!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouWadleyJohnson_2001_CuTa__MO_547744193826_000 Supported species : Cu Ta random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6.79532103496 Forces: 1 -2.77331746e+00 -6.21852302e+00 -6.63357147e+00 2 -8.09511774e+00 1.22986943e+01 -8.20344284e+00 3 7.40372258e-01 -8.46285986e+00 -1.43504813e+00 4 -4.02908097e+00 3.86160232e+00 3.90676414e+00 5 1.01417322e+01 -1.63246926e+01 -1.67043446e+00 6 3.00534964e+00 1.63558177e+00 -5.18971689e+00 7 3.75787921e+00 -2.17896004e+01 -2.02373470e+01 8 -7.75440247e+00 -8.89336704e+00 9.60388626e-01 9 -9.87083500e+00 -5.65721148e+00 -1.45101019e+01 10 -3.41330731e+00 1.63255305e+01 -1.58514235e+01 11 -2.29341316e+00 -1.27359993e+01 1.03561628e+01 12 -7.83216133e+00 1.34801424e+01 7.01372379e-02 13 -3.82428221e+00 -7.33097253e+00 -3.35004410e+01 14 5.31244751e+00 7.01774340e+00 -4.36128191e+00 15 2.85005159e+01 -3.91579206e+00 9.22246348e+00 16 3.69478487e+00 2.18082265e+01 1.16409270e+01 17 -8.64418549e+00 -3.50632739e+00 -3.54040830e+00 18 -2.88509598e+00 7.77039897e+00 3.17851538e+00 19 4.60975978e+00 -6.80880077e+00 5.21502758e+00 20 -2.96336040e+00 6.22614373e+00 3.98486632e+00 21 -8.10444845e+00 -8.21283839e+00 6.24404199e+00 22 1.33238271e+01 1.85750328e+01 1.61216376e+01 23 2.33368646e+00 -6.98029487e-01 4.35295128e+00 24 1.90649125e+00 8.45953805e-01 3.76988342e+00 25 -5.40134573e+00 -7.96642456e+00 9.86233010e+00 26 -5.40143493e+00 1.34103260e+01 -7.63902782e+00 27 8.49830041e+00 -2.52574803e+01 6.93386872e+00 28 -2.04998878e+01 1.70197506e+01 2.63158856e+00 29 -6.07143370e+00 -9.75555187e+00 3.18099708e+00 30 6.07002306e+00 1.02424037e+01 3.28046635e-01 31 1.14138967e+01 -7.81223687e+00 9.44143571e+00 32 6.54804366e+00 1.08291769e+01 1.13702115e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 38.6807472355 Forces: 1 1.55327526e+01 -1.34763813e+01 4.05483069e+00 2 -2.67837297e+01 8.63265203e+00 1.98670578e+01 3 2.54250570e-01 1.22494397e+00 -2.87507030e-01 4 1.05962745e+01 8.30929087e+00 -1.06733318e+00 5 1.75284899e+01 -3.56392963e+00 6.46166637e-01 6 -1.88276207e+01 2.00272573e+01 7.64470458e+00 7 -3.64267371e+00 -2.13110932e+01 -2.06933395e+01 8 -7.52127714e+00 -9.25725871e+00 5.95833103e-01 9 -1.78526770e+01 -1.60187429e+01 1.01028520e+01 10 -1.08352973e+01 4.40815869e+00 -8.51119459e+00 11 -2.91349324e+00 -1.22783753e+01 1.01192068e+01 12 3.18903213e+00 7.31551001e+00 4.91930826e+00 13 -2.99404142e+00 -8.32777561e+00 -2.83950311e+01 14 -8.01692968e+00 4.98990906e+00 -9.09950898e+00 15 2.31360179e+01 -3.74951900e+00 8.74954068e+00 16 5.26320260e+00 1.69219698e+01 1.20246315e+01 17 1.04167487e+01 -1.06849624e+01 -3.98317315e+00 18 -3.22410810e+00 7.03224600e+00 3.47964051e+00 19 4.41531869e+00 3.43463182e+00 3.89720505e+00 20 1.32917042e+01 2.02020656e+01 -6.25954857e+00 21 -8.47950258e+00 -2.37743749e+00 6.54217050e+00 22 -4.26540286e+00 2.80835792e+01 1.96194881e+01 23 -1.52554729e+01 -1.98161585e+01 -8.98900268e+00 24 2.15229354e+01 6.78316705e+00 -2.42096649e+01 25 -4.16943707e-01 -9.51401732e+00 9.80646072e+00 26 -4.52147069e+00 3.54394857e+00 -9.44054206e+00 27 1.83551070e+01 -2.56625889e+01 -1.12309715e+01 28 -2.18853320e+01 1.95510011e+01 -7.17028005e+00 29 -5.59909501e+00 -9.10099003e+00 3.70748464e+00 30 -3.83519505e-01 4.13351611e+00 2.62499671e+00 31 9.83732562e+00 -8.41842689e+00 7.57404275e+00 32 1.00794277e+01 8.96380974e+00 3.36147623e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ta (Configuration in file "config-F-Ta.xyz") ----------------------------------------------------------------------------------------------------- Energy = -25.4377239373 Forces: 1 -5.81448626e+00 -9.07018454e+00 -9.52834779e+00 2 -9.11434546e+00 -1.03501979e+01 -3.60243702e+01 3 1.09636474e+01 -3.48896709e+01 -1.81352773e+01 4 -3.05320957e+01 3.00901023e+01 -2.17570679e+01 5 -2.91624457e+00 -1.34438846e+01 -1.46001897e+01 6 1.45443704e+01 -8.05877928e+00 -1.59098142e+01 7 1.86110406e+01 -6.59915129e+00 -8.61226884e+00 8 2.28416290e+01 -1.50705512e+01 9.76693685e+00 9 -7.04009498e+00 1.75057356e+00 -7.82280926e+00 10 -5.07203334e+00 7.60699135e+00 -1.24571797e+01 11 -4.35738476e+01 1.56199624e+01 1.10170395e+01 12 -5.66967614e+00 7.61554266e+00 5.58068529e-01 13 9.42751463e+00 1.12319114e+01 -4.50749061e+01 14 1.48055780e+00 2.91405659e+00 -3.13131714e+00 15 2.67630870e+01 6.72698442e+00 1.42483450e+01 16 6.41055149e+00 2.06869206e+01 -2.28688672e+01 17 -3.57396929e+01 -4.83425075e+01 2.66707506e+01 18 2.07774530e+01 3.14604829e+01 -9.59443752e-01 19 1.01394929e+01 -2.62538092e+01 2.80770270e+01 20 -2.24551145e+01 1.14466929e+01 1.59698285e+01 21 -9.81099784e+00 -1.92106634e+01 1.02345974e+01 22 2.08705799e+01 1.07851357e+01 -1.26682131e+01 23 1.71397881e+01 -2.57195706e+01 1.35182999e+01 24 -1.99791354e+01 1.41549186e+01 1.72387858e+01 25 -1.04336861e+01 -8.94337473e+00 -1.27172570e+01 26 -1.59671397e+01 1.41765514e+01 2.01479160e+01 27 1.21740048e+01 -7.97704640e+00 1.09978419e+01 28 -1.03978115e+01 2.03988715e+01 1.13015065e+01 29 1.45837459e+01 8.01772098e+00 3.17312897e+01 30 2.09932312e+01 1.00365147e+01 1.37980164e+01 31 1.14330946e+01 1.85471512e+00 2.97474507e+00 32 -4.63738680e+00 7.35474259e+00 4.01633450e+00 MIXED STRUCTURE (pbc=False)-- Species = Cu Ta (Configuration in file "config-F-CuTa.xyz") ----------------------------------------------------------------------------------------------------- Energy = 83.643361934 Forces: 1 -4.42497588e+00 -9.15574922e+00 -9.55200413e+00 2 -1.43980496e+01 2.41217976e+01 -1.77136576e+01 3 -1.05680348e+01 -7.16152317e+00 1.69947573e+01 4 -5.78544529e+00 1.60417943e+00 9.87618086e+00 5 1.51802409e+01 -3.13522642e+01 -1.42315866e+01 6 1.52485429e+01 -6.68840459e-02 -2.04234031e+01 7 2.37489411e+01 -2.03464505e+01 -5.13180671e+00 8 -2.93015026e+01 -2.21594684e+01 -2.04225514e+01 9 -3.85583257e+01 -7.76564551e+00 -3.64604913e+01 10 -1.28083464e+01 5.85308408e+01 -1.97986564e+01 11 -2.93789845e+00 -3.77977462e+01 9.20717553e+00 12 -9.13857312e+00 1.41392588e+01 3.53257021e+00 13 3.38629014e+01 -2.47424287e+01 -3.17566362e+01 14 7.88733538e+00 1.38741769e+01 -1.24480960e+01 15 5.34907915e+01 2.26049927e+01 -1.78639553e+01 16 2.55945084e+01 2.80294810e+01 -1.72889289e+01 17 -1.48320454e+01 -2.84785533e+00 -1.38008177e+01 18 -2.39973343e+01 -2.14053550e+01 -2.27852081e+01 19 1.06462911e+01 -9.01884742e+00 1.45820885e+01 20 -9.08326929e+00 3.98170932e-01 6.23905264e+00 21 -2.62423124e+01 -1.77618576e+01 -8.28116295e+00 22 3.59441452e+01 -1.86435307e+01 1.69037319e+01 23 1.93039657e+01 -2.30868551e+00 2.36712618e+01 24 2.68284449e+01 -2.90702053e+01 4.97696381e+01 25 -2.53410771e+01 -1.17417273e+01 8.49897482e+00 26 -3.33729243e+01 4.01399431e+01 3.67027428e+01 27 -1.87359488e+01 2.44299524e+01 2.09407679e+01 28 -3.54802226e+00 4.74919631e+00 4.91866204e+00 29 -6.03237455e+00 2.03963035e+01 1.80612120e+01 30 1.96667630e+01 1.00653696e+01 -9.58888022e+00 31 1.59095678e+01 -7.83064537e+00 7.06468528e+00 32 -1.42059790e+01 1.80932064e+01 3.05843411e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==10726== Memcheck, a memory error detector ==10726== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==10726== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==10726== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001_CuTa__MO_547744193826_000 ==10726== ==10726== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==10726== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==10726== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==10726== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==10726== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==10726== by 0x4010732: call_init (dl-init.c:72) ==10726== by 0x4010732: _dl_init (dl-init.c:119) ==10726== by 0x40151FE: dl_open_worker (dl-open.c:522) ==10726== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==10726== by 0x40147C9: _dl_open (dl-open.c:605) ==10726== by 0x544CF95: dlopen_doit (dlopen.c:66) ==10726== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==10726== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==10726== by 0x544D734: _dlerror_run (dlerror.c:162) ==10726== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==10726== ==10726== ==10726== HEAP SUMMARY: ==10726== in use at exit: 12,293,091 bytes in 4,273 blocks ==10726== total heap usage: 189,377 allocs, 185,104 frees, 85,262,043 bytes allocated ==10726== ==10726== LEAK SUMMARY: ==10726== definitely lost: 0 bytes in 0 blocks ==10726== indirectly lost: 0 bytes in 0 blocks ==10726== possibly lost: 183,295 bytes in 113 blocks ==10726== still reachable: 12,109,796 bytes in 4,160 blocks ==10726== suppressed: 0 bytes in 0 blocks ==10726== Rerun with --leak-check=full to see details of leaked memory ==10726== ==10726== For counts of detected and suppressed errors, rerun with: -v ==10726== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2538 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.