Enter a model name: === Verification check vc-memory-leak start (2022-11-30 10:16:18) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_2019v2_C__MO_956135237832_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 = -233.9437614486629 Forces: 1 -4.70943633e-02 -2.95652174e-02 -4.25595658e-02 2 2.10192545e-02 2.63839870e-02 -6.28199139e-02 3 2.07396353e-02 -5.02156680e-02 1.41227122e-02 4 -5.88574552e-02 2.41702865e-02 3.70780345e-03 5 1.60353189e-02 -6.16198028e-02 -3.44426702e-02 6 5.47381060e-02 9.55832474e-03 -3.77359165e-02 7 -5.83781644e-02 2.16063466e-02 1.08880485e-01 8 -2.23720277e-02 9.99886119e-02 6.59755135e-02 9 -4.19124309e-02 -2.15542691e-02 -7.58413203e-02 10 3.14681878e-02 7.95949503e-02 -4.90180784e-02 11 7.17619966e-02 -3.12751394e-02 8.63601217e-02 12 -8.60875907e-02 7.25048671e-02 3.09464648e-02 13 3.12027583e-02 -3.55776957e-02 3.47959989e-02 14 4.09003380e-02 2.37305310e-02 -2.89970240e-02 15 -5.67037095e-02 -3.40706207e-02 -1.79855074e-02 16 -2.49507925e-02 -5.61625396e-02 5.45165600e-02 17 -6.65251076e-02 -5.42898196e-02 3.86811154e-03 18 6.66000491e-02 6.48132977e-02 -5.22006357e-02 19 1.61935157e-02 -6.63597103e-02 5.60212914e-02 20 -5.56473070e-02 2.33710494e-02 5.09193118e-02 21 4.44794446e-02 -5.31523772e-03 -9.49293859e-02 22 4.03847690e-02 -1.08031021e-03 -1.12114020e-02 23 2.48804539e-02 -2.96034240e-02 1.83287704e-02 24 -1.00634668e-03 1.14986434e-02 4.46044490e-02 25 2.08190840e-02 -2.94156836e-02 -4.06986816e-02 26 5.22482081e-02 -1.03435205e-02 -6.53771536e-02 27 2.56654998e-02 -3.76789371e-02 8.50773412e-03 28 -1.06432805e-01 6.14435281e-02 6.74604480e-02 29 -3.98969155e-02 -4.82044022e-02 -9.28677567e-02 30 5.13792963e-02 4.47637806e-02 -1.94167968e-02 31 2.61077417e-02 -9.83116778e-04 1.36937279e-02 32 9.24135889e-03 3.98869105e-02 6.33923049e-02 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -233.9437614486629 Forces: 1 -4.70943633e-02 -2.95652174e-02 -4.25595658e-02 2 2.10192545e-02 2.63839870e-02 -6.28199139e-02 3 2.07396353e-02 -5.02156680e-02 1.41227122e-02 4 -5.88574552e-02 2.41702865e-02 3.70780345e-03 5 1.60353189e-02 -6.16198028e-02 -3.44426702e-02 6 5.47381060e-02 9.55832474e-03 -3.77359165e-02 7 -5.83781644e-02 2.16063466e-02 1.08880485e-01 8 -2.23720277e-02 9.99886119e-02 6.59755135e-02 9 -4.19124309e-02 -2.15542691e-02 -7.58413203e-02 10 3.14681878e-02 7.95949503e-02 -4.90180784e-02 11 7.17619966e-02 -3.12751394e-02 8.63601217e-02 12 -8.60875907e-02 7.25048671e-02 3.09464648e-02 13 3.12027583e-02 -3.55776957e-02 3.47959989e-02 14 4.09003380e-02 2.37305310e-02 -2.89970240e-02 15 -5.67037095e-02 -3.40706207e-02 -1.79855074e-02 16 -2.49507925e-02 -5.61625396e-02 5.45165600e-02 17 -6.65251076e-02 -5.42898196e-02 3.86811154e-03 18 6.66000491e-02 6.48132977e-02 -5.22006357e-02 19 1.61935157e-02 -6.63597103e-02 5.60212914e-02 20 -5.56473070e-02 2.33710494e-02 5.09193118e-02 21 4.44794446e-02 -5.31523772e-03 -9.49293859e-02 22 4.03847690e-02 -1.08031021e-03 -1.12114020e-02 23 2.48804539e-02 -2.96034240e-02 1.83287704e-02 24 -1.00634668e-03 1.14986434e-02 4.46044490e-02 25 2.08190840e-02 -2.94156836e-02 -4.06986816e-02 26 5.22482081e-02 -1.03435205e-02 -6.53771536e-02 27 2.56654998e-02 -3.76789371e-02 8.50773412e-03 28 -1.06432805e-01 6.14435281e-02 6.74604480e-02 29 -3.98969155e-02 -4.82044022e-02 -9.28677567e-02 30 5.13792963e-02 4.47637806e-02 -1.94167968e-02 31 2.61077417e-02 -9.83116778e-04 1.36937279e-02 32 9.24135889e-03 3.98869105e-02 6.33923049e-02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==67913== Memcheck, a memory error detector ==67913== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==67913== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==67913== Command: python runner2.py DUNN_WenTadmor_2019v2_C__MO_956135237832_000 ==67913== ==68067== Warning: invalid file descriptor 1024 in syscall close() ==68067== Warning: invalid file descriptor 1025 in syscall close() ==68067== Warning: invalid file descriptor 1026 in syscall close() ==68067== Warning: invalid file descriptor 1027 in syscall close() ==68067== Use --log-fd= to select an alternative log fd. ==68067== Warning: invalid file descriptor 1028 in syscall close() ==68067== Warning: invalid file descriptor 1029 in syscall close() ==67913== Conditional jump or move depends on uninitialised value(s) ==67913== 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_956135237832_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==67913== 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_956135237832_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==67913== 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_956135237832_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==67913== 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_956135237832_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==67913== 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_956135237832_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==67913== 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) ==67913== 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) ==67913== 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) ==67913== 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) ==67913== 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) ==67913== by 0x12BDDD17B: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (pybind11.h:929) ==67913== by 0x5F3988: PyCFunction_Call (in /usr/bin/python3.8) ==67913== ==67913== ==67913== HEAP SUMMARY: ==67913== in use at exit: 2,259,886 bytes in 1,704 blocks ==67913== total heap usage: 419,123 allocs, 417,419 frees, 396,412,979 bytes allocated ==67913== ==67913== LEAK SUMMARY: ==67913== definitely lost: 0 bytes in 0 blocks ==67913== indirectly lost: 0 bytes in 0 blocks ==67913== possibly lost: 180,827 bytes in 103 blocks ==67913== still reachable: 2,079,027 bytes in 1,600 blocks ==67913== of which reachable via heuristic: ==67913== stdstring : 38 bytes in 1 blocks ==67913== suppressed: 32 bytes in 1 blocks ==67913== Rerun with --leak-check=full to see details of leaked memory ==67913== ==67913== Use --track-origins=yes to see where uninitialised values come from ==67913== For lists of detected and suppressed errors, rerun with: -s ==67913== ERROR SUMMARY: 4 errors from 1 contexts (suppressed: 7775 from 547) ================================================================================ 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) ===