!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_NicholAckland_2016_Na__MO_048172193005_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 = 143.94391760386833 Forces: 1 -3.99676753e+00 -1.08609065e+01 -8.94809175e+00 2 -3.50249228e+00 2.52455145e+00 -9.06845421e+00 3 2.32857943e+00 -7.58253052e+00 -2.42051323e+00 4 -6.80226025e+00 6.37450537e+00 6.12595956e+00 5 2.29199683e+00 -1.15035392e+01 -5.00126849e+00 6 6.65299469e+00 7.41595605e-01 -8.07844176e+00 7 6.30810554e+00 -1.77245430e+01 -1.25174021e+01 8 -1.12766278e+01 -1.11514491e+01 2.13721633e+00 9 -9.84835104e+00 5.24512459e-02 -1.19356011e+01 10 -4.12486886e+00 1.48067272e+01 -1.34081498e+01 11 -4.46240580e+00 -8.55864253e+00 7.29558682e+00 12 -7.99152977e+00 1.20723561e+01 -4.65096436e+00 13 9.10679645e-04 -2.53532796e+00 -2.55245719e+01 14 6.45567939e+00 6.28892856e+00 -4.09429326e+00 15 2.56223302e+01 5.23126338e+00 5.02863156e+00 16 5.35030855e+00 1.82980498e+01 7.43660430e+00 17 -1.12952652e+01 -6.21117601e+00 -9.38767975e-01 18 2.84822673e+00 6.90925703e+00 -3.85774012e+00 19 1.99273122e+00 -1.13288079e+01 7.42966656e+00 20 -7.37875472e+00 3.24615170e+00 6.88299867e+00 21 -6.35220579e+00 -8.19683916e+00 4.68104632e+00 22 1.31389488e+01 1.12622356e+01 1.13328211e+01 23 3.92817109e+00 -2.34420232e+00 6.70784785e+00 24 3.93354456e+00 1.36035093e+00 7.09172534e+00 25 -7.86877119e+00 -8.54203547e+00 4.81695806e+00 26 -3.40278697e+00 1.37536059e+01 -4.27389423e+00 27 4.93267336e+00 -1.61751421e+01 9.35429207e+00 28 -1.66079982e+01 1.39078387e+01 5.04145708e+00 29 -3.77181469e+00 -7.09874220e+00 3.49052888e+00 30 7.71445692e+00 1.05798186e+01 -3.30276551e+00 31 9.84593763e+00 -7.75189273e+00 1.15345734e+01 32 5.33730450e+00 1.01560896e+01 1.16330059e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Na (Configuration in file "config-T-Na.xyz") ----------------------------------------------------------------------------------------------------- Energy = 143.94391760386833 Forces: 1 -3.99676753e+00 -1.08609065e+01 -8.94809175e+00 2 -3.50249228e+00 2.52455145e+00 -9.06845421e+00 3 2.32857943e+00 -7.58253052e+00 -2.42051323e+00 4 -6.80226025e+00 6.37450537e+00 6.12595956e+00 5 2.29199683e+00 -1.15035392e+01 -5.00126849e+00 6 6.65299469e+00 7.41595605e-01 -8.07844176e+00 7 6.30810554e+00 -1.77245430e+01 -1.25174021e+01 8 -1.12766278e+01 -1.11514491e+01 2.13721633e+00 9 -9.84835104e+00 5.24512459e-02 -1.19356011e+01 10 -4.12486886e+00 1.48067272e+01 -1.34081498e+01 11 -4.46240580e+00 -8.55864253e+00 7.29558682e+00 12 -7.99152977e+00 1.20723561e+01 -4.65096436e+00 13 9.10679645e-04 -2.53532796e+00 -2.55245719e+01 14 6.45567939e+00 6.28892856e+00 -4.09429326e+00 15 2.56223302e+01 5.23126338e+00 5.02863156e+00 16 5.35030855e+00 1.82980498e+01 7.43660430e+00 17 -1.12952652e+01 -6.21117601e+00 -9.38767975e-01 18 2.84822673e+00 6.90925703e+00 -3.85774012e+00 19 1.99273122e+00 -1.13288079e+01 7.42966656e+00 20 -7.37875472e+00 3.24615170e+00 6.88299867e+00 21 -6.35220579e+00 -8.19683916e+00 4.68104632e+00 22 1.31389488e+01 1.12622356e+01 1.13328211e+01 23 3.92817109e+00 -2.34420232e+00 6.70784785e+00 24 3.93354456e+00 1.36035093e+00 7.09172534e+00 25 -7.86877119e+00 -8.54203547e+00 4.81695806e+00 26 -3.40278697e+00 1.37536059e+01 -4.27389423e+00 27 4.93267336e+00 -1.61751421e+01 9.35429207e+00 28 -1.66079982e+01 1.39078387e+01 5.04145708e+00 29 -3.77181469e+00 -7.09874220e+00 3.49052888e+00 30 7.71445692e+00 1.05798186e+01 -3.30276551e+00 31 9.84593763e+00 -7.75189273e+00 1.15345734e+01 32 5.33730450e+00 1.01560896e+01 1.16330059e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==58138== Memcheck, a memory error detector ==58138== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==58138== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==58138== Command: python runner2.py EAM_Dynamo_NicholAckland_2016_Na__MO_048172193005_000 ==58138== ==59626== Warning: invalid file descriptor 1048564 in syscall close() ==59626== Warning: invalid file descriptor 1048565 in syscall close() ==59626== Warning: invalid file descriptor 1048566 in syscall close() ==59626== Warning: invalid file descriptor 1048567 in syscall close() ==59626== Use --log-fd= to select an alternative log fd. ==59626== Warning: invalid file descriptor 1048568 in syscall close() ==59626== Warning: invalid file descriptor 1048569 in syscall close() ==59636== Warning: invalid file descriptor 1048564 in syscall close() ==59636== Warning: invalid file descriptor 1048565 in syscall close() ==59636== Warning: invalid file descriptor 1048566 in syscall close() ==59636== Warning: invalid file descriptor 1048567 in syscall close() ==59636== Use --log-fd= to select an alternative log fd. ==59636== Warning: invalid file descriptor 1048568 in syscall close() ==59636== Warning: invalid file descriptor 1048569 in syscall close() ==59806== Warning: invalid file descriptor 1048564 in syscall close() ==59806== Warning: invalid file descriptor 1048565 in syscall close() ==59806== Warning: invalid file descriptor 1048566 in syscall close() ==59806== Warning: invalid file descriptor 1048567 in syscall close() ==59806== Use --log-fd= to select an alternative log fd. ==59806== Warning: invalid file descriptor 1048568 in syscall close() ==59806== Warning: invalid file descriptor 1048569 in syscall close() ==59807== Warning: invalid file descriptor 1048564 in syscall close() ==59807== Warning: invalid file descriptor 1048565 in syscall close() ==59807== Warning: invalid file descriptor 1048566 in syscall close() ==59807== Warning: invalid file descriptor 1048567 in syscall close() ==59807== Use --log-fd= to select an alternative log fd. ==59807== Warning: invalid file descriptor 1048568 in syscall close() ==59807== Warning: invalid file descriptor 1048569 in syscall close() ==59808== Warning: invalid file descriptor 1048564 in syscall close() ==59808== Warning: invalid file descriptor 1048565 in syscall close() ==59808== Warning: invalid file descriptor 1048566 in syscall close() ==59808== Warning: invalid file descriptor 1048567 in syscall close() ==59808== Use --log-fd= to select an alternative log fd. ==59808== Warning: invalid file descriptor 1048568 in syscall close() ==59808== Warning: invalid file descriptor 1048569 in syscall close() ==59809== Warning: invalid file descriptor 1048564 in syscall close() ==59809== Warning: invalid file descriptor 1048565 in syscall close() ==59809== Warning: invalid file descriptor 1048566 in syscall close() ==59809== Warning: invalid file descriptor 1048567 in syscall close() ==59809== Use --log-fd= to select an alternative log fd. ==59809== Warning: invalid file descriptor 1048568 in syscall close() ==59809== Warning: invalid file descriptor 1048569 in syscall close() ==58138== ==58138== HEAP SUMMARY: ==58138== in use at exit: 1,718,292 bytes in 1,321 blocks ==58138== total heap usage: 31,120 allocs, 29,799 frees, 47,288,127 bytes allocated ==58138== ==58138== LEAK SUMMARY: ==58138== definitely lost: 0 bytes in 0 blocks ==58138== indirectly lost: 0 bytes in 0 blocks ==58138== possibly lost: 178,943 bytes in 97 blocks ==58138== still reachable: 1,539,349 bytes in 1,224 blocks ==58138== suppressed: 0 bytes in 0 blocks ==58138== Rerun with --leak-check=full to see details of leaked memory ==58138== ==58138== For counts of detected and suppressed errors, rerun with: -v ==58138== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11272 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.