[Users] ETK test suite build fails for me in linking

Mon Jan 26 13:26:29 CST 2015

Sara

Please update the thorn CactusBase/Fortran, then try again. The error should now be gone.

-erik

> On Jan 26, 2015, at 14:23 , Erik Schnetter <schnetter at gmail.com> wrote:
> 
> The routines Util_CacheMalloc and friends were recently removed from the Einstein Toolkit. By accident, the Fortran interfaces are still there. I will correct this shortly.
> 
> -erik
> 
>> On Jan 26, 2015, at 14:21 , So Ra Chung <so.chung at pop.belmont.edu> wrote:
>> 
>> Hi, I'm following the instructions on the page https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users
>> 
>> and during the final link I get an 'undefined reference' error (see below).  It seems that the routine Util_CacheMalloc is defined in the Fortran thorn in the file cctk_Cache.F90, however the object code never seems to be supplied, i.e.
>> % nm cctk_Cache.F90.o
>> appears to contain no symbols.
>> 
>> So, perhaps this is a compiler error, however no errors were thrown during the build process.
>> 
>> I'm not sure what to do at this point.  Can anyone advise me?
>> 
>> Thanks,
>> Sara Chung
>> 
>> 
>> ./simfactory/bin/sim build --thornlist=manifest/einsteintoolkit.th
>> ...
>> 
>> ..._______________________________________________________________
>> 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.)
>> 
>> Creating cactus_sim in /home/sorachung/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 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
>> 
>> /home/sorachung/Cactus/configs/sim/lib/libthorn_PUGH.a(Storage.c.o): In function `PUGH_EnableGArrayDataStorage':
>> /home/sorachung/Cactus/arrangements/CactusPUGH/PUGH/src/Storage.c:646: undefined reference to `Util_CacheMalloc'
>> collect2: error: ld returned 1 exit status
>> make[1]: *** [/home/sorachung/Cactus/exe/cactus_sim] Error 1
>> make: *** [sim] Error 2
>> sorachung at sorachung-N550JK:~/Cactus$
>> sorachung at sorachung-N550JK:~/Cactus$     grep -rnw . -e "Util_CacheMalloc"
>> ./repos/cactusbase/Fortran/src/cctk_Cache.F90:8:     subroutine Util_CacheMalloc (pointer, index, size, realstart)
>> ./repos/cactusbase/Fortran/src/cctk_Cache.F90:14:     end subroutine Util_CacheMalloc
>> ./repos/cactuspugh/PUGH/src/Storage.c~:538:   @calls      Util_CacheMalloc
>> ./repos/cactuspugh/PUGH/src/Storage.c~:646:        GA->data = Util_CacheMalloc (GA->arrayid,
>> ./repos/cactuspugh/PUGH/src/Storage.c:538:   @calls      Util_CacheMalloc
>> ./repos/cactuspugh/PUGH/src/Storage.c:646:        GA->data = Util_CacheMalloc (GA->arrayid,
>> ./.svn/pristine/de/def745e3379fad4f949c40f811f7efd7acc3d4bf.svn-base:40:   @routine    Util_CacheMalloc
>> ./.svn/pristine/de/def745e3379fad4f949c40f811f7efd7acc3d4bf.svn-base:75:void *Util_CacheMalloc(unsigned int idx,
>> ./.svn/pristine/8c/8c6f37c22be6bcd98ee2b3825f12269b225b6a77.svn-base:19:void *Util_CacheMalloc(unsigned _index,
>> Binary file ./configs/sim/lib/libthorn_PUGH.a matches
>> Binary file ./configs/sim/build/PUGH/Storage.c.o matches
>> ./configs/sim/build/PUGH/Storage.c:539:   @calls      Util_CacheMalloc
>> ./configs/sim/build/PUGH/Storage.c:647:        GA->data = Util_CacheMalloc (GA->arrayid,
>> ./configs/sim/build/Fortran/cctk_Cache.f90:7:     subroutine Util_CacheMalloc (pointer, index, size, realstart)
>> ./configs/sim/build/Fortran/cctk_Cache.f90:13:     end subroutine Util_CacheMalloc
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> 
> --
> Erik Schnetter <schnetter at gmail.com>
> http://www.perimeterinstitute.ca/personal/eschnetter/
> 
> My email is as private as my paper mail. I therefore support encrypting
> and signing email messages. Get my PGP key from https://sks-keyservers.net.
> 

--
Erik Schnetter <schnetter at gmail.com>
http://www.perimeterinstitute.ca/personal/eschnetter/

My email is as private as my paper mail. I therefore support encrypting
and signing email messages. Get my PGP key from https://sks-keyservers.net.

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