Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:19:56) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Mendelev_2015_Na__MO_094065024556_000 Supported species : Na random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Na (Configuration in file "config-F-Na.xyz") ----------------------------------------------------------------------------------------------------- Energy = 145.91353961266663 Forces: 1 -4.48067646e+00 -6.71474871e+00 -7.76210773e+00 2 -5.63957019e+00 1.28569349e+01 -7.06325468e+00 3 2.63538992e+00 -6.35730420e+00 2.59297120e-01 4 -6.07443717e+00 3.17965123e+00 3.52403837e+00 5 8.67139758e+00 -1.48833367e+01 -2.43686287e+00 6 4.45439733e+00 1.23176447e+00 -6.67460756e+00 7 4.27504488e+00 -1.91445820e+01 -1.69584007e+01 8 -1.24104338e+01 -4.40771794e+00 1.19072123e+00 9 -6.79712657e+00 -5.37428300e+00 -1.40119838e+01 10 -2.04557888e+00 1.13693507e+01 -1.25065891e+01 11 1.47882778e+01 -1.10992664e+01 -3.24951506e+00 12 -1.02304956e+01 1.47714069e+01 6.49085654e-01 13 -8.45442016e+00 -9.60522132e+00 -2.42746071e+01 14 6.97787690e+00 8.15730489e+00 -6.30965320e+00 15 2.24011961e+01 -5.77484512e+00 6.25494334e+00 16 5.40610594e-02 1.62988451e+01 9.10736536e+00 17 -1.14413194e+01 -6.11962079e+00 -3.42487706e+00 18 4.42648631e+00 9.14427962e+00 -4.28806829e+00 19 5.78088267e+00 -9.69860174e+00 8.16710191e+00 20 -6.45071349e+00 6.37128372e+00 6.75338698e+00 21 -9.00008195e+00 -6.78777415e+00 5.00627680e+00 22 1.33511955e+01 1.62759988e+01 1.23994920e+01 23 3.36580219e+00 -1.72312056e+00 7.36080647e+00 24 4.25060716e+00 -3.24729113e+00 4.77592543e+00 25 -1.35179775e+01 -4.99625803e+00 1.60889878e+01 26 -3.23806096e+00 1.26253346e+01 -6.92103488e+00 27 4.93709579e+00 -1.86426303e+01 6.46096321e+00 28 -1.93155755e+01 1.54696617e+01 3.75906592e+00 29 -6.54750700e+00 -9.29270005e+00 1.98811343e+00 30 7.56966750e+00 1.07540086e+01 2.91017689e+00 31 1.14487316e+01 -5.85847504e+00 8.29953456e+00 32 6.25586437e+00 1.12219520e+01 1.09262795e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Na (Configuration in file "config-T-Na.xyz") ----------------------------------------------------------------------------------------------------- Energy = 145.91353961266663 Forces: 1 -4.48067646e+00 -6.71474871e+00 -7.76210773e+00 2 -5.63957019e+00 1.28569349e+01 -7.06325468e+00 3 2.63538992e+00 -6.35730420e+00 2.59297120e-01 4 -6.07443717e+00 3.17965123e+00 3.52403837e+00 5 8.67139758e+00 -1.48833367e+01 -2.43686287e+00 6 4.45439733e+00 1.23176447e+00 -6.67460756e+00 7 4.27504488e+00 -1.91445820e+01 -1.69584007e+01 8 -1.24104338e+01 -4.40771794e+00 1.19072123e+00 9 -6.79712657e+00 -5.37428300e+00 -1.40119838e+01 10 -2.04557888e+00 1.13693507e+01 -1.25065891e+01 11 1.47882778e+01 -1.10992664e+01 -3.24951506e+00 12 -1.02304956e+01 1.47714069e+01 6.49085654e-01 13 -8.45442016e+00 -9.60522132e+00 -2.42746071e+01 14 6.97787690e+00 8.15730489e+00 -6.30965320e+00 15 2.24011961e+01 -5.77484512e+00 6.25494334e+00 16 5.40610594e-02 1.62988451e+01 9.10736536e+00 17 -1.14413194e+01 -6.11962079e+00 -3.42487706e+00 18 4.42648631e+00 9.14427962e+00 -4.28806829e+00 19 5.78088267e+00 -9.69860174e+00 8.16710191e+00 20 -6.45071349e+00 6.37128372e+00 6.75338698e+00 21 -9.00008195e+00 -6.78777415e+00 5.00627680e+00 22 1.33511955e+01 1.62759988e+01 1.23994920e+01 23 3.36580219e+00 -1.72312056e+00 7.36080647e+00 24 4.25060716e+00 -3.24729113e+00 4.77592543e+00 25 -1.35179775e+01 -4.99625803e+00 1.60889878e+01 26 -3.23806096e+00 1.26253346e+01 -6.92103488e+00 27 4.93709579e+00 -1.86426303e+01 6.46096321e+00 28 -1.93155755e+01 1.54696617e+01 3.75906592e+00 29 -6.54750700e+00 -9.29270005e+00 1.98811343e+00 30 7.56966750e+00 1.07540086e+01 2.91017689e+00 31 1.14487316e+01 -5.85847504e+00 8.29953456e+00 32 6.25586437e+00 1.12219520e+01 1.09262795e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==53718== Memcheck, a memory error detector ==53718== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==53718== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==53718== Command: python runner2.py EAM_Dynamo_Mendelev_2015_Na__MO_094065024556_000 ==53718== ==55191== Warning: invalid file descriptor 1048564 in syscall close() ==55191== Warning: invalid file descriptor 1048565 in syscall close() ==55191== Warning: invalid file descriptor 1048566 in syscall close() ==55191== Warning: invalid file descriptor 1048567 in syscall close() ==55191== Use --log-fd= to select an alternative log fd. ==55191== Warning: invalid file descriptor 1048568 in syscall close() ==55191== Warning: invalid file descriptor 1048569 in syscall close() ==55192== Warning: invalid file descriptor 1048564 in syscall close() ==55192== Warning: invalid file descriptor 1048565 in syscall close() ==55192== Warning: invalid file descriptor 1048566 in syscall close() ==55192== Warning: invalid file descriptor 1048567 in syscall close() ==55192== Use --log-fd= to select an alternative log fd. ==55192== Warning: invalid file descriptor 1048568 in syscall close() ==55192== Warning: invalid file descriptor 1048569 in syscall close() ==55332== Warning: invalid file descriptor 1048564 in syscall close() ==55332== Warning: invalid file descriptor 1048565 in syscall close() ==55332== Warning: invalid file descriptor 1048566 in syscall close() ==55332== Warning: invalid file descriptor 1048567 in syscall close() ==55332== Use --log-fd= to select an alternative log fd. ==55332== Warning: invalid file descriptor 1048568 in syscall close() ==55332== Warning: invalid file descriptor 1048569 in syscall close() ==55338== Warning: invalid file descriptor 1048564 in syscall close() ==55338== Warning: invalid file descriptor 1048565 in syscall close() ==55338== Warning: invalid file descriptor 1048566 in syscall close() ==55338== Warning: invalid file descriptor 1048567 in syscall close() ==55338== Use --log-fd= to select an alternative log fd. ==55338== Warning: invalid file descriptor 1048568 in syscall close() ==55338== Warning: invalid file descriptor 1048569 in syscall close() ==55340== Warning: invalid file descriptor 1048564 in syscall close() ==55340== Warning: invalid file descriptor 1048565 in syscall close() ==55340== Warning: invalid file descriptor 1048566 in syscall close() ==55340== Warning: invalid file descriptor 1048567 in syscall close() ==55340== Use --log-fd= to select an alternative log fd. ==55340== Warning: invalid file descriptor 1048568 in syscall close() ==55340== Warning: invalid file descriptor 1048569 in syscall close() ==55357== Warning: invalid file descriptor 1048564 in syscall close() ==55357== Warning: invalid file descriptor 1048565 in syscall close() ==55357== Warning: invalid file descriptor 1048566 in syscall close() ==55357== Warning: invalid file descriptor 1048567 in syscall close() ==55357== Use --log-fd= to select an alternative log fd. ==55357== Warning: invalid file descriptor 1048568 in syscall close() ==55357== Warning: invalid file descriptor 1048569 in syscall close() ==53718== ==53718== HEAP SUMMARY: ==53718== in use at exit: 1,718,292 bytes in 1,321 blocks ==53718== total heap usage: 31,120 allocs, 29,799 frees, 47,287,625 bytes allocated ==53718== ==53718== LEAK SUMMARY: ==53718== definitely lost: 0 bytes in 0 blocks ==53718== indirectly lost: 0 bytes in 0 blocks ==53718== possibly lost: 178,943 bytes in 97 blocks ==53718== still reachable: 1,539,349 bytes in 1,224 blocks ==53718== suppressed: 0 bytes in 0 blocks ==53718== Rerun with --leak-check=full to see details of leaked memory ==53718== ==53718== For counts of detected and suppressed errors, rerun with: -v ==53718== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11242 from 590) ================================================================================ 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 23:20:20) ===