Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:14:13) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_AdamsFoilesWolfer_1989Universal6_Ag__MO_681640899874_000 Supported species : Ag random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ag (Configuration in file "config-F-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 207.29076987976953 Forces: 1 -8.81123933e+00 -1.54177137e+01 -1.65464133e+01 2 -6.60420110e+00 9.95265292e+00 -1.45836721e+01 3 7.51817108e+00 -2.38614820e+01 -9.75788315e+00 4 -1.58721022e+01 8.16336140e+00 4.61364532e+00 5 -2.27002174e+00 -2.52602054e+01 -8.25418757e+00 6 1.59856288e+01 9.52770945e+00 -1.70626322e+01 7 1.70464021e+01 -3.67134075e+01 -2.20621692e+01 8 -1.71787890e+01 -1.46170718e+01 -4.98825531e+00 9 -1.62650727e+01 -1.19233026e+01 -2.79146752e+01 10 -5.05968450e+00 3.01638358e+01 -2.99579493e+01 11 -3.37687043e+00 -2.02808863e+01 3.23232421e+00 12 -2.00553873e+01 2.89286717e+01 1.57315132e+00 13 -4.33994857e+00 -1.95787790e+01 -5.36793270e+01 14 1.50534144e+01 1.84221065e+01 -1.31686495e+01 15 4.91817231e+01 -1.27399090e+01 4.44089656e+00 16 5.72562553e+00 4.50741321e+01 1.54470218e+01 17 -2.63415673e+01 -1.43482728e+01 -6.19874330e+00 18 5.28237169e+00 1.67012480e+01 9.55178174e+00 19 1.22181446e+01 -1.82253983e+01 1.55386007e+01 20 -1.16401138e+01 1.39491856e+01 1.34389514e+01 21 -1.87186735e+01 -1.79497553e+01 1.26640237e+01 22 2.99981075e+01 2.70195717e+01 2.11300386e+01 23 7.14709685e+00 -3.58056116e+00 1.54068377e+01 24 7.91262174e+00 -9.85728109e+00 1.03714639e+01 25 -2.15760905e+01 -1.12266359e+01 2.06192364e+01 26 -9.42187811e+00 3.20215669e+01 -1.30706427e+01 27 5.56145181e-01 -3.20792336e+01 1.71676232e+01 28 -3.31211877e+01 2.61306847e+01 8.74774133e+00 29 -1.00879794e+01 -1.60684616e+01 1.15809217e+01 30 1.72847207e+01 2.50494388e+01 6.07117404e+00 31 2.66256515e+01 -1.30465337e+01 1.97300491e+01 32 1.32049825e+01 2.56707250e+01 2.59197168e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ag (Configuration in file "config-T-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 207.29076987976953 Forces: 1 -8.81123933e+00 -1.54177137e+01 -1.65464133e+01 2 -6.60420110e+00 9.95265292e+00 -1.45836721e+01 3 7.51817108e+00 -2.38614820e+01 -9.75788315e+00 4 -1.58721022e+01 8.16336140e+00 4.61364532e+00 5 -2.27002174e+00 -2.52602054e+01 -8.25418757e+00 6 1.59856288e+01 9.52770945e+00 -1.70626322e+01 7 1.70464021e+01 -3.67134075e+01 -2.20621692e+01 8 -1.71787890e+01 -1.46170718e+01 -4.98825531e+00 9 -1.62650727e+01 -1.19233026e+01 -2.79146752e+01 10 -5.05968450e+00 3.01638358e+01 -2.99579493e+01 11 -3.37687043e+00 -2.02808863e+01 3.23232421e+00 12 -2.00553873e+01 2.89286717e+01 1.57315132e+00 13 -4.33994857e+00 -1.95787790e+01 -5.36793270e+01 14 1.50534144e+01 1.84221065e+01 -1.31686495e+01 15 4.91817231e+01 -1.27399090e+01 4.44089656e+00 16 5.72562553e+00 4.50741321e+01 1.54470218e+01 17 -2.63415673e+01 -1.43482728e+01 -6.19874330e+00 18 5.28237169e+00 1.67012480e+01 9.55178174e+00 19 1.22181446e+01 -1.82253983e+01 1.55386007e+01 20 -1.16401138e+01 1.39491856e+01 1.34389514e+01 21 -1.87186735e+01 -1.79497553e+01 1.26640237e+01 22 2.99981075e+01 2.70195717e+01 2.11300386e+01 23 7.14709685e+00 -3.58056116e+00 1.54068377e+01 24 7.91262174e+00 -9.85728109e+00 1.03714639e+01 25 -2.15760905e+01 -1.12266359e+01 2.06192364e+01 26 -9.42187811e+00 3.20215669e+01 -1.30706427e+01 27 5.56145181e-01 -3.20792336e+01 1.71676232e+01 28 -3.31211877e+01 2.61306847e+01 8.74774133e+00 29 -1.00879794e+01 -1.60684616e+01 1.15809217e+01 30 1.72847207e+01 2.50494388e+01 6.07117404e+00 31 2.66256515e+01 -1.30465337e+01 1.97300491e+01 32 1.32049825e+01 2.56707250e+01 2.59197168e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==12340== Memcheck, a memory error detector ==12340== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==12340== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==12340== Command: python runner2.py EAM_Dynamo_AdamsFoilesWolfer_1989Universal6_Ag__MO_681640899874_000 ==12340== ==14164== Warning: invalid file descriptor 1048564 in syscall close() ==14164== Warning: invalid file descriptor 1048565 in syscall close() ==14164== Warning: invalid file descriptor 1048566 in syscall close() ==14164== Warning: invalid file descriptor 1048567 in syscall close() ==14164== Use --log-fd= to select an alternative log fd. ==14164== Warning: invalid file descriptor 1048568 in syscall close() ==14164== Warning: invalid file descriptor 1048569 in syscall close() ==14170== Warning: invalid file descriptor 1048564 in syscall close() ==14170== Warning: invalid file descriptor 1048565 in syscall close() ==14170== Warning: invalid file descriptor 1048566 in syscall close() ==14170== Warning: invalid file descriptor 1048567 in syscall close() ==14170== Use --log-fd= to select an alternative log fd. ==14170== Warning: invalid file descriptor 1048568 in syscall close() ==14170== Warning: invalid file descriptor 1048569 in syscall close() ==14239== Warning: invalid file descriptor 1048564 in syscall close() ==14239== Warning: invalid file descriptor 1048565 in syscall close() ==14239== Warning: invalid file descriptor 1048566 in syscall close() ==14239== Warning: invalid file descriptor 1048567 in syscall close() ==14239== Use --log-fd= to select an alternative log fd. ==14239== Warning: invalid file descriptor 1048568 in syscall close() ==14239== Warning: invalid file descriptor 1048569 in syscall close() ==14244== Warning: invalid file descriptor 1048564 in syscall close() ==14244== Warning: invalid file descriptor 1048565 in syscall close() ==14244== Warning: invalid file descriptor 1048566 in syscall close() ==14244== Warning: invalid file descriptor 1048567 in syscall close() ==14244== Use --log-fd= to select an alternative log fd. ==14244== Warning: invalid file descriptor 1048568 in syscall close() ==14244== Warning: invalid file descriptor 1048569 in syscall close() ==14251== Warning: invalid file descriptor 1048564 in syscall close() ==14251== Warning: invalid file descriptor 1048565 in syscall close() ==14251== Warning: invalid file descriptor 1048566 in syscall close() ==14251== Warning: invalid file descriptor 1048567 in syscall close() ==14251== Use --log-fd= to select an alternative log fd. ==14251== Warning: invalid file descriptor 1048568 in syscall close() ==14251== Warning: invalid file descriptor 1048569 in syscall close() ==14255== Warning: invalid file descriptor 1048564 in syscall close() ==14255== Warning: invalid file descriptor 1048565 in syscall close() ==14255== Warning: invalid file descriptor 1048566 in syscall close() ==14255== Warning: invalid file descriptor 1048567 in syscall close() ==14255== Use --log-fd= to select an alternative log fd. ==14255== Warning: invalid file descriptor 1048568 in syscall close() ==14255== Warning: invalid file descriptor 1048569 in syscall close() ==12340== ==12340== HEAP SUMMARY: ==12340== in use at exit: 1,718,308 bytes in 1,321 blocks ==12340== total heap usage: 31,220 allocs, 29,899 frees, 39,119,300 bytes allocated ==12340== ==12340== LEAK SUMMARY: ==12340== definitely lost: 0 bytes in 0 blocks ==12340== indirectly lost: 0 bytes in 0 blocks ==12340== possibly lost: 178,943 bytes in 97 blocks ==12340== still reachable: 1,539,365 bytes in 1,224 blocks ==12340== suppressed: 0 bytes in 0 blocks ==12340== Rerun with --leak-check=full to see details of leaked memory ==12340== ==12340== For counts of detected and suppressed errors, rerun with: -v ==12340== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16370 from 612) ================================================================================ 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 23:14:36) ===