!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_WuTrinkle_2009_CuAg__MO_270337113239_005 Supported species : Ag Cu random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ag (Configuration in file "config-F-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 195.308871399 Forces: 1 -7.72080993e+00 -1.67240225e+01 -1.43952120e+01 2 -5.59063121e+00 7.23923631e+00 -1.60198075e+01 3 5.51123495e+00 -1.56921862e+01 -2.85852668e+00 4 -1.46718260e+01 8.11057250e+00 6.86166944e+00 5 2.02340908e+00 -2.15829247e+01 -9.49662313e+00 6 1.28921922e+01 2.57418373e+00 -1.51894848e+01 7 1.30091047e+01 -2.58553319e+01 -1.40896489e+01 8 -1.09959932e+01 -1.07601536e+01 4.58470116e+00 9 -1.06578627e+01 -1.47893665e+01 -2.38445348e+01 10 1.27883277e+01 2.21249788e+01 -1.80398993e+01 11 1.80579488e+00 -1.33500169e+01 -9.36588118e+00 12 -2.42029361e+01 2.14187888e+01 1.05586815e+01 13 -8.98239310e+00 -5.48443771e+00 -4.02707086e+01 14 1.22771707e+01 1.50458580e+01 -1.26465318e+01 15 3.70534826e+01 -8.06819278e+00 5.13531124e+00 16 -1.40286441e+00 3.62934907e+01 2.98813278e+00 17 -2.37463096e+01 -1.47718803e+01 -5.48493723e+00 18 8.79282305e+00 1.03659241e+01 -1.85523426e+00 19 8.67724462e+00 -1.76882860e+01 1.51900124e+01 20 -1.29395034e+01 9.76868389e+00 1.52256610e+01 21 -1.19586323e+01 -1.50777923e+01 6.92245831e+00 22 2.23383343e+01 1.72237868e+01 1.24718850e+01 23 7.45987962e+00 -4.29722749e+00 1.26062613e+01 24 1.43017683e+00 -4.49340348e+00 1.14659934e+01 25 -2.96052937e+01 -1.92401850e+00 1.38810292e+01 26 -6.24022826e+00 2.92317532e+01 -5.88491755e+00 27 4.43923580e-01 -2.21163926e+01 1.65313720e+01 28 -2.35884909e+01 1.76343313e+01 7.67531550e+00 29 4.21908416e-01 -1.44318578e+01 8.08781650e+00 30 1.56255574e+01 1.76437558e+01 3.25357637e+00 31 2.08587026e+01 -7.09329874e+00 1.53970287e+01 32 8.89450750e+00 1.95254462e+01 2.06050418e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ag (Configuration in file "config-T-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 392.054620804 Forces: 1 1.59730731e+01 -1.33366564e+01 3.14083333e+00 2 -1.47361870e+01 3.32678740e+00 1.25533921e+01 3 4.62494741e+00 5.70006233e+00 9.73490173e-01 4 1.20113025e+01 1.41980424e+01 9.82875669e+00 5 3.96808968e+00 -7.37576568e+00 -3.28326150e+00 6 -2.07977070e+01 2.08441929e+01 1.41331777e+00 7 -3.09947175e+00 -1.61707736e+01 -1.20245981e+01 8 -1.24050016e+01 -1.04990886e+01 5.70394279e+00 9 -1.18695828e+01 -2.66568986e+01 5.54921466e+00 10 1.29106254e+01 1.05600020e+01 -1.55119795e+00 11 2.02553199e+00 -1.36731100e+01 -9.08002872e+00 12 -1.14980436e+00 6.44910590e+00 1.94203817e+01 13 -7.02120496e+00 -6.62021306e+00 -2.34410665e+01 14 -1.26386476e+01 5.64496536e+00 -1.39921221e+01 15 2.11101115e+01 -7.89909112e+00 6.09056314e+00 16 -1.90831574e-01 2.00948332e+01 4.17972312e+00 17 4.57248957e+00 -1.62681889e+01 -6.67417798e+00 18 1.19147070e+01 1.06536626e+01 -2.02882779e+00 19 8.79659090e+00 3.09299371e+00 6.24196354e+00 20 1.26250688e+01 2.54649186e+01 -4.89685503e+00 21 -1.22500928e+01 1.89035328e+00 8.02515875e+00 22 -2.70332883e+00 2.75646734e+01 1.12271939e+01 23 -2.03744990e+01 -2.08044276e+01 -9.52916738e+00 24 1.19710804e+01 2.59444864e+00 -1.80053815e+01 25 -1.55009103e+01 -5.27354137e+00 1.35563400e+01 26 -3.84191796e+00 7.83591538e+00 -7.93214785e+00 27 9.80785077e+00 -2.48481340e+01 -1.03810556e+01 28 -2.21665389e+01 1.25633874e+01 -1.16332899e+01 29 4.63379042e-01 -1.46055668e+01 8.03003153e+00 30 3.00028270e+00 2.61050938e+00 5.48488960e+00 31 1.27030086e+01 -8.68239511e+00 6.47003928e+00 32 1.22675871e+01 1.16249970e+01 6.56394590e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = -48.2594167435 Forces: 1 -2.41182176e+00 -3.24056062e+00 -3.15558019e+00 2 4.90699971e+00 -3.87333263e+00 -4.02398206e+00 3 5.46501779e+00 -1.11975880e+01 -4.63356770e+00 4 -8.33688901e+00 4.25160016e+00 -4.74513229e+00 5 -1.13865057e+01 -3.72170680e+00 -1.00724101e+01 6 5.98315057e+00 8.24119208e-01 -2.94560106e+00 7 1.16515994e+01 -3.30646519e+00 1.03350754e+01 8 6.68341549e+00 8.21889394e+00 -1.76978580e+01 9 -9.12656637e+00 2.61406311e+00 -4.25519334e+00 10 5.33906348e+00 2.20992229e+00 -5.91527874e+00 11 7.91365691e+00 5.20669346e+00 -1.66573705e+00 12 -4.12606622e+00 2.01740076e+00 4.34294701e+00 13 -4.16023242e+00 1.51619021e+00 -3.10085862e+00 14 6.27558350e+00 2.68980918e+00 -6.41552115e+00 15 1.14333590e+01 -4.95599576e+00 -1.84015505e+00 16 -9.98662847e+00 8.60575127e+00 3.77839387e+00 17 -5.46935394e+00 -4.80510220e+00 6.91103715e+00 18 -8.66259345e+00 2.48823124e+00 1.24160899e+01 19 5.50120997e-01 -1.37961048e+00 1.03258929e-01 20 -1.97676543e+00 -6.13709109e-01 2.80811215e+00 21 4.33643447e+00 -1.57289246e+01 1.23632080e+01 22 5.41950725e+00 2.19311135e-01 -3.31481432e+00 23 2.47496553e+00 -6.69817040e+00 3.37916898e+00 24 -4.25903804e+00 2.01497742e+00 3.06206818e+00 25 -7.92700772e+00 5.62753136e+00 4.16354587e+00 26 -1.71301015e+00 2.73563070e+00 -3.55976233e+00 27 3.24371009e+00 -2.62328374e+00 4.05756257e+00 28 -3.35650429e+00 2.45104219e+00 2.17933038e-01 29 -3.61710267e+00 5.02221447e+00 4.69112862e+00 30 1.29949326e+00 7.56112332e-01 -2.35313727e-01 31 4.36436321e+00 -1.26153955e+00 2.17636246e+00 32 -8.24355039e-01 3.93649463e+00 2.77087351e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = -34.0171828795 Forces: 1 -4.76403572e-01 -4.56982110e+00 -2.25507774e+00 2 4.22643043e+00 -1.95062614e+00 1.68409238e+00 3 8.57174884e+00 -4.21258669e+00 -5.50020604e+00 4 -7.35091933e+00 4.28515043e+00 -5.13987076e+00 5 -1.38287922e+01 -2.33579035e+00 -8.00253950e+00 6 6.42145667e+00 4.25310872e+00 6.65783711e+00 7 1.01061604e+01 1.11853596e+00 1.04138439e+01 8 6.72656046e+00 8.17915288e+00 -1.77017615e+01 9 -7.26632288e+00 3.64681567e+00 -1.72444701e+00 10 5.38246416e+00 3.61443317e+00 -2.80138915e+00 11 7.94659548e+00 5.31429552e+00 -1.66659259e+00 12 -5.70098640e+00 -4.75626212e+00 3.58438929e+00 13 -6.41626219e+00 4.93765133e+00 5.31471961e+00 14 6.98759515e+00 5.33336423e+00 -1.05176137e+00 15 9.60360979e+00 -4.69945139e+00 -2.07498921e+00 16 -1.16853873e+01 4.97240462e+00 4.92941940e+00 17 2.26407643e+00 -3.39605109e+00 5.73065216e+00 18 -8.62152422e+00 2.53119697e+00 1.24493942e+01 19 1.72636784e+00 -3.59907884e+00 -3.05224288e+00 20 1.82019159e+00 -4.68737932e-01 7.53184683e-01 21 6.26362882e+00 -1.18425020e+01 1.17994292e+01 22 -3.20041854e+00 2.84139887e+00 -4.51863964e+00 23 2.22720701e+00 -9.90353699e+00 -1.56166586e+00 24 -7.13791886e+00 -1.02940363e+00 -8.52884327e+00 25 -5.08035870e+00 6.75806269e+00 4.33243900e+00 26 -2.87347558e+00 -3.64407701e+00 -1.21286978e+00 27 3.70797823e+00 -3.63698536e+00 1.78217004e-01 28 6.17388960e+00 4.87864140e+00 3.50383439e+00 29 -3.65416731e+00 5.04715162e+00 4.67472747e+00 30 -6.09575599e+00 -3.24893532e+00 -4.53605311e+00 31 1.32786751e+00 -7.76410749e+00 -5.97692169e+00 32 -2.09513535e+00 3.34658943e+00 1.29969118e+00 MIXED STRUCTURE (pbc=False)-- Species = Ag Cu (Configuration in file "config-F-AgCu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 42.4284158472 Forces: 1 -1.92999381e+00 -4.27855980e+00 -5.77279218e+00 2 -5.65260723e+00 -3.75221629e+00 -6.11772001e+00 3 -3.05350356e+00 -9.15523084e+00 -9.04998315e+00 4 -1.22744095e+01 5.94179478e+00 -5.94910438e+00 5 -5.98178971e+00 -1.06754305e+01 -1.00261173e+01 6 1.24303140e+01 1.63649730e+00 -6.88235595e+00 7 8.16606239e+00 -1.19479808e+01 8.00521245e-01 8 -6.61037583e+00 2.82595526e+00 -4.11026440e+00 9 -9.21243120e+00 -4.48975308e+00 -6.74635566e+00 10 -3.52257608e+00 1.96221264e+01 -2.77063983e+01 11 -6.75007414e+00 -1.24027514e+01 7.87914765e+00 12 -1.57725938e+01 1.11099356e+01 6.56609894e+00 13 5.62044376e+00 2.70740908e+00 -1.58817668e+01 14 1.29902199e+01 4.99949195e+00 -1.11251053e+01 15 6.72978147e+00 1.36749662e+00 1.93690211e+00 16 7.41232905e+00 1.40473171e+01 9.57444752e+00 17 -6.29066562e+00 -1.07830715e+01 3.28351960e+00 18 2.97984207e-02 -7.03399678e+00 6.06173266e+00 19 -9.11552646e-01 -8.31697058e+00 7.32207101e+00 20 -6.88231249e+00 1.11618981e+00 5.68108602e+00 21 6.25950549e+00 -8.87808303e+00 2.97911408e+00 22 1.92066940e+01 8.68200984e-01 8.40201457e+00 23 1.88907880e+00 -4.85787510e+00 4.87260033e+00 24 6.89037562e+00 -1.02027495e+01 1.09192029e+01 25 -1.10461684e+01 3.21143012e+00 -1.72959031e+00 26 -6.77797498e+00 1.07783692e+01 5.59760269e+00 27 -5.84910134e+00 1.67376758e+00 1.47999851e+01 28 -6.48735566e+00 9.33442981e+00 5.09499175e+00 29 1.27225625e+01 2.40084239e+00 1.59607573e+00 30 3.97173081e+00 1.76948277e+00 1.85472165e+00 31 5.01974652e+00 3.64286867e+00 4.51181073e-01 32 5.66684325e+00 7.72106375e+00 5.42453716e+00 MIXED STRUCTURE (pbc=True)-- Species = Ag Cu (Configuration in file "config-T-AgCu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 108.806218929 Forces: 1 4.64739028e+00 -6.43500846e-01 1.15711467e+00 2 -1.08033861e+01 -7.03044079e+00 5.32226668e+00 3 -3.71043591e+00 -8.88543637e-01 -6.92892369e+00 4 -1.33871548e+00 4.14854185e+00 -7.56435512e+00 5 -4.25333415e+00 3.91365036e+00 -5.13179000e+00 6 1.09758884e+01 4.16542429e+00 -8.45719373e-01 7 4.20036132e+00 1.91539793e-01 3.07411200e+00 8 -6.64827955e+00 3.18831601e+00 -4.13322407e+00 9 -3.40052536e+00 -1.11165448e+01 -3.61643839e+00 10 -3.65759316e+00 1.48835581e+01 -1.46395036e+01 11 -6.48241785e+00 -1.21625558e+01 7.94616518e+00 12 -2.90770298e+00 -9.91524748e+00 -7.79029428e+00 13 1.06296932e+01 1.01301222e+01 8.49189901e+00 14 8.39127700e+00 -6.81331990e+00 -1.29514878e+01 15 -2.64635593e+00 1.92435939e+00 4.88057556e+00 16 5.95554987e+00 -6.03168058e+00 8.58685830e+00 17 6.35677340e+00 7.27926058e+00 1.58055906e+01 18 1.11770879e-01 -6.95428665e+00 5.84998116e+00 19 -5.54619795e+00 2.11284788e+00 -2.33323861e+00 20 -3.68221300e+00 5.22261163e+00 7.69093426e-02 21 8.43802639e+00 8.48565206e+00 4.68804791e+00 22 7.38730864e+00 4.98415529e+00 1.07874457e+01 23 -5.39836905e+00 -8.22734708e-01 8.02111190e+00 24 8.32055005e+00 -1.34497931e+01 -1.73734808e+01 25 -6.35182384e+00 3.68285851e+00 -3.94774987e+00 26 -1.10513200e+01 -3.45030544e-01 2.65253194e+00 27 -1.10063856e+01 5.07536031e+00 -4.35779550e+00 28 -2.90141272e+00 8.35565859e+00 -4.25456980e+00 29 1.29263718e+01 2.25610249e+00 1.40855878e+00 30 -3.23503276e+00 -9.05102150e+00 1.98851451e+00 31 -3.31050769e+00 -5.07272050e-01 -2.63439248e-01 32 9.99104789e+00 -4.26804693e+00 5.39432679e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==7398== Memcheck, a memory error detector ==7398== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==7398== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==7398== Command: python runner2.py EAM_Dynamo_WuTrinkle_2009_CuAg__MO_270337113239_005 ==7398== ==7398== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==7398== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==7398== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7398== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7398== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7398== by 0x4010732: call_init (dl-init.c:72) ==7398== by 0x4010732: _dl_init (dl-init.c:119) ==7398== by 0x40151FE: dl_open_worker (dl-open.c:522) ==7398== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7398== by 0x40147C9: _dl_open (dl-open.c:605) ==7398== by 0x544CF95: dlopen_doit (dlopen.c:66) ==7398== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7398== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==7398== by 0x544D734: _dlerror_run (dlerror.c:162) ==7398== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==7398== ==7398== ==7398== HEAP SUMMARY: ==7398== in use at exit: 16,217,825 bytes in 4,274 blocks ==7398== total heap usage: 194,419 allocs, 190,145 frees, 87,272,142 bytes allocated ==7398== ==7398== LEAK SUMMARY: ==7398== definitely lost: 0 bytes in 0 blocks ==7398== indirectly lost: 0 bytes in 0 blocks ==7398== possibly lost: 182,735 bytes in 112 blocks ==7398== still reachable: 16,035,090 bytes in 4,162 blocks ==7398== suppressed: 0 bytes in 0 blocks ==7398== Rerun with --leak-check=full to see details of leaked memory ==7398== ==7398== For counts of detected and suppressed errors, rerun with: -v ==7398== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2520 from 172) ================================================================================ 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.