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<div class="moz-cite-prefix">On 07/06/2015 02:30 PM, Comer Duncan
wrote:<br>
</div>
<blockquote
cite="mid:CAEL1xhCh1X7NhVJj+BQ3eFugH71G=tzTqU1zg7g4MBUM-mF7yQ@mail.gmail.com"
type="cite">
<div dir="ltr">I have tried building ET for the current released
version. I am on a macbook pro running Yosemite. The build
script is:
<div><br>
</div>
<div>
<div>#!/bin/sh</div>
<div>rm -rf configs/sim</div>
<div>echo "done removing configs/sim"</div>
<div>simfactory/bin/sim build --optionlist=./myoptionlist.cfg
--thornlist=./<a moz-do-not-send="true"
href="http://cospluseinsteintkit.th">cospluseinsteintkit.th</a>
>build$1.log 2>&1</div>
</div>
</div>
</blockquote>
What's in "myoptionlist.cfg"?<br>
<br>
Cheers,<br>
Steve<br>
<blockquote
cite="mid:CAEL1xhCh1X7NhVJj+BQ3eFugH71G=tzTqU1zg7g4MBUM-mF7yQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div><br>
</div>
<div>The build goes along fine apparently until the final
executable. I copy below the part after which the build
chokes:</div>
<div><br>
</div>
<div>
<div>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</div>
<div>Formaline: Creating git master repository...</div>
<div>Formaline: Pushing source tree to master git
repository...</div>
<div>Undefined symbols for architecture x86_64:</div>
<div> "MPI::Win::Free()", referenced from:</div>
<div> vtable for MPI::Win in
libthorn_PeriodicCarpet.a(periodic.cc.o)</div>
<div> vtable for MPI::Win in
libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o)</div>
<div> vtable for MPI::Win in
libthorn_Carpet.a(helpers.cc.o)</div>
<div> vtable for MPI::Win in
libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o)</div>
<div> vtable for MPI::Win in
libthorn_CarpetIOASCII.a(ioascii.cc.o)</div>
<div> vtable for MPI::Win in
libthorn_CarpetIOBasic.a(iobasic.cc.o)</div>
<div> vtable for MPI::Win in
libthorn_CarpetIOHDF5.a(Input.cc.o)</div>
<div> ...</div>
<div> "MPI::Comm::Comm()", referenced from:</div>
<div> MPI::Intercomm::Merge(bool) const in
libthorn_PeriodicCarpet.a(periodic.cc.o)</div>
<div> MPI::Intracomm::Split(int, int) const in
libthorn_PeriodicCarpet.a(periodic.cc.o)</div>
<div> MPI::Intracomm::Create(MPI::Group const&) const
in libthorn_PeriodicCarpet.a(periodic.cc.o)</div>
<div> MPI::Graphcomm::Clone() const in
libthorn_PeriodicCarpet.a(periodic.cc.o)</div>
<div> MPI::Cartcomm::Clone() const in
libthorn_PeriodicCarpet.a(periodic.cc.o)</div>
<div> MPI::Intracomm::Clone() const in
libthorn_PeriodicCarpet.a(periodic.cc.o)</div>
<div> MPI::Intracomm::Create_graph(int, int const*, int
const*, bool) const in
libthorn_PeriodicCarpet.a(periodic.cc.o)</div>
<div> ...</div>
<div> "MPI::Datatype::Free()", referenced from:</div>
<div> vtable for MPI::Datatype in
libthorn_PeriodicCarpet.a(periodic.cc.o)</div>
<div> vtable for MPI::Datatype in
libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o)</div>
<div> vtable for MPI::Datatype in
libthorn_Carpet.a(helpers.cc.o)</div>
<div> vtable for MPI::Datatype in
libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o)</div>
<div> vtable for MPI::Datatype in
libthorn_CarpetIOASCII.a(ioascii.cc.o)</div>
<div> vtable for MPI::Datatype in
libthorn_CarpetIOBasic.a(iobasic.cc.o)</div>
<div> vtable for MPI::Datatype in
libthorn_CarpetIOHDF5.a(Input.cc.o)</div>
<div> ...</div>
<div> "_ompi_mpi_cxx_op_intercept", referenced from:</div>
<div> MPI::Op::Init(void (*)(void const*, void*, int,
MPI::Datatype const&), bool) in
libthorn_PeriodicCarpet.a(periodic.cc.o)</div>
<div> MPI::Op::Init(void (*)(void const*, void*, int,
MPI::Datatype const&), bool) in
libthorn_CT_MultiLevel.a(CT_MultiLevel.cc.o)</div>
<div> MPI::Op::Init(void (*)(void const*, void*, int,
MPI::Datatype const&), bool) in
libthorn_Carpet.a(helpers.cc.o)</div>
<div> MPI::Op::Init(void (*)(void const*, void*, int,
MPI::Datatype const&), bool) in
libthorn_CarpetEvolutionMask.a(evolution_mask.cc.o)</div>
<div> MPI::Op::Init(void (*)(void const*, void*, int,
MPI::Datatype const&), bool) in
libthorn_CarpetIOASCII.a(ioascii.cc.o)</div>
<div> MPI::Op::Init(void (*)(void const*, void*, int,
MPI::Datatype const&), bool) in
libthorn_CarpetIOBasic.a(iobasic.cc.o)</div>
<div> MPI::Op::Init(void (*)(void const*, void*, int,
MPI::Datatype const&), bool) in
libthorn_CarpetIOHDF5.a(Input.cc.o)</div>
<div> ...</div>
<div>ld: symbol(s) not found for architecture x86_64</div>
<div>collect2: error: ld returned 1 exit status</div>
<div>make[1]: *** [/Users/comerduncan/Cactus/exe/cactus_sim]
Error 1</div>
<div>make[1]: *** Waiting for unfinished jobs....</div>
<div>Formaline: Pushing to local repository
/Users/comerduncan/Cactus/../CactusSourceJar.git...</div>
<div>Formaline: Optimising git repository (slow only the first
time)...</div>
<div>make: *** [sim] Error 2</div>
</div>
<div><br>
</div>
<div>Is there likely a problem with openmpi again?? Here is
some info about the current ports:</div>
<div><br>
</div>
<div>
<div>port installed | grep openmpi</div>
<div>Warning: port definitions are more than two weeks old,
consider updating them by running 'port selfupdate'.</div>
<div> openmpi @1.7.5_3</div>
<div> openmpi-default @1.7.5_3+gcc49 (active)</div>
<div> openmpi-default @1.7.5_4+gcc49</div>
<div> openmpi-gcc49 @1.7.5_3+fortran (active)</div>
<div> openmpi-gcc49 @1.7.5_4+fortran</div>
</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>For gcc49 there is:</div>
<div><br>
</div>
<div>
<div> gcc49 @4.9.2_1</div>
<div> gcc49 @4.9.2_2 (active)</div>
<div> mpich-default @3.1.3_0+gcc49</div>
<div> mpich-default @3.1.4_0+gcc49</div>
<div> openmpi-default @1.7.5_3+gcc49 (active)</div>
<div> openmpi-default @1.7.5_4+gcc49</div>
<div> openmpi-gcc49 @1.7.5_3+fortran (active)</div>
<div> openmpi-gcc49 @1.7.5_4+fortran</div>
</div>
<div><br>
</div>
<div>I am also using the macports hdf5 patched:</div>
<div><br>
</div>
<div>
<div>port installed | grep hdf5</div>
<div><br>
</div>
<div> hdf5 @1.8.13_0+cxx+gcc46</div>
<div> hdf5 @1.8.14_0+cxx+gcc46</div>
<div> hdf5 @1.8.14_0+cxx+fortran+gfortran</div>
<div> hdf5 @1.8.15-patch1_0+cxx+fortran+gfortran (active)</div>
</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Thanks.</div>
<div><br>
</div>
<div>Comer</div>
<div><br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</blockquote>
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