!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EAM_Dynamo_NicholAckland_2016v2_Rb__MO_874930365376_000 Supported species : Rb random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Rb (Configuration in file "config-F-Rb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 432.9727906669036 Forces: 1 -9.11043361e+00 -3.88644935e+01 -2.95627532e+01 2 -1.00663594e+01 1.26395018e+01 -2.00496393e+01 3 1.27230983e+00 -2.48216617e+01 -6.31797612e+00 4 -1.82853827e+01 2.65417131e+01 2.31559646e+01 5 8.33628205e+00 -3.05135996e+01 -1.10533701e+01 6 1.42698287e+01 2.73541086e+00 -1.82806995e+01 7 1.64321992e+01 -6.80576987e+01 -5.97748642e+01 8 -5.91391367e+01 -5.09697875e+01 -2.30668581e+00 9 -1.52233055e+01 -2.50232425e+01 -4.77532642e+01 10 -6.95134810e+00 3.76682162e+01 -4.34920933e+01 11 -1.42616937e+01 -2.38522369e+01 9.11347595e+00 12 -2.93932601e+01 3.76138289e+01 2.51952832e+01 13 -1.17888587e+01 -1.70710252e+01 -8.19988372e+01 14 1.68039452e+01 1.68199364e+01 -9.86394178e+00 15 9.92786143e+01 2.94254501e+01 1.02827898e+01 16 2.01188865e+01 5.84594125e+01 2.80836014e+01 17 -4.33021402e+01 -3.28479040e+01 -2.94391708e+01 18 9.51030370e+00 2.05636949e+01 1.73198359e+00 19 2.30780327e+01 -2.69380104e+01 2.59160399e+01 20 -1.50874706e+01 2.73916921e+01 3.20182566e+01 21 -2.29137242e+01 -2.62668553e+01 1.32098879e+01 22 4.88301297e+01 4.56741466e+01 5.46285762e+01 23 1.51568705e+01 -8.40563702e+00 1.56535290e+01 24 2.92120912e-01 1.07438912e+01 1.64547887e+01 25 -3.06119385e+01 -6.58745716e+00 -1.05062701e+00 26 -1.35310338e+01 4.23954393e+01 -1.64865396e+01 27 3.29765036e+01 -7.08382777e+01 2.86698797e+01 28 -6.43822397e+01 5.69892783e+01 1.40473949e+01 29 -1.28196160e+01 -1.37292136e+01 1.90873471e+01 30 1.85672480e+01 2.34112189e+01 -1.32529725e+00 31 3.32570288e+01 -1.53716765e+01 2.76818345e+01 32 1.86876379e+01 3.10859460e+01 3.38251264e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Rb (Configuration in file "config-T-Rb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 432.9727906669036 Forces: 1 -9.11043361e+00 -3.88644935e+01 -2.95627532e+01 2 -1.00663594e+01 1.26395018e+01 -2.00496393e+01 3 1.27230983e+00 -2.48216617e+01 -6.31797612e+00 4 -1.82853827e+01 2.65417131e+01 2.31559646e+01 5 8.33628205e+00 -3.05135996e+01 -1.10533701e+01 6 1.42698287e+01 2.73541086e+00 -1.82806995e+01 7 1.64321992e+01 -6.80576987e+01 -5.97748642e+01 8 -5.91391367e+01 -5.09697875e+01 -2.30668581e+00 9 -1.52233055e+01 -2.50232425e+01 -4.77532642e+01 10 -6.95134810e+00 3.76682162e+01 -4.34920933e+01 11 -1.42616937e+01 -2.38522369e+01 9.11347595e+00 12 -2.93932601e+01 3.76138289e+01 2.51952832e+01 13 -1.17888587e+01 -1.70710252e+01 -8.19988372e+01 14 1.68039452e+01 1.68199364e+01 -9.86394178e+00 15 9.92786143e+01 2.94254501e+01 1.02827898e+01 16 2.01188865e+01 5.84594125e+01 2.80836014e+01 17 -4.33021402e+01 -3.28479040e+01 -2.94391708e+01 18 9.51030370e+00 2.05636949e+01 1.73198359e+00 19 2.30780327e+01 -2.69380104e+01 2.59160399e+01 20 -1.50874706e+01 2.73916921e+01 3.20182566e+01 21 -2.29137242e+01 -2.62668553e+01 1.32098879e+01 22 4.88301297e+01 4.56741466e+01 5.46285762e+01 23 1.51568705e+01 -8.40563702e+00 1.56535290e+01 24 2.92120912e-01 1.07438912e+01 1.64547887e+01 25 -3.06119385e+01 -6.58745716e+00 -1.05062701e+00 26 -1.35310338e+01 4.23954393e+01 -1.64865396e+01 27 3.29765036e+01 -7.08382777e+01 2.86698797e+01 28 -6.43822397e+01 5.69892783e+01 1.40473949e+01 29 -1.28196160e+01 -1.37292136e+01 1.90873471e+01 30 1.85672480e+01 2.34112189e+01 -1.32529725e+00 31 3.32570288e+01 -1.53716765e+01 2.76818345e+01 32 1.86876379e+01 3.10859460e+01 3.38251264e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==59343== Memcheck, a memory error detector ==59343== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==59343== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==59343== Command: python runner2.py EAM_Dynamo_NicholAckland_2016v2_Rb__MO_874930365376_000 ==59343== ==60808== Warning: invalid file descriptor 1048564 in syscall close() ==60808== Warning: invalid file descriptor 1048565 in syscall close() ==60808== Warning: invalid file descriptor 1048566 in syscall close() ==60808== Warning: invalid file descriptor 1048567 in syscall close() ==60808== Use --log-fd= to select an alternative log fd. ==60808== Warning: invalid file descriptor 1048568 in syscall close() ==60808== Warning: invalid file descriptor 1048569 in syscall close() ==60815== Warning: invalid file descriptor 1048564 in syscall close() ==60815== Warning: invalid file descriptor 1048565 in syscall close() ==60815== Warning: invalid file descriptor 1048566 in syscall close() ==60815== Warning: invalid file descriptor 1048567 in syscall close() ==60815== Use --log-fd= to select an alternative log fd. ==60815== Warning: invalid file descriptor 1048568 in syscall close() ==60815== Warning: invalid file descriptor 1048569 in syscall close() ==60959== Warning: invalid file descriptor 1048564 in syscall close() ==60959== Warning: invalid file descriptor 1048565 in syscall close() ==60959== Warning: invalid file descriptor 1048566 in syscall close() ==60959== Warning: invalid file descriptor 1048567 in syscall close() ==60959== Use --log-fd= to select an alternative log fd. ==60959== Warning: invalid file descriptor 1048568 in syscall close() ==60959== Warning: invalid file descriptor 1048569 in syscall close() ==60965== Warning: invalid file descriptor 1048564 in syscall close() ==60965== Warning: invalid file descriptor 1048565 in syscall close() ==60965== Warning: invalid file descriptor 1048566 in syscall close() ==60965== Warning: invalid file descriptor 1048567 in syscall close() ==60965== Use --log-fd= to select an alternative log fd. ==60965== Warning: invalid file descriptor 1048568 in syscall close() ==60965== Warning: invalid file descriptor 1048569 in syscall close() ==60968== Warning: invalid file descriptor 1048564 in syscall close() ==60968== Warning: invalid file descriptor 1048565 in syscall close() ==60968== Warning: invalid file descriptor 1048566 in syscall close() ==60968== Warning: invalid file descriptor 1048567 in syscall close() ==60968== Use --log-fd= to select an alternative log fd. ==60968== Warning: invalid file descriptor 1048568 in syscall close() ==60968== Warning: invalid file descriptor 1048569 in syscall close() ==60984== Warning: invalid file descriptor 1048564 in syscall close() ==60984== Warning: invalid file descriptor 1048565 in syscall close() ==60984== Warning: invalid file descriptor 1048566 in syscall close() ==60984== Warning: invalid file descriptor 1048567 in syscall close() ==60984== Use --log-fd= to select an alternative log fd. ==60984== Warning: invalid file descriptor 1048568 in syscall close() ==60984== Warning: invalid file descriptor 1048569 in syscall close() ==59343== ==59343== HEAP SUMMARY: ==59343== in use at exit: 1,718,292 bytes in 1,321 blocks ==59343== total heap usage: 31,120 allocs, 29,799 frees, 47,288,454 bytes allocated ==59343== ==59343== LEAK SUMMARY: ==59343== definitely lost: 0 bytes in 0 blocks ==59343== indirectly lost: 0 bytes in 0 blocks ==59343== possibly lost: 178,943 bytes in 97 blocks ==59343== still reachable: 1,539,349 bytes in 1,224 blocks ==59343== suppressed: 0 bytes in 0 blocks ==59343== Rerun with --leak-check=full to see details of leaked memory ==59343== ==59343== For counts of detected and suppressed errors, rerun with: -v ==59343== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16335 from 612) ================================================================================ 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.