import meshes from OpenFOAM

[kkumar20]

Hello Yvan,

As far as I see, snappyHexMesh makes polyhedral cells close to the boundry which generates some polygonal boundry faces at some locations. The decompose polyhedra doesn't do a good job at certain such locations.

I was just taking the easy way out and haven't tried the foamMeshToMed tool. I'll try that next. Thank you,

Kumar

[Ruonan]

Hello Kumar,

When you get the cgns format mesh, I think you can import it into Code_Saturne directly, instead of transfer cgns to med and then import it into Saturne. I use cgns format mesh, which works well.

Best regards,
Ruonan

[kkumar20]

Hello Ruonan,

Thanks for your input! I tried that first but cs was not able to recognize the cgns mesh saved by Paraview. It always results in read errors and applying adf2hdf or hdf2adf converters doesn't resolve the problems. I think the problem comes from the Paraview cgns writer. However I suppose this may not be a problem for cgns meshes generated by other commercial software.

Kumar

[Ruonan]

Hi Kumar,

Thanks for your explanation! Sorry I didn't realize this problem. Yes, I use ICEM to generate mesh and have no problem. Hope you can fix it soon!

Best regards,
Ruonan

[kkumar20]

Hi Ruonan,

I tried to compile foamMeshToMED utility using OpenFOAM versions 7 and 8 - it is really amazing that it compiles with both versions 7 and 8 with some minor changes in the code. However there is a glitch while linking with the library and I'm not able to resolve the issue.

I have code_saturne 7.0.0 with med-4.1.0 installed and I am trying to link the foamMedToMED application with the libmedC library from code_saturne, as required. My OF Make/options are as follows:

EXE_INC = \
/*-DFULLDEBUG -g -O0 -DNDEBUG \*/\
-std=c++11 \
-I/home/kumar/Code_Saturne/7.0.0/hdf5-1.10.6/arch/Linux_x86_64/include \
-I/home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/include \
-I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude \
-I$(LIB_SRC)/dynamicMesh/lnInclude

EXE_LIBS = \
-L/home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/lib/libmedC.so \
-lfiniteVolume \
-lmeshTools \
-ldynamicMesh

During the linking stage, I get the error:

g++ -std=c++11 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -O3 -DNoRepository -ftemplate-depth-100 -std=c++11 -I/home/kumar/Code_Saturne/7.0.0/hdf5-1.10.6/arch/Linux_x86_64/include -I/home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/include -I/opt/openfoam8/src/finiteVolume/lnInclude -I/opt/openfoam8/src/meshTools/lnInclude -I/opt/openfoam8/src/dynamicMesh/lnInclude -IlnInclude -I. -I/opt/openfoam8/src/OpenFOAM/lnInclude -I/opt/openfoam8/src/OSspecific/POSIX/lnInclude -fPIC -fuse-ld=bfd -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPInt32Opt/foamToMED.o -L/opt/openfoam8/platforms/linux64GccDPInt32Opt/lib \
-L/home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/lib/libmedC.so -lfiniteVolume -lmeshTools -ldynamicMesh -lOpenFOAM -ldl \
-lm -o /home/kumar/OpenFOAM/kumar-8/platforms/linux64GccDPInt32Opt/bin/foamMeshToMED
/usr/bin/ld.bfd: Make/linux64GccDPInt32Opt/foamToMED.o: in function `main':
foamToMED.C:(.text.startup+0x568): undefined reference to `MEDfileOpen'
collect2: error: ld returned 1 exit status
make: *** [/opt/openfoam8/wmake/makefiles/general:142: /home/kumar/OpenFOAM/kumar-8/platforms/linux64GccDPInt32Opt/bin/foamMeshToMED] Error 1

The error says there is an undefined reference to MEDfileOpen. But this C function is available in <medfile.h> as:

#ifdef __cplusplus
extern "C" {
#endif

/* File */
MEDC_EXPORT med_idt
MEDfileOpen(const char* const filename,
const med_access_mode accessmode);


I suppose that the linker is not able to find the function in the library libmedC. I am not able to understand why this happens. Can anyone who compiled it successfully please help me out?

Thanks
Kumar

[Yvan Fournier]

Hello,

Just in case, you can run "nm" on /home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/lib/libmedC.so to make sure the MEDfileOpen function is present in MED.

Not sure whether your link is static or dynamic, but in some cases, when building a stic executable/library, order of library appearance may be important.

But what really seems strange in your link line is this:

Code: Select all

-L/home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/lib/libmedC.so

Where I would expect:

Code: Select all

-L/home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/lib -lmedC

Or possibly

Code: Select all

/home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/lib/libmedC.so

(without -L or -l if you are passing the full path explicitely)

Best regards,

Yvan

[kkumar20]

Hello Yvan,

Thanks for your comments! I changed the order of library appearance as you suggested to:

EXE_LIBS = \
-lfiniteVolume \
-lmeshTools \
-ldynamicMesh \
-L/home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/lib -lmedC

Now the compilation works without errors:

g++ -std=c++11 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -O3 -DNoRepository -ftemplate-depth-100 -std=c++11 -I/home/kumar/Code_Saturne/7.0.0/hdf5-1.10.6/arch/Linux_x86_64/include -I/home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/include -I/opt/openfoam8/src/finiteVolume/lnInclude -I/opt/openfoam8/src/meshTools/lnInclude -I/opt/openfoam8/src/dynamicMesh/lnInclude -IlnInclude -I. -I/opt/openfoam8/src/OpenFOAM/lnInclude -I/opt/openfoam8/src/OSspecific/POSIX/lnInclude -fPIC -fuse-ld=bfd -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPInt32Opt/foamMeshToMED.o -L/opt/openfoam8/platforms/linux64GccDPInt32Opt/lib \
-lfiniteVolume -lmeshTools -ldynamicMesh -L/home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/lib -lmedC -lOpenFOAM -ldl \
-lm -o /home/kumar/OpenFOAM/kumar-8/platforms/linux64GccDPInt32Opt/bin/foamMeshToMED

However, when I execute the application I get the message:

$ foamMeshToMED
foamMeshToMED: error while loading shared libraries: libmedC.so.11: cannot open shared object file: No such file or directory

Perhaps some path issue?

[Yvan Fournier]

Hello,

Yes. You can try adding path information to the compilation/link command

Code: Select all

-Wl,,-rpath -Wl,/home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/lib

Or otherwise, add the path to your environment

Code: Select all

export LD_LIBRARY_PATH=/home/kumar/Code_Saturne/7.0.0/med-4.1.0/arch/Linux_x86_64/lib:$LD_LIBRARY_PATH

Before running the executable.

Best regards,

Yvan

[MatthieuM]

Hello everyone,

I'm using this topic because the encountered problem is quite close, but don't hesitate to precise to me if it's recommended to begin a new one.

So I would like to use meshes generated by OpenFoam utilities (snappyHexMesh, CfMesh) with Code_Saturne. I'm trying to use the existing tool foamMeshToMED mentionned in this topic and available on https://github.com/mortbauer/foamMeshToMED.

Here are the versions I'm currently using :
- Code_Saturne 7.0
- Openfoam 9
- MED 4.0.1 (from CS installation)
- hdf5-1.10.6 (from CS installation)

With some minor modifications, the compilation of the foamMeshToMED tool seems to remain globally OK (just some warnings), even with OpenFoam 9. But then, when I try to convert a mesh (a very simple cube meshed with blockMesh), I get the following output (and error) :

Code: Select all

Create time

--> FOAM Warning : 
    From function static Foam::instantList Foam::timeSelector::select0(Foam::Time&, const Foam::argList&)
    in file db/Time/timeSelector.C at line 269
    No time specified or available, selecting 'constant'
Read the mesh

Creating MEDfile
Writing Comment
Creating Mesh
Translating time = constant
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/hdfi/MEDfichierNo.c [39] : Impossible d'identifier un numéro de fichier correct à partir de l'identifiant :
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/hdfi/MEDfichierNo.c [40] : id = 0
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/misc/_MEDcheckVersion30.c [32] : Erreur d'appel de l'API 
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/misc/_MEDcheckVersion30.c [32] : MEDfileNumVersionRd
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/misc/_MEDcheckVersion30.c [33] : majeur = 0
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/misc/_MEDcheckVersion30.c [33] : mineur = 0
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/misc/_MEDcheckVersion30.c [33] : release = 0
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/hdfi/MEDfichierNo.c [39] : Impossible d'identifier un numéro de fichier correct à partir de l'identifiant :
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/hdfi/MEDfichierNo.c [40] : id = 0
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/misc/_MEDcheckVersion30.c [32] : Erreur d'appel de l'API 
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/misc/_MEDcheckVersion30.c [32] : MEDfileNumVersionRd
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/misc/_MEDcheckVersion30.c [33] : majeur = 0
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/misc/_MEDcheckVersion30.c [33] : mineur = 0
~/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/src/misc/_MEDcheckVersion30.c [33] : release = 0
#0  Foam::error::printStack(Foam::Ostream&) at ??:?
#1  Foam::sigSegv::sigHandler(int) at ??:?
#2  ? in "/lib/x86_64-linux-gnu/libc.so.6"
#3  MEDfilterClose in "/home/morelm/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/arch/Linux_x86_64/lib/libmedC.so.11"
#4  _MEDmeshAdvancedWr in "/home/morelm/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/arch/Linux_x86_64/lib/libmedC.so.11"
#5  MEDmeshElementConnectivityWr in "/home/morelm/Programmes/Code_Saturne/saturne_build/prod_7.0.2/med-4.1.0/arch/Linux_x86_64/lib/libmedC.so.11"
#6  ? in "/media/disque2/ProjPerso_d2/OpenFoam_v9/PROJECT_USER/foamMeshtoMED/foamMeshToMED"
#7  ? in "/media/disque2/ProjPerso_d2/OpenFoam_v9/PROJECT_USER/foamMeshtoMED/foamMeshToMED"
#8  ? in "/media/disque2/ProjPerso_d2/OpenFoam_v9/PROJECT_USER/foamMeshtoMED/foamMeshToMED"
#9  __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
#10  ? in "/media/disque2/ProjPerso_d2/OpenFoam_v9/PROJECT_USER/foamMeshtoMED/foamMeshToMED"
Erreur de segmentation (core dumped)

The error seems to suggest the generated MED file is not accepted by my MED libraries. Is there a possibility the mentionned tool foamMeshToMED is too old (8 years) compared to my currently MED version? What does this error suggest to you? kkumar20 was using same MED versions in the previous posts, but I don't know if he finally succeeded to use the tool.

Thank you for your help,
Best regards,

Matthieu

[Yvan Fournier]

Hello,

The best solution here would probably be to compile Foam2Med in debug mode and run it under a debugger to understand what is wrong. You may also experiment with using a MED library build with 32-bit or 64-bit integer sizes, but this is just a guess.

Best regards,

Yvan