Posted by Mark JIN View Post
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.


Quote:
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
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