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Problems decomposing the mesh with decomposePar: contains face labels out of range

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Old   March 18, 2015, 10:43
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Stephanie
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Hello Bruno,

the installation of OpenFOAM on Ubuntu 14.4 did a friend of me. Therefore he used a video from YouTube.
I'm deeply grateful for your help. I tried the code, you have posted and it worked

Unfortunately I've got a new mistake:

Code:
 --> FOAM FATAL ERROR: 
Cell 0contains face labels out of range: 6(0 1 2 -1 -1 -1) Max face index = 189587

    From function polyMesh::polyMesh
(
    const IOobject&,
    const Xfer<pointField>&,
    const Xfer<faceList>&,
    const Xfer<cellList>&
)

    in file meshes/polyMesh/polyMesh.C at line 654.

FOAM aborting

#0  Foam::error::printStack(Foam::Ostream&) at ??:?
#1  Foam::error::abort() at ??:?
#2   Foam::polyMesh::polyMesh(Foam::IOobject const&,  Foam::Xfer<Foam::Field<Foam::Vector<double> > >  const&, Foam::Xfer<Foam::List<Foam::face> > const&,  Foam::Xfer<Foam::List<Foam::cell> > const&, bool) at  ??:?
#3  
 at ??:?
#4  
 at ??:?
#5  __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
#6  
 at ??:?
Abgebrochen (Speicherabzug geschrieben)
I'm not sure, if it depends on runnig the case in parallel. I git these message when I type in <decomposePar>. When I did it the last time it run.. but now it doesn't work anymore.
Maybe you might help me again? It would be wonderful.

Thank you for your help,
best regards,

Stephie

Last edited by wyldckat; March 21, 2015 at 09:59. Reason: Added [CODE][/CODE]
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Old   March 21, 2015, 10:04
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Bruno Santos
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Hi Stephie,

My guess is that the mesh is damaged somehow. Run the following command:
Code:
checkMesh -allGeometry -allTopology
It will provide you with a detailed list of results on whether the mesh is OK or not.

If the mesh is OK, then I need to know a lot more details about the case you're trying to decompose, because that's a very generic error message. The details in specific are:
  • How did you generate the mesh?
  • Is the mesh OK?
  • How did you prepare the boundary conditions?
  • Does the case run in serial mode (i.e. not in parallel)?
  • What solver are/will you be using?
Best regards,
Bruno

PS: I've copied your post from here: mpirun not working in paralleö with OpenMPI (post #10) - to this new thread, because this new question is no longer an installation issue.
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Old   August 11, 2015, 12:02
Default Error in cyclic boundar condition
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Hashem Nowruzi
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Hello
i give a same error. my geometry is a simple cylinder, and i create it in a gambit. i specified a periodic BC for my mesh in gambit and then i convert it with fleunt3DMeshToFoam in a mdFoam solver of OpenFoam 2 1 1. then i change the boundary condition to "cyclic" and operate "foamUpgradecyclic". however, after this procedure, when i run "thendecomposePar", i give a below error:

Code:
stanford@stanford-Ideapad-Z460:~/Desktop/y$ decomposePar
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.1.1                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.1.1-221db2718bbb
Exec   : decomposePar
Date   : Aug 11 2015
Time   : 20:24:23
Host   : "stanford-Ideapad-Z460"
PID    : 4602
Case   : /home/stanford/Desktop/y
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh

Calculating distribution of cells
Selecting decompositionMethod scotch

Finished decomposition in 0.02999999999999999889 s

Calculating original mesh data

Distributing cells to processors

Distributing faces to processors

Distributing points to processors

Constructing processor meshes

Processor 0
    Number of cells = 650
    Number of faces shared with processor 1 = 123
    Number of faces shared with processor 3 = 60
    Number of processor patches = 2
    Number of processor faces = 183
    Number of boundary faces = 247


--> FOAM FATAL ERROR: 
Cell 637contains face labels out of range: 6(1721 1722 -1 788 1161 1418) Max face index = 2200

    From function polyMesh::polyMesh
(
    const IOobject&,
    const Xfer<pointField>&,
    const Xfer<faceList>&,
    const Xfer<cellList>&
)

    in file meshes/polyMesh/polyMesh.C at line 652.

FOAM aborting

#0  Foam::error::printStack(Foam::Ostream&) in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#1  Foam::error::abort() in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#2  Foam::polyMesh::polyMesh(Foam::IOobject const&, Foam::Xfer<Foam::Field<Foam::Vector<double> > > const&, Foam::Xfer<Foam::List<Foam::face> > const&, Foam::Xfer<Foam::List<Foam::cell> > const&, bool) in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#3  
 in "/opt/openfoam211/platforms/linux64GccDPOpt/bin/decomposePar"
#4  
 in "/opt/openfoam211/platforms/linux64GccDPOpt/bin/decomposePar"
#5  __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
#6  
 in "/opt/openfoam211/platforms/linux64GccDPOpt/bin/decomposePar"
Aborted (core dumped)
i do a bellow work for solve my erro, but i give same error
1) i change the writePrecision to 20
2) i use a cyclicAMI
3) i checkmy mesh and i give bellow error too
Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.1.1                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.1.1-221db2718bbb
Exec   : checkMesh -allGeometry -allTopology
Date   : Aug 11 2015
Time   : 20:28:13
Host   : "stanford-Ideapad-Z460"
PID    : 4640
Case   : /home/stanford/Desktop/y
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create polyMesh for time = 0

Time = 0

Mesh stats
    points:           3312
    faces:            8744
    internal faces:   7678
    cells:            2737
    boundary patches: 5
    point zones:      0
    face zones:       1
    cell zones:       1

Overall number of cells of each type:
    hexahedra:     2737
    prisms:        0
    wedges:        0
    pyramids:      0
    tet wedges:    0
    tetrahedra:    0
    polyhedra:     0

Checking topology...
 ****Problem with boundary patch 4 named wall of type wall. The patch should start on face no 7914 and the patch specifies 7916.
Possibly consecutive patches have this same problem. Suppressing future warnings.
 ***Boundary definition is in error.
    Cell to face addressing OK.
    Point usage OK.
    Upper triangular ordering OK.
    Face vertices OK.
    Topological cell zip-up check OK.
    Face-face connectivity OK.
    Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces ...
    Patch               Faces    Points   Surface topology                   Bounding box
    inlet_shadow_half0  59       92       ok (non-closed singly connected)   (-2.5000000000000000523e-09 -2.5000000000000000523e-09 0) (2.5000000000000000523e-09 2.5000000000000000523e-09 0)
    inlet_shadow_half1  59       76       ok (non-closed singly connected)   (-1.4993899989999999846e-09 -1.7738679869999999008e-09 0) (2.1029784929999998324e-09 1.5910149619999999247e-09 0)
    inlet_half0         59       95       ok (non-closed singly connected)   (-2.5000000000000000523e-09 -2.5000000000000000523e-09 0) (2.5000000000000000523e-09 2.5000000000000000523e-09 1.0000000000000000209e-08)
    inlet_half1         59       76       ok (non-closed singly connected)   (-1.4993899989999999846e-09 -1.980907757999999998e-09 1.0000000000000000209e-08) (2.1029784929999998324e-09 1.5910149619999999247e-09 1.0000000000000000209e-08)
    wall                828      864      ok (non-closed singly connected)   (-2.5000000000000000523e-09 -2.5000000000000000523e-09 0) (2.5000000000000000523e-09 2.5000000000000000523e-09 1.0000000000000000209e-08)

Checking geometry...
    Overall domain bounding box (-2.5000000000000000523e-09 -2.5000000000000000523e-09 0) (2.5000000000000000523e-09 2.5000000000000000523e-09 1.0000000000000000209e-08)
    Mesh (non-empty, non-wedge) directions (1 1 1)
    Mesh (non-empty) directions (1 1 1)
    Boundary openness (-2.6567998704002758746e-17 1.093434397528899584e-17 -1.5554229082299158587e-17) OK.
    Max cell openness = 3.045985297783277465e-16 OK.
    Max aspect ratio = 2.3968495768130080315 OK.
    Minumum face area = 7.4714845148913033615e-20. Maximum face area = 2.4279173380366694604e-19.  Face area magnitudes OK.
    Min volume = 3.1827001516200503896e-29. Max volume = 1.0580237499368877868e-28.  Total volume = 1.9535397429082647449e-25.  Cell volumes OK.
    Mesh non-orthogonality Max: 13.560431309723149695 average: 4.1513739650341596743
    Non-orthogonality check OK.
    Face pyramids OK.
    Max skewness = 3.0733065837817203914 OK.
    Coupled point location match (average 0) OK.
#0  Foam::error::printStack(Foam::Ostream&) in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#1  Foam::sigSegv::sigHandler(int) in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#2   in "/lib/x86_64-linux-gnu/libc.so.6"
#3  Foam::polyMeshTetDecomposition::checkFaceTets(Foam::polyMesh const&, double, bool, Foam::HashSet<int, Foam::Hash<int> >*) in "/opt/openfoam211/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#4  
 in "/opt/openfoam211/platforms/linux64GccDPOpt/bin/checkMesh"
#5  
 in "/opt/openfoam211/platforms/linux64GccDPOpt/bin/checkMesh"
#6  __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
#7  
 in "/opt/openfoam211/platforms/linux64GccDPOpt/bin/checkMesh"
Segmentation fault (core dumped)
best regards

Last edited by wyldckat; August 12, 2015 at 16:31. Reason: Added [CODE][/CODE] markers
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Old   August 12, 2015, 16:47
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Bruno Santos
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Greetings Hashemkabir,

If you could provide/share a simple mesh that reproduces this error message, I (or anyone else) could test with other versions/variant of OpenFOAM, for diagnosing if this problem has already been fixed in the more recent versions.

Because the first error message hints that the problem has something to do with an ill-formed face for cell number 637. This was either because the mesh was not converted with success, or because the two patches that were assigned with the type "cyclic" are incompatible.

The second error message is hinting at the same problem, but it isn't able to provide more specific details, but most likely has to do with the invalid face number "-1" that the first error message is referring to.

Without having a test case or mesh, I'm not able to diagnose any further. My guess is that you're using either a polyhedral mesh or a tetrahedral mesh, therefore my suggestion would be for you to generate an hexahedral mesh in Gambit and then convert it to OpenFOAM. Such a mesh should provide better results.

Beyond this, these errors reminds me of this thread: Problem with cyclic boundaries in Openfoam 2.3, mesh import from ICEM

Best regards,
Bruno
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