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Problem with compiling a new solver in a supercomputer cluster and EasyBuild |
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#1 |
Member
Al
Join Date: May 2019
Posts: 37
Rep Power: 7 ![]() |
Hi
I intended to employ my own solvers on a supercomputer cluster. I am receiving errors even though the solvers worked on my Linux machine and other clouds. Also, both my Linux Workstation and the supercomputer have the same openfoam version. A difference that may create this problem is that the supercomputer uses EasyBuild to install openfoam. To confirm that the problem is with the* compilation of a new solver in this supercomputer, I compiled icoFoam in "FOAM USER APPBIN." It failed. Error message: HTML Code:
/usr/bin/ld: Make/linux64CrayDPInt32Opt/icoFoam.o: in function `Foam::fv::laplacianScheme<Foam::Vector<double>, double>::New(Foam::fvMesh const&, Foam::Istream&)': icoFoam.C:(.text._ZN4Foam2fv15laplacianSchemeINS_6VectorIdEEdE3NewERKNS_6fvM eshERNS_7IstreamE[_ZN4Foam2fv15laplacianSchemeINS_6VectorIdEEdE3N ewERKNS_6fvMeshERNS_7IstreamE]+0x37): undefined reference to `Foam::fv::laplacianScheme<Foam::Vector<double>, double>::IstreamConstructorTablePtr_[abi:cxx11]' /usr/bin/ld: icoFoam.C: (.text._ZN4Foam2fv15laplacianSchemeINS_6VectorIdEEdE3NewERKNS_6fvM eshERNS_7IstreamE[_ZN4Foam2fv15laplacianSchemeINS_6VectorIdEEdE3N ewERKNS_6fvMeshERNS_7IstreamE]+0x1f9): undefined reference to `Foam::fv::laplacianScheme<Foam::Vector<double>, double>::IstreamConstructorTablePtr_[abi:cxx11]' /usr/bin/ld: Make/linux64CrayDPInt32Opt/icoFoam.o: (.data.rel.ro._ZTVN4Foam8OPstreamE[_ZTVN4Foam8OPstreamE]+0x80): undefined reference to `Foam::UOPstream::writeQuoted(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool)' Also the log file for the compilation is as follow. HTML Code:
Making dependency list for source file icoFoam.C CC -std=c++11 -m64 -pthread -DOPENFOAM=2106 -DWM_DP - DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor - Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -Wno- unknown-pragmas -O3 -DNoRepository -ftemplate-depth-100 - I/scratch/project_465000271/EasyBuild/SW/LUMI- 22.08/C/OpenFOAM/v2106-cpeGNU-22.08/src/finiteVolume/lnInclude - I/scratch/project_465000271/EasyBuild/SW/LUMI- 22.08/C/OpenFOAM/v2106-cpeGNU-22.08/src/meshTools/lnInclude -iquote. - IlnInclude -I/scratch/project_465000271/EasyBuild/SW/LUMI- 22.08/C/OpenFOAM/v2106-cpeGNU-22.08/src/OpenFOAM/lnInclude - I/scratch/project_465000271/EasyBuild/SW/LUMI- 22.08/C/OpenFOAM/v2106-cpeGNU-22.08/src/OSspecific/POSIX/lnInclude - fPIC -c icoFoam.C -o Make/linux64CrayDPInt32Opt/icoFoam.o CC -std=c++11 -m64 -pthread -DOPENFOAM=2106 -DWM_DP - DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor - Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -Wno- unknown-pragmas -O3 -DNoRepository -ftemplate-depth-100 - I/scratch/project_465000271/EasyBuild/SW/LUMI- 22.08/C/OpenFOAM/v2106-cpeGNU-22.08/src/finiteVolume/lnInclude - I/scratch/project_465000271/EasyBuild/SW/LUMI- 22.08/C/OpenFOAM/v2106-cpeGNU-22.08/src/meshTools/lnInclude -iquote. - IlnInclude -I/scratch/project_465000271/EasyBuild/SW/LUMI- 22.08/C/OpenFOAM/v2106-cpeGNU-22.08/src/OpenFOAM/lnInclude - I/scratch/project_465000271/EasyBuild/SW/LUMI- 22.08/C/OpenFOAM/v2106-cpeGNU-22.08/src/OSspecific/POSIX/lnInclude - fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64CrayDPInt32Opt/icoFoam.o - L/scratch/project_465000271/EasyBuild/SW/LUMI- 22.08/C/OpenFOAM/v2106-cpeGNU- 22.08/platforms/linux64CrayDPInt32Opt/lib \ -lfiniteVolume -lmeshTools -lOpenFOAM -ldl \ -lm -o /users/nujukamb/OpenFOAM/nujukamb- v2106/platforms/linux64CrayDPInt32Opt/bin/myIcoFoam I'll appreciate any help regarding this matter. Thanks |
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#2 | |
New Member
Konstantinos Missios
Join Date: Mar 2017
Location: Copenhagen, Denmark.
Posts: 12
Rep Power: 9 ![]() |
Hello aliyah.
I faced a similar issue. Although I can't recall the error message. I remember that the OpenFOAM easyconfig file of LUMI had an issue at some point and the installed OpenFOAM couldn't compile new code. A solution to that, provided by the LUMI support was: Quote:
Hope it helps. If not you could try compiling again OpenFOAM yourself. To do so, you can follow the instructions provided by prof H. Nilsson here http://www.tfd.chalmers.se/~hani/wik.../_Installation |
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#3 | |
Member
Al
Join Date: May 2019
Posts: 37
Rep Power: 7 ![]() |
Quote:
Just to highlight Lumi's alternative solution: By adding the following line to the bashrc file, the problem can be solved. Code:
export FOAM_EXTRA_CXXFLAGS="-D_GLIBCXX_USE_CXX11_ABI=0" |
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Tags |
cluster setup, easybuild, new solver |
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