[shimakasaei]

Hi all,
I have a simulation model which has boxes inside a flume. All geometeries are simple without any curvature or slope.
After running snappyHexMesh (I used it to generate boxes and refine mesh in area around blocks), I started the simulation and it was crashed showing an error that :No base point for face 11252089, 5(3950857 3977716 3977717 4849004 3950858), produces a decomposition that has a minimum volume greater than tolerance.
When I run checkMesh -allGeometery, it shows me concaveCells and Faces.
Here is what I have with checkMesh -allGeometery:
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create polyMesh for time = 0

Enabling all geometry checks.

Time = 0

Mesh stats
points: 126245292
faces: 376149362
internal faces: 374320813
cells: 124953645
faces per cell: 6.005989
boundary patches: 9
point zones: 0
face zones: 0
cell zones: 0

Overall number of cells of each type:
hexahedra: 124702557
prisms: 180
wedges: 0
pyramids: 0
tet wedges: 102
tetrahedra: 0
polyhedra: 250806
Breakdown of polyhedra by number of faces:
faces number of cells
5 232
6 2644
8 65
9 246235
11 12
12 1512
15 106

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 Bounding box
inlet 11250 11476 ok (non-closed singly connected) (0 0 0) (0 1.5 0.75)
outlet 11250 11476 ok (non-closed singly connected) (15 0 0) (15 1.5 0.75)
leftwall 294564 297016 ok (non-closed singly connected) (0 1.5 0) (15 1.5 0.75)
rightwall 294564 297016 ok (non-closed singly connected) (0 0 0) (15 0 0.75)
bottom 736800 740222 ok (non-closed singly connected) (0 0 0) (15 1.5 0)
top 223050 224851 ok (non-closed singly connected) (0 0 0.75) (15 1.5 0.75)
A3b1 85832 86310 ok (non-closed singly connected) (6.59994 0.1241463 0) (6.850059 0.3758527 0.75)
A3b2 85602 86097 ok (non-closed singly connected) (6.599942 0.6241819 0) (6.850127 0.875807 0.75)
A3b3 85637 86124 ok (non-closed singly connected) (6.599926 1.124148 0) (6.850074 1.375607 0.75)

Checking geometry...
Overall domain bounding box (0 0 0) (15 1.5 0.75)
Mesh has 3 geometric (non-empty/wedge) directions (1 1 1)
Mesh has 3 solution (non-empty) directions (1 1 1)
Boundary openness (-6.720224e-17 -1.083957e-13 2.300914e-12) OK.
Max cell openness = 2.821353e-16 OK.
Max aspect ratio = 5.383686 OK.
Minimum face area = 5.105227e-06. Maximum face area = 0.0001351346. Face area magnitudes OK.
Min volume = 1.352747e-08. Max volume = 1.234041e-06. Total volume = 16.7344. Cell volumes OK.
Mesh non-orthogonality Max: 53.93429 average: 1.296363
Non-orthogonality check OK.
Face pyramids OK.
Max skewness = 0.7117331 OK.
Coupled point location match (average 0) OK.
Face tets OK.
Min/max edge length = 0.002001521 0.0136275 OK.
*There are 461 faces with concave angles between consecutive edges. Max concave angle = 71.20371 degrees.
<<Writing 461 faces with concave angles to set concaveFaces
Face flatness (1 = flat, 0 = butterfly) : min = 0.8910414 average = 0.9999999
All face flatness OK.
Cell determinant (wellposedness) : minimum: 0.1489069 average: 8.041237
Cell determinant check OK.
***Concave cells (using face planes) found, number of cells: 244507
<<Writing 244507 concave cells to set concaveCells
Face interpolation weight : minimum: 0.106129 average: 0.4995235
Face interpolation weight check OK.
Face volume ratio : minimum: 0.01914057 average: 0.9975404
Face volume ratio check OK.

Failed 1 mesh checks.

End

I also attached picture of how concave cells look in paraview.

I would appreciate if anyone can help me solve this!!

Thanks,
Shima

[HPE]

- concavity should be ok.
- could you please attach the full error log file of the simulation?
- could you please do `checkMesh -allTopology -allGeometry`, and attach its log file?

[shimakasaei]

Attached is the error of the simulation, I also attached the result of running checkMesh -allGeometery command. I should run checkMesh -allTopology as well to get the results.

[shimakasaei]

Originally Posted by HPE

- concavity should be ok.
- could you please attach the full error log file of the simulation?
- could you please do `checkMesh -allTopology -allGeometry`, and attach its log file?

Attached is the error of the simulation, I also attached the result of running checkMesh -allGeometery command. I should run checkMesh -allTopology as well to get the results.

[HPE]

- the error log of the simulation is not full.
- can you decompose your case with fewer processors, and see if this helps.
- your mesh quality seems to be OK to me.

[shimakasaei]

Originally Posted by HPE

- the error log of the simulation is not full.
- can you decompose your case with fewer processors, and see if this helps.
- your mesh quality seems to be OK to me.

I tried to decompose my case on 16 processors and then run the snappyHexMesh and it shows me an error as well:

new cannot satisfy memory request.
This does not necessarily mean you have run out of virtual memory.
It could be due to a stack violation caused by e.g. bad use of pointers or an out of date shared library
[zagros-0-07:49305] *** Process received signal ***
[zagros-0-07:49305] Signal: Aborted (6)
[zagros-0-07:49305] Signal code: (-6)
new cannot satisfy memory request.
This does not necessarily mean you have run out of virtual memory.
It could be due to a stack violation caused by e.g. bad use of pointers or an out of date shared library
[zagros-0-07:49310] *** Process received signal ***
[zagros-0-07:49310] Signal: Aborted (6)
[zagros-0-07:49310] Signal code: (-6)
[zagros-0-07:49305] [ 0] [zagros-0-07:49310] /lib64/libc.so.6(+0x35250)[0x7f29a1703250]
[zagros-0-07:49305] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x7f29a17031d7]
[zagros-0-07:49305] [ 2] /lib64/libc.so.6(abort+0x148)[0x7f29a17048c8]
[zagros-0-07:49305] [ 3] [ 0] /lib64/libc.so.6(+0x35250)[0x7fb92d639250]
[zagros-0-07:49310] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x7fb92d6391d7]
[zagros-0-07:49310] [ 2] /lib64/libc.so.6(abort+0x148)[0x7fb92d63a8c8]
[zagros-0-07:49310] [ 3] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam8newErrorEv+0x54)[0x7fb92e6fa264]
[zagros-0-07:49310] [ 4] /opt/ohpc/pub/compiler/gcc/5.4.0/lib64/libstdc++.so.6(_Znwm+0x2c)[0x7fb92df6b04c]
[zagros-0-07:49310] [ 5] /opt/ohpc/pub/compiler/gcc/5.4.0/lib64/libstdc++.so.6(_Znam+0x9)[0x7fb92df6b0d9]
[zagros-0-07:49310] [ 6] snappyHexMesh(_ZN4Foam4ListIiE7setSizeEi+0x2e)[0x423b4e]
[zagros-0-07:49310] [ 7] new cannot satisfy memory request.
This does not necessarily mean you have run out of virtual memory.
It could be due to a stack violation caused by e.g. bad use of pointers or an out of date shared library/home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam8newErrorEv+0x54)[0x7f29a27c4264]
[zagros-0-07:49305] [ 4] /opt/ohpc/pub/compiler/gcc/5.4.0/lib64/libstdc++.so.6(_Znwm+0x2c)[0x7f29a203504c]
[zagros-0-07:49305] [ 5] /opt/ohpc/pub/compiler/gcc/5.4.0/lib64/libstdc++.so.6(_Znam+0x9)[0x7f29a20350d9]
[zagros-0-07:49305] [ 6] snappyHexMesh(_ZN4Foam4ListIiE7setSizeEi+0x2e)[0x423b4e]
[zagros-0-07:49305] [ 7] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so(_ZN4Foam11DynamicListIiLj0ELj2E Lj1EE6appendERKi+0x30)[0x7fb93220b020]
/home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libfiniteVolume.so(_ZN4Foam11DynamicListIiLj0ELj2E Lj1EE6appendERKi+0x30)[0x7f29a62d5020]
[zagros-0-07:49305] [ 8] [zagros-0-07:49310] [ 8] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libdynamicMesh.so(_ZN4Foam14polyTopoChange7addFace ERKNS_4faceEiiiiibiib+0xbd)[0x7f29a3a7414d]
[zagros-0-07:49305] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libdynamicMesh.so(_ZN4Foam14polyTopoChange7addFace ERKNS_4faceEiiiiibiib+0x28e)[0x7fb92f9aa31e]
[zagros-0-07:49310] [ 9] [ 9] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libdynamicMesh.so(_ZN4Foam14polyTopoChange9setActi onERKNS_10topoActionE+0x410)[0x7fb92f9ad6e0]
[zagros-0-07:49310] [10] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libdynamicMesh.so(_ZNK4Foam7hexRef87addFaceERNS_14 polyTopoChangeEiRKNS_4faceEii+0xd9)[0x7fb92fa18bb9]
[zagros-0-07:49310] [11] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libdynamicMesh.so(_ZN4Foam7hexRef813setRefinementE RKNS_4ListIiEERNS_14polyTopoChangeE+0x280e)[0x7fb92fa2c38e]
/home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libdynamicMesh.so(_ZN4Foam14polyTopoChange9setActi onERKNS_10topoActionE+0x410)[0x7f29a3a776e0]
[zagros-0-07:49305] [10] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libdynamicMesh.so(_ZNK4Foam7hexRef87addFaceERNS_14 polyTopoChangeEiRKNS_4faceEii+0xd9)[0x7f29a3ae2bb9]
[zagros-0-07:49305] [11] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libdynamicMesh.so(_ZN4Foam7hexRef813setRefinementE RKNS_4ListIiEERNS_14polyTopoChangeE+0x280e)[0x7f29a3af638e]
[zagros-0-07:49305] [12] [zagros-0-07:49310] [12] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libsnappyHexMesh.so(_ZN4Foam14meshRefinement6refin eERKNS_4ListIiEE+0x54)[0x7f29a31d7284]
[zagros-0-07:49305] [13] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libsnappyHexMesh.so(_ZN4Foam14meshRefinement16refi neAndBalanceERKNS_6stringERNS_19decompositionMetho dERNS_16fvMeshDistributeERKNS_4ListIiEEd+0x46)[0x7f29a31d76c6]
[zagros-0-07:49305] [14] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libsnappyHexMesh.so(_ZN4Foam14meshRefinement6refin eERKNS_4ListIiEE+0x54)[0x7fb92f10d284]
/home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libsnappyHexMesh.so(_ZN4Foam18snappyRefineDriver11 shellRefineERKNS_20refinementParametersEi+0xcff)[0x7f29a3124e8f]
[zagros-0-07:49305] [15] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libsnappyHexMesh.so(_ZN4Foam18snappyRefineDriver8d oRefineERKNS_10dictionaryERKNS_20refinementParamet ersERKNS_14snapParametersEbbS3_+0x59e)[0x7f29a312729e]
[zagros-0-07:49305] [16] snappyHexMesh[0x418cb8]
[zagros-0-07:49305] [17] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f29a16efb35]
[zagros-0-07:49305] [18] snappyHexMesh[0x41a2d2]
[zagros-0-07:49305] *** End of error message ***
[zagros-0-07:49310] [13] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libsnappyHexMesh.so(_ZN4Foam14meshRefinement16refi neAndBalanceERKNS_6stringERNS_19decompositionMetho dERNS_16fvMeshDistributeERKNS_4ListIiEEd+0x46)[0x7fb92f10d6c6]
[zagros-0-07:49310] [14] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libsnappyHexMesh.so(_ZN4Foam18snappyRefineDriver11 shellRefineERKNS_20refinementParametersEi+0xcff)[0x7fb92f05ae8f]
[zagros-0-07:49310] [15] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libsnappyHexMesh.so(_ZN4Foam18snappyRefineDriver8d oRefineERKNS_10dictionaryERKNS_20refinementParamet ersERKNS_14snapParametersEbbS3_+0x59e)[0x7fb92f05d29e]
[zagros-0-07:49310] [16] snappyHexMesh[0x418cb8]
[zagros-0-07:49310] [17] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7fb92d625b35]
[zagros-0-07:49310] [18] snappyHexMesh[0x41a2d2]
[zagros-0-07:49310] *** End of error message ***

[zagros-0-07:49303] *** Process received signal ***
[zagros-0-07:49303] Signal: Aborted (6)
[zagros-0-07:49303] Signal code: (-6)
[zagros-0-07:49303] [ 0] /lib64/libc.so.6(+0x35250)[0x7f02af181250]
[zagros-0-07:49303] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x7f02af1811d7]
[zagros-0-07:49303] [ 2] /lib64/libc.so.6(abort+0x148)[0x7f02af1828c8]
[zagros-0-07:49303] [ 3] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam8newErrorEv+0x54)[0x7f02b0242264]
[zagros-0-07:49303] [ 4] /opt/ohpc/pub/compiler/gcc/5.4.0/lib64/libstdc++.so.6(_Znwm+0x2c)[0x7f02afab304c]
[zagros-0-07:49303] [ 5] /opt/ohpc/pub/compiler/gcc/5.4.0/lib64/libstdc++.so.6(_Znam+0x9)[0x7f02afab30d9]
[zagros-0-07:49303] [ 6] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libdynamicMesh.so(_ZN4Foam14polyTopoChange19reorde rCompactFacesEiRKNS_4ListIiEE+0x23e)[0x7f02b14f26ce]
[zagros-0-07:49303] [ 7] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libdynamicMesh.so(_ZN4Foam14polyTopoChange7compact EbbRiRNS_4ListIiEES4_+0xc1b)[0x7f02b14f89ab]
[zagros-0-07:49303] [ 8] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libdynamicMesh.so(_ZN4Foam14polyTopoChange17compac tAndReorderERKNS_8polyMeshEbbbRiRNS_5FieldINS_6Vec torIdEEEERNS_4ListIiEESC_RNSA_INS_9objectMapEEESF_ SF_SF_SF_SF_SF_SF_RNSA_INS_3MapIiEEEESC_SC_SJ_+0x1 1b)[0x7f02b14f932b]
[zagros-0-07:49303] [ 9] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libdynamicMesh.so(_ZN4Foam14polyTopoChange10change MeshERNS_8polyMeshEbbbb+0x28d)[0x7f02b14fba2d]
[zagros-0-07:49303] [10] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libsnappyHexMesh.so(_ZN4Foam14meshRefinement6refin eERKNS_4ListIiEE+0x7b)[0x7f02b0c552ab]
[zagros-0-07:49303] [11] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libsnappyHexMesh.so(_ZN4Foam14meshRefinement16refi neAndBalanceERKNS_6stringERNS_19decompositionMetho dERNS_16fvMeshDistributeERKNS_4ListIiEEd+0x46)[0x7f02b0c556c6]
[zagros-0-07:49303] [12] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libsnappyHexMesh.so(_ZN4Foam18snappyRefineDriver11 shellRefineERKNS_20refinementParametersEi+0xcff)[0x7f02b0ba2e8f]
[zagros-0-07:49303] [13] /home/OpenFoam/OpenFOAM-v1612+/platforms/linux64GccDPInt32Opt/lib/libsnappyHexMesh.so(_ZN4Foam18snappyRefineDriver8d oRefineERKNS_10dictionaryERKNS_20refinementParamet ersERKNS_14snapParametersEbbS3_+0x59e)[0x7f02b0ba529e]
[zagros-0-07:49303] [14] snappyHexMesh[0x418cb8]
[zagros-0-07:49303] [15] /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f02af16db35]
[zagros-0-07:49303] [16] snappyHexMesh[0x41a2d2]
[zagros-0-07:49303] *** End of error message ***

Do you have any idea if these errors are related?