[ET Trac] [Einstein Toolkit] #1755: Problem with building on Ubuntu 14.04

Einstein Toolkit trac-noreply at einsteintoolkit.org
Fri Mar 20 01:12:17 CDT 2015 

#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?

-- 
Ticket URL: <https://trac.einsteintoolkit.org/ticket/1755#comment:2>
Einstein Toolkit <http://einsteintoolkit.org>
The Einstein Toolkit

More information about the Trac mailing list