[ET Trac] [Einstein Toolkit] #1764: Error with compilation of HWLOC

[Einstein Toolkit]

#1764: Error with compilation of HWLOC
------------------------------------+---------------------------------------
  Reporter:  maxim.barkov@…         |       Owner:  eschnett           
      Type:  defect                 |      Status:  assigned           
  Priority:  blocker                |   Milestone:  ET_2015_05         
 Component:  EinsteinToolkit thorn  |     Version:  development version
Resolution:                         |    Keywords:  HWLOC              
------------------------------------+---------------------------------------

Comment (by rhaas):

 Cactus (ET trunk) now fails to build (once again) on a freshly installed
 Ubuntu 15.04 with libnuma-dev installed (even when using HWLOC_DIR=BUILD
 and the very newest ubuntu.cfg) due to hwloc's configure script finding
 libnuma but Cactus not linking against it.

 The only real solution to this seems to me to move the call to "configure"
 from build.sh into detect.sh so that one can inspect the results of
 configure afterwards.

 Just blindly adding numa to HWLOC_LIBS will not work since the required
 library libnuma.a (for static linking as we now require this) is only
 present (in Ubunut at least) if libnuma-dev is installed.

 As far as I am concerned we need to be able to build on typical user
 Desktop machines (and laptops) out of the box. Typical, in my opinion,
 being the current version of OSX, Ubuntu, RedHat and possibly Debian and
 Fedora. Obviously we also need to be able to build on the public clusters
 so we cannot revert to dynamic linking again since it breaks all Crays.

 The error I get is:
 {{{
 Creating cactus_sim in /home/rhaas/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/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 local repository...
 Formaline: Pushing source tree to master git repository...
 Formaline: Pushing to local repository
 /home/rhaas/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/rhaas/Cactus/configs/sim/scratch/external/hwloc/lib/libhwloc.a
 (topology-linux.o): In function `hwloc_linux_set_thisthread_membind':
 /home/rhaas/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src
 /topology-linux.c:1302: undefined reference to `migrate_pages'
 /home/rhaas/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src
 /topology-linux.c:1314: undefined reference to `set_mempolicy'
 /home/rhaas/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src
 /topology-linux.c:1291: undefined reference to `set_mempolicy'
 /home/rhaas/Cactus/configs/sim/scratch/external/hwloc/lib/libhwloc.a
 (topology-linux.o): In function `hwloc_linux_set_area_membind':
 /home/rhaas/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src
 /topology-linux.c:1243: undefined reference to `mbind'
 /home/rhaas/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src
 /topology-linux.c:1224: undefined reference to `mbind'
 /home/rhaas/Cactus/configs/sim/scratch/external/hwloc/lib/libhwloc.a
 (topology-linux.o): In function `hwloc_linux_find_kernel_max_numnodes':
 /home/rhaas/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src
 /topology-linux.c:1347: undefined reference to `get_mempolicy'
 /home/rhaas/Cactus/configs/sim/scratch/external/hwloc/lib/libhwloc.a
 (topology-linux.o): In function `hwloc_linux_get_area_membind':
 /home/rhaas/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src
 /topology-linux.c:1445: undefined reference to `get_mempolicy'
 /home/rhaas/Cactus/configs/sim/scratch/external/hwloc/lib/libhwloc.a
 (topology-linux.o): In function `hwloc_linux_get_thisthread_membind':
 /home/rhaas/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src
 /topology-linux.c:1392: undefined reference to `get_mempolicy'
 collect2: error: ld returned 1 exit status
 /home/rhaas/Cactus/lib/make/make.configuration:149: recipe for target
 '/home/rhaas/Cactus/exe/cactus_sim' failed
 make[1]: *** [/home/rhaas/Cactus/exe/cactus_sim] Error 1
 Makefile:254: recipe for target 'sim' failed
 make: *** [sim] Error 2
 }}}

-- 
Ticket URL: <https://trac.einsteintoolkit.org/ticket/1764#comment:4>
Einstein Toolkit <http://einsteintoolkit.org>
The Einstein Toolkit