Enter a model name: === Verification check vc-memory-leak start (2022-11-30 10:16:20) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EDIP_LAMMPS_Marks_2000_C__MO_374144505645_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 = -60.03145604354536 Forces: 1 7.06084516e+00 1.01792369e+01 1.29916075e+01 2 -1.30271181e+00 -1.55955134e+01 -7.31253802e-01 3 -1.12132126e+01 1.24041714e+01 1.57081919e+00 4 5.52984536e+00 -1.56048137e+01 -3.96931702e+00 5 -4.91056208e-01 1.69836752e+01 -7.67233094e-01 6 -7.23437526e+00 -9.85931959e+00 2.60748117e-01 7 -3.50817230e+00 -5.54947881e+00 -3.88837731e-01 8 3.87718803e+00 -1.58884880e+01 6.62078913e+00 9 9.34334231e+00 1.69712457e+01 1.42574543e+01 10 -1.54098600e+01 -1.50738510e+01 9.92607854e+00 11 -3.51342651e+01 9.12763288e+00 -3.27233046e+00 12 1.32422163e+01 -1.62954006e+01 -5.27642388e+00 13 4.64139780e+00 3.83163689e+00 -1.47752943e+01 14 1.69249344e+00 2.20554037e+00 -6.68597789e-01 15 1.25708087e+01 -5.43005366e+00 -2.90498517e+00 16 -6.00967615e+00 1.86508435e+01 -9.49097945e+00 17 2.41141448e+01 1.26012896e+01 2.43761794e+00 18 -7.76807236e+00 -1.65703231e+01 3.94873391e+00 19 -1.11441746e+01 1.23524412e+01 -1.37783628e+01 20 3.33291082e+00 -7.84256993e+00 -6.64876926e+00 21 1.45163438e+01 1.34064796e+01 5.08793684e+00 22 1.05426184e+00 -8.20755333e+00 1.55436470e+01 23 -9.36331461e+00 2.84330866e+00 -1.25223769e+01 24 2.52784600e+00 -8.38501032e+00 -6.37029285e+00 25 1.47638411e+01 2.08923186e+01 4.52540949e+00 26 -1.10307647e+01 -1.47209381e+00 4.94737659e+00 27 -5.97273688e+00 6.82167743e+00 -7.37249866e+00 28 5.21680865e+00 -1.17673373e+01 -1.12781877e+01 29 8.32619502e+00 -6.25597967e+00 2.36668548e+01 30 2.79541772e+00 -4.01239093e+00 7.20280955e+00 31 -1.21784551e+01 1.33980310e+01 -8.92991976e+00 32 3.15494096e+00 -8.85935171e+00 -3.84222224e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -60.03145604354536 Forces: 1 7.06084516e+00 1.01792369e+01 1.29916075e+01 2 -1.30271208e+00 -1.55955131e+01 -7.31253759e-01 3 -1.12132126e+01 1.24041714e+01 1.57081919e+00 4 5.52984536e+00 -1.56048137e+01 -3.96931702e+00 5 -4.91055943e-01 1.69836749e+01 -7.67233137e-01 6 -7.23437526e+00 -9.85931959e+00 2.60748117e-01 7 -3.50817230e+00 -5.54947881e+00 -3.88837731e-01 8 3.87718803e+00 -1.58884880e+01 6.62078913e+00 9 9.34334231e+00 1.69712457e+01 1.42574543e+01 10 -1.54098600e+01 -1.50738510e+01 9.92607854e+00 11 -3.51342651e+01 9.12763288e+00 -3.27233046e+00 12 1.32422163e+01 -1.62954006e+01 -5.27642388e+00 13 4.64139780e+00 3.83163689e+00 -1.47752943e+01 14 1.69249344e+00 2.20554037e+00 -6.68597789e-01 15 1.25708087e+01 -5.43005366e+00 -2.90498517e+00 16 -6.00967615e+00 1.86508435e+01 -9.49097945e+00 17 2.41141448e+01 1.26012896e+01 2.43761794e+00 18 -7.76807236e+00 -1.65703231e+01 3.94873391e+00 19 -1.11441746e+01 1.23524412e+01 -1.37783628e+01 20 3.33291082e+00 -7.84256993e+00 -6.64876926e+00 21 1.45163438e+01 1.34064796e+01 5.08793684e+00 22 1.05426184e+00 -8.20755333e+00 1.55436470e+01 23 -9.36331461e+00 2.84330866e+00 -1.25223769e+01 24 2.52784600e+00 -8.38501032e+00 -6.37029285e+00 25 1.47638411e+01 2.08923186e+01 4.52540949e+00 26 -1.10307647e+01 -1.47209381e+00 4.94737659e+00 27 -5.97273688e+00 6.82167743e+00 -7.37249866e+00 28 5.21680865e+00 -1.17673373e+01 -1.12781877e+01 29 8.32619502e+00 -6.25597967e+00 2.36668548e+01 30 2.79541772e+00 -4.01239093e+00 7.20280955e+00 31 -1.21784551e+01 1.33980310e+01 -8.92991976e+00 32 3.15494096e+00 -8.85935171e+00 -3.84222224e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==204067== Memcheck, a memory error detector ==204067== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==204067== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==204067== Command: python runner2.py EDIP_LAMMPS_Marks_2000_C__MO_374144505645_000 ==204067== ==205373== Warning: invalid file descriptor 1024 in syscall close() ==205373== Warning: invalid file descriptor 1025 in syscall close() ==205373== Warning: invalid file descriptor 1026 in syscall close() ==205373== Warning: invalid file descriptor 1027 in syscall close() ==205373== Use --log-fd= to select an alternative log fd. ==205373== Warning: invalid file descriptor 1028 in syscall close() ==205373== Warning: invalid file descriptor 1029 in syscall close() ==204067== Mismatched free() / delete / delete [] ==204067== at 0x483CFBF: operator delete(void*) (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so) ==204067== by 0x12C6AF2F2: EDIPC::ProcessParameterFile(_IO_FILE*, int) (in /mmfs1/scratch/bwaters2/bwaters/job-1dabf7a8-d543-495e-afa4-4a3dc9822d2e-007-c872a7a5-edbd-475f-b5d2-26bc4b49f6da/VC_561022993723_004-and-MO_374144505645_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204067== by 0x12C65822D: EDIPImplementation::ProcessParameterFiles(KIM::ModelDriverCreate*, int, _IO_FILE* const*) (in /mmfs1/scratch/bwaters2/bwaters/job-1dabf7a8-d543-495e-afa4-4a3dc9822d2e-007-c872a7a5-edbd-475f-b5d2-26bc4b49f6da/VC_561022993723_004-and-MO_374144505645_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204067== by 0x12C65A2BB: EDIPImplementation::EDIPImplementation(KIM::ModelDriverCreate*, KIM::LengthUnit, KIM::EnergyUnit, KIM::ChargeUnit, KIM::TemperatureUnit, KIM::TimeUnit, int*) (in /mmfs1/scratch/bwaters2/bwaters/job-1dabf7a8-d543-495e-afa4-4a3dc9822d2e-007-c872a7a5-edbd-475f-b5d2-26bc4b49f6da/VC_561022993723_004-and-MO_374144505645_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204067== by 0x12C63F3D7: EDIP::EDIP(KIM::ModelDriverCreate*, KIM::LengthUnit, KIM::EnergyUnit, KIM::ChargeUnit, KIM::TemperatureUnit, KIM::TimeUnit, int*) (in /mmfs1/scratch/bwaters2/bwaters/job-1dabf7a8-d543-495e-afa4-4a3dc9822d2e-007-c872a7a5-edbd-475f-b5d2-26bc4b49f6da/VC_561022993723_004-and-MO_374144505645_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204067== by 0x12C6422EE: ModelDriverCreateRoutine (in /mmfs1/scratch/bwaters2/bwaters/job-1dabf7a8-d543-495e-afa4-4a3dc9822d2e-007-c872a7a5-edbd-475f-b5d2-26bc4b49f6da/VC_561022993723_004-and-MO_374144505645_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204067== 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) ==204067== 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) ==204067== 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) ==204067== 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) ==204067== 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) ==204067== by 0x12BDDD17B: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (pybind11.h:929) ==204067== Address 0xa8f7ab00 is 0 bytes inside a block of size 1,024 alloc'd ==204067== at 0x483C583: operator new[](unsigned long) (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so) ==204067== by 0x12C6AE8D4: EDIPC::ProcessParameterFile(_IO_FILE*, int) (in /mmfs1/scratch/bwaters2/bwaters/job-1dabf7a8-d543-495e-afa4-4a3dc9822d2e-007-c872a7a5-edbd-475f-b5d2-26bc4b49f6da/VC_561022993723_004-and-MO_374144505645_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204067== by 0x12C65822D: EDIPImplementation::ProcessParameterFiles(KIM::ModelDriverCreate*, int, _IO_FILE* const*) (in /mmfs1/scratch/bwaters2/bwaters/job-1dabf7a8-d543-495e-afa4-4a3dc9822d2e-007-c872a7a5-edbd-475f-b5d2-26bc4b49f6da/VC_561022993723_004-and-MO_374144505645_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204067== by 0x12C65A2BB: EDIPImplementation::EDIPImplementation(KIM::ModelDriverCreate*, KIM::LengthUnit, KIM::EnergyUnit, KIM::ChargeUnit, KIM::TemperatureUnit, KIM::TimeUnit, int*) (in /mmfs1/scratch/bwaters2/bwaters/job-1dabf7a8-d543-495e-afa4-4a3dc9822d2e-007-c872a7a5-edbd-475f-b5d2-26bc4b49f6da/VC_561022993723_004-and-MO_374144505645_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204067== by 0x12C63F3D7: EDIP::EDIP(KIM::ModelDriverCreate*, KIM::LengthUnit, KIM::EnergyUnit, KIM::ChargeUnit, KIM::TemperatureUnit, KIM::TimeUnit, int*) (in /mmfs1/scratch/bwaters2/bwaters/job-1dabf7a8-d543-495e-afa4-4a3dc9822d2e-007-c872a7a5-edbd-475f-b5d2-26bc4b49f6da/VC_561022993723_004-and-MO_374144505645_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204067== by 0x12C6422EE: ModelDriverCreateRoutine (in /mmfs1/scratch/bwaters2/bwaters/job-1dabf7a8-d543-495e-afa4-4a3dc9822d2e-007-c872a7a5-edbd-475f-b5d2-26bc4b49f6da/VC_561022993723_004-and-MO_374144505645_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204067== 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) ==204067== 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) ==204067== 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) ==204067== 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) ==204067== 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) ==204067== by 0x12BDDD17B: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (pybind11.h:929) ==204067== ==204067== ==204067== HEAP SUMMARY: ==204067== in use at exit: 2,257,559 bytes in 1,700 blocks ==204067== total heap usage: 47,824 allocs, 46,124 frees, 62,302,677 bytes allocated ==204067== ==204067== LEAK SUMMARY: ==204067== definitely lost: 0 bytes in 0 blocks ==204067== indirectly lost: 0 bytes in 0 blocks ==204067== possibly lost: 180,827 bytes in 103 blocks ==204067== still reachable: 2,076,700 bytes in 1,596 blocks ==204067== of which reachable via heuristic: ==204067== stdstring : 38 bytes in 1 blocks ==204067== suppressed: 32 bytes in 1 blocks ==204067== Rerun with --leak-check=full to see details of leaked memory ==204067== ==204067== For lists of detected and suppressed errors, rerun with: -s ==204067== ERROR SUMMARY: 4 errors from 1 contexts (suppressed: 7801 from 553) ================================================================================ 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 10:16:49) ===