!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Ackland_1987_Au__MO_754413982908_000 Supported species : Au random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Au (Configuration in file "config-F-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 219.89835428672725 Forces: 1 -1.07573253e+01 -1.77480638e+01 -1.71601652e+01 2 -5.59639623e+00 6.57552384e+00 -2.07934994e+01 3 8.02326047e+00 -2.16385151e+01 -5.19758619e+00 4 -1.82572085e+01 9.26499785e+00 6.19401699e+00 5 1.24294404e+00 -2.56816488e+01 -1.35802043e+01 6 1.67784519e+01 2.35358603e+00 -1.95551195e+01 7 1.75484565e+01 -2.86843739e+01 -1.22060495e+01 8 -1.15308614e+01 -1.18268873e+01 3.12296957e+00 9 -1.32519699e+01 -1.38212800e+01 -2.71374578e+01 10 1.06571375e+01 2.67859208e+01 -2.23222017e+01 11 -4.61907217e+00 -1.36231164e+01 -4.55517832e+00 12 -2.72056246e+01 2.26131898e+01 1.10755593e+01 13 -6.71457612e+00 -5.19308078e+00 -4.53946790e+01 14 1.55935697e+01 1.78539127e+01 -1.47581808e+01 15 4.37639920e+01 -6.98670898e+00 -1.30612965e+00 16 -1.86393669e+00 4.26006004e+01 2.82902585e+00 17 -2.60456668e+01 -1.30042290e+01 1.97233787e+00 18 5.68774780e+00 1.00396911e+01 4.21691423e+00 19 1.57216177e+00 -2.11185059e+01 1.61140330e+01 20 -1.37671427e+01 7.26794476e+00 1.31120242e+01 21 -1.03385485e+01 -2.46744767e+01 2.48352914e+00 22 2.92402724e+01 1.44876553e+01 1.06067582e+01 23 1.73399160e+01 -9.84475067e+00 1.54245830e+01 24 -6.05238780e+00 1.11004014e+01 1.82468133e+01 25 -3.19631350e+01 -5.71081716e+00 5.84882748e+00 26 -3.44161765e+00 3.38297179e+01 -6.27392941e+00 27 3.80077163e+00 -2.62293162e+01 2.27111654e+01 28 -2.51651308e+01 1.96953005e+01 1.25543908e+01 29 -8.99069212e+00 -1.62409737e+01 1.14456576e+01 30 2.30191851e+01 2.66439037e+01 1.26892555e+00 31 2.29718907e+01 -9.80181977e+00 2.58045203e+01 32 8.32153481e+00 2.07162181e+01 2.52083289e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Au (Configuration in file "config-T-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 219.89835428672725 Forces: 1 -1.07573253e+01 -1.77480638e+01 -1.71601652e+01 2 -5.59639623e+00 6.57552384e+00 -2.07934994e+01 3 8.02326047e+00 -2.16385151e+01 -5.19758619e+00 4 -1.82572085e+01 9.26499785e+00 6.19401699e+00 5 1.24294404e+00 -2.56816488e+01 -1.35802043e+01 6 1.67784519e+01 2.35358603e+00 -1.95551195e+01 7 1.75484565e+01 -2.86843739e+01 -1.22060495e+01 8 -1.15308614e+01 -1.18268873e+01 3.12296957e+00 9 -1.32519699e+01 -1.38212800e+01 -2.71374578e+01 10 1.06571375e+01 2.67859208e+01 -2.23222017e+01 11 -4.61907217e+00 -1.36231164e+01 -4.55517832e+00 12 -2.72056246e+01 2.26131898e+01 1.10755593e+01 13 -6.71457612e+00 -5.19308078e+00 -4.53946790e+01 14 1.55935697e+01 1.78539127e+01 -1.47581808e+01 15 4.37639920e+01 -6.98670898e+00 -1.30612965e+00 16 -1.86393669e+00 4.26006004e+01 2.82902585e+00 17 -2.60456668e+01 -1.30042290e+01 1.97233787e+00 18 5.68774780e+00 1.00396911e+01 4.21691423e+00 19 1.57216177e+00 -2.11185059e+01 1.61140330e+01 20 -1.37671427e+01 7.26794476e+00 1.31120242e+01 21 -1.03385485e+01 -2.46744767e+01 2.48352914e+00 22 2.92402724e+01 1.44876553e+01 1.06067582e+01 23 1.73399160e+01 -9.84475067e+00 1.54245830e+01 24 -6.05238780e+00 1.11004014e+01 1.82468133e+01 25 -3.19631350e+01 -5.71081716e+00 5.84882748e+00 26 -3.44161765e+00 3.38297179e+01 -6.27392941e+00 27 3.80077163e+00 -2.62293162e+01 2.27111654e+01 28 -2.51651308e+01 1.96953005e+01 1.25543908e+01 29 -8.99069212e+00 -1.62409737e+01 1.14456576e+01 30 2.30191851e+01 2.66439037e+01 1.26892555e+00 31 2.29718907e+01 -9.80181977e+00 2.58045203e+01 32 8.32153481e+00 2.07162181e+01 2.52083289e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==10553== Memcheck, a memory error detector ==10553== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==10553== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==10553== Command: python runner2.py EAM_Dynamo_Ackland_1987_Au__MO_754413982908_000 ==10553== ==12064== Warning: invalid file descriptor 1048564 in syscall close() ==12064== Warning: invalid file descriptor 1048565 in syscall close() ==12064== Warning: invalid file descriptor 1048566 in syscall close() ==12064== Warning: invalid file descriptor 1048567 in syscall close() ==12064== Use --log-fd= to select an alternative log fd. ==12064== Warning: invalid file descriptor 1048568 in syscall close() ==12064== Warning: invalid file descriptor 1048569 in syscall close() ==12069== Warning: invalid file descriptor 1048564 in syscall close() ==12069== Warning: invalid file descriptor 1048565 in syscall close() ==12069== Warning: invalid file descriptor 1048566 in syscall close() ==12069== Warning: invalid file descriptor 1048567 in syscall close() ==12069== Use --log-fd= to select an alternative log fd. ==12069== Warning: invalid file descriptor 1048568 in syscall close() ==12069== Warning: invalid file descriptor 1048569 in syscall close() ==12245== Warning: invalid file descriptor 1048564 in syscall close() ==12245== Warning: invalid file descriptor 1048565 in syscall close() ==12245== Warning: invalid file descriptor 1048566 in syscall close() ==12245== Warning: invalid file descriptor 1048567 in syscall close() ==12245== Use --log-fd= to select an alternative log fd. ==12245== Warning: invalid file descriptor 1048568 in syscall close() ==12245== Warning: invalid file descriptor 1048569 in syscall close() ==12248== Warning: invalid file descriptor 1048564 in syscall close() ==12248== Warning: invalid file descriptor 1048565 in syscall close() ==12248== Warning: invalid file descriptor 1048566 in syscall close() ==12248== Warning: invalid file descriptor 1048567 in syscall close() ==12248== Use --log-fd= to select an alternative log fd. ==12248== Warning: invalid file descriptor 1048568 in syscall close() ==12248== Warning: invalid file descriptor 1048569 in syscall close() ==12253== Warning: invalid file descriptor 1048564 in syscall close() ==12253== Warning: invalid file descriptor 1048565 in syscall close() ==12253== Warning: invalid file descriptor 1048566 in syscall close() ==12253== Warning: invalid file descriptor 1048567 in syscall close() ==12253== Use --log-fd= to select an alternative log fd. ==12253== Warning: invalid file descriptor 1048568 in syscall close() ==12253== Warning: invalid file descriptor 1048569 in syscall close() ==12261== Warning: invalid file descriptor 1048564 in syscall close() ==12261== Warning: invalid file descriptor 1048565 in syscall close() ==12261== Warning: invalid file descriptor 1048566 in syscall close() ==12261== Warning: invalid file descriptor 1048567 in syscall close() ==12261== Use --log-fd= to select an alternative log fd. ==12261== Warning: invalid file descriptor 1048568 in syscall close() ==12261== Warning: invalid file descriptor 1048569 in syscall close() ==10553== ==10553== HEAP SUMMARY: ==10553== in use at exit: 1,718,292 bytes in 1,321 blocks ==10553== total heap usage: 31,120 allocs, 29,799 frees, 47,287,140 bytes allocated ==10553== ==10553== LEAK SUMMARY: ==10553== definitely lost: 0 bytes in 0 blocks ==10553== indirectly lost: 0 bytes in 0 blocks ==10553== possibly lost: 178,943 bytes in 97 blocks ==10553== still reachable: 1,539,349 bytes in 1,224 blocks ==10553== suppressed: 0 bytes in 0 blocks ==10553== Rerun with --leak-check=full to see details of leaked memory ==10553== ==10553== For counts of detected and suppressed errors, rerun with: -v ==10553== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11236 from 585) ================================================================================ 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.