!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouJohnsonWadley_2004NISTretabulation_CuAgAu__MO_318213562153_000 Supported species : Ag Au 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 = 225.069373819 Forces: 1 -8.79972746e+00 -1.63190336e+01 -1.68902641e+01 2 -1.59165232e+01 2.44729576e+01 -2.21040707e+01 3 -2.22503404e+00 -2.37162948e+01 -2.55003975e+00 4 -1.36746791e+01 7.69179448e+00 8.04860116e+00 5 2.31020914e+01 -3.65502560e+01 -8.15602079e+00 6 8.97117565e+00 2.00794928e+00 -1.41619436e+01 7 1.32736150e+01 -5.14552019e+01 -4.55278667e+01 8 -1.51044312e+01 -1.79064924e+01 -8.53497653e+00 9 -1.88298417e+01 -2.66744376e+01 -4.50907039e+01 10 -2.28379021e+00 3.83966331e+01 -3.90079660e+01 11 -7.01684096e+00 -2.64150115e+01 1.61634230e+01 12 -2.81983654e+01 3.74377746e+01 2.04712818e+01 13 -7.86688298e+00 -2.00218182e+01 -7.46907422e+01 14 1.57656604e+01 1.92573000e+01 -1.32726313e+01 15 6.69935371e+01 -7.68823014e+00 1.63025334e+01 16 8.40268528e+00 5.41575373e+01 2.38858341e+01 17 -2.20996828e+01 -1.08166464e+01 -7.87505218e+00 18 -1.15078785e+01 1.43928080e+01 1.10855800e+01 19 9.52626797e+00 -1.88957633e+01 1.48690670e+01 20 -1.02111320e+01 1.36333925e+01 1.21807016e+01 21 -1.66908859e+01 -2.38599994e+01 1.52396037e+01 22 3.65355512e+01 3.79642023e+01 3.61049616e+01 23 8.48180150e+00 -4.16141430e+00 1.38368824e+01 24 4.68783129e+00 1.02780755e+00 1.34461667e+01 25 -2.07773551e+01 -6.21457076e+00 1.45740877e+01 26 -1.32897436e+01 3.47670298e+01 -1.56717784e+01 27 1.57695744e+01 -5.32523657e+01 1.98205622e+01 28 -4.69866786e+01 3.84827245e+01 8.50992857e+00 29 -1.16726519e+01 -1.68158591e+01 1.32145532e+01 30 1.76960877e+01 2.62116018e+01 2.15130803e+00 31 2.85051962e+01 -1.62021890e+01 2.44048366e+01 32 1.54410496e+01 2.70640714e+01 2.92241433e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ag (Configuration in file "config-T-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 448.233946516 Forces: 1 3.31516078e+01 -2.18094506e+01 8.09106962e+00 2 -5.43825151e+01 1.87211695e+01 4.21886639e+01 3 -5.55658362e+00 1.52546952e+00 1.55138998e+00 4 2.47661867e+01 1.82295824e+01 -1.54632898e+00 5 3.89915459e+01 -3.70778529e+00 -6.98678215e-01 6 -4.10729219e+01 4.21795909e+01 1.25525183e+01 7 -7.30623934e+00 -4.69937702e+01 -4.54506112e+01 8 -1.66572766e+01 -1.76569076e+01 -7.94467999e+00 9 -3.31022819e+01 -5.14314880e+01 1.08153098e+01 10 -1.70951093e+01 8.91379668e+00 -1.98523177e+01 11 -6.73777578e+00 -2.71685985e+01 1.79143689e+01 12 1.79643867e+01 1.58868615e+01 4.83941736e+01 13 -6.24889789e+00 -2.39468270e+01 -5.88674869e+01 14 -3.91789804e+01 1.28311676e+01 -2.87901748e+01 15 5.13521153e+01 -7.70376235e+00 1.70121354e+01 16 1.24325643e+01 3.69385900e+01 2.63785866e+01 17 2.36156105e+01 -2.39358754e+01 -1.07700950e+01 18 -1.11836007e+01 1.50974083e+01 1.07792683e+01 19 1.00931545e+01 8.20139014e+00 8.63982765e+00 20 2.90405915e+01 4.51239560e+01 -1.47546513e+01 21 -1.84580570e+01 -5.58076383e+00 1.61050912e+01 22 -6.23113164e+00 6.03568912e+01 4.40941454e+01 23 -3.55268556e+01 -4.00760528e+01 -1.53985721e+01 24 4.57115800e+01 1.41205191e+01 -5.08592360e+01 25 -4.87426247e+00 -1.15463762e+01 1.46392378e+01 26 -1.05670785e+01 7.54929073e+00 -2.08315593e+01 27 3.77869772e+01 -5.67460472e+01 -2.49216393e+01 28 -4.74611100e+01 4.04705999e+01 -1.80092371e+01 29 -1.18456604e+01 -1.73870981e+01 1.31226310e+01 30 3.52327366e+00 8.67180053e+00 2.67953692e+00 31 2.17439283e+01 -1.89763109e+01 1.62999032e+01 32 2.33128158e+01 1.98490298e+01 7.43741026e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Au (Configuration in file "config-F-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 199.390636617 Forces: 1 -9.79438730e+00 -1.34686467e+01 -1.50439805e+01 2 -1.01967407e+01 -2.20675300e+01 -6.11364781e+01 3 1.73751032e+01 -5.16516176e+01 -2.49966436e+01 4 -4.63108737e+01 3.37888282e+01 -3.39623094e+01 5 -9.55480964e+00 -2.26467522e+01 -2.44528176e+01 6 4.18265345e+01 -2.02598536e+01 -3.06214743e+01 7 1.91790445e+01 -1.34161347e+01 4.92418610e+00 8 2.73531798e+01 -2.56898910e+01 1.25075339e+01 9 -1.00780919e+01 3.36073327e+00 -1.09901012e+01 10 -8.18507691e+00 9.23587142e+00 -1.90497599e+01 11 -3.60761079e+01 3.65128595e+01 1.40177028e+01 12 -1.10773453e+01 1.55428880e+01 -5.51721180e+00 13 -4.86353341e+01 1.50602503e+01 -7.70469223e+01 14 9.60824923e+00 1.24433814e+01 -1.08407347e+01 15 7.56333829e+01 1.53616343e+01 5.36949274e+01 16 3.35789465e+00 2.83915410e+01 -2.67747616e+01 17 -4.96231688e+01 -6.60528026e+01 3.63725227e+01 18 2.57089464e+01 4.29694100e+01 -3.04784153e-01 19 8.05900548e+00 -3.63464342e+01 4.46022367e+01 20 -3.29972367e+01 1.33286948e+01 2.33118495e+01 21 -3.07403015e+00 -2.85951874e+01 -5.75580653e+00 22 3.07967328e+01 1.08639028e+01 -1.64624648e+01 23 3.02320323e+01 -3.50239212e+01 2.44621398e+01 24 -2.38764620e+01 2.09265111e+01 2.77671585e+01 25 -1.43906083e+01 3.68584771e+00 8.31829316e+00 26 -2.38501133e+01 2.05001395e+01 2.95932109e+01 27 1.10224928e+01 -7.89588592e+00 1.11805786e+01 28 -1.43249350e+01 1.61452267e+01 4.01999634e+00 29 8.91837053e+00 1.34472369e+01 3.49263652e+01 30 3.10924569e+01 1.70657710e+01 1.98606748e+01 31 1.65064377e+01 2.88664221e+00 6.11881476e+00 32 -4.62454187e+00 1.15972869e+01 7.27805953e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 0.28797836279 Forces: 1 -7.75353382e-01 -9.23020520e-01 -7.20547066e-01 2 -1.06777069e+01 -2.49566706e+00 -1.12547436e+01 3 -1.19424129e+01 -1.46439773e+01 2.27733091e+00 4 -9.70263173e+00 1.72332327e+00 -1.06570956e+01 5 -2.82473998e+00 -6.99430612e+00 -1.17877794e+01 6 9.39649693e+00 6.26426557e+00 -1.21374024e+01 7 7.55836706e+00 -1.29182985e+01 1.27956733e+01 8 1.28389090e+01 7.46949013e+00 8.46139308e+00 9 -8.54750165e+00 -1.41358439e+01 -1.03365773e+01 10 2.98199627e+00 9.32388812e+00 -1.23599493e+01 11 -1.21042346e+01 1.99226131e+00 -4.34988898e+00 12 -6.68610817e+00 1.08719909e+01 1.06435795e+01 13 1.40378093e+00 3.89707465e+00 -8.52697649e+00 14 2.69350668e+00 4.90244676e+00 -2.43411067e+00 15 9.72608697e+00 -2.45616054e+00 -2.70198785e+00 16 7.16615436e+00 1.79491953e+01 -4.75126033e+00 17 -4.26716732e+00 -8.90346888e+00 2.41285540e+00 18 1.22241660e+01 -6.93270933e+00 3.18077114e+00 19 -1.44051153e+01 -1.27911848e+01 1.24893983e+01 20 -1.16297341e+01 -1.13485163e+01 1.06637364e+01 21 7.65717597e+00 -5.73742776e+00 -1.28659506e+01 22 4.22932007e+00 1.34301993e+00 2.62164142e+00 23 5.95413726e+00 -2.23855318e+00 5.50008015e+00 24 1.09917881e+01 5.85877664e+00 5.11523377e+00 25 -1.27628761e+01 1.34384174e+01 -3.07886389e+00 26 1.54211864e+00 4.33201164e+00 -2.02360388e+00 27 4.15069826e+00 1.46555460e+01 5.15121468e+00 28 -3.89630881e+00 1.26016164e+00 3.82990424e+00 29 -8.12693158e+00 -1.88749233e+01 1.33243281e+01 30 1.97808394e+01 1.43877383e+01 -4.54274299e+00 31 9.92662374e+00 -1.16891112e+01 7.38611326e+00 32 -1.18733432e+01 1.34135610e+01 8.67622671e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 27.6860117904 Forces: 1 1.01545989e+01 -1.42422669e+01 6.84381087e+00 2 -1.25512594e+01 -1.07952851e+01 1.41020996e+01 3 -1.19320365e+01 -1.03539434e+01 2.00538691e+00 4 7.31525571e+00 5.95472694e-01 -1.84014680e+01 5 -1.05036518e+01 5.04664117e+00 -6.36246942e-01 6 -2.24573807e+00 1.54672028e+01 -4.11220302e+00 7 4.01141583e+00 -1.26161255e+01 1.34479139e+01 8 1.31826150e+01 6.89532220e+00 7.88145470e+00 9 -1.08632403e+01 -9.99171166e+00 -2.50564688e-01 10 -6.96777481e-01 8.17278152e+00 -8.14513940e+00 11 -1.25215839e+01 2.38256693e+00 -4.62288537e+00 12 -3.24439807e+00 9.81326723e+00 9.81024289e+00 13 -1.14590250e+00 5.98551458e+00 1.47394001e+01 14 1.53659382e+01 3.31083984e+00 1.98530671e+01 15 4.48171303e+00 -2.13727315e+00 -2.35529694e+00 16 7.71643592e+00 1.45056303e+01 -3.74815556e+00 17 -9.76952687e+00 2.20004545e+00 -2.09041930e+00 18 1.18378554e+01 -7.21459481e+00 3.62574125e+00 19 -1.38385698e+01 -5.54438996e+00 1.34355498e+01 20 -1.16446348e+01 -4.98581911e+00 -4.44113033e+00 21 9.19214999e+00 -6.33736842e-01 -1.41075275e+01 22 -1.30151541e+01 -9.45353242e-01 1.21092423e+01 23 8.81963042e+00 4.19863271e+00 -8.73040844e+00 24 1.46064117e+01 -2.78987116e+00 -1.59748395e+01 25 -4.42354934e+00 1.45530003e+01 -2.42927925e+00 26 5.75696004e+00 -1.17592589e+01 -3.80652313e+00 27 2.91322789e+00 1.96168663e+01 -1.72331649e+01 28 -4.88885992e-01 -2.09704002e+00 5.96616755e+00 29 -7.51827597e+00 -1.81558445e+01 1.36588436e+01 30 1.57311890e+01 1.41358227e+01 -6.14529031e+00 31 1.77045460e+01 -1.66065761e+01 -1.01919894e+01 32 -2.23867582e+01 3.98948360e+00 -1.00563886e+01 MIXED STRUCTURE (pbc=False)-- Species = Ag Au Cu (Configuration in file "config-F-AgAuCu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 67.969033417 Forces: 1 -5.43752080e+00 -5.22309369e+00 -3.95505144e+00 2 -3.26706204e+01 2.04326552e+01 -2.63193864e+01 3 -1.06898443e+01 -2.67804465e+01 -7.95872071e+00 4 -1.01818884e+01 1.09365579e+01 -5.45987924e+00 5 1.91143584e+01 -2.22517730e+01 -1.56286809e+01 6 1.84650356e+01 -1.25208226e+01 -1.34805426e+01 7 7.34129815e+00 -1.09698110e+01 -2.21255684e+00 8 1.47263129e+01 1.04769775e+01 1.77620478e+01 9 -7.82708521e+00 -4.52824673e+00 -4.47447162e+00 10 2.25364974e+00 1.46603017e+01 -1.39015308e+01 11 -4.43613639e+00 -1.94252508e+01 -1.33098821e+01 12 -1.07449529e+01 1.47854985e+01 -1.92448266e+00 13 -1.04958348e+01 9.19537721e+00 -1.86083884e+01 14 5.18117670e+00 5.49387416e+00 -1.24074432e+00 15 1.81452111e+01 2.74221789e+01 -1.62469826e+01 16 7.28271209e+00 1.21934028e+01 -2.11432745e+00 17 -1.23990660e+01 -1.07669584e+01 1.12036768e+01 18 -8.12123154e+00 3.10157499e+00 -3.30976840e+00 19 -1.37629997e+00 -1.17715804e+01 9.41365137e+00 20 -1.29399884e+01 -1.32856774e+01 1.19955339e+01 21 1.22554083e+01 -1.28793891e+01 1.36832338e+01 22 1.10360529e+01 -2.16252873e+01 1.81498838e+01 23 3.59355267e+00 -6.37791470e+00 3.17236133e+00 24 3.27923430e+00 -2.33783383e+00 1.53353108e+01 25 -1.93056399e+01 -1.27266825e+01 -1.21693923e+01 26 -1.36585815e+01 4.20922984e+01 4.32681025e+00 27 -3.70826768e+00 -8.62975099e+00 2.30990975e+01 28 -9.69300139e+00 2.06707492e+01 1.71739056e+01 29 2.40836614e+01 -1.71287499e+01 -2.07934955e+00 30 4.67776991e+00 5.13154433e+00 2.11540032e+00 31 8.26325483e+00 5.18695636e+00 4.88959987e+00 32 1.39872705e+01 1.74493217e+01 1.20736253e+01 MIXED STRUCTURE (pbc=True)-- Species = Ag Au Cu (Configuration in file "config-T-AgAuCu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 333.558915847 Forces: 1 -2.30341521e+00 2.95770291e+01 1.53024844e+01 2 -2.99898648e+01 2.76500438e+01 3.45359967e+00 3 -3.79981338e+00 -6.71767412e-01 -3.49114924e+00 4 9.75536611e+00 1.70770901e+01 -6.79164262e+00 5 3.25400015e+01 -2.88426494e+01 2.39718935e+01 6 1.28175896e+01 -2.32519572e+01 7.68083567e+00 7 -1.58536575e+01 -1.16697751e+00 -5.60836870e+00 8 1.47630039e+01 9.92127770e+00 1.95951696e+01 9 5.01242984e+01 1.98332907e+01 1.46710549e+02 10 1.79700575e+01 -1.10626052e+01 8.83085427e+00 11 -2.08240624e+00 -2.08935876e+01 -1.14599099e+01 12 -5.21045556e+00 -2.13584565e+01 -2.53870998e+01 13 -1.74715909e+01 1.43541616e-01 2.22651012e+01 14 -8.21967483e+00 -1.17426110e+01 3.22305740e+01 15 -2.77195277e+00 2.51490991e+01 -2.77136597e+01 16 9.30514453e+00 2.27131180e+00 -3.05291518e+00 17 3.38429281e+00 2.30269829e+01 2.81441609e+01 18 -7.66776238e+00 3.29396171e+00 -3.96867436e+00 19 -7.89828433e+00 -7.98948238e+00 -3.73201452e+01 20 4.63377560e+01 -8.31627352e+01 -3.87904404e+01 21 1.23670166e+01 -2.42798113e+00 1.33212521e+01 22 -3.44415041e+00 -2.19744175e+01 1.88761145e+01 23 -7.79083913e+00 2.93707777e+01 -2.14926275e+01 24 6.03086736e+00 1.09902968e+01 -2.19518578e+01 25 1.03680348e+01 -8.25309458e+00 -1.58715708e+01 26 -1.30425564e+01 2.79612991e+01 5.58036593e+00 27 -1.37516844e+00 -1.21187306e+01 8.32747669e+00 28 1.65726609e+01 5.32723582e+01 -4.45189493e+01 29 2.36368013e+01 -1.72079068e+01 -3.26348557e+00 30 -1.22041498e+01 -1.04517853e+01 3.00273310e+00 31 -1.15792336e+02 -9.36166116e+00 -7.05331325e+01 32 -9.05481358e+00 1.24000462e+01 -1.60775360e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==7905== Memcheck, a memory error detector ==7905== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==7905== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==7905== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_CuAgAu__MO_318213562153_000 ==7905== ==7905== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==7905== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==7905== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7905== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7905== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7905== by 0x4010732: call_init (dl-init.c:72) ==7905== by 0x4010732: _dl_init (dl-init.c:119) ==7905== by 0x40151FE: dl_open_worker (dl-open.c:522) ==7905== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7905== by 0x40147C9: _dl_open (dl-open.c:605) ==7905== by 0x544CF95: dlopen_doit (dlopen.c:66) ==7905== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7905== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==7905== by 0x544D734: _dlerror_run (dlerror.c:162) ==7905== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==7905== ==7905== ==7905== HEAP SUMMARY: ==7905== in use at exit: 23,507,116 bytes in 4,433 blocks ==7905== total heap usage: 235,213 allocs, 230,780 frees, 103,911,009 bytes allocated ==7905== ==7905== LEAK SUMMARY: ==7905== definitely lost: 0 bytes in 0 blocks ==7905== indirectly lost: 0 bytes in 0 blocks ==7905== possibly lost: 183,295 bytes in 113 blocks ==7905== still reachable: 23,323,821 bytes in 4,320 blocks ==7905== suppressed: 0 bytes in 0 blocks ==7905== Rerun with --leak-check=full to see details of leaked memory ==7905== ==7905== For counts of detected and suppressed errors, rerun with: -v ==7905== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2535 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.