!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Mishin_2004_NiAl__MO_101214310689_005 Supported species : Al Ni 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 = -27.7618627356 Forces: 1 -1.95102487e+00 -2.10367647e+00 -2.58474976e+00 2 -9.11778383e-01 1.82615386e+00 -4.42878345e+00 3 1.04169301e+00 -3.85492439e+00 2.39685181e-01 4 -3.60410342e+00 1.62802846e+00 1.10020848e+00 5 1.72868327e+00 -4.65210118e+00 -1.70390205e+00 6 2.13735709e+00 1.19157737e+00 -2.86000886e+00 7 2.26438453e+00 -5.69590831e+00 -3.64019379e+00 8 -2.58157310e+00 -1.48317737e+00 -1.22253972e-01 9 -4.21016656e+00 -1.94649374e+00 -5.46388592e+00 10 -2.26193551e-01 6.80741456e+00 -5.76808675e+00 11 -3.06451689e+00 -5.34254013e+00 3.00956686e+00 12 -4.85335732e+00 3.99260655e+00 1.42215533e+00 13 4.35882561e+00 -2.36008189e+00 -7.88017431e+00 14 1.50620761e+00 1.36040043e+00 -1.61009894e+00 15 6.52350307e+00 -8.02392554e-01 -3.02882122e+00 16 1.97884734e+00 7.83158232e+00 3.54283409e+00 17 -4.87295736e+00 -2.79864220e+00 -1.16118703e+00 18 1.44411707e+00 3.10726798e+00 -1.65853608e+00 19 1.22118948e+00 -4.86536222e+00 3.53999906e+00 20 -3.06528727e+00 2.45759269e+00 3.08063359e+00 21 -2.16638544e+00 -4.59034538e+00 8.74776532e-01 22 6.04507775e+00 3.21536955e+00 2.88000540e+00 23 1.83071101e+00 -8.43758953e-01 2.77002764e+00 24 8.60009515e-01 1.72533812e+00 3.48156076e+00 25 -4.57703947e+00 -3.11642235e+00 -1.15142738e+00 26 1.43727909e+00 6.22311407e+00 -2.22180230e+00 27 1.75383400e+00 -5.59125174e+00 4.96582029e+00 28 -5.80198380e+00 4.12926312e+00 2.99282677e+00 29 -2.95782803e+00 -2.40906239e+00 2.65386194e+00 30 3.44719765e+00 5.43477851e+00 4.22421370e-01 31 3.79912688e+00 -2.53667874e+00 4.45851644e+00 32 1.46615150e+00 4.06233246e+00 3.84901209e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 107.224380605 Forces: 1 2.94896641e+00 -1.88875370e+00 1.28265055e+00 2 -3.17634186e+00 2.16461424e+00 2.65646308e+00 3 -1.46726558e-01 1.86789490e+00 5.60616089e-01 4 2.54146576e+00 2.84181487e+00 -4.66264470e-01 5 3.13396462e+00 -1.04876424e+00 5.45471989e-01 6 -3.30661269e+00 4.92807528e+00 7.44512952e-01 7 -2.46026660e+00 -4.08217206e+00 -3.51605725e+00 8 -2.44864368e+00 -1.77896358e+00 -2.89519572e-01 9 -4.27887007e+00 -4.01792605e+00 1.06823645e+00 10 -8.95340333e-01 2.95320366e+00 -1.98688950e+00 11 -3.51301586e+00 -4.94543373e+00 2.57455508e+00 12 -7.65734482e-01 9.25074945e-01 1.37741081e+00 13 5.05866835e+00 -2.71850965e+00 -3.94134808e+00 14 -2.40554198e+00 -1.05400118e-02 -1.25454071e+00 15 3.02917861e+00 -2.49954672e-01 -2.86354776e+00 16 2.59856635e+00 3.92262572e+00 3.68558519e+00 17 1.06572791e+00 -2.41886131e+00 -8.78840044e-01 18 1.41014098e+00 2.75298273e+00 -1.36571177e+00 19 5.29023459e-01 -3.85746888e-01 9.23216318e-01 20 2.50241290e+00 4.95983144e+00 -1.16153861e+00 21 -2.01244038e+00 -9.45059627e-01 1.77316585e+00 22 1.49965429e-01 4.80226217e+00 3.43443470e+00 23 -4.48652104e+00 -4.03049786e+00 -6.28231982e-01 24 3.71750194e+00 2.30912720e+00 -3.98906217e+00 25 -2.59514316e-01 -3.47402338e+00 -8.36160464e-01 26 1.95689779e+00 7.13337213e-01 -2.05532439e+00 27 2.47160792e+00 -5.55741682e+00 -1.58956505e+00 28 -4.87508119e+00 3.21760406e+00 -2.45176532e-01 29 -2.40802758e+00 -2.11503165e+00 2.83977514e+00 30 2.77634794e-01 1.91314965e+00 8.98772703e-01 31 1.26700119e+00 -2.54468516e+00 2.45588867e+00 32 2.77995422e+00 1.94074232e+00 2.47022791e-01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -68.6284371536 Forces: 1 -6.20818653e-01 -1.41322743e+00 -1.18043647e+00 2 -1.12248378e+00 -2.57576566e+00 -5.81171928e+00 3 1.20179735e+00 -7.88249196e+00 -4.75147385e+00 4 -6.73597625e+00 3.45649413e+00 -2.61606070e+00 5 -2.91175092e+00 -2.55022415e+00 -4.17309038e+00 6 4.03298017e+00 -7.10216692e-01 -3.89513750e+00 7 4.50842794e+00 -1.64852008e+00 9.46324009e-01 8 4.30655194e+00 -2.36953334e+00 5.08920829e-01 9 -2.27157642e+00 1.97977322e+00 -9.89370763e-01 10 -1.81501649e+00 1.05112066e+00 -1.31850488e+00 11 -6.34243149e+00 3.95461900e+00 1.07746422e+00 12 -1.92771746e+00 1.30604193e+00 -2.40445376e+00 13 3.61868701e-01 1.34642216e+00 -7.98790648e+00 14 1.62678695e+00 1.34250038e+00 -2.25334037e+00 15 6.55196157e+00 1.11916285e+00 3.71416508e+00 16 1.28063341e-01 5.39327357e+00 -7.52778345e-01 17 -5.19185690e+00 -6.17361157e+00 1.41423051e+00 18 3.00530642e+00 3.37980515e+00 5.02795010e+00 19 3.12394244e+00 -3.28255710e+00 3.49387213e+00 20 -4.39283241e+00 1.61175621e+00 3.39758760e+00 21 -7.85898624e-01 -4.42691189e+00 3.08437166e+00 22 4.76690043e+00 2.03231863e+00 -3.30406715e+00 23 2.25799788e+00 -4.43533455e+00 2.63983828e+00 24 -4.11088560e+00 2.79634119e+00 2.98904943e+00 25 -2.34943153e+00 3.96712507e-01 -8.34050339e-01 26 -1.52105353e+00 2.47322381e+00 3.81521714e+00 27 3.62429236e+00 -2.43990687e+00 1.58999037e+00 28 -1.58004068e+00 2.86729937e+00 1.89100892e-01 29 1.65608417e+00 2.02135276e+00 6.58640654e+00 30 3.37428000e+00 1.88960629e+00 -2.04649165e+00 31 3.02767749e+00 -1.86207064e+00 1.06487352e+00 32 -3.87514840e+00 1.35254812e+00 2.77951962e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -49.5755346248 Forces: 1 2.83905960e+00 -4.17589178e+00 4.21716017e+00 2 -1.71136403e+00 -3.13329495e+00 -3.10410506e+00 3 -1.65854703e-01 -2.53829438e+00 -7.11787302e+00 4 -2.20264450e+00 4.07081414e+00 -1.52950973e+00 5 -6.25939089e+00 -4.29231810e-02 2.26284442e+00 6 6.41048153e-01 -5.64190456e-01 3.08044945e+00 7 1.65322439e+00 -5.22232140e-01 1.94608073e+00 8 4.11794216e+00 -2.47814493e+00 8.50899610e-01 9 1.92496494e+00 2.72987135e+00 4.31611396e+00 10 -1.64021055e+00 2.19163301e+00 3.76857515e+00 11 -6.49614623e+00 4.33614530e+00 1.29916726e+00 12 -1.11246940e+00 -1.11820346e+00 -3.42275434e+00 13 -7.37872843e-02 2.50180011e+00 -4.09562860e+00 14 3.98373945e+00 -3.51524921e+00 3.04772712e+00 15 3.87262470e+00 1.90737991e+00 4.51908316e+00 16 -8.24441979e-02 3.25970582e-01 -2.32547583e+00 17 -4.39774774e+00 -4.82135799e+00 2.94463798e+00 18 2.80869483e+00 3.65815363e+00 4.83996498e+00 19 4.24589500e+00 -1.75799640e+00 3.75512037e-01 20 2.91255812e+00 2.05426595e+00 -1.68745040e+00 21 4.32548646e-02 3.80280994e+00 3.40969927e+00 22 -1.74370627e+00 2.15394721e+00 -3.66357793e+00 23 1.63873935e+00 -3.84618111e+00 -3.95433809e+00 24 -6.03092997e+00 3.27340622e+00 -4.15494169e+00 25 5.52371508e-01 1.61764532e+00 -2.25386715e+00 26 -3.04202802e+00 -4.61259238e+00 6.24615316e+00 27 4.40283659e+00 -2.76076563e+00 -5.07318112e+00 28 -3.87134439e-01 5.05663420e+00 -3.39232277e+00 29 1.53418131e+00 2.26862968e+00 6.39538042e+00 30 5.51599746e+00 -2.73948281e+00 -6.40854503e-01 31 -2.38670182e+00 -6.53100208e-01 -4.02295041e+00 32 -4.95457237e+00 -2.66920554e+00 -3.08061822e+00 MIXED STRUCTURE (pbc=False)-- Species = Al Ni (Configuration in file "config-F-AlNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = -20.4310836233 Forces: 1 -3.59410146e+00 -4.47733636e+00 -3.43359064e+00 2 1.44292187e+01 1.35684331e+00 -1.40678383e+01 3 -1.67075556e+00 -6.86990241e+00 4.45307023e-01 4 -2.04743819e+01 -4.85323038e+00 1.22363600e+01 5 -9.04701325e+00 -8.64864868e+00 -3.41830217e+00 6 1.14824507e+01 9.97545076e+00 -7.79130482e+00 7 1.00829386e+01 -2.07022510e+01 -1.11709899e+01 8 2.35298948e+01 -2.19602568e+00 -1.44230884e+01 9 -3.80368988e+00 -2.47257906e+00 -1.36024241e+01 10 1.39558484e+00 4.16885659e+00 -1.09668185e+00 11 2.03579755e+00 4.98049561e+00 1.31560622e-01 12 -1.31541396e+01 2.79012868e+01 -2.40726003e+01 13 -4.01323838e+00 2.53507761e+00 -9.82231402e+00 14 2.16858715e+00 2.82644113e+00 -3.27767340e+00 15 1.02736771e+01 -5.83009067e+00 3.75416256e+00 16 -1.52694231e+01 5.67174593e+00 -5.95033730e+00 17 -2.71706317e+00 -3.26403502e+00 -2.65618093e+00 18 -2.07577967e+01 -4.14551803e+00 1.23693727e+01 19 -1.59098397e+00 -5.84037662e+00 4.30673467e+00 20 -1.55035485e+01 -8.90519785e+00 5.31739967e+00 21 -1.20821928e+00 -9.68678193e+00 3.70123961e+00 22 3.81618579e+00 1.58587272e+01 1.45890606e+01 23 6.34694590e-01 -6.12872523e-01 1.62633110e+00 24 1.10498586e+01 -3.83884885e+00 6.83750658e+00 25 -1.04159912e+01 -2.00055072e+01 1.96478852e+01 26 1.33786503e+01 6.29854197e+00 7.00454815e+00 27 -3.74899557e+00 1.51435496e+01 9.39487532e+00 28 -2.01755844e+00 3.52445512e+00 3.90000616e+00 29 8.69518320e+00 3.76909106e+00 -5.84419211e+00 30 1.14354276e+01 4.42485769e+00 8.33921940e+00 31 2.95992652e+00 -1.06621584e+00 2.71573412e+00 32 1.61882359e+00 4.97999773e+00 4.31021469e+00 MIXED STRUCTURE (pbc=True)-- Species = Al Ni (Configuration in file "config-T-AlNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 48.7602752806 Forces: 1 1.25787597e+01 -6.97736684e+00 9.75626764e+00 2 1.38719706e+01 5.78717810e-01 -1.08116930e+01 3 -2.59343031e+00 -6.01867244e-01 2.67903669e+00 4 -1.03130705e+01 -1.85184407e+00 1.01803273e+01 5 -1.62313104e+00 -2.75541222e+00 4.55724203e+00 6 5.68801534e+00 1.62357152e+01 -1.98815765e+00 7 4.13016330e+00 -1.98104500e+01 -1.25137813e+01 8 2.31872191e+01 -2.26346463e+00 -1.47253487e+01 9 3.38390361e+00 -5.38580761e+00 -1.16171063e+01 10 -3.21549051e+00 -5.27979789e+00 -4.02965160e-01 11 1.34349914e+00 5.23451958e+00 -6.14407878e-01 12 -7.60171152e+00 2.79215603e+01 -2.38861820e+01 13 -3.49046004e+00 3.00990396e+00 -7.82903768e+00 14 -5.59213826e+00 5.13271401e+00 -3.71001987e+00 15 -8.60772176e-01 -6.26081848e+00 -7.85272890e-01 16 -1.41266443e+01 -1.07214683e+00 -8.84479938e+00 17 6.91394053e+00 5.64768083e+00 -9.51530346e+00 18 -2.12146658e+01 -4.61026749e+00 1.25913668e+01 19 -7.52546662e+00 -1.68323614e+00 -2.82115509e+00 20 -1.20661248e+01 -8.89853515e+00 1.14537353e+00 21 -3.34839350e+00 -2.61782639e+00 6.87579998e+00 22 1.29620706e+00 1.61328609e+01 1.55689957e+01 23 -1.61075723e+01 -5.14571429e+00 -1.19279427e+01 24 1.05485066e+01 -3.52425100e+00 3.81289879e+00 25 6.28542087e+00 -2.49961536e+01 1.90819559e+01 26 1.27191220e+01 4.10741617e+00 7.74797450e+00 27 -2.72893067e+00 1.48975792e+01 7.57699681e+00 28 1.42283667e+01 2.42370556e+00 1.19559730e+01 29 8.65249961e+00 4.43988611e+00 -5.27326523e+00 30 -4.49378170e+00 6.35830672e+00 4.75527633e+00 31 -1.23150141e+01 -7.29317058e+00 8.25199405e+00 32 4.38920400e+00 -1.09243584e+00 7.28959120e-01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==4817== Memcheck, a memory error detector ==4817== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==4817== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==4817== Command: python runner2.py EAM_Dynamo_Mishin_2004_NiAl__MO_101214310689_005 ==4817== ==4817== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==4817== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==4817== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==4817== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==4817== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==4817== by 0x4010732: call_init (dl-init.c:72) ==4817== by 0x4010732: _dl_init (dl-init.c:119) ==4817== by 0x40151FE: dl_open_worker (dl-open.c:522) ==4817== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==4817== by 0x40147C9: _dl_open (dl-open.c:605) ==4817== by 0x544CF95: dlopen_doit (dlopen.c:66) ==4817== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==4817== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==4817== by 0x544D734: _dlerror_run (dlerror.c:162) ==4817== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==4817== ==4817== ==4817== HEAP SUMMARY: ==4817== in use at exit: 39,242,201 bytes in 4,274 blocks ==4817== total heap usage: 198,995 allocs, 194,721 frees, 113,066,113 bytes allocated ==4817== ==4817== LEAK SUMMARY: ==4817== definitely lost: 0 bytes in 0 blocks ==4817== indirectly lost: 0 bytes in 0 blocks ==4817== possibly lost: 182,735 bytes in 112 blocks ==4817== still reachable: 39,059,466 bytes in 4,162 blocks ==4817== suppressed: 0 bytes in 0 blocks ==4817== Rerun with --leak-check=full to see details of leaked memory ==4817== ==4817== For counts of detected and suppressed errors, rerun with: -v ==4817== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2518 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.