Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:26:57) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Al__MO_623376124862_001 Supported species : Al random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = -4.2450123135406574 Forces: 1 -2.59937807e+00 -5.28562918e+00 -5.63297820e+00 2 -2.18445696e+00 5.43112450e+00 -3.00182366e+00 3 3.35722728e+00 -4.29552704e+00 -1.51298600e+00 4 -3.04134362e+00 3.75619958e+00 3.10128635e+00 5 1.69391662e+00 -7.20269025e+00 -1.51423055e+00 6 3.15164705e+00 2.32310105e+00 -3.48511706e+00 7 3.46481756e+00 -1.23522814e+01 -1.10531332e+01 8 -7.49014028e+00 -3.03324572e+00 -1.17362995e+00 9 -5.76240215e+00 -7.53012247e+00 -8.28216186e+00 10 6.34474706e+00 9.08232232e+00 -6.52415473e+00 11 3.66312599e+00 -6.83764996e+00 -2.27951536e-01 12 -7.82863217e+00 8.81214303e+00 2.81397516e+00 13 -6.36051584e+00 -6.01427239e+00 -1.53767769e+01 14 4.12862772e+00 5.39503678e+00 -4.12449741e+00 15 1.29748834e+01 -6.95240355e+00 2.56891557e+00 16 -9.39438984e-01 1.15597629e+01 3.14090527e+00 17 -8.26443445e+00 -4.30619675e+00 -3.06018550e+00 18 2.60896392e+00 7.21908991e+00 -2.24396783e+00 19 3.89690083e+00 -7.52278641e+00 5.35614405e+00 20 -3.85323525e+00 5.43220909e+00 4.70221289e+00 21 -6.63673214e+00 -5.20993931e+00 2.60127685e+00 22 9.06311654e+00 1.17860775e+01 8.25225149e+00 23 2.97143094e+00 -1.38990476e+00 4.80200623e+00 24 1.08734061e+00 2.07261349e+00 2.89493480e+00 25 -6.18983666e+00 -4.25856818e+00 8.27468349e+00 26 -2.42762823e+00 8.05348804e+00 -5.40618003e+00 27 5.70009094e+00 -1.60327069e+01 3.91766701e+00 28 -1.31753544e+01 1.07487051e+01 1.95511485e+00 29 -4.14457728e+00 -4.82284986e+00 2.36196096e+00 30 4.78127341e+00 8.02284891e+00 4.55859553e+00 31 8.00105110e+00 -3.87341520e+00 4.33462604e+00 32 4.00894547e+00 7.22546723e+00 6.98321787e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = -4.2450123135406574 Forces: 1 -2.59937807e+00 -5.28562918e+00 -5.63297820e+00 2 -2.18445696e+00 5.43112450e+00 -3.00182366e+00 3 3.35722728e+00 -4.29552704e+00 -1.51298600e+00 4 -3.04134362e+00 3.75619958e+00 3.10128635e+00 5 1.69391662e+00 -7.20269025e+00 -1.51423055e+00 6 3.15164705e+00 2.32310105e+00 -3.48511706e+00 7 3.46481756e+00 -1.23522814e+01 -1.10531332e+01 8 -7.49014028e+00 -3.03324572e+00 -1.17362995e+00 9 -5.76240215e+00 -7.53012247e+00 -8.28216186e+00 10 6.34474706e+00 9.08232232e+00 -6.52415473e+00 11 3.66312599e+00 -6.83764996e+00 -2.27951536e-01 12 -7.82863217e+00 8.81214303e+00 2.81397516e+00 13 -6.36051584e+00 -6.01427239e+00 -1.53767769e+01 14 4.12862772e+00 5.39503678e+00 -4.12449741e+00 15 1.29748834e+01 -6.95240355e+00 2.56891557e+00 16 -9.39438984e-01 1.15597629e+01 3.14090527e+00 17 -8.26443445e+00 -4.30619675e+00 -3.06018550e+00 18 2.60896392e+00 7.21908991e+00 -2.24396783e+00 19 3.89690083e+00 -7.52278641e+00 5.35614405e+00 20 -3.85323525e+00 5.43220909e+00 4.70221289e+00 21 -6.63673214e+00 -5.20993931e+00 2.60127685e+00 22 9.06311654e+00 1.17860775e+01 8.25225149e+00 23 2.97143094e+00 -1.38990476e+00 4.80200623e+00 24 1.08734061e+00 2.07261349e+00 2.89493480e+00 25 -6.18983666e+00 -4.25856818e+00 8.27468349e+00 26 -2.42762823e+00 8.05348804e+00 -5.40618003e+00 27 5.70009094e+00 -1.60327069e+01 3.91766701e+00 28 -1.31753544e+01 1.07487051e+01 1.95511485e+00 29 -4.14457728e+00 -4.82284986e+00 2.36196096e+00 30 4.78127341e+00 8.02284891e+00 4.55859553e+00 31 8.00105110e+00 -3.87341520e+00 4.33462604e+00 32 4.00894547e+00 7.22546723e+00 6.98321787e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==20278== Memcheck, a memory error detector ==20278== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==20278== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==20278== Command: python runner2.py EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Al__MO_623376124862_001 ==20278== ==22106== Warning: invalid file descriptor 1048564 in syscall close() ==22106== Warning: invalid file descriptor 1048565 in syscall close() ==22106== Warning: invalid file descriptor 1048566 in syscall close() ==22106== Warning: invalid file descriptor 1048567 in syscall close() ==22106== Use --log-fd= to select an alternative log fd. ==22106== Warning: invalid file descriptor 1048568 in syscall close() ==22106== Warning: invalid file descriptor 1048569 in syscall close() ==22109== Warning: invalid file descriptor 1048564 in syscall close() ==22109== Warning: invalid file descriptor 1048565 in syscall close() ==22109== Warning: invalid file descriptor 1048566 in syscall close() ==22109== Warning: invalid file descriptor 1048567 in syscall close() ==22109== Use --log-fd= to select an alternative log fd. ==22109== Warning: invalid file descriptor 1048568 in syscall close() ==22109== Warning: invalid file descriptor 1048569 in syscall close() ==22140== Warning: invalid file descriptor 1048564 in syscall close() ==22140== Warning: invalid file descriptor 1048565 in syscall close() ==22140== Warning: invalid file descriptor 1048566 in syscall close() ==22140== Warning: invalid file descriptor 1048567 in syscall close() ==22140== Use --log-fd= to select an alternative log fd. ==22140== Warning: invalid file descriptor 1048568 in syscall close() ==22140== Warning: invalid file descriptor 1048569 in syscall close() ==22141== Warning: invalid file descriptor 1048564 in syscall close() ==22141== Warning: invalid file descriptor 1048565 in syscall close() ==22141== Warning: invalid file descriptor 1048566 in syscall close() ==22141== Warning: invalid file descriptor 1048567 in syscall close() ==22141== Use --log-fd= to select an alternative log fd. ==22141== Warning: invalid file descriptor 1048568 in syscall close() ==22141== Warning: invalid file descriptor 1048569 in syscall close() ==22143== Warning: invalid file descriptor 1048564 in syscall close() ==22143== Warning: invalid file descriptor 1048565 in syscall close() ==22143== Warning: invalid file descriptor 1048566 in syscall close() ==22143== Warning: invalid file descriptor 1048567 in syscall close() ==22143== Use --log-fd= to select an alternative log fd. ==22143== Warning: invalid file descriptor 1048568 in syscall close() ==22143== Warning: invalid file descriptor 1048569 in syscall close() ==22144== Warning: invalid file descriptor 1048564 in syscall close() ==22144== Warning: invalid file descriptor 1048565 in syscall close() ==22144== Warning: invalid file descriptor 1048566 in syscall close() ==22144== Warning: invalid file descriptor 1048567 in syscall close() ==22144== Use --log-fd= to select an alternative log fd. ==22144== Warning: invalid file descriptor 1048568 in syscall close() ==22144== Warning: invalid file descriptor 1048569 in syscall close() ==20278== ==20278== HEAP SUMMARY: ==20278== in use at exit: 1,718,292 bytes in 1,321 blocks ==20278== total heap usage: 30,944 allocs, 29,623 frees, 39,187,728 bytes allocated ==20278== ==20278== LEAK SUMMARY: ==20278== definitely lost: 0 bytes in 0 blocks ==20278== indirectly lost: 0 bytes in 0 blocks ==20278== possibly lost: 178,943 bytes in 97 blocks ==20278== still reachable: 1,539,349 bytes in 1,224 blocks ==20278== suppressed: 0 bytes in 0 blocks ==20278== Rerun with --leak-check=full to see details of leaked memory ==20278== ==20278== For counts of detected and suppressed errors, rerun with: -v ==20278== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16344 from 613) ================================================================================ 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 23:27:19) ===