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Bug in Dynamic 1Eq Eddy Viscosity LES Model Incompressible flow

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Old   November 19, 2008, 19:10
Default I was trying to run the channe
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I was trying to run the channel flow case with the dynamic one eq eddy viscosity LES model. I am using the latest Openfoam 1.5 version on Ubuntu Linux, which i pulled from the GIT repository. I got the following error message.

Create time

Create mesh for time = 0


Reading transportProperties

Reading field p

Reading field U

Reading/calculating face flux field phi

Selecting incompressible transport model Newtonian
Selecting LES turbulence model dynOneEqEddy
dynOneEqEddyCoeffs
{
ce 1.05;
filter simple;
}

Initializing with 0 pressure gradient


Starting time loop

Reading/calculating field UMean

Reading/calculating field pMean

Reading/calculating field UPrime2Mean

Reading/calculating field pPrime2Mean

Time = 0.2

Courant Number mean: 0.0522045 max: 0.362923
#0 Foam::error::printStack(Foam:stream&) in "/home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so"
#1 Foam::sigFpe::sigFpeHandler(int) in "/home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so"
#2 Uninterpreted: [0xb802f400]
#3 ?? in "/lib/tls/i686/cmov/libm.so.6"
#4 pow in "/lib/tls/i686/cmov/libm.so.6"
#5 Foam::pow(Foam::Field<double>&, Foam::UList<double> const&, double const&) in "/home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so"
#6 Foam::tmp<foam::geometricfield<double,> > Foam::pow<foam::fvpatchfield,>(Foam::tmp<foam::geo metricfield<double,> > const&, Foam::dimensioned<double> const&) in "/home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libincompressibleLESMod els.so"
#7 Foam::incompressible::LESModels::dynOneEqEddy::ce( Foam::GeometricField<foam::sym mtensor<double>, Foam::fvPatchField, Foam::volMesh> const&) const in "/home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libincompressibleLESMod els.so"
#8 Foam::incompressible::LESModels::dynOneEqEddy::cor rect(Foam::tmp<foam::geometric field<foam::tensor<double>, Foam::fvPatchField, Foam::volMesh> > const&) in "/home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libincompressibleLESMod els.so"
#9 Foam::incompressible::LESModel::correct() in "/home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libincompressibleLESMod els.so"
#10 main in "/home/harishg/OpenFOAM/OpenFOAM-1.5.x/applications/bin/linuxGccDPOpt/channelOod les"
#11 __libc_start_main in "/lib/tls/i686/cmov/libc.so.6"
#12 _start in "/home/harishg/OpenFOAM/OpenFOAM-1.5.x/applications/bin/linuxGccDPOpt/channelOod les"
Floating point exception
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Old   November 20, 2008, 07:27
Default I have just run dynOneEqEddy m
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I have just run dynOneEqEddy model on the channelOodles tutorial case without incident:

Selecting LES turbulence model dynOneEqEddy
dynOneEqEddyCoeffs
{
ce 1.05;
filter simple;
}

Initializing with 0 pressure gradient


Starting time loop

Time = 0.2

Courant Number mean: 0.0691206 max: 0.36731
DILUPBiCG: Solving for k, Initial residual = 0.0181897, Final residual = 7.27253e-06, No Iterations 2
bounding k, min: 0 max: 0.000863933 average: 6.6298e-05
DILUPBiCG: Solving for Ux, Initial residual = 0.011546, Final residual = 1.05515e-06, No Iterations 3
DILUPBiCG: Solving for Uy, Initial residual = 0.0616962, Final residual = 5.5491e-06, No Iterations 3
DILUPBiCG: Solving for Uz, Initial residual = 0.0589226, Final residual = 5.24922e-06, No Iterations 3
DICPCG: Solving for p, Initial residual = 0.189244, Final residual = 0.00788658, No Iterations 3
time step continuity errors : sum local = 1.08526e-05, global = 3.22043e-18, cumulative = 3.22043e-18
DICPCG: Solving for p, Initial residual = 0.0190868, Final residual = 8.88436e-07, No Iterations 96
time step continuity errors : sum local = 1.08773e-09, global = 1.36544e-19, cumulative = 3.35698e-18
Uncorrected Ubar = 0.133495 pressure gradient = 2.75168e-05
ExecutionTime = 3.89 s ClockTime = 4 s

.
.
.

I am unable to reproduce the failure you are getting. Could you try running in valgrind?

H
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Old   November 20, 2008, 19:47
Default I ran it with valgrind upto T=
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I ran it with valgrind upto T=0.4 with dt=0.2 and it ran.I did not have problems with the other LES models that I tried ( smagorinksy, oneeqeqqy, dynsmagorinsky, locdynsmagorinsky) before. This is the log of the run

==10159== Memcheck, a memory error detector.
==10159== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et al.
==10159== Using LibVEX rev 1854, a library for dynamic binary translation.
==10159== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP.
==10159== Using valgrind-3.3.1-Debian, a dynamic binary instrumentation framework.
==10159== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et al.
==10159== For more details, rerun with: -v
==10159==
/*---------------------------------------------------------------------------*\
| ========= | |
| \ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \ / O peration | Version: 1.5.x |
| \ / A nd | Web: http://www.OpenFOAM.org |
| \/ M anipulation | |
\*---------------------------------------------------------------------------*/
Exec : channelOodles
Date : Nov 20 2008
Time : 16:34:37
Host : harishg-desktop
PID : 10159
Case : /windows/dynamic_one_eq_eddy/channel395
nProcs : 1

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

Create mesh for time = 0


Reading transportProperties

Reading field p

Reading field U

Reading/calculating face flux field phi

Selecting incompressible transport model Newtonian
Selecting LES turbulence model dynOneEqEddy
dynOneEqEddyCoeffs
{
ce 1.05;
filter simple;
}

Initializing with 0 pressure gradient


Starting time loop

Reading/calculating field UMean

Reading/calculating field pMean

Reading/calculating field UPrime2Mean

Reading/calculating field pPrime2Mean

Time = 0.2

Courant Number mean: 0.0522045 max: 0.362923
DILUPBiCG: Solving for k, Initial residual = 0.015961, Final residual = 8.98421e-07, No Iterations 2
bounding k, min: 0 max: 0.000715794 average: 2.71055e-05
DILUPBiCG: Solving for Ux, Initial residual = 0.019267, Final residual = 2.87628e-06, No Iterations 3
DILUPBiCG: Solving for Uy, Initial residual = 0.060418, Final residual = 4.40496e-06, No Iterations 3
DILUPBiCG: Solving for Uz, Initial residual = 0.0578968, Final residual = 4.44615e-06, No Iterations 3
GAMG: Solving for p, Initial residual = 0.89089, Final residual = 4.32425e-07, No Iterations 13
time step continuity errors : sum local = 1.27939e-09, global = 9.27239e-19, cumulative = 9.27239e-19
GAMG: Solving for p, Initial residual = 0.0650577, Final residual = 4.38012e-07, No Iterations 9
time step continuity errors : sum local = 2.27455e-09, global = 9.31268e-19, cumulative = 1.85851e-18
Uncorrected Ubar = 0.133393 pressure gradient = 0.000545882
ExecutionTime = 226.18 s ClockTime = 235 s

Calculating averages

Time = 0.4

Courant Number mean: 0.0578568 max: 0.37128
DILUPBiCG: Solving for k, Initial residual = 0.00963296, Final residual = 1.55151e-07, No Iterations 2
bounding k, min: -1.05229e-12 max: 0.000719623 average: 2.71513e-05
DILUPBiCG: Solving for Ux, Initial residual = 0.0445695, Final residual = 9.25886e-07, No Iterations 3
DILUPBiCG: Solving for Uy, Initial residual = 0.234011, Final residual = 6.32796e-06, No Iterations 3
DILUPBiCG: Solving for Uz, Initial residual = 0.164481, Final residual = 3.60588e-06, No Iterations 3
GAMG: Solving for p, Initial residual = 0.945979, Final residual = 5.23357e-07, No Iterations 13
time step continuity errors : sum local = 1.35865e-09, global = 4.93432e-19, cumulative = 2.35194e-18
GAMG: Solving for p, Initial residual = 0.131621, Final residual = 9.82133e-07, No Iterations 9
time step continuity errors : sum local = 1.6846e-09, global = -1.29563e-18, cumulative = 1.0563e-18
Uncorrected Ubar = 0.133537 pressure gradient = 0.000263556
ExecutionTime = 322.4 s ClockTime = 336 s

Calculating averages

End

==10159== Invalid read of size 4
==10159== at 0x4EBD318: Foam::objectRegistry::checkOut(Foam::regIOobject&) const (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x4EB6853: Foam::regIOobject::checkOut() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x4EB6F50: Foam::regIOobject::~regIOobject() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x409CA97: Foam::GeometricField<foam::symmtensor<double>, Foam::fvPatchField, Foam::volMesh>::~GeometricField() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libincompressibleLESMode ls.so)
==10159== by 0x7F34189: Foam::fieldAverage::~fieldAverage() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libfieldAverage.so)
==10159== by 0x7F84566: Foam::-OutputFilterFunctionObject<foam::fieldaverage>::~O utputFilterFunctionObje ct() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libfieldAverage.so)
==10159== by 0x4EC20B9: Foam::functionObjectList::~functionObjectList() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x4ECA840: Foam::Time::~Time() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x805DFBF: main (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/applications/bin/linuxGccDPOpt/channelOodl es)
==10159== Address 0x58b9938 is not stack'd, malloc'd or (recently) free'd
==10159==
==10159== Invalid read of size 4
==10159== at 0x4EBD318: Foam::objectRegistry::checkOut(Foam::regIOobject&) const (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x4EB6853: Foam::regIOobject::checkOut() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x4EB6F50: Foam::regIOobject::~regIOobject() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x806D2A7: Foam::GeometricField<double,>::~GeometricField() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/applications/bin/linuxGccDPOpt/channelOodl es)
==10159== by 0x7F341D1: Foam::fieldAverage::~fieldAverage() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libfieldAverage.so)
==10159== by 0x7F84566: Foam::-OutputFilterFunctionObject<foam::fieldaverage>::~O utputFilterFunctionObje ct() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libfieldAverage.so)
==10159== by 0x4EC20B9: Foam::functionObjectList::~functionObjectList() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x4ECA840: Foam::Time::~Time() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x805DFBF: main (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/applications/bin/linuxGccDPOpt/channelOodl es)
==10159== Address 0x58b9948 is not stack'd, malloc'd or (recently) free'd
==10159==
==10159== Invalid read of size 4
==10159== at 0x4EBD318: Foam::objectRegistry::checkOut(Foam::regIOobject&) const (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x4EB6853: Foam::regIOobject::checkOut() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x4EB6F50: Foam::regIOobject::~regIOobject() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x806B427: Foam::GeometricField<foam::vector<double>, Foam::fvPatchField, Foam::volMesh>::~GeometricField() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/applications/bin/linuxGccDPOpt/channelOodl es)
==10159== by 0x7F342F1: Foam::fieldAverage::~fieldAverage() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libfieldAverage.so)
==10159== by 0x7F84566: Foam::-OutputFilterFunctionObject<foam::fieldaverage>::~O utputFilterFunctionObje ct() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libfieldAverage.so)
==10159== by 0x4EC20B9: Foam::functionObjectList::~functionObjectList() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x4ECA840: Foam::Time::~Time() (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/lib/linuxGccDPOpt/libOpenFOAM.so)
==10159== by 0x805DFBF: main (in /home/harishg/OpenFOAM/OpenFOAM-1.5.x/applications/bin/linuxGccDPOpt/channelOodl es)
==10159== Address 0x58b9858 is not stack'd, malloc'd or (recently) free'd
==10159==
==10159== Invalid free() / delete / delete[]
==10159== at 0x4024B4A: free (vg_replace_malloc.c:323)
==10159== by 0x53AE1EB: (within /lib/tls/i686/cmov/libc-2.8.90.so)
==10159== by 0x53ADCB9: __libc_freeres (in /lib/tls/i686/cmov/libc-2.8.90.so)
==10159== by 0x401F236: _vgnU_freeres (vg_preloaded.c:60)
==10159== by 0x5323163: _Exit (in /lib/tls/i686/cmov/libc-2.8.90.so)
==10159== by 0x529C68C: (below main) (in /lib/tls/i686/cmov/libc-2.8.90.so)
==10159== Address 0x5611328 is not stack'd, malloc'd or (recently) free'd
==10159==
==10159== ERROR SUMMARY: 5 errors from 4 contexts (suppressed: 84 from 2)
==10159== malloc/free: in use at exit: 320 bytes in 13 blocks.
==10159== malloc/free: 1,673,422 allocs, 1,673,410 frees, 5,280,162,639 bytes allocated.
==10159== For counts of detected errors, rerun with: -v
==10159== searching for pointers to 13 not-freed blocks.
==10159== checked 650,496 bytes.
==10159==
==10159== LEAK SUMMARY:
==10159== definitely lost: 156 bytes in 11 blocks.
==10159== possibly lost: 0 bytes in 0 blocks.
==10159== still reachable: 164 bytes in 2 blocks.
==10159== suppressed: 0 bytes in 0 blocks.
==10159== Rerun with --leak-check=full to see details of leaked memory.
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Old   November 27, 2008, 17:18
Default I confirm the bug, I have very
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I confirm the bug, I have very similar error, the case is different though. in my case it occurs only when run in parallel, i.e. with -parallel option, in serial execution it seems to work.
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Old   December 2, 2008, 16:51
Default I did a fresh install of OpenF
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I did a fresh install of OpenFOAM on another machine and the dynamic one equation model did not produce any errors for a serial execution. I think that there was some problem with how I cleaned the openfoam 1.5 installation before installing the openfoam 1.5.x from the git repository.
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Old   December 2, 2008, 19:18
Default serial execution works on my i
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serial execution works on my install also, try parallel.
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