Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:16:40) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_WilsonMendelev_2015_NiZr__MO_306032198193_000 Supported species : Ni Zr 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 = 13.5448952085 Forces: 1 -2.32990092e+01 -1.41426996e+01 -3.81168185e+01 2 -1.47754581e+01 2.11278158e+01 -4.10653205e+00 3 5.19683809e+01 -1.44370621e+01 1.28204208e+01 4 -1.61575963e+01 2.96273369e+01 1.02879503e+01 5 1.38673614e+01 -2.12995374e+01 5.58255789e-01 6 5.31658901e+00 9.64115595e+00 -1.48323858e+01 7 4.62686149e+00 -6.09073814e+01 -5.07687019e+01 8 -2.33378802e+01 -1.18324015e+01 -8.71581187e+00 9 -1.33228801e+00 -1.16900980e+01 -1.46817619e+01 10 -1.88752965e+01 1.43521134e+01 -3.00686519e+01 11 -1.14609347e+01 -2.13003189e+01 1.53091204e+00 12 -4.34776168e+00 1.94345258e+01 5.94838675e+00 13 -2.44329373e+01 -2.87606030e+01 -7.24079286e+01 14 6.46567729e+00 1.23631770e+01 -9.50668085e+00 15 6.19553009e+01 -3.31599906e+01 1.13151420e+01 16 6.50168811e+00 5.32467621e+01 3.53393846e+01 17 -1.63138620e+01 -5.23875404e+00 1.56577503e+01 18 -1.37608812e+01 2.11819710e+01 -3.71403524e+01 19 1.01711898e+01 -3.79372940e+01 1.10254869e+01 20 -1.68787424e+01 1.47583222e+01 7.12900946e+00 21 -2.67528298e+01 -1.17918844e+01 8.54280507e+00 22 2.69797506e+01 4.64806404e+01 4.26009757e+01 23 9.99923052e+00 -2.13596306e-01 1.50824380e+01 24 2.08340167e+01 6.87894029e+00 2.21440098e+01 25 -8.68880361e+00 -1.50695711e+01 5.86933102e+00 26 -8.75801575e+00 2.35020877e+01 -2.29389196e+01 27 2.38789921e+01 -6.17733975e+01 2.40045447e+01 28 -5.05512577e+01 4.55699239e+01 3.17428738e-01 29 -1.49588277e+01 -8.62040251e+00 1.46453754e+01 30 1.01170476e+01 3.04276610e+01 2.62796323e+01 31 2.52669524e+01 -1.08368848e+01 1.25198189e+01 32 1.67333433e+01 2.04194434e+01 1.96654869e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = 68.669304813 Forces: 1 9.71959817e+00 -5.48126302e+01 -1.04172542e+01 2 -4.20497438e+01 2.20818637e+01 4.23190769e+01 3 5.33690545e+01 -1.10197249e+01 1.36144727e+01 4 1.24323110e+01 3.94926151e+01 6.40687482e+00 5 2.39287687e+01 -1.18994440e+01 4.01955481e+00 6 -4.34498775e+01 4.34602319e+01 -6.50587472e+00 7 -6.51047312e+00 -5.89923420e+01 -5.57604414e+01 8 -2.39165268e+01 -1.27098966e+01 -8.87939171e+00 9 -8.95437069e+00 -2.45936871e+01 3.56155674e+00 10 -3.22955395e+01 4.66690979e+00 -2.01184565e+01 11 -1.24723939e+01 -2.20534862e+01 9.36814066e-01 12 2.60905998e+01 1.28421700e+01 1.78609833e+01 13 -2.36865853e+01 -3.13279356e+01 -7.15015765e+01 14 -2.36978874e+01 1.87137822e+01 -2.87410072e+01 15 5.93933078e+01 -3.46682944e+01 1.15269826e+01 16 5.73121197e+00 5.37466478e+01 3.55832115e+01 17 1.62086546e+01 -2.25089128e+01 2.12625708e+01 18 -1.40945308e+01 2.11257010e+01 -3.69195332e+01 19 1.08084505e+01 -1.90555905e+01 1.83909344e+01 20 1.25201998e+01 4.89603689e+01 -2.08337081e+01 21 -2.72039811e+01 -8.51299495e+00 1.02066681e+01 22 -3.79882355e+00 6.80883255e+01 6.01726699e+01 23 -1.81009399e+01 -2.71867700e+01 -1.14518214e+01 24 5.12241754e+01 1.19210231e+01 -2.55943246e+01 25 -6.36937593e+00 -1.70110718e+01 6.99009566e+00 26 -6.33013883e+00 1.14307868e+01 -3.22707401e+01 27 3.67705979e+01 -6.30904227e+01 8.24430961e+00 28 -5.54657550e+01 4.35566919e+01 -4.77109622e+00 29 -1.48404245e+01 -9.19071692e+00 1.60527322e+01 30 -2.33448486e+00 2.18087178e+01 3.36450611e+01 31 2.47465490e+01 -1.20622958e+01 1.23099856e+01 32 2.26283732e+01 1.88003812e+01 1.06606712e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Zr (Configuration in file "config-F-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 528.429166295 Forces: 1 -3.56265954e+01 -2.21963074e+01 -3.23691661e+01 2 -4.89831442e+01 2.75428311e+01 -5.95910346e+01 3 8.72248359e+00 -6.91919212e+01 -3.03291084e+00 4 -9.24789054e+01 1.71331406e+01 -8.30514601e+01 5 3.70931159e+01 -7.87229681e+01 -5.02208281e+01 6 4.77496718e+01 6.64369923e+00 -4.19866118e+01 7 3.68149313e+01 -3.62739172e+01 8.26492531e+00 8 3.85491041e+01 -3.61165146e+01 3.78188988e+01 9 -5.31353995e+01 -1.04253784e+01 -6.42470820e+01 10 3.29663184e+01 4.16268499e+01 -6.14206395e+01 11 2.68098147e+01 2.47863617e+01 -2.03777753e+01 12 -6.62509825e+01 5.18209955e+01 4.14715511e+01 13 9.74994605e+00 6.93395406e+01 -8.43790639e+01 14 1.88529255e+01 1.34969641e+01 -2.20757457e+01 15 5.34088315e+01 1.83927981e+01 -3.02857628e+01 16 2.78012285e+01 4.15967324e+01 -2.38318593e+01 17 -4.43624084e+01 -1.26464668e+02 5.68175543e+01 18 6.04350962e+01 -3.75157122e+01 2.42891683e+01 19 5.47955772e+00 -2.53913885e+01 2.57796596e+01 20 -6.75421299e+01 -7.89708949e+00 7.71368836e+01 21 2.33906111e+01 -4.84528372e+01 1.94221607e+01 22 7.90465508e+01 -7.40586800e+01 -3.98779617e+01 23 1.23391112e+01 -2.39012811e+01 1.29450315e+01 24 -1.89458613e+01 -5.78502109e+01 9.26160485e+01 25 -9.57967968e+01 6.86685963e+01 1.91768916e+01 26 -3.99556730e+01 5.66881269e+01 1.90288187e+01 27 -2.28565534e+01 3.04576964e+01 8.55038966e+01 28 -1.28854376e+01 1.69478411e+01 1.42821427e+01 29 -1.63034904e+01 4.71247289e+01 -3.57971194e+01 30 3.20990477e+01 6.67852424e+01 -1.64508745e+01 31 5.57568559e+01 2.07622002e+01 9.34191672e+01 32 8.05817581e+00 3.46445287e+01 4.10230971e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zr (Configuration in file "config-T-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 2740.27145607 Forces: 1 -1.03037894e+02 2.26129419e+01 5.86787233e+01 2 -3.79233497e+01 8.00811427e+01 2.60909020e+00 3 3.39168452e+01 3.15469416e+00 3.99825219e+01 4 -6.18937685e+01 6.49995222e+00 -1.13703878e+02 5 8.27307696e+01 -5.39447700e+01 2.75716770e+01 6 1.73839425e+01 2.26793534e+01 6.38949871e+01 7 2.24025122e+01 9.89110355e-01 4.68128759e+01 8 2.51117130e+01 -2.14588505e+01 6.24413945e+01 9 -2.01280922e+01 2.48825401e+00 -4.90417647e+01 10 5.69998161e+01 -1.10972208e+02 -1.92383198e+01 11 7.20641275e+01 2.82839215e+01 -1.62324169e+01 12 -6.02432049e+01 2.82931681e+01 5.34129406e+01 13 1.66150275e+01 9.05957423e+01 -3.54392601e+01 14 -5.99490684e+00 -5.41172497e+01 4.84667185e+00 15 -5.96906166e+01 4.46891038e+01 -5.28622014e+01 16 3.67068955e+01 -3.19773960e+01 -2.21857902e+01 17 -3.24596528e+01 -1.53463958e+02 3.73346358e+01 18 1.14306356e+02 -2.59443814e+01 -5.02359957e+00 19 3.42774986e+01 -1.51639550e+01 -1.19621411e+02 20 4.49139203e+01 -8.96809217e+00 9.42049047e+01 21 4.91636869e+01 1.06568291e+01 8.89371504e+00 22 -7.06409865e+01 -8.09399013e+01 -9.87561140e+01 23 -4.80465251e+01 -2.04932922e+01 -2.31331170e+01 24 -5.10575942e+01 -3.84157318e+01 1.97682970e+01 25 4.74190880e+00 9.94234569e+01 -2.31074430e-01 26 -2.83697881e+01 -7.04636694e+00 2.07730949e+01 27 -5.54945600e+00 4.75904747e+01 6.14864984e+01 28 1.43176477e+02 -2.06950772e+00 8.37816152e+01 29 -5.00704146e+01 6.35566225e+01 -7.19371449e+01 30 -1.21370819e+02 6.83385924e+01 -1.61479654e+02 31 -3.16157016e+01 4.45350398e+01 1.04683623e+02 32 3.35812744e+01 -3.94927390e+01 -2.29151931e+00 MIXED STRUCTURE (pbc=False)-- Species = Ni Zr (Configuration in file "config-F-NiZr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 242.737522628 Forces: 1 -3.25997144e+01 -1.46264819e+01 -2.75655159e+01 2 -2.95831230e+00 9.38827104e+00 -4.06931884e+01 3 6.67783769e+00 -4.92559539e+01 2.74229354e+01 4 -5.57521826e+01 8.51907472e+00 -4.21802598e+01 5 2.00305116e+01 -1.69974837e+01 -2.02967031e+01 6 2.22478055e+01 -8.52665033e+00 -1.16202017e+01 7 6.29145225e+01 -5.96227323e+01 -2.42238457e+01 8 -2.81139260e+01 1.90670706e+01 -3.85477558e+01 9 -3.74714712e+01 -5.87072026e+00 -2.06896339e+01 10 1.56519805e+01 2.84940265e+01 -7.91103017e+00 11 -4.79490847e+01 -6.22547675e+01 -7.62176260e+01 12 -2.41128556e+01 1.76069976e+01 -1.58032611e+01 13 -3.03145768e+01 -1.65598060e+01 -1.93212957e+01 14 2.48747864e+01 3.64537649e+01 -3.85551508e+00 15 3.21069787e+01 1.06815914e+01 -2.23294459e+01 16 6.41026733e+01 8.09034190e+01 -5.41644977e+01 17 -1.73447273e+01 -2.64537765e+01 3.42105285e+00 18 2.47070379e+01 -1.19315541e+01 5.60434949e+01 19 -8.38684983e-01 -4.77198306e+00 3.83136232e+00 20 -8.15525794e+00 -3.70209551e+00 9.92682764e+00 21 -2.28412266e+01 -5.56551149e+01 1.53034274e+01 22 8.05513348e+01 -8.41680660e+01 -2.23383607e+01 23 1.16375960e+01 -8.68134786e+00 1.46416305e+01 24 -1.07282505e+01 -2.48420505e+01 3.69428404e+01 25 -5.25736729e+01 -2.68279551e+01 -1.16170425e+00 26 -3.43414677e+01 9.37513449e+01 4.14297736e+01 27 -5.08911651e+01 -3.55902718e+01 5.10346902e+01 28 -2.37577408e+01 3.58574088e+01 3.26623459e+01 29 -8.45655827e+00 -1.03360981e-02 1.09259604e+00 30 3.84518387e+01 5.24050443e+01 -8.26676942e+00 31 5.77468230e+01 4.75254111e+01 1.18744253e+02 32 2.74991492e+01 7.56957223e+01 4.46893800e+01 MIXED STRUCTURE (pbc=True)-- Species = Ni Zr (Configuration in file "config-T-NiZr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 2041.97894598 Forces: 1 -6.64345936e+01 -1.64928726e+01 -3.09732316e+01 2 -1.06556005e+01 2.70579379e+00 3.77310705e+01 3 6.17121800e+01 -1.42915259e+01 7.22484065e+01 4 -1.43949409e+01 -1.36563609e+01 -7.03476115e+01 5 4.71534601e+01 -4.68701452e+01 3.24399533e+01 6 2.20818172e+01 -3.96518634e+01 5.71676232e+00 7 -8.61364317e+00 -8.04900138e+01 -4.74248252e+00 8 -6.56912463e+01 -9.42997860e+00 -1.12294347e+00 9 -4.31550217e+01 2.58842113e+00 1.33026147e+01 10 8.72708225e+00 2.82280207e+01 1.61823809e+01 11 -1.34985328e+01 -6.79151064e+01 -5.60457616e+01 12 -3.17980151e+01 3.90444279e+01 -1.03946357e+02 13 -2.33314658e+01 7.01104363e+00 9.93198711e+01 14 5.66345717e+01 8.44880520e+01 4.53579463e+01 15 -3.42646409e+01 9.69394122e+00 -9.99257858e+01 16 6.27283753e+01 8.59567007e+01 -3.07831267e+01 17 -4.09073797e+00 3.65941945e+01 3.14607867e+00 18 8.52156566e+01 -1.71801573e+01 5.19741354e+01 19 -2.81694598e+00 3.53769479e+01 -2.97945932e+01 20 1.02010721e+01 -4.68185328e+01 2.22649345e+01 21 -4.12461836e+01 -4.36940936e+01 -3.25252322e+01 22 1.08740650e+01 -1.21184053e+02 -4.98355972e+01 23 1.13295057e+01 1.61063402e+01 5.24031054e+01 24 -1.31228725e+01 -8.99649946e+01 -4.34258032e+01 25 9.95041193e+01 -2.93960372e+01 2.28720509e+01 26 2.01145420e+01 7.46729914e+01 4.45911084e+01 27 -4.17790692e+01 8.48909315e-01 -4.03449924e+01 28 3.99899767e+01 1.72942365e+01 8.97904080e+01 29 -6.51142714e+01 -3.86008118e+01 -4.95853683e+01 30 -1.14586305e+02 8.43373822e+01 -4.37056284e+01 31 3.76819571e+01 7.30578290e+01 9.71079358e+01 32 2.06457055e+01 7.76313152e+01 -1.93442480e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==7227== Memcheck, a memory error detector ==7227== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==7227== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==7227== Command: python runner2.py EAM_Dynamo_WilsonMendelev_2015_NiZr__MO_306032198193_000 ==7227== ==7227== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==7227== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==7227== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7227== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7227== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7227== by 0x4010732: call_init (dl-init.c:72) ==7227== by 0x4010732: _dl_init (dl-init.c:119) ==7227== by 0x40151FE: dl_open_worker (dl-open.c:522) ==7227== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7227== by 0x40147C9: _dl_open (dl-open.c:605) ==7227== by 0x544CF95: dlopen_doit (dlopen.c:66) ==7227== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7227== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==7227== by 0x544D734: _dlerror_run (dlerror.c:162) ==7227== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==7227== ==7227== ==7227== HEAP SUMMARY: ==7227== in use at exit: 40,113,417 bytes in 4,274 blocks ==7227== total heap usage: 206,726 allocs, 202,452 frees, 114,365,944 bytes allocated ==7227== ==7227== LEAK SUMMARY: ==7227== definitely lost: 0 bytes in 0 blocks ==7227== indirectly lost: 0 bytes in 0 blocks ==7227== possibly lost: 182,735 bytes in 112 blocks ==7227== still reachable: 39,930,682 bytes in 4,162 blocks ==7227== suppressed: 0 bytes in 0 blocks ==7227== Rerun with --leak-check=full to see details of leaked memory ==7227== ==7227== For counts of detected and suppressed errors, rerun with: -v ==7227== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2523 from 171) ================================================================================ 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 06:17:22) ===