Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:30:26) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Morse_Shifted_GirifalcoWeizer_1959MedCutoff_Ca__MO_562200212426_003 Supported species : Ca random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ca (Configuration in file "config-F-Ca.xyz") ----------------------------------------------------------------------------------------------------- Energy = 734.9001139750286 Forces: 1 -2.31882844e+01 -2.27176660e+01 -2.51116755e+01 2 -5.87671738e-01 7.25080402e+00 -3.41813568e+01 3 -4.01639021e+00 -3.19841507e+01 1.08270352e+01 4 -3.25444866e+01 4.80595406e+00 7.50821766e+00 5 1.55159684e+01 -3.15900357e+01 -2.21903578e+01 6 2.00584759e+01 -1.03163727e+00 -2.70769912e+01 7 2.28041326e+01 -4.21892506e+01 -2.29612383e+01 8 -2.35022696e+01 -1.95804790e+01 -7.02049146e+00 9 -2.39542251e+01 -1.09037409e-01 -3.78111120e+01 10 -6.50723936e+00 3.70440507e+01 -4.15355292e+01 11 -9.52245012e+00 -1.97500151e+01 8.47144637e-01 12 -3.41640369e+01 3.09521636e+01 -2.81857481e+00 13 3.87631131e+00 -9.61357885e+00 -5.53985976e+01 14 2.33356378e+01 2.25169724e+01 -1.75829548e+01 15 5.62835264e+01 1.98969144e+00 -1.17291279e+01 16 1.60423182e+01 4.85577383e+01 2.43088660e+00 17 -3.26347204e+01 -3.08856946e+01 -5.07183559e+00 18 4.54872773e+00 1.11673973e+01 -3.90561330e+00 19 5.99576367e-01 -3.14707856e+01 2.49361849e+01 20 -2.25909178e+01 9.56563235e+00 2.98135839e+01 21 -7.84333032e+00 -3.63451116e+01 8.04965590e+00 22 4.97425174e+01 8.72740883e+00 1.96377475e+01 23 1.96050115e+01 -1.27973361e+01 2.39420985e+01 24 1.24668442e+00 3.30914328e+00 2.98282180e+01 25 -3.62498172e+01 -5.67291761e+00 9.65825393e+00 26 -9.40422278e+00 4.09979153e+01 1.32050135e+01 27 1.94890479e+00 -2.08623820e+01 2.77400051e+01 28 -3.31594333e+01 2.84650613e+01 1.71882764e+01 29 -1.01208958e+01 7.23267374e-01 1.84439083e+01 30 3.19276237e+01 3.51903609e+01 1.60012696e+00 31 3.49923350e+01 -5.29570983e+00 3.75693971e+01 32 7.46264024e+00 3.06322267e+01 3.11697021e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ca (Configuration in file "config-T-Ca.xyz") ----------------------------------------------------------------------------------------------------- Energy = 734.9001139750286 Forces: 1 -2.31882844e+01 -2.27176660e+01 -2.51116755e+01 2 -5.87671738e-01 7.25080402e+00 -3.41813568e+01 3 -4.01639021e+00 -3.19841507e+01 1.08270352e+01 4 -3.25444866e+01 4.80595406e+00 7.50821766e+00 5 1.55159684e+01 -3.15900357e+01 -2.21903578e+01 6 2.00584759e+01 -1.03163727e+00 -2.70769912e+01 7 2.28041326e+01 -4.21892506e+01 -2.29612383e+01 8 -2.35022696e+01 -1.95804790e+01 -7.02049146e+00 9 -2.39542251e+01 -1.09037409e-01 -3.78111120e+01 10 -6.50723936e+00 3.70440507e+01 -4.15355292e+01 11 -9.52245012e+00 -1.97500151e+01 8.47144637e-01 12 -3.41640369e+01 3.09521636e+01 -2.81857481e+00 13 3.87631131e+00 -9.61357885e+00 -5.53985976e+01 14 2.33356378e+01 2.25169724e+01 -1.75829548e+01 15 5.62835264e+01 1.98969144e+00 -1.17291279e+01 16 1.60423182e+01 4.85577383e+01 2.43088660e+00 17 -3.26347204e+01 -3.08856946e+01 -5.07183559e+00 18 4.54872773e+00 1.11673973e+01 -3.90561330e+00 19 5.99576367e-01 -3.14707856e+01 2.49361849e+01 20 -2.25909178e+01 9.56563235e+00 2.98135839e+01 21 -7.84333032e+00 -3.63451116e+01 8.04965590e+00 22 4.97425174e+01 8.72740883e+00 1.96377475e+01 23 1.96050115e+01 -1.27973361e+01 2.39420985e+01 24 1.24668442e+00 3.30914328e+00 2.98282180e+01 25 -3.62498172e+01 -5.67291761e+00 9.65825393e+00 26 -9.40422278e+00 4.09979153e+01 1.32050135e+01 27 1.94890479e+00 -2.08623820e+01 2.77400051e+01 28 -3.31594333e+01 2.84650613e+01 1.71882764e+01 29 -1.01208958e+01 7.23267374e-01 1.84439083e+01 30 3.19276237e+01 3.51903609e+01 1.60012696e+00 31 3.49923350e+01 -5.29570983e+00 3.75693971e+01 32 7.46264024e+00 3.06322267e+01 3.11697021e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==63449== Memcheck, a memory error detector ==63449== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==63449== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==63449== Command: python runner2.py Morse_Shifted_GirifalcoWeizer_1959MedCutoff_Ca__MO_562200212426_003 ==63449== ==65060== Warning: invalid file descriptor 1048564 in syscall close() ==65060== Warning: invalid file descriptor 1048565 in syscall close() ==65060== Warning: invalid file descriptor 1048566 in syscall close() ==65060== Warning: invalid file descriptor 1048567 in syscall close() ==65060== Use --log-fd= to select an alternative log fd. ==65060== Warning: invalid file descriptor 1048568 in syscall close() ==65060== Warning: invalid file descriptor 1048569 in syscall close() ==65065== Warning: invalid file descriptor 1048564 in syscall close() ==65065== Warning: invalid file descriptor 1048565 in syscall close() ==65065== Warning: invalid file descriptor 1048566 in syscall close() ==65065== Warning: invalid file descriptor 1048567 in syscall close() ==65065== Use --log-fd= to select an alternative log fd. ==65065== Warning: invalid file descriptor 1048568 in syscall close() ==65065== Warning: invalid file descriptor 1048569 in syscall close() ==65150== Warning: invalid file descriptor 1048564 in syscall close() ==65150== Warning: invalid file descriptor 1048565 in syscall close() ==65150== Warning: invalid file descriptor 1048566 in syscall close() ==65150== Warning: invalid file descriptor 1048567 in syscall close() ==65150== Use --log-fd= to select an alternative log fd. ==65150== Warning: invalid file descriptor 1048568 in syscall close() ==65150== Warning: invalid file descriptor 1048569 in syscall close() ==65154== Warning: invalid file descriptor 1048564 in syscall close() ==65154== Warning: invalid file descriptor 1048565 in syscall close() ==65154== Warning: invalid file descriptor 1048566 in syscall close() ==65154== Warning: invalid file descriptor 1048567 in syscall close() ==65154== Use --log-fd= to select an alternative log fd. ==65154== Warning: invalid file descriptor 1048568 in syscall close() ==65154== Warning: invalid file descriptor 1048569 in syscall close() ==65159== Warning: invalid file descriptor 1048564 in syscall close() ==65159== Warning: invalid file descriptor 1048565 in syscall close() ==65159== Warning: invalid file descriptor 1048566 in syscall close() ==65159== Warning: invalid file descriptor 1048567 in syscall close() ==65159== Use --log-fd= to select an alternative log fd. ==65159== Warning: invalid file descriptor 1048568 in syscall close() ==65159== Warning: invalid file descriptor 1048569 in syscall close() ==65165== Warning: invalid file descriptor 1048564 in syscall close() ==65165== Warning: invalid file descriptor 1048565 in syscall close() ==65165== Warning: invalid file descriptor 1048566 in syscall close() ==65165== Warning: invalid file descriptor 1048567 in syscall close() ==65165== Use --log-fd= to select an alternative log fd. ==65165== Warning: invalid file descriptor 1048568 in syscall close() ==65165== Warning: invalid file descriptor 1048569 in syscall close() ==63449== ==63449== HEAP SUMMARY: ==63449== in use at exit: 1,718,292 bytes in 1,321 blocks ==63449== total heap usage: 31,396 allocs, 30,075 frees, 38,295,244 bytes allocated ==63449== ==63449== LEAK SUMMARY: ==63449== definitely lost: 0 bytes in 0 blocks ==63449== indirectly lost: 0 bytes in 0 blocks ==63449== possibly lost: 178,943 bytes in 97 blocks ==63449== still reachable: 1,539,349 bytes in 1,224 blocks ==63449== suppressed: 0 bytes in 0 blocks ==63449== Rerun with --leak-check=full to see details of leaked memory ==63449== ==63449== For counts of detected and suppressed errors, rerun with: -v ==63449== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16378 from 614) ================================================================================ 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 23:30:47) ===