[Users] Error while compiling ET on cluster

Mon Dec 3 16:42:00 CST 2018

Hi Rolland,

Sorry for the late response but I've been working on something else.
I haven't modified the thorn multipole, so that should not be an issue.
I've also tried using 'nm' and the output is :

0000000000000000 r .L_2il0floatpacket.28
0000000000000000 N .debug_info_seg
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U CCTK_VarIndex
U CCTK_Warn
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U DriscollHealy2DIntegral(double const*, int, int, double, double)
0000000000001c20 T Multipole_OutputComplex(_cGH*, _IO_FILE*, double, double)
00000000000004b0 T Multipole_OpenOutputFile(_cGH*, std::string const&)
0000000000000000 r _Z24Multipole_OpenOutputFileP4_cGHRKSs$$LSDA
0000000000002290 T Multipole_ScaleCartesian(int, int, double, double const*, double const*, double const*, double*, double*, double*)
0000000000000000 T Multipole_OutputArrayToFile(_cGH*, std::string const&, int, double const*, double const*, double const*, double const*, double const*, double const*)
00000000000017b0 T Multipole_OutputComplexToFile(_cGH*, std::string const&, double, double)
0000000000002080 T Multipole_OutputComplexToH5File(_cGH*, std::string const&, std::string const&, double, double)
0000000000000d10 t _INTERNAL_81__gpfs_pace2_project_pc1_jfuertes7_Cactus_configs_bbh_i15_build_Multipole_utils_cc_da37273b::__gnu_cxx::__exchange_and_add_dispatch(int*, int)
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0000000000000000 V std::integral_constant<bool, false>::value
0000000000000000 V std::integral_constant<bool, true>::value
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U std::ios_base::Init::~Init()
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w __pthread_key_create
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0000000000000194 d cctki_vi_test_simpson_result_high.19660.0.36
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The function 'Multipole_OutputComplexToH5File' seems to be there. I've also tried recompiling the thorn and nothing seems to change.

Thanks,
Jordi

On Nov 26 2018, at 11:42 am, Roland Haas <rhaas at illinois.edu> wrote:

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

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