Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:34:30) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : ThreeBodyCluster_SRS_StephensonRadnySmith_1996_Si__MO_604248666067_000 Supported species : Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 239.59131466835225 Forces: 1 -1.20748079e+01 -2.21043117e+01 -2.45677037e+01 2 -1.77536835e+01 -4.53104275e+00 -3.89350288e+01 3 -7.01890529e+00 -3.19102496e+01 -7.86185377e+00 4 -3.06679592e+01 6.46614244e+00 3.91082588e+00 5 9.93842534e+00 -3.92114273e+01 -2.82567510e+01 6 1.15042883e+01 -8.14091379e-01 -1.57978173e+01 7 3.04041514e+01 -3.64258933e+01 -2.69704864e+01 8 1.92711755e+01 -4.41353416e+01 -1.66180232e+01 9 -1.82282157e+01 -1.05741325e+01 -3.13804258e+01 10 -1.50043784e+01 4.58483829e+01 -4.44891705e+01 11 -2.27821781e+01 1.30381559e+01 -6.88089350e+00 12 -2.60416294e+01 2.46515568e+01 7.77750311e+00 13 1.44830726e+01 -9.09242192e+00 -5.82682008e+01 14 1.04029777e+01 7.95202808e+00 -6.04395652e+00 15 5.66195099e+01 6.97364988e+00 -7.82073105e-01 16 1.87208660e+01 4.93176679e+01 3.43990940e+00 17 -2.24613612e+01 -1.65061114e+01 -5.48112366e+00 18 -1.35977926e+01 5.00575821e-02 2.56656706e+01 19 6.75241924e+00 -2.14372101e+01 1.93693534e+01 20 -1.24708560e+01 6.71067075e+00 1.83228652e+01 21 -8.68498760e+00 -3.69759705e+01 2.20382714e+01 22 4.06520639e+01 1.34638661e+01 1.82718176e+01 23 9.32124263e+00 -2.90123068e+00 1.31486807e+01 24 4.05065116e+00 -5.54656076e+00 2.56120613e+01 25 -4.78285812e+01 2.93100019e-01 1.14088629e+01 26 -2.48978066e+01 5.84434871e+01 1.50998327e+01 27 5.79766034e+00 -1.95695626e+01 3.00538954e+01 28 -3.36315915e+01 3.03217660e+01 1.35554246e+01 29 1.29479106e+01 -2.45581792e-01 2.32695785e+01 30 2.26046825e+01 2.61421700e+01 3.86159614e+00 31 3.10163637e+01 -7.53014433e+00 2.83362641e+01 32 8.65727351e+00 1.98385828e+01 2.91910949e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 239.59131466835225 Forces: 1 -1.20748079e+01 -2.21043117e+01 -2.45677037e+01 2 -1.77536835e+01 -4.53104275e+00 -3.89350288e+01 3 -7.01890529e+00 -3.19102496e+01 -7.86185377e+00 4 -3.06679592e+01 6.46614244e+00 3.91082588e+00 5 9.93842534e+00 -3.92114273e+01 -2.82567510e+01 6 1.15042883e+01 -8.14091379e-01 -1.57978173e+01 7 3.04041514e+01 -3.64258933e+01 -2.69704864e+01 8 1.92711755e+01 -4.41353416e+01 -1.66180232e+01 9 -1.82282157e+01 -1.05741325e+01 -3.13804258e+01 10 -1.50043784e+01 4.58483829e+01 -4.44891705e+01 11 -2.27821781e+01 1.30381559e+01 -6.88089350e+00 12 -2.60416294e+01 2.46515568e+01 7.77750311e+00 13 1.44830726e+01 -9.09242192e+00 -5.82682008e+01 14 1.04029777e+01 7.95202808e+00 -6.04395652e+00 15 5.66195099e+01 6.97364988e+00 -7.82073105e-01 16 1.87208660e+01 4.93176679e+01 3.43990940e+00 17 -2.24613612e+01 -1.65061114e+01 -5.48112366e+00 18 -1.35977926e+01 5.00575821e-02 2.56656706e+01 19 6.75241924e+00 -2.14372101e+01 1.93693534e+01 20 -1.24708560e+01 6.71067075e+00 1.83228652e+01 21 -8.68498760e+00 -3.69759705e+01 2.20382714e+01 22 4.06520639e+01 1.34638661e+01 1.82718176e+01 23 9.32124263e+00 -2.90123068e+00 1.31486807e+01 24 4.05065116e+00 -5.54656076e+00 2.56120613e+01 25 -4.78285812e+01 2.93100019e-01 1.14088629e+01 26 -2.48978066e+01 5.84434871e+01 1.50998327e+01 27 5.79766034e+00 -1.95695626e+01 3.00538954e+01 28 -3.36315915e+01 3.03217660e+01 1.35554246e+01 29 1.29479106e+01 -2.45581792e-01 2.32695785e+01 30 2.26046825e+01 2.61421700e+01 3.86159614e+00 31 3.10163637e+01 -7.53014433e+00 2.83362641e+01 32 8.65727351e+00 1.98385828e+01 2.91910949e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==22901== Memcheck, a memory error detector ==22901== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==22901== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==22901== Command: python runner2.py ThreeBodyCluster_SRS_StephensonRadnySmith_1996_Si__MO_604248666067_000 ==22901== ==23441== Warning: invalid file descriptor 1048564 in syscall close() ==23441== Warning: invalid file descriptor 1048565 in syscall close() ==23441== Warning: invalid file descriptor 1048566 in syscall close() ==23441== Warning: invalid file descriptor 1048567 in syscall close() ==23441== Use --log-fd= to select an alternative log fd. ==23441== Warning: invalid file descriptor 1048568 in syscall close() ==23441== Warning: invalid file descriptor 1048569 in syscall close() ==23442== Warning: invalid file descriptor 1048564 in syscall close() ==23442== Warning: invalid file descriptor 1048565 in syscall close() ==23442== Warning: invalid file descriptor 1048566 in syscall close() ==23442== Warning: invalid file descriptor 1048567 in syscall close() ==23442== Use --log-fd= to select an alternative log fd. ==23442== Warning: invalid file descriptor 1048568 in syscall close() ==23442== Warning: invalid file descriptor 1048569 in syscall close() ==23455== Warning: invalid file descriptor 1048564 in syscall close() ==23455== Warning: invalid file descriptor 1048565 in syscall close() ==23455== Warning: invalid file descriptor 1048566 in syscall close() ==23455== Warning: invalid file descriptor 1048567 in syscall close() ==23455== Use --log-fd= to select an alternative log fd. ==23455== Warning: invalid file descriptor 1048568 in syscall close() ==23455== Warning: invalid file descriptor 1048569 in syscall close() ==23456== Warning: invalid file descriptor 1048564 in syscall close() ==23456== Warning: invalid file descriptor 1048565 in syscall close() ==23456== Warning: invalid file descriptor 1048566 in syscall close() ==23456== Warning: invalid file descriptor 1048567 in syscall close() ==23456== Use --log-fd= to select an alternative log fd. ==23456== Warning: invalid file descriptor 1048568 in syscall close() ==23456== Warning: invalid file descriptor 1048569 in syscall close() ==23457== Warning: invalid file descriptor 1048564 in syscall close() ==23457== Warning: invalid file descriptor 1048565 in syscall close() ==23457== Warning: invalid file descriptor 1048566 in syscall close() ==23457== Warning: invalid file descriptor 1048567 in syscall close() ==23457== Use --log-fd= to select an alternative log fd. ==23457== Warning: invalid file descriptor 1048568 in syscall close() ==23457== Warning: invalid file descriptor 1048569 in syscall close() ==23458== Warning: invalid file descriptor 1048564 in syscall close() ==23458== Warning: invalid file descriptor 1048565 in syscall close() ==23458== Warning: invalid file descriptor 1048566 in syscall close() ==23458== Warning: invalid file descriptor 1048567 in syscall close() ==23458== Use --log-fd= to select an alternative log fd. ==23458== Warning: invalid file descriptor 1048568 in syscall close() ==23458== Warning: invalid file descriptor 1048569 in syscall close() ==22901== ==22901== HEAP SUMMARY: ==22901== in use at exit: 1,718,308 bytes in 1,321 blocks ==22901== total heap usage: 31,118 allocs, 29,797 frees, 38,091,740 bytes allocated ==22901== ==22901== LEAK SUMMARY: ==22901== definitely lost: 0 bytes in 0 blocks ==22901== indirectly lost: 0 bytes in 0 blocks ==22901== possibly lost: 178,943 bytes in 97 blocks ==22901== still reachable: 1,539,365 bytes in 1,224 blocks ==22901== suppressed: 0 bytes in 0 blocks ==22901== Rerun with --leak-check=full to see details of leaked memory ==22901== ==22901== For counts of detected and suppressed errors, rerun with: -v ==22901== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16345 from 614) ================================================================================ 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 23:34:49) ===