Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:14:06) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Mendelev_2015_Na__MO_094065024556_000 Supported species : Na random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Na (Configuration in file "config-F-Na.xyz") ----------------------------------------------------------------------------------------------------- Energy = 145.913539613 Forces: 1 -4.48067646e+00 -6.71474871e+00 -7.76210773e+00 2 -5.63957019e+00 1.28569349e+01 -7.06325468e+00 3 2.63538992e+00 -6.35730420e+00 2.59297120e-01 4 -6.07443717e+00 3.17965123e+00 3.52403837e+00 5 8.67139758e+00 -1.48833367e+01 -2.43686287e+00 6 4.45439733e+00 1.23176447e+00 -6.67460756e+00 7 4.27504488e+00 -1.91445820e+01 -1.69584007e+01 8 -1.24104338e+01 -4.40771794e+00 1.19072123e+00 9 -6.79712657e+00 -5.37428300e+00 -1.40119838e+01 10 -2.04557888e+00 1.13693507e+01 -1.25065891e+01 11 1.47882778e+01 -1.10992664e+01 -3.24951506e+00 12 -1.02304956e+01 1.47714069e+01 6.49085654e-01 13 -8.45442016e+00 -9.60522132e+00 -2.42746071e+01 14 6.97787690e+00 8.15730489e+00 -6.30965320e+00 15 2.24011961e+01 -5.77484512e+00 6.25494334e+00 16 5.40610594e-02 1.62988451e+01 9.10736536e+00 17 -1.14413194e+01 -6.11962079e+00 -3.42487706e+00 18 4.42648631e+00 9.14427962e+00 -4.28806829e+00 19 5.78088267e+00 -9.69860174e+00 8.16710191e+00 20 -6.45071349e+00 6.37128372e+00 6.75338698e+00 21 -9.00008195e+00 -6.78777415e+00 5.00627680e+00 22 1.33511955e+01 1.62759988e+01 1.23994920e+01 23 3.36580219e+00 -1.72312056e+00 7.36080647e+00 24 4.25060716e+00 -3.24729113e+00 4.77592543e+00 25 -1.35179775e+01 -4.99625803e+00 1.60889878e+01 26 -3.23806096e+00 1.26253346e+01 -6.92103488e+00 27 4.93709579e+00 -1.86426303e+01 6.46096321e+00 28 -1.93155755e+01 1.54696617e+01 3.75906592e+00 29 -6.54750700e+00 -9.29270005e+00 1.98811343e+00 30 7.56966750e+00 1.07540086e+01 2.91017689e+00 31 1.14487316e+01 -5.85847504e+00 8.29953456e+00 32 6.25586437e+00 1.12219520e+01 1.09262795e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Na (Configuration in file "config-T-Na.xyz") ----------------------------------------------------------------------------------------------------- Energy = -197.063507941 Forces: 1 1.22787051e+01 -1.02383054e+01 3.41095137e+00 2 -2.11904976e+01 1.96093489e+00 2.27434631e+01 3 1.24161916e+00 4.30898419e+00 1.08321696e+00 4 8.48518640e+00 5.90125298e+00 -1.33298607e+00 5 1.48939177e+01 -7.40448899e-01 -9.67492587e-01 6 -1.65919568e+01 1.76819916e+01 6.58577082e+00 7 -4.04763808e+00 -1.68584766e+01 -1.70846031e+01 8 -1.09446652e+01 -7.12543630e+00 -3.16277018e-01 9 -1.28835678e+01 -1.43861406e+01 7.32459111e+00 10 -7.86817001e+00 6.65885017e-01 -5.20794769e+00 11 1.20389122e+01 -1.06132204e+01 -5.07536055e+00 12 1.34782524e+00 7.71824649e+00 3.17174764e+00 13 -5.21265782e+00 -9.63032700e+00 -2.00190650e+01 14 -6.68262351e+00 4.40408736e+00 -9.27837123e+00 15 1.82131823e+01 -4.74989117e+00 4.91626521e+00 16 2.75947095e+00 1.24635445e+01 8.81241677e+00 17 6.63927034e+00 -1.03762158e+01 -2.68582930e+00 18 2.99595971e+00 6.57502925e+00 -2.36793816e+00 19 5.24894123e+00 2.00653257e+00 4.77112723e+00 20 1.25854469e+01 1.95564619e+01 -4.17511937e+00 21 -8.28502485e+00 -1.87984389e-02 7.09400244e+00 22 -2.87003455e+00 2.32578150e+01 1.65700627e+01 23 -1.76879056e+01 -1.87816232e+01 -8.38395103e+00 24 2.11804942e+01 6.18195805e+00 -2.41414555e+01 25 -9.35896139e+00 -6.30464967e+00 1.74795146e+01 26 -2.88108081e+00 3.71721534e+00 -6.79050251e+00 27 1.16901110e+01 -1.91894719e+01 -9.29175321e+00 28 -1.96463427e+01 1.50512389e+01 -6.35849432e+00 29 -4.11778810e+00 -8.11076507e+00 5.11902740e+00 30 -2.30272849e-01 3.64752828e+00 6.59859276e+00 31 8.69644169e+00 -6.29194202e+00 5.34246591e+00 32 1.02037036e+01 8.31700617e+00 2.45393064e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==4134== Memcheck, a memory error detector ==4134== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==4134== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==4134== Command: python runner2.py EAM_Dynamo_Mendelev_2015_Na__MO_094065024556_000 ==4134== ==4134== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==4134== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==4134== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==4134== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==4134== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==4134== by 0x4010732: call_init (dl-init.c:72) ==4134== by 0x4010732: _dl_init (dl-init.c:119) ==4134== by 0x40151FE: dl_open_worker (dl-open.c:522) ==4134== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==4134== by 0x40147C9: _dl_open (dl-open.c:605) ==4134== by 0x544CF95: dlopen_doit (dlopen.c:66) ==4134== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==4134== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==4134== by 0x544D734: _dlerror_run (dlerror.c:162) ==4134== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==4134== ==4134== ==4134== HEAP SUMMARY: ==4134== in use at exit: 10,245,479 bytes in 3,960 blocks ==4134== total heap usage: 122,314 allocs, 118,354 frees, 64,866,919 bytes allocated ==4134== ==4134== LEAK SUMMARY: ==4134== definitely lost: 0 bytes in 0 blocks ==4134== indirectly lost: 0 bytes in 0 blocks ==4134== possibly lost: 182,191 bytes in 111 blocks ==4134== still reachable: 10,063,288 bytes in 3,849 blocks ==4134== suppressed: 0 bytes in 0 blocks ==4134== Rerun with --leak-check=full to see details of leaked memory ==4134== ==4134== For counts of detected and suppressed errors, rerun with: -v ==4134== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2509 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 06:14:35) ===