!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_2019v3_C__MO_714772088128_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 = -230.6810818408382 Forces: 1 -6.23745664e-02 -3.66298858e-02 -3.56892774e-02 2 2.47564453e-02 2.31779186e-03 -9.87291301e-02 3 -1.38234398e-03 -9.82801505e-02 -8.57311916e-04 4 -1.07540460e-01 -2.19646501e-03 -1.84266702e-02 5 2.38785822e-02 -7.15416273e-02 -4.52505321e-02 6 9.64113361e-02 -1.80574586e-02 -8.40170572e-02 7 -3.96087042e-02 6.07483114e-02 1.38937471e-02 8 -5.61738799e-03 7.57216828e-02 4.58192652e-02 9 -4.90226756e-02 3.56920844e-03 -9.14865916e-02 10 2.79518039e-02 7.69676183e-02 -4.16274985e-02 11 9.95737245e-02 -1.77356724e-02 5.20879742e-02 12 -8.80702800e-02 8.51313605e-02 3.12276156e-04 13 1.51210006e-02 -9.57509532e-03 3.44024653e-02 14 3.84111011e-02 3.37665763e-02 -4.73484669e-02 15 -3.58369106e-02 -1.10218595e-02 -1.29588621e-02 16 -2.91404177e-02 -1.63419335e-02 2.07357678e-02 17 -1.08988168e-01 -8.86527103e-02 9.17993834e-04 18 9.00821767e-02 5.13689543e-02 -6.23863611e-02 19 5.21378211e-02 -9.71669172e-02 8.74600377e-02 20 -1.11994237e-01 3.31215614e-02 1.03296611e-01 21 9.72699926e-03 -7.55028143e-02 -3.82479259e-03 22 8.93169542e-02 -2.00926309e-02 2.89499988e-03 23 4.08975994e-02 -3.00939345e-02 2.77856121e-02 24 1.31807474e-02 4.68168175e-04 6.72804590e-02 25 -7.58200390e-02 -2.07421109e-03 -3.69255646e-02 26 7.84772873e-02 -1.95635889e-02 -4.31524634e-02 27 7.05947748e-02 3.25138556e-02 3.74464730e-02 28 -1.37528531e-01 8.23835121e-02 1.00382235e-01 29 -2.44702561e-02 -2.94694740e-02 -7.63203067e-02 30 7.30493421e-02 5.61564248e-02 2.46020309e-03 31 2.91424905e-02 2.06835231e-02 4.07885239e-02 32 4.68478996e-03 2.90778800e-02 6.10362423e-02 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -230.6810818408382 Forces: 1 -6.23745664e-02 -3.66298858e-02 -3.56892774e-02 2 2.47564453e-02 2.31779186e-03 -9.87291301e-02 3 -1.38234398e-03 -9.82801505e-02 -8.57311916e-04 4 -1.07540460e-01 -2.19646501e-03 -1.84266702e-02 5 2.38785822e-02 -7.15416273e-02 -4.52505321e-02 6 9.64113361e-02 -1.80574586e-02 -8.40170572e-02 7 -3.96087042e-02 6.07483114e-02 1.38937471e-02 8 -5.61738799e-03 7.57216828e-02 4.58192652e-02 9 -4.90226756e-02 3.56920844e-03 -9.14865916e-02 10 2.79518039e-02 7.69676183e-02 -4.16274985e-02 11 9.95737245e-02 -1.77356724e-02 5.20879742e-02 12 -8.80702800e-02 8.51313605e-02 3.12276156e-04 13 1.51210006e-02 -9.57509532e-03 3.44024653e-02 14 3.84111011e-02 3.37665763e-02 -4.73484669e-02 15 -3.58369106e-02 -1.10218595e-02 -1.29588621e-02 16 -2.91404177e-02 -1.63419335e-02 2.07357678e-02 17 -1.08988168e-01 -8.86527103e-02 9.17993834e-04 18 9.00821767e-02 5.13689543e-02 -6.23863611e-02 19 5.21378211e-02 -9.71669172e-02 8.74600377e-02 20 -1.11994237e-01 3.31215614e-02 1.03296611e-01 21 9.72699926e-03 -7.55028143e-02 -3.82479259e-03 22 8.93169542e-02 -2.00926309e-02 2.89499988e-03 23 4.08975994e-02 -3.00939345e-02 2.77856121e-02 24 1.31807474e-02 4.68168175e-04 6.72804590e-02 25 -7.58200390e-02 -2.07421109e-03 -3.69255646e-02 26 7.84772873e-02 -1.95635889e-02 -4.31524634e-02 27 7.05947748e-02 3.25138556e-02 3.74464730e-02 28 -1.37528531e-01 8.23835121e-02 1.00382235e-01 29 -2.44702561e-02 -2.94694740e-02 -7.63203067e-02 30 7.30493421e-02 5.61564248e-02 2.46020309e-03 31 2.91424905e-02 2.06835231e-02 4.07885239e-02 32 4.68478996e-03 2.90778800e-02 6.10362423e-02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==253218== Memcheck, a memory error detector ==253218== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==253218== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==253218== Command: python runner2.py DUNN_WenTadmor_2019v3_C__MO_714772088128_000 ==253218== ==253376== Warning: invalid file descriptor 255988 in syscall close() ==253376== Warning: invalid file descriptor 255989 in syscall close() ==253376== Warning: invalid file descriptor 255990 in syscall close() ==253376== Warning: invalid file descriptor 255991 in syscall close() ==253376== Use --log-fd= to select an alternative log fd. ==253376== Warning: invalid file descriptor 255992 in syscall close() ==253376== Warning: invalid file descriptor 255993 in syscall close() ==253218== Conditional jump or move depends on uninitialised value(s) ==253218== at 0x114972997: NeuralNetwork::read_parameter_file(_IO_FILE*, int) (in /work2/08773/bwaters/stampede2/bwaters/job-48593a8e-64e0-42ef-b0c2-7c95e4689d7b-007-2bec10c8-26e5-4698-9c8d-5034d3b31a91/VC_561022993723_004-and-MO_714772088128_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==253218== by 0x11494CCAB: ANNImplementation::ProcessParameterFiles(KIM::ModelDriverCreate*, int, _IO_FILE* const*) (in /work2/08773/bwaters/stampede2/bwaters/job-48593a8e-64e0-42ef-b0c2-7c95e4689d7b-007-2bec10c8-26e5-4698-9c8d-5034d3b31a91/VC_561022993723_004-and-MO_714772088128_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==253218== by 0x11494D131: ANNImplementation::ANNImplementation(KIM::ModelDriverCreate*, KIM::LengthUnit, KIM::EnergyUnit, KIM::ChargeUnit, KIM::TemperatureUnit, KIM::TimeUnit, int*) (in /work2/08773/bwaters/stampede2/bwaters/job-48593a8e-64e0-42ef-b0c2-7c95e4689d7b-007-2bec10c8-26e5-4698-9c8d-5034d3b31a91/VC_561022993723_004-and-MO_714772088128_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==253218== by 0x11494A8B7: ANN::ANN(KIM::ModelDriverCreate*, KIM::LengthUnit, KIM::EnergyUnit, KIM::ChargeUnit, KIM::TemperatureUnit, KIM::TimeUnit, int*) (in /work2/08773/bwaters/stampede2/bwaters/job-48593a8e-64e0-42ef-b0c2-7c95e4689d7b-007-2bec10c8-26e5-4698-9c8d-5034d3b31a91/VC_561022993723_004-and-MO_714772088128_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==253218== by 0x11494A975: model_driver_create (in /work2/08773/bwaters/stampede2/bwaters/job-48593a8e-64e0-42ef-b0c2-7c95e4689d7b-007-2bec10c8-26e5-4698-9c8d-5034d3b31a91/VC_561022993723_004-and-MO_714772088128_000-1669765210/staged_job_files/repository/md/DUNN__MD_292677547454_000/libkim-api-model-driver.so) ==253218== by 0x1140C5F1E: 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) ==253218== by 0x1140C6E18: 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) ==253218== by 0x1140CB762: 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) ==253218== by 0x11407B246: 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) ==253218== by 0x113FDB6C7: 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) ==253218== by 0x113FF117B: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (pybind11.h:929) ==253218== by 0x5F3988: PyCFunction_Call (in /usr/bin/python3.8) ==253218== ==253218== ==253218== HEAP SUMMARY: ==253218== in use at exit: 2,259,907 bytes in 1,704 blocks ==253218== total heap usage: 419,109 allocs, 417,405 frees, 387,920,109 bytes allocated ==253218== ==253218== LEAK SUMMARY: ==253218== definitely lost: 0 bytes in 0 blocks ==253218== indirectly lost: 0 bytes in 0 blocks ==253218== possibly lost: 180,827 bytes in 103 blocks ==253218== still reachable: 2,079,048 bytes in 1,600 blocks ==253218== of which reachable via heuristic: ==253218== stdstring : 38 bytes in 1 blocks ==253218== suppressed: 32 bytes in 1 blocks ==253218== Rerun with --leak-check=full to see details of leaked memory ==253218== ==253218== Use --track-origins=yes to see where uninitialised values come from ==253218== For lists of detected and suppressed errors, rerun with: -s ==253218== ERROR SUMMARY: 4 errors from 1 contexts (suppressed: 7812 from 552) ================================================================================ 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.