Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:10:57) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_HepburnAckland_2008_FeC__MO_143977152728_005 Supported species : C Fe random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = C (Configuration in file "config-F-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -33.1719741128 Forces: 1 -1.41596773e+00 -7.93540066e+00 -5.31081386e+00 2 1.84693650e-01 -6.66677422e-01 -2.61364698e+00 3 1.81353679e-01 -2.83475969e+00 -8.91126701e-01 4 -3.26997390e+00 5.98110805e+00 3.45355275e+00 5 2.30893170e-02 -1.63583326e+00 -1.29548986e+00 6 1.90698024e+00 -9.31661891e-01 -8.44474187e-01 7 -3.00838583e+00 1.09332518e+01 1.15687518e+01 8 1.40305876e+01 7.76021036e+00 7.67246073e+00 9 -1.60980814e+00 5.77039485e-01 -2.62577115e+00 10 2.96862647e+00 1.70568055e+00 1.94354516e+00 11 4.39909670e+00 7.35108084e+00 5.66670185e+00 12 -3.06680207e+00 2.53227381e+00 -5.68695700e-01 13 -2.20109920e-01 1.14763352e+00 5.16451816e+00 14 4.42487485e+00 6.24447068e-01 1.75272483e+00 15 -1.22218528e+01 4.25554359e-01 -5.18679105e-01 16 -5.86187977e+00 -1.11239853e+01 9.87554923e-01 17 -2.32876594e+00 -2.04795887e+00 3.96031727e-01 18 -6.88645248e-01 -2.40487501e-01 8.32316794e-02 19 -3.74188754e-01 -2.80762721e+00 1.90777502e+00 20 -2.77157207e+00 -4.19383758e-02 2.46350848e+00 21 5.02580104e+00 -6.24423488e-01 -5.05972383e+00 22 -7.67909274e+00 -6.70791012e+00 -1.00342766e+01 23 1.63398231e+00 -7.94983069e-01 1.38607687e+00 24 3.63872383e-01 -1.63184323e-01 3.21080818e+00 25 2.84108269e+00 4.17507849e+00 -4.11407654e-01 26 1.06224153e+00 -8.99153861e+00 -1.34776934e+00 27 5.69549371e+00 1.92820627e+00 -9.99596508e-01 28 -2.94890508e+00 4.74953503e+00 -1.44008731e+00 29 6.67544670e+00 -1.28833455e+00 -7.97327023e+00 30 5.07024007e-01 -1.94449261e+00 2.90402366e+00 31 -9.09177058e+00 7.17342834e+00 -7.52544931e+00 32 4.63347364e+00 -6.28333100e+00 -1.10098748e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -4.05619782595 Forces: 1 -6.37197375e+00 -2.30661737e+00 -9.28060920e+00 2 4.62893133e-01 -3.26859323e+00 -5.25300064e+00 3 1.22199314e+01 -3.04930120e+00 -1.67852486e+00 4 -4.34944918e+00 -3.58574783e+00 1.53403134e+00 5 -5.84573872e-02 -2.64784887e-01 4.86481292e-02 6 1.06796608e+01 -7.55312488e+00 -2.73185205e+00 7 7.85587405e+00 -4.77440728e+00 -9.79346740e+00 8 2.52569814e+00 -2.27906385e+01 -6.68591830e+00 9 -5.17352745e+00 -7.54788498e+00 -1.76714002e+01 10 -9.77764664e+00 6.68171849e+00 -1.61446565e+01 11 -3.03548827e+01 -2.23084209e+00 -2.10976472e+01 12 -8.24579690e+00 3.19670008e+01 -1.42001082e+01 13 -3.34220869e+00 9.57962980e+00 -1.16490933e+01 14 2.71316475e+01 3.70237965e+00 -1.64529046e+01 15 6.66595662e+00 8.86128546e+00 -9.14875263e+00 16 -1.00778527e+01 7.23977196e+00 2.31565854e+01 17 -2.80089317e+01 -8.47442637e+00 -9.34428378e+00 18 -1.81275257e+00 -2.62674624e+01 -3.42350545e+01 19 1.53395531e+01 -1.42647153e+01 1.64012811e+01 20 -8.47586670e+00 3.91252140e+00 9.69602796e+00 21 -2.03514455e+01 -7.97093159e+00 -4.28882529e+00 22 9.90834796e+00 1.42178741e+00 9.40295133e+00 23 9.50554894e+00 -6.63467656e+00 1.25299247e+01 24 8.84808636e+00 4.33517636e+00 8.90477480e+00 25 -8.82516477e+00 -2.69317879e+01 1.59540134e+01 26 5.44768933e+00 1.04035397e+01 4.91157580e+00 27 3.05738094e+00 3.68478714e+01 3.31346748e+01 28 -2.05479739e+00 8.80698591e+00 1.27198326e+01 29 2.57576510e+01 9.34952098e+00 3.64762157e+01 30 2.64217285e+01 -1.98592801e-01 -2.30668783e+01 31 1.00618631e+00 -1.07029632e+00 3.84654134e+00 32 -2.55530801e+01 6.07564215e+00 2.40058985e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 74.7752081317 Forces: 1 -9.09216791e+00 3.65085664e+00 -1.09548385e+01 2 -3.29246505e+00 -1.22182426e+00 1.16123700e+01 3 9.67859139e+00 6.31177903e+01 -5.87155330e+01 4 1.92720616e+01 -2.39432263e+01 -5.50131055e+00 5 5.63339222e+00 7.30876161e+00 1.61087199e+01 6 5.73714892e+00 -1.53485171e+01 4.35088054e+00 7 9.64415921e+00 1.49826956e+01 1.63721360e+00 8 2.29430169e+00 -2.35095881e+01 -6.97721555e+00 9 2.84998917e+00 -7.94129733e+00 -1.99917560e+01 10 -1.34745126e+01 -8.30474568e+00 -1.73314534e+01 11 -2.98925892e+01 -5.14784421e+00 -2.22474567e+01 12 -1.27369112e+00 3.63730852e+01 -1.68960429e+01 13 -3.11283993e+00 1.56920520e+01 -5.80131224e+00 14 2.48781615e+01 -9.15776126e+00 -3.39628598e+01 15 -5.30633457e+01 6.07289388e+00 -3.06932044e+01 16 -1.22824313e+01 -6.98415346e-01 2.61030713e+01 17 -4.80375761e+01 1.77428508e+01 -4.09984263e+00 18 -1.19568809e+00 -2.50502511e+01 -3.65116736e+01 19 1.01087906e+01 -6.21681911e+00 1.96506143e+01 20 -9.01967392e+00 2.01834446e+00 3.23995681e+00 21 -2.28298191e+01 -8.14350389e-01 -8.87743066e+00 22 4.94580396e+00 -5.61796098e-01 1.23676797e+01 23 4.34617774e+01 4.44876215e+01 2.66992025e+01 24 1.44541026e+01 9.82371227e+00 -1.02259184e+01 25 3.07288495e+01 -2.04622721e+01 4.43255897e+01 26 2.94292488e+01 -7.32697525e+01 4.86962453e+01 27 3.95330933e+00 4.07552534e+01 3.04912961e+01 28 7.35516323e+00 9.33376674e+00 2.09369945e+01 29 2.61534367e+01 8.54092708e+00 3.72593623e+01 30 1.91030917e+01 -1.65842478e+01 -3.76613257e+01 31 -7.72478107e+00 -1.03297878e+00 -4.12896175e-02 32 -5.53897983e+01 -4.06349241e+01 2.30112673e+01 MIXED STRUCTURE (pbc=False)-- Species = C Fe (Configuration in file "config-F-CFe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -40.0490942854 Forces: 1 -1.47987711e+00 -9.33250578e-01 -1.34372569e+00 2 1.12244824e+01 -1.35806692e+01 2.17132239e+00 3 -3.22539322e+00 -8.95051440e+00 -9.45401968e+00 4 4.86046408e+00 8.32525626e+00 3.42735912e+00 5 4.02470722e+00 -2.89261664e+00 2.03512538e+00 6 2.78691016e+00 -2.51538351e+00 5.19076179e-01 7 4.81854987e-01 1.09464712e+00 -1.14341572e+00 8 -1.87488082e+00 -1.07040769e+00 -3.34970576e-01 9 -1.51269850e+01 1.72620871e+01 3.25505635e+00 10 -2.47853292e+01 -4.44167528e+00 -1.43066027e+01 11 -5.39540117e+00 -1.35376716e+00 2.52022761e-01 12 8.48091992e-01 -8.76223714e-01 1.06505657e+00 13 -1.66928528e+01 -1.45190095e+01 -3.85929773e+00 14 1.45002764e+01 2.30369799e+01 -8.68495543e+00 15 4.91487288e+00 -4.86228549e+00 1.55424410e+01 16 2.48587149e+01 2.85944772e+00 1.53104785e+01 17 -2.50923855e+01 6.23449351e+00 -2.58349099e+01 18 -4.91906995e+00 3.37527049e+01 -1.33791669e+01 19 -1.20716604e+00 -1.70674524e+01 6.28719502e+01 20 -1.44193989e+01 -3.12292029e+00 9.99063647e+00 21 4.54268888e+01 -1.05872736e+01 -2.71293820e+01 22 3.10195431e+00 -2.11697212e+00 -4.83835661e+00 23 -1.33391917e+00 5.39107640e-01 -1.40147082e+00 24 -2.33118277e+01 -3.23618033e+01 5.46800782e+00 25 5.58053845e+00 -4.73667939e+00 -1.59263031e+01 26 1.88068528e+00 -6.84400256e+00 -3.97413523e+00 27 4.54364689e+00 3.43220716e+00 4.56925969e+00 28 -1.39695562e+01 8.71973948e+00 5.68963676e+00 29 -1.02555044e+01 4.96107805e+00 -1.29543335e+00 30 -1.15538717e-01 -3.54168441e+00 -2.87496669e+00 31 3.32917373e+01 2.77408651e+01 3.66073416e+00 32 8.79259712e-01 -1.58402254e+00 -4.70512367e-02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==409== Memcheck, a memory error detector ==409== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==409== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==409== Command: python runner2.py EAM_Dynamo_HepburnAckland_2008_FeC__MO_143977152728_005 ==409== ==409== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==409== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==409== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==409== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==409== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==409== by 0x4010732: call_init (dl-init.c:72) ==409== by 0x4010732: _dl_init (dl-init.c:119) ==409== by 0x40151FE: dl_open_worker (dl-open.c:522) ==409== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==409== by 0x40147C9: _dl_open (dl-open.c:605) ==409== by 0x544CF95: dlopen_doit (dlopen.c:66) ==409== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==409== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==409== by 0x544D734: _dlerror_run (dlerror.c:162) ==409== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==409== ==409== ==409== HEAP SUMMARY: ==409== in use at exit: 110,077,704 bytes in 4,275 blocks ==409== total heap usage: 186,761 allocs, 182,486 frees, 193,983,144 bytes allocated ==409== ==409== LEAK SUMMARY: ==409== definitely lost: 0 bytes in 0 blocks ==409== indirectly lost: 0 bytes in 0 blocks ==409== possibly lost: 183,855 bytes in 114 blocks ==409== still reachable: 109,893,849 bytes in 4,161 blocks ==409== suppressed: 0 bytes in 0 blocks ==409== Rerun with --leak-check=full to see details of leaked memory ==409== ==409== For counts of detected and suppressed errors, rerun with: -v ==409== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2525 from 172) ================================================================================ 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 06:12:09) ===