#1755: Problem with building on Ubuntu 14.04 ------------------------------------+--------------------------------------- Reporter: maxim.barkov@… | Owner: Type: defect | Status: new Priority: major | Milestone: ET_2014_11 Component: Cactus | Version: development version Resolution: | Keywords: MPI build ------------------------------------+---------------------------------------
Comment (by maxim.barkov@…):
Dear Rhaas,
Thank you for your swift response. I have installed OpenMPI. As you recommended I rename config file and run following commands: {{{ mv ~/.cactus/config ~/.cactus/config_old ./simfactory/bin/sim cleanup ./simfactory/bin/sim setup --optionlist=ubuntu.cfg --runscript debian.sh ./simfactory/bin/sim build --thornlist=manifest/einsteintoolkit.th 2&> sim_2a_log.txt }}}
After that operations I got error message: {{{ Creating cactus_2 in /home/bmv/utils/soft/ET/Cactus/exe from EinsteinAnalysis/ADMAnalysis EinsteinBase/ADMBase EinsteinBase/ADMCoupling EinsteinBase/ADMMacros AEIThorns/ADMMass AEIThorns/AEILocalInterp EinsteinAnalysis/AHFinder EinsteinAnalysis/AHFinderDirect ExternalLibraries/BLAS CactusBase/Boundary 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/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 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/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: Creating git local repository... Formaline: Pushing source tree to master git repository... Formaline: Pushing to local repository /home/bmv/utils/soft/ET/Cactus/../CactusSourceJar.git... Formaline: Optimising git repository (slow only the first time)... Formaline: Done. Formaline: (Formaline has finished updating the git repositories. Formaline: If the build process seems to hang, some other command Formaline: is still running, e.g. the final link stage.) /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/external/hwloc/lib/libhwloc.a (topology-linux.o): In function `hwloc_linux_set_area_membind': /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/build/hwloc/hwloc-1.7.2/src /topology-linux.c:1230: undefined reference to `mbind' /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/build/hwloc/hwloc-1.7.2/src /topology-linux.c:1211: undefined reference to `mbind' /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/external/hwloc/lib/libhwloc.a (topology-linux.o): In function `hwloc_linux_set_thisthread_membind': /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/build/hwloc/hwloc-1.7.2/src /topology-linux.c:1289: undefined reference to `migrate_pages' /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/build/hwloc/hwloc-1.7.2/src /topology-linux.c:1301: undefined reference to `set_mempolicy' /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/build/hwloc/hwloc-1.7.2/src /topology-linux.c:1278: undefined reference to `set_mempolicy' /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/external/hwloc/lib/libhwloc.a (topology-linux.o): In function `hwloc_linux_find_kernel_max_numnodes': /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/build/hwloc/hwloc-1.7.2/src /topology-linux.c:1334: undefined reference to `get_mempolicy' /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/external/hwloc/lib/libhwloc.a (topology-linux.o): In function `hwloc_linux_get_area_membind': /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/build/hwloc/hwloc-1.7.2/src /topology-linux.c:1432: undefined reference to `get_mempolicy' /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/external/hwloc/lib/libhwloc.a (topology-linux.o): In function `hwloc_linux_get_thisthread_membind': /home/bmv/utils/soft/ET/Cactus/configs/2/scratch/build/hwloc/hwloc-1.7.2/src /topology-linux.c:1379: undefined reference to `get_mempolicy' collect2: error: ld returned 1 exit status make[1]: *** [/home/bmv/utils/soft/ET/Cactus/exe/cactus_2] Error 1 make: *** [2] Error 2
}}}
Nevertheless the example code start to work {{{ # modify parameter file for smaller memory footprint using sed sed '/CoordBase::d[xyz]/s/8/12/' <par/static_tov.par
par/static_tov_small.par
# start simulation, watch log output ./simfactory/bin/sim submit static_tov --parfile=par/static_tov_small.par --procs=1 --walltime=8:0:0 ./simfactory/bin/sim show-output --follow static_tov }}}
Could you please clarify that mean this Error massage? Should I ignore it?