!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MendelevKramerHao_2012_Ni__MO_832600236922_005 Supported species : Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = 10.107695872666579 Forces: 1 -2.33387180e+01 -1.41580701e+01 -3.81049839e+01 2 -1.49271849e+01 2.08990230e+01 -4.43337001e+00 3 5.17634891e+01 -1.45940555e+01 1.27735353e+01 4 -1.69140960e+01 2.80481920e+01 8.64787763e+00 5 1.38631555e+01 -2.14839707e+01 3.93325122e-01 6 5.53573626e+00 9.51077147e+00 -1.50785830e+01 7 4.92487638e+00 -6.13254713e+01 -5.07702514e+01 8 -2.30930077e+01 -1.27530993e+01 -9.17351959e+00 9 -1.54621441e+00 -1.17006071e+01 -1.49071575e+01 10 -1.89298625e+01 1.46862690e+01 -3.04474199e+01 11 -1.29570074e+01 -1.99337639e+01 1.53522941e+00 12 -3.13977834e+00 1.33563606e+01 1.38099989e+01 13 -2.41574016e+01 -2.85437082e+01 -7.31320450e+01 14 6.58760689e+00 1.24975518e+01 -9.73557769e+00 15 5.95982588e+01 -3.38767563e+01 1.11778570e+01 16 7.27820747e+00 5.41783563e+01 3.55246917e+01 17 -1.59893620e+01 -5.29559220e+00 1.62694394e+01 18 2.46771464e+00 1.85016859e+01 -3.85785654e+01 19 -8.78749426e+00 -3.29721080e+01 1.34105095e+01 20 -1.47579141e+01 1.96711386e+00 1.23391785e+01 21 -2.09682880e+01 -9.84627402e+00 1.50084534e+01 22 2.68126303e+01 4.64353728e+01 4.32758795e+01 23 4.55942209e+00 -2.02487784e+00 8.17814774e+00 24 2.13281101e+01 1.35515036e+01 1.74551324e+01 25 -7.22302915e+00 1.72620812e-01 4.98732114e+00 26 -1.37230007e+01 2.10158956e+01 -2.29228176e+01 27 2.52417017e+01 -6.14931984e+01 2.32822449e+01 28 -5.01360472e+01 4.22108080e+01 -5.32767865e+00 29 -1.38164243e+01 -7.66311265e+00 1.57178853e+01 30 1.20812880e+01 3.04994940e+01 2.64737013e+01 31 2.55207270e+01 -1.04554100e+01 1.24924950e+01 32 1.68419063e+01 2.05890569e+01 1.98590666e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = 10.107695872666579 Forces: 1 -2.33387180e+01 -1.41580701e+01 -3.81049839e+01 2 -1.49271849e+01 2.08990230e+01 -4.43337001e+00 3 5.17634891e+01 -1.45940555e+01 1.27735353e+01 4 -1.69140960e+01 2.80481920e+01 8.64787763e+00 5 1.38631555e+01 -2.14839707e+01 3.93325122e-01 6 5.53573626e+00 9.51077147e+00 -1.50785830e+01 7 4.92487638e+00 -6.13254713e+01 -5.07702514e+01 8 -2.30930077e+01 -1.27530993e+01 -9.17351959e+00 9 -1.54621441e+00 -1.17006071e+01 -1.49071575e+01 10 -1.89298625e+01 1.46862690e+01 -3.04474199e+01 11 -1.29570074e+01 -1.99337639e+01 1.53522941e+00 12 -3.13977834e+00 1.33563606e+01 1.38099989e+01 13 -2.41574016e+01 -2.85437082e+01 -7.31320450e+01 14 6.58760689e+00 1.24975518e+01 -9.73557769e+00 15 5.95982588e+01 -3.38767563e+01 1.11778570e+01 16 7.27820747e+00 5.41783563e+01 3.55246917e+01 17 -1.59893620e+01 -5.29559220e+00 1.62694394e+01 18 2.46771464e+00 1.85016859e+01 -3.85785654e+01 19 -8.78749426e+00 -3.29721080e+01 1.34105095e+01 20 -1.47579141e+01 1.96711386e+00 1.23391785e+01 21 -2.09682880e+01 -9.84627402e+00 1.50084534e+01 22 2.68126303e+01 4.64353728e+01 4.32758795e+01 23 4.55942209e+00 -2.02487784e+00 8.17814774e+00 24 2.13281101e+01 1.35515036e+01 1.74551324e+01 25 -7.22302915e+00 1.72620812e-01 4.98732114e+00 26 -1.37230007e+01 2.10158956e+01 -2.29228176e+01 27 2.52417017e+01 -6.14931984e+01 2.32822449e+01 28 -5.01360472e+01 4.22108080e+01 -5.32767865e+00 29 -1.38164243e+01 -7.66311265e+00 1.57178853e+01 30 1.20812880e+01 3.04994940e+01 2.64737013e+01 31 2.55207270e+01 -1.04554100e+01 1.24924950e+01 32 1.68419063e+01 2.05890569e+01 1.98590666e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==50076== Memcheck, a memory error detector ==50076== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==50076== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==50076== Command: python runner2.py EAM_Dynamo_MendelevKramerHao_2012_Ni__MO_832600236922_005 ==50076== ==51177== Warning: invalid file descriptor 1048564 in syscall close() ==51177== Warning: invalid file descriptor 1048565 in syscall close() ==51177== Warning: invalid file descriptor 1048566 in syscall close() ==51177== Warning: invalid file descriptor 1048567 in syscall close() ==51177== Use --log-fd= to select an alternative log fd. ==51177== Warning: invalid file descriptor 1048568 in syscall close() ==51177== Warning: invalid file descriptor 1048569 in syscall close() ==51179== Warning: invalid file descriptor 1048564 in syscall close() ==51179== Warning: invalid file descriptor 1048565 in syscall close() ==51179== Warning: invalid file descriptor 1048566 in syscall close() ==51179== Warning: invalid file descriptor 1048567 in syscall close() ==51179== Use --log-fd= to select an alternative log fd. ==51179== Warning: invalid file descriptor 1048568 in syscall close() ==51179== Warning: invalid file descriptor 1048569 in syscall close() ==51184== Warning: invalid file descriptor 1048564 in syscall close() ==51184== Warning: invalid file descriptor 1048565 in syscall close() ==51184== Warning: invalid file descriptor 1048566 in syscall close() ==51184== Warning: invalid file descriptor 1048567 in syscall close() ==51184== Use --log-fd= to select an alternative log fd. ==51184== Warning: invalid file descriptor 1048568 in syscall close() ==51184== Warning: invalid file descriptor 1048569 in syscall close() ==51185== Warning: invalid file descriptor 1048564 in syscall close() ==51185== Warning: invalid file descriptor 1048565 in syscall close() ==51185== Warning: invalid file descriptor 1048566 in syscall close() ==51185== Warning: invalid file descriptor 1048567 in syscall close() ==51185== Use --log-fd= to select an alternative log fd. ==51185== Warning: invalid file descriptor 1048568 in syscall close() ==51185== Warning: invalid file descriptor 1048569 in syscall close() ==51186== Warning: invalid file descriptor 1048564 in syscall close() ==51186== Warning: invalid file descriptor 1048565 in syscall close() ==51186== Warning: invalid file descriptor 1048566 in syscall close() ==51186== Warning: invalid file descriptor 1048567 in syscall close() ==51186== Use --log-fd= to select an alternative log fd. ==51186== Warning: invalid file descriptor 1048568 in syscall close() ==51186== Warning: invalid file descriptor 1048569 in syscall close() ==51187== Warning: invalid file descriptor 1048564 in syscall close() ==51187== Warning: invalid file descriptor 1048565 in syscall close() ==51187== Warning: invalid file descriptor 1048566 in syscall close() ==51187== Warning: invalid file descriptor 1048567 in syscall close() ==51187== Use --log-fd= to select an alternative log fd. ==51187== Warning: invalid file descriptor 1048568 in syscall close() ==51187== Warning: invalid file descriptor 1048569 in syscall close() ==50076== ==50076== HEAP SUMMARY: ==50076== in use at exit: 1,718,292 bytes in 1,321 blocks ==50076== total heap usage: 31,120 allocs, 29,799 frees, 47,288,649 bytes allocated ==50076== ==50076== LEAK SUMMARY: ==50076== definitely lost: 0 bytes in 0 blocks ==50076== indirectly lost: 0 bytes in 0 blocks ==50076== possibly lost: 178,943 bytes in 97 blocks ==50076== still reachable: 1,539,349 bytes in 1,224 blocks ==50076== suppressed: 0 bytes in 0 blocks ==50076== Rerun with --leak-check=full to see details of leaked memory ==50076== ==50076== For counts of detected and suppressed errors, rerun with: -v ==50076== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16327 from 599) ================================================================================ 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.