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Old   January 2, 2020, 17:39
Default Errors when running waves2foam
  #1
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Jinshi Chen
Join Date: Jan 2020
Location: Cambridge, MA
Posts: 10
Rep Power: 6
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Hi foamers,

I am new to waves2foam and this website. Yet I have encountered a problem when running waves2foam parallel with JOHNSWAP wave generator, wave absorption zone and k-omega SST turbulence model. The error exists after some seconds of running and the error code is shown below:

Code:
--------------------------------------------------------------------------
A process has executed an operation involving a call to the
"fork()" system call to create a child process.  Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your job may hang, crash, or produce silent
data corruption.  The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.

The process that invoked fork was:

  Local host:          [[33758,1],58] (PID 209108)

If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
--------------------------------------------------------------------------
[58] #0  Foam::error::printStack(Foam::Ostream&) at ??:?
[58] #1  Foam::sigSegv::sigHandler(int) at ??:?
[58] #2  ? in "/lib64/libc.so.6"
[58] #3  ? at btl_vader_component.c:?
[58] #4  opal_progress in "/vortexfs1/apps/openmpi-3.0.1/lib/libopen-pal.so.40"
[58] #5  mca_pml_ob1_recv at ??:?
[58] #6  MPI_Recv in "/vortexfs1/apps/openmpi-3.0.1/lib/libmpi.so.40"
[58] #7  Foam::UIPstream::read(Foam::UPstream::commsTypes, int, char*, long, int, int) at ??:?
[58] #8  void Foam::reduce<bool, Foam::andOp<bool> >(Foam::List<Foam::UPstream::commsStruct> const&, bool&, Foam::andOp<bool> const&, int, int) at ??:?
[58] #9  Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>::needReference() const at ??:?
[58] #10  main at ??:?
[58] #11  __libc_start_main in "/lib64/libc.so.6"
[58] #12  ? at ??:?
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 58 with PID 209108 on node pn054 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
I have searched through this Wiki and someone indicated that this could be due to the poorly chosen boundary condition. However, I still am not able to solve this problem after changing the boundary condition for days. My boundary conditions are:

Alpha.water:
Code:
internalField   uniform 0;

boundaryField
{
    inlet
    {
        type            waveAlpha;
        refValue        uniform 0;
        refGrad         uniform 0;
        valueFraction   uniform 1;
        value           uniform 0;
    }
    bottom
    {
        type            zeroGradient;
    }
    oceanbottom
    {
        type            zeroGradient;
    }
    outlet
    {
        type            zeroGradient;
    }
    atmosphere
    {
        type            inletOutlet;
        inletValue      uniform 0;
        value           uniform 0;
    }
    front
    {
        type            empty;
    }
    back
    {
        type            empty;
    }
}
k
Code:
internalField   uniform 1e-05;

boundaryField
{
    inlet
    {
        type            zeroGradient;
        value           uniform 1e-05;
    }
    outlet
    {
        type            zeroGradient;
        value           uniform 1e-05;
    }
    bottom
    {
        type            kqRWallFunction;
        value           uniform 1e-05;
    }
    oceanbottom
    {
        type            kqRWallFunction;
        value           uniform 1e-05;
    }
    atmosphere
    {
        type            inletOutlet;
        inletValue      uniform 1e-05;
        value           uniform 1e-05;
    }
    front
    {
        type            empty;
    }
    back
    {
        type            empty;
    }
}
nut
Code:
internalField   uniform 0;

boundaryField
{
    inlet
    {
        type            zeroGradient;
        value           uniform 0;
    }

    outlet
    {
        type            zeroGradient;
        value           uniform 0;
    }

    bottom
    {
        type            nutkWallFunction;
        Cmu             0.09;
        kappa           0.41;
        E               9.8;
        value           uniform 0;
    }
    oceanbottom
    {
        type            nutkWallFunction;
        Cmu             0.09;
        kappa           0.41;
        E               9.8;
        value           uniform 0;
    }

    atmosphere
    {
        type            calculated;
        value           uniform 0;
    }
    front
    {
        type            empty;
    }
    back
    {
        type            empty;
    }
}
omega
Code:
internalField   uniform 0.003;

boundaryField
{
    inlet
    {
        type            zeroGradient;
        value           0.003;
    }

    outlet
    {
        type            zeroGradient;
        value           0.003;
    }
    bottom
    {
        type            omegaWallFunction;
        value           0.003;
    }

    oceanbottom
    {
        type            omegaWallFunction;
        value           0.003;
    }

    atmosphere
    {
        type            inletOutlet;
        inletValue      0.003;
        value           0.003;
    }

    front
    {
        type            empty;
    }

    back
    {
        type            empty;
    }

}
U
Code:
internalField   uniform ( 0.0 0.0 0.0);

boundaryField
{
    inlet
    {
        type            waveVelocity;
        refValue        uniform ( 0 0 0 );
        refGradient     uniform ( 0 0 0 );
        valueFraction   uniform 1;
        value           uniform ( 0 0 0 );
    }
    bottom
    {
        type            fixedValue;
        value           uniform ( 0 0 0 );
    }
    oceanbottom
    {
        type            fixedValue;
        value           uniform ( 0 0 0 );
    }
    outlet
    {
        type            fixedValue;
        value           uniform ( 0 0 0 );
    }
    atmosphere
    {
        type            pressureInletOutletVelocity;
        value           uniform ( 0 0 0 );
    }
    front
    {
        type            empty;
    }
    back
    {
        type            empty;
    }

}
Thank you so much in advance!

Best,
Jinshi
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Old   January 17, 2022, 12:25
Default
  #2
FVP
New Member
 
Francisco Pinto
Join Date: Dec 2021
Posts: 4
Rep Power: 4
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Quote:
Originally Posted by JinshiC View Post
Hi foamers,

I am new to waves2foam and this website. Yet I have encountered a problem when running waves2foam parallel with JOHNSWAP wave generator, wave absorption zone and k-omega SST turbulence model. The error exists after some seconds of running and the error code is shown below:

Code:
--------------------------------------------------------------------------
A process has executed an operation involving a call to the
"fork()" system call to create a child process.  Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your job may hang, crash, or produce silent
data corruption.  The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.

The process that invoked fork was:

  Local host:          [[33758,1],58] (PID 209108)

If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
--------------------------------------------------------------------------
[58] #0  Foam::error::printStack(Foam::Ostream&) at ??:?
[58] #1  Foam::sigSegv::sigHandler(int) at ??:?
[58] #2  ? in "/lib64/libc.so.6"
[58] #3  ? at btl_vader_component.c:?
[58] #4  opal_progress in "/vortexfs1/apps/openmpi-3.0.1/lib/libopen-pal.so.40"
[58] #5  mca_pml_ob1_recv at ??:?
[58] #6  MPI_Recv in "/vortexfs1/apps/openmpi-3.0.1/lib/libmpi.so.40"
[58] #7  Foam::UIPstream::read(Foam::UPstream::commsTypes, int, char*, long, int, int) at ??:?
[58] #8  void Foam::reduce<bool, Foam::andOp<bool> >(Foam::List<Foam::UPstream::commsStruct> const&, bool&, Foam::andOp<bool> const&, int, int) at ??:?
[58] #9  Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh>::needReference() const at ??:?
[58] #10  main at ??:?
[58] #11  __libc_start_main in "/lib64/libc.so.6"
[58] #12  ? at ??:?
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 58 with PID 209108 on node pn054 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
I have searched through this Wiki and someone indicated that this could be due to the poorly chosen boundary condition. However, I still am not able to solve this problem after changing the boundary condition for days. My boundary conditions are:

Alpha.water:
Code:
internalField   uniform 0;

boundaryField
{
    inlet
    {
        type            waveAlpha;
        refValue        uniform 0;
        refGrad         uniform 0;
        valueFraction   uniform 1;
        value           uniform 0;
    }
    bottom
    {
        type            zeroGradient;
    }
    oceanbottom
    {
        type            zeroGradient;
    }
    outlet
    {
        type            zeroGradient;
    }
    atmosphere
    {
        type            inletOutlet;
        inletValue      uniform 0;
        value           uniform 0;
    }
    front
    {
        type            empty;
    }
    back
    {
        type            empty;
    }
}
k
Code:
internalField   uniform 1e-05;

boundaryField
{
    inlet
    {
        type            zeroGradient;
        value           uniform 1e-05;
    }
    outlet
    {
        type            zeroGradient;
        value           uniform 1e-05;
    }
    bottom
    {
        type            kqRWallFunction;
        value           uniform 1e-05;
    }
    oceanbottom
    {
        type            kqRWallFunction;
        value           uniform 1e-05;
    }
    atmosphere
    {
        type            inletOutlet;
        inletValue      uniform 1e-05;
        value           uniform 1e-05;
    }
    front
    {
        type            empty;
    }
    back
    {
        type            empty;
    }
}
nut
Code:
internalField   uniform 0;

boundaryField
{
    inlet
    {
        type            zeroGradient;
        value           uniform 0;
    }

    outlet
    {
        type            zeroGradient;
        value           uniform 0;
    }

    bottom
    {
        type            nutkWallFunction;
        Cmu             0.09;
        kappa           0.41;
        E               9.8;
        value           uniform 0;
    }
    oceanbottom
    {
        type            nutkWallFunction;
        Cmu             0.09;
        kappa           0.41;
        E               9.8;
        value           uniform 0;
    }

    atmosphere
    {
        type            calculated;
        value           uniform 0;
    }
    front
    {
        type            empty;
    }
    back
    {
        type            empty;
    }
}
omega
Code:
internalField   uniform 0.003;

boundaryField
{
    inlet
    {
        type            zeroGradient;
        value           0.003;
    }

    outlet
    {
        type            zeroGradient;
        value           0.003;
    }
    bottom
    {
        type            omegaWallFunction;
        value           0.003;
    }

    oceanbottom
    {
        type            omegaWallFunction;
        value           0.003;
    }

    atmosphere
    {
        type            inletOutlet;
        inletValue      0.003;
        value           0.003;
    }

    front
    {
        type            empty;
    }

    back
    {
        type            empty;
    }

}
U
Code:
internalField   uniform ( 0.0 0.0 0.0);

boundaryField
{
    inlet
    {
        type            waveVelocity;
        refValue        uniform ( 0 0 0 );
        refGradient     uniform ( 0 0 0 );
        valueFraction   uniform 1;
        value           uniform ( 0 0 0 );
    }
    bottom
    {
        type            fixedValue;
        value           uniform ( 0 0 0 );
    }
    oceanbottom
    {
        type            fixedValue;
        value           uniform ( 0 0 0 );
    }
    outlet
    {
        type            fixedValue;
        value           uniform ( 0 0 0 );
    }
    atmosphere
    {
        type            pressureInletOutletVelocity;
        value           uniform ( 0 0 0 );
    }
    front
    {
        type            empty;
    }
    back
    {
        type            empty;
    }

}
Thank you so much in advance!

Best,
Jinshi
Hello Jinshi,

Did you fix this problem? I think it might be related with your compilation. It means that the compilation was not succeded.
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Old   January 18, 2022, 11:23
Default
  #3
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Tony Zhang
Join Date: Nov 2019
Location: soton
Posts: 45
Rep Power: 6
zyfsoton is on a distinguished road
Quote:
Originally Posted by FVP View Post
Hello Jinshi,

Did you fix this problem? I think it might be related with your compilation. It means that the compilation was not succeded.
Hi Francisco,

I think I had a similar problem when simulating a ship in wave conditions.

Instead of using waves2Foam, I am using OpenFOAM its own wave generation tool.

As far as I know, OpenFOAM has included its own wave generation tool since OFv5.

To start with, I copied the DTCHullWave tutorial case into my own directory then I replaced the STL file and then did my own blockMesh, refineMesh and snappyHexMesh etc. Then I did renumberMesh, the error reported:

--> FOAM FATAL IO ERROR:
Essential entry 'value' missing

file: /home/OpenFOAM/OpenFOAM-7/run/KCSDRIFTINWAVE/0/U.boundaryField.inlet from line 31 to line 31.

Then I had to add value in alpha.water and U files in 0 folder (value $internalField; in both inlet BCs in both files)

Then setWaves and decomposePar ran smoothly without any error.

Finally, running interFoam, error reads: Unknown patchField type waveVelocity for patch type patch; (/0/U.boundaryField.inlet)

I think the same error will reported in 0/alpha.water.inlet as well for Unknown patchField type waveAlpha for patch type patch;

Please let me know if you have any hint to resolve this issue! Many thanks and Btw I am using OF version 7 and the patches of waveAlpha and waveVelocity should have been included in OFv7, and I can run DTCHullWave tutorial case without any error!

Btw, I am not sure whether it is worth installing a third party wave generation tool eg. wave2Foam in OpenFOAM v7?

Any help will be appreciated!
Tony

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Old   January 18, 2022, 11:45
Default
  #4
FVP
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Francisco Pinto
Join Date: Dec 2021
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Rep Power: 4
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Quote:
Originally Posted by zyfsoton View Post



Btw, I am not sure whether it is worth installing a third party wave generation tool eg. wave2Foam in OpenFOAM v7?

Any help will be appreciated!
Tony

Dear Tony,

I would suggest you to make sure that the openfoam is well installed in your ubuntu machine.
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