Hello Jodi, I have never seen such an error (unless one has buggy code and eg declares and calls a function with a different function signature than is actually available as a function definition).
So assuming that you did not modify the Multipole thorn, my guess would be that there could have been some (previous) failure in the build process that may have left a corrupted .o file behind. This can happen for a variety of reasons eg running of quota, the compiler being terminated (killed) at the wrong time (maybe out of memory, maybe a crash of the login node, maybe the admins killed some processes for whatever reason, maybe the file system had issues). If you want to, you could check the file sizes of the file: /gpfs/pace2/project/pc1/jfuertes7/Cactus/configs/bbh_i15/build/Multipole/utils.cc.o which should contain the function in question (you can run nm -C /gpfs/pace2/project/pc1/jfuertes7/Cactus/configs/bbh_i15/build/Multipole/utils.cc.o to see what functions are defined inside). If this file has size of 0 bytes then this is your culprit. As a first try (if you have not yet done so) I would also try and see if the error goes away once you force Multipole to be recompiled eg by running: touch /gpfs/pace2/project/pc1/jfuertes7/Cactus/arrangements/EinsteinAnalysis/Multipole/src/* then build once more. Yours, Roland > Hi, > > My name is Jordi Manyer from the astrophysics department in Georgia Tech. I'm > trying to build the ET on the cluster Cygnus and I've encountered a problem > that I think might be related to one of your thorns: > After compiling the thorns, Formaline starts creating tarballs and eventually > outputs an error: > > Formaline: Creating configuration git repository... > Formaline: Updating files in git repository... > Creating Formaline tarball for thorn Carpet > Creating Formaline tarball for thorn CarpetIOASCII > Creating Formaline tarball for thorn CarpetIOBasic > Creating Formaline tarball for thorn CarpetIOScalar > Creating Formaline tarball for thorn CarpetInterp > Creating Formaline tarball for thorn CarpetReduce > Creating Formaline tarball for thorn CarpetRegrid > Creating Formaline tarball for thorn CarpetRegrid2 > Creating Formaline tarball for thorn CarpetSlab > Creating Formaline tarball for thorn WeightedReduce > ________________________________________________________________________ > Creating cactus_bbh_i15 in /gpfs/pace2/project/pc1/jfuertes7/Cactus/exe from > EinsteinBase/ADMBase EinsteinBase/ADMCoupling EinsteinBase/ADMMacros > GTThorns/ADM_EJP Numerical/AEILocalInterp EinsteinAnalysis/AHFinderDirect > ExternalLibraries/BLAS GTThorns/Baum CactusBase/Boundary Carpet/Carpet > Carpet/CarpetIOASCII Carpet/CarpetIOBasic Carpet/CarpetIOScalar > Carpet/CarpetInterp Carpet/CarpetLib Carpet/CarpetReduce Carpet/CarpetRegrid > Carpet/CarpetRegrid2 Carpet/CarpetSlab Carpet/CarpetTracker > CactusBase/CartGrid3D EinsteinBase/Constants CactusBase/CoordBase > EinsteinBase/CoordGauge Carpet/CycleClock CactusNumerical/Dissipation > EinsteinBase/EOS_Base EinsteinEOS/EOS_IdealFluid CactusElliptic/EllBase > CactusElliptic/EllSOR GTThorns/ExternalEtaBeta CactusUtils/Formaline > CactusBase/Fortran ExternalLibraries/GSL KrancNumericalTools/GenericFD > CactusConnect/HTTPD CactusConnect/HTTPDExtra GTThorns/IHSpin > CactusBase/IOASCII CactusBase/IOBasic CactusBase/IOUtil CactusBase/InitBase > Kranc/Kranc2BSSNChi ExternalLibraries/LAPACK CactusNumerical/LocalInterp > CactusNumerical/LocalReduce Carpet/LoopControl ExternalLibraries/MPI > GTThorns/MinTracker CactusNumerical/MoL EinsteinAnalysis/Multipole > CactusUtils/NaNChecker CactusUtils/Nice CactusPUGH/PUGH CactusPUGH/PUGHInterp > CactusPUGH/PUGHReduce CactusPUGH/PUGHSlab CactusNumerical/Periodic > GTThorns/ProperDistance GTThorns/Psi4Analysis > EinsteinAnalysis/QuasiLocalMeasures CactusNumerical/ReflectionSymmetry > CactusNumerical/RotatingSymmetry180 CactusNumerical/RotatingSymmetry90 > GTThorns/RunStats GTThorns/ShiftTracker CactusNumerical/Slab > CactusConnect/Socket CactusNumerical/SpaceMask GTThorns/SphereIntegrate > GTThorns/SphereRad CactusNumerical/SphericalSurface > EinsteinBase/StaticConformal CactusNumerical/SummationByParts > CactusBase/SymBase CactusUtils/SystemTopology EinsteinUtils/TGRtensor > GTThorns/TeukolskyADMBase CactusBase/Time CactusUtils/TimerReport > Carpet/Timers EinsteinBase/TmunuBase CactusUtils/Trigger > GTThorns/TwoPunctures CactusUtils/Vectors GTThorns/WaveExtract > GTThorns/WeightedReduce EinsteinAnalysis/WeylScal4 GTThorns/Ylm_Decomp > ExternalLibraries/hwloc ExternalLibraries/libjpeg ExternalLibraries/zlib > fatal: bad revision 'HEAD' > Formaline: Committing source tree to git repository... > Formaline: Created git tag > build-bbh_i15-login-s1.pace.gatech.edu-jfuertes7-2018.11.21-15.14.51-28991 > Formaline: Updated git branch > config-bbh_i15-login-s1.pace.gatech.edu-gpfs-pace2-project-pc1-jfuertes7-Cactus > Formaline: Optimising git repository (slow only the first time)... > /gpfs/pace2/project/pc1/jfuertes7/Cactus/configs/bbh_i15/lib/libthorn_Multipole.a(multipole.cc.o): > In function > `_INTERNAL_85__gpfs_pace2_project_pc1_jfuertes7_Cactus_configs_bbh_i15_build_Multipole_multipole_cc_d1a966a7::output_modes(_cGH*, > Multipole::variable_desc const*, double const*, Multipole::mode_array > const&)': > /gpfs/pace2/project/pc1/jfuertes7/Cactus/configs/bbh_i15/build/Multipole/multipole.cc:128: > undefined reference to `Multipole_OutputComplexToH5File(_cGH*, > Multipole::variable_desc const*, double const*, Multipole::mode_array const&)' > make[1]: *** [/gpfs/pace2/project/pc1/jfuertes7/Cactus/exe/cactus_bbh_i15] > Error 1 > make[1]: *** Waiting for unfinished jobs.... > Formaline: Pushing to master git repository... > Formaline: Optimising git repository (slow only the first time)... > Formaline: Pushing to local git repository > /gpfs/pace2/project/pc1/jfuertes7/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.) > make: *** [bbh_i15] Error 2 > > > Have you ever encountered something similar? The compiler in intel 15.0 with > mvapich2 2.1 and mkl 11.2 > > Thanks, > Jordi > > > > -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu .
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