Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:11:42) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_LiuLiuBorucki_1999_AlCu__MO_020851069572_000 Supported species : Al Cu 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 = 81.8164887686 Forces: 1 -5.60108033e+00 -6.60589052e+00 -6.85002679e+00 2 -1.48318987e+00 3.24657708e+00 -9.78575913e+00 3 3.87847106e+00 -1.02483632e+01 -8.10624060e-01 4 -8.71455672e+00 1.57290987e+00 4.07836511e+00 5 -1.78769751e+00 -1.23665735e+01 -8.59059818e+00 6 9.53846339e+00 2.78842867e+00 -1.17742989e+01 7 9.37789944e+00 -1.10487126e+01 6.64897269e-01 8 -2.94281098e+00 -3.91904355e+00 2.03287285e+00 9 -5.40033329e+00 -3.29351751e+00 -1.23880563e+01 10 2.15508563e+00 1.11657663e+01 -1.11040748e+01 11 -4.83608166e+00 -6.69929003e+00 -4.20584750e+00 12 -1.22403862e+01 1.12111381e+01 2.48054369e+00 13 -2.68118797e-01 -2.64060838e+00 -1.54076334e+01 14 7.48578256e+00 9.59971058e+00 -6.63639262e+00 15 1.45605678e+01 -4.64570943e+00 5.27659488e-01 16 2.11727219e+00 1.67847085e+01 -2.88806034e+00 17 -1.50487085e+01 -7.78336703e+00 -3.58398693e+00 18 9.31223528e-01 2.00784155e+00 -1.17127876e+00 19 3.12037068e+00 -1.49068636e+01 9.38509526e+00 20 -7.73919588e+00 8.16274792e+00 8.57298852e+00 21 -6.01679081e+00 -1.09828485e+01 3.70879203e-01 22 1.21854474e+01 7.03452420e+00 1.83161584e+00 23 5.38173116e+00 -2.53595721e+00 9.78088305e+00 24 5.54273802e+00 1.30521386e+00 9.48094437e+00 25 -1.45410149e+01 -6.51993509e+00 8.98419116e-01 26 -6.70368737e-01 1.97548519e+01 -1.27743671e+00 27 -3.69684044e+00 -5.95731581e+00 1.38153358e+01 28 -1.01925035e+01 6.57058837e+00 8.21297752e+00 29 4.16074056e+00 -6.67837094e+00 3.05222227e+00 30 6.39452123e+00 1.06497540e+01 1.03618672e-01 31 9.84941509e+00 -6.29028677e+00 9.00957665e+00 32 4.49994831e+00 1.12678927e+01 1.21751798e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 179.260221553 Forces: 1 6.37840128e+00 -6.25549200e-01 1.69536351e+00 2 -5.97168637e-01 4.17230200e+00 2.65131180e+00 3 2.38647750e+00 8.72278195e+00 2.09474745e+00 4 7.19322888e+00 5.00746019e+00 1.54601262e+00 5 1.78947613e+00 -2.57723959e+00 -4.09174274e+00 6 -3.80505927e+00 8.08995285e+00 -5.63978811e+00 7 -3.84357320e+00 -6.29328901e+00 2.20031880e+00 8 -3.56544462e+00 -3.90886608e+00 2.44511453e+00 9 -3.56692127e+00 -7.86234256e+00 -1.51020811e+00 10 1.04320401e+00 2.55549516e+00 5.10789398e-01 11 -4.83658258e+00 -6.92423914e+00 -4.44076200e+00 12 -1.69833498e+00 1.99443237e+00 1.44367328e+00 13 1.35728397e+00 -4.77711807e+00 -4.88736300e+00 14 -2.96140619e+00 2.42032328e+00 -4.25902049e+00 15 4.91766034e+00 -4.61578914e+00 8.48173456e-01 16 4.17633279e+00 5.10093466e+00 -5.13485727e-01 17 -6.03709333e-01 -3.24018070e+00 -4.35050846e+00 18 1.72417933e+00 2.19529227e+00 -1.43711745e+00 19 2.53292092e+00 -2.52113903e+00 3.05297264e+00 20 2.48219048e+00 1.24989093e+01 -2.54142916e+00 21 -6.36221014e+00 -2.71458550e-01 8.35511213e-01 22 5.07101068e-01 9.74123766e+00 2.14327155e+00 23 -7.55900926e+00 -4.73037135e+00 2.36070038e+00 24 5.73064059e+00 4.54690101e+00 -2.59099161e+00 25 -4.32157773e+00 -9.44987144e+00 1.15794293e+00 26 8.16647800e-01 5.81300667e+00 -1.03032799e+00 27 -3.29951398e-01 -8.01885324e+00 1.10644827e+00 28 -9.36883240e+00 8.42791815e-01 -7.36066562e-01 29 3.89455299e+00 -6.87577763e+00 3.10110333e+00 30 -4.65508553e+00 7.41746457e-01 2.52802726e+00 31 4.30267079e+00 -7.38219515e+00 3.66687784e+00 32 6.84189766e+00 5.63071228e+00 2.64045116e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = -16.5147048537 Forces: 1 -4.85404694e+00 -6.28848013e+00 -6.14673618e+00 2 8.20434301e+00 -6.08051047e+00 -7.22249963e+00 3 6.97487487e+00 -1.67498136e+01 -7.61671913e+00 4 -1.24688035e+01 4.20697706e+00 -6.38239996e+00 5 -1.07408179e+01 -6.69470837e+00 -8.70459008e+00 6 1.03225924e+01 1.90375288e+00 -4.89143896e+00 7 1.18120671e+01 -6.88360106e+00 8.20899495e+00 8 4.79482472e+00 6.20683262e+00 -1.29204882e+01 9 -1.34759249e+01 4.90851312e+00 -8.71112814e+00 10 5.08245807e+00 2.86134083e+00 -4.19934824e+00 11 1.26478931e+01 9.98739591e+00 -3.60625085e+00 12 -5.61518018e+00 3.28991224e+00 3.24806905e+00 13 -6.46391463e+00 4.58502930e+00 -2.37019669e+00 14 3.25318019e+00 4.08790087e+00 -1.35303113e+00 15 1.54478653e+01 -5.40900268e+00 -5.88855232e+00 16 -7.07667008e+00 1.37994301e+01 -4.16251524e+00 17 -9.73091362e+00 -9.23709382e+00 8.64278366e+00 18 -8.13352047e+00 2.76963478e+00 1.52349637e+01 19 2.77921761e+00 -2.57501153e+00 1.07035134e+00 20 -3.03822777e+00 3.44104346e+00 4.51159210e+00 21 5.40831731e+00 -1.67076519e+01 9.79995412e+00 22 7.89474720e+00 4.10604879e+00 -8.19304128e+00 23 3.11447038e+00 -9.74052490e+00 7.76862360e+00 24 -8.22211177e+00 -1.54028365e+00 6.02829132e+00 25 -1.25590195e+01 5.71026660e+00 6.83586116e+00 26 4.76063480e+00 7.32137006e+00 -5.45824738e+00 27 5.25911783e+00 -6.55301840e+00 7.82702481e+00 28 -1.01387807e+01 3.88310061e+00 4.08526299e+00 29 -3.62108984e+00 3.49188659e+00 9.56207434e+00 30 4.12514192e+00 2.46658038e+00 -1.96628198e+00 31 8.06048421e+00 3.05861359e-01 3.87686295e+00 32 -3.80320812e+00 5.12682286e+00 3.09275527e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 26.684718065 Forces: 1 -3.11389717e+00 -8.02122637e+00 3.85063155e+00 2 5.53458570e+00 -3.39629845e+00 4.45033835e-01 3 8.20778575e+00 -7.93389072e+00 -1.24815030e+01 4 -1.01292939e+01 3.96877300e+00 -7.23738477e+00 5 -1.30739276e+01 -2.73165160e+00 -2.54416122e+00 6 6.76250103e+00 4.46260188e+00 1.49660645e+01 7 6.93495806e+00 -1.48967489e+00 8.16621321e+00 8 5.20791034e+00 5.80244124e+00 -1.30853356e+01 9 -8.87651167e+00 5.80155207e+00 -4.71323431e+00 10 4.82044096e+00 2.68413106e-01 1.02700537e+00 11 1.23749075e+01 1.00598576e+01 -3.88877944e+00 12 -3.24204848e-01 6.27165242e-03 4.64058458e+00 13 -1.25797059e+01 7.49868187e+00 1.47255425e+01 14 7.84053060e+00 7.66002895e+00 1.07901078e+01 15 9.81050908e+00 -6.69193452e+00 -5.69683836e+00 16 -8.54861082e+00 9.24117548e+00 -3.32219812e+00 17 2.46744091e+00 -7.83907511e+00 2.02418939e+00 18 -8.31750634e+00 2.53102299e+00 1.54296589e+01 19 8.53502606e+00 -2.96793869e+00 -9.05064187e+00 20 1.59287613e+01 1.00861752e+01 1.53623249e+00 21 6.09490493e+00 -1.40264112e+01 1.02653729e+01 22 -8.96303738e+00 9.11491523e+00 -1.18687617e+01 23 -6.78255076e+00 -1.50404030e+01 3.11714697e+00 24 -1.20521455e+01 -6.45320106e+00 -1.20479528e+01 25 -9.01921295e+00 6.35268251e+00 7.82934233e+00 26 6.20643340e+00 -3.40200966e+00 -7.06303393e-01 27 5.31397432e+00 -7.05918174e+00 2.81434623e+00 28 3.52005871e+00 3.39926577e+00 5.29795725e+00 29 -3.12319696e+00 3.53428133e+00 9.79977514e+00 30 -5.99692871e+00 -5.09608558e+00 -9.82455249e+00 31 7.07337170e+00 -3.23161817e+00 -1.17041224e+01 32 -1.17333698e+01 5.59246089e+00 -8.55343563e+00 MIXED STRUCTURE (pbc=False)-- Species = Al Cu (Configuration in file "config-F-AlCu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 22.588688497 Forces: 1 -4.61734066e+00 -6.89059583e+00 -5.84263621e+00 2 2.19681623e+00 -3.06356631e+00 -1.33641571e+01 3 -3.11735037e+00 -1.48461975e+01 7.85002272e-01 4 -1.07720557e+01 -2.24850442e+00 7.46889467e+00 5 -1.16288151e+00 -5.30728447e+00 -7.90756070e+00 6 5.57895962e+00 3.36721226e+00 -5.19265196e+00 7 6.94947492e+00 -7.20401839e+00 2.03797340e+00 8 2.03985212e+00 -2.18800755e+00 -3.77598727e+00 9 -1.04501006e+01 4.07632427e+00 -1.32572845e+01 10 2.55676509e+00 6.26937262e+00 -2.22134586e+00 11 4.62826655e+00 1.90293872e+00 -7.92860223e-01 12 -7.99523044e+00 9.93908655e+00 -2.57890335e+00 13 3.49658927e+00 3.18258344e+00 -1.27834472e+01 14 3.08802131e+00 5.12551980e+00 -6.52621325e+00 15 8.08855868e+00 -5.81830086e+00 4.76337109e+00 16 -2.88983259e+00 1.07692034e+01 -3.25982624e+00 17 -3.17981733e+00 -2.22377746e+00 -1.28116739e+00 18 -8.51272281e+00 -6.25795537e+00 3.97362292e-01 19 -1.03619391e+00 -2.30599266e+00 3.99187594e+00 20 -6.15999229e+00 -4.58104340e+00 8.44069324e+00 21 -3.81045925e+00 -1.31096690e+01 -4.35435232e-01 22 1.31823467e+01 5.12889239e+00 3.54757774e+00 23 4.47125817e+00 -2.58660909e+00 4.67307043e+00 24 5.66565880e+00 -1.23470398e+00 1.39351485e+01 25 -1.47364575e+01 -5.20247617e+00 -1.28824226e+00 26 2.73783318e+00 1.40930486e+01 1.93685445e-01 27 -3.89533205e+00 2.70256153e+00 8.89164136e+00 28 -3.23685811e+00 5.95224408e+00 7.55746128e+00 29 1.05782544e+01 3.46974931e+00 2.55938580e+00 30 4.41770334e+00 7.86410259e+00 -1.00252255e+00 31 3.99113506e+00 -5.39851296e+00 6.92126659e+00 32 1.90513160e+00 6.62437583e+00 5.34583123e+00 MIXED STRUCTURE (pbc=True)-- Species = Al Cu (Configuration in file "config-T-AlCu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 61.1115704729 Forces: 1 6.48429216e+00 -8.94793155e+00 -2.47543092e+00 2 3.20987774e+00 -3.68922694e+00 -5.77362550e+00 3 -3.70212905e+00 -5.33044678e+00 1.92842658e+00 4 2.63340458e+00 1.45110339e-01 8.84170052e+00 5 1.03692910e+00 -1.47951200e+00 3.46632948e+00 6 -7.28955224e+00 1.00080068e+01 -3.23141506e+00 7 2.49166098e+00 -3.57212204e+00 1.95482367e+00 8 2.51439237e+00 -1.82899563e+00 -3.68784228e+00 9 -3.69057355e+00 4.51897379e+00 -5.47987413e+00 10 -3.84986340e+00 -4.04537025e+00 7.98180309e+00 11 4.56825317e+00 1.72950978e+00 -7.25128340e-01 12 9.76160957e-01 1.06352834e+01 4.14818936e-01 13 3.81304997e+00 5.27564670e+00 -6.33083173e+00 14 -6.30820957e+00 5.52769278e+00 -6.85646664e+00 15 -4.45641454e+00 -7.46737775e+00 2.82759831e+00 16 -3.16898427e+00 1.95367774e+00 -3.96340756e+00 17 7.30640837e+00 5.60908761e+00 -4.74694598e+00 18 -8.51691863e+00 -6.12830367e+00 2.67999920e-01 19 -7.92036723e+00 8.91391867e+00 -5.13787806e+00 20 -3.65924753e+00 -8.58653984e+00 -1.67267978e+00 21 -4.90812433e+00 -6.49691237e+00 -1.04738411e+00 22 9.53313981e+00 6.05699984e+00 3.60446352e+00 23 -2.78324816e+00 2.12390209e+00 3.78767865e-01 24 4.97882625e+00 -8.69667482e-01 4.76004894e+00 25 -3.52493225e+00 -7.71816928e+00 -2.67670803e+00 26 2.32320229e+00 8.92939184e+00 2.01607658e+00 27 -3.58218465e+00 2.35959498e+00 5.67255503e+00 28 6.04427388e+00 5.82880766e-01 7.13528549e+00 29 1.05634013e+01 3.38982453e+00 2.59849707e+00 30 -5.32660659e+00 2.56949539e+00 -5.10309608e+00 31 -7.00378282e+00 -7.66868024e+00 9.56487801e+00 32 1.12138659e+01 -6.49974118e+00 -4.50535881e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1348== Memcheck, a memory error detector ==1348== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1348== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==1348== Command: python runner2.py EAM_Dynamo_LiuLiuBorucki_1999_AlCu__MO_020851069572_000 ==1348== ==1348== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==1348== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==1348== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==1348== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==1348== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==1348== by 0x4010732: call_init (dl-init.c:72) ==1348== by 0x4010732: _dl_init (dl-init.c:119) ==1348== by 0x40151FE: dl_open_worker (dl-open.c:522) ==1348== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==1348== by 0x40147C9: _dl_open (dl-open.c:605) ==1348== by 0x544CF95: dlopen_doit (dlopen.c:66) ==1348== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==1348== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==1348== by 0x544D734: _dlerror_run (dlerror.c:162) ==1348== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==1348== ==1348== ==1348== HEAP SUMMARY: ==1348== in use at exit: 7,130,829 bytes in 4,274 blocks ==1348== total heap usage: 192,866 allocs, 188,592 frees, 77,157,305 bytes allocated ==1348== ==1348== LEAK SUMMARY: ==1348== definitely lost: 0 bytes in 0 blocks ==1348== indirectly lost: 0 bytes in 0 blocks ==1348== possibly lost: 182,735 bytes in 112 blocks ==1348== still reachable: 6,948,094 bytes in 4,162 blocks ==1348== suppressed: 0 bytes in 0 blocks ==1348== Rerun with --leak-check=full to see details of leaked memory ==1348== ==1348== For counts of detected and suppressed errors, rerun with: -v ==1348== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2525 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 06:12:17) ===