Issue building python wrapper with CGNS support (problems with static/dynamic HDF5 dependencies)

[paspro]

Describe the bug

I am unable to complete the compilation of SU2 v7.3.0 on Fedora 35 using the GCC compiler.
There is a problem when trying to link with the system's libz library.

/usr/bin/ld: /usr/lib64/libz.a(deflate.o): warning: relocation against `z_errmsg' in read-only section `.text'
/usr/bin/ld: /usr/lib64/libz.a(zutil.o): relocation R_X86_64_PC32 against symbol `z_errmsg' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status

To Reproduce

I configured the source code with the commands:

module load mkl/latest
module load mpi/openmpi-x86_64

CFLAGS="-mtune=native -march=native -fPIC" CXXFLAGS="-mtune=native -march=native -fPIC" LDFLAGS="-fPIC" CC=$(which mpiicc) CC=$(which mpicc) CXX=$(which mpicxx) ./meson.py --prefix=/home/panos/Applications/SU2 --optimization=3 -Denable-cgns=true -Denable-mkl=true -Denable-autodiff=true -Denable-directdiff=true -Denable-pywrapper=true -Dwith-mpi=enabled build

Message: -------------------------------------------------------------------------
         |    ___ _   _ ___                                                      |
         |   / __| | | |_  )   Release 7.3.0 "Blackbird"                         |
         |   \__ \ |_| |/ /                                                      |
         |   |___/\___//___|   Meson Configuration Summary                       |
         |                                                                       |
         -------------------------------------------------------------------------

         Option          Value
         ---------------------
         TecIO:          true
         CGNS:           true
         AD (reverse):   true
         AD (forward):   true
         Python Wrapper: true
         Intel-MKL:      true
         OpenBlas:       false
         PaStiX:         false
         Mixed Float:    false
         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=/home/panos/Applications/SU2/bin
         export SU2_HOME=/home/panos/Development/SU2/SU2_SRC
         export PATH=$PATH:$SU2_RUN
         export PYTHONPATH=$PYTHONPATH:$SU2_RUN

         Use './ninja -C build install' to compile and install SU2

Build targets in project: 25

SU2 7.3.0 "Blackbird"

  User defined options
    optimization     : 3
    prefix           : /home/panos/Applications/SU2
    enable-autodiff  : true
    enable-cgns      : true
    enable-directdiff: true
    enable-mkl       : true
    enable-pywrapper : true
    with-mpi         : enabled

Found ninja-1.10.0.git at /home/panos/Development/SU2/SU2_SRC/ninja

When compiling the process fails when trying to link with the libz library:

[1357/1358] Linking target SU2_PY/pySU2/_pysu2ad.so
FAILED: SU2_PY/pySU2/_pysu2ad.so
/usr/lib64/openmpi/bin/mpicxx  -o SU2_PY/pySU2/_pysu2ad.so SU2_PY/pySU2/_pysu2ad.so.p/meson-generated_pySU2ad.cxx.o SU2_CFD/src/libSU2core_AD.a.p/definition_structure.cpp.o SU2_CFD/src/libSU2core_AD.a.p/python_wrapper_structure.cpp.o SU2_CFD/src/libSU2core_AD.a.p/CMarkerProfileReaderFVM.cpp.o SU2_CFD/src/libSU2core_AD.a.p/fluid_CFluidModel.cpp.o SU2_CFD/src/libSU2core_AD.a.p/fluid_CIdealGas.cpp.o SU2_CFD/src/libSU2core_AD.a.p/fluid_CPengRobinson.cpp.o SU2_CFD/src/libSU2core_AD.a.p/fluid_CVanDerWaalsGas.cpp.o SU2_CFD/src/libSU2core_AD.a.p/fluid_CNEMOGas.cpp.o SU2_CFD/src/libSU2core_AD.a.p/fluid_CMutationTCLib.cpp.o SU2_CFD/src/libSU2core_AD.a.p/fluid_CSU2TCLib.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_COutputFactory.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CAdjElasticityOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CAdjFlowOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CAdjFlowCompOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CAdjFlowIncOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CAdjHeatOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CBaselineOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CMultizoneOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CElasticityOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CFlowCompOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CFlowCompFEMOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CFVMOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CFlowOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CFlowIncOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CHeatOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CMeshOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_CNEMOCompOutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_output_physics.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_COutput.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_output_structure_legacy.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CParallelDataSorter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CFVMDataSorter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CFEMDataSorter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CSurfaceFEMDataSorter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CSurfaceFVMDataSorter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CParallelFileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CParaviewFileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CParaviewBinaryFileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CTecplotFileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CTecplotBinaryFileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CCSVFileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CSTLFileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CSU2FileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CSU2BinaryFileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CParaviewXMLFileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CParaviewVTMFileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CSU2MeshFileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_filewriter_CCGNSFileWriter.cpp.o SU2_CFD/src/libSU2core_AD.a.p/output_tools_CWindowingTools.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CIncNSVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CTransLMVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CAdjEulerVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CHeatVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CTurbVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CScalarVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CSpeciesVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CAdjNSVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CBaselineVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CDiscAdjFEABoundVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CDiscAdjMeshBoundVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CFEABoundVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CDiscAdjVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CTurbSAVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CFEAVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CMeshVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CMeshBoundVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CMeshElement.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CRadVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CRadP1Variable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CTurbSSTVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CNSVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CAdjTurbVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CFlowVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CIncEulerVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CEulerVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CNEMOEulerVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CNEMONSVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/variables_CSobolevSmoothingVariable.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CSolverFactory.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CAdjEulerSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CAdjNSSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CAdjTurbSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CBaselineSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CBaselineSolver_FEM.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CDiscAdjFEASolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CDiscAdjMeshSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CRadSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CRadP1Solver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CDiscAdjSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CEulerSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CFEASolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CFEM_DG_EulerSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CFEM_DG_NSSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CHeatSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CIncEulerSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CIncNSSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CMeshSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CNEMOEulerSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CNEMONSSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CNSSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CTemplateSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CSpeciesSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CTransLMSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CTurbSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CTurbSASolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CTurbSSTSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CFEASolverBase.cpp.o SU2_CFD/src/libSU2core_AD.a.p/solvers_CGradientSmoothingSolver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_CNumerics.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_template.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_transition.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_heat.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_radiation.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_flow_convection_roe.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_flow_convection_fds.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_flow_convection_fvs.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_flow_convection_cusp.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_flow_convection_hllc.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_flow_convection_ausm_slau.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_flow_convection_centered.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_flow_flow_diffusion.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_flow_flow_sources.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_NEMO_CNEMONumerics.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_NEMO_convection_lax.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_NEMO_convection_roe.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_NEMO_convection_ausm.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_NEMO_convection_ausmplusup2.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_NEMO_convection_ausmpwplus.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_NEMO_convection_msw.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_NEMO_NEMO_diffusion.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_NEMO_NEMO_sources.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_continuous_adjoint_adj_convection.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_continuous_adjoint_adj_diffusion.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_continuous_adjoint_adj_sources.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_scalar_scalar_sources.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_turbulent_turb_sources.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_species_species_sources.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_elasticity_CFEAElasticity.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_elasticity_CFEALinearElasticity.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_elasticity_CFEANonlinearElasticity.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_elasticity_nonlinear_models.cpp.o SU2_CFD/src/libSU2core_AD.a.p/numerics_CGradSmoothing.cpp.o SU2_CFD/src/libSU2core_AD.a.p/.._include_numerics_simd_CNumericsSIMD.cpp.o SU2_CFD/src/libSU2core_AD.a.p/interfaces_CInterface.cpp.o SU2_CFD/src/libSU2core_AD.a.p/interfaces_cfd_CConservativeVarsInterface.cpp.o SU2_CFD/src/libSU2core_AD.a.p/interfaces_cfd_CMixingPlaneInterface.cpp.o SU2_CFD/src/libSU2core_AD.a.p/interfaces_cfd_CSlidingInterface.cpp.o SU2_CFD/src/libSU2core_AD.a.p/interfaces_cht_CConjugateHeatInterface.cpp.o SU2_CFD/src/libSU2core_AD.a.p/interfaces_fsi_CDisplacementsInterface.cpp.o SU2_CFD/src/libSU2core_AD.a.p/interfaces_fsi_CFlowTractionInterface.cpp.o SU2_CFD/src/libSU2core_AD.a.p/interfaces_fsi_CDiscAdjFlowTractionInterface.cpp.o SU2_CFD/src/libSU2core_AD.a.p/drivers_CDriver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/drivers_CMultizoneDriver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/drivers_CSinglezoneDriver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/drivers_CDiscAdjMultizoneDriver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/drivers_CDiscAdjSinglezoneDriver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/drivers_CDummyDriver.cpp.o SU2_CFD/src/libSU2core_AD.a.p/integration_CIntegration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/integration_CIntegrationFactory.cpp.o SU2_CFD/src/libSU2core_AD.a.p/integration_CSingleGridIntegration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/integration_CMultiGridIntegration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/integration_CNewtonIntegration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/integration_CStructuralIntegration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/integration_CFEM_DG_Integration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/iteration_CIteration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/iteration_CIterationFactory.cpp.o SU2_CFD/src/libSU2core_AD.a.p/iteration_CAdjFluidIteration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/iteration_CDiscAdjFluidIteration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/iteration_CDiscAdjHeatIteration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/iteration_CDiscAdjFEAIteration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/iteration_CFEAIteration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/iteration_CFEMFluidIteration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/iteration_CFluidIteration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/iteration_CHeatIteration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/iteration_CTurboIteration.cpp.o SU2_CFD/src/libSU2core_AD.a.p/limiters_CLimiterDetails.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,_pysu2ad.so -fPIC -mtune=native -march=native -fPIC -Wl,-rpath,/usr/lib64/openmpi/lib -Wl,-rpath-link,/usr/lib64/openmpi/lib Common/src/libSU2CommonAD.a externals/cgns/libcgns.a externals/cgns/hdf5/libsu2hdf5.a externals/metis/libmetis.a externals/parmetis/libparmetis.a externals/tecio/teciompisrc/libteciompi.a /usr/lib64/libpython3.10.so /usr/lib64/libz.a -lm -ldl -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -Wl,--enable-new-dtags /usr/lib64/openmpi/lib/libmpi.so -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -Wl,--enable-new-dtags /usr/lib64/openmpi/lib/libmpi_cxx.so -Wl,--start-group /opt/intel/oneapi/mkl/latest/lib/pkgconfig/../../lib/intel64/libmkl_intel_lp64.a /opt/intel/oneapi/mkl/latest/lib/pkgconfig/../../lib/intel64/libmkl_sequential.a /opt/intel/oneapi/mkl/latest/lib/pkgconfig/../../lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -Wl,--end-group -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -Wl,--enable-new-dtags -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -Wl,--enable-new-dtags -Wl,--start-group -Wl,--end-group -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -Wl,--enable-new-dtags -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -Wl,--enable-new-dtags -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -Wl,--enable-new-dtags -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -Wl,--enable-new-dtags -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -Wl,--enable-new-dtags -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -Wl,--enable-new-dtags -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -Wl,--enable-new-dtags -Wl,-rpath -Wl,/usr/lib64/openmpi/lib -Wl,--enable-new-dtags
/usr/bin/ld: /usr/lib64/libz.a(deflate.o): warning: relocation against `z_errmsg' in read-only section `.text'
/usr/bin/ld: /usr/lib64/libz.a(zutil.o): relocation R_X86_64_PC32 against symbol `z_errmsg' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.

I do use the -fPIC option for the compilation process but even if I remove it from the configuration execution line I still get the same linking error.

Desktop (please complete the following information):

• OS: Linux (Fedora 35)
• C++ 11.2.1 20220127 (Red Hat 11.2.1-9) (GCC)
• MPI implementation and version: OpenMPI v4.1.1
• SU2 Version: v7.3.0

[pcarruscag]

Have you tried:
a) Not forcing CC and CXX to be one of the OpenMPI wrappers
b) Since you are forcing the wrappers, -Dwith-mpi=custom

[pcarruscag]

Correction for b) it's -Dcustom-mpi=true

[paspro]

The problem is not related to the OpenMPI library but the system's libz library and the fact that apparently it is not compiled using the -fPIC option (to create Position Independent Code, which means that the generated machine code is not dependent on being located at a specific address in order to work) but SU2 is compiled or must be compiled with this option in order to work.

[pcarruscag]

(I don't usually build the python wrapper locally)
On Ubuntu 18 (GCC 7.5) I can confirm the same problem linking the python wrapper library with default meson options.
However, passing -fPIC in CXXFLAGS and LDFLAGS solves the issue, clang-10 does not have this fPIC problem, and looking around I found other reports of this issue being particular to GCC (xoreaxeaxeax/rosenbridge#1).

Maybe in your case the environment variables are not making it to the compiler wrapper? (it looks like you are using a cluster and they can be funny...) Try giving a wrong value to CXXFLAGS (e.g. fPIK), meson should fail when it tests the compiler.

So in summary I don't think we should change the defaults of the build system, but I'll ask other devs if they've had the same problem.
I'll change the tittle to make it easier for folks with the same issue to find this.
Please do let us know what solution you find, we may at least add a warning to ours doc.

[aa-g]

Hey ! I recently encountered this issue as well. It seems that on some systems, the libz is available both as a static .a and dynamic .so library. It seems, in some cases, that the former is not compiled with the -fPIC flag by default.

Unfortunately, the HDF5 code packaged with SU2 seems to prefer linking to the former when it is available, leading to errors when compiling the Python API (this flag is required for Python extensions).

The following worked for me: in externals/cgns/hdf5/meson.build, line 28 (and presumably 29, if the same issue exists for szip), you can change the static: true argument to static: false. When (re)configuring, meson should now pick up the shared library instead.

Please let me know if this worked for you also !

[paspro]

This worked for me.

[martin-g]

I face the same issue with the new Docker images (based on Ubuntu 20.04).
#1619
https://github.com/su2code/SU2/runs/6384596072?check_suite_focus=true

Neither the proposed change by @aa-g :

diff --git externals/cgns/hdf5/meson.build externals/cgns/hdf5/meson.build
index f85d5ba86d..c7655a6d1e 100644
--- externals/cgns/hdf5/meson.build
+++ externals/cgns/hdf5/meson.build
@@ -25,8 +25,8 @@ hdf5_conf_data.set('version', '1.12.1')
 ext_deps = []
 
 
-opt_zlib = dependency('zlib', required: false, static: true)
-opt_szip = dependency('szip', required: false, static: true)
+opt_zlib = dependency('zlib', required: false, static: false)
+opt_szip = dependency('szip', required: false, static: false)
 
 if opt_zlib.found() and cc.has_header('zlib.h')
   if cc.has_function('inflate', dependencies: opt_zlib, prefix: '#include <zlib.h>')

nor the extra compiler/linker flags seems to help me:

LDFLAGS="-fPIC" CFLAGS="-fPIC" CXXFLAGS="-fPIC" ./docker/build/compileSU2.sh -b refs/pull/1619/merge -f "-Denable-pywrapper=true -Dwith-mpi=disabled -Denable-tests=true --warnlevel=0 --werror"

[martin-g]

Actually @aa-g 's way works!
I had to make the change in src/SU2_refs_pull_1619_merge/externals/cgns/hdf5/meson.build, not in externals/cgns/hdf5/meson.build because ./docker/build/compileSU2.sh checks out the code of the PR!

[pcarruscag]

Ok, we should make that change official, do you see any problems @MicK7 ?
@aa-g @martin-g can one of you open a PR for this? Thanks.