Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:25:31) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MagneticCubic_DerletNguyenDudarev_2007_Nb__MO_218026715338_002 Supported species : Nb random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Nb (Configuration in file "config-F-Nb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 621.0161371242644 Forces: 1 -2.58041776e+01 -4.81135521e+01 -4.98888636e+01 2 -4.60253116e+01 7.94676641e+01 -5.06321677e+01 3 8.98759962e+00 -3.54978721e+01 1.34012483e+01 4 -2.74781161e+01 3.13516739e+01 2.82829318e+01 5 7.46958808e+01 -1.01504167e+02 -2.85932643e+01 6 1.75245444e+01 1.12968476e+01 -3.55077671e+01 7 6.14359225e+01 -1.64417061e+02 -1.45794217e+02 8 -1.12948326e+02 -9.27300004e+01 -2.69384037e+01 9 -5.92708930e+01 -8.42728939e+01 -1.28927868e+02 10 -1.56638267e+01 1.31670412e+02 -1.37431032e+02 11 -6.01772400e+01 -1.01533334e+02 5.56649328e+01 12 -8.86674838e+01 9.56648414e+01 7.46674917e+01 13 -2.18523894e+01 -9.15553250e+01 -2.52810741e+02 14 5.44458828e+01 6.93624379e+01 -4.61791628e+01 15 2.35877072e+02 -6.90478705e+01 1.36886970e+01 16 2.85036260e+01 2.13198212e+02 6.38878001e+01 17 -1.20645181e+02 -8.31682809e+01 -4.54233669e+01 18 8.94582696e+01 1.11861043e+02 -1.05355958e+02 19 4.59355086e+01 -1.33974601e+02 8.30860571e+01 20 -9.21577570e+01 5.09756532e+01 1.07178971e+02 21 -8.51530479e+01 -6.68069903e+01 4.78808274e+01 22 1.25497180e+02 1.15375725e+02 1.18604060e+02 23 2.41547842e+01 -1.18352230e+01 3.70435636e+01 24 3.67448088e+01 3.28314629e+01 4.43661292e+01 25 -1.01297438e+02 -3.39517754e+01 -3.66071705e+01 26 -4.60800454e+01 1.44762686e+02 -6.23510156e+01 27 4.87794388e+01 -1.78155191e+02 1.02928515e+02 28 -1.39168894e+02 1.26415920e+02 5.06483874e+01 29 -5.12423884e+01 -7.71814445e+01 8.09369902e+01 30 7.43969785e+01 1.08892379e+02 5.17345447e+01 31 1.03721101e+02 -4.90821435e+01 7.01311353e+01 32 6.34739174e+01 9.97007685e+01 1.08308715e+02 MONOATOMIC STRUCTURE (pbc=True)-- Species = Nb (Configuration in file "config-T-Nb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 621.0161371242644 Forces: 1 -2.58041776e+01 -4.81135521e+01 -4.98888636e+01 2 -4.60253116e+01 7.94676641e+01 -5.06321677e+01 3 8.98759962e+00 -3.54978721e+01 1.34012483e+01 4 -2.74781161e+01 3.13516739e+01 2.82829318e+01 5 7.46958808e+01 -1.01504167e+02 -2.85932643e+01 6 1.75245444e+01 1.12968476e+01 -3.55077671e+01 7 6.14359225e+01 -1.64417061e+02 -1.45794217e+02 8 -1.12948326e+02 -9.27300004e+01 -2.69384037e+01 9 -5.92708930e+01 -8.42728939e+01 -1.28927868e+02 10 -1.56638267e+01 1.31670412e+02 -1.37431032e+02 11 -6.01772400e+01 -1.01533334e+02 5.56649328e+01 12 -8.86674838e+01 9.56648414e+01 7.46674917e+01 13 -2.18523894e+01 -9.15553250e+01 -2.52810741e+02 14 5.44458828e+01 6.93624379e+01 -4.61791628e+01 15 2.35877072e+02 -6.90478705e+01 1.36886970e+01 16 2.85036260e+01 2.13198212e+02 6.38878001e+01 17 -1.20645181e+02 -8.31682809e+01 -4.54233669e+01 18 8.94582696e+01 1.11861043e+02 -1.05355958e+02 19 4.59355086e+01 -1.33974601e+02 8.30860571e+01 20 -9.21577570e+01 5.09756532e+01 1.07178971e+02 21 -8.51530479e+01 -6.68069903e+01 4.78808274e+01 22 1.25497180e+02 1.15375725e+02 1.18604060e+02 23 2.41547842e+01 -1.18352230e+01 3.70435636e+01 24 3.67448088e+01 3.28314629e+01 4.43661292e+01 25 -1.01297438e+02 -3.39517754e+01 -3.66071705e+01 26 -4.60800454e+01 1.44762686e+02 -6.23510156e+01 27 4.87794388e+01 -1.78155191e+02 1.02928515e+02 28 -1.39168894e+02 1.26415920e+02 5.06483874e+01 29 -5.12423884e+01 -7.71814445e+01 8.09369902e+01 30 7.43969785e+01 1.08892379e+02 5.17345447e+01 31 1.03721101e+02 -4.90821435e+01 7.01311353e+01 32 6.34739174e+01 9.97007685e+01 1.08308715e+02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==7883== Memcheck, a memory error detector ==7883== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==7883== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==7883== Command: python runner2.py EAM_MagneticCubic_DerletNguyenDudarev_2007_Nb__MO_218026715338_002 ==7883== ==8943== Warning: invalid file descriptor 1048564 in syscall close() ==8943== Warning: invalid file descriptor 1048565 in syscall close() ==8943== Warning: invalid file descriptor 1048566 in syscall close() ==8943== Warning: invalid file descriptor 1048567 in syscall close() ==8943== Use --log-fd= to select an alternative log fd. ==8943== Warning: invalid file descriptor 1048568 in syscall close() ==8943== Warning: invalid file descriptor 1048569 in syscall close() ==8949== Warning: invalid file descriptor 1048564 in syscall close() ==8949== Warning: invalid file descriptor 1048565 in syscall close() ==8949== Warning: invalid file descriptor 1048566 in syscall close() ==8949== Warning: invalid file descriptor 1048567 in syscall close() ==8949== Use --log-fd= to select an alternative log fd. ==8949== Warning: invalid file descriptor 1048568 in syscall close() ==8949== Warning: invalid file descriptor 1048569 in syscall close() Potential info: Nb potential Atomic number: 41 ==9033== Warning: invalid file descriptor 1048564 in syscall close() ==9033== Warning: invalid file descriptor 1048565 in syscall close() ==9033== Warning: invalid file descriptor 1048566 in syscall close() ==9033== Warning: invalid file descriptor 1048567 in syscall close() ==9033== Use --log-fd= to select an alternative log fd. ==9033== Warning: invalid file descriptor 1048568 in syscall close() ==9033== Warning: invalid file descriptor 1048569 in syscall close() ==9035== Warning: invalid file descriptor 1048564 in syscall close() ==9035== Warning: invalid file descriptor 1048565 in syscall close() ==9035== Warning: invalid file descriptor 1048566 in syscall close() ==9035== Warning: invalid file descriptor 1048567 in syscall close() ==9035== Use --log-fd= to select an alternative log fd. ==9035== Warning: invalid file descriptor 1048568 in syscall close() ==9035== Warning: invalid file descriptor 1048569 in syscall close() ==9052== Warning: invalid file descriptor 1048564 in syscall close() ==9052== Warning: invalid file descriptor 1048565 in syscall close() ==9052== Warning: invalid file descriptor 1048566 in syscall close() ==9052== Warning: invalid file descriptor 1048567 in syscall close() ==9052== Use --log-fd= to select an alternative log fd. ==9052== Warning: invalid file descriptor 1048568 in syscall close() ==9052== Warning: invalid file descriptor 1048569 in syscall close() ==9066== Warning: invalid file descriptor 1048564 in syscall close() ==9066== Warning: invalid file descriptor 1048565 in syscall close() ==9066== Warning: invalid file descriptor 1048566 in syscall close() ==9066== Warning: invalid file descriptor 1048567 in syscall close() ==9066== Use --log-fd= to select an alternative log fd. ==9066== Warning: invalid file descriptor 1048568 in syscall close() ==9066== Warning: invalid file descriptor 1048569 in syscall close() Potential info: Nb potential Atomic number: 41 Potential info: Nb potential Atomic number: 41 ==7883== ==7883== HEAP SUMMARY: ==7883== in use at exit: 1,718,308 bytes in 1,321 blocks ==7883== total heap usage: 31,167 allocs, 29,846 frees, 38,178,518 bytes allocated ==7883== ==7883== LEAK SUMMARY: ==7883== definitely lost: 0 bytes in 0 blocks ==7883== indirectly lost: 0 bytes in 0 blocks ==7883== possibly lost: 178,943 bytes in 97 blocks ==7883== still reachable: 1,539,365 bytes in 1,224 blocks ==7883== suppressed: 0 bytes in 0 blocks ==7883== Rerun with --leak-check=full to see details of leaked memory ==7883== ==7883== For counts of detected and suppressed errors, rerun with: -v ==7883== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16374 from 616) ================================================================================ 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 23:25:54) === Potential info: Nb potential Atomic number: 41 Potential info: Nb potential Atomic number: 41 Potential info: Nb potential Atomic number: 41