!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_JustoBazantKaxiras_1998_Si__MO_315965276297_000 Supported species : Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 116.62318182459161 Forces: 1 8.49109123e-02 4.75333427e-01 9.62948095e-01 2 -5.77099309e+00 8.14177825e-01 -1.24050299e+01 3 5.71830024e-01 -1.57169193e+01 -6.32666611e+00 4 -1.47359105e+01 -4.48036070e+00 9.03752073e-01 5 -5.99405950e+00 -9.39262466e+00 -1.30717530e+01 6 1.76640256e+01 -1.96093447e+00 -2.01752085e+01 7 6.29911449e+00 -2.24097160e+01 -1.95489640e-01 8 -3.32287825e+00 -3.57388215e+00 -6.68641050e+00 9 -1.65437218e+01 -8.85539553e+00 -1.82999192e+01 10 9.21929285e+00 1.27556434e+01 -1.16526710e+01 11 -1.52276968e+01 -4.10097258e+00 -1.12745992e+00 12 -2.25139910e+01 1.73647592e+01 -4.51460291e+00 13 1.05346453e+01 -5.34856304e+00 -2.06688945e+01 14 -1.47629449e+00 7.97568639e+00 -4.89224447e+00 15 2.82361539e+01 8.69911979e+00 -8.33783850e+00 16 7.31240814e+00 2.22644248e+01 5.15601332e+00 17 -1.15846736e+01 -8.31558219e+00 -8.18814306e+00 18 -1.96715349e+00 1.52097953e+00 2.32962757e-01 19 9.89842521e-01 -9.76509773e+00 1.39553698e+01 20 -1.55387724e+01 2.89688281e+00 8.19064797e+00 21 3.32972994e-01 -1.32621587e+01 6.98795495e+00 22 2.09945855e+01 4.18926535e+00 5.37057918e+00 23 4.27269693e+00 1.43916382e-01 4.12385880e+00 24 3.72408601e+00 -6.44816624e+00 3.10136347e+01 25 -2.76542932e+01 1.37227458e-01 4.14067863e+00 26 -3.96142145e+00 1.80237308e+01 -1.84622138e+00 27 -2.99551579e+00 -1.03292189e+01 1.54023835e+01 28 -1.17496632e+01 8.46214522e+00 6.91349747e+00 29 1.65996013e+01 -1.82617401e+00 7.54408111e+00 30 1.52730348e+01 1.07021437e+01 -1.46479965e+00 31 1.33404653e+01 -7.79464759e+00 1.66563813e+01 32 5.58737182e+00 1.71549778e+01 1.22986085e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 116.62318182459161 Forces: 1 8.49109123e-02 4.75333427e-01 9.62948095e-01 2 -5.77099309e+00 8.14177825e-01 -1.24050299e+01 3 5.71830024e-01 -1.57169193e+01 -6.32666611e+00 4 -1.47359105e+01 -4.48036070e+00 9.03752073e-01 5 -5.99405950e+00 -9.39262466e+00 -1.30717530e+01 6 1.76640256e+01 -1.96093447e+00 -2.01752085e+01 7 6.29911449e+00 -2.24097160e+01 -1.95489640e-01 8 -3.32287825e+00 -3.57388215e+00 -6.68641050e+00 9 -1.65437218e+01 -8.85539553e+00 -1.82999192e+01 10 9.21929285e+00 1.27556434e+01 -1.16526710e+01 11 -1.52276968e+01 -4.10097258e+00 -1.12745992e+00 12 -2.25139910e+01 1.73647592e+01 -4.51460291e+00 13 1.05346453e+01 -5.34856304e+00 -2.06688945e+01 14 -1.47629449e+00 7.97568639e+00 -4.89224447e+00 15 2.82361539e+01 8.69911979e+00 -8.33783850e+00 16 7.31240814e+00 2.22644248e+01 5.15601332e+00 17 -1.15846736e+01 -8.31558219e+00 -8.18814306e+00 18 -1.96715349e+00 1.52097953e+00 2.32962757e-01 19 9.89842521e-01 -9.76509773e+00 1.39553698e+01 20 -1.55387724e+01 2.89688281e+00 8.19064797e+00 21 3.32972994e-01 -1.32621587e+01 6.98795495e+00 22 2.09945855e+01 4.18926535e+00 5.37057918e+00 23 4.27269693e+00 1.43916382e-01 4.12385880e+00 24 3.72408601e+00 -6.44816624e+00 3.10136347e+01 25 -2.76542932e+01 1.37227458e-01 4.14067863e+00 26 -3.96142145e+00 1.80237308e+01 -1.84622138e+00 27 -2.99551579e+00 -1.03292189e+01 1.54023835e+01 28 -1.17496632e+01 8.46214522e+00 6.91349747e+00 29 1.65996013e+01 -1.82617401e+00 7.54408111e+00 30 1.52730348e+01 1.07021437e+01 -1.46479965e+00 31 1.33404653e+01 -7.79464759e+00 1.66563813e+01 32 5.58737182e+00 1.71549778e+01 1.22986085e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==204078== Memcheck, a memory error detector ==204078== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==204078== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==204078== Command: python runner2.py EDIP_LAMMPS_JustoBazantKaxiras_1998_Si__MO_315965276297_000 ==204078== ==205505== Warning: invalid file descriptor 1024 in syscall close() ==205505== Warning: invalid file descriptor 1025 in syscall close() ==205505== Warning: invalid file descriptor 1026 in syscall close() ==205505== Warning: invalid file descriptor 1027 in syscall close() ==205505== Use --log-fd= to select an alternative log fd. ==205505== Warning: invalid file descriptor 1028 in syscall close() ==205505== Warning: invalid file descriptor 1029 in syscall close() ==204078== Mismatched free() / delete / delete [] ==204078== at 0x483CFBF: operator delete(void*) (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so) ==204078== by 0x12C6E81B1: EDIPSingle::ProcessParameterFile(_IO_FILE*, int, std::vector, std::allocator >, std::allocator, std::allocator > > > const&) (in /mmfs1/scratch/bwaters2/bwaters/job-1dabf7a8-d543-495e-afa4-4a3dc9822d2e-007-c872a7a5-edbd-475f-b5d2-26bc4b49f6da/VC_561022993723_004-and-MO_315965276297_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204078== by 0x12C658C47: 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_315965276297_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204078== 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_315965276297_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204078== 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_315965276297_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204078== 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_315965276297_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204078== 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) ==204078== 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) ==204078== 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) ==204078== 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) ==204078== 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) ==204078== by 0x12BDDD17B: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (pybind11.h:929) ==204078== Address 0xa8f7ed70 is 0 bytes inside a block of size 1,024 alloc'd ==204078== at 0x483C583: operator new[](unsigned long) (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so) ==204078== by 0x12C6E7859: EDIPSingle::ProcessParameterFile(_IO_FILE*, int, std::vector, std::allocator >, std::allocator, std::allocator > > > const&) (in /mmfs1/scratch/bwaters2/bwaters/job-1dabf7a8-d543-495e-afa4-4a3dc9822d2e-007-c872a7a5-edbd-475f-b5d2-26bc4b49f6da/VC_561022993723_004-and-MO_315965276297_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204078== by 0x12C658C47: 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_315965276297_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204078== 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_315965276297_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204078== 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_315965276297_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204078== 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_315965276297_000-1669765225/staged_job_files/repository/md/EDIP_LAMMPS__MD_783584031339_000/libkim-api-model-driver.so) ==204078== 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) ==204078== 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) ==204078== 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) ==204078== 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) ==204078== 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) ==204078== by 0x12BDDD17B: pybind11::cpp_function::dispatcher(_object*, _object*, _object*) (pybind11.h:929) ==204078== ==204078== ==204078== HEAP SUMMARY: ==204078== in use at exit: 2,257,591 bytes in 1,700 blocks ==204078== total heap usage: 47,810 allocs, 46,110 frees, 127,626,544 bytes allocated ==204078== ==204078== LEAK SUMMARY: ==204078== definitely lost: 0 bytes in 0 blocks ==204078== indirectly lost: 0 bytes in 0 blocks ==204078== possibly lost: 180,827 bytes in 103 blocks ==204078== still reachable: 2,076,732 bytes in 1,596 blocks ==204078== of which reachable via heuristic: ==204078== stdstring : 38 bytes in 1 blocks ==204078== suppressed: 32 bytes in 1 blocks ==204078== Rerun with --leak-check=full to see details of leaked memory ==204078== ==204078== For lists of detected and suppressed errors, rerun with: -s ==204078== ERROR SUMMARY: 4 errors from 1 contexts (suppressed: 7784 from 554) ================================================================================ 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.