View Issue Details

IDProjectCategoryView StatusLast Update
0000980OpenFOAMBugpublic2015-01-01 14:31
ReporterAndrea Assigned Tohenry  
PrioritynormalSeverityminorReproducibilityalways
Status closedResolutionunable to reproduce 
Platformx86_64OSCentOS OS Version6.4
Summary0000980: ReconstructParMesh doesn't work in interDyMFoam
DescriptionI have a problem in reconstructing a decomposed case of interDyMFoam solver. I tried, as suggested on the forum, to run reconstructParMesh and reconstructPar alternating for each time step. ReconstructParMesh works with no issue but reconstructPar -time does not. I got this error every time:

Create time

Create mesh for time = 0

Time = 0.002

#0 Foam::error::printStack(Foam::Ostream&) in "/home/aferrari/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#1 Foam::sigSegv::sigHandler(int) in "/home/aferrari/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#2 in "/lib64/libc.so.6"
#3 Foam::objectRegistry::checkOut(Foam::regIOobject&) const in "/home/aferrari/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#4 Foam::regIOobject::~regIOobject() in "/home/aferrari/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
#5 Foam::IOList<int>::~IOList() in "/home/aferrari/OpenFOAM/aferrari-2.1.0/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"
#6 Foam::processorMeshes::read() in "/home/aferrari/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libreconstruct.so"
#7 Foam::processorMeshes::readUpdate() in "/home/aferrari/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libreconstruct.so"
#8
 in "/home/aferrari/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/bin/reconstructPar"
#9 __libc_start_main in "/lib64/libc.so.6"
#10
 in "/home/aferrari/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64GccDPOpt/bin/reconstructPar"
Segmentation fault


I tried on cluster's nodes with 128/256/512 Gb of RAM.
TagsNo tags attached.

Activities

user4

2013-09-02 12:36

  ~0002446

- Does the parallel mesh 'checkMesh' ok? E.g.

mpirun -np xxxx checkMesh -allGeometry -allTopology -parallel -time 0.002

- Does the reconstructed mesh 'checkMesh' ok? E.g.

checkMesh -allGeometry -allTopology -time 0.002

- Are you using any special boundary conditions? What if you e.g. replace all boundary conditions with zeroGradient or fixedValue.

Andrea

2013-09-02 12:52

reporter   ~0002447

-parallel mesh check

Time = 0.002

Mesh stats
    points: 261734
    faces: 666734
    internal faces: 588796
    cells: 203533
    boundary patches: 8
    point zones: 0
    face zones: 0
    cell zones: 0

Overall number of cells of each type:
    hexahedra: 193173
    prisms: 0
    wedges: 0
    pyramids: 0
    tet wedges: 0
    tetrahedra: 0
    polyhedra: 10360

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.
    Number of regions: 1 (OK).

Checking geometry...
    Overall domain bounding box (-0.001 -0.001 0) (0 0 0.003)
    Mesh (non-empty, non-wedge) directions (1 1 1)
    Mesh (non-empty) directions (1 1 1)
    Boundary openness (-1.02055e-17 6.84269e-18 8.7025e-17) OK.
    Max cell openness = 3.31693e-16 OK.
    Max aspect ratio = 3.15505 OK.
    Minumum face area = 9.21589e-12. Maximum face area = 1.27538e-09. Face area magnitudes OK.
    Min volume = 5.76032e-17. Max volume = 3.19841e-14. Total volume = 1.76644e-09. Cell volumes OK.
    Mesh non-orthogonality Max: 51.2789 average: 12.1025
    Non-orthogonality check OK.
    Face pyramids OK.
    Max skewness = 3.19152 OK.
    Coupled point location match (average 0) OK.
    Face tets OK.
    Min/max edge length = 2.94876e-06 4.97295e-05 OK.
    All angles in faces OK.
    Face flatness (1 = flat, 0 = butterfly) : average = 1 min = 0.999972
    All face flatness OK.
    Cell determinant (wellposedness) : minimum: 0 average: 9.45532
 ***Cells with small determinant found, number of cells: 40
  <<Writing 40 under-determined cells to set underdeterminedCells
 ***Concave cells (using face planes) found, number of cells: 7287
  <<Writing 7287 concave cells to set concaveCells

Failed 2 mesh checks.

End




-reconstructed mesh check

Create polyMesh for time = 0.002

Time = 0.002

Mesh stats
    points: 229776
    faces: 636476
    internal faces: 619054
    cells: 203533
    boundary patches: 7
    point zones: 0
    face zones: 0
    cell zones: 0

Overall number of cells of each type:
    hexahedra: 193173
    prisms: 0
    wedges: 0
    pyramids: 0
    tet wedges: 0
    tetrahedra: 0
    polyhedra: 10360

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.
    Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces ...
    Patch Faces Points Surface topology Bounding box
    entrata 384 421 ok (non-closed singly connected) (-0.0005 -0.0005 0.003) (0 0 0.003)
    uscita 1024 1081 ok (non-closed singly connected) (-0.001 -0.001 0) (0 0 0)
    symmetry1 5095 5397 ok (non-closed singly connected) (0 -0.001 0) (0 0 0.003)
    symmetry2 5095 5397 ok (non-closed singly connected) (-0.001 0 0) (0 0 0.003)
    leftThroat 1280 1353 ok (non-closed singly connected) (-0.0005 -0.0005 0.002) (0 0 0.003)
    fixedWall 1984 2142 ok (non-closed singly connected) (-0.001 -0.001 0.002) (0 0 0.002)
    leftWall 2560 2673 ok (non-closed singly connected) (-0.001 -0.001 0) (0 0 0.002)

Checking geometry...
    Overall domain bounding box (-0.001 -0.001 0) (0 0 0.003)
    Mesh (non-empty, non-wedge) directions (1 1 1)
    Mesh (non-empty) directions (1 1 1)
    Boundary openness (1.96299e-14 1.94952e-14 -1.72773e-17) OK.
    Max cell openness = 3.31693e-16 OK.
    Max aspect ratio = 3.15505 OK.
    Minumum face area = 9.21589e-12. Maximum face area = 1.27538e-09. Face area magnitudes OK.
    Min volume = 5.76032e-17. Max volume = 3.19841e-14. Total volume = 1.76644e-09. Cell volumes OK.
    Mesh non-orthogonality Max: 51.2789 average: 12.0186
    Non-orthogonality check OK.
    Face pyramids OK.
    Max skewness = 3.19152 OK.
    Coupled point location match (average 0) OK.
    Face tets OK.
    Min/max edge length = 2.94876e-06 4.97295e-05 OK.
    All angles in faces OK.
    Face flatness (1 = flat, 0 = butterfly) : average = 1 min = 0.999972
    All face flatness OK.
    Cell determinant (wellposedness) : minimum: 0.773735 average: 11.3061
    Cell determinant check OK.
 ***Concave cells (using face planes) found, number of cells: 7287
  <<Writing 7287 concave cells to set concaveCells

Failed 1 mesh checks.

End


Just a comment if it was not clear before: i am using dynamic mesh refinement during the simulation. The concave cells come from the refinement step. The original mesh is ok.

-I am using symmetry BC on two sides. I'll try with zeroGradient.

user4

2013-09-05 08:53

  ~0002465

Does it work with 2.2.x?

henry

2015-01-01 14:31

manager   ~0003447

Orphaned report

Issue History

Date Modified Username Field Change
2013-08-28 16:25 Andrea New Issue
2013-09-02 12:36 user4 Note Added: 0002446
2013-09-02 12:52 Andrea Note Added: 0002447
2013-09-05 08:53 user4 Note Added: 0002465
2015-01-01 14:31 henry Note Added: 0003447
2015-01-01 14:31 henry Status new => closed
2015-01-01 14:31 henry Assigned To => henry
2015-01-01 14:31 henry Resolution open => unable to reproduce