[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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