Enter a model name: === Verification check vc-memory-leak start (2022-11-30 10:16:19) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! VERIFICATION CHECK: vc-memory-leak !!!!! !!!!! !!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Description: Check that the model has no memory leaks. This is tested using the Valgrind memory debugging tool (http://valgrind.org) by performing a series of energy and force calculations on a randomly distorted face-centered cubic (FCC) cube base structure for both non-periodic and periodic boundary conditions. Separate configurations are tested for each species supported by the model, as well as one containing a random distribution of all species. Configurations used for testing are provided as auxiliary files. Author: Ellad Tadmor and Daniel S. Karls ----------------------------------------------------------------------------------------------------- Results for KIM Model : DUNN_WenTadmor_2019v1_C__MO_584345505904_000 Supported species : C random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = C (Configuration in file "config-F-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -236.69098362816206 Forces: 1 -1.18283727e-03 -6.33276175e-03 -3.71346155e-03 2 6.13549686e-05 2.01480463e-02 2.02260434e-02 3 7.77520312e-03 7.22611565e-03 3.73318840e-03 4 1.96461800e-02 1.72857869e-02 8.87313286e-03 5 2.21791718e-03 7.80022223e-03 1.23758437e-02 6 -1.15770308e-04 5.91300732e-04 -8.81476330e-04 7 -9.60857256e-03 8.26268340e-03 -5.79839094e-03 8 -1.90510363e-02 -5.73820066e-03 3.09616401e-02 9 1.27272679e-02 -9.78734350e-03 1.31844930e-02 10 -4.85770158e-03 -3.82604556e-03 2.30468339e-03 11 -9.38371998e-03 -3.43725249e-03 8.30135689e-03 12 6.07713991e-03 -6.12569427e-03 3.32190524e-03 13 -8.83591347e-03 -1.96008560e-02 -9.94782898e-03 14 5.68062074e-03 4.40315384e-03 -6.10549379e-03 15 1.31857245e-02 -5.96811546e-03 -1.04053998e-04 16 -1.26314813e-02 2.26936567e-03 1.83200555e-02 17 -3.91669497e-03 2.16853261e-03 -4.35995318e-03 18 2.20284408e-02 2.40836151e-02 -2.57846721e-02 19 7.62352823e-03 3.09711493e-03 2.77901519e-03 20 4.71356382e-03 5.15210975e-03 -2.42504763e-03 21 -1.29910694e-02 8.28894046e-03 -8.97272727e-03 22 -1.63310636e-02 1.62571940e-02 1.30192222e-03 23 4.11825197e-03 -5.04530690e-03 5.40156113e-03 24 -7.07916604e-03 1.91643597e-02 -1.57650529e-02 25 1.48389609e-02 -1.81220345e-02 -1.65050211e-02 26 2.78078357e-02 -3.34807099e-02 -3.72242203e-03 27 1.97206833e-02 -1.55404733e-02 -9.06122974e-03 28 -8.10484401e-03 6.96059612e-03 3.36521916e-03 29 -2.40919304e-02 1.23160459e-02 1.23138515e-02 30 -9.15491287e-03 -9.19815098e-03 6.83072198e-03 31 -2.14902413e-02 -7.65156387e-03 -2.25458145e-02 32 6.04282298e-04 -1.56206740e-02 -1.79019877e-02 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -236.69098362816206 Forces: 1 -1.18283727e-03 -6.33276175e-03 -3.71346155e-03 2 6.13549686e-05 2.01480463e-02 2.02260434e-02 3 7.77520312e-03 7.22611565e-03 3.73318840e-03 4 1.96461800e-02 1.72857869e-02 8.87313286e-03 5 2.21791718e-03 7.80022223e-03 1.23758437e-02 6 -1.15770308e-04 5.91300732e-04 -8.81476330e-04 7 -9.60857256e-03 8.26268340e-03 -5.79839094e-03 8 -1.90510363e-02 -5.73820066e-03 3.09616401e-02 9 1.27272679e-02 -9.78734350e-03 1.31844930e-02 10 -4.85770158e-03 -3.82604556e-03 2.30468339e-03 11 -9.38371998e-03 -3.43725249e-03 8.30135689e-03 12 6.07713991e-03 -6.12569427e-03 3.32190524e-03 13 -8.83591347e-03 -1.96008560e-02 -9.94782898e-03 14 5.68062074e-03 4.40315384e-03 -6.10549379e-03 15 1.31857245e-02 -5.96811546e-03 -1.04053998e-04 16 -1.26314813e-02 2.26936567e-03 1.83200555e-02 17 -3.91669497e-03 2.16853261e-03 -4.35995318e-03 18 2.20284408e-02 2.40836151e-02 -2.57846721e-02 19 7.62352823e-03 3.09711493e-03 2.77901519e-03 20 4.71356382e-03 5.15210975e-03 -2.42504763e-03 21 -1.29910694e-02 8.28894046e-03 -8.97272727e-03 22 -1.63310636e-02 1.62571940e-02 1.30192222e-03 23 4.11825197e-03 -5.04530690e-03 5.40156113e-03 24 -7.07916604e-03 1.91643597e-02 -1.57650529e-02 25 1.48389609e-02 -1.81220345e-02 -1.65050211e-02 26 2.78078357e-02 -3.34807099e-02 -3.72242203e-03 27 1.97206833e-02 -1.55404733e-02 -9.06122974e-03 28 -8.10484401e-03 6.96059612e-03 3.36521916e-03 29 -2.40919304e-02 1.23160459e-02 1.23138515e-02 30 -9.15491287e-03 -9.19815098e-03 6.83072198e-03 31 -2.14902413e-02 -7.65156387e-03 -2.25458145e-02 32 6.04282298e-04 -1.56206740e-02 -1.79019877e-02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==67914== Memcheck, a memory error detector ==67914== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==67914== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==67914== Command: python runner2.py DUNN_WenTadmor_2019v1_C__MO_584345505904_000 ==67914== ==68062== Warning: invalid file descriptor 1024 in syscall close() ==68062== Warning: invalid file descriptor 1025 in syscall close() ==68062== Warning: invalid file descriptor 1026 in syscall close() ==68062== Warning: invalid file descriptor 1027 in syscall close() ==68062== Use --log-fd= to select an alternative log fd. ==68062== Warning: invalid file descriptor 1028 in syscall close() ==68062== Warning: invalid file descriptor 1029 in syscall close() ==67914== Conditional jump or move depends on uninitialised value(s) ==67914== at 0x12C75E997: NeuralNetwork::read_parameter_file(_IO_FILE*, int) (in /mmfs1/scratch/bwaters2/bwaters/job-2d0c0de2-5d09-4d2e-95d7-164529315322-007-758a2dc8-413f-49c2-8cca-a58df9148549/VC_561022993723_004-and-MO_584345505904_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==67914== by 0x12C738CAB: ANNImplementation::ProcessParameterFiles(KIM::ModelDriverCreate*, int, _IO_FILE* const*) (in /mmfs1/scratch/bwaters2/bwaters/job-2d0c0de2-5d09-4d2e-95d7-164529315322-007-758a2dc8-413f-49c2-8cca-a58df9148549/VC_561022993723_004-and-MO_584345505904_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==67914== by 0x12C739131: ANNImplementation::ANNImplementation(KIM::ModelDriverCreate*, KIM::LengthUnit, KIM::EnergyUnit, KIM::ChargeUnit, KIM::TemperatureUnit, KIM::TimeUnit, int*) (in /mmfs1/scratch/bwaters2/bwaters/job-2d0c0de2-5d09-4d2e-95d7-164529315322-007-758a2dc8-413f-49c2-8cca-a58df9148549/VC_561022993723_004-and-MO_584345505904_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==67914== by 0x12C7368B7: ANN::ANN(KIM::ModelDriverCreate*, KIM::LengthUnit, KIM::EnergyUnit, KIM::ChargeUnit, KIM::TemperatureUnit, KIM::TimeUnit, int*) (in /mmfs1/scratch/bwaters2/bwaters/job-2d0c0de2-5d09-4d2e-95d7-164529315322-007-758a2dc8-413f-49c2-8cca-a58df9148549/VC_561022993723_004-and-MO_584345505904_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==67914== by 0x12C736975: model_driver_create (in /mmfs1/scratch/bwaters2/bwaters/job-2d0c0de2-5d09-4d2e-95d7-164529315322-007-758a2dc8-413f-49c2-8cca-a58df9148549/VC_561022993723_004-and-MO_584345505904_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==67914== by 0x12BEB1F1E: KIM::ModelImplementation::InitializeParameterizedModel(KIM::LengthUnit, KIM::EnergyUnit, KIM::ChargeUnit, KIM::TemperatureUnit, KIM::TimeUnit, KIM::Collections*) (in /usr/local/lib/libkim-api.so.2.2.1) ==67914== by 0x12BEB2E18: KIM::ModelImplementation::ModelCreate(KIM::Numbering, KIM::LengthUnit, KIM::EnergyUnit, KIM::ChargeUnit, KIM::TemperatureUnit, KIM::TimeUnit, std::__cxx11::basic_string, std::allocator > const&) (in /usr/local/lib/libkim-api.so.2.2.1) ==67914== by 0x12BEB7762: KIM::ModelImplementation::Create(KIM::Numbering, KIM::LengthUnit, KIM::EnergyUnit, KIM::ChargeUnit, KIM::TemperatureUnit, KIM::TimeUnit, std::__cxx11::basic_string, std::allocator > const&, int*, KIM::ModelImplementation**) (in /usr/local/lib/libkim-api.so.2.2.1) ==67914== by 0x12BE67246: KIM::Model::Create(KIM::Numbering, KIM::LengthUnit, KIM::EnergyUnit, KIM::ChargeUnit, KIM::TemperatureUnit, KIM::TimeUnit, std::__cxx11::basic_string, std::allocator > const&, int*, KIM::Model**) (in /usr/local/lib/libkim-api.so.2.2.1) ==67914== by 0x12BDC76C7: void pybind11::cpp_function::initialize, std::allocator > const&)#21}, pybind11::tuple, KIM::Numbering const&, KIM::LengthUnit const&, KIM::EnergyUnit const&, KIM::ChargeUnit const&, KIM::TemperatureUnit const&, KIM::TimeUnit const&, std::__cxx11::basic_string, std::allocator > const&, pybind11::name, pybind11::scope, pybind11::sibling, char [115], pybind11::arg, char [115], char [115], char [115], char [115], char [115], char [115]>(pybind11_init_model(pybind11::module_&)::{lambda(KIM::Numbering const&, KIM::LengthUnit const&, KIM::EnergyUnit const&, KIM::ChargeUnit const&, KIM::TemperatureUnit const&, KIM::TimeUnit const&, std::__cxx11::basic_string, std::allocator > const&)#21}&&, pybind11::tuple (*)(KIM::Numbering const&, KIM::LengthUnit const&, KIM::EnergyUnit const&, KIM::ChargeUnit const&, KIM::TemperatureUnit const&, KIM::TimeUnit const&, std::__cxx11::basic_string, std::allocator > const&), pybind11::name const&, pybind11::scope const&, pybind11::sibling const&, char const (&) [115], pybind11::arg const&, char const (&) [115], char const (&) [115], char const (&) [115], char const (&) [115], char const (&) [115], char const (&) [115])::{lambda(pybind11::detail::function_call&)#3}::_FUN(pybind11::detail::function_call) (KIM_Model_bind.cpp:400) ==67914== by 0x12BDDD17B: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (pybind11.h:929) ==67914== by 0x5F3988: PyCFunction_Call (in /usr/bin/python3.8) ==67914== ==67914== ==67914== HEAP SUMMARY: ==67914== in use at exit: 2,259,886 bytes in 1,704 blocks ==67914== total heap usage: 419,123 allocs, 417,419 frees, 396,413,001 bytes allocated ==67914== ==67914== LEAK SUMMARY: ==67914== definitely lost: 0 bytes in 0 blocks ==67914== indirectly lost: 0 bytes in 0 blocks ==67914== possibly lost: 180,827 bytes in 103 blocks ==67914== still reachable: 2,079,027 bytes in 1,600 blocks ==67914== of which reachable via heuristic: ==67914== stdstring : 38 bytes in 1 blocks ==67914== suppressed: 32 bytes in 1 blocks ==67914== Rerun with --leak-check=full to see details of leaked memory ==67914== ==67914== Use --track-origins=yes to see where uninitialised values come from ==67914== For lists of detected and suppressed errors, rerun with: -s ==67914== ERROR SUMMARY: 4 errors from 1 contexts (suppressed: 7774 from 548) ================================================================================ To pass this verification check the number of bytes that are "definitely lost" or "indirectly lost" must be zero. NOTE that Valgrind will typically report non-zero "possibly lost" bytes due to Python's internal memory allocation and garbage collection that it does not monitor. Full Valgrind output written to auxiliary file "valgrind.out" Grade: P Comment: No memory leak detected. === Verification check vc-memory-leak end (2022-11-30 10:18:36) ===