Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:16:55) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Al__MO_519613893196_000 Supported species : Al 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 = 57.5719215854 Forces: 1 -4.28387653e+00 -7.77792863e+00 -8.31603626e+00 2 -3.54319971e+00 4.92805859e+00 -8.02998680e+00 3 5.23227090e+00 -1.41212785e+01 -5.72444393e+00 4 -1.07235526e+01 5.10482101e+00 1.88396367e-01 5 -1.16053232e+00 -1.31712384e+01 -4.34135274e+00 6 8.14518996e+00 4.94404541e+00 -8.78653196e+00 7 8.23201189e+00 -2.20632076e+01 -1.45855690e+01 8 -1.05605668e+01 -8.82251796e+00 -1.66425604e+00 9 -8.52560271e+00 -6.17938538e+00 -1.43903631e+01 10 -3.20287807e+00 1.59183757e+01 -1.63063696e+01 11 -3.47429194e+00 -1.03386247e+01 2.01213295e+00 12 -1.01845262e+01 1.36695374e+01 1.86154312e+00 13 -3.72464184e+00 -1.06572864e+01 -3.19674470e+01 14 7.71132736e+00 9.44566978e+00 -6.36044465e+00 15 2.97602956e+01 -3.94350048e+00 5.86573649e+00 16 4.06356804e+00 2.54701685e+01 9.59171512e+00 17 -1.55619046e+01 -9.92772945e+00 -2.29025391e+00 18 8.24634623e+00 1.04893503e+01 7.01050268e+00 19 3.70122063e+00 -1.18833240e+01 6.72168849e+00 20 -6.19269358e+00 7.14906806e+00 7.59051684e+00 21 -9.38120091e+00 -1.06722759e+01 6.17793587e+00 22 1.73837869e+01 1.66581517e+01 1.13021445e+01 23 4.58679609e+00 -2.64040944e+00 9.50512398e+00 24 2.34395822e+00 5.07955552e+00 5.42169638e+00 25 -1.22800992e+01 -4.42521904e+00 7.38464042e+00 26 -4.82579682e+00 1.76727063e+01 -6.84885294e+00 27 6.50144329e+00 -2.33413641e+01 1.06452375e+01 28 -2.00536629e+01 1.64634617e+01 5.01322171e+00 29 -5.93330061e+00 -9.60120726e+00 7.62647640e+00 30 8.68932457e+00 1.30527112e+01 -1.00088330e+00 31 1.23543975e+01 -9.18574281e+00 1.25158151e+01 32 6.66039016e+00 1.27065589e+01 1.41782673e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 194.319447772 Forces: 1 2.17409274e+01 -1.58675133e+01 4.79481468e+00 2 -2.06633749e+01 6.01726871e+00 2.43968924e+01 3 4.41510046e+00 -4.81754419e-01 -4.15814642e+00 4 6.68810480e+00 1.02441265e+01 -5.38317702e+00 5 3.24076078e+00 -3.61030523e+00 -2.17606352e-01 6 -2.29016852e+01 2.67389071e+01 2.68431403e+01 7 -2.12011221e+00 -1.96496414e+01 -1.43753857e+01 8 -1.12058605e+01 -8.78978300e+00 -1.52813146e+00 9 -1.39124776e+01 -1.69052988e+01 9.99465421e+00 10 -7.55243795e+00 8.30525717e+00 -6.52163096e+00 11 -3.40294992e+00 -1.04152947e+01 2.13919369e+00 12 2.12899411e+00 5.35255493e+00 6.71463973e+00 13 -2.95387108e+00 -1.29041415e+01 -2.44076575e+01 14 -6.35675279e+00 4.33499573e+00 -1.04005059e+01 15 2.15374204e+01 -3.99676820e+00 5.71440168e+00 16 5.32672789e+00 1.67263575e+01 1.07373757e+01 17 4.64484867e+00 -1.50570415e+01 -1.67171595e+00 18 9.63848399e+00 1.06123263e+01 6.99624906e+00 19 3.65212473e+00 1.27808048e+00 4.20114981e+00 20 2.64776722e+01 2.70275056e+01 -4.63933567e+00 21 -9.89265881e+00 -1.11298240e+00 6.74033094e+00 22 -3.20369142e+00 2.56064156e+01 1.47200901e+01 23 -2.59491781e+01 -2.63810513e+01 -2.92354999e+01 24 2.04280400e+01 8.59402327e+00 -2.70809025e+01 25 -4.34804083e+00 -6.88854020e+00 7.17266482e+00 26 -3.49133936e+00 4.23463053e+00 -8.77966769e+00 27 1.52951945e+01 -2.45344109e+01 -8.80405480e+00 28 -2.02885598e+01 1.77390530e+01 -5.27661503e+00 29 -5.93394200e+00 -9.68361985e+00 7.58131698e+00 30 -1.10698773e-01 5.09032557e+00 1.37304505e+00 31 8.65434573e+00 -1.06664577e+01 8.76071389e+00 32 1.04188855e+01 9.04277654e+00 3.59935984e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==7553== Memcheck, a memory error detector ==7553== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==7553== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==7553== Command: python runner2.py EAM_Dynamo_Zhakhovsky_2009_Al__MO_519613893196_000 ==7553== ==7553== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==7553== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==7553== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7553== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7553== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7553== by 0x4010732: call_init (dl-init.c:72) ==7553== by 0x4010732: _dl_init (dl-init.c:119) ==7553== by 0x40151FE: dl_open_worker (dl-open.c:522) ==7553== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7553== by 0x40147C9: _dl_open (dl-open.c:605) ==7553== by 0x544CF95: dlopen_doit (dlopen.c:66) ==7553== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7553== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==7553== by 0x544D734: _dlerror_run (dlerror.c:162) ==7553== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==7553== ==7553== ==7553== HEAP SUMMARY: ==7553== in use at exit: 9,115,651 bytes in 3,961 blocks ==7553== total heap usage: 116,125 allocs, 112,164 frees, 63,058,737 bytes allocated ==7553== ==7553== LEAK SUMMARY: ==7553== definitely lost: 0 bytes in 0 blocks ==7553== indirectly lost: 0 bytes in 0 blocks ==7553== possibly lost: 182,191 bytes in 111 blocks ==7553== still reachable: 8,933,460 bytes in 3,850 blocks ==7553== suppressed: 0 bytes in 0 blocks ==7553== Rerun with --leak-check=full to see details of leaked memory ==7553== ==7553== For counts of detected and suppressed errors, rerun with: -v ==7553== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2503 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. === Verification check vc-memory-leak end (2018-12-15 06:17:21) ===