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November 12, 2019, 10:08 |
InterFoam and dynamicMesh fatal error
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#1 |
Member
Rasmus Iwersen
Join Date: Jan 2019
Location: Denmark
Posts: 81
Rep Power: 8 |
Hi all,
I am modelling at free surface flow around a circular cylinder, and wanted to test if using a dynamic mesh provides better results (or the same results faster) compared to adding refinement regions. As far as i understand, dynamicMesh is implemented in interFoam now, i.e. interDyMFoam is not neede as an application entry in controlDict.. I have inserted a dynamicMeshDict into the constant folder, however i get the following error message: PIMPLE: iteration 1 Selected 28439 cells for refinement out of 5438309. Refined from 5438309 to 5637382 cells. Selected 0 split points out of a possible 28439. GAMGPCG: Solving for pcorr, Initial residual = 1, Final residual = 6.32677819096724e-07, No Iterations 13 GAMGPCG: Solving for pcorr, Initial residual = 0.0735650686648364, Final residual = 4.40914813615931e-07, No Iterations 8 GAMGPCG: Solving for pcorr, Initial residual = 0.0131704358701754, Final residual = 5.89343910326883e-07, No Iterations 7 GAMGPCG: Solving for pcorr, Initial residual = 0.00467343802369218, Final residual = 8.00701739157435e-07, No Iterations 5 time step continuity errors : sum local = 3.20448209727168e-11, global = 2.59233061624815e-12, cumulative = 2.13480562902331e-12 smoothSolver: Solving for alpha.water, Initial residual = 3.58916897985575e-07, Final residual = 1.03775942356476e-11, No Iterations 1 Phase-1 volume fraction = 0.750000228067901 Min(alpha.water) = 0 Max(alpha.water) = 1.00000118060983 MULES: Correcting alpha.water Phase-1 volume fraction = 0.750000228067562 Min(alpha.water) = -2.22688585361915e-28 Max(alpha.water) = 1.00000116828149 GAMG: Solving for p_rgh, Initial residual = 1, Final residual = 6.75927310402766e-07, No Iterations 27 GAMG: Solving for p_rgh, Initial residual = 0.000209978335423724, Final residual = 9.67682932467685e-07, No Iterations 5 GAMG: Solving for p_rgh, Initial residual = 4.13560844904846e-05, Final residual = 7.91966998151843e-07, No Iterations 3 GAMG: Solving for p_rgh, Initial residual = 1.45645557196383e-05, Final residual = 2.40593904610264e-07, No Iterations 3 [VAC-PC-WIN10:05389] *** Process received signal *** [VAC-PC-WIN10:05389] Signal: Segmentation fault (11) [VAC-PC-WIN10:05389] Signal code: (-6) [VAC-PC-WIN10:05389] Failing at address: 0x3e80000150d [VAC-PC-WIN10:05389] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7f31d0aaef20] [VAC-PC-WIN10:05389] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f31d0aaee97] [VAC-PC-WIN10:05389] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7f31d0aaef20] [VAC-PC-WIN10:05389] [ 3] interFoam(_ZN4Foam8subtractIddNS_12fvPatchFieldENS _7volMeshEEEvRNS_14GeometricFieldINS_9typeOfSumIT_ T0_E4typeET1_T2_EERKNS3_IS5_S9_SA_EERKNS3_IS6_S9_S A_EE+0x269)[0x7f31d7c70de9] [VAC-PC-WIN10:05389] [ 4] interFoam(_ZN4FoammiIddNS_12fvPatchFieldENS_7volMe shEEENS_3tmpINS_14GeometricFieldINS_9typeOfSumIT_T 0_E4typeET1_T2_EEEERKNS4_IS6_SA_SB_EERKNS4_IS7_SA_ SB_EE+0x31b)[0x7f31d7cd535b] [VAC-PC-WIN10:05389] [ 5] interFoam(_ZN4Foam14GeometricFieldIdNS_12fvPatchFi eldENS_7volMeshEE5relaxEd+0x63)[0x7f31d7cd8543] [VAC-PC-WIN10:05389] [ 6] interFoam(_ZN4Foam14GeometricFieldIdNS_12fvPatchFi eldENS_7volMeshEE5relaxEv+0x147)[0x7f31d7cd8997] [VAC-PC-WIN10:05389] [ 7] interFoam(+0x4ea18)[0x7f31d7c4ea18] [VAC-PC-WIN10:05389] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f31d0a91b97] [VAC-PC-WIN10:05389] [ 9] interFoam(+0x567ea)[0x7f31d7c567ea] [VAC-PC-WIN10:05389] *** End of error message *** [VAC-PC-WIN10:05390] *** Process received signal *** [VAC-PC-WIN10:05390] Signal: Segmentation fault (11) [VAC-PC-WIN10:05390] Signal code: (-6) [VAC-PC-WIN10:05390] Failing at address: 0x3e80000150e [VAC-PC-WIN10:05390] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7fe158aaef20] [VAC-PC-WIN10:05390] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7fe158aaee97] [VAC-PC-WIN10:05390] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7fe158aaef20] [VAC-PC-WIN10:05390] [ 3] interFoam(_ZN4Foam8subtractIddNS_12fvPatchFieldENS _7volMeshEEEvRNS_14GeometricFieldINS_9typeOfSumIT_ T0_E4typeET1_T2_EERKNS3_IS5_S9_SA_EERKNS3_IS6_S9_S A_EE+0x269)[0x7fe15fc70de9] [VAC-PC-WIN10:05390] [ 4] interFoam(_ZN4FoammiIddNS_12fvPatchFieldENS_7volMe shEEENS_3tmpINS_14GeometricFieldINS_9typeOfSumIT_T 0_E4typeET1_T2_EEEERKNS4_IS6_SA_SB_EERKNS4_IS7_SA_ SB_EE+0x31b)[0x7fe15fcd535b] [VAC-PC-WIN10:05390] [ 5] interFoam(_ZN4Foam14GeometricFieldIdNS_12fvPatchFi eldENS_7volMeshEE5relaxEd+0x63)[0x7fe15fcd8543] [VAC-PC-WIN10:05390] [ 6] interFoam(_ZN4Foam14GeometricFieldIdNS_12fvPatchFi eldENS_7volMeshEE5relaxEv+0x147)[0x7fe15fcd8997] [VAC-PC-WIN10:05390] [ 7] interFoam(+0x4ea18)[0x7fe15fc4ea18] [VAC-PC-WIN10:05390] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7fe158a91b97] [VAC-PC-WIN10:05390] [ 9] interFoam(+0x567ea)[0x7fe15fc567ea] [VAC-PC-WIN10:05390] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 0 on node VAC-PC-WIN10 exited on signal 11 (Segmentation fault). Looking into the log.interFoam output following error is found: GAMG: Solving for p_rgh, Initial residual = 1.45645557196383e-05, Final residual = 2.40593904610264e-07, No Iterations 3 [VAC-PC-WIN10:05389] *** Process received signal *** [VAC-PC-WIN10:05389] Signal: Segmentation fault (11) [VAC-PC-WIN10:05389] Signal code: (-6) [VAC-PC-WIN10:05389] Failing at address: 0x3e80000150d [VAC-PC-WIN10:05389] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7f31d0aaef20] [VAC-PC-WIN10:05389] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f31d0aaee97] [VAC-PC-WIN10:05389] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7f31d0aaef20] [VAC-PC-WIN10:05389] [ 3] interFoam(_ZN4Foam8subtractIddNS_12fvPatchFieldENS _7volMeshEEEvRNS_14GeometricFieldINS_9typeOfSumIT_ T0_E4typeET1_T2_EERKNS3_IS5_S9_SA_EERKNS3_IS6_S9_S A_EE+0x269)[0x7f31d7c70de9] [VAC-PC-WIN10:05389] [ 4] interFoam(_ZN4FoammiIddNS_12fvPatchFieldENS_7volMe shEEENS_3tmpINS_14GeometricFieldINS_9typeOfSumIT_T 0_E4typeET1_T2_EEEERKNS4_IS6_SA_SB_EERKNS4_IS7_SA_ SB_EE+0x31b)[0x7f31d7cd535b] [VAC-PC-WIN10:05389] [ 5] interFoam(_ZN4Foam14GeometricFieldIdNS_12fvPatchFi eldENS_7volMeshEE5relaxEd+0x63)[0x7f31d7cd8543] [VAC-PC-WIN10:05389] [ 6] interFoam(_ZN4Foam14GeometricFieldIdNS_12fvPatchFi eldENS_7volMeshEE5relaxEv+0x147)[0x7f31d7cd8997] [VAC-PC-WIN10:05389] [ 7] interFoam(+0x4ea18)[0x7f31d7c4ea18] [VAC-PC-WIN10:05389] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f31d0a91b97] [VAC-PC-WIN10:05389] [ 9] interFoam(+0x567ea)[0x7f31d7c567ea] [VAC-PC-WIN10:05389] *** End of error message *** [VAC-PC-WIN10:05390] *** Process received signal *** [VAC-PC-WIN10:05390] Signal: Segmentation fault (11) [VAC-PC-WIN10:05390] Signal code: (-6) [VAC-PC-WIN10:05390] Failing at address: 0x3e80000150e [VAC-PC-WIN10:05390] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7fe158aaef20] [VAC-PC-WIN10:05390] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7fe158aaee97] [VAC-PC-WIN10:05390] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7fe158aaef20] [VAC-PC-WIN10:05390] [ 3] interFoam(_ZN4Foam8subtractIddNS_12fvPatchFieldENS _7volMeshEEEvRNS_14GeometricFieldINS_9typeOfSumIT_ T0_E4typeET1_T2_EERKNS3_IS5_S9_SA_EERKNS3_IS6_S9_S A_EE+0x269)[0x7fe15fc70de9] [VAC-PC-WIN10:05390] [ 4] interFoam(_ZN4FoammiIddNS_12fvPatchFieldENS_7volMe shEEENS_3tmpINS_14GeometricFieldINS_9typeOfSumIT_T 0_E4typeET1_T2_EEEERKNS4_IS6_SA_SB_EERKNS4_IS7_SA_ SB_EE+0x31b)[0x7fe15fcd535b] [VAC-PC-WIN10:05390] [ 5] interFoam(_ZN4Foam14GeometricFieldIdNS_12fvPatchFi eldENS_7volMeshEE5relaxEd+0x63)[0x7fe15fcd8543] [VAC-PC-WIN10:05390] [ 6] interFoam(_ZN4Foam14GeometricFieldIdNS_12fvPatchFi eldENS_7volMeshEE5relaxEv+0x147)[0x7fe15fcd8997] [VAC-PC-WIN10:05390] [ 7] interFoam(+0x4ea18)[0x7fe15fc4ea18] [VAC-PC-WIN10:05390] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7fe158a91b97] [VAC-PC-WIN10:05390] [ 9] interFoam(+0x567ea)[0x7fe15fc567ea] [VAC-PC-WIN10:05390] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 0 on node VAC-PC-WIN10 exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- I cant really see where the error is. It is important to note that if i run interFoam without the dynamicMeshDict in the constant folder, the case runs normally... What am i missing? Is there an initialization i haven't done prior to using the dynamicMesh? For reference, the dynamicMeshDict is as follows: FoamFile { version 2.0; format ascii; class dictionary; location "constant"; object dynamicMeshDict; } // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // dynamicFvMesh dynamicRefineFvMesh; dynamicRefineFvMeshCoeffs { // How often to refine refineInterval 1; // Field to be refinement on field alpha.water; // Refine field inbetween lower..upper lowerRefineLevel 0.1; upperRefineLevel 0.99; // If value < unrefineLevel unrefine unrefineLevel 10; // Have slower than 2:1 refinement nBufferLayers 1; // Refine cells only up to maxRefinement levels maxRefinement 2; // Stop refinement if maxCells reached maxCells 6000000; // Flux field and corresponding velocity field. Fluxes on changed // faces get recalculated by interpolating the velocity. Use 'none' // on surfaceScalarFields that do not need to be reinterpolated. correctFluxes ( (phi none) (nHatf none) (rhoPhi none) (alphaPhi0.water none) //Inserted due to error provided by OpenFOAM (alphaPhiUn none) //Inserted due to error provided by OpenFOAM (ghf none) ); // Write the refinement level as a volScalarField dumpLevel true; } // ************************************************** *********************** // I appreciate your time! /Rasmus %%---------------------------EDIT--------------------%% I've included: "cellDisplacement.*" { solver GAMG; tolerance 1e-5; relTol 0; smoother GaussSeidel; cacheAgglomeration true; nCellsInCoarsestLevel 10; agglomerator faceAreaPair; mergeLevels 1; } In the fvSolution, which reduced the first error I've listed to only being shown once instead of the two errors starting with *** Process received signal ***... Last edited by Rasmusiwersen; November 12, 2019 at 10:30. Reason: Update on status |
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November 12, 2019, 12:04 |
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#2 |
Member
Cyrille Bonamy
Join Date: Mar 2015
Location: Grenoble, France
Posts: 85
Rep Power: 11 |
have you tried to run an interfoam tutorial with dynamic mesh to be sure it does not come from the installation?
I see the keyword win10 in the log. Do you use an openfoam windows10 version? |
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November 13, 2019, 01:31 |
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#3 | |
Member
Rasmus Iwersen
Join Date: Jan 2019
Location: Denmark
Posts: 81
Rep Power: 8 |
Hi, thank you for reading my (way too long) question!
Quote:
No I am running on ubuntu, it is just installed through powershell on windows10. |
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November 13, 2019, 02:27 |
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#4 |
Member
Cyrille Bonamy
Join Date: Mar 2015
Location: Grenoble, France
Posts: 85
Rep Power: 11 |
Ok, your mesh is 3D? (because dynamicMesh support only 3D mesh)
Is it based on tetra or hex? |
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November 13, 2019, 02:31 |
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#5 |
Member
Rasmus Iwersen
Join Date: Jan 2019
Location: Denmark
Posts: 81
Rep Power: 8 |
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November 13, 2019, 02:42 |
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#6 |
Member
Cyrille Bonamy
Join Date: Mar 2015
Location: Grenoble, France
Posts: 85
Rep Power: 11 |
in fvSolution, there is the pcorr section, but your log says that everything is fine...
I have no idea. |
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November 13, 2019, 02:47 |
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#7 | |
Member
Rasmus Iwersen
Join Date: Jan 2019
Location: Denmark
Posts: 81
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Quote:
I am trying to run the same case on a bigger computer. If it works, i'll let you know. /Rasmus |
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November 13, 2019, 02:51 |
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#8 |
Member
Cyrille Bonamy
Join Date: Mar 2015
Location: Grenoble, France
Posts: 85
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Ha! I thought about the memory problem, but I can not think that it is the problem because the refinement is not huge.
You are passing from 5438309 to 5637382 cells. |
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November 13, 2019, 03:52 |
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#9 | |
Member
Rasmus Iwersen
Join Date: Jan 2019
Location: Denmark
Posts: 81
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Quote:
[ip-172-31-1-177:10360] *** Process received signal *** [ip-172-31-1-177:10360] Signal: Floating point exception (8) [ip-172-31-1-177:10360] Signal code: (-6) [ip-172-31-1-177:10360] Failing at address: 0x3e800002878 [ip-172-31-1-177:10360] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7f1612cb3f20] [ip-172-31-1-177:10360] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f1612cb3e97] [ip-172-31-1-177:10360] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7f1612cb3f20] [ip-172-31-1-177:10360] [ 3] /home/ubuntu/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so(_ZNK4Foam2fv15cellLimi$ [ip-172-31-1-177:10360] [ 4] /home/ubuntu/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so(_ZNK4Foam2fv10gradSche$ [ip-172-31-1-177:10360] [ 5] /home/ubuntu/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so(_ZNK4Foam2fv15correcte$ [ip-172-31-1-177:10360] [ 6] /home/ubuntu/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so(_ZNK4Foam2fv15correcte$ [ip-172-31-1-177:10360] [ 7] /home/ubuntu/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so(_ZNK4Foam2fv13limitedS$ [ip-172-31-1-177:10360] [ 8] /home/ubuntu/OpenFOAM/OpenFOAM-v1906/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so(_ZN4Foam2fv20gaussLapl$ [ip-172-31-1-177:10360] [ 9] interFoam(+0x98eff)[0x55556367ceff] [ip-172-31-1-177:10360] [10] interFoam(+0x4e52c)[0x55556363252c] [ip-172-31-1-177:10360] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f1612c96b97] [ip-172-31-1-177:10360] [12] interFoam(+0x567ea)[0x55556363a7ea] [ip-172-31-1-177:10360] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 4 with PID 0 on node ip-172-31-1-177 exited on signal 8 (Floating point exception). Now i am dealing with a floating point exception.. |
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November 13, 2019, 03:56 |
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#10 |
Member
Cyrille Bonamy
Join Date: Mar 2015
Location: Grenoble, France
Posts: 85
Rep Power: 11 |
FPE == division by 0... Perhaps a problem with the mesh (a cell with zero volume)? What is the output of checkmesh?
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November 13, 2019, 03:57 |
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#11 | |
Member
Rasmus Iwersen
Join Date: Jan 2019
Location: Denmark
Posts: 81
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Quote:
Doesn't look like there are any problems.. Create mesh for time = 0 Time = 0 Mesh stats points: 5668407 faces: 16544381 internal faces: 16345753 cells: 5438309 faces per cell: 6.04786046544983 boundary patches: 8 point zones: 0 face zones: 0 cell zones: 0 Overall number of cells of each type: hexahedra: 5277916 prisms: 53760 wedges: 0 pyramids: 0 tet wedges: 0 tetrahedra: 0 polyhedra: 106633 Breakdown of polyhedra by number of faces: faces number of cells 6 20414 9 68682 12 16694 15 762 18 81 Checking topology... Boundary definition OK. Cell to face addressing OK. Point usage OK. Upper triangular ordering OK. Face vertices OK. Number of regions: 1 (OK). Checking patch topology for multiply connected surfaces... Patch Faces Points Surface topology inlet 3450 3596 ok (non-closed singly connected) atmosphere 1150 1276 ok (non-closed singly connected) outlet 4600 4756 ok (non-closed singly connected) top 20798 21314 ok (non-closed singly connected) bottom 25910 26478 ok (non-closed singly connected) back 4800 4961 ok (non-closed singly connected) front 4800 4961 ok (non-closed singly connected) cylinder1 133120 133328 ok (non-closed singly connected) Checking faceZone topology for multiply connected surfaces... No cellZones found. Checking geometry... Overall domain bounding box (0 0 0) (60 45 40.0000000000001) Mesh has 3 geometric (non-empty/wedge) directions (1 1 1) Mesh has 3 solution (non-empty) directions (1 1 1) Boundary openness (-5.58520569744795e-15 -1.45795060987434e-16 1.2460434568671e-15) OK. Max cell openness = 3.62473640382341e-16 OK. Max aspect ratio = 9.42523631287193 OK. Minimum face area = 0.000167617667811691. Maximum face area = 0.539799921057025. Face area magnitudes OK. Min volume = 1.0727931765941e-05. Max volume = 0.214606872044131. Total volume = 107874.685055143. Cell volumes OK. Mesh non-orthogonality Max: 51.9162638698642 average: 7.15419368319089 Non-orthogonality check OK. Face pyramids OK. Max skewness = 0.683329567945927 OK. Coupled point location match (average 0) OK. Mesh OK. End |
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February 23, 2020, 04:51 |
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#12 |
New Member
mengge
Join Date: Feb 2020
Posts: 8
Rep Power: 6 |
hi, i am encountering the same problem with Floating point exception, do you have any idea on how to solve that?
and it doesn't seem like something is wrong with checkmesh. Thanks. |
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