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Segmentation fault (core dumped)

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Old   December 16, 2016, 08:38
Default Segmentation fault (core dumped)
  #1
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zhoubiao
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who can help me think the error source ? I have spent several days on it. Please help. Thanks in advance!
Best regards
Zhou
HTML Code:
[#48#zhou@zhou-All-Series ~/OpenFOAM/zhou-2.2.x/run/f/20161215/20161209]$checkMesh -allTopology -allGeometry
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.2.x                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.2.x-1f35a0ff2a58
Exec   : checkMesh -allTopology -allGeometry
Date   : Dec 16 2016
Time   : 21:40:24
Host   : "zhou-All-Series"
PID    : 18490
Case   : /home/zhou/OpenFOAM/zhou-2.2.x/run/f/20161215/20161209
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

--> FOAM Warning : 
    From function dlOpen(const fileName&, const bool)
    in file POSIX.C at line 1179
    dlopen error : /home/zhou/OpenFOAM/zhou-2.2.x/platforms/linux64GccDPOpt/lib/libfvPatchFieldsPyrolysis.so: undefined symbol: _ZTIN4Foam11basicThermoE
--> FOAM Warning : 
    From function dlLibraryTable::open(const fileName&, const bool)
    in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
    could not load "libfvPatchFieldsPyrolysis.so"
Create polyMesh for time = 0

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

Enabling all geometry checks.

Time = 0

Mesh stats
    points:           544563
    faces:            1599538
    internal faces:   1549262
    cells:            524800
    faces per cell:   6
    boundary patches: 10
    point zones:      0
    face zones:       7
    cell zones:       0

Overall number of cells of each type:
    hexahedra:     524800
    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.
    Topological cell zip-up check OK.
    Number of identical duplicate faces (baffle faces): 5618
    Face-face connectivity OK.
  <<Writing 11236 faces with non-standard edge connectivity to set edgeFaces
    Number of regions: 1 (OK).

Checking patch topology for multiply connected surfaces...
    Patch               Faces    Points   Surface topology                   Bounding box
    wall                6560     6723     ok (non-closed singly connected)   (-2 -2 0) (-2 2 4.1)
    side                19680    20003    ok (non-closed singly connected)   (-2 -2 0) (2 2 4.1)
    outlet              6400     6561     ok (non-closed singly connected)   (-2 -2 4.1) (2 2 4.1)
    ground              5616     5832     ok (non-closed singly connected)   (-2 -2 0) (2 2 0)
    burner              144      169      ok (non-closed singly connected)   (-1.9 -0.3 0) (-1.3 0.3 0)
    floor               640      709      ok (non-closed singly connected)   (-1.9 -0.7 0) (-0.5 0.7 0)
    baffle1DWall_master 2990     3107     ok (non-closed singly connected)   (-1.9 -0.7 0) (-0.5 0.7 1.4)
    baffle1DWall_slave  2990     3107     ok (non-closed singly connected)   (-1.9 -0.7 0) (-0.5 0.7 1.4)
    baffle1DWall_slave1 2628     2782     ok (non-closed singly connected)   (-0.5 -0.9 0) (-0.5 0.9 4.1)
    region0_to_panelRegion_panel2628     2782     ok (non-closed singly connected)   (-0.5 -0.9 0) (-0.5 0.9 4.1)

Checking geometry...
    Overall domain bounding box (-2 -2 0) (2 2 4.1)
    Mesh (non-empty, non-wedge) directions (1 1 1)
    Mesh (non-empty) directions (1 1 1)
    Boundary openness (2.91283e-17 -8.9876e-17 4.44964e-17) OK.
    Max cell openness = 1.73472e-16 OK.
    Max aspect ratio = 1 OK.
    Minimum face area = 0.0025. Maximum face area = 0.0025.  Face area magnitudes OK.
    Min volume = 0.000125. Max volume = 0.000125.  Total volume = 65.6.  Cell volumes OK.
    Mesh non-orthogonality Max: 0 average: 0
    Non-orthogonality check OK.
    Face pyramids OK.
    Max skewness = 2.00012e-11 OK.
    Coupled point location match (average 0) OK.
    Face tets OK.
    Min/max edge length = 0.05 0.05 OK.
    All angles in faces OK.
    Face flatness (1 = flat, 0 = butterfly) : average = 1  min = 1
    All face flatness OK.
    Cell determinant (wellposedness) : minimum: 1 average: 7.62223
    Cell determinant check OK.
    Concave cell check OK.

Mesh OK.

End
HTML Code:
[#21#zhou@zhou-All-Series ~/OpenFOAM/zhou-2.2.x/run/f/20161215/20161209]$fireFoam
/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.2.x                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.2.x-1f35a0ff2a58
Exec   : fireFoam
Date   : Dec 16 2016
Time   : 21:19:58
Host   : "zhou-All-Series"
PID    : 17763
Case   : /home/zhou/OpenFOAM/zhou-2.2.x/run/f/20161215/20161209
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

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
FireFOAM Build Version:  9f8ab38ff7dce6108bc5b4c155b18de7c8a3c4ba
FireFOAM Build Time Stamp:  Fri Dec 16 20:33:03 JST 2016
****************************************************
Create time

Create mesh for time = 0


Reading g
Creating combustion model

Selecting combustion model eddyDissipationModel<psiThermoCombustion,gasHThermoPhysics>
Selecting thermodynamics package 
{
    type            hePsiThermo;
    mixture         singleStepReactingMixture;
    transport       sutherland;
    thermo          janaf;
    energy          sensibleEnthalpy;
    equationOfState perfectGas;
    specie          specie;
}

Selecting chemistryReader foamChemistryReader
--> FOAM Warning : 
    From function entry::getKeyword(keyType&, Istream&)
    in file db/dictionary/entry/entryIO.C at line 80
    Reading /home/zhou/OpenFOAM/zhou-2.2.x/run/f/20161215/20161209/0/N2
    found on line 102 the punctuation token '*'
    expected either } or EOF
--> FOAM Warning : 
    From function entry::getKeyword(keyType&, Istream&)
    in file db/dictionary/entry/entryIO.C at line 80
    Reading /home/zhou/OpenFOAM/zhou-2.2.x/run/f/20161215/20161209/0/N2
    found on line 102 the punctuation token '/'
    expected either } or EOF
Fuel heat of combustion :4.63572e+07
stoichiometric air-fuel ratio :15.5715
stoichiometric oxygen-fuel ratio :3.62829
Maximum products mass concentrations:
    H2O: 0.0986136
    CO2: 0.180679
    N2: 0.720707
Combustion mode: explicit
Reading thermophysical properties

Creating component thermo properties:
    multi-component carrier - 5 species
    no liquid components
    no solid components
Creating field rho

Reading field p_rgh

Reading field U

Reading/calculating face flux field phi

Creating turbulence model

Selecting turbulence model type LESModel
Selecting LES turbulence model oneEqEddy
Selecting LES delta type cubeRootVol
oneEqEddyCoeffs
{
    Prt             1;
    ce              1.048;
    ck              0.094;
}

stoichiometric mixture fraction is = 0.0603444
Creating field DpDt

Calculating field g.h

Creating pyrolysis model collection
Selecting pyrolysisModel reactingOneDim21
    Selecting region model functions
    none
Selecting chemistry type 
{
    chemistrySolver ode;
    chemistryThermo pyrolysisChemistryModel;
}

chemistryTypeName ode<pyrolysisChemistryModel<basicSolidChemistryModel,constIso<hConst<rhoConst<specie>>,sensibleEnthalpy>,sutherland<janaf<perfectGas<specie>>,sensibleEnthalpy>>>
Selecting thermodynamics package 
{
    type            heSolidThermo;
    mixture         reactingMixture;
    transport       constIso;
    thermo          hConst;
    energy          sensibleEnthalpy;
    equationOfState rhoConst;
    specie          specie;
}

Selecting chemistryReader foamChemistryReader
pyrolysisChemistryModel: 
Number of solids = 2
Number of gases = 1
"v^4.86 = char + gas";

Selecting ODE solver SIBS
Selecting radiationModel opaqueSolid
Selecting absorptionEmissionModel greyMeanSolidAbsorptionEmission
Selecting scatterModel none
Selecting radiationModel fvDOM
Selecting absorptionEmissionModel constRadFractionEmission
Selecting scatterModel constantScatter
fvDOM : Allocated 16 rays with average orientation:
	I0 : omega : 	0.785398
	I1 : omega : 	0.785398
	I2 : omega : 	0.785398
	I3 : omega : 	0.785398
	I4 : omega : 	0.785398
	I5 : omega : 	0.785398
	I6 : omega : 	0.785398
	I7 : omega : 	0.785398
	I8 : omega : 	0.785398
	I9 : omega : 	0.785398
	I10 : omega : 	0.785398
	I11 : omega : 	0.785398
	I12 : omega : 	0.785398
	I13 : omega : 	0.785398
	I14 : omega : 	0.785398
	I15 : omega : 	0.785398


Constructing reacting cloud
Constructing particle injection models
Selecting injection model none

Constructing surface film model
Selecting surfaceFilmModel none
    Selecting region model functions
    none
Courant Number mean: 0 max: 0
Starting time loop
cellSource HRR:all(c0):
    total cells  = 524800
    total volume = 65.6



faceSource patchBurner:
    total faces  = 144
    total area   = 0.36


faceSource patchPanel:
    total faces  = 2628
    total area   = 6.57


faceSource patchOutlet:
    total faces  = 6400
    total area   = 16


faceSource patchPanelSolidRegion:
    total faces  = 2628
    total area   = 6.57


faceSource patchPanelQr:
    total faces  = 2628
    total area   = 6.57


faceSource patchWallQr:
    total faces  = 6560
    total area   = 16.4


faceSource patchSideQr:
    total faces  = 19680
    total area   = 49.2


faceSource patchBurnerQr:
    total faces  = 144
    total area   = 0.36


faceSource patchOutletQr:
    total faces  = 6400
    total area   = 16


faceSource patchGroundQr:
    total faces  = 5616
    total area   = 14.04


faceSource patchPanelQin:
    total faces  = 2628
    total area   = 6.57


faceSource patchPanelConvectiveHeatFlux:
    total faces  = 2628
    total area   = 6.57


surfaces patchSamplingGas: Reading surface description:
    pyrolysisPatch

Courant Number mean: 0 max: 0
deltaT = 0.00952381
Time = 0.00952381

diagonal:  Solving for rho, Initial residual = 0, Final residual = 0, No Iterations 0
DILUPBiCG:  Solving for Ux, Initial residual = 1, Final residual = 2.91856e-08, No Iterations 1
DILUPBiCG:  Solving for Uy, Initial residual = 1, Final residual = 3.02462e-08, No Iterations 1
DILUPBiCG:  Solving for Uz, Initial residual = 1, Final residual = 3.28988e-08, No Iterations 1
DILUPBiCG:  Solving for O2, Initial residual = 0.999447, Final residual = 1.89125e-15, No Iterations 2
DILUPBiCG:  Solving for H2O, Initial residual = 0, Final residual = 0, No Iterations 0
DILUPBiCG:  Solving for C3H8, Initial residual = 1, Final residual = 2.17871e-15, No Iterations 2
DILUPBiCG:  Solving for CO2, Initial residual = 0, Final residual = 0, No Iterations 0
      O2	min/ave/max  =	     0.23301	     0.23301	     0.23301
     H2O	min/ave/max  =	           0	           0	           0
    C3H8	min/ave/max  =	-6.9622e-127	  3.3546e-16	  6.3517e-14
     CO2	min/ave/max  =	           0	           0	           0
      N2	min/ave/max  =	     0.76699	     0.76699	     0.76699
#0  Foam::error::printStack(Foam::Ostream&) at ??:?
#1  Foam::sigSegv::sigHandler(int) at ??:?
#2   in "/lib/x86_64-linux-gnu/libc.so.6"
#3  Foam::mapDistribute::mapDistribute(Foam::List<int> const&, Foam::List<int> const&) at ??:?
#4  Foam::mappedPatchBase::calcMapping() const at ??:?
#5  Foam::compressible::thermalBaffle1DFvPatchScalarField<Foam::constIsoSolidTransport<Foam::species::thermo<Foam::hConstThermo<Foam::rhoConst<Foam::specie> >, Foam::sensibleEnthalpy> > >::updateCoeffs() at ??:?
#6  Foam::mixedFvPatchField<double>::evaluate(Foam::UPstream::commsTypes) at ??:?
#7  Foam::mixedEnergyFvPatchScalarField::updateCoeffs() at ??:?
#8  Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>::GeometricBoundaryField::updateCoeffs() at ??:?
#9  Foam::fvMatrix<double>::fvMatrix(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&, Foam::dimensionSet const&) at ??:?
#10  Foam::tmp<Foam::fvMatrix<double> > Foam::fvm::Sp<double>(Foam::DimensionedField<double, Foam::volMesh> const&, Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&) at ??:?
#11  Foam::tmp<Foam::fvMatrix<double> > Foam::fvm::Sp<double>(Foam::tmp<Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> > const&, Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&) at ??:?
#12  Foam::radiation::radiationModel::Sh(Foam::fluidThermo&) const at ??:?
#13  
 at ??:?
#14  __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
#15  
 at ??:?
Segmentation fault (core dumped)
Attached Files
File Type: txt error.txt (19.5 KB, 10 views)
File Type: txt log.blockMesh.txt (2.6 KB, 4 views)
File Type: txt checkMesh -allTopology -allGeometry.txt (4.7 KB, 1 views)
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Old   March 7, 2017, 06:49
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Louis Gagnon
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Hello Zhou,
You may have more luck if you post a test case to this thread: Adding New phaseCompressible Turbulence Model
Regards,
-Louis
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Old   March 7, 2017, 11:53
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Mahdi Hosseinali
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Hi,

The first log says it cannot find your library named "libfvPatchFieldsPyrolysis.so", and there's an error in the second one. I'm not quiet acquainted with the models you are using, but it seems the second part is complaining about a bad dictionary.
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Old   March 13, 2017, 21:05
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Quote:
Originally Posted by louisgag View Post
Hello Zhou,
You may have more luck if you post a test case to this thread: Adding New phaseCompressible Turbulence Model
Regards,
-Louis
Thanks very much!
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Old   March 13, 2017, 21:06
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Quote:
Originally Posted by anishtain4 View Post
Hi,

The first log says it cannot find your library named "libfvPatchFieldsPyrolysis.so", and there's an error in the second one. I'm not quiet acquainted with the models you are using, but it seems the second part is complaining about a bad dictionary.
Thanks very much. I will try it again.
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