Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:18:25) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouWadleyJohnson_2001NISTretabulation_CuTa__MO_950828638160_000 Supported species : Cu Ta 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 = 6.79528356524 Forces: 1 -2.77330435e+00 -6.21824665e+00 -6.63342091e+00 2 -8.09520555e+00 1.22987978e+01 -8.20332609e+00 3 7.40197865e-01 -8.46300210e+00 -1.43506432e+00 4 -4.02898909e+00 3.86143123e+00 3.90657706e+00 5 1.01418552e+01 -1.63245246e+01 -1.67039560e+00 6 3.00535070e+00 1.63557037e+00 -5.18982421e+00 7 3.75789881e+00 -2.17890628e+01 -2.02372121e+01 8 -7.75460211e+00 -8.89357279e+00 9.60551052e-01 9 -9.87088645e+00 -5.65714322e+00 -1.45102004e+01 10 -3.41367195e+00 1.63257711e+01 -1.58516914e+01 11 -2.29290889e+00 -1.27365745e+01 1.03561913e+01 12 -7.83208452e+00 1.34801532e+01 7.00819699e-02 13 -3.82456995e+00 -7.33117576e+00 -3.35003565e+01 14 5.31236812e+00 7.01771258e+00 -4.36122381e+00 15 2.85006823e+01 -3.91579070e+00 9.22239047e+00 16 3.69498439e+00 2.18083428e+01 1.16410011e+01 17 -8.64426759e+00 -3.50628527e+00 -3.54054198e+00 18 -2.88512699e+00 7.77074044e+00 3.17849300e+00 19 4.60959156e+00 -6.80892022e+00 5.21517262e+00 20 -2.96317223e+00 6.22600337e+00 3.98476818e+00 21 -8.10443220e+00 -8.21292337e+00 6.24425215e+00 22 1.33238395e+01 1.85747051e+01 1.61214993e+01 23 2.33364531e+00 -6.97980835e-01 4.35287572e+00 24 1.90659467e+00 8.46141096e-01 3.76993608e+00 25 -5.40146350e+00 -7.96654053e+00 9.86219222e+00 26 -5.40108665e+00 1.34104123e+01 -7.63865073e+00 27 8.49876949e+00 -2.52578139e+01 6.93392009e+00 28 -2.05003384e+01 1.70200366e+01 2.63161871e+00 29 -6.07155001e+00 -9.75578159e+00 3.18090675e+00 30 6.07015661e+00 1.02426166e+01 3.28093640e-01 31 1.14141223e+01 -7.81244280e+00 9.44139100e+00 32 6.54760355e+00 1.08293472e+01 1.13699955e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 38.6806887883 Forces: 1 1.55331024e+01 -1.34763031e+01 4.05480831e+00 2 -2.67838177e+01 8.63284370e+00 1.98674948e+01 3 2.53718162e-01 1.22490169e+00 -2.87543921e-01 4 1.05960829e+01 8.30887183e+00 -1.06727017e+00 5 1.75286685e+01 -3.56328712e+00 6.45947346e-01 6 -1.88277007e+01 2.00275887e+01 7.64460222e+00 7 -3.64250904e+00 -2.13104113e+01 -2.06934540e+01 8 -7.52146718e+00 -9.25756216e+00 5.95890386e-01 9 -1.78524365e+01 -1.60188339e+01 1.01026741e+01 10 -1.08359080e+01 4.40834119e+00 -8.51142182e+00 11 -2.91303539e+00 -1.22788804e+01 1.01192016e+01 12 3.18945208e+00 7.31548815e+00 4.91918754e+00 13 -2.99430536e+00 -8.32784209e+00 -2.83951801e+01 14 -8.01730270e+00 4.98997965e+00 -9.09960277e+00 15 2.31365162e+01 -3.74932288e+00 8.74949553e+00 16 5.26357715e+00 1.69218765e+01 1.20249188e+01 17 1.04169562e+01 -1.06850255e+01 -3.98331325e+00 18 -3.22417589e+00 7.03260624e+00 3.47968913e+00 19 4.41520541e+00 3.43457121e+00 3.89735865e+00 20 1.32916432e+01 2.02018357e+01 -6.25933174e+00 21 -8.47957166e+00 -2.37778007e+00 6.54244987e+00 22 -4.26518405e+00 2.80834057e+01 1.96193119e+01 23 -1.52557377e+01 -1.98163849e+01 -8.98924304e+00 24 2.15231224e+01 6.78333028e+00 -2.42097082e+01 25 -4.17101858e-01 -9.51404606e+00 9.80630663e+00 26 -4.52101987e+00 3.54380915e+00 -9.44009889e+00 27 1.83553069e+01 -2.56629391e+01 -1.12310021e+01 28 -2.18858767e+01 1.95512016e+01 -7.17037247e+00 29 -5.59928373e+00 -9.10108975e+00 3.70753722e+00 30 -3.83492222e-01 4.13357293e+00 2.62539222e+00 31 9.83748771e+00 -8.41841296e+00 7.57410688e+00 32 1.00790869e+01 8.96389709e+00 3.36116946e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ta (Configuration in file "config-F-Ta.xyz") ----------------------------------------------------------------------------------------------------- Energy = -25.4376265184 Forces: 1 -5.81417775e+00 -9.06996178e+00 -9.52820515e+00 2 -9.11366308e+00 -1.03513188e+01 -3.60231916e+01 3 1.09635061e+01 -3.48879874e+01 -1.81353149e+01 4 -3.05319522e+01 3.00892133e+01 -2.17567380e+01 5 -2.91585854e+00 -1.34439445e+01 -1.46004199e+01 6 1.45438598e+01 -8.05823280e+00 -1.59094948e+01 7 1.86121513e+01 -6.59920902e+00 -8.61339667e+00 8 2.28412286e+01 -1.50707395e+01 9.76683223e+00 9 -7.04053179e+00 1.75077324e+00 -7.82313712e+00 10 -5.07203513e+00 7.60705623e+00 -1.24578934e+01 11 -4.35753754e+01 1.56205518e+01 1.10158966e+01 12 -5.67023013e+00 7.61608331e+00 5.58291471e-01 13 9.42713173e+00 1.12310771e+01 -4.50740383e+01 14 1.48065831e+00 2.91413697e+00 -3.13138579e+00 15 2.67632187e+01 6.72610615e+00 1.42483387e+01 16 6.41314775e+00 2.06868998e+01 -2.28696299e+01 17 -3.57384136e+01 -4.83406932e+01 2.66698096e+01 18 2.07759358e+01 3.14576883e+01 -9.57941806e-01 19 1.01402460e+01 -2.62530666e+01 2.80757753e+01 20 -2.24554925e+01 1.14467515e+01 1.59694513e+01 21 -9.81253815e+00 -1.92115431e+01 1.02353724e+01 22 2.08711259e+01 1.07850917e+01 -1.26678124e+01 23 1.71411057e+01 -2.57210629e+01 1.35184226e+01 24 -1.99797811e+01 1.41563023e+01 1.72388259e+01 25 -1.04335549e+01 -8.94286078e+00 -1.27168552e+01 26 -1.59684325e+01 1.41769361e+01 2.01493228e+01 27 1.21746690e+01 -7.97787438e+00 1.09979279e+01 28 -1.03985598e+01 2.03993330e+01 1.13010700e+01 29 1.45844100e+01 8.01805566e+00 3.17311384e+01 30 2.09922149e+01 1.00366267e+01 1.37972052e+01 31 1.14335172e+01 1.85489936e+00 2.97500952e+00 32 -4.63753027e+00 7.35491206e+00 4.01676489e+00 MIXED STRUCTURE (pbc=False)-- Species = Cu Ta (Configuration in file "config-F-CuTa.xyz") ----------------------------------------------------------------------------------------------------- Energy = 83.6433919275 Forces: 1 -4.42476265e+00 -9.15547237e+00 -9.55172291e+00 2 -1.43988105e+01 2.41224496e+01 -1.77144283e+01 3 -1.05684134e+01 -7.16205116e+00 1.69950604e+01 4 -5.78552876e+00 1.60396598e+00 9.87607112e+00 5 1.51809641e+01 -3.13531787e+01 -1.42318890e+01 6 1.52482496e+01 -6.69133126e-02 -2.04230699e+01 7 2.37494518e+01 -2.03465203e+01 -5.13258469e+00 8 -2.93009562e+01 -2.21601845e+01 -2.04217834e+01 9 -3.85582806e+01 -7.76484479e+00 -3.64610227e+01 10 -1.28084257e+01 5.85292417e+01 -1.97987441e+01 11 -2.93875425e+00 -3.77965652e+01 9.20855950e+00 12 -9.13863270e+00 1.41394055e+01 3.53240071e+00 13 3.38621210e+01 -2.47413017e+01 -3.17572987e+01 14 7.88745301e+00 1.38748366e+01 -1.24484301e+01 15 5.34914780e+01 2.26052368e+01 -1.78634754e+01 16 2.55949619e+01 2.80292946e+01 -1.72890611e+01 17 -1.48320781e+01 -2.84768056e+00 -1.38006155e+01 18 -2.39971801e+01 -2.14046278e+01 -2.27846359e+01 19 1.06460396e+01 -9.01850995e+00 1.45818200e+01 20 -9.08319630e+00 3.97844944e-01 6.23881331e+00 21 -2.62427133e+01 -1.77615696e+01 -8.28070736e+00 22 3.59438736e+01 -1.86439100e+01 1.69039231e+01 23 1.93043965e+01 -2.30874785e+00 2.36717421e+01 24 2.68288876e+01 -2.90724249e+01 4.97714567e+01 25 -2.53408325e+01 -1.17416486e+01 8.49913444e+00 26 -3.33737705e+01 4.01389165e+01 3.67021187e+01 27 -1.87364122e+01 2.44299288e+01 2.09403095e+01 28 -3.54832296e+00 4.74955857e+00 4.91881671e+00 29 -6.03087037e+00 2.03972676e+01 1.80588493e+01 30 1.96664096e+01 1.00652078e+01 -9.58871225e+00 31 1.59095038e+01 -7.83075237e+00 7.06469848e+00 32 -1.42058487e+01 1.80937487e+01 3.05844072e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==9533== Memcheck, a memory error detector ==9533== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==9533== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==9533== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_CuTa__MO_950828638160_000 ==9533== ==9533== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==9533== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==9533== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9533== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9533== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9533== by 0x4010732: call_init (dl-init.c:72) ==9533== by 0x4010732: _dl_init (dl-init.c:119) ==9533== by 0x40151FE: dl_open_worker (dl-open.c:522) ==9533== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==9533== by 0x40147C9: _dl_open (dl-open.c:605) ==9533== by 0x544CF95: dlopen_doit (dlopen.c:66) ==9533== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==9533== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==9533== by 0x544D734: _dlerror_run (dlerror.c:162) ==9533== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==9533== ==9533== ==9533== HEAP SUMMARY: ==9533== in use at exit: 12,293,283 bytes in 4,273 blocks ==9533== total heap usage: 189,377 allocs, 185,104 frees, 85,262,623 bytes allocated ==9533== ==9533== LEAK SUMMARY: ==9533== definitely lost: 0 bytes in 0 blocks ==9533== indirectly lost: 0 bytes in 0 blocks ==9533== possibly lost: 183,295 bytes in 113 blocks ==9533== still reachable: 12,109,988 bytes in 4,160 blocks ==9533== suppressed: 0 bytes in 0 blocks ==9533== Rerun with --leak-check=full to see details of leaked memory ==9533== ==9533== For counts of detected and suppressed errors, rerun with: -v ==9533== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2534 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. === Verification check vc-memory-leak end (2018-12-15 06:18:57) ===