[Orgogozo]

Dear Foamers,

I'm a beginners in the use of OF and I try to make a 3D parallel resolution of a solute transport problem in a flow cell partly occupied by a fluid phase flowing, with convection and diffusion of the solute, and by an immobile phase in which there is only diffusive transport and a first order reaction of consumption. The flowfield is computed previously and is introduced by the use of mapFields.

I am implementing a user modified solver, in which I try to force the boundedness of the solute concentration between 0 and the concentration of injection; the use of limitedVanLeer schemes, bounded snGradSchemes, etc improve the boundedness but it is not totally efficient. So additionnaly I write directly in the source code (fully shown at the end of this message) something like :

D = alpha1*cinj+(1-alpha1)*cinj;

Ads = alpha1*0+(1-alpha1)*0;

c = min(max(c,Ads),D);

just after my solve command, in which Ads and D are volScalarFields containing the minimum and maximum desired concentration.

I manage to compile my solver (called bioFoam2), but when I run it in my case by typing

mpirun -np 4 bioFoam2 -parallel

, it gives me the error message written below. And when the three lines for forcing boundedness shown above are not written in the source code, it runs, but it diverges quite quickly.

Does anyone have an idea of what is my mistake ? Thanks by advance.

Kind regards,

Laurent

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ERROR MESSAGE:

p { margin-bottom: 0.21cm; } [2] #3



[1] in "/home/laurent/OpenFOAM/laurent-1.7.1/applications/bin/linuxGccDPOpt/bioFoam2"
[1] #4 [3] in "/home/laurent/OpenFOAM/laurent-1.7.1/applications/bin/linuxGccDPOpt/bioFoam2"
[3] #4 [0] in "/home/laurent/OpenFOAM/laurent-1.7.1/applications/bin/linuxGccDPOpt/bioFoam2"
[0] #4
[2] in "/home/laurent/OpenFOAM/laurent-1.7.1/applications/bin/linuxGccDPOpt/bioFoam2"
[2] #4

[1] in "/home/laurent/OpenFOAM/laurent-1.7.1/applications/bin/linuxGccDPOpt/bioFoam2"
[1] #5 __libc_start_main
[3] in "/home/laurent/OpenFOAM/laurent-1.7.1/applications/bin/linuxGccDPOpt/bioFoam2"
[3] #5 __libc_start_main[2] in "/home/laurent/OpenFOAM/laurent-1.7.1/applications/bin/linuxGccDPOpt/bioFoam2"
[2] #5 __libc_start_main[0] in "/home/laurent/OpenFOAM/laurent-1.7.1/applications/bin/linuxGccDPOpt/bioFoam2"
[0] #5 __libc_start_main in "/lib/tls/i686/cmov/libc.so.6"
[3] #6 in "/lib/tls/i686/cmov/libc.so.6"
[1] #6 in "/lib/tls/i686/cmov/libc.so.6"
[2] #6 in "/lib/tls/i686/cmov/libc.so.6"
[0] #6



--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[2] in "/home/laurent/OpenFOAM/laurent-1.7.1/applications/bin/linuxGccDPOpt/bioFoam2"
[3] in "/home/laurent/OpenFOAM/laurent-1.7.1/applications/bin/linuxGccDPOpt/bioFoam2"
[1] in "/home/laurent/OpenFOAM/laurent-1.7.1/applications/bin/linuxGccDPOpt/bioFoam2"
--------------------------------------------------------------------------
mpirun has exited due to process rank 2 with PID 9779 on
node etna exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[etna:09776] 2 more processes have sent help message help-mpi-api.txt / mpi-abort
[etna:09776] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages


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CREATEFIELDS.H of bioFoam2:

Info<< "Reading transportProperties\n" << endl;

IOdictionary transportProperties
(
IOobject
(
"transportProperties",
runTime.constant(),
mesh,
IOobject::MUST_READ,
IOobject::NO_WRITE
)
);

dimensionedScalar Deau
(
transportProperties.lookup("Deau")
);

dimensionedScalar Dbio
(
transportProperties.lookup("Dbio")
);

dimensionedScalar Adsbio
(
transportProperties.lookup("Adsbio")
);

dimensionedScalar cinj
(
transportProperties.lookup("cinj")
);

Info<< "Reading field c\n" << endl;
volScalarField c
(
IOobject
(
"c",
runTime.timeName(),
mesh,
IOobject::MUST_READ,
IOobject::AUTO_WRITE
),
mesh
);

Info<< "Reading field alpha1\n" << endl;
volScalarField alpha1
(
IOobject
(
"alpha1",
runTime.timeName(),
mesh,
IOobject::MUST_READ,
IOobject::AUTO_WRITE
),
mesh
);

Info<< "Reading field D\n" << endl;
volScalarField D
(
IOobject
(
"D",
runTime.timeName(),
mesh,
IOobject::MUST_READ,
IOobject::AUTO_WRITE
),
mesh
);

Info<< "Reading field Ads\n" << endl;
volScalarField Ads
(
IOobject
(
"Ads",
runTime.timeName(),
mesh,
IOobject::MUST_READ,
IOobject::AUTO_WRITE
),
mesh
);


Info<< "Reading field U\n" << endl;
volVectorField U
(
IOobject
(
"U",
runTime.timeName(),
mesh,
IOobject::MUST_READ,
IOobject::AUTO_WRITE
),
mesh
);


# include "createPhi.H"



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BIOFOAM2.C, source code of bioFoam2:

\*---------------------------------------------------------------------------*/

#include "fvCFD.H"

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

int main(int argc, char *argv[])
{
#include "setRootCase.H"

#include "createTime.H"
#include "createMesh.H"
#include "createFields.H"
#include "initContinuityErrs.H"

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

Info<< "\nStarting time loop\n" << endl;


while (runTime.loop())
{

Info<< "Time = " << runTime.timeName() << nl << endl;

#include "CourantNo.H"

D = alpha1*Deau+(1-alpha1)*Dbio;

Ads = (1-alpha1)*Adsbio;

solve
(
fvm::ddt(c)
- fvm::laplacian(D,c)
+ Ads*c
==
- fvm::div((phi),c)
);

D = alpha1*cinj+(1-alpha1)*cinj;

Ads = alpha1*0+(1-alpha1)*0;

c = min(max(c,Ads),D);

runTime.write();

Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
<< " ClockTime = " << runTime.elapsedClockTime() << " s"
<< nl << endl;
}

Info<< "End\n" << endl;

return 0;
}


// ************************************************** *********************** //


------------------------------------------------------------------------------------------------------------------------
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LOG OF THE RUN WHICH GIVE ME THE ERROR MESSAGE SHOWN ABOVE

/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.7.x |
| \\ / A nd | Web: www.OpenFOAM.com |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 1.7.x-131caa989cd3
Exec : bioFoam2 -parallel
Date : Jun 01 2011
Time : 16:35:08
Host : etna
PID : 9777
Case : /home/laurent/OpenFOAM/laurent-1.7.1/run/LO_OF_1.7.1/biofilmLCPME/cell3Dtransport
nProcs : 4
Slaves :
3
(
etna.9778
etna.9779
etna.9780
)

Pstream initialized with:
floatTransfer : 0
nProcsSimpleSum : 0
commsType : nonBlocking
SigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Create mesh for time = 0.099952

Reading transportProperties

Reading field c

Reading field alpha1

Reading field D

Reading field Ads

Reading field U

Reading/calculating face flux field phi


Starting time loop

Time = 0.100352

Courant Number mean: 6.3162635e-05 max: 0.40167238
GAMG: Solving for c, Initial residual = 1, Final residual = 7.4663329e-10, No Iterations 3