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Old   September 27, 2013, 15:01
Default compilation problem on cluster
  #521
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Join Date: Dec 2009
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katakgoreng is on a distinguished road
Hi Niels,

Currently, I'm moving to cluster computing for simulation using waves2Foam.
I have some difficulty compiling waves2Foam on the cluster.
Available version of OpenFOAM is 2.1.0 on the cluster.
Compiling the wave2Foam library was a success.
The compilation fails for the solver, pre and post processing as follows:

FOR SOLVER :
Code:
=====================================
    COMPILE SOLVERS
=====================================
Making dependency list for source file waveFoam.C
SOURCE=waveFoam.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/transportModels -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/transportModels/incompressible/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/transportModels/interfaceProperties/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/turbulenceModels/incompressible/turbulenceModel -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude -DOFVERSION=210 -DEXTBRANCH=0 -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2Foam/lnInclude -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2FoamSampling/lnInclude -IlnInclude -I. -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/waveFoam.o
/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude/readTimeControls.H: In function ‘int main(int, char**)’:
/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude/readTimeControls.H:38: warning: unused variable ‘maxDeltaT’
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/transportModels -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/transportModels/incompressible/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/transportModels/interfaceProperties/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/turbulenceModels/incompressible/turbulenceModel -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude -DOFVERSION=210 -DEXTBRANCH=0 -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2Foam/lnInclude -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2FoamSampling/lnInclude -IlnInclude -I. -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPOpt/waveFoam.o -L/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib \
	     -ltwoPhaseInterfaceProperties -lincompressibleTransportModels -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteVolume -L/home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/lib -lwaves2Foam -lwaves2FoamSampling -lOpenFOAM -ldl   -lm -o /home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/bin/waveFoam
/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libincompressibleRASModels.so: undefined reference to `memcpy@GLIBC_2.14'
collect2: ld returned 1 exit status
make: *** [/home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/bin/waveFoam] Error 1
FOR PRE-PROCESSING:

Code:
=====================================
    COMPILE PRE-PROCESSING
=====================================
Making dependency list for source file faceSetToSTL.C
make[1]: Entering directory `/export71/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/applications/utilities/preProcessing/faceSetToSTL'
SOURCE=faceSetToSTL.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/triSurface/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude -IlnInclude -I. -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/faceSetToSTL.o
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/triSurface/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude -IlnInclude -I. -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPOpt/faceSetToSTL.o -L/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib \
	     -lOpenFOAM -ltriSurface -lfiniteVolume -lOpenFOAM -ldl   -lm -o /home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/bin/faceSetToSTL
/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so: undefined reference to `memcpy@GLIBC_2.14'
collect2: ld returned 1 exit status
make[1]: *** [/home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/bin/faceSetToSTL] Error 1
make[1]: Leaving directory `/export71/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/applications/utilities/preProcessing/faceSetToSTL'
make: *** [faceSetToSTL] Error 2
Making dependency list for source file relaxationZoneLayout.C
make[1]: Entering directory `/export71/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/applications/utilities/preProcessing/relaxationZoneLayout'
SOURCE=relaxationZoneLayout.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude -DOFVERSION=210 -DEXTBRANCH=0 -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2Foam/lnInclude -IlnInclude -I. -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/relaxationZoneLayout.o
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude -DOFVERSION=210 -DEXTBRANCH=0 -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2Foam/lnInclude -IlnInclude -I. -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPOpt/relaxationZoneLayout.o -L/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib \
	     -lfiniteVolume -L/home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/lib -lwaves2Foam -lOpenFOAM -ldl   -lm -o /home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/bin/relaxationZoneLayout
/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libfiniteVolume.so: undefined reference to `memcpy@GLIBC_2.14'
collect2: ld returned 1 exit status
make[1]: *** [/home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/bin/relaxationZoneLayout] Error 1
make[1]: Leaving directory `/export71/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/applications/utilities/preProcessing/relaxationZoneLayout'
make: *** [relaxationZoneLayout] Error 2
Making dependency list for source file setWaveField.C
make[1]: Entering directory `/export71/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/applications/utilities/preProcessing/setWaveField'
SOURCE=setWaveField.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude -DOFVERSION=210 -DEXTBRANCH=0 -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2Foam/lnInclude -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2FoamProcessing/lnInclude -IlnInclude -I. -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/setWaveField.o
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude -DOFVERSION=210 -DEXTBRANCH=0 -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2Foam/lnInclude -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2FoamProcessing/lnInclude -IlnInclude -I. -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPOpt/setWaveField.o -L/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib \
	     -lfiniteVolume -L/home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/lib -lwaves2Foam -lwaves2FoamProcessing -lOpenFOAM -ldl   -lm -o /home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/bin/setWaveField
/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libfiniteVolume.so: undefined reference to `memcpy@GLIBC_2.14'
collect2: ld returned 1 exit status
make[1]: *** [/home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/bin/setWaveField] Error 1
make[1]: Leaving directory `/export71/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/applications/utilities/preProcessing/setWaveField'
make: *** [setWaveField] Error 2
Making dependency list for source file setWaveParameters.C
make[1]: Entering directory `/export71/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/applications/utilities/preProcessing/setWaveParameters'
SOURCE=setWaveParameters.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -DOFVERSION=210 -DEXTBRANCH=0 -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2Foam/lnInclude -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2FoamProcessing/lnInclude -I/apps/gsl/1.8/include -IlnInclude -I. -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/setWaveParameters.o
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -DOFVERSION=210 -DEXTBRANCH=0 -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2Foam/lnInclude -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2FoamProcessing/lnInclude -I/apps/gsl/1.8/include -IlnInclude -I. -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPOpt/setWaveParameters.o -L/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib \
	     -lfiniteVolume -L/apps/gsl/1.8/lib -lgsl -lgslcblas -L/home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/lib -lwaves2Foam -lwaves2FoamProcessing -lOpenFOAM -ldl   -lm -o /home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/bin/setWaveParameters
/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libfiniteVolume.so: undefined reference to `memcpy@GLIBC_2.14'
collect2: ld returned 1 exit status
make[1]: *** [/home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/bin/setWaveParameters] Error 1
make[1]: Leaving directory `/export71/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/applications/utilities/preProcessing/setWaveParameters'
make: *** [setWaveParameters] Error 2
Making dependency list for source file waveGaugesNProbes.C
make[1]: Entering directory `/export71/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/applications/utilities/preProcessing/waveGaugesNProbes'
SOURCE=waveGaugesNProbes.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/triSurface/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2FoamProcessing/lnInclude  -IlnInclude -I. -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/waveGaugesNProbes.o
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/triSurface/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/finiteVolume/lnInclude -I/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/src/waves2FoamProcessing/lnInclude  -IlnInclude -I. -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPOpt/waveGaugesNProbes.o -L/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib \
	     -lOpenFOAM -ltriSurface -lfiniteVolume -L/home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/lib -lwaves2FoamProcessing -lOpenFOAM -ldl   -lm -o /home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/bin/waveGaugesNProbes
/apps/OpenFOAM/2.1.0//OpenFOAM-2.1.0/platforms/linux64GccDPOpt/lib/libOpenFOAM.so: undefined reference to `memcpy@GLIBC_2.14'
collect2: ld returned 1 exit status
make[1]: *** [/home/ehk112/OpenFOAM/ehk112-2.1.0/platforms/linux64GccDPOpt/bin/waveGaugesNProbes] Error 1
make[1]: Leaving directory `/export71/home/ehk112/OpenFOAM/ehk112-2.1.0/applications/utilities/waves2Foam/applications/utilities/preProcessing/waveGaugesNProbes'
make: *** [waveGaugesNProbes] Error 2
make: Target `application' not remade because of errors.
It would be grateful if you could take a look at the problem.

Kind regards,
katakgoreng
katakgoreng is offline  

Old   September 28, 2013, 19:43
Default
  #522
ngj
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Niels Gjoel Jacobsen
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@Katakgoreng: You seem to be using a rather old version of glibc on the cluster. I would advice you to talk with your system administrator and ask, how OpenFoam was compiled in the first place.

@David: When you do not bother to give information on OpenFoam version, what you are trying to do in waves2Foam, and how the simulation crashes, nobody will have the slightest chance to help you. If you look on the wiki, and long list of changes between version is available. This might be helpful.

Kind regards,

Niels
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Old   October 4, 2013, 15:59
Default
  #523
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Hi Niels,

In regards to compilation of waves2Foam on the cluster (red hat enterprise linux), I managed to compile the latest version of OpenFOAM (2.2.x) from the Centos - OpenFOAM built project.
I encounter another problem with the current waves2Foam compilation.

My current system is as follows:
Code:
Red Hat Enterprise Linux Server release 6.4 (Santiago)
Linux login-3 2.6.32-358.11.1.el6.x86_64 #1 SMP Wed May 15 10:48:38 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux
The error code that I got:
Code:
=====================================
    COMPILE LIBRARY
=====================================
'/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/lib/libwaves2Foam.so' is up to date.
'/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/lib/libwaves2FoamProcessing.so' is up to date.
SOURCE=surfaceElevation/sampledSurfaceElevationFunctionObject/sampledSurfaceElevationFunctionObject.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -DOFVERSION=220 -DEXTBRANCH=0 -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/finiteVolume/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/meshTools/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/sampling/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/lagrangian/basic/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/fileFormats/lnInclude -I/apps/gsl/1.8/include -IlnInclude -I. -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/sampledSurfaceElevationFunctionObject.o
In file included from /home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude/OutputFilterFunctionObject.H:225:0,
                 from surfaceElevation/sampledSurfaceElevationFunctionObject/sampledSurfaceElevationFunctionObject.H:43,
                 from surfaceElevation/sampledSurfaceElevationFunctionObject/sampledSurfaceElevationFunctionObject.C:27:
/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude/OutputFilterFunctionObject.C: In instantiation of ‘bool Foam::OutputFilterFunctionObject<OutputFilter>::timeSet() [with OutputFilter = Foam::sampledSurfaceElevation]’:
surfaceElevation/sampledSurfaceElevationFunctionObject/sampledSurfaceElevationFunctionObject.C:44:1:   required from here
/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude/OutputFilterFunctionObject.C:215:9: error: ‘class Foam::sampledSurfaceElevation’ has no member named ‘timeSet’
make: *** [Make/linux64GccDPOpt/sampledSurfaceElevationFunctionObject.o] Error 1

=====================================
    COMPILE SOLVERS
=====================================
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/transportModels -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/transportModels/incompressible/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/transportModels/interfaceProperties/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/turbulenceModels/incompressible/turbulenceModel -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/transportModels/twoPhaseMixture/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/finiteVolume/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/meshTools/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/fvOptions/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/sampling/lnInclude -DOFVERSION=220 -DEXTBRANCH=0 -DXVERSION=1 -I/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/src/waves2Foam/lnInclude -I/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/src/waves2FoamSampling/lnInclude -IlnInclude -I. -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPOpt/waveFoam.o -L/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib \
	     -linterfaceProperties -ltwoPhaseInterfaceProperties -lincompressibleTransportModels -lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleLESModels -lfiniteVolume -lmeshTools -lfvOptions -lsampling -L/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/lib -lwaves2Foam -lwaves2FoamSampling -lOpenFOAM -ldl   -lm -o /home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/waveFoam
/usr/bin/ld: cannot find -ltwoPhaseInterfaceProperties
collect2: error: ld returned 1 exit status
make: *** [/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/waveFoam] Error 1

=====================================
    COMPILE PRE-PROCESSING
=====================================
make[1]: Entering directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/preProcessing/faceSetToSTL'
make[1]: `/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/faceSetToSTL' is up to date.
make[1]: Leaving directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/preProcessing/faceSetToSTL'
make[1]: Entering directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/preProcessing/relaxationZoneLayout'
make[1]: `/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/relaxationZoneLayout' is up to date.
make[1]: Leaving directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/preProcessing/relaxationZoneLayout'
make[1]: Entering directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/preProcessing/setWaveField'
make[1]: `/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/setWaveField' is up to date.
make[1]: Leaving directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/preProcessing/setWaveField'
make[1]: Entering directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/preProcessing/setWaveParameters'
make[1]: `/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/setWaveParameters' is up to date.
make[1]: Leaving directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/preProcessing/setWaveParameters'
make[1]: Entering directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/preProcessing/waveGaugesNProbes'
make[1]: `/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/waveGaugesNProbes' is up to date.
make[1]: Leaving directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/preProcessing/waveGaugesNProbes'

=====================================
    COMPILE POST-PROCESSING
=====================================
make[1]: Entering directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/postProcessing/postProcessWaves2Foam'
make[1]: `/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/postProcessWaves2Foam' is up to date.
make[1]: Leaving directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/postProcessing/postProcessWaves2Foam'
make[1]: Entering directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/postProcessing/surfaceElevation'
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/finiteVolume/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/meshTools/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/sampling/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/lagrangian/basic/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/fileFormats/lnInclude -DOFVERSION=220 -DEXTBRANCH=0 -I/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/src/waves2Foam/lnInclude -I/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/src/waves2FoamSampling/lnInclude  -IlnInclude -I. -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPOpt/surfaceElevation.o -L/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib \
	     -lfiniteVolume -lmeshTools -lsampling -lsurfMesh -ltriSurface -llagrangian -lfileFormats -L/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/lib -lwaves2Foam -lwaves2FoamSampling -lOpenFOAM -ldl   -lm -o /home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/surfaceElevation
/usr/bin/ld: cannot find -lwaves2FoamSampling
collect2: error: ld returned 1 exit status
make[1]: *** [/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/surfaceElevation] Error 1
make[1]: Leaving directory `/export71/home/ehk112/OpenFOAM/ehk112-2.2.x/applications/utilities/waves2Foam/applications/utilities/postProcessing/surfaceElevation'
make: *** [surfaceElevation] Error 2
make: Target `application' not remade because of errors.
Could you point to where I could have made mistakes.

Kind regards,
katakgoreng
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Old   October 5, 2013, 06:34
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  #524
ngj
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Good morning Katakgoreng,

For some reason it is not recognised that you are using the 2.2.x version, and I suspect that the compilation script thinks that you are using 2.2.0. This would explain the error in compiling the waves2FoamSampling library, because the function timeSet was introduced between the two versions mentioned above.

I would like to see the output of your environmental variables in waves2Foam and potential error messages bashrc script for waves2Foam, so could you please post everything that goes into log.compile, when you execute the compilation as follows:
Code:
./Allwmake > log.compile 2>&1
I suspect that the problem with the twoPhaseProperties is also related to a wrong identification of the solvers, because this might as well have changed between 2.2.x and 2.2.0. I believe it has been discussed above, but maintaining cross-version compatibility for the most recent releases has been a bit of a pain, so I am happy that you report these issues, since I only have 2.2.0 and 2.2.1 on my machine.

Kind regards,

Niels
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Old   October 7, 2013, 05:18
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Quote:
Originally Posted by ngj View Post
Good morning Katakgoreng,

For some reason it is not recognised that you are using the 2.2.x version, and I suspect that the compilation script thinks that you are using 2.2.0. This would explain the error in compiling the waves2FoamSampling library, because the function timeSet was introduced between the two versions mentioned above.

I would like to see the output of your environmental variables in waves2Foam and potential error messages bashrc script for waves2Foam, so could you please post everything that goes into log.compile, when you execute the compilation as follows:
Code:
./Allwmake > log.compile 2>&1
I suspect that the problem with the twoPhaseProperties is also related to a wrong identification of the solvers, because this might as well have changed between 2.2.x and 2.2.0. I believe it has been discussed above, but maintaining cross-version compatibility for the most recent releases has been a bit of a pain, so I am happy that you report these issues, since I only have 2.2.0 and 2.2.1 on my machine.

Kind regards,

Niels
Hi Niels,

The log files is as link below:
http://sdrv.ms/18Jq32A

Kind regards,
katakgoreng
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Old   October 7, 2013, 14:45
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  #526
ngj
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Hi Katakgoreng,

I have found a solution, so please make an update of your svn-repository. It turned out that I had forgotten to add the XVERSION-flag in the options files. This resolves the problem with compiling libwaves2FoamSampling.so.

With respect to the problem with compiling the solver, I have to come up with a solution. Up to know it has been enough to replace .x in 2.2.x with 2.2.0 and the solvers have been compatible. It turns out that the naming 2.2.x now refers to the git-version of 2.2.1, which requires another solver
This means basically that I will have to come up with a solution, such that the compilation structure is both back- and forward compatible. For now, I will kindly ask you to manually execute the following commands from the waves2Foam directory:

Code:
cd applications/solvers/solvers221/waveFoam
wclean
wmake
As the solver structure for 2.2.1. is actually working (i.e. compiling) with 2.2.x, this resolves your problem. I will think of a more permanent and automatic solution, but for now, this is a path forward.

Kind regards

Niels
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Old   October 8, 2013, 07:19
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Quote:
Originally Posted by ngj View Post
Hi Katakgoreng,

I have found a solution, so please make an update of your svn-repository. It turned out that I had forgotten to add the XVERSION-flag in the options files. This resolves the problem with compiling libwaves2FoamSampling.so.

With respect to the problem with compiling the solver, I have to come up with a solution. Up to know it has been enough to replace .x in 2.2.x with 2.2.0 and the solvers have been compatible. It turns out that the naming 2.2.x now refers to the git-version of 2.2.1, which requires another solver
This means basically that I will have to come up with a solution, such that the compilation structure is both back- and forward compatible. For now, I will kindly ask you to manually execute the following commands from the waves2Foam directory:

Code:
cd applications/solvers/solvers221/waveFoam
wclean
wmake
As the solver structure for 2.2.1. is actually working (i.e. compiling) with 2.2.x, this resolves your problem. I will think of a more permanent and automatic solution, but for now, this is a path forward.

Kind regards

Niels
Hi Niels,

Many thanks for your help. The problem was sorted out. I have managed to get wave2Foam up and running on the cluster.

Kind regards,
katakgoreng
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Old   October 9, 2013, 11:13
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Is there any way to check if I installed waveFoam correctly? As the same way I was able to check icoFoam -help when I installed OpenFOAM? I copied all the files as the wiki says but it doesn't recognize the waveFoam -help
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Old   October 9, 2013, 11:34
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  #529
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Hello everyone,

It may be inappropriate for me to ask here. But this has troubled me for a long time. Sorry about this anyway.

My problem is I cannot make an animation out of the image files output from paraView, either using convert or ffmpeg. Does anyone has a solution for me? Thanks in advance.

Version: ImageMagick 6.6.9-7 2012-08-17 Q16 http://www.imagemagick.org
Copyright: Copyright (C) 1999-2011 ImageMagick Studio LLC
Features: OpenMP

ffmpeg version 0.8.5-4:0.8.5-0ubuntu0.12.04.1, Copyright (c) 2000-2012 the Libav developers


convert *.png movie.mpg

convert: delegate failed `"ffmpeg" -v -1 -mbd rd -trellis 2 -cmp 2 -subcmp 2 -g 300 -pass 1/2 -i "%M%%d.jpg" "%u.%m" 2> "%Z"' @ error/delegate.c/InvokeDelegate/1058.


When using ffmpeg -i animation*.jpg movie.mpeg, it gives lots of output in the terminal, but still cannot see anything in the video.

Stream #0.0 -> #80.0
Press ctrl-c to stop encoding
frame= 1 fps= 0 q=5.3 Lq=5.3 q=5.3 q=5.3 q=5.3 q=5.3 q=5.3 q=5.3 q=5.3 q=5.3 q=5.3 q=5.3
...
q=5.3 q=5.3 q=5.3 q=5.3 q=5.3 q=5.3 q=5.3 q=5.3 q=4.9 size= -0kB time=0.04 bitrate= -4.4kbits/s
video:3139kB audio:0kB global headers:0kB muxing overhead -100.000684%
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Old   October 9, 2013, 12:30
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  #530
ngj
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Hallo Arthur,

That would probably mean that the compilation of waves2Foam has not been successful. I have quickly tried on both OF1.6-ext and OF2.2.1, and on both versions the "-help" option works.

Have you been running any of the tutorials successfully? If no, then return to the compilation step.

Kind regards,

Niels
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Old   October 9, 2013, 12:57
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Mr.Ngj would you mind if I send you a PM?
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Old   October 10, 2013, 08:11
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Ni Niels,

I'm trying to simulate wave breaking/vertical jetting due to focusing waves event (very high steepness). So far, I have managed to go to steepness, Akc of 0.2 and 0.3 without breaking. However, as I reach Akc 0.4, the simulation stop with error code as follows :

Code:
MULES: Solving for alpha1
Phase-1 volume fraction = 0.699903  Min(alpha1) = -3.7219e-19  Max(alpha1) = 1.36268
DILUPBiCG:  Solving for Ux, Initial residual = 0.00387945, Final residual = 1.89691e-10, No Iterations 4
DILUPBiCG:  Solving for Uy, Initial residual = 0.00468833, Final residual = 6.7893e-10, No Iterations 3
GAMG:  Solving for p_rgh, Initial residual = 0.0247348, Final residual = 8.56019e-08, No Iterations 8
GAMG:  Solving for p_rgh, Initial residual = 8.55912e-08, Final residual = 8.55912e-08, No Iterations 0
time step continuity errors : sum local = 1.15524e-09, global = -6.6881e-10, cumulative = -5.17334e-07
GAMG:  Solving for p_rgh, Initial residual = 0.000950645, Final residual = 6.40902e-08, No Iterations 6
GAMG:  Solving for p_rgh, Initial residual = 6.38803e-08, Final residual = 6.38803e-08, No Iterations 0
time step continuity errors : sum local = 8.65e-10, global = 3.06962e-11, cumulative = -5.17304e-07
GAMG:  Solving for p_rgh, Initial residual = 4.12761e-05, Final residual = 5.01357e-08, No Iterations 3
GAMG:  Solving for p_rgh, Initial residual = 5.01163e-08, Final residual = 7.33679e-09, No Iterations 2
time step continuity errors : sum local = 9.93841e-11, global = -1.08676e-11, cumulative = -5.17315e-07
ExecutionTime = 11862.1 s  ClockTime = 11913 s

Courant Number mean: 0.00701962 max: 0.307835
Interface Courant Number mean: 9.04814e-05 max: 0.21481
deltaT = 0.00117681
Time = 22.3717

MULES: Solving for alpha1
Phase-1 volume fraction = 0.6999  Min(alpha1) = -1.76375e-19  Max(alpha1) = 1.36617
DILUPBiCG:  Solving for Ux, Initial residual = 0.00313601, Final residual = 1.90061e-10, No Iterations 4
DILUPBiCG:  Solving for Uy, Initial residual = 0.00375741, Final residual = 1.75008e-10, No Iterations 4
[0] #0  Foam::error::printStack(Foam::Ostream&) in "/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[0] #1  Foam::sigFpe::sigHandler(int) in "/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[0] #2   in "/lib64/libc.so.6"
[0] #3  Foam::GAMGSolver::scale(Foam::Field<double>&, Foam::Field<double>&, Foam::lduMatrix const&, Foam::FieldField<Foam::Field, double> const&, Foam::UPtrList<Foam::lduInterfaceField const> const&, Foam::Field<double> const&, unsigned char) const in "/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[0] #4  Foam::GAMGSolver::Vcycle(Foam::PtrList<Foam::lduMatrix::smoother> const&, Foam::Field<double>&, Foam::Field<double> const&, Foam::Field<double>&, Foam::Field<double>&, Foam::Field<double>&, Foam::PtrList<Foam::Field<double> >&, Foam::PtrList<Foam::Field<double> >&, unsigned char) const in "/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[0] #5  Foam::GAMGSolver::solve(Foam::Field<double>&, Foam::Field<double> const&, unsigned char) const in "/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"
[0] #6  Foam::fvMatrix<double>::solveSegregated(Foam::dictionary const&) in "/home/ehk112/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"
[0] #7  Foam::fvMatrix<double>::solve(Foam::dictionary const&) in "/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/waveFoam"
[0] #8  
[0]  in "/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/waveFoam"
[0] #9  __libc_start_main in "/lib64/libc.so.6"
[0] #10  
[0]  in "/home/ehk112/OpenFOAM/ehk112-2.2.x/platforms/linux64GccDPOpt/bin/waveFoam"
[cx1-5-15-2:16953] *** Process received signal ***
[cx1-5-15-2:16953] Signal: Floating point exception (8)
[cx1-5-15-2:16953] Signal code:  (-6)
[cx1-5-15-2:16953] Failing at address: 0x7a2b300004239
[cx1-5-15-2:16953] [ 0] /lib64/libc.so.6(+0x32920) [0x2ac14c5af920]
[cx1-5-15-2:16953] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x2ac14c5af8a5]
[cx1-5-15-2:16953] [ 2] /lib64/libc.so.6(+0x32920) [0x2ac14c5af920]
[cx1-5-15-2:16953] [ 3] /home/ehk112/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZNK4Foam10GAMGSolver5scaleERNS_5FieldIdEES3_RKNS_9lduMatrixERKNS_10FieldFieldIS1_dEERKNS_8UPtrListIKNS_17lduInterfaceFieldEEERKS2_h+0xba) [0x2ac14b66be7a]
[cx1-5-15-2:16953] [ 4] /home/ehk112/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZNK4Foam10GAMGSolver6VcycleERKNS_7PtrListINS_9lduMatrix8smootherEEERNS_5FieldIdEERKS8_S9_S9_S9_RNS1_IS8_EESD_h+0x1186) [0x2ac14b66ecc6]
[cx1-5-15-2:16953] [ 5] /home/ehk112/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so(_ZNK4Foam10GAMGSolver5solveERNS_5FieldIdEERKS2_h+0x3a8) [0x2ac14b670308]
[cx1-5-15-2:16953] [ 6] /home/ehk112/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libfiniteVolume.so(_ZN4Foam8fvMatrixIdE15solveSegregatedERKNS_10dictionaryE+0x118) [0x2ac1495bf168]
[cx1-5-15-2:16953] [ 7] waveFoam(_ZN4Foam8fvMatrixIdE5solveERKNS_10dictionaryE+0x11c) [0x459c9c]
[cx1-5-15-2:16953] [ 8] waveFoam() [0x48694e]
[cx1-5-15-2:16953] [ 9] /lib64/libc.so.6(__libc_start_main+0xfd) [0x2ac14c59bcdd]
[cx1-5-15-2:16953] [10] waveFoam() [0x4334d5]
[cx1-5-15-2:16953] *** End of error message ***
I'm not sure what the problem is.
Is the error due to problem with the probe? At breaking point, alpha1 would have multiple values causing the interpolation operation for the probe to crash.
Or is it due to the simulation has reach minimum time step?

# UPDATE :

A closer inspection for the alpha1 value from the log reveals the following.

1. For wave with steepness, Akc = 0.2, the alpha1 has a limit of 1 and 0 for every time step as follows:



2. For wave with steepness, Akc = 0.3, the alpha1 does not sustain the limit of 1 and 0 between 22 to 27 s. The simulation however managed to get stable and revert alpha1 to the limit of 1 and 0.



3. For wave reaching the breaking limit Akc=0.4, alpha1 shoot up higher than 1 and the simulation blows up



(blue and red line correspond to minimum and maximum value of alpha1 respectively)

Any idea on tackling this problem with unboundedness of alpha1 is highly appreciated.

Kind regards,
katakgoreng

Last edited by katakgoreng; October 13, 2013 at 13:27.
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Old   October 10, 2013, 14:21
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  #533
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Arthur Loginow
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Hello, I am trying to install waveFoam, so far I have some doubts:

1. Which is the best OF version to work with waveFoam?

2. I did the step 3 from the waves2Foam wiki (This is copy the interFoam source code and modify it)

3. Now I have to proceed with the step number 8 (Is this correct or should I do this step before the step number 3?)

4.At this point I am not sure what to do when it says:

-Obtain the source code via SVN as described above

-Execute the Allwmake script in the folder waves2Foam

What really means by source code?
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Old   October 11, 2013, 14:48
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I made the changes to both the interFoam and the interDyMFoam files and when I try to finish the installation with the wmake command I get the following error:

could not open file relaxationZone.H for source file waveDyMFoam.C
could not open file readWaveProperties.H for source file waveDyMFoam.C
SOURCE=waveDyMFoam.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-100 -I.. -I/opt/openfoam221/src/transportModels/twoPhaseMixture/lnInclude -I/opt/openfoam221/src/transportModels -I/opt/openfoam221/src/transportModels/incompressible/lnInclude -I/opt/openfoam221/src/transportModels/interfaceProperties/lnInclude -I/opt/openfoam221/src/turbulenceModels/incompressible/turbulenceModel -I/opt/openfoam221/src/finiteVolume/lnInclude -I/opt/openfoam221/src/dynamicMesh/lnInclude -I/opt/openfoam221/src/dynamicFvMesh/lnInclude -I./../../../../../src/lnInclude -I/opt/openfoam221/src/meshTools/lnInclude -I/opt/openfoam221/src/fvOptions/lnInclude -I/opt/openfoam221/src/sampling/lnInclude -IlnInclude -I. -I/opt/openfoam221/src/OpenFOAM/lnInclude -I/opt/openfoam221/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/waveDyMFoam.o
waveDyMFoam.C:44:28: fatal error: relaxationZone.H: No such file or directory
compilation terminated.
make: *** [Make/linux64GccDPOpt/waveDyMFoam.o] Error 1


Any help?
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Old   October 12, 2013, 04:44
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Hi Arthur,

You say above that you are unsure on how to use SVN and obtain the source code. I suppose that you are experiencing problems with compiling waveDymFoam simply because you have not obtained the source code from the svn-repository.

This is done by executing the command stated on the wiki, which starts with something like:

Code:
svn co
After this step, you have to compile the source code as also described on the wiki by executing the Allwmake script as in

Code:
./Allwmake
You do not need to make your own waveFoam solver for OF221, since it already comes along with waves2Foam, but if you need to use the moving meshes in OpenFoam, you need to create your own waveDymFoam solver. In that regard please note the NB-statement, which tells you that you should not do exactly as given on the wiki, as the described is partly outdated. Use the existing solvers to see, which modifications are required.

Kind regards

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Old   October 12, 2013, 13:39
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Neil thanks for your reply, when I run the ./Allwmake command I get the following error:

=====================================
ENVIRONMENTAL VARIABLES
=====================================
WAVES_XVERSION=0
WM_PROJECT_VERSION_NUMBER=221
WAVES_SOL=/home/arthur/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam/applications/solvers/solvers221
WAVES_POST=/home/arthur/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam/applications/utilities/postProcessing
WAVES_UTIL=/home/arthur/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam/applications/utilities
EXTBRANCH=0
WAVES_APPBIN=/home/arthur/OpenFOAM/arthur-2.2.1/platforms/linux64GccDPOpt/bin
WAVES_TUT=/home/arthur/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam/tutorials
WAVES_GSL_INCLUDE=/usr/include
WAVES_GSL_LIB=/usr/lib64
WAVES_PRE=/home/arthur/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam/applications/utilities/preProcessing
WAVES_SRC=/home/arthur/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam/src
WAVES_DIR=/home/arthur/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam
WAVES_LIBBIN=/home/arthur/OpenFOAM/arthur-2.2.1/platforms/linux64GccDPOpt/lib


FATAL ERROR.
The directory path /home/arthur/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam does not exist.
Correct the path in bin/bashrc

Please note that once bin/bashrc is created, bin/bashrc.org is only an
inactive file. The latter is also the only of the two files, which is
updated through the SVN-repository.

EXITING


I tried the same creating the

/home/arthur/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam

Directory but still getting another error, what I am doing wrong?
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Old   October 12, 2013, 15:08
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Note that the error message does not advice you to create the given directory, but to adjust bin/bashrc, such that it is pointing to the location, where you have placed waves2Foam.

Kind regards

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Old   October 12, 2013, 18:33
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I was able to compile the application but now when I try to run the solver (waveFoam) at the tutorial (periodicSolitary) I get the following error:

arthur@ubuntu:~/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam/tutorials/waveFoam/periodicSolitary$ waveFoam
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.2.1 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.2.1-57f3c3617a2d
Exec : waveFoam
Date : Oct 12 2013
Time : 18:31:03
Host : "ubuntu"
PID : 10165
Case : /home/arthur/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam/tutorials/waveFoam/periodicSolitary
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

Create mesh for time = 0



--> FOAM FATAL IO ERROR:
cannot open file

file: /home/arthur/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam/tutorials/waveFoam/periodicSolitary/system/fvSchemes at line 0.

From function regIOobject::readStream()
in file db/regIOobject/regIOobjectRead.C at line 87.

FOAM exiting

Any suggestion?
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Old   October 13, 2013, 06:42
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Hi Arthur,

Execute the Allrun script. This will take care of cross-version compatibility of the tutorial cases.

Kind regards

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Old   October 13, 2013, 16:55
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Neils, thanks for your reply, I did what you said, I was able to generate the mesh without any problem, however I get this error when I try to run the solver:

--> FOAM FATAL IO ERROR:
Cannot find patchField entry for cyclic cyclic1_half0
Is your field uptodate with split cyclics?
Run foamUpgradeCyclics to convert mesh and fields to split cyclics.

file: /home/arthur/OpenFOAM/arthur-2.2.1/applications/utilities/waves2Foam/tutorials/waveFoam/periodicSolitary/0/p_rgh.boundaryField from line 25 to line 47.

From function GeometricField<Type, PatchField, GeoMesh>::GeometricBoundaryField::readField(const DimensionedField<Type, GeoMesh>&, const dictionary&)


in file /opt/openfoam221/src/OpenFOAM/lnInclude/GeometricBoundaryField.C at line 181.

FOAM exiting

By this I understand that I have to specify the cyclic at the cyclic boundary, is this correct?

Last edited by Maralady; October 13, 2013 at 18:53.
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