Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:23:52) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouWadleyJohnson_2001NISTretabulation_Cu__MO_759493141826_000 Supported species : Cu random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6.795293823122359 Forces: 1 -2.77330438e+00 -6.21824697e+00 -6.63342124e+00 2 -8.09520852e+00 1.22987976e+01 -8.20333509e+00 3 7.40194608e-01 -8.46300657e+00 -1.43506474e+00 4 -4.02899510e+00 3.86142815e+00 3.90657679e+00 5 1.01418553e+01 -1.63245248e+01 -1.67039587e+00 6 3.00535725e+00 1.63556813e+00 -5.18982865e+00 7 3.75789945e+00 -2.17890633e+01 -2.02372122e+01 8 -7.75460204e+00 -8.89357285e+00 9.60550963e-01 9 -9.87088723e+00 -5.65714325e+00 -1.45102012e+01 10 -3.41367043e+00 1.63257739e+01 -1.58516951e+01 11 -2.29290887e+00 -1.27365745e+01 1.03561913e+01 12 -7.83209051e+00 1.34801585e+01 7.00816282e-02 13 -3.82456593e+00 -7.33117349e+00 -3.35003614e+01 14 5.31237306e+00 7.01771740e+00 -4.36122776e+00 15 2.85006824e+01 -3.91579049e+00 9.22239029e+00 16 3.69498459e+00 2.18083429e+01 1.16410011e+01 17 -8.64427081e+00 -3.50628579e+00 -3.54053948e+00 18 -2.88512709e+00 7.77074035e+00 3.17849308e+00 19 4.60958933e+00 -6.80892284e+00 5.21517361e+00 20 -2.96317825e+00 6.22599739e+00 3.98477672e+00 21 -8.10443048e+00 -8.21292529e+00 6.24425324e+00 22 1.33238429e+01 1.85747027e+01 1.61214990e+01 23 2.33365367e+00 -6.97985421e-01 4.35288376e+00 24 1.90659345e+00 8.46139017e-01 3.76993899e+00 25 -5.40146753e+00 -7.96653770e+00 9.86219051e+00 26 -5.40108676e+00 1.34104123e+01 -7.63865069e+00 27 8.49876888e+00 -2.52578137e+01 6.93392042e+00 28 -2.05003415e+01 1.70200400e+01 2.63162260e+00 29 -6.07154999e+00 -9.75578160e+00 3.18090670e+00 30 6.07016441e+00 1.02426247e+01 3.28093707e-01 31 1.14141231e+01 -7.81244282e+00 9.44139178e+00 32 6.54760303e+00 1.08293484e+01 1.13699973e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6.795293823122359 Forces: 1 -2.77330438e+00 -6.21824697e+00 -6.63342124e+00 2 -8.09520852e+00 1.22987976e+01 -8.20333509e+00 3 7.40194608e-01 -8.46300657e+00 -1.43506474e+00 4 -4.02899510e+00 3.86142815e+00 3.90657679e+00 5 1.01418553e+01 -1.63245248e+01 -1.67039587e+00 6 3.00535725e+00 1.63556813e+00 -5.18982865e+00 7 3.75789945e+00 -2.17890633e+01 -2.02372122e+01 8 -7.75460204e+00 -8.89357285e+00 9.60550963e-01 9 -9.87088723e+00 -5.65714325e+00 -1.45102012e+01 10 -3.41367043e+00 1.63257739e+01 -1.58516951e+01 11 -2.29290887e+00 -1.27365745e+01 1.03561913e+01 12 -7.83209051e+00 1.34801585e+01 7.00816282e-02 13 -3.82456593e+00 -7.33117349e+00 -3.35003614e+01 14 5.31237306e+00 7.01771740e+00 -4.36122776e+00 15 2.85006824e+01 -3.91579049e+00 9.22239029e+00 16 3.69498459e+00 2.18083429e+01 1.16410011e+01 17 -8.64427081e+00 -3.50628579e+00 -3.54053948e+00 18 -2.88512709e+00 7.77074035e+00 3.17849308e+00 19 4.60958933e+00 -6.80892284e+00 5.21517361e+00 20 -2.96317825e+00 6.22599739e+00 3.98477672e+00 21 -8.10443048e+00 -8.21292529e+00 6.24425324e+00 22 1.33238429e+01 1.85747027e+01 1.61214990e+01 23 2.33365367e+00 -6.97985421e-01 4.35288376e+00 24 1.90659345e+00 8.46139017e-01 3.76993899e+00 25 -5.40146753e+00 -7.96653770e+00 9.86219051e+00 26 -5.40108676e+00 1.34104123e+01 -7.63865069e+00 27 8.49876888e+00 -2.52578137e+01 6.93392042e+00 28 -2.05003415e+01 1.70200400e+01 2.63162260e+00 29 -6.07154999e+00 -9.75578160e+00 3.18090670e+00 30 6.07016441e+00 1.02426247e+01 3.28093707e-01 31 1.14141231e+01 -7.81244282e+00 9.44139178e+00 32 6.54760303e+00 1.08293484e+01 1.13699973e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==89321== Memcheck, a memory error detector ==89321== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==89321== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==89321== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Cu__MO_759493141826_000 ==89321== ==91266== Warning: invalid file descriptor 1048564 in syscall close() ==91266== Warning: invalid file descriptor 1048565 in syscall close() ==91266== Warning: invalid file descriptor 1048566 in syscall close() ==91266== Warning: invalid file descriptor 1048567 in syscall close() ==91266== Use --log-fd= to select an alternative log fd. ==91266== Warning: invalid file descriptor 1048568 in syscall close() ==91266== Warning: invalid file descriptor 1048569 in syscall close() ==91275== Warning: invalid file descriptor 1048564 in syscall close() ==91275== Warning: invalid file descriptor 1048565 in syscall close() ==91275== Warning: invalid file descriptor 1048566 in syscall close() ==91275== Warning: invalid file descriptor 1048567 in syscall close() ==91275== Use --log-fd= to select an alternative log fd. ==91275== Warning: invalid file descriptor 1048568 in syscall close() ==91275== Warning: invalid file descriptor 1048569 in syscall close() ==91399== Warning: invalid file descriptor 1048564 in syscall close() ==91399== Warning: invalid file descriptor 1048565 in syscall close() ==91399== Warning: invalid file descriptor 1048566 in syscall close() ==91399== Warning: invalid file descriptor 1048567 in syscall close() ==91399== Use --log-fd= to select an alternative log fd. ==91399== Warning: invalid file descriptor 1048568 in syscall close() ==91399== Warning: invalid file descriptor 1048569 in syscall close() ==91402== Warning: invalid file descriptor 1048564 in syscall close() ==91402== Warning: invalid file descriptor 1048565 in syscall close() ==91402== Warning: invalid file descriptor 1048566 in syscall close() ==91402== Warning: invalid file descriptor 1048567 in syscall close() ==91402== Use --log-fd= to select an alternative log fd. ==91402== Warning: invalid file descriptor 1048568 in syscall close() ==91402== Warning: invalid file descriptor 1048569 in syscall close() ==91409== Warning: invalid file descriptor 1048564 in syscall close() ==91409== Warning: invalid file descriptor 1048565 in syscall close() ==91409== Warning: invalid file descriptor 1048566 in syscall close() ==91409== Warning: invalid file descriptor 1048567 in syscall close() ==91409== Use --log-fd= to select an alternative log fd. ==91409== Warning: invalid file descriptor 1048568 in syscall close() ==91409== Warning: invalid file descriptor 1048569 in syscall close() ==91416== Warning: invalid file descriptor 1048564 in syscall close() ==91416== Warning: invalid file descriptor 1048565 in syscall close() ==91416== Warning: invalid file descriptor 1048566 in syscall close() ==91416== Warning: invalid file descriptor 1048567 in syscall close() ==91416== Use --log-fd= to select an alternative log fd. ==91416== Warning: invalid file descriptor 1048568 in syscall close() ==91416== Warning: invalid file descriptor 1048569 in syscall close() ==89321== ==89321== HEAP SUMMARY: ==89321== in use at exit: 1,718,292 bytes in 1,321 blocks ==89321== total heap usage: 31,120 allocs, 29,799 frees, 40,378,415 bytes allocated ==89321== ==89321== LEAK SUMMARY: ==89321== definitely lost: 0 bytes in 0 blocks ==89321== indirectly lost: 0 bytes in 0 blocks ==89321== possibly lost: 178,943 bytes in 97 blocks ==89321== still reachable: 1,539,349 bytes in 1,224 blocks ==89321== suppressed: 0 bytes in 0 blocks ==89321== Rerun with --leak-check=full to see details of leaked memory ==89321== ==89321== For counts of detected and suppressed errors, rerun with: -v ==89321== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 13369 from 596) ================================================================================ 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 23:24:14) ===