!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MendelevSrolovitzAckland_2005_AlFe__MO_577453891941_005 Supported species : Al Fe random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 67.3024758695 Forces: 1 -5.17615352e+00 -9.09316694e+00 -9.74047603e+00 2 -3.91384177e+00 5.79155160e+00 -9.45080433e+00 3 6.44890609e+00 -1.65093325e+01 -6.31170667e+00 4 -1.28613729e+01 5.85704691e+00 -6.75236886e-02 5 -1.48635088e+00 -1.54277856e+01 -5.21518068e+00 6 9.60004671e+00 5.92238838e+00 -1.03633654e+01 7 9.75829990e+00 -2.56022885e+01 -1.66474768e+01 8 -1.27572188e+01 -1.00975512e+01 -1.69649347e+00 9 -1.01089008e+01 -7.15651703e+00 -1.70426230e+01 10 -3.61387176e+00 1.89667802e+01 -1.91791019e+01 11 -4.10712501e+00 -1.24652334e+01 2.33689183e+00 12 -1.19936691e+01 1.60707555e+01 2.27984507e+00 13 -3.83451653e+00 -1.26452267e+01 -3.70943782e+01 14 9.14739642e+00 1.10912196e+01 -7.50176652e+00 15 3.46379155e+01 -4.89779530e+00 6.22720114e+00 16 4.41541071e+00 3.00569845e+01 1.10503471e+01 17 -1.84391879e+01 -1.18955443e+01 -2.50739053e+00 18 1.03912862e+01 1.25488858e+01 8.02472500e+00 19 4.25839756e+00 -1.40691820e+01 8.00422326e+00 20 -7.32074188e+00 8.44902707e+00 9.04461347e+00 21 -1.11413228e+01 -1.25668192e+01 6.96852302e+00 22 2.03979232e+01 1.93744073e+01 1.30891680e+01 23 5.51282025e+00 -3.02507488e+00 1.11447491e+01 24 2.59622483e+00 6.33435966e+00 5.97389885e+00 25 -1.43751726e+01 -5.34688962e+00 8.60273427e+00 26 -5.50750118e+00 2.10373643e+01 -8.15958328e+00 27 7.40201013e+00 -2.72615324e+01 1.25734257e+01 28 -2.32913243e+01 1.91234954e+01 6.14752448e+00 29 -7.19820976e+00 -1.20236674e+01 9.20496086e+00 30 1.04380976e+01 1.55073959e+01 -1.01655278e+00 31 1.43841433e+01 -1.10029876e+01 1.46519952e+01 32 7.73760308e+00 1.49549322e+01 1.66695969e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 258.516403908 Forces: 1 2.56440562e+01 -1.86623551e+01 5.91253149e+00 2 -2.56196157e+01 6.94411425e+00 3.10358148e+01 3 5.44122522e+00 -2.88716757e-01 -4.55017162e+00 4 7.73942485e+00 1.22704121e+01 -6.58322178e+00 5 3.36751640e+00 -4.56708576e+00 -2.33465258e-01 6 -2.73560139e+01 3.33253246e+01 3.63665888e+01 7 -3.14820504e+00 -2.30842343e+01 -1.64047877e+01 8 -1.31974921e+01 -1.02961773e+01 -1.64346777e+00 9 -1.67003327e+01 -1.99420577e+01 1.11815720e+01 10 -8.41432648e+00 1.03865142e+01 -7.23325301e+00 11 -4.44665745e+00 -1.24730922e+01 2.29704243e+00 12 2.39153029e+00 6.58723216e+00 8.02684421e+00 13 -2.83872329e+00 -1.54445141e+01 -2.83558652e+01 14 -7.08538227e+00 5.10790080e+00 -1.22047303e+01 15 2.48472567e+01 -4.85837472e+00 5.72063039e+00 16 5.89565614e+00 1.99575360e+01 1.24024818e+01 17 5.22891323e+00 -1.80935545e+01 -2.18775762e+00 18 1.20439181e+01 1.25566497e+01 7.87625392e+00 19 4.38068686e+00 1.38106613e+00 4.78012899e+00 20 3.27883547e+01 3.30496684e+01 -5.21091424e+00 21 -1.16074792e+01 -1.20491296e+00 7.69258552e+00 22 -3.59107753e+00 2.99098411e+01 1.70077213e+01 23 -3.20427312e+01 -3.37707204e+01 -3.90576279e+01 24 2.55965008e+01 1.07045209e+01 -3.45027739e+01 25 -5.03941376e+00 -8.36762395e+00 8.43212709e+00 26 -3.97266913e+00 5.15837589e+00 -1.04353341e+01 27 1.74531960e+01 -2.89123198e+01 -1.01012787e+01 28 -2.39568822e+01 2.06524183e+01 -5.89055842e+00 29 -7.05670988e+00 -1.19322256e+01 9.33109665e+00 30 1.96703690e-01 6.16039596e+00 1.93087248e+00 31 1.04032003e+01 -1.29721901e+01 1.03700938e+01 32 1.26555723e+01 1.07181849e+01 4.23082188e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -4.57009115193 Forces: 1 -3.64145989e+00 -4.20087457e+00 -3.88482588e+00 2 -2.15008585e+01 2.72398439e+01 -2.27149335e+01 3 -2.15000940e+01 -2.36406418e+01 3.83011575e+00 4 -1.02315483e+01 2.90110227e+00 3.75553484e+00 5 2.45474230e+01 -3.92604926e+01 -1.36420920e+01 6 6.09028530e+00 4.77398163e+00 -8.37918470e+00 7 2.67384432e+00 -5.73039818e+00 3.50683936e+00 8 2.15932487e+01 1.78746502e+01 1.03499906e+01 9 -3.84829775e+00 -7.79669836e-01 -3.24992492e+00 10 -2.34697124e+01 1.23977035e+01 -1.59392628e+01 11 -1.32561769e+01 -2.91148264e-01 -8.98486643e+00 12 -3.13201639e+00 1.04277886e+01 -8.41218377e+00 13 1.23049976e+01 -2.56353837e+01 -2.71734045e+01 14 1.15435731e+00 1.31492612e+00 -5.87222987e-01 15 3.89530034e+00 -4.31761901e+00 -3.10059524e+00 16 1.68129453e+01 2.71874192e+01 2.88377554e+01 17 -1.20197318e+01 -8.56382389e+00 -1.02646426e+01 18 -9.45330294e+00 2.84455397e+01 1.74844763e+00 19 1.17416924e+01 -2.33995463e+01 2.17379881e+01 20 -1.82269114e+01 1.68186278e+01 6.12309775e+00 21 1.71786565e+01 -2.95377548e+01 4.33141049e-01 22 3.14127448e+00 2.47215141e+01 -2.68047371e+01 23 7.46256471e+00 -2.57185917e+01 2.62056782e+01 24 1.84537493e+00 6.85363080e-01 9.71660097e+00 25 -8.16776525e+00 -9.63086564e+00 7.06243750e+00 26 4.85238015e-01 1.21360442e+01 -3.04702454e+00 27 -5.76073779e+00 3.71932036e+00 1.64221130e+01 28 -4.18964042e+00 7.85964961e-01 4.82191960e+00 29 1.28159890e+01 -4.96078504e+00 1.12860628e+00 30 1.21252823e+01 9.28760392e+00 7.00903735e-01 31 1.96010333e+00 9.38764716e-01 1.02712157e+00 32 5.69676250e-01 4.01143737e+00 8.77660957e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 27.13933597 Forces: 1 1.74236244e+01 -6.53542055e+00 -7.81200330e+00 2 -3.90720731e+01 3.34261274e+01 3.01079156e+00 3 -2.33262870e+01 -2.29186908e+01 5.37393827e+00 4 -4.15432227e+00 4.37559995e+00 6.08201917e+00 5 2.80141633e+01 -4.01172893e+01 -1.15180184e+01 6 -5.12670331e+00 1.42472119e+01 -1.93559437e+00 7 -1.19526763e+01 -4.29555665e+00 1.29703214e+01 8 2.34522641e+01 1.98665166e+01 1.33982299e+01 9 7.11706216e+00 1.88323553e-01 6.70951700e-01 10 -2.60309854e+01 9.98608086e+00 -1.36103454e+01 11 -1.37990272e+01 -2.18896379e-01 -8.89943194e+00 12 6.86578995e+00 7.36734127e+00 -1.11233420e+01 13 1.36799957e+01 -2.67287819e+01 -2.03424848e+01 14 2.15023462e+00 -4.20527330e+00 1.19320351e+01 15 -7.60616586e+00 -5.59383453e+00 -2.27580718e+00 16 1.87044206e+01 2.32141541e+01 3.32023802e+01 17 -5.92603034e+00 -4.81156208e+00 -1.84991226e+01 18 -9.37913975e+00 3.18656546e+01 -1.47602952e-01 19 1.41245323e+01 -1.95647967e+01 1.79607533e+01 20 -1.72399835e+01 1.89646141e+01 2.44820229e+00 21 2.51133722e+01 -1.90981612e+01 -5.13249094e+00 22 -2.46761642e+00 2.91527323e+01 -2.93527377e+01 23 7.30276552e-02 -2.27144604e+01 2.60460187e+01 24 1.82465601e+01 4.92491362e+00 -1.49928372e+01 25 -2.74251194e+00 -1.24206438e+01 9.39224998e+00 26 -3.36211640e+00 -6.78481377e+00 -5.96071701e+00 27 -8.50027505e+00 4.89793127e+00 1.15125237e+01 28 -2.29129103e+00 -9.76994083e+00 1.75117682e+00 29 1.36791969e+01 -6.70812015e+00 7.37144366e-01 30 7.39214443e+00 8.46565927e+00 2.78794552e+00 31 -5.75556767e+00 2.34251857e+00 -7.51969245e+00 32 -7.30361586e+00 -7.99137101e-01 -1.54453871e-01 MIXED STRUCTURE (pbc=False)-- Species = Al Fe (Configuration in file "config-F-AlFe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 36.7734331777 Forces: 1 -6.54333501e+00 -9.58728339e+00 -6.81131241e+00 2 7.70032809e+00 -5.83421308e+00 -1.82078867e+01 3 -1.96411392e+01 -1.63495569e+01 -1.42155919e+01 4 -1.83522701e+01 -5.30688970e+00 5.89752184e+00 5 -2.16009165e+01 -1.07366756e+01 -2.43009660e+01 6 1.11136786e+01 -2.02005392e+01 -3.63985883e+01 7 2.60821077e+01 -1.15311587e+01 1.76987485e+01 8 -2.02666718e-01 1.63213671e+01 -7.86469486e+00 9 -3.34917593e+01 -2.25890322e+01 -2.01016651e+01 10 1.83010880e+01 3.54971237e+01 -4.55620846e+00 11 1.91884629e+01 5.64724378e+00 1.76655195e+01 12 -1.03757284e+01 3.06721682e+01 -2.11984555e+01 13 -3.03531632e-01 -1.08945746e+01 -1.83129817e+01 14 8.19381901e+00 4.03150961e+00 -5.90534000e+00 15 3.88798019e+00 3.52915191e+01 2.13878324e+01 16 -2.63761387e+00 1.45839636e+01 1.59615010e+01 17 -6.63388872e+00 -6.73519174e+00 3.17610855e-01 18 7.67362356e+00 4.06191842e+00 -2.10060286e+01 19 -9.89632909e+00 -1.73784147e+01 1.24746356e+01 20 -2.65407349e+01 -1.86187421e+00 1.91077482e+01 21 2.03474914e+01 -1.84061335e+01 2.34576862e+01 22 1.60583846e+01 -8.01565907e+00 8.85403740e+00 23 2.88711537e-01 -3.84278922e-01 -8.62640944e-02 24 1.25485322e+01 8.56822802e+00 1.02544908e+01 25 -1.05680521e+01 -2.90627227e+01 1.87508515e+01 26 -8.45723873e+00 1.08840117e+01 -1.71533650e+01 27 5.92839597e+00 1.64169492e+00 1.44318187e+01 28 -6.42721470e+00 8.26281844e+00 7.11580141e+00 29 -2.70952921e+00 6.73195456e+00 -1.18788347e+00 30 1.41845747e+01 8.59245616e+00 -1.24541321e+01 31 8.12026347e+00 -4.49114019e+00 1.07285433e+01 32 4.76450628e+00 8.57736122e+00 2.56570171e+01 MIXED STRUCTURE (pbc=True)-- Species = Al Fe (Configuration in file "config-T-AlFe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 74.8668671375 Forces: 1 -1.00313289e+01 9.25043606e+00 -7.06822010e+00 2 6.43307467e+00 -6.67473659e+00 -7.27271746e+00 3 -2.21115175e+01 -9.37279066e+00 -1.38062959e+01 4 -4.96633752e+00 -5.41937024e+00 6.36247837e+00 5 -3.14385483e+01 8.21036224e+00 -2.17817140e+01 6 5.16400252e+00 -1.92531990e+01 -3.78638433e+01 7 1.64945463e+01 1.65171855e+00 2.41851836e+01 8 -1.65994749e-02 1.57872191e+01 -8.15255950e+00 9 -4.84441569e+01 -1.97473598e+01 -8.65082403e-01 10 2.73636390e+01 2.04670139e+01 -3.53058183e-01 11 1.83980158e+01 5.69999381e+00 1.83510795e+01 12 -4.89038596e+00 2.26547164e+01 -2.20411402e+01 13 9.07030988e+00 -1.10571187e+01 -5.94044223e+00 14 1.48561659e+01 -2.17832080e+01 -1.27751160e+01 15 6.15520380e-01 3.60867802e+01 2.09286818e+01 16 -2.07152687e+00 2.11573303e+00 1.77726586e+01 17 3.42862553e-01 -2.56989505e+00 4.05670048e-01 18 6.58714628e+00 4.92187995e+00 -2.08568541e+01 19 -8.65197354e+00 -1.65350726e+01 8.09733671e+00 20 -2.16431754e+01 -5.35563586e+00 1.79712310e+01 21 2.09217680e+01 -1.03755204e+01 2.17483615e+01 22 4.84491608e+00 -7.23754031e+00 9.97073967e+00 23 -6.59525545e-01 8.30151044e+00 -2.14489531e+00 24 1.51599345e+01 9.05706422e+00 5.57217337e+00 25 -2.33151577e+00 -2.70377686e+01 1.57678387e+01 26 -1.05721037e+01 5.99196989e+00 -1.55348261e+01 27 1.23701944e+01 -3.18218369e+00 -1.97109654e+01 28 -9.17363104e-01 2.61823192e+00 6.62022916e+00 29 -2.54962812e+00 6.83315978e+00 -7.59241103e-01 30 5.65593554e+00 3.76221783e+00 -1.07331713e+01 31 1.19662011e+00 -3.46219205e+00 1.04928245e+01 32 5.82103463e+00 5.65358426e+00 2.34136561e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==3549== Memcheck, a memory error detector ==3549== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3549== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==3549== Command: python runner2.py EAM_Dynamo_MendelevSrolovitzAckland_2005_AlFe__MO_577453891941_005 ==3549== ==3549== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==3549== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==3549== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==3549== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==3549== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==3549== by 0x4010732: call_init (dl-init.c:72) ==3549== by 0x4010732: _dl_init (dl-init.c:119) ==3549== by 0x40151FE: dl_open_worker (dl-open.c:522) ==3549== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==3549== by 0x40147C9: _dl_open (dl-open.c:605) ==3549== by 0x544CF95: dlopen_doit (dlopen.c:66) ==3549== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==3549== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==3549== by 0x544D734: _dlerror_run (dlerror.c:162) ==3549== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==3549== ==3549== ==3549== HEAP SUMMARY: ==3549== in use at exit: 39,869,697 bytes in 4,274 blocks ==3549== total heap usage: 198,931 allocs, 194,657 frees, 113,692,102 bytes allocated ==3549== ==3549== LEAK SUMMARY: ==3549== definitely lost: 0 bytes in 0 blocks ==3549== indirectly lost: 0 bytes in 0 blocks ==3549== possibly lost: 182,735 bytes in 112 blocks ==3549== still reachable: 39,686,962 bytes in 4,162 blocks ==3549== suppressed: 0 bytes in 0 blocks ==3549== Rerun with --leak-check=full to see details of leaked memory ==3549== ==3549== For counts of detected and suppressed errors, rerun with: -v ==3549== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2517 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.