Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:13:48) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_AcklandTichyVitek_1987v2_Cu__MO_762798677854_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 = -59.23876383634842 Forces: 1 -4.02797770e-01 -1.45112483e+00 -1.18704229e+00 2 -2.54527065e-01 5.91567478e-01 -1.70721683e+00 3 1.30488260e+00 -3.19713588e+00 -2.40398019e+00 4 -2.22069426e+00 1.03335778e+00 4.80566220e-01 5 -1.74902882e-01 -2.55305533e+00 -8.01491769e-01 6 1.15955561e+00 1.13190338e+00 -1.32096354e+00 7 2.08279094e+00 -3.96799448e+00 -2.47385014e+00 8 -2.48097030e+00 -1.65451314e+00 -9.00722946e-01 9 -2.89091928e+00 -1.56077548e+00 -3.74376297e+00 10 6.83784581e-01 4.36525578e+00 -3.09398902e+00 11 -1.08801896e+00 -2.71258315e+00 1.58618640e+00 12 -2.62902236e+00 2.58789983e+00 1.45083480e+00 13 7.74103800e-01 -2.30092400e+00 -6.45857489e+00 14 1.72193988e+00 1.60985611e+00 -1.47772577e+00 15 6.30932482e+00 -2.04321883e+00 -1.56898527e+00 16 -1.19737457e+00 6.42459240e+00 1.09254444e+00 17 -4.25294068e+00 -1.83669388e+00 -4.00819123e-01 18 1.07471132e+00 3.36622641e+00 6.43834436e-01 19 1.14750694e+00 -2.40229741e+00 2.68941584e+00 20 -1.40668755e+00 1.64005055e+00 1.66517996e+00 21 -1.56957579e+00 -3.64486250e+00 9.50277566e-01 22 4.70921588e+00 2.39640295e+00 1.95413418e+00 23 1.82774548e+00 -9.25946559e-01 1.69358639e+00 24 -1.60616470e+00 1.54763024e+00 1.46013658e+00 25 -2.98784730e+00 -2.09686534e+00 -1.01643945e+00 26 3.19836519e-01 4.22413578e+00 -2.43038095e+00 27 1.03122000e+01 -1.38250837e+01 3.43324464e+00 28 -1.24454626e+01 1.24063281e+01 2.10047506e+00 29 -2.73472367e+00 -2.09762634e+00 3.08464211e+00 30 3.00295707e+00 4.05895616e+00 1.09088268e+00 31 2.97709729e+00 -1.67655599e+00 2.74077062e+00 32 9.34977000e-01 2.56309395e+00 2.86923325e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = -59.23876383634842 Forces: 1 -4.02797770e-01 -1.45112483e+00 -1.18704229e+00 2 -2.54527065e-01 5.91567478e-01 -1.70721683e+00 3 1.30488260e+00 -3.19713588e+00 -2.40398019e+00 4 -2.22069426e+00 1.03335778e+00 4.80566220e-01 5 -1.74902882e-01 -2.55305533e+00 -8.01491769e-01 6 1.15955561e+00 1.13190338e+00 -1.32096354e+00 7 2.08279094e+00 -3.96799448e+00 -2.47385014e+00 8 -2.48097030e+00 -1.65451314e+00 -9.00722946e-01 9 -2.89091928e+00 -1.56077548e+00 -3.74376297e+00 10 6.83784581e-01 4.36525578e+00 -3.09398902e+00 11 -1.08801896e+00 -2.71258315e+00 1.58618640e+00 12 -2.62902236e+00 2.58789983e+00 1.45083480e+00 13 7.74103800e-01 -2.30092400e+00 -6.45857489e+00 14 1.72193988e+00 1.60985611e+00 -1.47772577e+00 15 6.30932482e+00 -2.04321883e+00 -1.56898527e+00 16 -1.19737457e+00 6.42459240e+00 1.09254444e+00 17 -4.25294068e+00 -1.83669388e+00 -4.00819123e-01 18 1.07471132e+00 3.36622641e+00 6.43834436e-01 19 1.14750694e+00 -2.40229741e+00 2.68941584e+00 20 -1.40668755e+00 1.64005055e+00 1.66517996e+00 21 -1.56957579e+00 -3.64486250e+00 9.50277566e-01 22 4.70921588e+00 2.39640295e+00 1.95413418e+00 23 1.82774548e+00 -9.25946559e-01 1.69358639e+00 24 -1.60616470e+00 1.54763024e+00 1.46013658e+00 25 -2.98784730e+00 -2.09686534e+00 -1.01643945e+00 26 3.19836519e-01 4.22413578e+00 -2.43038095e+00 27 1.03122000e+01 -1.38250837e+01 3.43324464e+00 28 -1.24454626e+01 1.24063281e+01 2.10047506e+00 29 -2.73472367e+00 -2.09762634e+00 3.08464211e+00 30 3.00295707e+00 4.05895616e+00 1.09088268e+00 31 2.97709729e+00 -1.67655599e+00 2.74077062e+00 32 9.34977000e-01 2.56309395e+00 2.86923325e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==8092== Memcheck, a memory error detector ==8092== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==8092== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==8092== Command: python runner2.py EAM_Dynamo_AcklandTichyVitek_1987v2_Cu__MO_762798677854_000 ==8092== ==9587== Warning: invalid file descriptor 1048564 in syscall close() ==9587== Warning: invalid file descriptor 1048565 in syscall close() ==9587== Warning: invalid file descriptor 1048566 in syscall close() ==9587== Warning: invalid file descriptor 1048567 in syscall close() ==9587== Use --log-fd= to select an alternative log fd. ==9587== Warning: invalid file descriptor 1048568 in syscall close() ==9587== Warning: invalid file descriptor 1048569 in syscall close() ==9594== Warning: invalid file descriptor 1048564 in syscall close() ==9594== Warning: invalid file descriptor 1048565 in syscall close() ==9594== Warning: invalid file descriptor 1048566 in syscall close() ==9594== Warning: invalid file descriptor 1048567 in syscall close() ==9594== Use --log-fd= to select an alternative log fd. ==9594== Warning: invalid file descriptor 1048568 in syscall close() ==9594== Warning: invalid file descriptor 1048569 in syscall close() ==9752== Warning: invalid file descriptor 1048564 in syscall close() ==9752== Warning: invalid file descriptor 1048565 in syscall close() ==9752== Warning: invalid file descriptor 1048566 in syscall close() ==9752== Warning: invalid file descriptor 1048567 in syscall close() ==9752== Use --log-fd= to select an alternative log fd. ==9752== Warning: invalid file descriptor 1048568 in syscall close() ==9752== Warning: invalid file descriptor 1048569 in syscall close() ==9761== Warning: invalid file descriptor 1048564 in syscall close() ==9761== Warning: invalid file descriptor 1048565 in syscall close() ==9761== Warning: invalid file descriptor 1048566 in syscall close() ==9761== Warning: invalid file descriptor 1048567 in syscall close() ==9761== Use --log-fd= to select an alternative log fd. ==9761== Warning: invalid file descriptor 1048568 in syscall close() ==9761== Warning: invalid file descriptor 1048569 in syscall close() ==9765== Warning: invalid file descriptor 1048564 in syscall close() ==9765== Warning: invalid file descriptor 1048565 in syscall close() ==9765== Warning: invalid file descriptor 1048566 in syscall close() ==9765== Warning: invalid file descriptor 1048567 in syscall close() ==9765== Use --log-fd= to select an alternative log fd. ==9765== Warning: invalid file descriptor 1048568 in syscall close() ==9765== Warning: invalid file descriptor 1048569 in syscall close() ==9768== Warning: invalid file descriptor 1048564 in syscall close() ==9768== Warning: invalid file descriptor 1048565 in syscall close() ==9768== Warning: invalid file descriptor 1048566 in syscall close() ==9768== Warning: invalid file descriptor 1048567 in syscall close() ==9768== Use --log-fd= to select an alternative log fd. ==9768== Warning: invalid file descriptor 1048568 in syscall close() ==9768== Warning: invalid file descriptor 1048569 in syscall close() ==8092== ==8092== HEAP SUMMARY: ==8092== in use at exit: 1,718,292 bytes in 1,321 blocks ==8092== total heap usage: 31,348 allocs, 30,027 frees, 47,320,266 bytes allocated ==8092== ==8092== LEAK SUMMARY: ==8092== definitely lost: 0 bytes in 0 blocks ==8092== indirectly lost: 0 bytes in 0 blocks ==8092== possibly lost: 178,943 bytes in 97 blocks ==8092== still reachable: 1,539,349 bytes in 1,224 blocks ==8092== suppressed: 0 bytes in 0 blocks ==8092== Rerun with --leak-check=full to see details of leaked memory ==8092== ==8092== For counts of detected and suppressed errors, rerun with: -v ==8092== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16329 from 599) ================================================================================ 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 23:14:12) ===