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groovyBC in openFOAM-2.0 for parabolic velocity bc

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Old   August 26, 2013, 04:27
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  #21
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Illya Shevchuk
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The version was 0.2.3 (next to last according to Swak4Foam-Wiki) and suitable to OF up to 2.2 (2.1 is the one I use).

Now I've got v0.2.4 (release, available via svn, must be the latest one), but the errors are still there.

There are also a couple of other error related to openmpi (see attachment for the full log)
Code:
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Waitall'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Abort'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_double'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Get_count'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Init'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Probe'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Send'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Allreduce'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_packed'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Buffer_detach'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Bsend'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_byte'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Irecv'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Recv'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_comm_world'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Get_processor_name'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Test'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Isend'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Finalize'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_op_sum'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Buffer_attach'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_size'
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_rank'
. Somehow, swak is looking for the "OF-internal" openmpi, while an external is used. I think I'm missing something.

Best regards,
Ilya
Attached Files
File Type: gz log.Allwmake.gz (14.6 KB, 5 views)
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Old   August 26, 2013, 07:02
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  #22
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Bernhard Gschaider
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Quote:
Originally Posted by linch View Post
The version was 0.2.3 (next to last according to Swak4Foam-Wiki) and suitable to OF up to 2.2 (2.1 is the one I use).

Now I've got v0.2.4 (release, available via svn, must be the latest one), but the errors are still there.

There are also a couple of other error related to openmpi (see attachment for the full log)
Code:
/home/shevchuk/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Waitall'
. Somehow, swak is looking for the "OF-internal" openmpi, while an external is used. I think I'm missing something.

Best regards,
Ilya
Have you ever tried compiling other software than swak with that installation? Because it seems that this is a problem with the installation, not swak. swak doesn't specify which MPI to use but uses the options that wmake automatically generates (have a look for instance at Utilities/replayTransientBC/Make/options - that is one of the links that is failing and it uses only standard-options).

What version of Linux are you using?
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Old   August 26, 2013, 11:06
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Illya Shevchuk
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Thanks Bernhard,

the problem was indeed somewhere else. I was looking for it for a while with our admin, who takes care of the cluster. Finally, his conclusion was that the openmpi installed on the cluster was compiled with intel compiler while OF uses gcc. However, compiling ThirdPartys and src's caused no errors, these errors occurred only while compiling some application and swak4foam. After recompiling the openmpi with gcc, everything was ok.

Nevertheless, the warnings
Quote:
could not open file [...] for source file [...]
are still there. But since there are no errors, I think it's ok.

Thank you for the hints and best regards,
Ilya
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Old   July 10, 2015, 09:44
Default groovyBC problems
  #24
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Hi guys,


it's my first time using groovyBC and I'm trying to set up a parabolic profile of inlet velocity. What I'm doing is editing the U file to have the following code for inlet

Code:
inlet
    {
        type               groovyBC;
    variables          "yp = pts().y; minY = min(yp); maxY = max(yp); rad = 0.5*(maxY - minY); vavg = 0.23;";
    valueExpression    "2.0*vavg*(1.0-pow(pos().y/rad, 2))*normal()";
    value              uniform (10 0 0);
    }
and also I edited the controlDict file in system to include

Code:
libs ("libOpenFOAM.so"
      "libsimpleSwakFunctionObjects.so"
      "libswakFunctionObjects.so"
      "libgroovyBC.so"
);
But, when I run the case I get the following message

Code:
Create time

Create mesh for time = 0

Selecting dynamicFvMesh dynamicMotionSolverFvMesh
Selecting motion solver: displacementSBRStress
Selecting motion diffusion: inverseDistance
Reading field p

Reading field U

Reading/calculating face flux field phi

Selecting incompressible transport model Newtonian
Selecting turbulence model type laminar
Reading field rAU if present

No field sources present


PIMPLE: no residual control data found. Calculations will employ 2 corrector loops


Starting time loop

Courant Number mean: 0.00054139691 max: 0.023902054
deltaT = 0.00011990408
Time = 0.00011990408

DICPCG:  Solving for cellDisplacementx, Initial residual = 0, Final residual = 0, No Iterations 0
DICPCG:  Solving for cellDisplacementy, Initial residual = 0, Final residual = 0, No Iterations 0
word::stripInvalid() called for word yp
    For debug level (= 2) > 1 this is considered fatal
Aborted (core dumped)
Anyone knows what I'm doing wrong?
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Old   August 23, 2015, 22:41
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Xavier Pivan
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Hi Bernhard,

I use openfoam/2.3.0 on a virtual machine (MASSIVE). I try to implement a zero flux condition via swaf4foam. I have swak4foam/2.3.0. I guess it is well installed as the answer to the command module show swak4foam/2.3.0

-------------------------------------------------------------------
/usr/local/Modules/modulefiles/swak4foam/2.3.0:

conflict swak4foam
module load openfoam/2.3.0
module load bison
module-whatis An OpenFOAM library that combines the functionality of groovyBC (boundary conditions) and funkySetFields (set fields) (v2.3.0)
prepend-path LD_LIBRARY_PATH /usr/local/swak4foam/2.3.0/lib
prepend-path PATH /usr/local/swak4foam/2.3.0/bin
prepend-path MANPATH /usr/local/swak4foam/2.3.0/man
setenv GCONV_PATH /usr/lib64/gconv/
setenv SWAK4FOAM_SRC /usr/local/swak4foam/2.3.0/Libraries
-------------------------------------------------------------------





So the installation seems to be complete. When I try to set up the path of the plug-in

libs (
"libgroovyBC.so"
);

I have a FOAM:WARNING

--> FOAM Warning :
From function dlOpen(const fileName&, const bool)
in file POSIX.C at line 1179
dlopen error : libgroovyBC.so: cannot open shared object file: No such file or directory
--> FOAM Warning :
From function dlLibraryTable:pen(const fileName&, const bool)
in file db/dynamicLibrary/dlLibraryTable/dlLibraryTable.C at line 99
could not load "libgroovyBC.so"

The foam warning doesn't stop the program as this isn't a fatal error. But I need to use this groovyBC for my boundary condition. My boundary condition is:

upperWall
{
type groovyBC;
value uniform (0 0 0);
valueExpression "0.001*T-DT*fvc::snGrad(T)"
}

And as expected I now have a fatal error:

--> FOAM FATAL IO ERROR:
Unknown patchField type groovyBC for patch type patch

Valid patchField types are :.......


Do you have any idea how I can solve this problem? Why do I receive a foam warning for the .so file while swak4foam is apparently well installed.
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