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
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
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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Hello Jordi,
sorry for the late response.
The function 'Multipole_OutputComplexToH5File' seems to be there. I've also tried recompiling the thorn and nothing seems to change.
The function is not quite there. The error is about
Multipole_OutputComplexToH5File(_cGH*, Multipole::variable_desc const*, double const*, Multipole::mode_array const&)
while the functions found is
Multipole_OutputComplexToH5File(_cGH*, std::string const&, std::string const&, double, double)
ie it takes different arguments.
I had a look at the source code in utils.cc and (in line 179) it defines two different functions
Multipole_OutputComplexToH5File
depending on whether or not
HAVE_CAPABILITY_HDF5
is true.
The one missing is the one defined in the "true" branch of the #if statement while the one found is in the "false" branch ie used when no HDF5 functionality is present.
This clearly a bug in the code and went undetected since we always compile Cactus with HDF5 support.
Most likely you also want HDF5 support since it is used for checkpoint / recovery.
You should check that you have the thorn
ExternalLibaries/HDF5
listed in your ThornList and that also succeeded in building the HDF5 library or could find one in the system (this was output at the beginning of the compilation process but is hard to notice).
You can check for the presence of the file
configs/sim/bindings/Configuration/Capabilities/make.HDF5.defn
which should exist and contain lines like this (they will differ a bit for you of course):
include /home/rhaas/postdoc/gr/cactus/ET_trunk/configs/sim/bindings/Configuration/Capabilities/make.ZLIB.defn INC_DIRS += $(HDF5_INC_DIRS) INC_DIRS_F += $(HDF5_INC_DIRS) HDF5_BUILD = HDF5_ENABLE_CXX = no HDF5_ENABLE_FORTRAN = yes LIBSZ_DIR = LIBZ_DIR = HDF5_INSTALL_DIR = HDF5_DIR = /usr HDF5_ENABLE_CXX = no HDF5_ENABLE_FORTRAN = yes HDF5_INC_DIRS = /usr/lib/x86_64-linux-gnu/hdf5/serial /usr/include/hdf5/serial HDF5_LIB_DIRS = /usr/lib/x86_64-linux-gnu/hdf5/serial HDF5_LIBS = hdf5hl_fortran hdf5_fortran hdf5_hl hdf5 sz z m z HAVE_CAPABILITY_HDF5 = 1
ie it should end in HAVE_CAPBILITY_HDF5
Yours, Roland
users@lists.einsteintoolkit.org
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Haas, Roland -
Jordi Manyer -
Roland Haas