segmentation problem wind windPlantPisoSolver

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Ruben.Pabello
Posts: 7
Joined: Fri Feb 14, 2014 2:12 am
Organization: DTU
Location: Denmark

segmentation problem wind windPlantPisoSolver

Postby Ruben.Pabello » Mon Aug 18, 2014 3:27 am

Hello foamers,

I am trying to simulate a wind turbine in a wind tunnel using a modified pisoSolver, My steps are:

mpirun -np 20 blockMesh > log.blockMesh 2>&1
refineMeshByCellSetLocal 3
decomposePar -cellDist -force > log.decomposePar 2>&1
mpirun -np 20 windPlantPisoSolver -parallel > log.windPlantPisoSolver.1 2>&1

This is the log resulting from this run

Code: Select all

Pstream initialized with:
    floatTransfer     : 0
    nProcsSimpleSum   : 0
    commsType         : nonBlocking
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 for time = 0

Reading gravitational acceleration...
Reading planetary body rotation rate...
Creating/Reading velocity field, U...
Creating mean velocity field, Umean...
Creating fluctuating velocity field, Uprime...
Creating the resolved Reynolds stress field, UprimeUprimeMean...
Creating the resolved turbulent kinetic energy field, k...
Creating/Calculating face flux field, phi...
Reading temperature field, T...
Creating mean temperature field, Tmean...
Creating fluctuating temperature field, Tprime...
Creating the temperature-velocity correlation field, TprimeUprimeMean...
Creating/Reading deviation from hydrostatic pressure field, pd...
Reading pressure field reference information...
Reading transport properties...
Selecting incompressible transport model Newtonian
Reading atmospheric boundary layer properties...
     Specified wind at 90 m is from 225 degrees at 9 m/s
     This is a wind vector of (6.364 6.364 0) m/s, where +x is east and +y is north
                               N
                               0
                               |

                    W 270 --       --  90 E

                               |
                              180
                               S
Thrust from Body Force = 0    Thrust from Act. Line = 41.329    Ratio = 0
Torque from Body Force = 0    Torque from Act. Line = 2.7109    Ratio = 0
Creating the kinematic density field, rhok...
Creating the turbulent viscosity field, nuLES...
Calculating LES filter widths, deltaLES...
Creating the turbulent thermal diffusivity field, kappaLES...
Creating the divergence of the deviatoric SGS stresses field, divDevR...
Creating the divergence of the SGS temperature flux field, divq...
Initializing with 0 pressure (pd) gradient...

Courant Number mean: 0.23309 max: 0.25

Total number of cell center height levels: 10
26000    5.439
26000    5.439
26000    5.439
26000    5.439
26000    5.439
26000    5.439
26000    5.439
26000    5.439
26000    5.439
26000    5.439
Total number of cell face height levels: 11

0    26000    26000    30.217
26000    0    26000    30.217
26000    0    26000    30.217
26000    0    26000    30.217
26000    0    26000    30.217
26000    0    26000    30.217
26000    0    26000    30.217
26000    0    26000    30.217
26000    0    26000    30.217
26000    0    26000    30.217
0    26000    26000    30.217
meanTimeSum = 0    corrTimeSum = 0

Entering time loop...

[14] #0  Foam::error::printStack(Foam::Ostream&)Courant Number mean: 0.23309 max: 0.25
Time = 0.0001    Time Step = 1
 at ??:?
[14] #1  Foam::sigSegv::sigHandler(int)[1] #0  Foam::error::printStack(Foam::Ostream&)[6] #0  Foam::error::printStack(Foam::Ostream&)[3] #0  [7] #0  Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)[9] #0  Foam::error::printStack(Foam::Ostream&)[0] #0  Foam::error::printStack(Foam::Ostream&)[17] #0  [13] #0  Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)[5] #0  Foam::error::printStack(Foam::Ostream&)[2] #0  Foam::error::printStack(Foam::Ostream&)[10] [15] #0  Foam::error::printStack(Foam::Ostream&)[18] [8] #0  Foam::error::printStack(Foam::Ostream&)#0  Foam::error::printStack(Foam::Ostream&)[12] #[16] ##0  Foam::error::printStack(Foam::Ostream&)0[4]   Foam::error::printStack(Foam::Ostream&)0  Foam::error::printStack(Foam::Ostream&)[19] [11] #0  Foam::error::printStack(Foam::Ostream&)#0  Foam::error::printStack(Foam::Ostream&)#0  Foam::error::printStack(Foam::Ostream&) at ??:?
[14] #2  Uninterpreted:
[14] #3  Foam::surfaceInterpolationScheme<Foam::Tensor<double> >::interpolate(Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::tmp<Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> > const&) at ??:?
[2] #1  Foam::sigSegv::sigHandler(int) at ??:?
[0] #1  Foam::sigSegv::sigHandler(int) at ??:?
[6] #1  Foam::sigSegv::sigHandler(int) at ??:?
[7] #1  Foam::sigSegv::sigHandler(int) at ??:?
[3] #1  Foam::sigSegv::sigHandler(int) at ??:?
[11] #1  Foam::sigSegv::sigHandler(int) at ??:?
[17] #1  Foam::sigSegv::sigHandler(int) at ??:?
[15] #1  Foam::sigSegv::sigHandler(int) at ??:?
[12] #1  Foam::sigSegv::sigHandler(int) at ??:?
[4] #1  Foam::sigSegv::sigHandler(int) at ??:?
[1] #1  Foam::sigSegv::sigHandler(int) at ??:?
[18] #1  Foam::sigSegv::sigHandler(int) at ??:?
[9] #1  Foam::sigSegv::sigHandler(int) at ??:?
[13] #1  Foam::sigSegv::sigHandler(int) at ??:?
[16] #1  Foam::sigSegv::sigHandler(int) at ??:?
[19] #1  Foam::sigSegv::sigHandler(int) at ??:?
[8] #1  Foam::sigSegv::sigHandler(int) at ??:?
[5] #1  Foam::sigSegv::sigHandler(int) at ??:?
[10] #1  Foam::sigSegv::sigHandler(int) at  at ??:?
[6] #2  Uninterpreted:
[6] #3  Foam::surfaceInterpolationScheme<Foam::Tensor<double> >::interpolate(Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::tmp<Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> > const&) at ??:?
[17] #2  Uninterpreted:
[17] #3  Foam::surfaceInterpolationScheme<Foam::Tensor<double> >::interpolate(Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::tmp<Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> > const&) at ??:?
[15] #2  Uninterpreted:
[15] #3  Foam::surfaceInterpolationScheme<Foam::Tensor<double> >::interpolate(Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::tmp<Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> > const&)??:?
[2] #2  Uninterpreted:
[2] #3  Foam::surfaceInterpolationScheme<Foam::Tensor<double> >::interpolate(Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::tmp<Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> > const&) at ??:?
[13] #2  Uninterpreted:
[13] #3  Foam::surfaceInterpolationScheme<Foam::Tensor<double> >::interpolate(Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::tmp<Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> > const&) at ??:?
[3] #2  Uninterpreted:
[3] #3  Foam::surfaceInterpolationScheme<Foam::Tensor<double> >::interpolate(Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::tmp<Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> > const&) at ??:?
[4] #2  Uninterpreted:


[9]  at ??:?
[9] #6  __libc_start_main at ??:?
[17] #5   at ??:?
[19] #5   at ??:?
[3] #5   at ??:?
[10] #5 

[4]  at ??:?
[4] #6  __libc_start_main at ??:?
[1] #5   in "/lib/i386-linux-gnu/libc.so.6"
[9] #7  [13]  at ??:?
[13] #6  __libc_start_main[14]  at ??:?
[14] #6  __libc_start_main
[6]  at ??:?
[6] #6  __libc_start_main at ??:?
[0] #5  [17]  at ??:?
[17] #6  __libc_start_main[15]  at ??:?
[15] #6  __libc_start_main

 in "/lib/i386-linux-gnu/libc.so.6"
[4] #7 

 in "/lib/i386-linux-gnu/libc.so.6"
[6] #7   at ??:?
[12] #5  [8]  at ??:?
[8] #6  __libc_start_main at ??:?
[18] #4  Foam::surfaceInterpolationScheme<Foam::Tensor<double> >::interpolate(Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh> const&) const at ??:?
[2] #5  [3]  at ??:?
[3] #6  __libc_start_main
 in "/lib/i386-linux-gnu/libc.so.6"
[13] #7   at ??:?
[16] #5 
 in "/lib/i386-linux-gnu/libc.so.6"
[14] #7   in "/lib/i386-linux-gnu/libc.so.6"
[3] #7   at ??:?
[5] #5   in "/lib/i386-linux-gnu/libc.so.6"
[17] #7 
 in "/lib/i386-linux-gnu/libc.so.6"
[15] #7  [11]  at ??:?
[11] #6  __libc_start_main[1]  at ??:?
[1] #6  __libc_start_main
[10]  at ??:?
[10] #6  __libc_start_main[19]  at ??:?
[19] #6  __libc_start_main




 in "/lib/i386-linux-gnu/libc.so.6"
[11] #7 
[9]  at ??:?
[pabello-VirtualBox:03884] *** Process received signal ***
[pabello-VirtualBox:03884] Signal: Segmentation fault (11)
[pabello-VirtualBox:03884] Signal code:  (-6)
[pabello-VirtualBox:03884] Failing at address: 0xf2c
[pabello-VirtualBox:03884] [ 0] [0xb77c740c]
[pabello-VirtualBox:03884] [ 1] [0xb77c7424]
[pabello-VirtualBox:03884] [ 2] /lib/i386-linux-gnu/libc.so.6(gsignal+0x4f) [0xb591f1df]
[pabello-VirtualBox:03884] [ 3] /home/pabello/OpenFOAM/OpenFOAM-2.1.1/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam7sigSegv10sigHandlerEi+0x60) [0xb6018dd0]
[pabello-VirtualBox:03884] [ 4] [0xb77c7400]
[pabello-VirtualBox:03884] [ 5] /home/pabello/OpenFOAM/OpenFOAM-2.1.1/platforms/linuxGccDPOpt/lib/libfiniteVolume.so(_ZN4Foam26surfaceInterpolationSchemeINS_6TensorIdEEE11interpolateERKNS_14GeometricFieldIS2_NS_12fvPatchFieldENS_7volMeshEEERKNS_3tmpINS4_IdNS_13fvsPatchFieldENS_11surfaceMeshEEEEE+0x24a) [0xb6b73baa]
[pabello-VirtualBox:03884] [ 6] /home/pabello/OpenFOAM/OpenFOAM-2.1.1/platforms/linuxGccDPOpt/lib/libfiniteVolume.so(_ZNK4Foam26surfaceInterpolationSchemeINS_6TensorIdEEE11interpolateERKNS_14GeometricFieldIS2_NS_12fvPatchFieldENS_7volMeshEEE+0x65) [0xb6bacc95]
[pabello-VirtualBox:03884] [ 7] windPlantPisoSolver() [0x808f666]
[pabello-VirtualBox:03884] [ 8] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0xb590a4d3]
[pabello-VirtualBox:03884] [ 9] windPlantPisoSolver() [0x8098391]
[pabello-VirtualBox:03884] *** End of error message ***

[6]  at ??:?
[pabello-VirtualBox:03881] *** Process received signal ***
[pabello-VirtualBox:03881] Signal: Segmentation fault (11)
[pabello-VirtualBox:03881] Signal code:  (-6)
[pabello-VirtualBox:03881] Failing at address: 0xf29
[pabello-VirtualBox:03881] [ 0] [0xb777540c]
[pabello-VirtualBox:03881] [ 1] [0xb7775424]
[pabello-VirtualBox:03881] [ 2] /lib/i386-linux-gnu/libc.so.6(gsignal+0x4f) [0xb58cd1df]
[pabello-VirtualBox:03881] [ 3] /home/pabello/OpenFOAM/OpenFOAM-2.1.1/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam7sigSegv10sigHandlerEi+0x60) [0xb5fc6dd0]
[pabello-VirtualBox:03881] [ 4] [0xb7775400]
[pabello-VirtualBox:03881] [ 5] /home/pabello/OpenFOAM/OpenFOAM-2.1.1/platforms/linuxGccDPOpt/lib/libfiniteVolume.so(_ZN4Foam26surfaceInterpolationSchemeINS_6TensorIdEEE11interpolateERKNS_14GeometricFieldIS2_NS_12fvPatchFieldENS_7volMeshEEERKNS_3tmpINS4_IdNS_13fvsPatchFieldENS_11surfaceMeshEEEEE+0x24a) [0xb6b21baa]
[pabello-VirtualBox:03881] [ 6] /home/pabello/OpenFOAM/OpenFOAM-2.1.1/platforms/linuxGccDPOpt/lib/libfiniteVolume.so(_ZNK4Foam26surfaceInterpolationSchemeINS_6TensorIdEEE11interpolateERKNS_14GeometricFieldIS2_NS_12fvPatchFieldENS_7volMeshEEE+0x65) [0xb6b5ac95]
[pabello-VirtualBox:03881] [ 7] windPlantPisoSolver() [0x808f666]
[pabello-VirtualBox:03881] [ 8] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0xb58b84d3]
[pabello-VirtualBox:03881] [ 9] windPlantPisoSolver() [0x8098391]
[pabello-VirtualBox:03881] *** End of error message ***
[2]  at ??:?
[2] #6  __libc_start_main
[3]  at ??:?
[pabello-VirtualBox:03877] *** Process received signal ***
[pabello-VirtualBox:03877] Signal: Segmentation fault (11)
[pabello-VirtualBox:03877] Signal code:  (-6)
[pabello-VirtualBox:03877] Failing at address: 0xf25
[pabello-VirtualBox:03877] [ 0] [0xb77bb40c]
[pabello-VirtualBox:03877] [ 1] [0xb77bb424]
[pabello-VirtualBox:03877] [ 2] /lib/i386-linux-gnu/libc.so.6(gsignal+0x4f) [0xb59131df]
[pabello-VirtualBox:03877] [ 3] /home/pabello/OpenFOAM/OpenFOAM-2.1.1/platforms/linuxGccDPOpt/lib/libOpenFOAM.so(_ZN4Foam7sigSegv10sigHandlerEi+0x60) [0xb600cdd0]
[pabello-VirtualBox:03877] [ 4] [0xb77bb400]
[pabello-VirtualBox:03877] [ 5] /home/pabello/OpenFOAM/OpenFOAM-2.1.1/platforms/linuxGccDPOpt/lib/libfiniteVolume.so(_ZN4Foam26surfaceInterpolationSchemeINS_6TensorIdEEE11interpolateERKNS_14GeometricFieldIS2_NS_12fvPatchFieldENS_7volMeshEEERKNS_3tmpINS4_IdNS_13fvsPatchFieldENS_11surfaceMeshEEEEE+0x24a) [0xb6b67baa]
[pabello-VirtualBox:03877] [ 6] /home/pabello/OpenFOAM/OpenFOAM-2.1.1/platforms/linuxGccDPOpt/lib/libfiniteVolume.so(_ZNK4Foam26surfaceInterpolationSchemeINS_6TensorIdEEE11interpolateERKNS_14GeometricFieldIS2_NS_12fvPatchFieldENS_7volMeshEEE+0x65) [0xb6ba0c95]
[pabello-VirtualBox:03877] [ 7] windPlantPisoSolver() [0x808f666]
[pabello-VirtualBox:03877] [ 8] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0xb58fe4d3]
[pabello-VirtualBox:03877] [ 9] windPlantPisoSolver() [0x8098391]
[pabello-VirtualBox:03877] *** End of error message ***
 in "/lib/i386-linux-gnu/libc.so.6"
[8] #7   in "/lib/i386-linux-gnu/libc.so.6"
[10] #7   in "/lib/i386-linux-gnu/libc.so.6"
[1] #7  --------------------------------------------------------------------------
mpirun noticed that process rank 6 with PID 3881 on node pabello-VirtualBox exited on signal 11 (Segmentation fault).



I am not able to pin point where the error might be. I checked the mesh and there are no errors:

Code: Select all

/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  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
Date   : Aug 18 2014
Time   : 10:08:17
Host   : "pabello-VirtualBox"
PID    : 4212
Case   : /home/pabello/OpenFOAM/tutorials/NTNU_TSR6_anm
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:           314721
    faces:            832100
    internal faces:   727900
    cells:            260000
    boundary patches: 6
    point zones:      0
    face zones:       0
    cell zones:       0

Overall number of cells of each type:
    hexahedra:     260000
    prisms:        0
    wedges:        0
    pyramids:      0
    tet wedges:    0
    tetrahedra:    0
    polyhedra:     0

Checking topology...
    Boundary definition OK.
    Cell to face addressing OK.
    Point usage OK.
    Upper triangular ordering OK.
    Face vertices OK.
    Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces ...
    Patch               Faces    Points   Surface topology                 
    bottom              26000    28611    ok (non-closed singly connected) 
    top                 26000    28611    ok (non-closed singly connected) 
    inlet               26000    28611    ok (non-closed singly connected) 
    outlet              26000    28611    ok (non-closed singly connected) 
    side1               100      121      ok (non-closed singly connected) 
    side2               100      121      ok (non-closed singly connected) 

Checking geometry...
    Overall domain bounding box (0 0 0) (11.15 2.71 1.8)
    Mesh (non-empty, non-wedge) directions (1 1 1)
    Mesh (non-empty) directions (1 1 1)
    Boundary openness (4.6541e-18 -2.2222e-14 1.292e-14) OK.
    Max cell openness = 9.5256e-17 OK.
    Max aspect ratio = 67.75 OK.
    Minumum face area = 0.00072. Maximum face area = 0.04878.  Face area magnitudes OK.
    Min volume = 0.00019512. Max volume = 0.0002439.  Total volume = 54.39.  Cell volumes OK.
    Mesh non-orthogonality Max: 0 average: 0
    Non-orthogonality check OK.
    Face pyramids OK.
    Max skewness = 1.2813e-11 OK.
    Coupled point location match (average 0) OK.

Mesh OK.

End


Any idea what I might need to look into??

Greets,
Ruben

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