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January 21, 2022, 12:26 |
Error during compilation (python-wrapper)
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#1 |
New Member
Wim Cardoen
Join Date: Jan 2022
Posts: 1
Rep Power: 0 |
Hello,
I tried to compile the SU2 code on a machine (OS:Centos7) using the following modules: module purge module load gcc/10.2.0 # gcc/10.2.0 module load python/3.9.7 # python/3.9.7 (compiled with gcc/10.2.0) module load openblas/0.3.19-st # openblas 0.3.19 (Single threaded) module load impi/2019.5.281 # IMPI MPI library module load cmake export CC=mpicc export CXX=mpicxx export CFLAGS=" -O2 -fPIC " export CXXFLAGS=" ${CXXFLAGS} " export PYTHONPATH=/uufs/chpc.utah.edu/sys/installdir/su2/pylib/3.9.7/lib/python3.9/site-packages:$PYTHONPATH I used the following flags: ./meson.py mybuild -Dcustom-mpi=true -Dwith-mpi=enabled -Denable-mpp=true -Denable-openblas=true -Denable-pywrapper=true \ -Denable-autodiff=true -Denable-mixedprec=true --prefix=/uufs/chpc.utah.edu/sys/installdir/su2/7.2.1 Program swig found: YES (/bin/swig) Message: Using mpi4py from /uufs/chpc.utah.edu/sys/installdir/su2/pylib/3.9.7/lib/python3.9/site-packages/mpi4py/include Dependency python found: YES (pkgconfig) Program install.sh found: YES (/bin/sh /uufs/chpc.utah.edu/sys/srcdir/su2/7.2.1/SU2_PY/pySU2/install.sh) Message: ------------------------------------------------------------------------- | ___ _ _ ___ | | / __| | | |_ ) Release 7.2.1 "Blackbird" | | \__ \ |_| |/ / | | |___/\___//___| Meson Configuration Summary | | | ------------------------------------------------------------------------- Option Value --------------------- TecIO: true CGNS: true AD (reverse): true AD (forward): false Python Wrapper: true Intel-MKL: false OpenBlas: true PaStiX: false Mixed Float: true libROM: false Please be sure to add the $SU2_HOME and $SU2_RUN environment variables, and update your $PATH (and $PYTHONPATH if applicable) with $SU2_RUN Based on the input to this configuration, add these lines to your .bashrc file: export SU2_RUN=/uufs/chpc.utah.edu/sys/installdir/su2/7.2.1/bin export SU2_HOME=/uufs/chpc.utah.edu/sys/srcdir/su2/7.2.1 export PATH=$PATH:$SU2_RUN export PYTHONPATH=$PYTHONPATH:$SU2_RUN Use './ninja -C mybuild install' to compile and install SU2 Message: To run SU2 with Mutation++ library, add these lines to your .bashrc file: export MPP_DATA_DIRECTORY=$SU2_HOME/subprojects/Mutationpp/data export LD_LIBRARY_PATH=$SU2_HOME/<build_dir>/subprojects/Mutationpp At the end of the compilation I obtained the following error: Build targets in project: 21 SU2 7.2.1 "Blackbird" Subprojects Mutationpp: YES Found ninja-1.10.0.git at /uufs/chpc.utah.edu/sys/srcdir/su2/7.2.1/ninja ./ninja -C build install [608/810] Compiling C++ object SU2_CFD/src/libSU2core.a.p/drivers_CDriver.cpp.o In file included from ../subprojects/Mutationpp/src/utilities/Utilities.h:45, from ../subprojects/Mutationpp/src/kinetics/RateLaws.h:35, from ../subprojects/Mutationpp/src/kinetics/RateLawGroup.h:41, from ../subprojects/Mutationpp/src/kinetics/RateManager.h:31, from ../subprojects/Mutationpp/src/kinetics/Kinetics.h:33, from ../subprojects/Mutationpp/src/general/Mixture.h:34, from ../subprojects/Mutationpp/src/general/mutation++.h:31, from ../SU2_CFD/src/drivers/../../include/numerics/NEMO/convection/../../../fluid/CMutationTCLib.hpp:33, from ../SU2_CFD/src/drivers/../../include/numerics/NEMO/convection/../CNEMONumerics.hpp:32, from ../SU2_CFD/src/drivers/../../include/numerics/NEMO/convection/roe.hpp:30, from ../SU2_CFD/src/drivers/CDriver.cpp:67: ../subprojects/Mutationpp/src/utilities/XMLite.h: In member function ‘bool Mutation::Utilities::IO::XmlElement::getChildEleme ntObject(const string&, T&) const’: ../subprojects/Mutationpp/src/utilities/XMLite.h:288:5: warning: no return statement in function returning non-void [-Wreturn-type] 288 | } | ^ [789/810] Generating 'SU2_PY/pySU2/_pysu2.so.p/pySU2.cxx'. FAILED: SU2_PY/pySU2/_pysu2.so.p/pySU2.cxx /bin/swig -DHAVE_CGNS -DNDEBUG -DUSE_MIXED_PRECISION -DHAVE_MPI -DHAVE_METIS -DHAVE_PARMETIS -DHAVE_TECIO -DTECIOMPI -DHAVE_BLAS -DHAVE_LAPACK -DHAVE_MPP -c++ -python -I/uufs/chpc.utah.edu/sys/installdir/su2/pylib/3.9.7/lib/python3.9/site-packages/mpi4py/include -outdir /uufs/chpc.utah.edu/sys/srcdir/su2/7.2.1/mybuild/SU2_PY/pySU2 -o ./SU2_PY/pySU2/_pysu2.so.p/pySU2.cxx ../SU2_PY/pySU2/pySU2.i ../SU2_PY/pySU2/../../Common/include/code_config.hpp:60: Error: Syntax error in input(1). [798/810] Compiling C++ object SU2_CFD/src/libSU2core_AD.a.p/.._include_numerics_simd_CNumericsSIMD.cpp.o ninja: build stopped: subcommand failed. When I removed the option "-Denable-pywrapper=true" from the meson CMD line I was able to compile the code. Before compiling the SU2 code I installed MPI4PY with the same version of gcc and impi. module purge module load gcc/10.2.0 module load python/3.9.7 module load impi/2019.5.281 export CC=mpicc export CXX=mpicxx export CFLAGS=" -m64 -O2 -fPIC " export CXXFLAGS=" ${CFLAGS} " cd /uufs/chpc.utah.edu/sys/srcdir/su2/pylib/mpi4py/3.1.3 python3 setup.py build python3 setup.py install --prefix=/uufs/chpc.utah.edu/sys/installdir/su2/pylib/3.9.7 export PYTHONPATH=/uufs/chpc.utah.edu/sys/installdir/su2/pylib/3.9.7/lib/python3.9/site-packages:$PYTHONPATH Any idea what I should do to resolve the compilation issue? Thank you, Wim |
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March 13, 2022, 23:29 |
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#2 |
New Member
ChenYingJie
Join Date: Feb 2022
Posts: 6
Rep Power: 4 |
I have the same problem, do you have a solution now?
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Tags |
python wrapper |
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