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Error while running SnappyHex in parallel

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Old   February 8, 2016, 08:42
Default Error while running SnappyHex in parallel
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Myth
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Hi this is Mithun, I am relatively new to OF. I am trying to do a snappyHex mesh in parallel. In order to do so I follow this sequence.
blockMesh
decomposePar
foamJob -s -p renumberMesh -overwrite
foamJob -s -p snappyHexMesh -overwrite

The error that I receive is as follows
I would appreciate if someone can help me in layman's terms.

Quote:
Smoothing patch points ...
Smoothing iteration 0
Found 78 non-manifold point(s).
Scaling iteration 0
Moving mesh using displacement scaling : min:1 max:1
Correcting 2-D mesh motion--> FOAM Warning :
From function motionSmootherAlgo::modifyMotionPoints(pointField& )
in file motionSmoother/motionSmootherAlgo.C at line 660
2D mesh-motion probably not correct in parallel
--> FOAM Warning :
From function twoDPointCorrector::calcAddressing()
in file twoDPointCorrector/twoDPointCorrector.C at line 145
the number of vertices in the geometry is odd - this should not be the case for a 2-D case. Please check the geometry.
--> FOAM Warning :
From function twoDPointCorrector::calcAddressing()
in file twoDPointCorrector/twoDPointCorrector.C at line 154
The number of points in the mesh is not equal to twice the number of edges normal to the plane - this may be OK only for wedge geometries.
Please check the geometry or adjust the orthogonality tolerance.

Number of normal edges: 514721 number of points: 549703
...done
[5] processorPolyPatch::calcGeometry : Writing my 904 faces to OBJ file "/home/mithun/Mithun/2016/Tutorials/run/gearMain/gearSnappy/processor5/procBoundary5to4_faces.obj"
[3] processorPolyPatch::calcGeometry : Writing my 2310 faces to OBJ file "/home/mithun/Mithun/2016/Tutorials/run/gearMain/gearSnappy/processor3/procBoundary3to4_faces.obj"
[1] processorPolyPatch::calcGeometry : Writing my 1770 faces to OBJ file "/home/mithun/Mithun/2016/Tutorials/run/gearMain/gearSnappy/processor1/procBoundary1to4_faces.obj"
[4] processorPolyPatch::calcGeometry : Writing my 2310 faces to OBJ file "/home/mithun/Mithun/2016/Tutorials/run/gearMain/gearSnappy/processor4/procBoundary4to3_faces.obj"
[0] processorPolyPatch::calcGeometry : Writing my 1904 faces to OBJ file "/home/mithun/Mithun/2016/Tutorials/run/gearMain/gearSnappy/processor0/procBoundary0to1_faces.obj"
[2] processorPolyPatch::calcGeometry : Writing my 1227 faces to OBJ file "/home/mithun/Mithun/2016/Tutorials/run/gearMain/gearSnappy/processor2/procBoundary2to5_faces.obj"
[2] processorPolyPatch::calcGeometry : Dumping cell centre lines between corresponding face centres to OBJ file"/home/mithun/Mithun/2016/Tutorials/run/gearMain/gearSnappy/processor2/procBoundary2to5_faceCentresConnections.obj"
[5] processorPolyPatch::calcGeometry : Dumping cell centre lines between corresponding face centres to OBJ file"/home/mithun/Mithun/2016/Tutorials/run/gearMain/gearSnappy/processor5/procBoundary5to4_faceCentresConnections.obj"
[3] processorPolyPatch::calcGeometry : Dumping cell centre lines between corresponding face centres to OBJ file"/home/mithun/Mithun/2016/Tutorials/run/gearMain/gearSnappy/processor3/procBoundary3to4_faceCentresConnections.obj"
[1] processorPolyPatch::calcGeometry : Dumping cell centre lines between corresponding face centres to OBJ file"/home/mithun/Mithun/2016/Tutorials/run/gearMain/gearSnappy/processor1/procBoundary1to4_faceCentresConnections.obj"
[0] processorPolyPatch::calcGeometry : Dumping cell centre lines between corresponding face centres to OBJ file"/home/mithun/Mithun/2016/Tutorials/run/gearMain/gearSnappy/processor0/procBoundary0to1_faceCentresConnections.obj"
[2]
[2]
[2] --> FOAM FATAL ERROR:
[2] face 631 area does not match neighbour by 0.07483415% -- possible face ordering problem.
patchrocBoundary2to5 my area:0.001681062 neighbour area:0.001679805 matching tolerance:1.158685e-07
Mesh face:1269055 vertices:4((19.18875 27.09357 1.375) (19.16188 27.09614 1.375) (19.16188 27.09494 1.4375) (19.18875 27.09535 1.4375))
If you are certain your matching is correct you can increase the 'matchTolerance' setting in the patch dictionary in the boundary file.
Rerun with processor debug flag set for more information.
[2]
[2] From function processorPolyPatch::calcGeometry()
[2] in file meshes/polyMesh/polyPatches/constraint/processor/processorPolyPatch.C at line 243.
[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.
--------------------------------------------------------------------------
[5]
[5]
[5] --> FOAM FATAL ERROR:
[5] face 114 area does not match neighbour by 0.8646605% -- possible face ordering problem.
patchrocBoundary5to4 my area:0.002833827 neighbour area:0.002858436 matching tolerance:1.941542e-07
Mesh face:1264819 vertices:4((15.59821 66.95923 1) (15.53375 66.95 1) (15.53375 66.90625 1) (15.5875 66.90625 1))
If you are certain your matching is correct you can increase the 'matchTolerance' setting in the patch dictionary in the boundary file.
Rerun with processor debug flag set for more information.
[5]
[5] From function processorPolyPatch::calcGeometry()
[5] in file meshes/polyMesh/polyPatches/constraint/processor/processorPolyPatch.C at line 243.
[5]
FOAM parallel run exiting
[5]
[4] processorPolyPatch::calcGeometry : Dumping cell centre lines between corresponding face centres to OBJ file"/home/mithun/Mithun/2016/Tutorials/run/gearMain/gearSnappy/processor4/procBoundary4to3_faceCentresConnections.obj"
[3]
[3]
[3] --> FOAM FATAL ERROR:
[3] face 145 area does not match neighbour by 0.07211154% -- possible face ordering problem.
patchrocBoundary3to4 my area:0.006368358 neighbour area:0.006372952 matching tolerance:4.568779e-07
Mesh face:1258886 vertices:4((-15.16007 65.90185 0.75) (-15.21125 65.9 0.75) (-15.21125 65.9 0.625) (-15.16061 65.90215 0.625))
If you are certain your matching is correct you can increase the 'matchTolerance' setting in the patch dictionary in the boundary file.
Rerun with processor debug flag set for more information.
[3]
[3] From function processorPolyPatch::calcGeometry()
[3] in file meshes/polyMesh/polyPatches/constraint/processor/processorPolyPatch.C at line 243.
[3]
FOAM parallel run exiting
[3]
[1]
[1]
[1] --> FOAM FATAL ERROR:
[1] face 99 area does not match neighbour by 1.773816% -- possible face ordering problem.
patchrocBoundary1to4 my area:0.02959001 neighbour area:0.03011958 matching tolerance:1.935907e-06
Mesh face:1269768 vertices:7((-3.225 22.5875 0.75) (-3.225 22.5875 0.875) (-3.225 22.5875 1) (-3.17125 22.5875 1) (-3.108149 22.57815 1) (-3.108149 22.57815 0.875) (-3.103837 22.57564 0.75))
If you are certain your matching is correct you can increase the 'matchTolerance' setting in the patch dictionary in the boundary file.
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 243.
[1]
FOAM parallel run exiting
[1]
[0]
[0]
[0] --> FOAM FATAL ERROR:
[0] face 698 area does not match neighbour by 2.012861% -- possible face ordering problem.
patchrocBoundary0to1 my area:0.005005237 neighbour area:0.004905493 matching tolerance:4.359999e-07
Mesh face:1268901 vertices:5((-15.26722 10.5982 0.5) (-15.265 10.57812 0.5) (-15.26436 10.5574 0.5) (-15.26371 10.55757 0.375) (-15.26943 10.59639 0.375))
If you are certain your matching is correct you can increase the 'matchTolerance' setting in the patch dictionary in the boundary file.
Rerun with processor debug flag set for more information.
[0]
[0] From function processorPolyPatch::calcGeometry()
[0] in file meshes/polyMesh/polyPatches/constraint/processor/processorPolyPatch.C at line 243.
[0]
FOAM parallel run exiting
[0]
[4]
[4]
[4] --> FOAM FATAL ERROR:
[4] face 145 area does not match neighbour by 0.07211154% -- possible face ordering problem.
patchrocBoundary4to3 my area:0.006372952 neighbour area:0.006368358 matching tolerance:4.567569e-07
Mesh face:1267388 vertices:4((-15.16007 65.90185 0.75) (-15.1606 65.90338 0.625) (-15.21125 65.9 0.625) (-15.21125 65.9 0.75))
If you are certain your matching is correct you can increase the 'matchTolerance' setting in the patch dictionary in the boundary file.
Rerun with processor debug flag set for more information.
[4]
[4] From function processorPolyPatch::calcGeometry()
[4] in file meshes/polyMesh/polyPatches/constraint/processor/processorPolyPatch.C at line 243.
[4]
FOAM parallel run exiting
[4]
--------------------------------------------------------------------------
mpirun has exited due to process rank 2 with PID 3228 on
node PFSNSQ855105 exiting improperly. There are two reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).

Last edited by mg.mithun; February 8, 2016 at 08:46. Reason: text modification
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Old   February 10, 2016, 14:13
Default Same here
  #2
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Aaron E.
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Yup, I found this post because I'm getting the same error. And worse is that I'm reconstructing a simulation from a case setup that I did last year, and it meshed just fine. The difference is that I've upgraded OpenFOAM to 3.0 since then, but I'm not sure how that would effect snappyHexMesh.

Perhaps its time to downgrade OpenFOAM and give it another try, but I still wish I knew what this error meant.
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