!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_WilliamsMishinHamilton_2006_CuAg__MO_128703483589_005 Supported species : Ag 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 = 195.308221552 Forces: 1 -7.72174222e+00 -1.67216810e+01 -1.43947267e+01 2 -5.59014268e+00 7.23724229e+00 -1.60199933e+01 3 5.51173130e+00 -1.56913911e+01 -2.85696781e+00 4 -1.46711888e+01 8.10855696e+00 6.85938596e+00 5 2.02289700e+00 -2.15819623e+01 -9.49821528e+00 6 1.28915238e+01 2.57425947e+00 -1.51896482e+01 7 1.30103478e+01 -2.58537092e+01 -1.40884739e+01 8 -1.09954124e+01 -1.07617967e+01 4.58639407e+00 9 -1.06593494e+01 -1.47908050e+01 -2.38453263e+01 10 1.27899021e+01 2.21251289e+01 -1.80382749e+01 11 1.80839984e+00 -1.33477444e+01 -9.36558561e+00 12 -2.42026856e+01 2.14185199e+01 1.05598923e+01 13 -8.98405977e+00 -5.48383734e+00 -4.02714425e+01 14 1.22771927e+01 1.50460211e+01 -1.26466570e+01 15 3.70568133e+01 -8.06706907e+00 5.13744701e+00 16 -1.40644053e+00 3.62932543e+01 2.98611435e+00 17 -2.37455716e+01 -1.47715531e+01 -5.48472712e+00 18 8.79221068e+00 1.03652431e+01 -1.85667993e+00 19 8.67568493e+00 -1.76878275e+01 1.51892361e+01 20 -1.29392843e+01 9.76914867e+00 1.52265307e+01 21 -1.19564704e+01 -1.50770600e+01 6.92384565e+00 22 2.23365767e+01 1.72218050e+01 1.24692233e+01 23 7.45910203e+00 -4.29809436e+00 1.26062924e+01 24 1.43070875e+00 -4.49416691e+00 1.14673643e+01 25 -2.96069252e+01 -1.92421514e+00 1.38808373e+01 26 -6.23809439e+00 2.92320700e+01 -5.88376647e+00 27 4.45562196e-01 -2.21159941e+01 1.65314391e+01 28 -2.35898570e+01 1.76347828e+01 7.67520784e+00 29 4.21105803e-01 -1.44321625e+01 8.08816132e+00 30 1.56264268e+01 1.76432971e+01 3.25283236e+00 31 2.08593811e+01 -7.09320951e+00 1.53966533e+01 32 8.89165745e+00 1.95249498e+01 2.06036276e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ag (Configuration in file "config-T-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 392.053533151 Forces: 1 1.59711515e+01 -1.33316187e+01 3.14145609e+00 2 -1.47344357e+01 3.32509958e+00 1.25507414e+01 3 4.62523473e+00 5.70084603e+00 9.75285078e-01 4 1.20142235e+01 1.41959345e+01 9.82717355e+00 5 3.96798156e+00 -7.37397189e+00 -3.28512385e+00 6 -2.07978421e+01 2.08431001e+01 1.41126539e+00 7 -3.09881480e+00 -1.61695456e+01 -1.20222666e+01 8 -1.24042288e+01 -1.05007829e+01 5.70600107e+00 9 -1.18707331e+01 -2.66587182e+01 5.54836184e+00 10 1.29115666e+01 1.05591889e+01 -1.55080426e+00 11 2.02811104e+00 -1.36707361e+01 -9.07971855e+00 12 -1.14965172e+00 6.44761180e+00 1.94216586e+01 13 -7.02245358e+00 -6.61873643e+00 -2.34419811e+01 14 -1.26402458e+01 5.64437617e+00 -1.39918784e+01 15 2.11136846e+01 -7.89640800e+00 6.09214177e+00 16 -1.94597832e-01 2.00948427e+01 4.17803876e+00 17 4.57345125e+00 -1.62673474e+01 -6.67287595e+00 18 1.19137206e+01 1.06528815e+01 -2.03031934e+00 19 8.79426374e+00 3.09300493e+00 6.24270184e+00 20 1.26254312e+01 2.54667569e+01 -4.89679027e+00 21 -1.22481732e+01 1.89051104e+00 8.02636848e+00 22 -2.70555075e+00 2.75625701e+01 1.12253458e+01 23 -2.03749807e+01 -2.08062004e+01 -9.52979809e+00 24 1.19705645e+01 2.59228675e+00 -1.80031091e+01 25 -1.55008828e+01 -5.27393415e+00 1.35562381e+01 26 -3.83924859e+00 7.83675802e+00 -7.93044711e+00 27 9.80903880e+00 -2.48490136e+01 -1.03810869e+01 28 -2.21655646e+01 1.25648689e+01 -1.16335804e+01 29 4.62626963e-01 -1.46060472e+01 8.03038073e+00 30 2.99850822e+00 2.61075645e+00 5.48382183e+00 31 1.27026830e+01 -8.68262780e+00 6.46932670e+00 32 1.22651624e+01 1.16242940e+01 6.56347286e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 11.0306791369 Forces: 1 -5.80570596e+00 -7.54623261e+00 -7.44110838e+00 2 1.32655746e+01 -6.29872263e+00 -8.57718874e+00 3 1.13996595e+01 -2.37616563e+01 -9.36702603e+00 4 -1.75593489e+01 9.11994690e+00 -9.66579595e+00 5 -2.37146096e+01 -8.45868002e+00 -2.16429338e+01 6 6.66064921e+00 8.16557467e+00 -5.62767889e+00 7 2.49194920e+01 -7.43681476e+00 2.16256657e+01 8 1.45854342e+01 2.16164331e+01 -3.56360321e+01 9 -1.91982613e+01 4.98030038e+00 -9.61281928e+00 10 5.30246950e+00 8.17378383e+00 -7.43113460e+00 11 1.74986915e+01 1.06936962e+01 -3.25900250e+00 12 -4.79176617e+00 2.95040504e+00 3.81934053e+00 13 -1.76732739e+01 -1.75257442e+01 -5.90345564e+00 14 1.96804502e+01 1.59236829e+01 -5.24955636e+00 15 1.67892931e+01 -1.05626086e+01 -5.00304759e+00 16 -1.45352843e+01 1.88282548e+01 4.00906558e+00 17 -1.35668983e+01 -1.29976609e+01 9.52831484e+00 18 -1.60190304e+01 6.78525542e+00 2.45387357e+01 19 1.41040459e+01 -1.64932197e+01 4.57003211e+00 20 -1.27220015e+01 1.89810565e+01 4.28898775e+00 21 9.65437510e+00 -3.19222308e+01 2.73098318e+01 22 1.66928939e+01 -9.37913036e+00 -2.13764236e+00 23 1.83956505e+00 -6.11093014e+00 3.64479864e+00 24 -6.10349975e+00 -1.18436832e+01 1.81615985e+01 25 -1.76602561e+01 1.02782764e+01 1.25357785e+01 26 1.15080833e+00 6.43059421e+00 -4.64907035e+00 27 3.59310960e+00 -6.84480477e+00 8.72283441e+00 28 -7.72988560e+00 4.26621430e+00 1.46073933e+00 29 -1.01857525e+01 1.78487403e+01 -1.38111013e+01 30 3.06959858e+00 4.40384049e+00 -2.15278867e+00 31 2.06907627e+01 -8.60276423e+00 9.21442656e+00 32 -1.36312988e+01 1.63388277e+01 3.73723267e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 77.573320804 Forces: 1 -6.65544220e+00 -1.03095859e+01 1.19979761e+01 2 1.22278471e+01 -3.77284224e+00 1.91737832e+00 3 1.28719646e+01 -1.35485675e+01 -1.55604531e+01 4 -1.52063692e+01 8.72982533e+00 -1.02835942e+01 5 -2.81315508e+01 -1.40358375e+00 -1.64625998e+01 6 3.33848915e+00 1.56506420e+01 1.25310791e+01 7 1.84689146e+01 1.77094922e+00 2.16712890e+01 8 1.47905377e+01 2.14355211e+01 -3.57454676e+01 9 -1.47717712e+01 4.92226040e+00 -5.51459849e+00 10 5.76838870e+00 1.00853342e+01 2.04181179e+00 11 1.74435524e+01 1.09205006e+01 -3.39992425e+00 12 2.04434451e+00 -4.69098054e+00 4.25804028e+00 13 -2.78974689e+01 -2.21128884e+01 2.75608438e+01 14 2.42261674e+01 5.43156728e+01 6.27406138e+01 15 1.10940325e+01 -1.12649520e+01 -5.23126155e+00 16 -1.77109804e+01 1.18960703e+01 6.13658861e+00 17 -3.01620382e+00 -7.67222051e+00 5.58275632e+00 18 -1.60770115e+01 6.70299359e+00 2.47210964e+01 19 2.53300100e+01 -1.97125075e+01 -1.10773562e+01 20 -6.13592371e-02 2.47956780e+01 -3.35080019e+00 21 1.17255046e+01 -2.84437562e+01 2.73745783e+01 22 6.85560625e-01 -6.53636788e+00 -3.86851053e+00 23 -7.77581103e+00 -1.47803461e+01 -5.36993733e+00 24 -9.98026089e+00 -1.84262187e+01 -1.23320337e+00 25 -8.45176414e+00 1.33867905e+01 1.23219240e+01 26 1.73572170e+00 -5.84877906e+00 1.41531501e+00 27 3.71243659e+00 -9.06231355e+00 -4.97964453e-01 28 3.15561531e+01 1.70424836e+01 -4.75180911e-01 29 -1.01533574e+01 1.79054759e+01 -1.40520293e+01 30 -1.09989213e+01 -2.06182933e+00 -1.24496152e+01 31 8.92371200e+00 -6.70634808e+01 -5.31082670e+01 32 -2.90550652e+01 2.71510223e+01 -2.45905274e+01 MIXED STRUCTURE (pbc=False)-- Species = Ag Cu (Configuration in file "config-F-AgCu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 100.661068469 Forces: 1 -5.14266106e+00 -4.25545000e+00 -5.54070037e+00 2 -4.26541669e+00 5.47136619e+00 -2.18773956e+01 3 1.48169111e+01 -2.74045524e+01 -9.16599885e+00 4 -2.71125969e+01 -4.86036965e+00 -7.25604328e+00 5 -2.54414277e+00 -1.71837076e+01 -2.02232475e+01 6 1.12905896e+01 -1.05116342e+01 -3.10237567e+01 7 1.74193682e+01 -1.84148982e+01 -7.20933199e+00 8 1.34110209e+01 7.30922511e+00 -6.76191205e+00 9 -6.85587871e+00 6.83201884e+00 -1.16107732e+01 10 -1.31143461e+01 1.68166985e+01 -2.06787175e+01 11 2.06063313e+01 2.62539757e+00 -8.88766716e+00 12 -2.39566064e+01 1.81351690e+01 -7.28232046e+00 13 2.14294220e+00 -6.36408560e+00 -9.60416197e+00 14 8.24575929e+00 5.04743288e+00 -4.88981996e+00 15 5.87834280e+00 2.49146240e+01 1.88808747e+01 16 9.47766046e+00 6.52704309e+00 1.41016212e+01 17 -2.87840902e+01 -1.08766116e+01 -5.73142262e+00 18 -3.43180470e+00 -3.20745367e+00 2.43948248e+01 19 8.24233989e+00 -1.13808104e+01 2.33637600e+01 20 -1.04492789e+01 -7.49871823e+00 1.80216972e+01 21 -1.21862574e+01 -2.08932368e+01 -8.35235478e+00 22 1.30654044e+01 8.15224459e+00 1.72308166e+01 23 1.48953956e+01 -8.62229139e+00 1.38475902e+01 24 1.56025271e+00 1.16175857e+01 1.66609376e+01 25 -2.19613449e+01 5.14856558e+00 5.15807926e+00 26 1.83088151e+01 1.32231384e+01 -7.53449974e+00 27 3.54498063e+00 -1.14158343e+01 1.50770440e+01 28 -2.59343799e+01 1.16635220e+01 1.77839094e+01 29 -1.07918936e+01 -1.66847517e+00 -1.74043313e+01 30 9.17129382e+00 1.53952463e+01 -5.97754307e+00 31 1.72921439e+01 -8.55322727e+00 2.17309519e+01 32 7.16114618e+00 1.42320788e+01 1.07598912e+01 MIXED STRUCTURE (pbc=True)-- Species = Ag Cu (Configuration in file "config-T-AgCu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 228.814047677 Forces: 1 6.73363323e+00 2.21747856e+01 -1.33108146e+01 2 -5.19947941e+00 3.72025986e+00 -4.68944734e+00 3 1.58032817e+01 -8.23327015e+00 -3.83146281e+00 4 -2.51150492e+00 -5.03095708e+00 -4.53434481e+00 5 -5.58697828e+00 3.06714684e-01 -1.32761531e+01 6 -2.08876271e+01 -3.28023101e+01 -3.04137583e+01 7 4.89052078e+00 -1.11424254e+00 4.61457388e+00 8 1.33360729e+01 7.40879914e+00 -6.71803075e+00 9 2.46910204e+01 2.41499241e+01 -1.19389128e+01 10 -1.71926010e-01 -5.44705405e+00 -1.12812520e+01 11 2.06002085e+01 2.57271612e+00 -8.86304560e+00 12 -8.18588152e+00 1.23063463e+00 -1.60094795e+01 13 9.68548791e+00 -1.13108651e+01 7.49634641e+00 14 -1.41694453e+01 -2.13570522e+01 -3.04172700e+00 15 -1.54483218e+01 2.33536838e+01 2.39105616e+01 16 1.78408412e+00 -1.69017251e+01 7.30978640e+00 17 -3.02712963e+01 1.61071540e+01 -1.21182689e+00 18 -3.14322383e+00 -2.92622905e+00 2.40864582e+01 19 1.13944550e+01 1.77937127e+01 2.92125265e+01 20 1.02355625e+01 -1.77641793e+01 1.50699730e+01 21 -6.01100782e+00 2.46362576e+00 -1.05087986e+00 22 -1.29658116e+01 2.37571428e+00 1.09027851e+01 23 2.00852579e+01 6.51769746e+00 2.12948461e+00 24 5.26025285e+00 1.30138827e+01 3.90270590e+00 25 -2.81717186e+00 8.43633134e+00 6.24882824e+00 26 3.15530026e+01 -2.26650095e+01 -2.02016339e+01 27 -4.43564017e+00 -9.31166170e+00 -1.30269700e+00 28 -1.84411692e+01 -7.15734222e+00 1.88611992e+01 29 -1.08865823e+01 -2.08110169e+00 -1.76302256e+01 30 -1.56278744e+01 6.96981086e+00 -4.29720921e+00 31 -3.29951376e+00 7.83126038e-01 1.75846520e+01 32 4.00761520e+00 4.72442647e+00 2.27302010e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==7068== Memcheck, a memory error detector ==7068== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==7068== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==7068== Command: python runner2.py EAM_Dynamo_WilliamsMishinHamilton_2006_CuAg__MO_128703483589_005 ==7068== ==7068== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==7068== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==7068== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7068== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7068== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7068== by 0x4010732: call_init (dl-init.c:72) ==7068== by 0x4010732: _dl_init (dl-init.c:119) ==7068== by 0x40151FE: dl_open_worker (dl-open.c:522) ==7068== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7068== by 0x40147C9: _dl_open (dl-open.c:605) ==7068== by 0x544CF95: dlopen_doit (dlopen.c:66) ==7068== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7068== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==7068== by 0x544D734: _dlerror_run (dlerror.c:162) ==7068== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==7068== ==7068== ==7068== HEAP SUMMARY: ==7068== in use at exit: 39,099,049 bytes in 4,273 blocks ==7068== total heap usage: 194,504 allocs, 190,231 frees, 112,525,986 bytes allocated ==7068== ==7068== LEAK SUMMARY: ==7068== definitely lost: 0 bytes in 0 blocks ==7068== indirectly lost: 0 bytes in 0 blocks ==7068== possibly lost: 182,735 bytes in 112 blocks ==7068== still reachable: 38,916,314 bytes in 4,161 blocks ==7068== suppressed: 0 bytes in 0 blocks ==7068== Rerun with --leak-check=full to see details of leaked memory ==7068== ==7068== For counts of detected and suppressed errors, rerun with: -v ==7068== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2519 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.