Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:34:10) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : ThreeBodyBondOrder_PPM_PurjaPunMishin_2017_Si__MO_566683736730_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 = 160.61459235488687 Forces: 1 -1.31160937e+01 -1.31110315e+01 -2.04527122e+01 2 -1.07050335e+01 1.33622003e+01 -1.95862150e+01 3 5.19190384e+00 -1.60328893e+01 1.19040818e+01 4 -1.48596769e+01 6.95006696e+00 5.24055022e+00 5 1.23829464e+01 -2.55275903e+01 -9.38907583e+00 6 1.18750923e+01 5.53726625e+00 -1.48932859e+01 7 1.26725126e+01 -5.37689636e+01 -4.56556314e+01 8 -4.39915076e+01 -3.59332026e+01 -3.79348956e+00 9 -2.61487403e+01 -3.20119078e+00 -2.76362240e+01 10 -1.36715150e+01 3.91637624e+01 -3.79467552e+01 11 -6.56884130e+00 -3.16227651e+01 1.89159753e+01 12 -2.14424865e+01 4.97382034e+01 -2.62206869e+01 13 -2.52040985e+00 -1.68214820e+01 -7.51029194e+01 14 1.31669453e+01 1.35300396e+01 -7.34230064e+00 15 7.88637389e+01 1.26422708e+01 7.80495489e+00 16 1.43411330e+01 5.37640572e+01 2.56943286e+01 17 -2.14250658e+01 -1.58222939e+01 -4.97650152e+00 18 1.19349035e+01 1.77277031e+01 -1.22347369e+01 19 9.13263423e+00 -2.20030289e+01 1.77480335e+01 20 -1.38421834e+01 9.06617441e+00 1.41095281e+01 21 -2.67197778e+01 -2.19470282e+01 9.71997323e+00 22 4.19388829e+01 3.49309481e+01 4.25434349e+01 23 1.12558955e+01 -2.10162921e+00 1.87898691e+01 24 3.06694124e+00 -4.68801889e+00 1.21894679e+01 25 -1.41612664e+01 -3.71553972e+01 3.86927907e+01 26 -1.13794395e+01 3.56887873e+01 -1.31677658e+01 27 1.45336555e+01 -5.10586167e+01 2.21571496e+01 28 -4.72285449e+01 3.78119970e+01 7.46923709e+00 29 -1.32381107e+01 -1.27535966e+01 1.52246585e+01 30 1.49807756e+01 1.90788722e+01 8.33659279e-01 31 2.93435060e+01 -9.99063994e+00 2.14988742e+01 32 1.63372260e+01 2.45470156e+01 2.78617334e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 160.61459235488687 Forces: 1 -1.31160937e+01 -1.31110315e+01 -2.04527122e+01 2 -1.07050335e+01 1.33622003e+01 -1.95862150e+01 3 5.19190384e+00 -1.60328893e+01 1.19040818e+01 4 -1.48596769e+01 6.95006696e+00 5.24055022e+00 5 1.23829464e+01 -2.55275903e+01 -9.38907583e+00 6 1.18750923e+01 5.53726625e+00 -1.48932859e+01 7 1.26725126e+01 -5.37689636e+01 -4.56556314e+01 8 -4.39915076e+01 -3.59332026e+01 -3.79348956e+00 9 -2.61487403e+01 -3.20119078e+00 -2.76362240e+01 10 -1.36715150e+01 3.91637624e+01 -3.79467552e+01 11 -6.56884130e+00 -3.16227651e+01 1.89159753e+01 12 -2.14424865e+01 4.97382034e+01 -2.62206869e+01 13 -2.52040985e+00 -1.68214820e+01 -7.51029194e+01 14 1.31669453e+01 1.35300396e+01 -7.34230064e+00 15 7.88637389e+01 1.26422708e+01 7.80495489e+00 16 1.43411330e+01 5.37640572e+01 2.56943286e+01 17 -2.14250658e+01 -1.58222939e+01 -4.97650152e+00 18 1.19349035e+01 1.77277031e+01 -1.22347369e+01 19 9.13263423e+00 -2.20030289e+01 1.77480335e+01 20 -1.38421834e+01 9.06617441e+00 1.41095281e+01 21 -2.67197778e+01 -2.19470282e+01 9.71997323e+00 22 4.19388829e+01 3.49309481e+01 4.25434349e+01 23 1.12558955e+01 -2.10162921e+00 1.87898691e+01 24 3.06694124e+00 -4.68801889e+00 1.21894679e+01 25 -1.41612664e+01 -3.71553972e+01 3.86927907e+01 26 -1.13794395e+01 3.56887873e+01 -1.31677658e+01 27 1.45336555e+01 -5.10586167e+01 2.21571496e+01 28 -4.72285449e+01 3.78119970e+01 7.46923709e+00 29 -1.32381107e+01 -1.27535966e+01 1.52246585e+01 30 1.49807756e+01 1.90788722e+01 8.33659279e-01 31 2.93435060e+01 -9.99063994e+00 2.14988742e+01 32 1.63372260e+01 2.45470156e+01 2.78617334e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==17786== Memcheck, a memory error detector ==17786== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==17786== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==17786== Command: python runner2.py ThreeBodyBondOrder_PPM_PurjaPunMishin_2017_Si__MO_566683736730_000 ==17786== ==20460== Warning: invalid file descriptor 1048564 in syscall close() ==20460== Warning: invalid file descriptor 1048565 in syscall close() ==20460== Warning: invalid file descriptor 1048566 in syscall close() ==20460== Warning: invalid file descriptor 1048567 in syscall close() ==20460== Use --log-fd= to select an alternative log fd. ==20460== Warning: invalid file descriptor 1048568 in syscall close() ==20460== Warning: invalid file descriptor 1048569 in syscall close() ==20462== Warning: invalid file descriptor 1048564 in syscall close() ==20462== Warning: invalid file descriptor 1048565 in syscall close() ==20462== Warning: invalid file descriptor 1048566 in syscall close() ==20462== Warning: invalid file descriptor 1048567 in syscall close() ==20462== Use --log-fd= to select an alternative log fd. ==20462== Warning: invalid file descriptor 1048568 in syscall close() ==20462== Warning: invalid file descriptor 1048569 in syscall close() ==20489== Warning: invalid file descriptor 1048564 in syscall close() ==20489== Warning: invalid file descriptor 1048565 in syscall close() ==20489== Warning: invalid file descriptor 1048566 in syscall close() ==20489== Warning: invalid file descriptor 1048567 in syscall close() ==20489== Use --log-fd= to select an alternative log fd. ==20489== Warning: invalid file descriptor 1048568 in syscall close() ==20489== Warning: invalid file descriptor 1048569 in syscall close() ==20491== Warning: invalid file descriptor 1048564 in syscall close() ==20491== Warning: invalid file descriptor 1048565 in syscall close() ==20491== Warning: invalid file descriptor 1048566 in syscall close() ==20491== Warning: invalid file descriptor 1048567 in syscall close() ==20491== Use --log-fd= to select an alternative log fd. ==20491== Warning: invalid file descriptor 1048568 in syscall close() ==20491== Warning: invalid file descriptor 1048569 in syscall close() ==20493== Warning: invalid file descriptor 1048564 in syscall close() ==20493== Warning: invalid file descriptor 1048565 in syscall close() ==20493== Warning: invalid file descriptor 1048566 in syscall close() ==20493== Warning: invalid file descriptor 1048567 in syscall close() ==20493== Use --log-fd= to select an alternative log fd. ==20493== Warning: invalid file descriptor 1048568 in syscall close() ==20493== Warning: invalid file descriptor 1048569 in syscall close() ==20498== Warning: invalid file descriptor 1048564 in syscall close() ==20498== Warning: invalid file descriptor 1048565 in syscall close() ==20498== Warning: invalid file descriptor 1048566 in syscall close() ==20498== Warning: invalid file descriptor 1048567 in syscall close() ==20498== Use --log-fd= to select an alternative log fd. ==20498== Warning: invalid file descriptor 1048568 in syscall close() ==20498== Warning: invalid file descriptor 1048569 in syscall close() ==17786== ==17786== HEAP SUMMARY: ==17786== in use at exit: 1,718,308 bytes in 1,321 blocks ==17786== total heap usage: 31,227 allocs, 29,906 frees, 38,094,563 bytes allocated ==17786== ==17786== LEAK SUMMARY: ==17786== definitely lost: 0 bytes in 0 blocks ==17786== indirectly lost: 0 bytes in 0 blocks ==17786== possibly lost: 178,943 bytes in 97 blocks ==17786== still reachable: 1,539,365 bytes in 1,224 blocks ==17786== suppressed: 0 bytes in 0 blocks ==17786== Rerun with --leak-check=full to see details of leaked memory ==17786== ==17786== For counts of detected and suppressed errors, rerun with: -v ==17786== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16372 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 23:34:33) ===