[Clouch]

Hello everyone,


I would like to perform computations on a case with a custom boundary condition, but I have some trouble making it work on a HPC cluster. I'm following the procedure given at the following link (from p19) which is based on the weirOverFlow tutorial, as the case I want to work on is similar :

http://www.tfd.chalmers.se/~hani/kur...key_report.pdf


The concept is to copy an existing boundary condition (the closest to our new boundary condition), modify it, compile with wmake and sourcing the new *.so library in the system/controlDict file of the case. I have done it on both the weirOverFlow tutorial and my personal case, and both on serial and parallel on my computer : it works.


Now I would like to perform this calculations on a HPC cluster and I have some troubles : I have copied the variableHeightFlowRateInletVelocity boundary condition *.H and *.C files in a personal src/ directory, renamed it and compiled with wmake without errors. When I run any of these commands on the weirOverFlow case : blockMesh, setFields, interFoam, this error occurs :

Create time

#0  Foam::error::printStack(Foam::Ostream&) at ??:?
#1  Foam::sigSegv::sigHandler(int) at ??:?
#2  ? in "/lib64/libc.so.6"
#3  ? at depthOutletVelocityFvPatchVectorField.C:?
#4  ? in "/lib64/ld-linux-x86-64.so.2"
#5  ? in "/lib64/ld-linux-x86-64.so.2"
#6  ? in "/lib64/ld-linux-x86-64.so.2"
#7  _dl_catch_exception in "/lib64/libc.so.6"
#8  ? in "/lib64/ld-linux-x86-64.so.2"
#9  ? in "/lib64/libdl.so.2"
#10  _dl_catch_exception in "/lib64/libc.so.6"
#11  _dl_catch_error in "/lib64/libc.so.6"
#12  ? in "/lib64/libdl.so.2"
#13  dlopen in "/lib64/libdl.so.2"
#14  Foam::dlOpen(Foam::fileName const&, bool) at ??:?
#15  Foam::dlLibraryTable::open(Foam::fileName const&, bool) at ??:?
#16  Foam::dlLibraryTable::open(Foam::dictionary const&, Foam::word const&) at ??:?
#17  Foam::Time::Time(Foam::word const&, Foam::argList const&, Foam::word const&, Foam::word const&) at ??:?
#18  ? at ??:?
#19  __libc_start_main in "/lib64/libc.so.6"
#20  ? at ??:?
Segmentation fault (core dumped)

I've recompiled the copied boundary condition in debug mode (export WM_COMPILE_OPTION=Debug), this is what happens when I execute again the program :

Create time

#0  Foam::error::printStack(Foam::Ostream&) at ??:?
#1  Foam::sigSegv::sigHandler(int) at ??:?
#2  ? in "/lib64/libc.so.6"
#3  std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::size() const in "/lib64/libstdc++.so.6"
#4  _ZSteqIcEN9__gnu_cxx11__enable_ifIXsr3std9__is_charIT_EE7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS2_St11char_traitsIS2_ESaIS2_EEESC_ at /usr/include/c++/8/bits/basic_string.h:6058
#5  Foam::HashTable<Foam::tmp<Foam::fvPatchField<Foam::Vector<double> > > (*)(Foam::fvPatchField<Foam::Vector<double> > const&, Foam::fvPatch const&, Foam::DimensionedField<Foam::Vector<double>, Foam::volMesh> const&, Foam::fvPatchFieldMapper const&), Foam::word, Foam::string::hash>::set(Foam::word const&, Foam::tmp<Foam::fvPatchField<Foam::Vector<double> > > (* const&)(Foam::fvPatchField<Foam::Vector<double> > const&, Foam::fvPatch const&, Foam::DimensionedField<Foam::Vector<double>, Foam::volMesh> const&, Foam::fvPatchFieldMapper const&), bool) at /gpfslocalsup/spack_soft/openfoam-org/7/intel-19.0.5-hsmolp2atuki34neiwvbtp7tqsaxwvdm/src/OpenFOAM/lnInclude/HashTable.C:246
#6  Foam::HashTable<Foam::tmp<Foam::fvPatchField<Foam::Vector<double> > > (*)(Foam::fvPatchField<Foam::Vector<double> > const&, Foam::fvPatch const&, Foam::DimensionedField<Foam::Vector<double>, Foam::volMesh> const&, Foam::fvPatchFieldMapper const&), Foam::word, Foam::string::hash>::insert(Foam::word const&, Foam::tmp<Foam::fvPatchField<Foam::Vector<double> > > (* const&)(Foam::fvPatchField<Foam::Vector<double> > const&, Foam::fvPatch const&, Foam::DimensionedField<Foam::Vector<double>, Foam::volMesh> const&, Foam::fvPatchFieldMapper const&)) at /gpfslocalsup/spack_soft/openfoam-org/7/intel-19.0.5-hsmolp2atuki34neiwvbtp7tqsaxwvdm/src/OpenFOAM/lnInclude/HashTableI.H:85
#7  Foam::fvPatchField<Foam::Vector<double> >::addpatchMapperConstructorToTable<Foam::depthOutletVelocityFvPatchVectorField>::addpatchMapperConstructorToTable(Foam::word const&) at /gpfslocalsup/spack_soft/openfoam-org/7/intel-19.0.5-hsmolp2atuki34neiwvbtp7tqsaxwvdm/src/finiteVolume/lnInclude/fvPatchField.H:137
#8  ? at /gpfsdswork/projects/rech/hhg/umo91rl/src/depthOutletVelocity/depthOutletVelocityFvPatchVectorField.C:145
#9  ? at /usr/include/c++/8/iostream:74
#10  ? in "/lib64/ld-linux-x86-64.so.2"
#11  ? in "/lib64/ld-linux-x86-64.so.2"
#12  ? in "/lib64/ld-linux-x86-64.so.2"
#13  _dl_catch_exception in "/lib64/libc.so.6"
#14  ? in "/lib64/ld-linux-x86-64.so.2"
#15  ? in "/lib64/libdl.so.2"
#16  _dl_catch_exception in "/lib64/libc.so.6"
#17  _dl_catch_error in "/lib64/libc.so.6"
#18  ? in "/lib64/libdl.so.2"
#19  dlopen in "/lib64/libdl.so.2"
#20  Foam::dlOpen(Foam::fileName const&, bool) at ??:?
#21  Foam::dlLibraryTable::open(Foam::fileName const&, bool) at ??:?
#22  Foam::dlLibraryTable::open(Foam::dictionary const&, Foam::word const&) at ??:?
#23  Foam::Time::Time(Foam::word const&, Foam::argList const&, Foam::word const&, Foam::word const&) at ??:?
#24  ? at ??:?
#25  __libc_start_main in "/lib64/libc.so.6"
#26  ? at ??:?
Segmentation fault (core dumped)

Could you please help me debug this problem ? I don't know if it's a problem of compiler, of directory, ...



Regards,


Clouch

[scleakey]

Hello, this is my OSCFD report I think I answered you by email back in 2020, but just in case anyone else is reading this, the depthOutletVelocity boundary condition can be fixed to work in parallel by changing one line in the code. See http://www.tfd.chalmers.se/~hani/kur...key/Errata.pdf for the very brief instructions!