!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MendelevFangYe_2015_AlSm__MO_338600200739_000 Supported species : Al Sm 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 = 85.5039081674 Forces: 1 -8.70757931e+00 -1.12689296e+01 -1.37867814e+01 2 -6.37520162e+00 1.10813860e+01 -1.46274238e+01 3 -2.97565847e+00 -1.54313868e+01 7.48426882e+00 4 -1.27060338e+01 6.02008606e+00 3.33000634e+00 5 1.30173776e+01 -1.84933855e+01 -1.04517266e+01 6 7.41673833e+00 1.37969579e+00 -1.11959178e+01 7 9.62391583e+00 -2.94763734e+01 -1.97109679e+01 8 -5.81410571e+00 -2.08340509e+01 -1.00928570e+01 9 -7.13009966e+00 -1.05751909e+01 -1.92911348e+01 10 -3.15177927e+00 1.64146120e+01 -1.97121934e+01 11 -3.87231005e+00 -7.05268305e+00 -2.47441914e+01 12 -1.58114922e+01 1.97549348e+01 4.96654541e+00 13 -5.24392723e+00 -8.50741142e+00 -4.11382895e+01 14 9.82635282e+00 1.05855197e+01 -7.43748702e+00 15 4.24063124e+01 2.51068665e+00 3.39895248e+00 16 8.46408570e+00 3.68981912e+01 4.86073909e+00 17 -1.22930718e+01 -8.54422950e+00 -1.50474606e+00 18 -5.52163502e+00 -7.32472615e+00 1.02840709e+01 19 3.99261220e+00 -1.12026022e+01 8.87375894e+00 20 -7.42907998e+00 5.40545650e+00 7.30681880e+00 21 -9.04411621e+00 -1.51709683e+01 8.80599827e+00 22 2.38575020e+01 1.53776763e+01 1.91834907e+01 23 5.11949354e+00 -3.16490107e+00 8.89518615e+00 24 1.14876618e+00 -4.59353870e+00 1.06791581e+01 25 -3.64630567e+01 7.95847100e-01 1.94724217e+01 26 -9.83912816e+00 2.95940266e+01 -9.41182423e-01 27 4.17354492e+00 -2.43059833e+01 1.49335697e+01 28 -2.45823899e+01 1.95978386e+01 6.07546044e+00 29 9.92631334e+00 -4.33803602e+00 2.19376761e+01 30 1.22896163e+01 1.50385020e+01 4.35282258e-01 31 1.76200412e+01 -6.93387011e+00 1.45337205e+01 32 8.07799268e+00 1.67638076e+01 1.91777744e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 772.767459956 Forces: 1 3.98380384e+01 -1.79805892e+01 -4.81260701e+00 2 -2.40550274e+01 1.92162869e+01 1.16528842e+01 3 -1.39454955e+00 2.47125431e+01 3.74252539e+01 4 2.31951769e+01 3.06240708e+01 6.04034836e+00 5 3.88603005e+01 1.62692329e+01 -1.95005712e+01 6 -5.94494475e+01 6.04679373e+01 9.64948657e+00 7 -1.61523404e+01 -3.60454742e+01 -2.27986020e+01 8 -2.53184116e+01 -2.72106095e+01 -2.51089904e+00 9 -2.80532908e+01 -5.56291732e+01 6.21033485e+00 10 -8.61027837e+00 -5.08268763e+00 -2.57131520e+01 11 -3.08240588e+00 -3.45857463e+01 -2.12527887e+01 12 -6.97891367e-01 2.75603558e+00 3.73025334e+01 13 -5.60960022e-01 -3.37235901e+01 -5.79167948e+01 14 -3.07720861e+01 1.06538547e+00 -3.25306477e+01 15 4.95923372e+01 -5.35445301e+00 1.24944228e+01 16 2.29436876e+01 3.85844433e+01 2.52207761e+01 17 2.55530566e+01 -1.78573055e+01 5.68004819e+00 18 4.93319471e-01 -1.29899270e+00 2.07416849e+01 19 1.38402633e+01 2.28791047e+01 -3.43643938e+00 20 2.69135176e+01 5.08168360e+01 -2.26306933e+01 21 -2.20335131e+01 4.96182549e+00 2.48655475e+01 22 -9.25089505e-01 5.61463329e+01 4.95243991e+01 23 -3.88825818e+01 -3.74493573e+01 -4.56194323e+01 24 2.67437729e+01 2.25713347e+00 -3.55767805e+01 25 -3.79475019e+01 -1.59622133e+01 3.98255682e+01 26 -1.19855693e+01 2.53354734e+01 -6.12604357e+00 27 2.08590599e+01 -6.12091549e+01 -2.54660213e+01 28 -4.92587560e+01 2.36403364e+01 -2.61368316e+01 29 1.33087824e+01 -2.61727446e+01 3.95510491e+01 30 2.97943125e+00 7.27558787e-02 1.61115987e+01 31 1.96977180e+01 -2.10272588e+01 1.00463585e+01 32 3.43612387e+01 1.67836167e+01 -3.13990069e-01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Sm (Configuration in file "config-F-Sm.xyz") ----------------------------------------------------------------------------------------------------- Energy = 733.680576245 Forces: 1 -3.88782721e+01 -3.29330018e+01 -2.35898017e+01 2 -2.73239845e+01 -4.40248104e+00 -6.88883774e+01 3 -2.71503227e+01 -1.22065388e+02 -6.70347536e+01 4 -5.81569232e+01 -2.60291263e+01 -3.11132640e+01 5 2.17445402e+01 -5.03194866e+01 -2.60676530e+01 6 4.69098608e+01 -1.22710473e+01 -1.78018924e+01 7 3.15335283e+01 -1.78591534e+01 -1.36668295e+01 8 1.07520998e+02 1.62347196e+01 -4.30532449e+01 9 -3.56401001e+01 -5.24794413e+00 -3.27918817e+01 10 -2.51131662e+01 3.69214219e+01 -6.02377602e+01 11 -2.65206583e+01 2.83156003e+01 1.73271402e+01 12 -3.91922685e+01 3.80475390e+01 8.73753602e+00 13 2.22041748e+01 2.24733583e+01 -4.89278840e+01 14 3.74588658e+01 2.44776604e+01 -3.76102311e+01 15 2.56984171e+01 -3.73942734e+01 -2.76909848e+01 16 2.17178498e+01 4.18651443e+01 2.75930545e+01 17 -8.20937763e+01 -6.40936640e+01 -4.24050428e+01 18 -1.93006189e+01 5.78157118e+01 1.24565891e+02 19 6.84518761e+01 -3.77248083e+01 8.35824648e+01 20 -4.76080900e+01 1.89819917e+01 4.98333340e+01 21 -7.48441737e+00 -3.46937101e+01 1.05346739e+01 22 3.36296237e+01 -1.51571277e+01 -3.70674895e+01 23 2.47333042e+01 -2.19110244e+01 2.81434775e+01 24 1.75587740e+01 -3.97662009e+01 5.25512502e+01 25 -3.40443695e+01 3.47346238e+01 1.95189911e+01 26 -6.80659250e+01 7.88327217e+01 -1.55715925e+01 27 -8.93108736e+01 -4.13297287e+00 7.62240968e+01 28 -1.04317814e+01 1.56260164e+01 1.67380560e+01 29 9.03343369e+01 -4.94245151e+01 -7.47421088e+01 30 3.18489249e+01 5.31143712e+01 2.93558781e+01 31 3.35701952e+01 3.15542040e+01 4.48178003e+01 32 2.14002783e+01 7.64308413e+01 7.87371475e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Sm (Configuration in file "config-T-Sm.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1403.802801 Forces: 1 -3.80649016e+01 -3.39582224e+00 1.98599991e+01 2 -4.43510844e+01 -1.20613395e+00 1.74149641e+01 3 -2.85210603e+01 -8.24969426e+01 -6.72389754e+01 4 -2.52755244e+01 -2.72425440e+01 -3.96649767e+01 5 2.73312211e+01 -1.09135582e+01 7.28572770e-01 6 5.56538892e+01 -3.64594140e+01 7.71507312e+01 7 1.49127445e+01 3.33680118e+01 -2.21494831e+01 8 1.04436665e+02 2.05758572e+01 -3.88169238e+01 9 6.50510113e+01 -8.71957449e+01 1.27801352e+02 10 -1.84213149e+01 -1.23505441e+01 -3.18414351e+01 11 -2.33970991e+01 2.72031151e+01 2.57643040e+01 12 8.19929800e+00 1.40708666e+01 -4.08210150e+00 13 7.67889582e+00 6.62052415e+01 4.75173073e+01 14 -2.45542774e+01 4.48942537e+01 1.46866475e+01 15 -3.35884062e+01 -4.46460632e+01 -3.27224637e+01 16 1.06146711e+01 -7.54611633e+00 3.82460873e+01 17 -3.60824996e+01 -1.60795330e+01 -5.54623502e+01 18 -1.76342411e+01 6.47100954e+01 1.20200947e+02 19 6.51327684e+01 -2.53252924e+01 2.57197544e+01 20 2.29799318e+01 3.44849300e+01 3.06996236e+01 21 -1.58656837e+01 4.78621147e+01 -1.95160604e+01 22 -8.89988633e+01 -6.00642536e+01 -3.94292267e+01 23 -2.98124797e+01 -2.50126972e+01 2.54881942e+01 24 1.37590067e+01 -6.51323907e+01 -8.92874020e+01 25 8.00057066e+01 6.45503775e+01 -1.85138375e+00 26 -5.80289513e+01 2.76227310e+01 -2.20588818e+01 27 -9.50302881e+01 4.15628840e+00 2.42542853e+01 28 6.46133073e+01 1.07219113e+02 -9.33577763e+01 29 8.50392608e+01 -5.75265616e+01 -8.27860402e+01 30 4.23304901e+00 -1.31882031e+00 2.26528193e+01 31 -6.16654281e+01 -1.44542039e+01 -4.78407922e+01 32 9.65067683e+00 2.14436408e+01 6.99206837e+01 MIXED STRUCTURE (pbc=False)-- Species = Al Sm (Configuration in file "config-F-AlSm.xyz") ----------------------------------------------------------------------------------------------------- Energy = 304.667748175 Forces: 1 -1.03339132e+01 -1.14465664e+01 -9.28724501e+00 2 -2.45953177e+00 -7.07035615e+00 -3.44681181e+01 3 8.64454466e+00 -4.81623007e+01 -2.77598077e+01 4 -5.08651808e+01 1.34669833e+01 -4.37248969e+01 5 -9.85730409e+00 -3.60020597e+01 -4.09911129e+01 6 2.89908316e+01 -4.92794728e+00 -1.70144927e+01 7 2.72211567e+01 -1.92257097e+01 8.69502671e+00 8 3.70360997e+00 -8.74123534e+00 1.51552832e+00 9 -2.06175347e+01 -3.54454051e+00 -2.92804618e+01 10 5.46575468e-01 1.13861343e+01 -1.34536047e+01 11 -1.16391143e+01 1.81419418e+01 -5.21018414e+00 12 -1.43699592e+01 3.10650098e+01 9.33524213e+00 13 -9.97796991e+00 1.63651796e+01 -4.09183795e+01 14 1.29758815e+01 1.20558954e+01 -1.27040220e+01 15 3.57166738e+01 3.80372445e+00 1.62090891e+01 16 -1.19615767e+01 3.64341767e+01 -2.54648014e+01 17 -4.35579505e+01 -4.71084065e+01 2.17050526e+01 18 1.22336775e+01 3.03329887e+01 2.18675353e+01 19 -1.20884372e+01 -3.12124415e+01 2.64987740e+01 20 -2.55483365e+01 4.69459334e+00 2.96402063e+01 21 1.49630611e+01 -6.02506108e+01 -2.32713611e+01 22 2.63838014e+01 7.09090811e+00 5.00168812e+00 23 3.22460195e+01 -1.22965871e+01 2.01606706e+01 24 1.23756017e+01 2.55644170e+01 4.99884795e+01 25 -3.11231751e+01 1.64157441e+01 9.62167803e+00 26 -1.17675332e+01 2.24349690e+01 4.10827320e+00 27 1.88681732e+01 -9.76280963e+00 2.66903399e+01 28 -3.58364301e+01 2.75583837e+01 1.01525946e+01 29 8.41337242e+00 -1.34919921e+00 1.31393975e+01 30 3.42273894e+01 1.14833018e+01 2.46234624e+01 31 1.70966382e+01 -7.95233641e-02 1.11383719e+01 32 7.39693889e+00 1.28859429e+01 1.34570779e+01 MIXED STRUCTURE (pbc=True)-- Species = Al Sm (Configuration in file "config-T-AlSm.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1952.34084519 Forces: 1 9.46561203e+01 4.19704063e+01 -8.15916999e+01 2 9.47484670e+01 5.10766676e+01 1.26743504e+02 3 9.78794180e+00 -8.43589589e+00 -4.78398648e+01 4 1.03177234e+01 7.55241132e+01 -1.60383308e+01 5 -4.59661025e+01 5.92259002e-01 -1.84957804e+01 6 6.79274989e+01 8.53610933e+00 -4.26027430e+01 7 -2.29114779e+01 4.34116112e+00 5.15468540e+01 8 -7.38975366e+01 -4.50474746e-01 2.93907739e+01 9 3.17780147e+01 -5.37151773e+01 4.26600326e+01 10 -6.78733065e+01 -2.12123135e+01 7.02804299e+01 11 -6.49366508e+01 1.96494791e+00 2.79875210e+00 12 6.23609825e+01 -8.56034150e+01 4.79747806e+01 13 -6.67507402e+01 2.95217189e+01 -5.63948986e+01 14 -2.32321956e+01 -5.09547204e+01 -1.26259215e+01 15 6.99857972e+01 2.35802664e+01 4.97366029e+01 16 -4.93560199e+01 -2.84792459e+01 -5.19657284e+01 17 3.08632808e+00 -3.29174683e+00 4.16635622e+01 18 -2.03896210e+01 8.24943253e+01 3.47561587e+01 19 -6.86583014e+01 2.83852551e+01 2.94300837e+01 20 -1.16158508e+02 3.24229007e+01 -1.41591650e+02 21 -8.47652495e+00 4.30941146e+01 -2.40088556e+01 22 2.40647712e+01 6.03375652e+01 4.74399585e+01 23 7.58202691e+01 5.41365867e+01 2.53751118e+01 24 -1.37797479e+01 6.75888063e+01 -8.96839260e+00 25 5.45445996e+01 3.86536813e+00 1.35655335e+01 26 -8.78882972e+01 -9.41234195e+01 -2.89994927e+01 27 -1.05658088e+01 -5.78984842e+01 -2.84814358e+01 28 2.97159540e+01 -5.19783657e+00 -6.46525153e+01 29 -4.08344084e+01 -5.87124026e+01 7.08531075e+00 30 8.80636008e+01 -5.25286869e+01 1.59283704e+01 31 4.37204226e+01 -2.92287787e+01 -1.46929099e+01 32 2.10967565e+01 -5.95999739e+01 2.57439952e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2399== Memcheck, a memory error detector ==2399== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2399== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==2399== Command: python runner2.py EAM_Dynamo_MendelevFangYe_2015_AlSm__MO_338600200739_000 ==2399== ==2399== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==2399== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==2399== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2399== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2399== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2399== by 0x4010732: call_init (dl-init.c:72) ==2399== by 0x4010732: _dl_init (dl-init.c:119) ==2399== by 0x40151FE: dl_open_worker (dl-open.c:522) ==2399== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2399== by 0x40147C9: _dl_open (dl-open.c:605) ==2399== by 0x544CF95: dlopen_doit (dlopen.c:66) ==2399== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2399== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==2399== by 0x544D734: _dlerror_run (dlerror.c:162) ==2399== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==2399== ==2399== ==2399== HEAP SUMMARY: ==2399== in use at exit: 40,155,945 bytes in 4,274 blocks ==2399== total heap usage: 207,113 allocs, 202,839 frees, 114,813,185 bytes allocated ==2399== ==2399== LEAK SUMMARY: ==2399== definitely lost: 0 bytes in 0 blocks ==2399== indirectly lost: 0 bytes in 0 blocks ==2399== possibly lost: 182,735 bytes in 112 blocks ==2399== still reachable: 39,973,210 bytes in 4,162 blocks ==2399== suppressed: 0 bytes in 0 blocks ==2399== Rerun with --leak-check=full to see details of leaked memory ==2399== ==2399== For counts of detected and suppressed errors, rerun with: -v ==2399== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2523 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.