Problem compiling roadrunner C++ version
Closed this issue · 4 comments
matthiaskoenig commented
Hi all,
I have problems getting roadrunner compiled. I followed the online documentation and information I got from @steffenger.
I can build the LLVM and roadrunner-deps, but it seems the linkink step when building roadrunner is failing. Not sure what I am doing wrong here.
The error I get is the following:
[ 51%] Linking CXX shared library ../lib/libroadrunner.so
cd /home/mkoenig/git/porous_media/buildroadrunner/roadrunner/build/source && /usr/bin/cmake -E cmake_link_script CMakeFiles/roadrunner.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -std=c++17 -O3 -DNDEBUG -shared -Wl,-soname,libroadrunner.so -o ../lib/libroadrunner.so CMakeFiles/roadrunner.dir/rrConfig.cpp.o CMakeFiles/roadrunner.dir/rrConstants.cpp.o CMakeFiles/roadrunner.dir/rrException.cpp.o CMakeFiles/roadrunner.dir/rrGetOptions.cpp.o CMakeFiles/roadrunner.dir/rrLogger.cpp.o CMakeFiles/roadrunner.dir/rrExecutableModel.cpp.o CMakeFiles/roadrunner.dir/rrRoadRunner.cpp.o CMakeFiles/roadrunner.dir/rrRoadRunnerOptions.cpp.o CMakeFiles/roadrunner.dir/rrStringUtils.cpp.o CMakeFiles/roadrunner.dir/rrUtils.cpp.o CMakeFiles/roadrunner.dir/Integrator.cpp.o CMakeFiles/roadrunner.dir/CVODEIntegrator.cpp.o CMakeFiles/roadrunner.dir/Dictionary.cpp.o CMakeFiles/roadrunner.dir/GillespieIntegrator.cpp.o CMakeFiles/roadrunner.dir/RK4Integrator.cpp.o CMakeFiles/roadrunner.dir/RK45Integrator.cpp.o CMakeFiles/roadrunner.dir/NLEQ1Solver.cpp.o CMakeFiles/roadrunner.dir/NLEQ2Solver.cpp.o CMakeFiles/roadrunner.dir/NLEQSolver.cpp.o CMakeFiles/roadrunner.dir/rrNLEQ1Interface.cpp.o CMakeFiles/roadrunner.dir/rrNLEQ2Interface.cpp.o CMakeFiles/roadrunner.dir/rrTestSuiteModelSimulation.cpp.o CMakeFiles/roadrunner.dir/rrIniKey.cpp.o CMakeFiles/roadrunner.dir/rrIniSection.cpp.o CMakeFiles/roadrunner.dir/rrIniFile.cpp.o CMakeFiles/roadrunner.dir/rrFileName.cpp.o CMakeFiles/roadrunner.dir/rrRoadRunnerData.cpp.o CMakeFiles/roadrunner.dir/rrSelectionRecord.cpp.o CMakeFiles/roadrunner.dir/ExecutableModelFactory.cpp.o CMakeFiles/roadrunner.dir/rrVersionInfo.cpp.o CMakeFiles/roadrunner.dir/rrSparse.cpp.o CMakeFiles/roadrunner.dir/rrSBMLModelSimulation.cpp.o CMakeFiles/roadrunner.dir/rrSBMLReader.cpp.o CMakeFiles/roadrunner.dir/SBMLValidator.cpp.o CMakeFiles/roadrunner.dir/SteadyStateSolver.cpp.o CMakeFiles/roadrunner.dir/Solver.cpp.o CMakeFiles/roadrunner.dir/Setting.cpp.o CMakeFiles/roadrunner.dir/ForwardSensitivitySolver.cpp.o CMakeFiles/roadrunner.dir/RegistrationFactory.cpp.o CMakeFiles/roadrunner.dir/SensitivitySolverFactory.cpp.o CMakeFiles/roadrunner.dir/SteadyStateSolverFactory.cpp.o CMakeFiles/roadrunner.dir/IntegratorFactory.cpp.o CMakeFiles/roadrunner.dir/KinsolSteadyStateSolver.cpp.o CMakeFiles/roadrunner.dir/FixedPointIteration.cpp.o CMakeFiles/roadrunner.dir/NewtonIteration.cpp.o CMakeFiles/roadrunner.dir/BasicNewtonIteration.cpp.o CMakeFiles/roadrunner.dir/LinesearchNewtonIteration.cpp.o CMakeFiles/roadrunner.dir/KinsolErrHandler.cpp.o CMakeFiles/roadrunner.dir/SVD.cpp.o CMakeFiles/roadrunner.dir/SteadyStateSolverDecorator.cpp.o CMakeFiles/roadrunner.dir/PresimulationDecorator.cpp.o CMakeFiles/roadrunner.dir/PresimulationProgramDecorator.cpp.o CMakeFiles/roadrunner.dir/ApproxSteadyStateDecorator.cpp.o CMakeFiles/roadrunner.dir/conservation/ConservationExtension.cpp.o CMakeFiles/roadrunner.dir/conservation/ConservationDocumentPlugin.cpp.o CMakeFiles/roadrunner.dir/conservation/ConservedMoietyPlugin.cpp.o CMakeFiles/roadrunner.dir/conservation/ConservedMoietyConverter.cpp.o CMakeFiles/roadrunner.dir/rrRoadRunnerMap.cpp.o CMakeFiles/roadrunner.dir/llvm/ASTNodeCodeGen.cpp.o CMakeFiles/roadrunner.dir/llvm/ASTNodeFactory.cpp.o CMakeFiles/roadrunner.dir/llvm/AssignmentRuleEvaluator.cpp.o CMakeFiles/roadrunner.dir/llvm/CodeGenBase.cpp.o CMakeFiles/roadrunner.dir/llvm/EvalConversionFactorCodeGen.cpp.o CMakeFiles/roadrunner.dir/llvm/EvalInitialConditionsCodeGen.cpp.o CMakeFiles/roadrunner.dir/llvm/EvalRateRuleRatesCodeGen.cpp.o CMakeFiles/roadrunner.dir/llvm/EvalReactionRatesCodeGen.cpp.o CMakeFiles/roadrunner.dir/llvm/EvalVolatileStoichCodeGen.cpp.o CMakeFiles/roadrunner.dir/llvm/EventAssignCodeGen.cpp.o CMakeFiles/roadrunner.dir/llvm/EventQueue.cpp.o CMakeFiles/roadrunner.dir/llvm/EventTriggerCodeGen.cpp.o CMakeFiles/roadrunner.dir/llvm/FunctionResolver.cpp.o CMakeFiles/roadrunner.dir/llvm/GetEventValuesCodeGen.cpp.o CMakeFiles/roadrunner.dir/llvm/GetInitialValuesCodeGen.cpp.o CMakeFiles/roadrunner.dir/llvm/GetValuesCodeGen.cpp.o CMakeFiles/roadrunner.dir/llvm/Jit.cpp.o CMakeFiles/roadrunner.dir/llvm/JitFactory.cpp.o CMakeFiles/roadrunner.dir/llvm/KineticLawParameterResolver.cpp.o CMakeFiles/roadrunner.dir/llvm/LLJit.cpp.o CMakeFiles/roadrunner.dir/llvm/LLVMCompiler.cpp.o CMakeFiles/roadrunner.dir/llvm/LLVMExecutableModel.cpp.o CMakeFiles/roadrunner.dir/llvm/LLVMModelData.cpp.o CMakeFiles/roadrunner.dir/llvm/LLVMModelDataSymbols.cpp.o CMakeFiles/roadrunner.dir/llvm/LLVMModelGenerator.cpp.o CMakeFiles/roadrunner.dir/llvm/LLVMModelSymbols.cpp.o CMakeFiles/roadrunner.dir/llvm/LoadSymbolResolverBase.cpp.o CMakeFiles/roadrunner.dir/llvm/MCJit.cpp.o CMakeFiles/roadrunner.dir/llvm/ModelDataIRBuilder.cpp.o CMakeFiles/roadrunner.dir/llvm/ModelDataSymbolResolver.cpp.o CMakeFiles/roadrunner.dir/llvm/ModelGeneratorContext.cpp.o CMakeFiles/roadrunner.dir/llvm/ModelInitialValueSymbolResolver.cpp.o CMakeFiles/roadrunner.dir/llvm/ModelResources.cpp.o CMakeFiles/roadrunner.dir/llvm/Random.cpp.o CMakeFiles/roadrunner.dir/llvm/SBMLInitialValueSymbolResolver.cpp.o CMakeFiles/roadrunner.dir/llvm/SBMLModelObjectCache.cpp.o CMakeFiles/roadrunner.dir/llvm/SBMLSupportFunctions.cpp.o CMakeFiles/roadrunner.dir/llvm/SetInitialValuesCodeGen.cpp.o CMakeFiles/roadrunner.dir/llvm/SetValuesCodeGen.cpp.o -Wl,-rpath,:::::::::::::::::::::: -lpthread -ldl -lm -lcurses /usr/lib/x86_64-linux-gnu/libform.so /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcJIT.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMPasses.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMObjCARCOpts.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCoroutines.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMipo.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMInstrumentation.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMVectorize.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMLinker.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMIRReader.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAsmParser.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMFrontendOpenMP.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMJITLink.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86Disassembler.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86AsmParser.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86CodeGen.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCFGuard.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMGlobalISel.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86Desc.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86Info.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMCDisassembler.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMSelectionDAG.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAsmPrinter.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDebugInfoMSF.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDebugInfoDWARF.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCodeGen.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMScalarOpts.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMInstCombine.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAggressiveInstCombine.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMTransformUtils.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBitWriter.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMCJIT.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMExecutionEngine.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMTarget.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAnalysis.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMProfileData.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMRuntimeDyld.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcTargetProcess.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcShared.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMObject.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMTextAPI.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMCParser.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBitReader.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMC.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDebugInfoCodeView.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCore.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMRemarks.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBitstreamReader.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBinaryFormat.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMSupport.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDemangle.a -lcurses /usr/lib/x86_64-linux-gnu/libform.so /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/librr-libstruct-static.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsbml-static.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libz.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libnleq2-static.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libnleq1-static.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/liblapack.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libblas.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libf2c.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_generic.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_nvecserial.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_nvecmanyvector.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunmatrixband.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunmatrixdense.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunmatrixsparse.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsolband.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsoldense.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsolpcg.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsolspbcgs.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsolspfgmr.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsolspgmr.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsolsptfqmr.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunnonlinsolnewton.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunnonlinsolfixedpoint.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_cvodes.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_kinsol.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libPocoFoundation.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libPocoNet.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libPocoXML.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libexpat.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcJIT.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMPasses.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMObjCARCOpts.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCoroutines.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMipo.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMInstrumentation.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMVectorize.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMLinker.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMIRReader.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAsmParser.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMFrontendOpenMP.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMJITLink.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86Disassembler.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86AsmParser.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86CodeGen.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCFGuard.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMGlobalISel.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86Desc.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86Info.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMCDisassembler.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMSelectionDAG.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAsmPrinter.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDebugInfoMSF.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDebugInfoDWARF.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCodeGen.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMScalarOpts.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMInstCombine.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAggressiveInstCombine.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMTransformUtils.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBitWriter.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMCJIT.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMExecutionEngine.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMTarget.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAnalysis.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMProfileData.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMRuntimeDyld.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcTargetProcess.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcShared.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMObject.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMTextAPI.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMCParser.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBitReader.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMC.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDebugInfoCodeView.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCore.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMRemarks.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBitstreamReader.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBinaryFormat.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMSupport.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDemangle.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libz.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunmatrixband.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunmatrixdense.a -lm /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libPocoFoundation.a -lpthread -ldl -lrt
make[2]: Leaving directory '/home/mkoenig/git/porous_media/buildroadrunner/roadrunner/build'
/usr/bin/make -f wrappers/C/CMakeFiles/roadrunner_c_api-static.dir/build.make wrappers/C/CMakeFiles/roadrunner_c_api-static.dir/build
make[2]: Leaving directory '/home/mkoenig/git/porous_media/buildroadrunner/roadrunner/build'
/usr/bin/make -f wrappers/C/CMakeFiles/roadrunner_c_api.dir/build.make wrappers/C/CMakeFiles/roadrunner_c_api.dir/build
make[2]: Entering directory '/home/mkoenig/git/porous_media/buildroadrunner/roadrunner/build'
make[2]: Nothing to be done for 'wrappers/C/CMakeFiles/roadrunner_c_api-static.dir/build'.
make[2]: Leaving directory '/home/mkoenig/git/porous_media/buildroadrunner/roadrunner/build'
make[2]: Entering directory '/home/mkoenig/git/porous_media/buildroadrunner/roadrunner/build'
[ 51%] Built target roadrunner_c_api-static
[ 51%] Linking CXX shared library ../../lib/libroadrunner_c_api.so
cd /home/mkoenig/git/porous_media/buildroadrunner/roadrunner/build/wrappers/C && /usr/bin/cmake -E cmake_link_script CMakeFiles/roadrunner_c_api.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -std=c++17 -O3 -DNDEBUG -shared -Wl,-soname,libroadrunner_c_api.so -o ../../lib/libroadrunner_c_api.so CMakeFiles/roadrunner_c_api.dir/rrcStringList.cpp.o CMakeFiles/roadrunner_c_api.dir/rrArrayList.cpp.o CMakeFiles/roadrunner_c_api.dir/rrArrayListItem.cpp.o CMakeFiles/roadrunner_c_api.dir/rrArrayListItemBase.cpp.o CMakeFiles/roadrunner_c_api.dir/rrc_api.cpp.o CMakeFiles/roadrunner_c_api.dir/rrc_logging_api.cpp.o CMakeFiles/roadrunner_c_api.dir/rrc_nom_api.cpp.o CMakeFiles/roadrunner_c_api.dir/rrc_libstruct_api.cpp.o CMakeFiles/roadrunner_c_api.dir/rrc_utilities.cpp.o CMakeFiles/roadrunner_c_api.dir/rrc_cpp_support.cpp.o -Wl,-rpath,:::::::::::::::::::::: ../../lib/libroadrunner-static.a -lpthread -ldl -lm -lcurses /usr/lib/x86_64-linux-gnu/libform.so /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcJIT.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMPasses.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMObjCARCOpts.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCoroutines.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMipo.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMInstrumentation.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMVectorize.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMLinker.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMIRReader.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAsmParser.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMFrontendOpenMP.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMJITLink.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86Disassembler.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86AsmParser.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86CodeGen.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCFGuard.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMGlobalISel.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86Desc.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86Info.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMCDisassembler.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMSelectionDAG.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAsmPrinter.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDebugInfoMSF.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDebugInfoDWARF.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCodeGen.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMScalarOpts.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMInstCombine.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAggressiveInstCombine.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMTransformUtils.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBitWriter.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMCJIT.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMExecutionEngine.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMTarget.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAnalysis.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMProfileData.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMRuntimeDyld.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcTargetProcess.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcShared.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMObject.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMTextAPI.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMCParser.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBitReader.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMC.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDebugInfoCodeView.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCore.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMRemarks.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBitstreamReader.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBinaryFormat.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMSupport.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDemangle.a -lcurses /usr/lib/x86_64-linux-gnu/libform.so /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/librr-libstruct-static.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsbml-static.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libz.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libnleq2-static.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libnleq1-static.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/liblapack.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libblas.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libf2c.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_generic.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_nvecserial.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_nvecmanyvector.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunmatrixband.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunmatrixdense.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunmatrixsparse.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsolband.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsoldense.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsolpcg.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsolspbcgs.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsolspfgmr.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsolspgmr.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunlinsolsptfqmr.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunnonlinsolnewton.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunnonlinsolfixedpoint.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_cvodes.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_kinsol.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libPocoFoundation.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libPocoNet.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libPocoXML.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libexpat.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcJIT.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMPasses.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMObjCARCOpts.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCoroutines.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMipo.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMInstrumentation.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMVectorize.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMLinker.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMIRReader.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAsmParser.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMFrontendOpenMP.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMJITLink.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86Disassembler.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86AsmParser.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86CodeGen.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCFGuard.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMGlobalISel.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86Desc.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMX86Info.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMCDisassembler.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMSelectionDAG.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAsmPrinter.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDebugInfoMSF.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDebugInfoDWARF.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCodeGen.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMScalarOpts.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMInstCombine.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAggressiveInstCombine.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMTransformUtils.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBitWriter.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMCJIT.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMExecutionEngine.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMTarget.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMAnalysis.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMProfileData.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMRuntimeDyld.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcTargetProcess.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcShared.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMObject.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMTextAPI.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMCParser.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBitReader.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMMC.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDebugInfoCodeView.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMCore.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMRemarks.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBitstreamReader.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMBinaryFormat.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMSupport.a /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMDemangle.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libz.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunmatrixband.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libsundials_sunmatrixdense.a /home/mkoenig/git/porous_media/buildroadrunner/libroadrunner-deps-release/lib/libPocoFoundation.a -lpthread -ldl -lrt -lm
/usr/bin/ld: /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcJIT.a: error adding symbols: no more archived files
collect2: error: ld returned 1 exit status
make[2]: *** [source/CMakeFiles/roadrunner.dir/build.make:1773: lib/libroadrunner.so] Error 1
make[2]: Leaving directory '/home/mkoenig/git/porous_media/buildroadrunner/roadrunner/build'
make[1]: *** [CMakeFiles/Makefile2:182: source/CMakeFiles/roadrunner.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
/usr/bin/ld: /home/mkoenig/git/porous_media/buildroadrunner/llvm-13.x-release/lib/libLLVMOrcJIT.a: error adding symbols: no more archived files
collect2: error: ld returned 1 exit status
make[2]: *** [wrappers/C/CMakeFiles/roadrunner_c_api.dir/build.make:382: lib/libroadrunner_c_api.so] Error 1
make[2]: Leaving directory '/home/mkoenig/git/porous_media/buildroadrunner/roadrunner/build'
make[1]: *** [CMakeFiles/Makefile2:208: wrappers/C/CMakeFiles/roadrunner_c_api.dir/all] Error 2
make[1]: Leaving directory '/home/mkoenig/git/porous_media/buildroadrunner/roadrunner/build'
make: *** [Makefile:139: all] Error 2I am using the following to build the dependencies and roadrunner:
## Setup build directory
```bash
mkdir buildroadrunner
cd buildroadrunnerBuild LLVM
git clone https://github.com/sys-bio/llvm-13.x.git
cd llvm-13.x/llvm
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX="../../../llvm-13.x-release" -DCMAKE_BUILD_TYPE="Release" ..
cmake --build . --parallel 10 --target install --config Release
cd ../../../Roadrunner dependencies
git clone https://github.com/sys-bio/libroadrunner-deps.git --recurse-submodules
cd libroadrunner-deps
git switch release
mkdir build
cd build
rm -rf ../../libroadrunner-deps-release
cmake -DCMAKE_INSTALL_PREFIX="../../libroadrunner-deps-release" -DCMAKE_BUILD_TYPE="Release" ..
# cmake -DCMAKE_INSTALL_PREFIX="../../libroadrunner-deps-release" -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_BUILD_TYPE="Release" -DCMAKE_CXX_COMPILER="/opt/hlrs/non-spack/2022-02/compiler/gcc/11.2.0/bin/c++" -DCMAKE_C_COMPILER="/opt/hlrs/non-spack/2022-02/compiler/gcc/11.2.0/bin/gcc" ..
cmake --build . --parallel 10 --target install --config Release
cd ../../Roadrunner
git clone https://github.com/sys-bio/roadrunner.git
cd roadrunner
git switch release
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX="../../roadrunner-release" -DLLVM_INSTALL_PREFIX="../../llvm-13.x-release" -DRR_DEPENDENCIES_INSTALL_PREFIX="../../libroadrunner-deps-release" -DCMAKE_BUILD_TYPE="Release" ..
cmake --build . --parallel 10 --target install --config Releasehsauro commented
Has something because even I have been able
build roadrunner using the install instructions in the past.
luciansmith commented
The error message is one I've not seen before. Just doing a google search led me to https://stackoverflow.com/questions/18151810/no-more-archived-files-linker-error and https://stackoverflow.com/questions/2765240/could-not-read-symbols-archive-has-no-index-run-ranlib-to-add-one which seem to indicate that the file might be corrupt? Or that the object files are in the wrong format?
Either way, I would wipe the build directory for llvm and build it from scratch. Sorry, I know that takes many hours...
-Lucian
matthiaskoenig commented
Hi Lucian,
thanks for the input. I will try this. When using multiple cores LLVM builds in a few minutes, so is not too bad.
Best Matthias
matthiaskoenig commented
Perfect, this solved the issue. I had to build LLVM without parallel for things to work.