[Users] build error at end
Comer Duncan
comer.duncan at gmail.com
Mon Jul 6 14:30:13 CDT 2015
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 >build$1.log 2>&1
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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