Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:18:53) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouWadleyJohnson_2001NISTretabulation_Pd__MO_993644691224_000 Supported species : Pd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Pd (Configuration in file "config-F-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 169.661941822 Forces: 1 -6.80019334e+00 -2.78499358e+01 -2.18283806e+01 2 -7.68465195e+00 9.40018420e+00 -1.84477183e+01 3 1.05563859e+01 -2.25495873e+01 -1.18161909e+01 4 -1.54525832e+01 1.95642255e+01 1.68643545e+01 5 7.06096220e+00 -2.51822128e+01 -8.68685236e+00 6 1.05362893e+01 5.65895501e+00 -1.30019846e+01 7 1.59086712e+01 -4.97739384e+01 -4.10910084e+01 8 -1.42994964e+01 -1.06643514e+01 -7.59294847e+00 9 -1.79669591e+01 -2.18271907e+01 -4.47093148e+01 10 -3.42665038e+00 3.80725649e+01 -3.86603613e+01 11 -1.21422191e+01 -2.63405832e+01 1.92181972e+01 12 -2.64725129e+01 3.27679930e+01 2.22490767e+01 13 -4.41344611e+00 -3.01869936e+01 -7.23629565e+01 14 1.78869563e+01 2.55293851e+01 -2.28550770e+01 15 6.60139158e+01 -1.97157281e+01 2.38403149e+01 16 -2.44991633e+00 6.12628380e+01 2.40253936e+01 17 -2.86669656e+01 -1.24669653e+01 3.14704978e+00 18 6.05004113e+00 1.96080728e+01 3.85924573e+00 19 3.25611713e+00 -2.21853913e+01 1.21722628e+01 20 -1.20240766e+01 8.19522713e+00 1.02566453e+01 21 -1.90820654e+01 -2.06059050e+01 1.52150288e+01 22 3.72691058e+01 3.74713819e+01 3.26391425e+01 23 6.98713281e+00 -3.69006843e+00 1.42790717e+01 24 7.35386669e+00 4.28736425e+00 1.18194043e+01 25 -2.35599611e+01 -7.11407053e+00 -3.14757706e-01 26 -1.24886529e+01 3.65090239e+01 -1.45419238e+01 27 1.60838735e+01 -4.98789973e+01 2.35248802e+01 28 -4.44790276e+01 3.77446052e+01 1.01911543e+01 29 -1.13239106e+01 -1.89818367e+01 1.52946036e+01 30 1.89222326e+01 3.07615663e+01 -1.99941365e+00 31 2.48400733e+01 -2.36987296e+01 2.97400800e+01 32 1.40076650e+01 2.58790984e+01 2.95729825e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pd (Configuration in file "config-T-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 458.224886411 Forces: 1 3.92757235e+01 -3.90111794e+01 1.76466376e+00 2 -5.38492259e+01 6.77665067e+00 6.47313736e+01 3 8.88629581e+00 3.63457788e+00 -7.26400432e+00 4 2.06136916e+01 3.63556951e+01 2.89289935e+01 5 1.75102900e+01 -3.22956831e+00 -2.39154024e+00 6 -5.71154862e+01 5.47036125e+01 2.18686285e+01 7 -8.16464481e+00 -4.52737818e+01 -4.23322473e+01 8 -1.75130327e+01 -9.02428107e+00 -5.93839136e+00 9 -3.34122141e+01 -4.97577553e+01 9.31432646e+00 10 -1.25962938e+01 2.17817865e+01 -1.97430924e+01 11 -1.05683983e+01 -2.93359618e+01 2.39027292e+01 12 2.18462883e+01 1.38246296e+01 5.22699085e+01 13 -3.40840445e+00 -3.75721699e+01 -5.74397282e+01 14 -3.46491336e+01 1.97696492e+01 -4.22137881e+01 15 4.97377970e+01 -2.72660669e+01 2.87183583e+01 16 2.58957597e-01 4.30297305e+01 2.88996390e+01 17 1.76602341e+01 -3.09217769e+01 3.78581245e+00 18 9.82095178e+00 2.29514745e+01 2.33565931e+00 19 5.72813917e+00 3.83170957e+00 7.84007501e+00 20 4.03614611e+01 5.00480081e+01 -1.79129637e+01 21 -2.30940588e+01 -1.44948504e+00 1.53181020e+01 22 -5.32851513e-01 6.82965775e+01 3.55957785e+01 23 -4.23975400e+01 -5.76257401e+01 -3.92272592e+01 24 5.77495217e+01 1.78411916e+01 -7.10052011e+01 25 -8.52439289e+00 -1.43653721e+01 -2.16887654e+00 26 -9.35187895e+00 9.25726112e+00 -2.15365542e+01 27 3.99442683e+01 -5.73781141e+01 -2.27817247e+01 28 -4.73650395e+01 4.50424109e+01 -1.56408125e+01 29 -1.25925698e+01 -2.16046203e+01 1.42959379e+01 30 4.39765336e+00 1.55064325e+01 -2.61744672e+00 31 1.78835769e+01 -2.88110544e+01 2.29049706e+01 32 2.34603150e+01 1.99755297e+01 7.73867389e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==10114== Memcheck, a memory error detector ==10114== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==10114== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==10114== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Pd__MO_993644691224_000 ==10114== ==10114== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==10114== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==10114== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==10114== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==10114== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==10114== by 0x4010732: call_init (dl-init.c:72) ==10114== by 0x4010732: _dl_init (dl-init.c:119) ==10114== by 0x40151FE: dl_open_worker (dl-open.c:522) ==10114== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==10114== by 0x40147C9: _dl_open (dl-open.c:605) ==10114== by 0x544CF95: dlopen_doit (dlopen.c:66) ==10114== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==10114== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==10114== by 0x544D734: _dlerror_run (dlerror.c:162) ==10114== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==10114== ==10114== ==10114== HEAP SUMMARY: ==10114== in use at exit: 5,906,617 bytes in 3,961 blocks ==10114== total heap usage: 115,015 allocs, 111,054 frees, 59,353,773 bytes allocated ==10114== ==10114== LEAK SUMMARY: ==10114== definitely lost: 0 bytes in 0 blocks ==10114== indirectly lost: 0 bytes in 0 blocks ==10114== possibly lost: 182,191 bytes in 111 blocks ==10114== still reachable: 5,724,426 bytes in 3,850 blocks ==10114== suppressed: 0 bytes in 0 blocks ==10114== Rerun with --leak-check=full to see details of leaked memory ==10114== ==10114== For counts of detected and suppressed errors, rerun with: -v ==10114== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2510 from 175) ================================================================================ 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 06:19:18) ===