Enter a model name: === Verification check vc-memory-leak start (2019-08-09 02:14:40) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Sim_LAMMPS_MEAM_EtesamiAsadi_2018_Fe__SM_267016608755_000 Supported species : Fe random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -23.99869677587374 Forces: 1 -3.71151860e+00 -6.13157326e+00 -7.45301427e+00 2 -7.94581135e+00 1.32678884e+01 -5.30482482e+00 3 1.78111793e+00 -6.31423732e+00 3.37613841e+00 4 -3.84282234e+00 5.42837984e+00 4.50028266e+00 5 9.59726785e+00 -1.58499682e+01 -2.86356267e+00 6 2.91931345e+00 1.88558064e+00 -3.66389208e+00 7 2.99762201e+00 -2.01611314e+01 -2.04708908e+01 8 -6.33490297e+00 -4.99705366e+00 -5.62632612e+00 9 -6.90823559e+00 -3.53065513e+00 -1.00438364e+01 10 -3.87681006e+00 1.21806757e+01 -1.24351292e+01 11 -5.05000880e+00 -7.93024785e+00 7.00399062e+00 12 -5.16486061e+00 6.06326989e+00 3.20715403e+00 13 -5.98621659e+00 -7.59160885e+00 -2.96621128e+01 14 4.37021651e+00 5.66593835e+00 -3.24116090e+00 15 2.65304554e+01 -4.68966542e+00 8.53695793e+00 16 2.42571378e+00 1.85036221e+01 8.66606125e+00 17 -5.26788863e+00 -2.40989740e+00 -2.87265070e+00 18 -4.94221140e+00 1.47595984e+00 4.86158328e+00 19 3.83697371e+00 -4.63553579e+00 3.47794822e+00 20 -2.28334975e+00 3.90192783e+00 2.43180155e+00 21 -7.44583712e+00 -8.42056505e+00 8.77635252e+00 22 1.55721463e+01 1.43327518e+01 1.25025063e+01 23 2.77008699e+00 -1.06110091e+00 4.97500936e+00 24 -1.48470899e+00 7.55461667e-01 2.73747625e+00 25 -7.13059233e+00 -5.23963385e+00 -2.89554236e+00 26 -3.77988799e+00 1.13713635e+01 -5.30878231e+00 27 1.61900942e+01 -2.53186584e+01 8.28691960e+00 28 -2.36485374e+01 2.13914011e+01 4.41121061e+00 29 -3.98541063e+00 -3.25218203e+00 6.43806303e+00 30 5.19101764e+00 7.90865970e+00 2.39207076e+00 31 9.17508587e+00 -4.14728243e+00 6.62722850e+00 32 5.43249949e+00 7.54811652e+00 8.63297057e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -23.99869677587374 Forces: 1 -3.71151860e+00 -6.13157326e+00 -7.45301427e+00 2 -7.94581135e+00 1.32678884e+01 -5.30482482e+00 3 1.78111793e+00 -6.31423732e+00 3.37613841e+00 4 -3.84282234e+00 5.42837984e+00 4.50028266e+00 5 9.59726785e+00 -1.58499682e+01 -2.86356267e+00 6 2.91931345e+00 1.88558064e+00 -3.66389208e+00 7 2.99762201e+00 -2.01611314e+01 -2.04708908e+01 8 -6.33490297e+00 -4.99705366e+00 -5.62632612e+00 9 -6.90823559e+00 -3.53065513e+00 -1.00438364e+01 10 -3.87681006e+00 1.21806757e+01 -1.24351292e+01 11 -5.05000880e+00 -7.93024785e+00 7.00399062e+00 12 -5.16486061e+00 6.06326989e+00 3.20715403e+00 13 -5.98621659e+00 -7.59160885e+00 -2.96621128e+01 14 4.37021651e+00 5.66593835e+00 -3.24116090e+00 15 2.65304554e+01 -4.68966542e+00 8.53695793e+00 16 2.42571378e+00 1.85036221e+01 8.66606125e+00 17 -5.26788863e+00 -2.40989740e+00 -2.87265070e+00 18 -4.94221140e+00 1.47595984e+00 4.86158328e+00 19 3.83697371e+00 -4.63553579e+00 3.47794822e+00 20 -2.28334975e+00 3.90192783e+00 2.43180155e+00 21 -7.44583712e+00 -8.42056505e+00 8.77635252e+00 22 1.55721463e+01 1.43327518e+01 1.25025063e+01 23 2.77008699e+00 -1.06110091e+00 4.97500936e+00 24 -1.48470899e+00 7.55461667e-01 2.73747625e+00 25 -7.13059233e+00 -5.23963385e+00 -2.89554236e+00 26 -3.77988799e+00 1.13713635e+01 -5.30878231e+00 27 1.61900942e+01 -2.53186584e+01 8.28691960e+00 28 -2.36485374e+01 2.13914011e+01 4.41121061e+00 29 -3.98541063e+00 -3.25218203e+00 6.43806303e+00 30 5.19101764e+00 7.90865970e+00 2.39207076e+00 31 9.17508587e+00 -4.14728243e+00 6.62722850e+00 32 5.43249949e+00 7.54811652e+00 8.63297057e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==36707== Memcheck, a memory error detector ==36707== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==36707== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==36707== Command: python runner2.py Sim_LAMMPS_MEAM_EtesamiAsadi_2018_Fe__SM_267016608755_000 ==36707== ==37363== Warning: invalid file descriptor 1048564 in syscall close() ==37363== Warning: invalid file descriptor 1048565 in syscall close() ==37363== Warning: invalid file descriptor 1048566 in syscall close() ==37363== Warning: invalid file descriptor 1048567 in syscall close() ==37363== Use --log-fd= to select an alternative log fd. ==37363== Warning: invalid file descriptor 1048568 in syscall close() ==37363== Warning: invalid file descriptor 1048569 in syscall close() ==37365== Warning: invalid file descriptor 1048564 in syscall close() ==37365== Warning: invalid file descriptor 1048565 in syscall close() ==37365== Warning: invalid file descriptor 1048566 in syscall close() ==37365== Warning: invalid file descriptor 1048567 in syscall close() ==37365== Use --log-fd= to select an alternative log fd. ==37365== Warning: invalid file descriptor 1048568 in syscall close() ==37365== Warning: invalid file descriptor 1048569 in syscall close() ==37367== Warning: invalid file descriptor 1048564 in syscall close() ==37367== Warning: invalid file descriptor 1048565 in syscall close() ==37367== Warning: invalid file descriptor 1048566 in syscall close() ==37367== Warning: invalid file descriptor 1048567 in syscall close() ==37367== Use --log-fd= to select an alternative log fd. ==37367== Warning: invalid file descriptor 1048568 in syscall close() ==37367== Warning: invalid file descriptor 1048569 in syscall close() ==37368== Warning: invalid file descriptor 1048564 in syscall close() ==37368== Warning: invalid file descriptor 1048565 in syscall close() ==37368== Warning: invalid file descriptor 1048566 in syscall close() ==37368== Warning: invalid file descriptor 1048567 in syscall close() ==37368== Use --log-fd= to select an alternative log fd. ==37368== Warning: invalid file descriptor 1048568 in syscall close() ==37368== Warning: invalid file descriptor 1048569 in syscall close() ==37369== Warning: invalid file descriptor 1048564 in syscall close() ==37369== Warning: invalid file descriptor 1048565 in syscall close() ==37369== Warning: invalid file descriptor 1048566 in syscall close() ==37369== Warning: invalid file descriptor 1048567 in syscall close() ==37369== Use --log-fd= to select an alternative log fd. ==37369== Warning: invalid file descriptor 1048568 in syscall close() ==37369== Warning: invalid file descriptor 1048569 in syscall close() ==37370== Warning: invalid file descriptor 1048564 in syscall close() ==37370== Warning: invalid file descriptor 1048565 in syscall close() ==37370== Warning: invalid file descriptor 1048566 in syscall close() ==37370== Warning: invalid file descriptor 1048567 in syscall close() ==37370== Use --log-fd= to select an alternative log fd. ==37370== Warning: invalid file descriptor 1048568 in syscall close() ==37370== Warning: invalid file descriptor 1048569 in syscall close() ==37371== Warning: invalid file descriptor 1048564 in syscall close() ==37371== Warning: invalid file descriptor 1048565 in syscall close() ==37371== Warning: invalid file descriptor 1048566 in syscall close() ==37371== Warning: invalid file descriptor 1048567 in syscall close() ==37371== Use --log-fd= to select an alternative log fd. ==37371== Warning: invalid file descriptor 1048568 in syscall close() ==37371== Warning: invalid file descriptor 1048569 in syscall close() ==37372== Warning: invalid file descriptor 1048564 in syscall close() ==37372== Warning: invalid file descriptor 1048565 in syscall close() ==37372== Warning: invalid file descriptor 1048566 in syscall close() ==37372== Warning: invalid file descriptor 1048567 in syscall close() ==37372== Use --log-fd= to select an alternative log fd. ==37372== Warning: invalid file descriptor 1048568 in syscall close() ==37372== Warning: invalid file descriptor 1048569 in syscall close() ==36707== ==36707== HEAP SUMMARY: ==36707== in use at exit: 1,780,635 bytes in 1,488 blocks ==36707== total heap usage: 28,650 allocs, 27,162 frees, 48,635,882 bytes allocated ==36707== ==36707== LEAK SUMMARY: ==36707== definitely lost: 0 bytes in 0 blocks ==36707== indirectly lost: 0 bytes in 0 blocks ==36707== possibly lost: 178,423 bytes in 96 blocks ==36707== still reachable: 1,602,212 bytes in 1,392 blocks ==36707== suppressed: 0 bytes in 0 blocks ==36707== Rerun with --leak-check=full to see details of leaked memory ==36707== ==36707== For counts of detected and suppressed errors, rerun with: -v ==36707== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16419 from 607) ================================================================================ 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 (2019-08-09 02:15:06) ===