Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:27:36) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 ----------------------------------------------------------------------------------------------------- Results for KIM Model : LJ_Shifted_Bernardes_1958HighCutoff_Xe__MO_796748253903_003 Supported species : Xe random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Xe (Configuration in file "config-F-Xe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 84329.85386640938 Forces: 1 -8.65010024e+03 -2.48969600e+04 -3.35475393e+04 2 -6.51660370e+01 4.48640273e+03 -4.31048601e+03 3 1.50055977e+04 -1.33428708e+04 5.04957194e+03 4 -8.06263366e+03 3.58494117e+04 2.59949173e+04 5 1.70723472e+02 -5.03429349e+03 -3.26032603e+03 6 1.37146511e+03 8.49481808e+02 -2.50245410e+03 7 -3.74172868e+03 -3.28358790e+04 -3.37401899e+04 8 -1.13543212e+04 -1.18068402e+04 2.60483979e+03 9 -3.81068390e+02 -1.61570540e+03 -2.20749151e+03 10 -7.09672247e+03 3.47845860e+03 -8.79166521e+03 11 -1.01317788e+04 -1.08881103e+04 -2.75264146e+02 12 -2.82856947e+03 7.89926254e+03 -3.78417319e+03 13 -1.74265682e+04 -7.93558989e+03 -3.43041702e+04 14 4.69316495e+03 5.02264499e+03 -2.01313268e+03 15 3.25577001e+04 6.19123902e+03 2.01625863e+04 16 1.01075843e+04 2.19070705e+04 1.41399069e+04 17 -6.54433528e+03 -2.87947498e+03 3.09795135e+03 18 -2.04713192e+01 1.17178445e+05 -1.10618460e+05 19 3.71329882e+03 -1.17146056e+05 1.11221111e+05 20 -2.83114664e+03 1.62956381e+03 1.98276299e+03 21 -9.32647312e+03 -6.12777584e+03 -5.32009122e+02 22 1.75328301e+04 3.37010981e+04 2.60296076e+04 23 1.47971723e+04 -7.55816462e+03 1.08156432e+04 24 -9.93756152e+03 7.46618746e+03 3.66872751e+03 25 -4.81706933e+03 -8.02571038e+03 7.14319748e+03 26 3.28689519e+02 8.47951977e+03 -5.45391470e+03 27 3.02833928e+04 -3.92149609e+04 7.07568697e+03 28 -3.85078113e+04 3.29779674e+04 9.33249360e+01 29 -1.52355180e+04 -1.51510938e+04 -2.12270666e+04 30 7.41856471e+03 9.07045742e+03 -2.70431964e+03 31 1.77540424e+04 -6.75779071e+03 1.41020409e+04 32 1.22481735e+03 1.50300655e+04 1.60907864e+04 MONOATOMIC STRUCTURE (pbc=True)-- Species = Xe (Configuration in file "config-T-Xe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 84329.85386640938 Forces: 1 -8.65010024e+03 -2.48969600e+04 -3.35475393e+04 2 -6.51660370e+01 4.48640273e+03 -4.31048601e+03 3 1.50055977e+04 -1.33428708e+04 5.04957194e+03 4 -8.06263366e+03 3.58494117e+04 2.59949173e+04 5 1.70723472e+02 -5.03429349e+03 -3.26032603e+03 6 1.37146511e+03 8.49481808e+02 -2.50245410e+03 7 -3.74172868e+03 -3.28358790e+04 -3.37401899e+04 8 -1.13543212e+04 -1.18068402e+04 2.60483979e+03 9 -3.81068390e+02 -1.61570540e+03 -2.20749151e+03 10 -7.09672247e+03 3.47845860e+03 -8.79166521e+03 11 -1.01317788e+04 -1.08881103e+04 -2.75264146e+02 12 -2.82856947e+03 7.89926254e+03 -3.78417319e+03 13 -1.74265682e+04 -7.93558989e+03 -3.43041702e+04 14 4.69316495e+03 5.02264499e+03 -2.01313268e+03 15 3.25577001e+04 6.19123902e+03 2.01625863e+04 16 1.01075843e+04 2.19070705e+04 1.41399069e+04 17 -6.54433528e+03 -2.87947498e+03 3.09795135e+03 18 -2.04713192e+01 1.17178445e+05 -1.10618460e+05 19 3.71329882e+03 -1.17146056e+05 1.11221111e+05 20 -2.83114664e+03 1.62956381e+03 1.98276299e+03 21 -9.32647312e+03 -6.12777584e+03 -5.32009122e+02 22 1.75328301e+04 3.37010981e+04 2.60296076e+04 23 1.47971723e+04 -7.55816462e+03 1.08156432e+04 24 -9.93756152e+03 7.46618746e+03 3.66872751e+03 25 -4.81706933e+03 -8.02571038e+03 7.14319748e+03 26 3.28689519e+02 8.47951977e+03 -5.45391470e+03 27 3.02833928e+04 -3.92149609e+04 7.07568697e+03 28 -3.85078113e+04 3.29779674e+04 9.33249360e+01 29 -1.52355180e+04 -1.51510938e+04 -2.12270666e+04 30 7.41856471e+03 9.07045742e+03 -2.70431964e+03 31 1.77540424e+04 -6.75779071e+03 1.41020409e+04 32 1.22481735e+03 1.50300655e+04 1.60907864e+04 ================================================================================ VALGRIND OUTPUT ================================================================================ ==28697== Memcheck, a memory error detector ==28697== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==28697== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==28697== Command: python runner2.py LJ_Shifted_Bernardes_1958HighCutoff_Xe__MO_796748253903_003 ==28697== ==31096== Warning: invalid file descriptor 1048564 in syscall close() ==31096== Warning: invalid file descriptor 1048565 in syscall close() ==31096== Warning: invalid file descriptor 1048566 in syscall close() ==31096== Warning: invalid file descriptor 1048567 in syscall close() ==31096== Use --log-fd= to select an alternative log fd. ==31096== Warning: invalid file descriptor 1048568 in syscall close() ==31096== Warning: invalid file descriptor 1048569 in syscall close() ==31100== Warning: invalid file descriptor 1048564 in syscall close() ==31100== Warning: invalid file descriptor 1048565 in syscall close() ==31100== Warning: invalid file descriptor 1048566 in syscall close() ==31100== Warning: invalid file descriptor 1048567 in syscall close() ==31100== Use --log-fd= to select an alternative log fd. ==31100== Warning: invalid file descriptor 1048568 in syscall close() ==31100== Warning: invalid file descriptor 1048569 in syscall close() ==31178== Warning: invalid file descriptor 1048564 in syscall close() ==31178== Warning: invalid file descriptor 1048565 in syscall close() ==31178== Warning: invalid file descriptor 1048566 in syscall close() ==31178== Warning: invalid file descriptor 1048567 in syscall close() ==31178== Use --log-fd= to select an alternative log fd. ==31178== Warning: invalid file descriptor 1048568 in syscall close() ==31178== Warning: invalid file descriptor 1048569 in syscall close() ==31186== Warning: invalid file descriptor 1048564 in syscall close() ==31186== Warning: invalid file descriptor 1048565 in syscall close() ==31186== Warning: invalid file descriptor 1048566 in syscall close() ==31186== Warning: invalid file descriptor 1048567 in syscall close() ==31186== Use --log-fd= to select an alternative log fd. ==31186== Warning: invalid file descriptor 1048568 in syscall close() ==31186== Warning: invalid file descriptor 1048569 in syscall close() ==31193== Warning: invalid file descriptor 1048564 in syscall close() ==31193== Warning: invalid file descriptor 1048565 in syscall close() ==31193== Warning: invalid file descriptor 1048566 in syscall close() ==31193== Warning: invalid file descriptor 1048567 in syscall close() ==31193== Use --log-fd= to select an alternative log fd. ==31193== Warning: invalid file descriptor 1048568 in syscall close() ==31193== Warning: invalid file descriptor 1048569 in syscall close() ==31194== Warning: invalid file descriptor 1048564 in syscall close() ==31194== Warning: invalid file descriptor 1048565 in syscall close() ==31194== Warning: invalid file descriptor 1048566 in syscall close() ==31194== Warning: invalid file descriptor 1048567 in syscall close() ==31194== Use --log-fd= to select an alternative log fd. ==31194== Warning: invalid file descriptor 1048568 in syscall close() ==31194== Warning: invalid file descriptor 1048569 in syscall close() ==28697== ==28697== HEAP SUMMARY: ==28697== in use at exit: 1,718,292 bytes in 1,321 blocks ==28697== total heap usage: 30,945 allocs, 29,624 frees, 38,087,219 bytes allocated ==28697== ==28697== LEAK SUMMARY: ==28697== definitely lost: 0 bytes in 0 blocks ==28697== indirectly lost: 0 bytes in 0 blocks ==28697== possibly lost: 178,943 bytes in 97 blocks ==28697== still reachable: 1,539,349 bytes in 1,224 blocks ==28697== suppressed: 0 bytes in 0 blocks ==28697== Rerun with --leak-check=full to see details of leaked memory ==28697== ==28697== For counts of detected and suppressed errors, rerun with: -v ==28697== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16348 from 602) ================================================================================ 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 (2019-08-08 23:27:57) ===