[Rasmusiwersen]

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 ***...

[cyss38]

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?

[Rasmusiwersen]

Hi, thank you for reading my (way too long) question!

Originally Posted by cyss38

have you tried to run an interfoam tutorial with dynamic mesh to be sure it does not come from the installation?
?

Yeah, I've tried running dambBreakWithObstacle which seems to fine just fine.

Originally Posted by cyss38

I see the keyword win10 in the log. Do you use an openfoam windows10 version?

No I am running on ubuntu, it is just installed through powershell on windows10.

[cyss38]

Ok, your mesh is 3D? (because dynamicMesh support only 3D mesh)


Is it based on tetra or hex?

[Rasmusiwersen]

Originally Posted by cyss38

Ok, your mesh is 3D? (because dynamicMesh support only 3D mesh)

Oh, i didn't know that. But yes, the mesh is in 3D.

Originally Posted by cyss38

Is it based on tetra or hex?

It is based on Hexahedras..

[cyss38]

in fvSolution, there is the pcorr section, but your log says that everything is fine...
I have no idea.

[Rasmusiwersen]

Originally Posted by cyss38

in fvSolution, there is the pcorr section, but your log says that everything is fine...
I have no idea.

Okay, well thank you for trying anyway! I've found a post suggesting it might be a problem with lack of memory, mpirun problems: exited on signal 11 (segmentation fault)

I am trying to run the same case on a bigger computer. If it works, i'll let you know.

/Rasmus

[cyss38]

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.

[Rasmusiwersen]

Originally Posted by cyss38

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.

So i tried a larger machine and got a different error:
[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..

[cyss38]

FPE == division by 0... Perhaps a problem with the mesh (a cell with zero volume)? What is the output of checkmesh?

[Rasmusiwersen]

Originally Posted by cyss38

FPE == division by 0... Perhaps a problem with the mesh (a cell with zero volume)? What is the output of checkmesh?

Yeah, some non physical phenomena.

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

[mengge]

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.