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Problem with compiling a new solver in a supercomputer cluster and EasyBuild

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Old   November 20, 2022, 08:27
Default Problem with compiling a new solver in a supercomputer cluster and EasyBuild
  #1
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Al
Join Date: May 2019
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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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Old   February 9, 2023, 04:11
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  #2
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Konstantinos Missios
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Location: Copenhagen, Denmark.
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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:
Please find `v2106-cpeGNU-22.08/wmake/rules/linux64Cray/c++` file in your OpenFOAM project directory and add `-D_GLIBCXX_USE_CXX11_ABI=0` in the line number 10, so it will look like this:

c++FLAGS = $(c++ARCH) $(GFLAGS) $(c++WARN) $(c++OPT) $(c++DBUG)
c++$(ptFLAGS)
$(LIB_HEADER_DIRS) -fPIC -D_GLIBCXX_USE_CXX11_ABI=0

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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Old   February 9, 2023, 08:23
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  #3
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Al
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Quote:
Originally Posted by missios View Post
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:



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
Thanks, Konstantinos. In fact, I was in touch with LUMI people, and they proposed a solution quite similar to the one you proposed.

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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