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[snappyHexMesh] SnappyHexMesh running killed! |
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October 2, 2016, 09:54 |
SnappyHexMesh running killed!
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#1 |
Member
JIN WEIGUO
Join Date: Sep 2016
Posts: 35
Rep Power: 10 |
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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October 3, 2016, 10:13 |
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#2 |
New Member
Join Date: Jun 2016
Location: Malaga, Spain
Posts: 15
Rep Power: 10 |
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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October 4, 2016, 00:19 |
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#3 |
Member
JIN WEIGUO
Join Date: Sep 2016
Posts: 35
Rep Power: 10 |
Thanks Daniel, I have solved the issue!
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March 12, 2020, 17:50 |
SnappyHexMesh Killed
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#4 | |
Member
Mondal
Join Date: Sep 2018
Location: Canberra ACT
Posts: 68
Rep Power: 8 |
Hi Mark, Though it is a old thread, it could be beneficial for me as I am encountered the same problem. Quote:
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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November 9, 2021, 10:50 |
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#5 |
New Member
Anton
Join Date: Nov 2021
Location: Saint-Petersburg
Posts: 10
Rep Power: 4 |
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? |
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November 11, 2021, 07:57 |
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#6 |
New Member
Anton
Join Date: Nov 2021
Location: Saint-Petersburg
Posts: 10
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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.
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June 11, 2022, 11:20 |
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#7 |
Senior Member
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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.
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June 14, 2022, 01:37 |
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#8 |
New Member
Anton
Join Date: Nov 2021
Location: Saint-Petersburg
Posts: 10
Rep Power: 4 |
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