Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:22:25) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Zhakhovsky_2009_Al__MO_519613893196_000 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 = 57.5719215854353 Forces: 1 -4.28387653e+00 -7.77792863e+00 -8.31603626e+00 2 -3.54319971e+00 4.92805859e+00 -8.02998680e+00 3 5.23227090e+00 -1.41212785e+01 -5.72444393e+00 4 -1.07235526e+01 5.10482101e+00 1.88396367e-01 5 -1.16053232e+00 -1.31712384e+01 -4.34135274e+00 6 8.14518996e+00 4.94404541e+00 -8.78653196e+00 7 8.23201189e+00 -2.20632076e+01 -1.45855690e+01 8 -1.05605668e+01 -8.82251796e+00 -1.66425604e+00 9 -8.52560271e+00 -6.17938538e+00 -1.43903631e+01 10 -3.20287807e+00 1.59183757e+01 -1.63063696e+01 11 -3.47429194e+00 -1.03386247e+01 2.01213295e+00 12 -1.01845262e+01 1.36695374e+01 1.86154312e+00 13 -3.72464184e+00 -1.06572864e+01 -3.19674470e+01 14 7.71132736e+00 9.44566978e+00 -6.36044465e+00 15 2.97602956e+01 -3.94350048e+00 5.86573649e+00 16 4.06356804e+00 2.54701685e+01 9.59171512e+00 17 -1.55619046e+01 -9.92772945e+00 -2.29025391e+00 18 8.24634623e+00 1.04893503e+01 7.01050268e+00 19 3.70122063e+00 -1.18833240e+01 6.72168849e+00 20 -6.19269358e+00 7.14906806e+00 7.59051684e+00 21 -9.38120091e+00 -1.06722759e+01 6.17793587e+00 22 1.73837869e+01 1.66581517e+01 1.13021445e+01 23 4.58679609e+00 -2.64040944e+00 9.50512398e+00 24 2.34395822e+00 5.07955552e+00 5.42169638e+00 25 -1.22800992e+01 -4.42521904e+00 7.38464042e+00 26 -4.82579682e+00 1.76727063e+01 -6.84885294e+00 27 6.50144329e+00 -2.33413641e+01 1.06452375e+01 28 -2.00536629e+01 1.64634617e+01 5.01322171e+00 29 -5.93330061e+00 -9.60120726e+00 7.62647640e+00 30 8.68932457e+00 1.30527112e+01 -1.00088330e+00 31 1.23543975e+01 -9.18574281e+00 1.25158151e+01 32 6.66039016e+00 1.27065589e+01 1.41782673e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 57.5719215854353 Forces: 1 -4.28387653e+00 -7.77792863e+00 -8.31603626e+00 2 -3.54319971e+00 4.92805859e+00 -8.02998680e+00 3 5.23227090e+00 -1.41212785e+01 -5.72444393e+00 4 -1.07235526e+01 5.10482101e+00 1.88396367e-01 5 -1.16053232e+00 -1.31712384e+01 -4.34135274e+00 6 8.14518996e+00 4.94404541e+00 -8.78653196e+00 7 8.23201189e+00 -2.20632076e+01 -1.45855690e+01 8 -1.05605668e+01 -8.82251796e+00 -1.66425604e+00 9 -8.52560271e+00 -6.17938538e+00 -1.43903631e+01 10 -3.20287807e+00 1.59183757e+01 -1.63063696e+01 11 -3.47429194e+00 -1.03386247e+01 2.01213295e+00 12 -1.01845262e+01 1.36695374e+01 1.86154312e+00 13 -3.72464184e+00 -1.06572864e+01 -3.19674470e+01 14 7.71132736e+00 9.44566978e+00 -6.36044465e+00 15 2.97602956e+01 -3.94350048e+00 5.86573649e+00 16 4.06356804e+00 2.54701685e+01 9.59171512e+00 17 -1.55619046e+01 -9.92772945e+00 -2.29025391e+00 18 8.24634623e+00 1.04893503e+01 7.01050268e+00 19 3.70122063e+00 -1.18833240e+01 6.72168849e+00 20 -6.19269358e+00 7.14906806e+00 7.59051684e+00 21 -9.38120091e+00 -1.06722759e+01 6.17793587e+00 22 1.73837869e+01 1.66581517e+01 1.13021445e+01 23 4.58679609e+00 -2.64040944e+00 9.50512398e+00 24 2.34395822e+00 5.07955552e+00 5.42169638e+00 25 -1.22800992e+01 -4.42521904e+00 7.38464042e+00 26 -4.82579682e+00 1.76727063e+01 -6.84885294e+00 27 6.50144329e+00 -2.33413641e+01 1.06452375e+01 28 -2.00536629e+01 1.64634617e+01 5.01322171e+00 29 -5.93330061e+00 -9.60120726e+00 7.62647640e+00 30 8.68932457e+00 1.30527112e+01 -1.00088330e+00 31 1.23543975e+01 -9.18574281e+00 1.25158151e+01 32 6.66039016e+00 1.27065589e+01 1.41782673e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==75107== Memcheck, a memory error detector ==75107== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==75107== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==75107== Command: python runner2.py EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_000 ==75107== ==76227== Warning: invalid file descriptor 1048564 in syscall close() ==76227== Warning: invalid file descriptor 1048565 in syscall close() ==76227== Warning: invalid file descriptor 1048566 in syscall close() ==76227== Warning: invalid file descriptor 1048567 in syscall close() ==76227== Use --log-fd= to select an alternative log fd. ==76227== Warning: invalid file descriptor 1048568 in syscall close() ==76227== Warning: invalid file descriptor 1048569 in syscall close() ==76228== Warning: invalid file descriptor 1048564 in syscall close() ==76228== Warning: invalid file descriptor 1048565 in syscall close() ==76228== Warning: invalid file descriptor 1048566 in syscall close() ==76228== Warning: invalid file descriptor 1048567 in syscall close() ==76228== Use --log-fd= to select an alternative log fd. ==76228== Warning: invalid file descriptor 1048568 in syscall close() ==76228== Warning: invalid file descriptor 1048569 in syscall close() ==76335== Warning: invalid file descriptor 1048564 in syscall close() ==76335== Warning: invalid file descriptor 1048565 in syscall close() ==76335== Warning: invalid file descriptor 1048566 in syscall close() ==76335== Warning: invalid file descriptor 1048567 in syscall close() ==76335== Use --log-fd= to select an alternative log fd. ==76335== Warning: invalid file descriptor 1048568 in syscall close() ==76335== Warning: invalid file descriptor 1048569 in syscall close() ==76341== Warning: invalid file descriptor 1048564 in syscall close() ==76341== Warning: invalid file descriptor 1048565 in syscall close() ==76341== Warning: invalid file descriptor 1048566 in syscall close() ==76341== Warning: invalid file descriptor 1048567 in syscall close() ==76341== Use --log-fd= to select an alternative log fd. ==76341== Warning: invalid file descriptor 1048568 in syscall close() ==76341== Warning: invalid file descriptor 1048569 in syscall close() ==76347== Warning: invalid file descriptor 1048564 in syscall close() ==76347== Warning: invalid file descriptor 1048565 in syscall close() ==76347== Warning: invalid file descriptor 1048566 in syscall close() ==76347== Warning: invalid file descriptor 1048567 in syscall close() ==76347== Use --log-fd= to select an alternative log fd. ==76347== Warning: invalid file descriptor 1048568 in syscall close() ==76347== Warning: invalid file descriptor 1048569 in syscall close() ==76353== Warning: invalid file descriptor 1048564 in syscall close() ==76353== Warning: invalid file descriptor 1048565 in syscall close() ==76353== Warning: invalid file descriptor 1048566 in syscall close() ==76353== Warning: invalid file descriptor 1048567 in syscall close() ==76353== Use --log-fd= to select an alternative log fd. ==76353== Warning: invalid file descriptor 1048568 in syscall close() ==76353== Warning: invalid file descriptor 1048569 in syscall close() ==75107== ==75107== HEAP SUMMARY: ==75107== in use at exit: 1,718,292 bytes in 1,321 blocks ==75107== total heap usage: 31,120 allocs, 29,799 frees, 45,726,714 bytes allocated ==75107== ==75107== LEAK SUMMARY: ==75107== definitely lost: 0 bytes in 0 blocks ==75107== indirectly lost: 0 bytes in 0 blocks ==75107== possibly lost: 178,943 bytes in 97 blocks ==75107== still reachable: 1,539,349 bytes in 1,224 blocks ==75107== suppressed: 0 bytes in 0 blocks ==75107== Rerun with --leak-check=full to see details of leaked memory ==75107== ==75107== For counts of detected and suppressed errors, rerun with: -v ==75107== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11243 from 587) ================================================================================ 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 23:22:49) ===