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[Other] Sysmalloc on checkMesh in foam-ext but not in openfoam

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Old   July 3, 2018, 03:54
Default Sysmalloc on checkMesh in foam-ext but not in openfoam
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Henrik Johansson
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Hi,

I been working on a rotor-stator setup for a gas turbine for a while. I am using mixing plane and cyclic GGI which works well.

The problem I'm having is that some meshes won't work at all even if the check mesh say that they are okay. I started using Salome 8.4 which I think works well. So some meshes works and some don't. I have hade working 4M cell meshes and working 1M cell ones. But in between those it is really common that I get the following error in foam extended:

Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | foam-extend: Open Source CFD                    |
|  \\    /   O peration     | Version:     4.0                                |
|   \\  /    A nd           | Web:         http://www.foam-extend.org         |
|    \\/     M anipulation  | For copyright notice see file Copyright         |
\*---------------------------------------------------------------------------*/
Build    : 4.0-54c9f83b540c
Exec     : checkMesh -allTopology -allGeometry
Date     : Jul 03 2018
Time     : 09:29:41
Host     : henrik-linux
PID      : 2630
CtrlDict : "/media/henrik/Scratchen/OpenFOAM/Turbine_3D_2018_06_28_1Stage/system/controlDict"
Case     : /media/henrik/Scratchen/OpenFOAM/Turbine_3D_2018_06_28_1Stage
nProcs   : 1
SigFpe   : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Create polyMesh for time = 0

Initializing the GGI interpolator between master/shadow patches: StatorLeft1_CyclicGgi/StatorRight1_CyclicGgi
Initializing the GGI interpolator between master/shadow patches: Mapped_S11/Mapped_R11
Initializing the GGI interpolator between master/shadow patches: Mapped_R12/Mapped_S12
Initializing the GGI interpolator between master/shadow patches: RotorLeft1_CyclicGgi/RotorRight1_CyclicGgi
Initializing the mixingPlane interpolator between master/shadow patches: Stator1_MixingPlane/Rotor1_MixingPlane
Time = 0

checkMesh: malloc.c:2394: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed.
./RunParallel: line 76:  2630 Aborted                 (core dumped) checkMesh -allTopology -allGeometry
But if I run the same in OpenFOAM it works:

Code:
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  5.x                                   |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 5.x-197d9d3bf20a
Exec   : checkMesh -allTopology -allGeometry
Date   : Jul 03 2018
Time   : 09:34:51
Host   : "henrik-linux"
PID    : 3076
I/O    : uncollated
Case   : /media/henrik/Scratchen/OpenFOAM/Turbine_3D_2018_06_28_1Stage
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

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

--> FOAM Warning : 
    From function void* Foam::dlOpen(const Foam::fileName&, bool)
    in file POSIX.C at line 1210
    dlopen error : liblduSolvers.so: cannot open shared object file: No such file or directory
--> FOAM Warning : 
    From function bool Foam::dlLibraryTable::open(const Foam::fileName&, bool)
    in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 105
    could not load "liblduSolvers.so"
Create polyMesh for time = 0

Enabling all (cell, face, edge, point) topology checks.

Enabling all geometry checks.

Time = 0

Mesh stats
    points:           427629
    faces:            4654715
    internal faces:   4514529
    cells:            2292311
    faces per cell:   4
    boundary patches: 15
    point zones:      0
    face zones:       14
    cell zones:       3

Overall number of cells of each type:
    hexahedra:     0
    prisms:        0
    wedges:        0
    pyramids:      0
    tet wedges:    0
    tetrahedra:    2292311
    polyhedra:     0

Checking topology...
    Boundary definition OK.
    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.
  <<Writing 18 cells with zero or one non-boundary face to set oneInternalFaceCells
  <<Writing 2719 cells with two non-boundary faces to set twoInternalFacesCells
   *Number of regions: 4
    The mesh has multiple regions which are not connected by any face.
  <<Writing region information to "0/cellToRegion"
  <<Writing region 0 (fully disconnected) with 455784 cells to cellSet region0
  <<Writing region 1 (fully disconnected) with 1584343 cells to cellSet region1
  <<Writing region 2 (fully disconnected) with 234883 cells to cellSet region2
  <<Writing region 3 (fully disconnected) with 17301 cells to cellSet region3

Checking patch topology for multiply connected surfaces...
    Patch               Faces    Points   Surface topology                   Bounding box
    Inlet               3920     2057     ok (non-closed singly connected)   (-0.02 -0.0120377 0.132616) (-0.02 0.00753666 0.159)
    NoSlip_outlet       0        0        ok (empty)                        
    Stator1_Wall        39843    20314    ok (non-closed singly connected)   (-0.02 -0.012046 0.125463) (0.00819958 0.0454419 0.159)
    StatorLeft1_CyclicGgi13150    6773     ok (non-closed singly connected)   (-0.02 0.0062674 0.125463) (0.00819958 0.0454419 0.158822)
    StatorRight1_CyclicGgi14350    7376     ok (non-closed singly connected)   (-0.02 -0.012046 0.129936) (0.00819958 0.0283832 0.159)
    Stator1_MixingPlane 4249     2224     ok (non-closed singly connected)   (0.00819958 0.0263732 0.125463) (0.00819958 0.0454419 0.156797)
    Rotor1_MixingPlane  3205     1687     ok (non-closed singly connected)   (0.00819959 0.0488003 0.118773) (0.00819959 0.0718993 0.147766)
    Mapped_S11          2888     1526     ok (non-closed singly connected)   (0.00899959 0.0488003 0.118773) (0.00899959 0.0718993 0.147766)
    Mapped_R11          2888     1526     ok (non-closed singly connected)   (0.00899959 0.0488003 0.118773) (0.00899959 0.0718993 0.147766)
    Mapped_R12          2757     1461     ok (non-closed singly connected)   (0.0302599 0.041634 0.122006) (0.0302599 0.0650237 0.150408)
    Mapped_S12          3386     1779     ok (non-closed singly connected)   (0.0302599 0.041634 0.122006) (0.0302599 0.0650237 0.150408)
    Rotor1_Wall         31748    16271    ok (non-closed singly connected)   (0.00819959 0.041634 0.117621) (0.0377594 0.074133 0.154228)
    RotorLeft1_CyclicGgi7380     3931     ok (non-closed singly connected)   (0.00819959 0.052948 0.117621) (0.0377594 0.074133 0.148758)
    RotorRight1_CyclicGgi7222     3851     ok (non-closed singly connected)   (0.00819959 0.041634 0.122779) (0.0377594 0.0610352 0.154228)
    Outlet              3200     1691     ok (non-closed singly connected)   (0.0377594 0.0423978 0.123783) (0.0377594 0.0669385 0.154228)

Checking geometry...
    Overall domain bounding box (-0.02 -0.012046 0.117621) (0.0377594 0.074133 0.159)
    Mesh has 3 geometric (non-empty/wedge) directions (1 1 1)
    Mesh has 3 solution (non-empty) directions (1 1 1)
    Boundary openness (-1.88151293589e-16 1.4288885673e-16 1.96336517238e-16) OK.
    Max cell openness = 2.61820300845e-16 OK.
    Max aspect ratio = 4.87346861298 OK.
    Minimum face area = 1.19702539533e-08. Maximum face area = 5.85207947017e-07.  Face area magnitudes OK.
    Min volume = 6.301377e-13. Max volume = 1.30156332142e-10.  Total volume = 1.9940836701e-05.  Cell volumes OK.
    Mesh non-orthogonality Max: 56.0133342939 average: 14.2472929393
    Non-orthogonality check OK.
    Face pyramids OK.
    Max skewness = 0.707953587696 OK.
    Coupled point location match (average 0) OK.
    Face tets OK.
    Min/max edge length = 0.000151175924009 0.00139489908237 OK.
  <<Writing 3060 near (closer than 1.11692389939e-07 apart) points to set nearPoints
    All angles in faces OK.
    All face flatness OK.
    Cell determinant (wellposedness) : minimum: 0 average: 1.66173120708
 ***Cells with small determinant (< 0.001) found, number of cells: 2737
  <<Writing 2737 under-determined cells to set underdeterminedCells
    Concave cell check OK.
    Face interpolation weight : minimum: 0.194846604054 average: 0.454086792589
    Face interpolation weight check OK.
    Face volume ratio : minimum: 0.241999356936 average: 0.839798039088
    Face volume ratio check OK.

Failed 1 mesh checks.

End
The checkMesh errors and warnings above are all elements with faces on the boundary. Aka more than one face on the boundary and therefore foam complains about it. The near points are nodes on the boundary between different regions.

I have been struggling with this problem for over half a year and can't figure it out. Can anyone help me?


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