Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:14:35) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_AgrawalMishraWard_2013_Be__MO_404563086984_000 Supported species : Be random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Be (Configuration in file "config-F-Be.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1.4235801087420363 Forces: 1 -4.40315132e+00 -6.79032703e+00 -1.08838404e+01 2 -1.00641885e+01 1.23566952e+01 -1.43340204e+00 3 1.19120159e+01 -6.66524419e+00 -4.58922723e+00 4 -1.41751574e+00 1.10598805e+01 5.95112293e+00 5 4.95486011e+00 -1.60940847e+01 1.08091530e+00 6 5.72386447e+00 5.05449558e+00 -2.22833069e+00 7 5.71033846e+00 -2.06860329e+01 -2.97020799e+01 8 -5.25972996e+00 -3.83401352e+00 -1.32328126e+01 9 -1.05582552e+00 -7.58605240e+00 -9.18977950e+00 10 -5.62084413e+00 8.47595478e+00 -1.24052241e+01 11 -1.52674234e+01 -1.22508102e+01 1.06488494e+01 12 -2.38815852e+00 8.56844796e+00 5.97113193e+00 13 -1.34030736e+00 -1.00645611e+01 -2.88294028e+01 14 3.60095280e+00 9.41798084e+00 -8.69173252e+00 15 1.90929936e+01 -1.81565615e+01 8.83953233e+00 16 2.85625094e+00 1.49813833e+01 1.49040467e+01 17 -1.16217430e+01 -2.04715492e+00 2.41704477e+00 18 3.24868441e+00 6.75456000e+00 -2.24229246e+00 19 7.53872189e+00 -8.45968437e+00 5.12827060e+00 20 -4.40377014e+00 7.23622987e+00 4.14818415e+00 21 -1.20945766e+01 -5.29844904e+00 1.54794650e+01 22 1.07557073e+01 1.46574802e+01 1.33769060e+01 23 1.31713161e+01 -7.56012475e+00 2.47784275e+00 24 -1.21170542e+01 8.85817282e+00 1.07662862e+00 25 -3.73763750e+00 -5.39242320e+00 -2.60689851e+00 26 -4.27942333e-01 8.79546286e+00 -1.08137794e+01 27 2.37935114e+01 -3.47256954e+01 8.02996229e+00 28 -2.85836398e+01 2.65042228e+01 2.46401580e+00 29 -5.59038644e+00 9.79727561e+00 1.26370199e+01 30 1.83277829e+00 1.28077252e+01 1.14205463e+01 31 7.83073841e+00 -6.06944503e+00 3.73026623e+00 32 3.37116029e+00 6.35469668e+00 7.06705116e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Be (Configuration in file "config-T-Be.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1.4235801087420363 Forces: 1 -4.40315132e+00 -6.79032703e+00 -1.08838404e+01 2 -1.00641885e+01 1.23566952e+01 -1.43340204e+00 3 1.19120159e+01 -6.66524419e+00 -4.58922723e+00 4 -1.41751574e+00 1.10598805e+01 5.95112293e+00 5 4.95486011e+00 -1.60940847e+01 1.08091530e+00 6 5.72386447e+00 5.05449558e+00 -2.22833069e+00 7 5.71033846e+00 -2.06860329e+01 -2.97020799e+01 8 -5.25972996e+00 -3.83401352e+00 -1.32328126e+01 9 -1.05582552e+00 -7.58605240e+00 -9.18977950e+00 10 -5.62084413e+00 8.47595478e+00 -1.24052241e+01 11 -1.52674234e+01 -1.22508102e+01 1.06488494e+01 12 -2.38815852e+00 8.56844796e+00 5.97113193e+00 13 -1.34030736e+00 -1.00645611e+01 -2.88294028e+01 14 3.60095280e+00 9.41798084e+00 -8.69173252e+00 15 1.90929936e+01 -1.81565615e+01 8.83953233e+00 16 2.85625094e+00 1.49813833e+01 1.49040467e+01 17 -1.16217430e+01 -2.04715492e+00 2.41704477e+00 18 3.24868441e+00 6.75456000e+00 -2.24229246e+00 19 7.53872189e+00 -8.45968437e+00 5.12827060e+00 20 -4.40377014e+00 7.23622987e+00 4.14818415e+00 21 -1.20945766e+01 -5.29844904e+00 1.54794650e+01 22 1.07557073e+01 1.46574802e+01 1.33769060e+01 23 1.31713161e+01 -7.56012475e+00 2.47784275e+00 24 -1.21170542e+01 8.85817282e+00 1.07662862e+00 25 -3.73763750e+00 -5.39242320e+00 -2.60689851e+00 26 -4.27942333e-01 8.79546286e+00 -1.08137794e+01 27 2.37935114e+01 -3.47256954e+01 8.02996229e+00 28 -2.85836398e+01 2.65042228e+01 2.46401580e+00 29 -5.59038644e+00 9.79727561e+00 1.26370199e+01 30 1.83277829e+00 1.28077252e+01 1.14205463e+01 31 7.83073841e+00 -6.06944503e+00 3.73026623e+00 32 3.37116029e+00 6.35469668e+00 7.06705116e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==16067== Memcheck, a memory error detector ==16067== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==16067== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==16067== Command: python runner2.py EAM_Dynamo_AgrawalMishraWard_2013_Be__MO_404563086984_000 ==16067== ==17778== Warning: invalid file descriptor 1048564 in syscall close() ==17778== Warning: invalid file descriptor 1048565 in syscall close() ==17778== Warning: invalid file descriptor 1048566 in syscall close() ==17778== Warning: invalid file descriptor 1048567 in syscall close() ==17778== Use --log-fd= to select an alternative log fd. ==17778== Warning: invalid file descriptor 1048568 in syscall close() ==17778== Warning: invalid file descriptor 1048569 in syscall close() ==17779== Warning: invalid file descriptor 1048564 in syscall close() ==17779== Warning: invalid file descriptor 1048565 in syscall close() ==17779== Warning: invalid file descriptor 1048566 in syscall close() ==17779== Warning: invalid file descriptor 1048567 in syscall close() ==17779== Use --log-fd= to select an alternative log fd. ==17779== Warning: invalid file descriptor 1048568 in syscall close() ==17779== Warning: invalid file descriptor 1048569 in syscall close() ==17832== Warning: invalid file descriptor 1048564 in syscall close() ==17832== Warning: invalid file descriptor 1048565 in syscall close() ==17832== Warning: invalid file descriptor 1048566 in syscall close() ==17832== Warning: invalid file descriptor 1048567 in syscall close() ==17832== Use --log-fd= to select an alternative log fd. ==17832== Warning: invalid file descriptor 1048568 in syscall close() ==17832== Warning: invalid file descriptor 1048569 in syscall close() ==17833== Warning: invalid file descriptor 1048564 in syscall close() ==17833== Warning: invalid file descriptor 1048565 in syscall close() ==17833== Warning: invalid file descriptor 1048566 in syscall close() ==17833== Warning: invalid file descriptor 1048567 in syscall close() ==17833== Use --log-fd= to select an alternative log fd. ==17833== Warning: invalid file descriptor 1048568 in syscall close() ==17833== Warning: invalid file descriptor 1048569 in syscall close() ==17834== Warning: invalid file descriptor 1048564 in syscall close() ==17834== Warning: invalid file descriptor 1048565 in syscall close() ==17834== Warning: invalid file descriptor 1048566 in syscall close() ==17834== Warning: invalid file descriptor 1048567 in syscall close() ==17834== Use --log-fd= to select an alternative log fd. ==17834== Warning: invalid file descriptor 1048568 in syscall close() ==17834== Warning: invalid file descriptor 1048569 in syscall close() ==17836== Warning: invalid file descriptor 1048564 in syscall close() ==17836== Warning: invalid file descriptor 1048565 in syscall close() ==17836== Warning: invalid file descriptor 1048566 in syscall close() ==17836== Warning: invalid file descriptor 1048567 in syscall close() ==17836== Use --log-fd= to select an alternative log fd. ==17836== Warning: invalid file descriptor 1048568 in syscall close() ==17836== Warning: invalid file descriptor 1048569 in syscall close() ==16067== ==16067== HEAP SUMMARY: ==16067== in use at exit: 1,718,308 bytes in 1,321 blocks ==16067== total heap usage: 31,217 allocs, 29,896 frees, 60,261,889 bytes allocated ==16067== ==16067== LEAK SUMMARY: ==16067== definitely lost: 0 bytes in 0 blocks ==16067== indirectly lost: 0 bytes in 0 blocks ==16067== possibly lost: 178,943 bytes in 97 blocks ==16067== still reachable: 1,539,365 bytes in 1,224 blocks ==16067== suppressed: 0 bytes in 0 blocks ==16067== Rerun with --leak-check=full to see details of leaked memory ==16067== ==16067== For counts of detected and suppressed errors, rerun with: -v ==16067== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16343 from 604) ================================================================================ 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 23:15:01) ===