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 U CCTK_CreateDirectory U CCTK_Equals U CCTK_VWarn U CCTK_VarIndex U CCTK_Warn U CCTKi_VarDataPtrI U _Unwind_Resume U Simpson2DIntegral(double const*, int, int, double, double) U Midpoint2DIntegral(double const*, int, int, double, double) 0000000000001240 T Multipole_Output1D(_cGH*, std::string const&, int, double const*, double const*, mp_coord, double const*) 0000000000002430 T Multipole_Integrate(int, int, double const*, double const*, double const*, double const*, double const*, double const*, double*, double*) 00000000000020a0 T Multipole_CoordSetup(int, int, double*, double*, double*, double*, double*) 0000000000000d30 T Multipole_OutputArray(_cGH*, _IO_FILE*, int, double const*, double const*, double const*, double const*, double const*, double const*) U Trapezoidal2DIntegral(double const*, int, int, double, double) 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) 0000000000000011 b _INTERNAL_81__gpfs_pace2_project_pc1_jfuertes7_Cactus_configs_bbh_i15_build_Multipole_utils_cc_da37273b::std::__ioinit U std::string::_Rep::_M_destroy(std::allocator<char> const&) U std::string::_Rep::_S_empty_rep_storage U std::string::append(char const*, unsigned long) U std::string::append(std::string const&) U std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&) 0000000000000000 V std::integral_constant<bool, false>::value 0000000000000000 V std::integral_constant<bool, true>::value U std::ios_base::Init::Init() U std::ios_base::Init::~Init() U operator new[](unsigned long) U __cxa_atexit U __dso_handle U __gxx_personality_v0 w __pthread_key_create 0000000000002820 t __sti__$E 0000000000000010 b allocated_memory.19720.0.40 0000000000000058 d cctki_vi_coarse_dx.19225.0.31 00000000000000b0 d cctki_vi_coarse_dx.19462.0.32 0000000000000000 d cctki_vi_coarse_dx.19488.0.33 0000000000000108 d cctki_vi_coarse_dx.19513.0.34 00000000000001b8 d cctki_vi_coarse_dx.19637.0.35 0000000000000160 d cctki_vi_coarse_dx.19660.0.36 000000000000005c d cctki_vi_coarse_dy.19225.0.31 00000000000000b4 d cctki_vi_coarse_dy.19462.0.32 0000000000000004 d cctki_vi_coarse_dy.19488.0.33 000000000000010c d cctki_vi_coarse_dy.19513.0.34 00000000000001bc d cctki_vi_coarse_dy.19637.0.35 0000000000000164 d cctki_vi_coarse_dy.19660.0.36 0000000000000060 d cctki_vi_coarse_dz.19225.0.31 00000000000000b8 d cctki_vi_coarse_dz.19462.0.32 0000000000000008 d cctki_vi_coarse_dz.19488.0.33 0000000000000110 d cctki_vi_coarse_dz.19513.0.34 00000000000001c0 d cctki_vi_coarse_dz.19637.0.35 0000000000000168 d cctki_vi_coarse_dz.19660.0.36 0000000000000064 d cctki_vi_harmonic_im.19225.0.31 00000000000000bc d cctki_vi_harmonic_im.19462.0.32 000000000000000c d cctki_vi_harmonic_im.19488.0.33 0000000000000114 d cctki_vi_harmonic_im.19513.0.34 00000000000001c4 d cctki_vi_harmonic_im.19637.0.35 000000000000016c d cctki_vi_harmonic_im.19660.0.36 0000000000000068 d cctki_vi_harmonic_re.19225.0.31 00000000000000c0 d cctki_vi_harmonic_re.19462.0.32 0000000000000010 d cctki_vi_harmonic_re.19488.0.33 0000000000000118 d cctki_vi_harmonic_re.19513.0.34 00000000000001c8 d cctki_vi_harmonic_re.19637.0.35 0000000000000170 d cctki_vi_harmonic_re.19660.0.36 000000000000006c d cctki_vi_r.19225.0.31 00000000000000c4 d cctki_vi_r.19462.0.32 0000000000000014 d cctki_vi_r.19488.0.33 000000000000011c d cctki_vi_r.19513.0.34 00000000000001cc d cctki_vi_r.19637.0.35 0000000000000174 d cctki_vi_r.19660.0.36 0000000000000070 d cctki_vi_test_driscollhealy_pi_symmetry.19225.0.31 00000000000000c8 d cctki_vi_test_driscollhealy_pi_symmetry.19462.0.32 0000000000000018 d cctki_vi_test_driscollhealy_pi_symmetry.19488.0.33 0000000000000120 d cctki_vi_test_driscollhealy_pi_symmetry.19513.0.34 00000000000001d0 d cctki_vi_test_driscollhealy_pi_symmetry.19637.0.35 0000000000000178 d cctki_vi_test_driscollhealy_pi_symmetry.19660.0.36 0000000000000074 d cctki_vi_test_midpoint_convergence_order.19225.0.31 00000000000000cc d cctki_vi_test_midpoint_convergence_order.19462.0.32 000000000000001c d cctki_vi_test_midpoint_convergence_order.19488.0.33 0000000000000124 d cctki_vi_test_midpoint_convergence_order.19513.0.34 00000000000001d4 d cctki_vi_test_midpoint_convergence_order.19637.0.35 000000000000017c d cctki_vi_test_midpoint_convergence_order.19660.0.36 0000000000000078 d cctki_vi_test_midpoint_pi_symmetry.19225.0.31 00000000000000d0 d cctki_vi_test_midpoint_pi_symmetry.19462.0.32 0000000000000020 d cctki_vi_test_midpoint_pi_symmetry.19488.0.33 0000000000000128 d cctki_vi_test_midpoint_pi_symmetry.19513.0.34 00000000000001d8 d cctki_vi_test_midpoint_pi_symmetry.19637.0.35 0000000000000180 d cctki_vi_test_midpoint_pi_symmetry.19660.0.36 000000000000007c d cctki_vi_test_midpoint_result_high.19225.0.31 00000000000000d4 d cctki_vi_test_midpoint_result_high.19462.0.32 0000000000000024 d cctki_vi_test_midpoint_result_high.19488.0.33 000000000000012c d cctki_vi_test_midpoint_result_high.19513.0.34 00000000000001dc d cctki_vi_test_midpoint_result_high.19637.0.35 0000000000000184 d cctki_vi_test_midpoint_result_high.19660.0.36 0000000000000080 d cctki_vi_test_midpoint_result_low.19225.0.31 00000000000000d8 d cctki_vi_test_midpoint_result_low.19462.0.32 0000000000000028 d cctki_vi_test_midpoint_result_low.19488.0.33 0000000000000130 d cctki_vi_test_midpoint_result_low.19513.0.34 00000000000001e0 d cctki_vi_test_midpoint_result_low.19637.0.35 0000000000000188 d cctki_vi_test_midpoint_result_low.19660.0.36 0000000000000084 d cctki_vi_test_simpson_convergence_order.19225.0.31 00000000000000dc d cctki_vi_test_simpson_convergence_order.19462.0.32 000000000000002c d cctki_vi_test_simpson_convergence_order.19488.0.33 0000000000000134 d cctki_vi_test_simpson_convergence_order.19513.0.34 00000000000001e4 d cctki_vi_test_simpson_convergence_order.19637.0.35 000000000000018c d cctki_vi_test_simpson_convergence_order.19660.0.36 0000000000000088 d cctki_vi_test_simpson_pi_symmetry.19225.0.31 00000000000000e0 d cctki_vi_test_simpson_pi_symmetry.19462.0.32 0000000000000030 d cctki_vi_test_simpson_pi_symmetry.19488.0.33 0000000000000138 d cctki_vi_test_simpson_pi_symmetry.19513.0.34 00000000000001e8 d cctki_vi_test_simpson_pi_symmetry.19637.0.35 0000000000000190 d cctki_vi_test_simpson_pi_symmetry.19660.0.36 000000000000008c d cctki_vi_test_simpson_result_high.19225.0.31 00000000000000e4 d cctki_vi_test_simpson_result_high.19462.0.32 0000000000000034 d cctki_vi_test_simpson_result_high.19488.0.33 000000000000013c d cctki_vi_test_simpson_result_high.19513.0.34 00000000000001ec d cctki_vi_test_simpson_result_high.19637.0.35 0000000000000194 d cctki_vi_test_simpson_result_high.19660.0.36 0000000000000090 d cctki_vi_test_simpson_result_low.19225.0.31 00000000000000e8 d cctki_vi_test_simpson_result_low.19462.0.32 0000000000000038 d cctki_vi_test_simpson_result_low.19488.0.33 0000000000000140 d cctki_vi_test_simpson_result_low.19513.0.34 00000000000001f0 d cctki_vi_test_simpson_result_low.19637.0.35 0000000000000198 d cctki_vi_test_simpson_result_low.19660.0.36 0000000000000094 d cctki_vi_test_trapezoidal_convergence_order.19225.0.31 00000000000000ec d cctki_vi_test_trapezoidal_convergence_order.19462.0.32 000000000000003c d cctki_vi_test_trapezoidal_convergence_order.19488.0.33 0000000000000144 d cctki_vi_test_trapezoidal_convergence_order.19513.0.34 00000000000001f4 d cctki_vi_test_trapezoidal_convergence_order.19637.0.35 000000000000019c d cctki_vi_test_trapezoidal_convergence_order.19660.0.36 0000000000000098 d cctki_vi_test_trapezoidal_pi_symmetry.19225.0.31 00000000000000f0 d cctki_vi_test_trapezoidal_pi_symmetry.19462.0.32 0000000000000040 d cctki_vi_test_trapezoidal_pi_symmetry.19488.0.33 0000000000000148 d cctki_vi_test_trapezoidal_pi_symmetry.19513.0.34 00000000000001f8 d cctki_vi_test_trapezoidal_pi_symmetry.19637.0.35 00000000000001a0 d cctki_vi_test_trapezoidal_pi_symmetry.19660.0.36 000000000000009c d cctki_vi_test_trapezoidal_result_high.19225.0.31 00000000000000f4 d cctki_vi_test_trapezoidal_result_high.19462.0.32 0000000000000044 d cctki_vi_test_trapezoidal_result_high.19488.0.33 000000000000014c d cctki_vi_test_trapezoidal_result_high.19513.0.34 00000000000001fc d cctki_vi_test_trapezoidal_result_high.19637.0.35 00000000000001a4 d cctki_vi_test_trapezoidal_result_high.19660.0.36 00000000000000a0 d cctki_vi_test_trapezoidal_result_low.19225.0.31 00000000000000f8 d cctki_vi_test_trapezoidal_result_low.19462.0.32 0000000000000048 d cctki_vi_test_trapezoidal_result_low.19488.0.33 0000000000000150 d cctki_vi_test_trapezoidal_result_low.19513.0.34 0000000000000200 d cctki_vi_test_trapezoidal_result_low.19637.0.35 00000000000001a8 d cctki_vi_test_trapezoidal_result_low.19660.0.36 00000000000000a4 d cctki_vi_x.19225.0.31 00000000000000fc d cctki_vi_x.19462.0.32 000000000000004c d cctki_vi_x.19488.0.33 0000000000000154 d cctki_vi_x.19513.0.34 0000000000000204 d cctki_vi_x.19637.0.35 00000000000001ac d cctki_vi_x.19660.0.36 00000000000000a8 d cctki_vi_y.19225.0.31 0000000000000100 d cctki_vi_y.19462.0.32 0000000000000050 d cctki_vi_y.19488.0.33 0000000000000158 d cctki_vi_y.19513.0.34 0000000000000208 d cctki_vi_y.19637.0.35 00000000000001b0 d cctki_vi_y.19660.0.36 00000000000000ac d cctki_vi_z.19225.0.31 0000000000000104 d cctki_vi_z.19462.0.32 0000000000000054 d cctki_vi_z.19488.0.33 000000000000015c d cctki_vi_z.19513.0.34 000000000000020c d cctki_vi_z.19637.0.35 00000000000001b4 d cctki_vi_z.19660.0.36 U cos U fclose 0000000000000008 b fi.19720.0.40 U fopen U fprintf U fputc U fputs 0000000000000000 b fr.19720.0.40 U iorest_ U multipolerest_ U sin
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@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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