Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:21:00) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_PunMishin_2012_Co__MO_885079680379_005 Supported species : Co random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Co (Configuration in file "config-F-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = 390.16525532170294 Forces: 1 -6.50233106e+01 -1.90447977e+02 -2.57368486e+02 2 -3.55074174e-02 3.59428617e+01 -3.01002340e+01 3 9.57556007e+01 -1.03150350e+02 6.69210542e+01 4 -6.92610824e+01 2.72365883e+02 1.93337564e+02 5 7.53148934e-01 -3.60498971e+01 -2.30384110e+01 6 7.84069399e+00 7.63660920e+00 -1.63731383e+01 7 -2.20300752e+01 -2.58361328e+02 -2.71491457e+02 8 -8.73822274e+01 -9.67732567e+01 1.38205877e+01 9 -1.52093964e+00 -6.24410052e+00 -4.99534180e+00 10 -5.54190456e+01 2.39556399e+01 -6.54123187e+01 11 -2.01218350e+02 -1.04411033e+02 -1.23697266e+02 12 -3.05025913e+00 1.13454264e+01 -2.58365428e-01 13 -1.35966824e+02 -6.30569647e+01 -2.63517824e+02 14 3.42314485e+01 3.70065027e+01 -1.33637496e+01 15 2.51813144e+02 3.32019467e+01 1.41532454e+02 16 8.53043826e+01 2.41967496e+02 2.02781936e+01 17 -4.13069064e+01 -1.29516955e+02 -1.38993647e+02 18 6.45539752e+01 -3.69968639e+01 8.39154512e+00 19 2.09861744e+01 -2.18242345e+01 1.71584720e+01 20 -1.15193280e+01 1.21408537e+02 1.40096676e+02 21 -1.08112288e+02 -5.21486845e+01 -1.08963535e+01 22 1.46717007e+02 2.62291858e+02 2.16753381e+02 23 5.28660697e+01 -1.08259742e+01 8.70146618e+01 24 -1.06669963e+01 3.11878499e+01 2.17667619e+01 25 -6.75355567e+01 4.24080225e+01 -9.27332846e+00 26 -7.82344503e+01 2.04518142e+02 -8.71589498e+01 27 1.63180048e+02 -3.12030945e+02 6.09629142e+01 28 -2.21733179e+02 1.98291437e+02 6.15398446e+01 29 1.86815604e+02 -1.44702608e+02 2.02677669e+02 30 1.20427504e+01 2.64982221e+01 1.39786814e+01 31 2.87156450e+01 -2.36506296e+01 4.13593860e+00 32 2.84406338e+01 4.01653689e+01 4.55724728e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Co (Configuration in file "config-T-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = 390.16525532170294 Forces: 1 -6.50233106e+01 -1.90447977e+02 -2.57368486e+02 2 -3.55074174e-02 3.59428617e+01 -3.01002340e+01 3 9.57556007e+01 -1.03150350e+02 6.69210542e+01 4 -6.92610824e+01 2.72365883e+02 1.93337564e+02 5 7.53148934e-01 -3.60498971e+01 -2.30384110e+01 6 7.84069399e+00 7.63660920e+00 -1.63731383e+01 7 -2.20300752e+01 -2.58361328e+02 -2.71491457e+02 8 -8.73822274e+01 -9.67732567e+01 1.38205877e+01 9 -1.52093964e+00 -6.24410052e+00 -4.99534180e+00 10 -5.54190456e+01 2.39556399e+01 -6.54123187e+01 11 -2.01218350e+02 -1.04411033e+02 -1.23697266e+02 12 -3.05025913e+00 1.13454264e+01 -2.58365428e-01 13 -1.35966824e+02 -6.30569647e+01 -2.63517824e+02 14 3.42314485e+01 3.70065027e+01 -1.33637496e+01 15 2.51813144e+02 3.32019467e+01 1.41532454e+02 16 8.53043826e+01 2.41967496e+02 2.02781936e+01 17 -4.13069064e+01 -1.29516955e+02 -1.38993647e+02 18 6.45539752e+01 -3.69968639e+01 8.39154512e+00 19 2.09861744e+01 -2.18242345e+01 1.71584720e+01 20 -1.15193280e+01 1.21408537e+02 1.40096676e+02 21 -1.08112288e+02 -5.21486845e+01 -1.08963535e+01 22 1.46717007e+02 2.62291858e+02 2.16753381e+02 23 5.28660697e+01 -1.08259742e+01 8.70146618e+01 24 -1.06669963e+01 3.11878499e+01 2.17667619e+01 25 -6.75355567e+01 4.24080225e+01 -9.27332846e+00 26 -7.82344503e+01 2.04518142e+02 -8.71589498e+01 27 1.63180048e+02 -3.12030945e+02 6.09629142e+01 28 -2.21733179e+02 1.98291437e+02 6.15398446e+01 29 1.86815604e+02 -1.44702608e+02 2.02677669e+02 30 1.20427504e+01 2.64982221e+01 1.39786814e+01 31 2.87156450e+01 -2.36506296e+01 4.13593860e+00 32 2.84406338e+01 4.01653689e+01 4.55724728e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==62502== Memcheck, a memory error detector ==62502== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==62502== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==62502== Command: python runner2.py EAM_Dynamo_PunMishin_2012_Co__MO_885079680379_005 ==62502== ==63647== Warning: invalid file descriptor 1048564 in syscall close() ==63647== Warning: invalid file descriptor 1048565 in syscall close() ==63647== Warning: invalid file descriptor 1048566 in syscall close() ==63647== Warning: invalid file descriptor 1048567 in syscall close() ==63647== Use --log-fd= to select an alternative log fd. ==63647== Warning: invalid file descriptor 1048568 in syscall close() ==63647== Warning: invalid file descriptor 1048569 in syscall close() ==63648== Warning: invalid file descriptor 1048564 in syscall close() ==63648== Warning: invalid file descriptor 1048565 in syscall close() ==63648== Warning: invalid file descriptor 1048566 in syscall close() ==63648== Warning: invalid file descriptor 1048567 in syscall close() ==63648== Use --log-fd= to select an alternative log fd. ==63648== Warning: invalid file descriptor 1048568 in syscall close() ==63648== Warning: invalid file descriptor 1048569 in syscall close() ==63649== Warning: invalid file descriptor 1048564 in syscall close() ==63649== Warning: invalid file descriptor 1048565 in syscall close() ==63649== Warning: invalid file descriptor 1048566 in syscall close() ==63649== Warning: invalid file descriptor 1048567 in syscall close() ==63649== Use --log-fd= to select an alternative log fd. ==63649== Warning: invalid file descriptor 1048568 in syscall close() ==63649== Warning: invalid file descriptor 1048569 in syscall close() ==63650== Warning: invalid file descriptor 1048564 in syscall close() ==63650== Warning: invalid file descriptor 1048565 in syscall close() ==63650== Warning: invalid file descriptor 1048566 in syscall close() ==63650== Warning: invalid file descriptor 1048567 in syscall close() ==63650== Use --log-fd= to select an alternative log fd. ==63650== Warning: invalid file descriptor 1048568 in syscall close() ==63650== Warning: invalid file descriptor 1048569 in syscall close() ==63651== Warning: invalid file descriptor 1048564 in syscall close() ==63651== Warning: invalid file descriptor 1048565 in syscall close() ==63651== Warning: invalid file descriptor 1048566 in syscall close() ==63651== Warning: invalid file descriptor 1048567 in syscall close() ==63651== Use --log-fd= to select an alternative log fd. ==63651== Warning: invalid file descriptor 1048568 in syscall close() ==63651== Warning: invalid file descriptor 1048569 in syscall close() ==63652== Warning: invalid file descriptor 1048564 in syscall close() ==63652== Warning: invalid file descriptor 1048565 in syscall close() ==63652== Warning: invalid file descriptor 1048566 in syscall close() ==63652== Warning: invalid file descriptor 1048567 in syscall close() ==63652== Use --log-fd= to select an alternative log fd. ==63652== Warning: invalid file descriptor 1048568 in syscall close() ==63652== Warning: invalid file descriptor 1048569 in syscall close() ==62502== ==62502== HEAP SUMMARY: ==62502== in use at exit: 1,718,292 bytes in 1,321 blocks ==62502== total heap usage: 31,120 allocs, 29,799 frees, 47,287,734 bytes allocated ==62502== ==62502== LEAK SUMMARY: ==62502== definitely lost: 0 bytes in 0 blocks ==62502== indirectly lost: 0 bytes in 0 blocks ==62502== possibly lost: 178,943 bytes in 97 blocks ==62502== still reachable: 1,539,349 bytes in 1,224 blocks ==62502== suppressed: 0 bytes in 0 blocks ==62502== Rerun with --leak-check=full to see details of leaked memory ==62502== ==62502== For counts of detected and suppressed errors, rerun with: -v ==62502== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11240 from 591) ================================================================================ 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 23:21:22) ===