!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Zhakhovsky_2009_Au__MO_173248269481_000 Supported species : Au random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Au (Configuration in file "config-F-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 555.741514433 Forces: 1 -1.78932969e+01 -3.97662065e+01 -4.04486677e+01 2 -4.29201791e+01 7.21031967e+01 -4.39900607e+01 3 5.54688769e+00 -2.60367680e+01 1.06976226e+01 4 -2.47417231e+01 2.87757052e+01 2.34154219e+01 5 6.24963009e+01 -8.94478125e+01 -1.41756885e+01 6 1.57410134e+01 6.21940589e+00 -2.79298546e+01 7 2.87923029e+01 -1.31569160e+02 -1.24494985e+02 8 -6.86457540e+01 -5.34625481e+01 -1.36394317e+01 9 -3.23214652e+01 -6.33934376e+01 -9.27366829e+01 10 -1.20628903e+01 7.85460477e+01 -8.97021818e+01 11 -3.37148593e+01 -6.06333052e+01 3.14933922e+01 12 -5.81939110e+01 7.30044069e+01 5.85253849e+01 13 -3.55877345e+01 -5.97675688e+01 -1.80523737e+02 14 3.57646048e+01 4.57180662e+01 -3.22188219e+01 15 1.59762635e+02 -4.45520512e+01 2.59380647e+01 16 2.01693541e+01 1.33450188e+02 5.73278330e+01 17 -8.04170427e+01 -5.58563390e+01 -2.82740709e+01 18 6.07016455e+01 7.83243357e+01 -7.43537905e+01 19 2.73445387e+01 -9.31452221e+01 5.78414070e+01 20 -6.53213461e+01 3.10486092e+01 7.49045263e+01 21 -5.57892098e+01 -4.50387797e+01 3.09146217e+01 22 9.18493151e+01 9.81100321e+01 1.01747674e+02 23 2.05746866e+01 -8.95829167e+00 2.80155863e+01 24 2.38582567e+01 2.06668657e+01 3.19864569e+01 25 -6.14289713e+01 -1.92234257e+01 -2.08102711e+01 26 -2.72196507e+01 8.91164260e+01 -4.08353615e+01 27 6.26287484e+01 -1.39555969e+02 6.46405109e+01 28 -1.21791431e+02 1.10551228e+02 3.10772609e+01 29 -3.26776198e+01 -4.12074605e+01 4.30882833e+01 30 4.55029355e+01 7.18718438e+01 3.78561296e+01 31 6.97978747e+01 -3.02954247e+01 4.67498455e+01 32 4.01959855e+01 6.44034128e+01 6.79135842e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Au (Configuration in file "config-T-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1087.60999472 Forces: 1 8.64322259e+01 -6.02374998e+01 1.99317355e+01 2 -1.49755824e+02 8.00731773e+01 1.22557211e+02 3 -7.02087250e-01 3.06615309e+01 1.98775528e+01 4 6.45435392e+01 5.40182874e+01 -1.85511985e+00 5 1.01943066e+02 -1.57702538e+01 1.02253800e+01 6 -1.06286057e+02 1.00054043e+02 2.22242797e+01 7 -1.81286497e+01 -1.15912067e+02 -1.26572116e+02 8 -7.13403106e+01 -5.25279809e+01 -1.24397632e+01 9 -7.34930341e+01 -1.24917476e+02 5.02132924e+01 10 -5.27750605e+01 5.62704252e+00 -4.67951110e+01 11 -3.28179812e+01 -6.19181675e+01 3.32544414e+01 12 5.61473073e+01 2.44438629e+01 1.15717647e+02 13 -3.32147570e+01 -7.08616033e+01 -1.48652908e+02 14 -9.15610597e+01 2.87785437e+01 -7.08631252e+01 15 1.31432526e+02 -4.47115439e+01 2.91027641e+01 16 2.89723673e+01 9.66748486e+01 6.30689098e+01 17 2.92727843e+01 -9.48477738e+01 -3.16606655e+01 18 6.57145554e+01 7.96706426e+01 -7.62136804e+01 19 2.85064627e+01 -2.95070552e+01 4.83965879e+01 20 1.60084099e+01 9.85077178e+01 9.98275577e+00 21 -5.69938357e+01 -8.85265068e+00 3.36896798e+01 22 -1.81330917e+01 1.54610323e+02 1.20052054e+02 23 -7.33994530e+01 -8.28911900e+01 -3.16907498e+01 24 1.36968187e+02 3.80626402e+01 -1.39726357e+02 25 -2.90431669e+01 -3.23931949e+01 -1.84078029e+01 26 -2.02917917e+01 2.69427309e+01 -5.41151767e+01 27 1.20172760e+02 -1.45021530e+02 -4.29856191e+01 28 -1.25747928e+02 1.17891264e+02 -3.52558975e+01 29 -3.32827916e+01 -4.23723218e+01 4.25750266e+01 30 9.56551367e+00 3.38467600e+01 4.54861800e+01 31 5.34341666e+01 -3.64738049e+01 3.27417878e+01 32 5.78530076e+01 4.93526985e+01 1.81368060e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==7563== Memcheck, a memory error detector ==7563== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==7563== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==7563== Command: python runner2.py EAM_Dynamo_Zhakhovsky_2009_Au__MO_173248269481_000 ==7563== ==7563== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==7563== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==7563== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7563== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7563== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7563== by 0x4010732: call_init (dl-init.c:72) ==7563== by 0x4010732: _dl_init (dl-init.c:119) ==7563== by 0x40151FE: dl_open_worker (dl-open.c:522) ==7563== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7563== by 0x40147C9: _dl_open (dl-open.c:605) ==7563== by 0x544CF95: dlopen_doit (dlopen.c:66) ==7563== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7563== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==7563== by 0x544D734: _dlerror_run (dlerror.c:162) ==7563== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==7563== ==7563== ==7563== HEAP SUMMARY: ==7563== in use at exit: 9,114,747 bytes in 3,960 blocks ==7563== total heap usage: 116,125 allocs, 112,165 frees, 63,058,547 bytes allocated ==7563== ==7563== LEAK SUMMARY: ==7563== definitely lost: 0 bytes in 0 blocks ==7563== indirectly lost: 0 bytes in 0 blocks ==7563== possibly lost: 182,191 bytes in 111 blocks ==7563== still reachable: 8,932,556 bytes in 3,849 blocks ==7563== suppressed: 0 bytes in 0 blocks ==7563== Rerun with --leak-check=full to see details of leaked memory ==7563== ==7563== For counts of detected and suppressed errors, rerun with: -v ==7563== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2507 from 170) ================================================================================ 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.