!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_LandaWynblattSiegel_2000_AlPb__MO_699137396381_005 Supported species : Al Pb 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 = 77.8419161646 Forces: 1 -5.63475388e+00 -6.10293752e+00 -6.51304297e+00 2 -1.11633824e+00 2.81206122e+00 -9.68237737e+00 3 3.49855173e+00 -9.81138414e+00 -6.60716797e-02 4 -8.70555062e+00 1.07715421e+00 3.74285926e+00 5 -1.74690763e+00 -1.18796476e+01 -8.34862244e+00 6 9.45050750e+00 2.48838569e+00 -1.12766034e+01 7 8.60152431e+00 -1.01200558e+01 6.23591798e-01 8 -2.24980956e+00 -3.48935773e+00 1.78098901e+00 9 -5.14701442e+00 -2.49925766e+00 -1.18657855e+01 10 1.69843119e+00 1.06452921e+01 -1.04341185e+01 11 -4.52045904e+00 -6.29827893e+00 -3.16730678e+00 12 -1.16190202e+01 1.05248158e+01 2.12535682e+00 13 3.56418781e-01 -2.30885596e+00 -1.43870709e+01 14 6.96158217e+00 8.77239568e+00 -6.19887955e+00 15 1.40532494e+01 -4.21115832e+00 1.00230464e-01 16 1.40257270e+00 1.57340720e+01 -2.65399759e+00 17 -1.41606805e+01 -7.48882633e+00 -3.15369131e+00 18 8.78558018e-01 1.81754843e+00 -1.68049780e+00 19 2.33018618e+00 -1.42966680e+01 9.07463891e+00 20 -7.36115098e+00 7.38551864e+00 8.04849583e+00 21 -4.86010951e+00 -1.04578255e+01 1.89186568e-01 22 1.16050403e+01 6.28662338e+00 1.55010797e+00 23 4.97356196e+00 -2.61977153e+00 9.35688063e+00 24 5.46290702e+00 1.20841736e+00 9.46710192e+00 25 -1.37914897e+01 -5.86899739e+00 2.09305047e-01 26 -1.94998296e-01 1.83618130e+01 -1.20784063e+00 27 -3.63583628e+00 -4.89738544e+00 1.33722885e+01 28 -9.72479737e+00 6.19941562e+00 8.20341202e+00 29 3.38339831e+00 -5.88217920e+00 2.40156257e+00 30 6.19899459e+00 9.89585181e+00 1.53724193e-01 31 9.48330751e+00 -5.56234805e+00 8.66608016e+00 32 4.13012458e+00 1.05855701e+01 1.15700948e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 173.007083585 Forces: 1 5.29126161e+00 9.62393216e-02 1.04663375e+00 2 8.16684564e-02 3.81114133e+00 2.32900562e+00 3 2.06571637e+00 8.03311079e+00 2.29050663e+00 4 6.55756956e+00 4.33955961e+00 1.23705566e+00 5 1.70893682e+00 -2.33836465e+00 -3.74015259e+00 6 -2.66503924e+00 7.25283295e+00 -5.51494977e+00 7 -4.51851288e+00 -5.31251541e+00 2.14914766e+00 8 -2.89511756e+00 -3.47523929e+00 2.21116978e+00 9 -2.98896637e+00 -6.70951005e+00 -1.81324986e+00 10 5.51039661e-01 2.10343471e+00 8.99060544e-01 11 -4.52265215e+00 -6.52292046e+00 -3.40282057e+00 12 -1.52991863e+00 1.75743371e+00 1.30109658e+00 13 1.88106612e+00 -4.35018751e+00 -4.04777820e+00 14 -2.66280916e+00 2.00263253e+00 -3.50784039e+00 15 4.39902404e+00 -4.25817830e+00 4.63169688e-01 16 3.16082405e+00 4.63673571e+00 -3.29354472e-01 17 -7.97555945e-01 -2.91317361e+00 -3.70167982e+00 18 1.69642580e+00 2.02696782e+00 -1.95096104e+00 19 1.56433098e+00 -2.77114871e+00 2.48149218e+00 20 1.99524316e+00 1.10988167e+01 -2.21273748e+00 21 -5.28699021e+00 2.36105705e-01 6.50148951e-01 22 4.73662070e-01 8.68098867e+00 1.61644903e+00 23 -6.92855199e+00 -4.17812834e+00 2.36744481e+00 24 5.35269155e+00 4.39560986e+00 -2.16553447e+00 25 -3.99901958e+00 -8.47133935e+00 4.92835825e-01 26 1.21283145e+00 4.83671158e+00 -6.42243793e-01 27 -6.58771891e-01 -6.73867537e+00 1.48838291e+00 28 -8.40796331e+00 5.60602720e-01 -2.85155703e-01 29 3.12424941e+00 -6.10075220e+00 2.44803776e+00 30 -3.73292951e+00 1.31168649e-01 2.24119070e+00 31 3.96652714e+00 -6.72288507e+00 3.32294080e+00 32 6.51173018e+00 4.86292595e+00 2.27868927e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Pb (Configuration in file "config-F-Pb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3393.70338137 Forces: 1 -1.17380032e+02 -1.40123046e+02 -1.43423582e+02 2 7.25291442e+00 -5.20302209e+01 -2.37991406e+02 3 -2.77921858e+01 -2.51976667e+02 -3.56816154e+01 4 -2.07358032e+02 -4.34510393e+01 -2.44867767e+01 5 5.40481269e+00 -1.52117871e+02 -1.43162249e+02 6 1.45669497e+02 1.58170776e+00 -1.61788121e+02 7 1.56040343e+02 -1.54475953e+02 -1.35813985e+01 8 3.93852677e+01 -5.31904732e+01 -4.14392229e+01 9 -1.74321525e+02 4.99158488e+01 -1.43133600e+02 10 -1.01977190e+01 1.71848021e+02 -1.47684852e+02 11 -3.03501396e+01 9.38991210e+01 -2.21651160e+01 12 -1.40926967e+02 1.44303012e+02 -1.37386606e+01 13 3.08718740e+01 1.65524478e+01 -2.04908375e+02 14 1.11157633e+02 9.74276022e+01 -1.20691068e+02 15 1.90309489e+02 4.36001942e+01 -3.40563267e+01 16 5.37720510e+01 1.82106596e+02 -2.80506273e+01 17 -1.90273103e+02 -1.58697783e+02 5.14507632e+01 18 -1.16084455e+01 -3.75128606e+01 7.27922134e+01 19 -1.88294709e+01 -1.19134605e+02 1.29696558e+02 20 -1.57779974e+02 -3.78660561e+01 1.60212656e+02 21 3.17233198e+01 -2.14268677e+02 5.90621944e+01 22 2.37520739e+02 -4.01681928e+01 9.72758805e+00 23 1.29836497e+02 -1.44432508e+02 1.16575032e+02 24 -3.28998287e+01 -5.12210450e+01 2.25003147e+02 25 -1.77744641e+02 5.93385091e+01 1.63566408e+01 26 -2.37517741e+01 2.22477223e+02 2.19371649e+00 27 -1.87213942e+01 4.38998683e+01 1.91176878e+02 28 -1.53303650e+02 1.40667784e+02 9.27580343e+01 29 3.48907942e+01 5.02790002e+01 3.58649188e+01 30 1.45211933e+02 1.59607336e+02 6.91569840e+00 31 1.61333803e+02 3.20471487e+01 1.80168925e+02 32 1.28579148e+01 1.41115576e+02 1.66028033e+02 MIXED STRUCTURE (pbc=False)-- Species = Al Pb (Configuration in file "config-F-AlPb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 889.546642399 Forces: 1 -6.02881854e+00 -1.83756733e+01 -1.64193665e+01 2 3.58331834e+01 -9.20295651e+01 -1.54689650e+02 3 5.01355104e+01 -1.45653761e+02 -2.81268133e+01 4 -1.57204636e+02 -8.70155978e+00 -3.75645995e+01 5 8.10042796e+00 -2.64061200e+01 -1.76238618e+01 6 5.53498199e+01 -3.14145843e+01 -2.79622117e+01 7 2.38417804e+01 -1.75204837e+01 5.13957170e+00 8 2.05559860e+01 -3.92444421e+00 -3.20339755e+00 9 -1.22350338e+02 5.24224719e+01 -1.17761090e+02 10 -7.69820646e+00 9.94292135e+01 -7.09925937e+01 11 1.27909486e+01 4.89832047e+01 2.12475635e+01 12 -1.61027671e+01 2.85992530e+01 4.55841243e-01 13 9.69564620e+01 4.15034731e+01 -7.75065130e+01 14 1.52467466e+01 9.70991638e+00 -9.04599428e+00 15 3.00424099e+01 7.26239176e+00 -1.16802177e+00 16 9.45011700e+00 2.30715077e+01 -1.72628618e+00 17 -1.19006852e+02 -1.21424522e+02 4.79228480e+01 18 7.08777769e+01 -3.69756649e+01 2.71819379e+01 19 -6.38851173e+00 -1.98353875e+01 2.22240083e+01 20 -1.10346906e+02 -3.21965810e+01 1.19576852e+02 21 1.53449698e+01 -3.01904106e+01 1.33985125e+00 22 7.58718613e+01 -1.94565235e+01 2.18268576e+01 23 1.25413631e+01 -1.03305428e+01 8.25346733e+00 24 1.43701615e+01 -3.47003915e+00 2.42409799e+01 25 -2.65759038e+01 1.91159579e+01 9.67915843e+00 26 -3.64317331e+01 1.26177243e+02 -2.89270786e+00 27 3.05538612e+01 4.32983744e+01 1.52756141e+02 28 -3.78875065e+01 4.80668173e+01 4.47548651e+01 29 5.84885413e+00 1.30702524e+01 1.48279499e+01 30 3.66596473e+01 3.42922877e+01 9.46718415e+00 31 2.22140549e+01 -1.79531301e-01 1.77138611e+01 32 3.43623752e+00 2.30830294e+01 1.80741690e+01 MIXED STRUCTURE (pbc=True)-- Species = Al Pb (Configuration in file "config-T-AlPb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 4425.63888631 Forces: 1 -2.66925364e-01 3.81101987e+00 1.75773087e+00 2 6.75892693e+01 -7.94116960e+01 6.55354239e+00 3 6.80162089e+01 -2.45556893e+01 2.23961965e+00 4 -3.81619665e+01 6.33985680e+00 -1.09962620e+01 5 1.77362449e+00 -8.22022629e-02 8.15561874e-01 6 -6.69886270e+01 -4.94263204e+01 2.10118494e+00 7 -1.03618692e+01 3.57551553e+00 9.75050856e+00 8 4.86486953e+00 3.24247588e+00 -8.37564625e-01 9 -9.09045796e+01 3.92972568e+01 3.78522815e+01 10 3.24403094e+01 9.53163071e+01 -9.96482608e+00 11 2.69807165e+01 7.48627363e-01 7.36206165e+01 12 6.30721355e+00 -1.53922574e+00 2.70624386e+00 13 4.91541247e+01 1.63189593e+01 -6.81893593e+00 14 -1.73158647e+01 -1.14225889e+01 -1.51418746e+00 15 -1.98458235e+01 1.25000695e+00 -8.74240284e+00 16 1.05354290e+01 -9.14960773e+00 3.65488452e+00 17 -2.06167001e+01 -3.14521703e+01 -2.49617033e+00 18 1.00730098e+02 2.53812779e-02 -6.16233970e+00 19 -3.58111900e+00 -4.44037586e+00 -3.81296202e+00 20 -3.20370144e+01 -2.76533955e+01 -1.04181835e-01 21 4.91305160e+00 -5.66660484e+00 -8.43543026e+00 22 -7.95937623e+01 5.64231019e+01 -1.34007712e+01 23 -7.29055575e+00 -1.33062228e+00 -5.52293309e+00 24 1.42033851e+01 7.15453896e-01 -1.52016570e+00 25 -1.48420923e+01 1.02279524e+01 -3.65282120e-01 26 2.17134468e+01 -2.00825292e+01 -2.25008257e+01 27 5.52742436e+01 -9.61402891e+00 -4.59307391e+01 28 -3.17932362e+01 5.51943970e+01 3.81807593e+01 29 1.21113650e+00 1.33167552e+01 -9.96261918e+00 30 -3.65466854e+01 -3.39488129e+01 -2.32242369e+01 31 -7.97301979e+00 7.02612637e+00 1.06938627e+00 32 1.24127146e+01 -3.05332344e+00 2.01051592e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==783== Memcheck, a memory error detector ==783== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==783== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==783== Command: python runner2.py EAM_Dynamo_LandaWynblattSiegel_2000_AlPb__MO_699137396381_005 ==783== ==783== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==783== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==783== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==783== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==783== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==783== by 0x4010732: call_init (dl-init.c:72) ==783== by 0x4010732: _dl_init (dl-init.c:119) ==783== by 0x40151FE: dl_open_worker (dl-open.c:522) ==783== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==783== by 0x40147C9: _dl_open (dl-open.c:605) ==783== by 0x544CF95: dlopen_doit (dlopen.c:66) ==783== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==783== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==783== by 0x544D734: _dlerror_run (dlerror.c:162) ==783== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==783== ==783== ==783== HEAP SUMMARY: ==783== in use at exit: 7,131,640 bytes in 4,275 blocks ==783== total heap usage: 189,679 allocs, 185,404 frees, 77,114,043 bytes allocated ==783== ==783== LEAK SUMMARY: ==783== definitely lost: 0 bytes in 0 blocks ==783== indirectly lost: 0 bytes in 0 blocks ==783== possibly lost: 183,295 bytes in 113 blocks ==783== still reachable: 6,948,345 bytes in 4,162 blocks ==783== suppressed: 0 bytes in 0 blocks ==783== Rerun with --leak-check=full to see details of leaked memory ==783== ==783== For counts of detected and suppressed errors, rerun with: -v ==783== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2524 from 174) ================================================================================ 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.