!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_OnatDurukanoglu_2014_CuNi__MO_592013496703_005 Supported species : Cu Ni 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 = 6.40057287749 Forces: 1 -2.29727846e+00 -5.73965244e+00 -6.07356996e+00 2 -6.80698058e+00 1.11853473e+01 -6.60392287e+00 3 3.48815101e-01 -7.99880229e+00 -1.56619428e+00 4 -3.23927963e+00 4.61374285e+00 4.22299017e+00 5 8.61202706e+00 -1.45071216e+01 -8.34554157e-01 6 2.56517367e+00 2.80926778e+00 -5.06908709e+00 7 4.49398640e+00 -2.06935257e+01 -1.80578483e+01 8 -6.54769068e+00 -6.93512815e+00 -6.69838055e+00 9 -9.20464344e+00 -5.25765764e+00 -1.30609263e+01 10 -3.52838595e+00 1.52728287e+01 -1.48471178e+01 11 -4.27424088e+00 -1.17671303e+01 1.12699258e+01 12 -6.06445680e+00 8.60940187e+00 3.15244323e+00 13 -2.77224773e+00 -1.00503740e+01 -2.93797977e+01 14 4.84396363e+00 6.66686472e+00 -3.99433398e+00 15 2.63565172e+01 -4.65260926e+00 5.78852898e+00 16 3.58214180e+00 2.08247985e+01 1.04907342e+01 17 -7.63752738e+00 -2.95880242e+00 -3.30765614e+00 18 -5.93123672e+00 6.17799205e+00 5.86170820e+00 19 3.13268660e+00 -6.53135961e+00 4.33061047e+00 20 -2.42385016e+00 5.58189695e+00 3.57194686e+00 21 -8.31706078e+00 -9.81001066e+00 3.31617437e+00 22 1.41096020e+01 1.59423223e+01 1.54505725e+01 23 5.61749357e+00 -2.19849714e+00 5.06838639e+00 24 -7.95090299e-01 5.63152751e+00 4.54876691e+00 25 -6.55085768e+00 -6.71245257e+00 2.24103610e-01 26 -4.59210526e+00 1.35475217e+01 -7.28657915e+00 27 8.56140644e+00 -2.34129408e+01 8.80131705e+00 28 -1.77175773e+01 1.56235437e+01 3.63932823e+00 29 -5.76979651e+00 -6.04833922e+00 6.36376683e+00 30 5.44172198e+00 9.49396104e+00 1.80019775e+00 31 1.04645089e+01 -6.75006679e+00 8.29100868e+00 32 6.34026196e+00 1.00434535e+01 1.05874581e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 26.3025558015 Forces: 1 1.48764830e+01 -1.15056892e+01 2.41244450e+00 2 -1.80281956e+01 1.36804596e+01 9.58305467e+00 3 1.32726721e-01 9.98588542e-01 -4.23529334e-01 4 9.13846083e+00 8.84470059e+00 -1.87438198e+00 5 1.45321596e+01 -4.88470469e+00 4.16882136e+00 6 -1.36900015e+01 2.03263339e+01 1.26341318e+01 7 -2.35103248e+00 -1.97614108e+01 -1.82881693e+01 8 -6.51203104e+00 -6.78304489e+00 -6.67066673e+00 9 -1.63645972e+01 -1.50950696e+01 9.00550857e+00 10 -1.03427945e+01 4.07229364e+00 -8.14921896e+00 11 -3.97819214e+00 -1.14306949e+01 1.11595850e+01 12 4.41971809e+00 3.35820805e+00 7.31926294e+00 13 -2.49626633e+00 -1.16768295e+01 -2.43502858e+01 14 -7.43471145e+00 4.50211552e+00 -8.49405976e+00 15 2.14334119e+01 -4.90339554e+00 5.69134318e+00 16 4.86404325e+00 1.57254587e+01 1.10363043e+01 17 8.65273303e+00 -9.78778980e+00 -2.36432911e+00 18 -5.68198267e+00 6.16953995e+00 5.70379732e+00 19 2.98278234e+00 2.63667545e+00 3.88122596e+00 20 8.24860138e+00 1.59769255e+01 -4.29295325e+00 21 -8.49337414e+00 -4.44301705e+00 3.54412088e+00 22 -2.38878524e+00 2.45528001e+01 1.85183146e+01 23 -5.84635379e+00 -1.88379956e+01 -1.20795112e+01 24 9.84740197e+00 8.66406251e+00 -1.57854498e+01 25 -1.70466084e+00 -8.71836818e+00 3.45896953e-01 26 -3.45913350e+00 4.06509073e+00 -9.43114645e+00 27 1.78864482e+01 -2.39684630e+01 -7.74008855e+00 28 -1.96664461e+01 1.88447745e+01 -5.32804846e+00 29 -5.71849248e+00 -5.85641027e+00 6.03677114e+00 30 -9.86410996e-01 4.49311573e+00 3.93138035e+00 31 8.98071486e+00 -7.69145940e+00 6.99677411e+00 32 9.14777685e+00 8.43319940e+00 3.30310108e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -7.29101510405 Forces: 1 -5.12210122e+00 -1.03103634e+00 -4.95441227e+00 2 -2.48386541e+00 -8.73173993e+00 -1.36766452e+01 3 -1.04372341e+00 -6.85924256e+00 2.01891935e+00 4 -2.21485893e+01 -3.67026323e+00 -1.54223785e+01 5 -7.30095910e+00 -8.07702619e+00 -1.37543896e+01 6 6.01239918e+00 5.40141474e+00 -9.10447571e+00 7 8.48546469e+00 -7.18523893e+00 1.33265934e+01 8 8.84751559e+00 1.62396080e+00 1.94563061e+00 9 -1.31996827e+01 5.68122485e-01 -7.51543707e+00 10 -1.37948611e+01 2.16348999e+01 -5.91188506e+00 11 -1.27359744e+00 -4.58304796e+00 -1.70236902e+00 12 -7.12642456e+00 7.68979760e+00 3.31234404e+00 13 1.97372966e+01 -1.00151491e+01 -9.83524342e+00 14 2.48093331e+00 5.71168093e+00 -3.62284257e+00 15 3.95333414e+00 3.61237694e+00 -2.13880056e-01 16 2.13477018e+01 8.27405834e+00 -1.52355614e+01 17 -5.67658862e+00 -7.89437159e+00 4.11657976e+00 18 2.16692400e+01 -1.46928693e+01 1.34532292e+01 19 -6.70546582e+00 -1.93395021e+00 1.42846608e+01 20 -2.29586482e+00 -2.91329703e-01 2.59909748e+00 21 1.05424020e+01 -1.43648968e+00 -8.21882006e+00 22 1.06161268e+01 -7.67142997e+00 6.66131138e+00 23 -8.99571699e-01 7.67273235e-01 -8.37111893e-01 24 5.58145075e+00 -1.27137128e+01 9.86256405e+00 25 -1.63331679e+01 1.17416057e+01 3.15081701e+00 26 -1.70499572e+01 1.08426301e+01 2.14374983e+01 27 -6.18190398e+00 6.06141846e+00 8.97230244e+00 28 1.06996117e-01 2.24052384e+00 1.22051401e+00 29 3.39025868e+00 6.44214460e+00 1.96743930e+00 30 3.97401532e+00 4.03205112e+00 -8.92717281e+00 31 9.75821342e+00 -7.94780126e+00 9.04775914e+00 32 -7.86702417e+00 8.09073990e+00 1.55536443e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -26.8404522521 Forces: 1 4.71990137e+00 -3.15732870e+00 6.77511317e+00 2 -1.79369098e+00 -1.19135179e+01 -4.72056491e+00 3 -1.26199677e+00 -2.65598944e+00 2.56939978e+00 4 5.16819771e+00 -8.88865049e+00 -2.32304883e+01 5 -9.75462223e+00 -3.09684004e+00 -9.38340211e+00 6 -5.54351333e+00 1.35809059e+01 5.09676727e+00 7 6.21912790e+00 -2.38183506e+00 1.34488663e+01 8 8.34551726e+00 2.01940023e+00 2.23834752e+00 9 1.59505407e+00 -3.90498259e-01 -8.44461096e+00 10 -1.30099953e+01 1.89509593e+01 -2.35306024e+00 11 -1.10669706e+00 -4.74206253e+00 -1.54651852e+00 12 3.04668422e+00 1.74916995e+00 8.50037736e+00 13 2.02622677e+01 -6.74523981e+00 1.51114979e+01 14 -6.48547900e+00 1.53481651e+01 6.45071108e+00 15 -1.00217326e+01 6.91754258e+00 2.54306974e+00 16 1.89864788e+01 -1.87870941e+00 -1.58067591e+01 17 -3.93963876e+00 1.96033309e+00 3.30005525e+00 18 2.15762301e+01 -1.40867661e+01 1.27581899e+01 19 -9.74424624e+00 4.20564366e+00 1.29419368e+01 20 7.39656747e+00 1.11691297e+01 -1.25668303e+01 21 1.16193878e+01 9.06429981e+00 -6.15804557e+00 22 -1.05206078e+01 -5.85925433e+00 1.90588105e+01 23 -1.76991366e+01 5.08868672e-01 -1.23890087e+01 24 7.77369836e+00 -1.97620341e+01 -2.14142808e-01 25 -4.78058230e+00 5.08349735e+00 2.29097289e+00 26 -1.60408400e+01 2.20293132e+00 1.94674708e+01 27 -1.36323473e+01 6.30182508e+00 -8.91073905e+00 28 1.92957876e+01 -8.00110132e+00 4.67121871e+00 29 2.98907988e+00 6.11840089e+00 1.67833091e+00 30 -1.48856644e+01 5.11423009e+00 -1.75509712e+01 31 6.14028662e+00 -2.08518382e+01 -9.61992952e+00 32 -4.91347616e+00 4.11636293e+00 -6.00606465e+00 MIXED STRUCTURE (pbc=False)-- Species = Cu Ni (Configuration in file "config-F-CuNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 40.1787895565 Forces: 1 -4.90276553e+00 -7.37409611e+00 -4.56174083e+00 2 1.66638645e+01 -6.28460948e+00 -2.00552195e+01 3 -1.95367658e+01 -8.95662031e+00 1.98587641e-01 4 -2.82996621e+01 -8.76337141e+00 4.33889866e+00 5 3.59717913e+00 -6.17830049e+00 -1.38559705e+01 6 4.20228225e+00 7.39912025e+00 -1.22607098e+01 7 1.29356242e+01 -1.76926417e+01 4.51465448e+00 8 -2.09150582e+01 9.19706595e+00 -2.63388874e+01 9 -9.38738537e+00 5.01480063e+00 -8.43678378e+00 10 -2.03762218e+01 9.55522328e+00 -2.64634976e+01 11 1.20939766e+01 1.70616893e+01 -2.92114759e+01 12 -1.00244226e+01 1.14229219e+01 -6.65266285e+00 13 5.16177951e+00 -1.01195779e+01 -1.20085332e+01 14 1.71731932e+00 2.19664346e+00 -2.57007810e+00 15 1.20195088e+01 1.24281006e+00 -1.05005505e+01 16 1.96125524e+01 1.17629101e+01 2.43648250e+01 17 -7.90053480e+00 -1.73540916e+01 -1.51287801e+01 18 7.06777119e+00 -2.48672827e+01 2.31595340e+01 19 1.47798459e+01 -6.88580878e+00 1.04957989e+01 20 -1.17712422e+01 1.85881094e+01 1.12999160e+01 21 4.26639860e+00 -1.54398290e+01 1.64374154e+01 22 2.90888656e+01 -4.12863887e+00 2.83355917e+01 23 1.97124714e+00 -1.94435921e+00 9.96070198e-01 24 -5.90875657e+00 -1.68879071e+00 4.84402988e+00 25 -3.61433899e+01 -3.97471161e+00 1.16464247e+01 26 1.59677787e+01 2.20744305e+01 -2.10333667e+00 27 9.80205759e+00 -1.48418784e+01 1.49796196e+01 28 -1.45468143e+01 1.16212567e+01 1.02797634e+01 29 6.36303340e+00 1.17660523e+01 1.34682886e+01 30 1.24555025e+00 7.53783773e+00 5.94505043e+00 31 6.67368036e+00 6.97225487e+00 3.54961128e+00 32 4.48270392e+00 3.08148185e+00 1.29414678e+00 MIXED STRUCTURE (pbc=True)-- Species = Cu Ni (Configuration in file "config-T-CuNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 21.9550645724 Forces: 1 1.56675489e+01 -1.29692443e+01 -5.86881072e+00 2 1.64536222e+01 -6.39695069e+00 -1.78497534e+01 3 -1.94273933e+01 -2.13033928e+00 6.60925621e-01 4 -2.24240546e+01 -8.18405149e+00 4.72300786e+00 5 5.50062509e+00 9.69910609e+00 -9.11763005e+00 6 -1.05004956e+01 1.84000207e+01 -6.59060856e+00 7 5.25307696e+00 -4.15462327e+00 4.70110385e+00 8 -2.09001066e+01 9.11283728e+00 -2.60302398e+01 9 -7.99318450e+00 1.54471398e+00 -3.21572137e+00 10 -3.19098606e+01 -1.12332784e+00 -1.42574701e+01 11 1.17458776e+01 1.68607187e+01 -2.87927291e+01 12 1.74713417e+00 8.10943368e+00 -5.47404770e+00 13 5.05041442e+00 -1.00769830e+01 -6.15675144e+00 14 -4.38510033e+00 -5.47745351e+00 -6.68185180e+00 15 5.05233002e+00 3.66996572e-01 -1.11989687e+01 16 1.95987471e+01 3.20231547e+00 2.38790920e+01 17 -8.44949517e+00 -5.94945916e-01 -1.61399127e+01 18 7.16860114e+00 -2.43782574e+01 2.23651311e+01 19 1.54957570e+01 -2.26749409e+00 1.01737906e+01 20 -3.65286906e+00 1.34600668e+01 8.84167119e+00 21 3.31693009e+00 -8.77862362e+00 1.77577104e+01 22 2.52491052e+01 -3.83904833e+00 2.66522754e+01 23 5.49162744e+00 9.45517915e-01 -8.31758912e+00 24 -7.03662681e+00 -2.65058667e+00 -6.52411644e-01 25 -2.93130916e+01 -4.73045675e+00 1.18111742e+01 26 1.88992966e+01 1.05079638e+01 -3.99037149e+00 27 1.17638853e+01 -1.46121292e+01 1.06471124e+01 28 -1.30511823e+01 5.53564681e+00 1.40030532e+01 29 5.84952263e+00 1.12173834e+01 1.30270727e+01 30 -4.94168655e+00 -5.40494253e+00 1.26609984e+01 31 -9.24582493e-01 1.26740888e+01 3.18863540e+00 32 5.60562773e+00 -3.86735199e+00 -1.47578867e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==5434== Memcheck, a memory error detector ==5434== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==5434== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==5434== Command: python runner2.py EAM_Dynamo_OnatDurukanoglu_2014_CuNi__MO_592013496703_005 ==5434== ==5434== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==5434== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==5434== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5434== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5434== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5434== by 0x4010732: call_init (dl-init.c:72) ==5434== by 0x4010732: _dl_init (dl-init.c:119) ==5434== by 0x40151FE: dl_open_worker (dl-open.c:522) ==5434== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==5434== by 0x40147C9: _dl_open (dl-open.c:605) ==5434== by 0x544CF95: dlopen_doit (dlopen.c:66) ==5434== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==5434== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==5434== by 0x544D734: _dlerror_run (dlerror.c:162) ==5434== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==5434== ==5434== ==5434== HEAP SUMMARY: ==5434== in use at exit: 35,868,325 bytes in 4,274 blocks ==5434== total heap usage: 198,995 allocs, 194,721 frees, 109,340,473 bytes allocated ==5434== ==5434== LEAK SUMMARY: ==5434== definitely lost: 0 bytes in 0 blocks ==5434== indirectly lost: 0 bytes in 0 blocks ==5434== possibly lost: 182,735 bytes in 112 blocks ==5434== still reachable: 35,685,590 bytes in 4,162 blocks ==5434== suppressed: 0 bytes in 0 blocks ==5434== Rerun with --leak-check=full to see details of leaked memory ==5434== ==5434== For counts of detected and suppressed errors, rerun with: -v ==5434== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2525 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.