CFD Online Discussion Forums - Mesquite - Adaptive mesh refinement / coarsening?

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- - Mesquite - Adaptive mesh refinement / coarsening? (https://www.cfd-online.com/Forums/openfoam-solving/110813-mesquite-adaptive-mesh-refinement-coarsening.html)

Hi,

Well is a way way way much slower, probably 5 times. In any case, all my previous cases are not working fine. At the moment I am playing with the length scales to see if I find the right values.

Regards,

Joel

Dear Sandeep:

I have run different cases on 4 processors. I have the same problem.

First: dynamicTopoFvMesh run well
but after various time steps > 200, I have this error

Code:

 ~~~ Mesh Quality Statistics ~~~ 

 Min: 0.551996

 Max: 0.999803

 Mean: 0.900042

 Cells: 386866

 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 



 Topo modifier time: 1.29494 s

 Bisections :: Total: 0, Surface: 0

 Collapses  :: Total: 0, Surface: 0

 Swaps      :: Total: 3, Surface: 0

 Mapping time: 1.1e-05 s

[manjaro:04482] *** Process received signal ***

[manjaro:04482] Signal: Floating point exception (8)

[manjaro:04482] Signal code:  (-6)

[manjaro:04482] Failing at address: 0x3e800001182

[manjaro:04482] [ 0] /usr/lib/libc.so.6(+0x35390) [0x7faf21a21390]

[manjaro:04482] [ 1] /usr/lib/libc.so.6(gsignal+0x39) [0x7faf21a21319]

[manjaro:04482] [ 2] /usr/lib/libc.so.6(+0x35390) [0x7faf21a21390]

[manjaro:04482] [ 3] /home/olivier/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64Gcc46DPOpt/libfiniteVolume.so(_ZNK4Foam19coupledFvPatchFieldINS_6TensorIdEEE5writeERNS_7OstreamE+0x122) [0x7faf2494d962]

[manjaro:04482] [ 4] /home/olivier/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64Gcc46DPOpt/libfiniteVolume.so(_ZN4FoamlsINS_6TensorIdEENS_12fvPatchFieldENS_7volMeshEEERNS_7OstreamES6_RKNS_14GeometricFieldIT_T0_T1_EE+0x15a) [0x7faf249d763a]

[manjaro:04482] [ 5] /home/olivier/OpenFOAM/olivier-1.6-ext/lib/linux64Gcc46DPOpt/libdynamicTopoFvMesh.so(_ZNK4Foam11coupledInfoINS_17dynamicTopoFvMeshEE4sendINS_14GeometricFieldINS_6TensorIdEENS_12fvPatchFieldENS_7volMeshEEEEEvRKNS_4ListINS_4wordEEERKSB_RKNSA_IiEERNS_8OSstreamE+0x88) [0x7faf1411f078]

[manjaro:04482] [ 6] /home/olivier/OpenFOAM/olivier-1.6-ext/lib/linux64Gcc46DPOpt/libdynamicTopoFvMesh.so(_ZN4Foam17dynamicTopoFvMesh18initFieldTransfersERNS_4ListINS_4wordEEERNS1_IS3_EERNS1_INS1_IcEEEES9_+0x8c8) [0x7faf140ba9b8]

[manjaro:04482] [ 7] /home/olivier/OpenFOAM/olivier-1.6-ext/lib/linux64Gcc46DPOpt/libdynamicTopoFvMesh.so(_ZN4Foam17dynamicTopoFvMesh9resetMeshEv+0x468) [0x7faf13ff82a8]

[manjaro:04482] [ 8] /home/olivier/OpenFOAM/olivier-1.6-ext/lib/linux64Gcc46DPOpt/libdynamicTopoFvMesh.so(_ZN4Foam17dynamicTopoFvMesh6updateEv+0x1ae) [0x7faf13ffaf5e]

[manjaro:04482] [ 9] sixDOFFoam() [0x419632]

[manjaro:04482] [10] /usr/lib/libc.so.6(__libc_start_main+0xf5) [0x7faf21a0db05]

[manjaro:04482] [11] sixDOFFoam() [0x41d239]

[manjaro:04482] *** End of error message ***

--------------------------------------------------------------------------

mpirun noticed that process rank 1 with PID 4482 on node manjaro exited on signal 8 (Floating point exception).

I will attempt to run with debug mode, to obtain more details.

Regards

Olivier

Dear Sandeep

I tested your latest version (01/15) in debug mode: fatal error: cells already calculated. When I run on one processor I have not this error.

Code:

[0]  Mapping Faces: 267

[0]  Mapping Cells: 228

[0]  Load starts: 4(0 66 133 200)

[0]  Load sizes: 4(66 67 67 67)

[0]  Load starts: 4(0 57 114 171)

[0]  Load sizes: 4{57}

[1]  Mapping Faces: 55

[1]  Mapping Cells: 30

[1]  Load starts: 4(0 13 27 41)

[1]  Load sizes: 4(13 14 14 14)

[1]  Load starts: 4(0 7 15 23)

[1]  Load sizes: 4(7 8 8 7)

[manjaro:04287] *** Process received signal ***

[manjaro:04287] Signal: Segmentation fault (11)

[manjaro:04287] Signal code:  (-6)

[manjaro:04287] Failing at address: 0x3e8000010bf

[2]  Mapping Faces: 16

[2]  Mapping Cells: 8

[2]  Load starts: 4(0 4 8 12)

[2]  Load sizes: 4{4}

[2]  Load starts: 4(0 2 4 6)

[2]  Load sizes: 4{2}

[3]  Mapping Faces: 87

[3]  Mapping Cells: 66

[3]  Load starts: 4(0 21 43 65)

[3]  Load sizes: 4(21 22 22 22)

[3]  Load starts: 4(0 16 33 50)

[3]  Load sizes: 4(16 17 17 16)

*** Error in `sixDOFFoam': double free or corruption (fasttop): 0x0000000001daab60 ***

[3] 

[3] 

[3] --> FOAM FATAL ERROR: 

[3] cells already calculated

[3] 

[3]     From function primitiveMesh::calcCells() const

[manjaro:04290] *** Process received signal ***

[3]     in file meshes/primitiveMesh/primitiveMeshCells.C at line 114.

[3] 

FOAM parallel run aborting

[3] 

[manjaro:04290] Signal: Segmentation fault (11)

[manjaro:04290] Signal code:  (-6)

[manjaro:04290] Failing at address: 0x3e8000010c2

[manjaro:04289] *** Process received signal ***

[manjaro:04289] Signal: Segmentation fault (11)

[manjaro:04289] Signal code:  (-6)

[manjaro:04289] Failing at address: 0x3e8000010c1

[manjaro:04289] [ 0] /usr/lib/libc.so.6(+0x35390) [0x7f792029a390]

[manjaro:04289] [ 1] /usr/lib/libc.so.6(gsignal+0x39) [0x7f792029a319]

[manjaro:04289] [ 2] /usr/lib/libc.so.6(+0x35390) [0x7f792029a390]

[manjaro:04289] [ 3] /home/olivier/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64Gcc46DPOpt/libOpenFOAM.so(_ZN4Foam16invertManyToManyINS_4ListIiEES2_EEviRKNS_5UListIT_EERNS1_IT0_EE+0x66) [0x7f79213d6736]

[manjaro:04289] [ 4] /home/olivier/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64Gcc46DPOpt/libOpenFOAM.so(_ZNK4Foam13primitiveMesh10cellPointsEv+0x7f) [0x7f79213da99f]

[manjaro:04289] [ 5] /home/olivier/OpenFOAM/olivier-1.6-ext/lib/linux64Gcc46DPOpt/libdynamicTopoFvMesh.so(_ZNK4Foam16cellSetAlgorithm8containsEi+0x25) [0x7f79129aece5]

[manjaro:04289] [ 6] /home/olivier/OpenFOAM/olivier-1.6-ext/lib/linux64Gcc46DPOpt/libdynamicTopoFvMesh.so(_ZN4Foam17dynamicTopoFvMesh21computeCoupledWeightsEiiRNS_4ListIiEERNS_5FieldIdEERNS4_INS_6VectorIdEEEEb+0x269) [0x7f7912917689]

[manjaro:04289] [ 7] /home/olivier/OpenFOAM/olivier-1.6-ext/lib/linux64Gcc46DPOpt/libdynamicTopoFvMesh.so(_ZN4Foam17dynamicTopoFvMesh14computeMappingEdbbiiii+0x405) [0x7f79128b30d5]

[manjaro:04289] [ 8] /home/olivier/OpenFOAM/olivier-1.6-ext/lib/linux64Gcc46DPOpt/libdynamicTopoFvMesh.so(_ZN4Foam17dynamicTopoFvMesh20computeMappingThreadEPv+0x126) [0x7f79128b65b6]

[manjaro:04289] [ 9] /home/olivier/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64Gcc46DPOpt/libOpenFOAM.so(_ZN4Foam13multiThreader10poolThreadEPv+0x6e) [0x7f79215548fe]

[manjaro:04289] [10] /usr/lib/libpthread.so.0(+0x80a2) [0x7f791fbd10a2]

[manjaro:04289] [11] /usr/lib/libc.so.6(clone+0x6d) [0x7f792034a3dd]

[manjaro:04289] *** End of error message ***

Regards,

Olivier

Olivier,

I've posted a fix for the floating-point exception issue. I'm not sure what's going on with the cellCells error - does it occur only in Debug?

[EDIT:]
Also - are you running this multi-threaded (i.e., threads > 1)?

Thanks

Sandeep,

I tested your latest version. The error is still there.

does it occur only in Debug?
==> no

are you running this multi-threaded (i.e., threads > 1)?
==> yes

Regards

Okay.. I'll look into the multi-threaded issue. Can you try with single-threaded for now, and see if the rest works?

Thanks

I've fixed the multi-threading issue as well. Hopefully, it should work now.

Sandeep:

Yes it works very fine, congratulation. However, now after various time steps, I have a problem at the boundaries, sorry

Quote:

~~~ Mesh Quality Statistics ~~~
Min: 0.351905
Max: 1
Mean: 0.832525
Cells: 159046
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[1]
[2]
[2]
[2] --> FOAM FATAL ERROR:
[2] face 30 area does not match neighbour by 0.0101978% -- possible face ordering problem.
patch: procBoundary2to1 my area:4.1039e-09 neighbour area: 4.10432e-09 matching tolerance: 0.0001
Mesh face: 76429 vertices: 3((0.0111005 0.0171076 0.0104443) (0.0110425 0.0170291 0.0105041) (0.0111254 0.0170277 0.0104461))
Rerun with processor debug flag set for more information.[1]
[1] --> FOAM FATAL ERROR:
[1] face 30 area does not match neighbour by 0.0101978% -- possible face ordering problem.
patch: procBoundary1to2 my area:4.10432e-09 neighbour area: 4.1039e-09 matching tolerance: 0.0001
Mesh face: 79637 vertices: 3((0.0111005 0.0171076 0.0104443) (0.0111254 0.0170277 0.0104461) (0.0110425 0.0170291 0.0105041))
Rerun with processor debug flag set for more information.
[1]
[1] From function processorPolyPatch::calcGeometry()
[1] in file meshes/polyMesh/polyPatches/constraint/processor/processorPolyPatch.C at line 216.
[1]
FOAM parallel run exiting
[1]

[2]
[2] From function processorPolyPatch::calcGeometry()
[2] in file meshes/polyMesh/polyPatches/constraint/processor/processorPolyPatch.C at line 216.
[2]
FOAM parallel run exiting
[2]
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 1 with PID 5264 on
node manjaro exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[manjaro:05262] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[manjaro:05262] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

Tomorrow, I will run in debug mode

Regards,

Olivier

Sandeep:

I carried out a run in debub mode:

Quote:

~~~ Mesh Quality Statistics ~~~
Min: 0.351905
Max: 1
Mean: 0.832525
Cells: 159046
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

From function void fvMesh::movePoints(const mapPolyMesh& meshMap)
in file fvMesh/fvMesh.C at line 594
Grabbing old cell volumes.
tmp<scalarField> polyMesh::movePoints(const pointField&) : Moving points for time 0.00042 index 42
Moving object leastSquaresVectors
Moving object mesquiteMotionSolver
Done moving
[1] [2]
[1]
[1] --> FOAM FATAL ERROR:
[1]
[2]
[2] --> FOAM FATAL ERROR:
[2] face 30 area does not match neighbour by 0.0101978% -- possible face ordering problem.
patch: procBoundary2to1 my area:4.1039e-09 neighbour area: 4.10432e-09 matching tolerance: 0.0001
Mesh face: 76429 vertices: 3((0.0111005 0.0171076 0.0104443) (0.0110425 0.0170291 0.0105041) (0.0111254 0.0170277 0.0104461))
Rerun with processor debug flag set for more information.
[2]
[2] From function processorPolyPatch::calcGeometry()
[2] in file meshes/polyMesh/polyPatches/constraint/processor/processorPolyPatch.Cface 30 area does not match neighbour by 0.0101978% -- possible face ordering problem.
patch: procBoundary1to2 my area:4.10432e-09 neighbour area: 4.1039e-09 matching tolerance: 0.0001
Mesh face: 79637 vertices: 3((0.0111005 0.0171076 0.0104443) (0.0111254 0.0170277 0.0104461) (0.0110425 0.0170291 0.0105041))
Rerun with processor debug flag set for more information.
[1]
[1] From function processorPolyPatch::calcGeometry()
[1] in file meshes/polyMesh/polyPatches/constraint/processor/processorPolyPatch.C at line at line 216.
[2]
FOAM parallel run exiting
[2]
216.
[1]
FOAM parallel run exiting

Regards,

Olivier

Could you give me a test case that I can work with?

Hi Sandeep,

A good day to you! I have modified the solver (it can work now in parallel and take in account viscous forces). Now, I am working with foam3.0 and I use parMetis method.

The solver works fine during various time steps, about 30000, up to an error:
<

Code:

ExecutionTime = 179843 s  ClockTime = 183110 s



Courant Number mean: 0.000429068 max: 0.007494 velocity magnitude: 0.346252

Time = 0.28947





 ~~~ Mesh Quality Statistics ~~~ 

 Min: 0.074796

 Max: 0.999982

 Mean: 0.849104

 Cells: 132815

 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 



 Topo modifier time: 0.687138 s

 Bisections :: Total: 0, Surface: 0

 Collapses  :: Total: 0, Surface: 0

 Swaps      :: Total: 3, Surface: 2

 Mapping time: 7e-06 s

 Reordering time: 0.03978 s

[1] 

[1] 

[1] --> FOAM FATAL ERROR: 

[1]  Mapping for inserted boundary face is incorrect. Found an empty masterObjects list.

 Face: 46348

 Patch: particle1

[1] 

[1]     From function void topoPatchMapper::calcInsertedFaceAddressing() const

[1]     in file fieldMapping/topoPatchMapper.C at line 137.

[1] 

FOAM parallel run aborting

[1]

code>

When I run another test case, I have the same error but on another patch.

Have you an idea?

Regards,

Olivier

Olivier,

If you are able to reproduce this consistently, then it would be helpful if you could write out the mesh at the time-step just prior to the crash, and then restart the simulation with a higher debug level (valid up to level 5) to produce more output. This should write out a few VTK files (related to the swaps) that you can visualize, and would also help me figure out what might be wrong.

Glad to know that you're finding this useful.

Hi Sandeep,

I have the same error than the one at post #91 from this page when running the GDI engine case. Bruno (wyldckat) have been helping me to resolve the issues with relation to the case, from the problem with the load balancing process and the loading of the parMetis libraries to the one with debbuging the dynamic mesh. Here are the results:

http://www.cfd-online.com/Forums/ope...balancing.html

I have sent to you through a private message the link to the debug package "turbDyMEngineFoam4subdomains.debug_at_358.3_3 58.4 .tar.gz" as well as the original case.

Thank you very much, Alvaro.

Tutorial for openFoam 2.3.0

I am using openFoam 2.3.0 and I managed to compile both the mesquite and the dynamicTopoFvMesh. I could run the text example circCylinder3d by Mooney (7th openFoam workshop) after initial hitch.

However I do not understand the other tutorials.

ballTranslation: The controlDict file does not have solver name. When I try to run the case with the 'Allrun' file that came with the case, it creates an empty log file and stops.
needleValveClosure: The controlDict file has line 'application icoFoamAutoMotion' which is suppose is the solver name. When I I try to run the case with the 'Allrun' file that came with the case, it creates a log file with following line.

Code:

/opt/openfoam230/bin/tools/RunFunctions: line 52: icoFoamAutoMotion: command not found
projectile: The controlDict file does not have solver name and there is no 'Allrun' file with the case.

Here is link to Kyle Mooney's files from the workshop.

Of course the tutorials were for old openFoam versions but can someone can please suggest modifications for openFoam2.3.0.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

In addition I have a case where a cube with in another cube is rotating with some speed. I want the mesh to update while the cube is rotating. Of course with current setup it does not. It would be nice if someone can help me fix this case. Here is link to the case.

http://www.mediafire.com/download/mb...bject_mod3.zip

Points between two slip boundaries do not move correctly with mesquiteMotionSolver

Hello ,

I would like to use Mesquite Motion Solver coupled with dynamicTopoFvMesh to simulate a case with a deforming boundary (which is deformed based on calculated data) .

I created a simple case based on the circCylinder3dHex tutorial but I got a problem. The points on the line between two slip boundaries do not move correctly as showed in pictures. I uploaded my case and please help me find out where did I make a mistake...(I am using Foam-extend 3.1)

By the way, I would like to use Mesquite Motion solver with interDyMFoam. However, the alpha1 value is not correct when the mesh is deformed. Could someone give me some suggestions about how to solve this problem ?

Thanks in advance !

Best regards !

Lu ZHOU