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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