[Users] build error at end

Steven R. Brandt sbrandt at cct.lsu.edu
Mon Jul 6 15:03:17 CDT 2015


On 07/06/2015 02:30 PM, Comer Duncan wrote:
> I have tried building ET for the current released version.  I am on a 
> macbook pro running Yosemite.  The build script is:
>
> #!/bin/sh
> rm -rf configs/sim
> echo "done removing configs/sim"
> simfactory/bin/sim build --optionlist=./myoptionlist.cfg 
> --thornlist=./cospluseinsteintkit.th <http://cospluseinsteintkit.th> 
> >build$1.log 2>&1
What's in "myoptionlist.cfg"?

Cheers,
Steve
>
> The build goes along fine apparently until the final executable. I 
> copy below the part after which the build chokes:
>
> Creating cactus_sim in /Users/comerduncan/Cactus/exe from 
> EinsteinAnalysis/ADMAnalysis EinsteinBase/ADMBase 
> EinsteinBase/ADMCoupling EinsteinBase/ADMMacros AEIThorns/ADMMass 
> AEIThorns/AEILocalInterp EinsteinAnalysis/AHFinder 
> EinsteinAnalysis/AHFinderDirect ExternalLibraries/BLAS 
> CactusBase/Boundary Cosmology/CT_Analytic Cosmology/CT_MultiLevel 
> EinsteinAnalysis/CalcK Carpet/Carpet Carpet/CarpetEvolutionMask 
> Carpet/CarpetIOASCII Carpet/CarpetIOBasic Carpet/CarpetIOHDF5 
> Carpet/CarpetIOScalar Carpet/CarpetIntegrateTest Carpet/CarpetInterp 
> Carpet/CarpetInterp2 Carpet/CarpetLib Carpet/CarpetMask 
> Carpet/CarpetProlongateTest Carpet/CarpetReduce Carpet/CarpetRegrid 
> Carpet/CarpetRegrid2 Carpet/CarpetRegridTest Carpet/CarpetSlab 
> Carpet/CarpetTracker CactusBase/CartGrid3D CactusNumerical/Cartoon2D 
> EinsteinBase/Constants CactusBase/CoordBase EinsteinBase/CoordGauge 
> Carpet/CycleClock CactusExamples/DemoInterp 
> CactusNumerical/Dissipation EinsteinInitialData/DistortedBHIVP 
> EinsteinAnalysis/EHFinder EinsteinBase/EOS_Base EinsteinEOS/EOS_Hybrid 
> EinsteinEOS/EOS_IdealFluid EinsteinEOS/EOS_Omni 
> EinsteinEOS/EOS_Polytrope EinsteinExact/EinsteinExact_Test 
> CactusElliptic/EllBase CactusElliptic/EllSOR EinsteinInitialData/Exact 
> EinsteinAnalysis/Extract ExternalLibraries/FFTW3 
> CactusExamples/FleshInfo CactusUtils/Formaline CactusBase/Fortran 
> EinsteinEvolve/GRHydro EinsteinEvolve/GRHydro_InitData 
> ExternalLibraries/GSL EinsteinExact/GaugeWave 
> KrancNumericalTools/GenericFD ExternalLibraries/HDF5 
> CactusConnect/HTTPD CactusConnect/HTTPDExtra CactusExamples/HelloWorld 
> Carpet/HighOrderWaveTest EinsteinBase/HydroBase 
> EinsteinAnalysis/Hydro_Analysis EinsteinInitialData/Hydro_InitExcision 
> EinsteinInitialData/IDAnalyticBH EinsteinInitialData/IDAxiBrillBH 
> EinsteinInitialData/IDAxiOddBrillBH EinsteinInitialData/IDBrillData 
> EinsteinInitialData/IDConstraintViolate EinsteinInitialData/IDFileADM 
> EinsteinInitialData/IDLinearWaves CactusWave/IDScalarWave 
> CactusWave/IDScalarWaveC CactusWave/IDScalarWaveCXX 
> CactusWave/IDScalarWaveElliptic CactusExamples/IDWaveMoL 
> CactusBase/IOASCII CactusBase/IOBasic CactusPUGHIO/IOHDF5 
> CactusPUGHIO/IOHDF5Util CactusIO/IOJpeg CactusBase/IOUtil 
> CactusBase/InitBase CactusNumerical/InterpToArray 
> EinsteinExact/KerrSchild ExternalLibraries/LAPACK 
> ExternalLibraries/LORENE CactusNumerical/LocalInterp 
> CactusNumerical/LocalInterp2 CactusNumerical/LocalReduce 
> Carpet/LoopControl McLachlan/ML_ADMConstraints 
> McLachlan/ML_ADMQuantities McLachlan/ML_BSSN McLachlan/ML_BSSN_Helper 
> McLachlan/ML_BSSN_Test McLachlan/ML_CCZ4 McLachlan/ML_CCZ4_Helper 
> McLachlan/ML_CCZ4_Test McLachlan/ML_WaveToy McLachlan/ML_WaveToy_Test 
> ExternalLibraries/MPI CactusUtils/MemSpeed 
> EinsteinInitialData/Meudon_Bin_BH EinsteinInitialData/Meudon_Bin_NS 
> EinsteinInitialData/Meudon_Mag_NS EinsteinExact/Minkowski 
> CactusNumerical/MoL EinsteinExact/ModifiedSchwarzschildBL 
> EinsteinAnalysis/Multipole CactusUtils/NaNCatcher 
> CactusUtils/NaNChecker EinsteinEvolve/NewRad CactusUtils/Nice 
> EinsteinInitialData/NoExcision CactusUtils/NoMPI CactusNumerical/Noise 
> CactusNumerical/Norms PITTNullCode/NullConstr PITTNullCode/NullDecomp 
> PITTNullCode/NullEvolve PITTNullCode/NullExact PITTNullCode/NullGrid 
> PITTNullCode/NullInterp PITTNullCode/NullNews PITTNullCode/NullPsiInt 
> PITTNullCode/NullSHRExtract PITTNullCode/NullVars 
> ExternalLibraries/OpenSSL EinsteinAnalysis/Outflow 
> ExternalLibraries/PAPI CactusPUGH/PUGH CactusPUGH/PUGHInterp 
> CactusPUGH/PUGHReduce CactusPUGH/PUGHSlab CactusNumerical/Periodic 
> LSUThorns/PeriodicCarpet CactusExamples/Poisson 
> AEIThorns/PunctureTracker LSUThorns/QuasiLocalMeasures 
> Carpet/ReductionTest Carpet/ReductionTest2 Carpet/ReductionTest3 
> CactusNumerical/ReflectionSymmetry Carpet/RegridSyncTest 
> EinsteinInitialData/RotatingDBHIVP CactusNumerical/RotatingSymmetry180 
> CactusNumerical/RotatingSymmetry90 CactusExamples/SampleBoundary 
> CactusExamples/SampleIO EinsteinUtils/SetMask_SphericalSurface 
> EinsteinExact/ShiftedGaugeWave CactusNumerical/Slab 
> CactusNumerical/SlabTest CactusConnect/Socket 
> CactusNumerical/SpaceMask PITTNullCode/SphericalHarmonicDecomp 
> PITTNullCode/SphericalHarmonicRecon CactusNumerical/SphericalSurface 
> EinsteinBase/StaticConformal LSUThorns/SummationByParts 
> CactusBase/SymBase AEIThorns/SystemStatistics 
> CactusUtils/SystemTopology CactusElliptic/TATelliptic 
> EinsteinUtils/TGRtensor EinsteinInitialData/TOVSolver 
> CactusUtils/TerminationTrigger CactusTest/TestArrays 
> Carpet/TestCarpetGridInfo CactusTest/TestComplex 
> CactusTest/TestCoordinates CactusTest/TestFortranCrayPointers 
> CactusTest/TestFortranDependencies1 
> CactusTest/TestFortranDependencies2 CactusTest/TestFpointerNULL 
> CactusTest/TestFreeF90 CactusTest/TestGlobalReduce 
> CactusTest/TestInclude1 CactusTest/TestInclude2 
> CactusNumerical/TestLocalInterp2 CactusNumerical/TestLocalReduce 
> CactusTest/TestLoop Carpet/TestLoopControl CactusTest/TestMath 
> CactusTest/TestMoL CactusTest/TestPar CactusTest/TestReduce 
> CactusTest/TestSchedule CactusTest/TestStrings CactusTest/TestTable 
> CactusTest/TestTimers CactusTest/TestTypes CactusBase/Time 
> CactusExamples/TimerInfo CactusUtils/TimerReport Carpet/Timers 
> EinsteinBase/TmunuBase AEIThorns/Trigger 
> EinsteinInitialData/TwoPunctures EinsteinExact/Vaidya2 
> LSUThorns/Vectors CactusWave/WaveBinarySource CactusExamples/WaveMoL 
> CactusExamples/WaveToy1DF77 CactusExamples/WaveToy2DF77 
> CactusWave/WaveToyC CactusWave/WaveToyCXX CactusWave/WaveToyExtra 
> CactusWave/WaveToyF77 CactusWave/WaveToyF90 CactusWave/WaveToyFreeF90 
> EinsteinAnalysis/WeylScal4 ExternalLibraries/hwloc 
> ExternalLibraries/libjpeg ExternalLibraries/zlib
> Formaline: Creating git master repository...
> Formaline: Pushing source tree to master git repository...
> Undefined symbols for architecture x86_64:
>   "MPI::Win::Free()", referenced from:
>       vtable for MPI::Win in libthorn_PeriodicCarpet.a(periodic.cc.o)
>       vtable for MPI::Win in libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o)
>       vtable for MPI::Win in libthorn_Carpet.a(helpers.cc.o)
>       vtable for MPI::Win in 
> libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o)
>       vtable for MPI::Win in libthorn_CarpetIOASCII.a(ioascii.cc.o)
>       vtable for MPI::Win in libthorn_CarpetIOBasic.a(iobasic.cc.o)
>       vtable for MPI::Win in libthorn_CarpetIOHDF5.a(Input.cc.o)
>       ...
>   "MPI::Comm::Comm()", referenced from:
>       MPI::Intercomm::Merge(bool) const in 
> libthorn_PeriodicCarpet.a(periodic.cc.o)
>       MPI::Intracomm::Split(int, int) const in 
> libthorn_PeriodicCarpet.a(periodic.cc.o)
>       MPI::Intracomm::Create(MPI::Group const&) const in 
> libthorn_PeriodicCarpet.a(periodic.cc.o)
>       MPI::Graphcomm::Clone() const in 
> libthorn_PeriodicCarpet.a(periodic.cc.o)
>       MPI::Cartcomm::Clone() const in 
> libthorn_PeriodicCarpet.a(periodic.cc.o)
>       MPI::Intracomm::Clone() const in 
> libthorn_PeriodicCarpet.a(periodic.cc.o)
>       MPI::Intracomm::Create_graph(int, int const*, int const*, bool) 
> const in libthorn_PeriodicCarpet.a(periodic.cc.o)
>       ...
>   "MPI::Datatype::Free()", referenced from:
>       vtable for MPI::Datatype in libthorn_PeriodicCarpet.a(periodic.cc.o)
>       vtable for MPI::Datatype in 
> libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o)
>       vtable for MPI::Datatype in libthorn_Carpet.a(helpers.cc.o)
>       vtable for MPI::Datatype in 
> libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o)
>       vtable for MPI::Datatype in libthorn_CarpetIOASCII.a(ioascii.cc.o)
>       vtable for MPI::Datatype in libthorn_CarpetIOBasic.a(iobasic.cc.o)
>       vtable for MPI::Datatype in libthorn_CarpetIOHDF5.a(Input.cc.o)
>       ...
>   "_ompi_mpi_cxx_op_intercept", referenced from:
>       MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype 
> const&), bool) in libthorn_PeriodicCarpet.a(periodic.cc.o)
>       MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype 
> const&), bool) in libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o)
>       MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype 
> const&), bool) in libthorn_Carpet.a(helpers.cc.o)
>       MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype 
> const&), bool) in libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o)
>       MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype 
> const&), bool) in libthorn_CarpetIOASCII.a(ioascii.cc.o)
>       MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype 
> const&), bool) in libthorn_CarpetIOBasic.a(iobasic.cc.o)
>       MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype 
> const&), bool) in libthorn_CarpetIOHDF5.a(Input.cc.o)
>       ...
> ld: symbol(s) not found for architecture x86_64
> collect2: error: ld returned 1 exit status
> make[1]: *** [/Users/comerduncan/Cactus/exe/cactus_sim] Error 1
> make[1]: *** Waiting for unfinished jobs....
> Formaline: Pushing to local repository 
> /Users/comerduncan/Cactus/../CactusSourceJar.git...
> Formaline: Optimising git repository (slow only the first time)...
> make: *** [sim] Error 2
>
> Is there likely a problem with openmpi again??  Here is some info 
> about the current ports:
>
> port installed | grep openmpi
> Warning: port definitions are more than two weeks old, consider 
> updating them by running 'port selfupdate'.
>   openmpi @1.7.5_3
>   openmpi-default @1.7.5_3+gcc49 (active)
>   openmpi-default @1.7.5_4+gcc49
>   openmpi-gcc49 @1.7.5_3+fortran (active)
>   openmpi-gcc49 @1.7.5_4+fortran
>
> Note that I had elected to activate openmpi-gcc49 @1.7.5_3+fortran 
> (active) rather than openmpi-gcc49 @1.7.5_4+fortran because with _4 
> the build crashed.
>
> For gcc49 there is:
>
>   gcc49 @4.9.2_1
>   gcc49 @4.9.2_2 (active)
>   mpich-default @3.1.3_0+gcc49
>   mpich-default @3.1.4_0+gcc49
>   openmpi-default @1.7.5_3+gcc49 (active)
>   openmpi-default @1.7.5_4+gcc49
>   openmpi-gcc49 @1.7.5_3+fortran (active)
>   openmpi-gcc49 @1.7.5_4+fortran
>
> I am also using the macports hdf5 patched:
>
> port installed | grep hdf5
>
>   hdf5 @1.8.13_0+cxx+gcc46
>   hdf5 @1.8.14_0+cxx+gcc46
>   hdf5 @1.8.14_0+cxx+fortran+gfortran
>   hdf5 @1.8.15-patch1_0+cxx+fortran+gfortran (active)
>
> Can I get some further help on resolving this?  I have not updated 
> macports in a few weeks as I did not want to possibly pollute what did 
> work a while back.
>
> Thanks.
>
> Comer
>
>
>
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