!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MendelevAstaRahman_2009_AlMg__MO_658278549784_005 Supported species : Al Mg 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 = 66960.7119986 Forces: 1 -5.18529568e+03 -5.36572181e+03 -3.66556210e+03 2 -1.12756895e+04 -1.76213890e+04 -2.88005372e+04 3 -1.12534786e+04 -2.07145106e+04 -3.19848529e+03 4 -2.16870557e+04 -1.18148094e+04 -5.81655945e+03 5 -2.92946408e+03 -2.02017981e+04 -1.48068945e+04 6 1.71413794e+04 -6.86875481e+03 -2.11211094e+04 7 2.26327987e+04 -3.22111864e+04 -5.93921067e+03 8 3.00718249e+04 -8.12208322e+04 -3.85729164e+04 9 -2.03626733e+04 2.57473675e+03 -2.22367991e+04 10 -7.47041613e+03 2.55656115e+04 -2.42955928e+04 11 -7.51540691e+04 8.99947462e+03 -4.11725125e+04 12 -2.14604349e+04 1.66502157e+04 -3.39578293e+03 13 1.88815772e+04 1.99243145e+04 -5.38305442e+04 14 1.04981588e+04 1.07700406e+04 -1.06462062e+04 15 6.25982178e+04 2.55405309e+04 -2.73456344e+04 16 1.20500271e+04 6.57076064e+04 -2.30346467e+04 17 -5.95038846e+03 -5.77224258e+03 2.59811557e+03 18 -3.05621754e+04 -3.20093058e+04 2.56936329e+04 19 -4.04444673e+03 -7.32684546e+03 6.33392908e+03 20 -5.97454975e+03 -2.72236402e+03 5.66194660e+03 21 4.02556082e+03 -2.61635107e+04 1.35240738e+04 22 3.41910935e+04 -2.04987593e+04 1.50936985e+04 23 3.55829464e+03 -5.51837036e+03 5.35548671e+03 24 1.88444115e+03 -1.39123652e+04 2.55842206e+04 25 -3.46161889e+04 8.92058326e+03 1.87762432e+04 26 -2.44783687e+04 4.05225149e+04 2.12838417e+04 27 -1.60873997e+04 3.24169396e+03 2.42722896e+04 28 -7.51885970e+03 4.25531728e+03 7.74166477e+03 29 3.47729261e+04 3.16031565e+04 8.71010064e+04 30 2.79234381e+04 2.54368703e+04 4.98234515e+03 31 2.86722371e+04 1.29180036e+03 3.51701556e+04 32 -2.89102097e+03 1.89382983e+04 2.87063435e+04 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 15893714.0181 Forces: 1 1.20907123e+05 -2.74171265e+04 2.41100488e+05 2 3.42090095e+05 8.71322146e+04 -1.74056071e+05 3 2.19538862e+05 1.56511067e+06 1.04243388e+06 4 7.45215784e+05 1.88517869e+05 1.28916375e+06 5 9.83495768e+05 1.09868904e+06 -4.38541669e+05 6 -1.08482762e+06 1.41493589e+05 -6.33044374e+05 7 -4.55373476e+05 -1.72970335e+05 2.90102944e+05 8 -8.37084959e+05 -1.37299029e+06 6.60369371e+05 9 -1.09138934e+06 -1.65691301e+06 5.22086705e+05 10 2.48735779e+05 8.82558254e+05 -4.28322017e+05 11 -5.77622854e+05 -1.97132109e+06 9.04881975e+05 12 -3.84463467e+05 3.98804400e+05 8.39500218e+05 13 8.75173350e+04 -1.20019726e+06 -2.11229491e+06 14 -6.09259775e+05 5.56948115e+05 -9.69066703e+05 15 1.50568792e+06 -8.62665620e+05 8.71203445e+05 16 6.05091926e+05 1.76307487e+06 1.08778433e+06 17 -2.49795903e+05 4.79638537e+05 -1.04799449e+06 18 4.00480232e+05 1.20108722e+05 -2.54636355e+04 19 1.51652639e+06 1.32174007e+06 -2.74429676e+05 20 1.27020668e+05 1.09655545e+06 -1.02716388e+06 21 -2.99021793e+05 7.14432546e+05 4.53557922e+05 22 -1.86315004e+05 5.80130943e+05 6.72203122e+05 23 -1.43924043e+06 -1.30630731e+05 -3.30318998e+05 24 -6.02601123e+04 -2.79533646e+05 -8.77121868e+05 25 -5.21295463e+05 -1.40618663e+06 1.75864589e+05 26 3.71241902e+05 7.84879067e+05 -2.42406103e+05 27 1.36840252e+06 -2.67324459e+06 -1.26852558e+06 28 -2.21105766e+06 6.92609165e+05 -9.67477143e+05 29 8.90262817e+04 -1.24471001e+06 1.43566607e+06 30 -3.32537438e+05 3.63713988e+05 9.95089429e+05 31 -5.98821747e+04 -3.92750060e+05 -2.18945670e+05 32 1.66844888e+06 5.55392881e+05 -4.45835456e+05 MONOATOMIC STRUCTURE (pbc=False)-- Species = Mg (Configuration in file "config-F-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 77.6487058333 Forces: 1 -2.23423685e+00 -2.47861181e+00 -2.87715257e+00 2 -3.63814838e+00 -1.40811135e+00 -8.12191327e+00 3 -2.37294835e+00 -9.92128428e+00 -2.98617722e+00 4 -7.69879532e+00 5.70151564e+00 -6.85840267e+00 5 -8.26546167e-02 -7.52104611e+00 -8.18036011e+00 6 5.71217423e+00 -1.60788679e+00 -6.81600563e+00 7 6.25141512e+00 -4.45433493e+00 2.16997358e-01 8 1.10436598e+00 2.18613320e+00 -1.96920036e+00 9 -9.90282033e+00 -3.49279408e+00 -9.00547132e+00 10 -2.78081941e+00 1.48064413e+01 -1.18546411e+01 11 1.66847568e+00 -6.37929409e+00 9.87988151e+00 12 -9.33257274e+00 1.39936963e+01 1.64570204e+00 13 4.40222173e+00 -7.41741344e+00 -8.07968033e+00 14 4.27443561e+00 9.58583702e+00 -1.04539499e+01 15 1.19545456e+01 -6.72233422e+00 5.67761562e+00 16 -1.46722408e+00 1.05331302e+01 3.01432469e+00 17 -5.37501954e+00 -1.05365822e+01 8.59640714e+00 18 -3.20676837e+00 1.87117523e+00 1.37729514e+00 19 -4.06507704e+00 -6.25206884e+00 9.44040554e+00 20 -7.85607189e+00 -7.71446892e+00 5.19803411e+00 21 -1.16060680e-01 -1.21319410e+01 2.75095098e+00 22 1.74464295e+01 2.98986432e+00 1.39162709e+00 23 2.89130664e+00 -2.17857152e+00 2.05130754e+00 24 -2.25397391e+00 -3.55541365e+00 6.94899430e+00 25 -6.86778984e+00 2.50169151e+00 -3.21753979e+00 26 -1.34262212e+00 6.03922314e+00 2.06552205e+00 27 6.36598845e+00 3.31200368e+00 7.66392712e+00 28 -3.06072776e+00 6.03277595e+00 3.20847399e+00 29 3.09882769e-01 4.18634258e+00 1.14630078e+00 30 8.59712721e+00 4.30543472e+00 -5.00250367e+00 31 7.50858196e+00 -1.87086332e-01 6.12128087e+00 32 -4.83261920e+00 5.91397873e+00 7.02795003e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mg (Configuration in file "config-T-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 281.402956652 Forces: 1 1.74799422e+01 8.36693555e+00 4.43556237e+00 2 -4.69608997e+00 -4.01253842e+00 -2.95393644e+00 3 -2.19538062e+00 2.23916488e+00 -3.41701295e+00 4 1.37007069e+00 1.07657692e+01 -6.83454687e+00 5 -9.57479278e+00 1.16637464e+01 4.94766582e+00 6 1.74111645e+01 -1.04985570e+01 1.66226460e+01 7 1.82960436e+00 2.92684082e+00 7.96518205e+00 8 -3.42705327e-01 5.13867832e+00 -2.26712981e-01 9 9.05541956e-01 -7.91404297e+00 -3.51703251e+00 10 -3.96014996e+00 1.49003465e+01 -6.29200661e+00 11 2.90483717e+00 -1.03515496e+01 1.49982446e+01 12 -6.65184171e+00 7.49194770e+00 7.03688654e+00 13 3.09725396e+00 -7.96819365e+00 2.00397512e+00 14 8.58994830e+00 -1.10275957e+00 7.23885616e+00 15 7.08652477e-01 -9.51384576e+00 1.72439584e+01 16 -3.56240619e+00 -8.10978490e-01 8.79050487e+00 17 7.32373131e-01 -9.62167448e+00 1.26142613e+01 18 -3.78593286e+00 2.30651050e+00 1.23930882e+00 19 -1.93891333e+01 8.97146937e+00 4.28057776e+00 20 -3.58313131e+00 -9.68550072e+00 -1.88766710e+00 21 -1.64594366e-01 -4.94807735e+00 2.50233124e+00 22 1.12184341e+01 5.39676906e+00 3.59552597e+00 23 3.05162072e+00 1.57720361e+01 -1.71552642e+01 24 -1.98940848e+01 -5.27811458e+00 -2.06620402e+01 25 -1.30662513e+00 1.79649729e+00 -6.90827932e+00 26 -2.82702946e+00 -5.66027037e+00 3.31486812e+00 27 7.80101065e+00 7.53716647e-01 -6.43293900e+00 28 8.34183740e+00 2.71800402e+00 -6.05525797e+00 29 -4.38510924e-01 4.99851398e+00 1.35368641e+00 30 6.29740895e+00 -1.38690591e+00 -1.54170436e+01 31 3.09051510e+00 -2.91169006e+00 -1.00464290e+01 32 -1.24578069e+01 -1.45422475e+01 -1.23778727e+01 MIXED STRUCTURE (pbc=False)-- Species = Al Mg (Configuration in file "config-F-AlMg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 406.810810967 Forces: 1 -5.12196138e+01 -6.89132969e+01 -7.58157336e+01 2 -3.94214086e+00 -1.05581829e+02 -1.99207597e+02 3 5.15801775e+01 -2.12896223e+02 -9.44532491e+01 4 -6.90967648e+02 -3.58321569e+02 -4.98353998e+02 5 2.00086255e+01 -3.78767704e+01 -3.97939794e+01 6 9.38961212e+01 -2.66868932e+01 -5.06210496e+01 7 6.96407084e+01 -5.85891105e+01 -1.42008589e+01 8 1.84248115e+02 -1.01113469e+02 -9.04265885e+01 9 -1.40855735e+02 2.41668927e+01 -1.68847851e+02 10 -5.70380861e+00 1.02475310e+02 -9.77778872e+01 11 -3.84539790e+02 7.60582695e+02 -4.29352395e+02 12 -2.77257547e+02 2.57937401e+02 -5.08988910e+01 13 2.90173560e+02 9.96603616e+00 -3.55064593e+02 14 7.41950737e+01 5.05501542e+01 -5.35544793e+01 15 1.15136261e+02 7.64638572e+00 -1.01159095e+01 16 3.19595033e+02 3.75469517e+02 -1.10047384e+02 17 -1.00846359e+02 -1.50317537e+02 7.42045308e+00 18 -1.56919486e+02 -6.32565712e+02 8.68231999e+02 19 1.52755632e+01 -1.41463929e+02 1.69440757e+02 20 -1.72550409e+02 -3.38331199e+01 2.98412093e+02 21 1.88556438e+02 -1.94824836e+02 5.61381657e+01 22 2.09773049e+02 -2.57695735e+01 3.45709258e+01 23 2.03725401e+01 -1.40291628e+01 1.39621066e+01 24 1.59711706e+02 -3.81223713e+01 1.96091206e+02 25 -2.69834124e+02 1.25596420e+02 1.38786614e+02 26 1.67074383e+01 1.73548160e+02 9.79239489e+01 27 3.81320398e+01 7.03984783e+01 1.79816122e+02 28 -2.19450166e+01 3.11289125e+01 3.49631516e+01 29 2.46834011e+02 1.07018411e+02 1.44643629e+02 30 1.06932135e+02 6.19243942e+01 3.26607387e+01 31 3.71096768e+01 1.23943174e+01 2.91892133e+01 32 1.87034056e+01 3.01019160e+01 3.62813194e+01 MIXED STRUCTURE (pbc=True)-- Species = Al Mg (Configuration in file "config-T-AlMg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 75608.2759314 Forces: 1 1.84371929e+04 -1.09091790e+04 -2.36384135e+04 2 3.56689277e+03 -1.08949506e+03 -8.72607207e+03 3 -1.68709620e+03 -2.06023648e+03 -6.26143311e+02 4 -9.67000532e+02 -9.25928482e+02 -1.02616801e+04 5 -8.40898464e+03 2.03903243e+03 -9.30038817e+03 6 -8.47557008e+03 2.11098846e+04 -2.65889379e+04 7 -9.17126808e+02 -6.12936721e+03 9.26598046e+03 8 -6.72556775e+03 6.14820940e+02 -1.90564146e+03 9 2.26757731e+03 2.31211474e+03 -9.45794722e+03 10 -2.63280817e+03 1.32819450e+03 -8.84539995e+03 11 -6.64418518e+03 9.66848143e+03 3.59721347e+03 12 1.81147736e+04 -8.97258140e+03 3.17389071e+03 13 -6.74863442e+03 -1.47373764e+04 -2.89142361e+04 14 7.24875413e+03 -6.74913163e+03 -3.29264968e+04 15 3.95376793e+03 -2.56799894e+03 1.00306245e+03 16 -1.86753638e+04 1.54641331e+04 7.50180542e+03 17 8.48872533e+03 -6.86366432e+03 1.18929056e+04 18 1.85919406e+04 -1.11872590e+03 3.51559666e+04 19 2.93593629e+03 -6.00221411e+03 -2.88166765e+03 20 5.65770249e+03 6.92553864e+03 -5.48125787e+02 21 -2.21213326e+04 -8.89032477e+03 2.27453032e+04 22 3.80748663e+03 1.66654446e+04 1.51561983e+04 23 1.47729787e+03 -3.24598465e+03 1.42172631e+03 24 -9.28458700e+03 2.98350621e+03 7.90280122e+03 25 1.81642594e+02 7.13784674e+03 9.72628418e+03 26 -3.43088553e+03 -3.48133204e+02 8.70445369e+03 27 -2.89692187e+03 2.86749572e+03 -1.14919165e+03 28 4.06842843e+03 -2.88519374e+03 -3.32712201e+03 29 -8.04963898e+02 1.18664352e+03 1.00552252e+04 30 3.28387567e+03 -9.91974250e+03 2.46513848e+04 31 2.28521647e+03 3.69994764e+03 7.76078256e+01 32 -3.94618262e+03 -5.87807057e+02 -2.93434577e+03 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2335== Memcheck, a memory error detector ==2335== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2335== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==2335== Command: python runner2.py EAM_Dynamo_MendelevAstaRahman_2009_AlMg__MO_658278549784_005 ==2335== ==2335== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==2335== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==2335== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2335== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2335== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2335== by 0x4010732: call_init (dl-init.c:72) ==2335== by 0x4010732: _dl_init (dl-init.c:119) ==2335== by 0x40151FE: dl_open_worker (dl-open.c:522) ==2335== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2335== by 0x40147C9: _dl_open (dl-open.c:605) ==2335== by 0x544CF95: dlopen_doit (dlopen.c:66) ==2335== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2335== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==2335== by 0x544D734: _dlerror_run (dlerror.c:162) ==2335== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==2335== ==2335== ==2335== HEAP SUMMARY: ==2335== in use at exit: 40,085,513 bytes in 4,274 blocks ==2335== total heap usage: 205,862 allocs, 201,588 frees, 114,312,212 bytes allocated ==2335== ==2335== LEAK SUMMARY: ==2335== definitely lost: 0 bytes in 0 blocks ==2335== indirectly lost: 0 bytes in 0 blocks ==2335== possibly lost: 182,735 bytes in 112 blocks ==2335== still reachable: 39,902,778 bytes in 4,162 blocks ==2335== suppressed: 0 bytes in 0 blocks ==2335== Rerun with --leak-check=full to see details of leaked memory ==2335== ==2335== For counts of detected and suppressed errors, rerun with: -v ==2335== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2518 from 173) ================================================================================ 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.