Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:06:27) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_AcklandTichyVitek_1987_Ni__MO_977363131043_005 Supported species : Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -69.5378601467 Forces: 1 -1.18945546e+00 -2.81076452e+00 -3.17033844e+00 2 -1.83389818e+00 4.40844108e+00 -2.97553374e+00 3 1.42917281e+00 -3.15382631e+00 5.79645225e-01 4 -2.01850629e+00 1.80238651e+00 1.55305912e+00 5 3.37362328e+00 -5.17228295e+00 -1.22901339e+00 6 9.01113370e-01 1.25215377e+00 -2.16469487e+00 7 2.64427186e+00 -7.20845495e+00 -5.76030570e+00 8 -5.34822112e+00 -3.05435639e+00 -3.87416710e-01 9 -4.34024019e+00 -3.55711179e+00 -6.21582046e+00 10 7.81096818e-01 7.17517136e+00 -6.08150001e+00 11 -4.18314881e-01 -5.85406632e+00 3.62134587e+00 12 -4.08579013e+00 5.78506348e+00 1.76943731e+00 13 -8.66569618e-01 -4.20257285e+00 -1.10070265e+01 14 2.78624734e+00 3.57748396e+00 -2.18583819e+00 15 9.90291574e+00 -3.68468539e+00 1.27004438e+00 16 4.28892700e-01 9.31573729e+00 2.90019886e+00 17 -5.84908463e+00 -3.04473777e+00 -2.10176335e+00 18 2.62619662e+00 5.78065251e+00 -7.88270288e-01 19 3.45043284e+00 -4.07881906e+00 3.75082164e+00 20 -2.36422455e+00 3.92653717e+00 2.82669886e+00 21 -4.77306126e+00 -4.01012443e+00 1.22911135e+00 22 5.99045274e+00 6.01578268e+00 4.94300326e+00 23 2.01513330e+00 -1.05289162e+00 2.12543758e+00 24 -1.81736722e+00 7.02261555e-01 1.53327519e+00 25 -3.29995928e+00 -3.40351018e+00 3.64780759e+00 26 -1.90698976e+00 6.46382303e+00 -3.92300991e+00 27 1.71066833e+00 -9.77056727e+00 3.34583818e+00 28 -6.24371257e+00 4.86754298e+00 1.36317991e+00 29 -3.34391744e+00 -4.44066501e+00 2.16131154e+00 30 3.29014636e+00 5.31925299e+00 9.88538166e-01 31 5.90209448e+00 -2.77187094e+00 3.30333811e+00 32 2.46685401e+00 4.87901742e+00 5.07843943e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -65.7040825129 Forces: 1 5.46673183e+00 -3.87120548e+00 1.28722525e+00 2 -3.85634609e+00 3.83501467e+00 1.16211571e+00 3 1.00767698e+00 2.10747500e+00 7.72495417e-01 4 4.38572353e+00 3.41181205e+00 -7.38452258e-01 5 5.69709960e+00 -1.33857403e+00 -4.68004641e-01 6 -4.26804573e+00 5.81558832e+00 1.99957102e+00 7 -1.81730404e+00 -6.41248188e+00 -5.82803833e+00 8 -4.50460306e+00 -3.67930116e+00 -7.52821133e-01 9 -6.47959915e+00 -7.21717432e+00 1.92379266e+00 10 -1.13091442e+00 3.65067284e+00 -2.38895238e+00 11 -1.34802220e+00 -5.38113122e+00 3.05789642e+00 12 6.28576245e-01 2.90911366e+00 2.41535384e+00 13 -3.82090024e-01 -3.80685471e+00 -8.08622160e+00 14 -3.25715163e+00 2.15011304e+00 -2.69857963e+00 15 6.76162422e+00 -3.07060314e+00 3.15559620e-01 16 1.54696694e+00 6.75723512e+00 2.94905615e+00 17 2.01112951e+00 -4.51415371e+00 -2.00297553e+00 18 1.90188071e+00 4.75171260e+00 -9.71739341e-02 19 2.17619291e+00 6.81650078e-01 2.52047026e+00 20 2.53399227e+00 7.39594720e+00 -1.47231590e+00 21 -3.89889133e+00 -7.88730547e-01 1.83689928e+00 22 -4.63121480e-01 8.55433142e+00 6.05113311e+00 23 -4.82756645e+00 -5.51157634e+00 -1.02964118e+00 24 -1.36205800e-01 1.74107438e+00 -4.14898323e+00 25 -9.92094580e-01 -4.17282100e+00 3.61636578e+00 26 -1.49331747e+00 1.66437113e+00 -3.79030498e+00 27 3.93842152e+00 -9.25395781e+00 -3.11400122e+00 28 -6.04388524e+00 4.22642343e+00 -2.45751498e+00 29 -2.68193183e+00 -3.69408439e+00 2.79214051e+00 30 -5.22310739e-04 1.99075555e+00 2.48716933e+00 31 5.29257525e+00 -2.95168784e+00 2.41464273e+00 32 4.23302132e+00 4.02104706e+00 1.47209382e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==28096== Memcheck, a memory error detector ==28096== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==28096== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==28096== Command: python runner2.py EAM_Dynamo_AcklandTichyVitek_1987_Ni__MO_977363131043_005 ==28096== ==28096== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==28096== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==28096== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==28096== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==28096== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==28096== by 0x4010732: call_init (dl-init.c:72) ==28096== by 0x4010732: _dl_init (dl-init.c:119) ==28096== by 0x40151FE: dl_open_worker (dl-open.c:522) ==28096== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==28096== by 0x40147C9: _dl_open (dl-open.c:605) ==28096== by 0x544CF95: dlopen_doit (dlopen.c:66) ==28096== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==28096== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==28096== by 0x544D734: _dlerror_run (dlerror.c:162) ==28096== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==28096== ==28096== ==28096== HEAP SUMMARY: ==28096== in use at exit: 9,926,077 bytes in 3,961 blocks ==28096== total heap usage: 112,725 allocs, 108,764 frees, 63,726,454 bytes allocated ==28096== ==28096== LEAK SUMMARY: ==28096== definitely lost: 0 bytes in 0 blocks ==28096== indirectly lost: 0 bytes in 0 blocks ==28096== possibly lost: 182,191 bytes in 111 blocks ==28096== still reachable: 9,743,886 bytes in 3,850 blocks ==28096== suppressed: 0 bytes in 0 blocks ==28096== Rerun with --leak-check=full to see details of leaked memory ==28096== ==28096== For counts of detected and suppressed errors, rerun with: -v ==28096== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2509 from 170) ================================================================================ 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 (2018-12-15 06:06:57) ===