Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:22:23) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : LJ_Truncated_Nguyen_2005_Ar__MO_398194508715_001 Supported species : Ar random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ar (Configuration in file "config-F-Ar.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6451.21600399 Forces: 1 -6.65411924e+02 -1.92169609e+03 -2.58819182e+03 2 -5.37656981e+00 3.44876359e+02 -3.29283254e+02 3 1.15674186e+03 -1.02636403e+03 3.89254529e+02 4 -6.19267569e+02 2.76665043e+03 2.00780429e+03 5 1.29526964e+01 -3.85396249e+02 -2.49512481e+02 6 1.03903208e+02 6.54630519e+01 -1.90483376e+02 7 -2.92879183e+02 -2.53386571e+03 -2.60629449e+03 8 -8.75590646e+02 -9.10647137e+02 2.00126982e+02 9 -2.82310589e+01 -1.24119990e+02 -1.68246871e+02 10 -5.46519292e+02 2.65848149e+02 -6.75798986e+02 11 -7.80083713e+02 -8.39315833e+02 -2.11589524e+01 12 -2.16345472e+02 6.07088936e+02 -2.91901279e+02 13 -1.34639943e+03 -6.11325421e+02 -2.64446654e+03 14 3.60081510e+02 3.85451266e+02 -1.53641841e+02 15 2.51017270e+03 4.78211907e+02 1.55731472e+03 16 7.79960670e+02 1.68672300e+03 1.09111790e+03 17 -5.01645757e+02 -2.19868356e+02 2.38297610e+02 18 -2.90342280e+00 9.06017207e+03 -8.55422209e+03 19 2.86888039e+02 -9.05649965e+03 8.59902939e+03 20 -2.16118072e+02 1.24872924e+02 1.51014272e+02 21 -7.18568247e+02 -4.69473315e+02 -4.08518812e+01 22 1.35101531e+03 2.60220687e+03 2.01155078e+03 23 1.13943129e+03 -5.81905998e+02 8.31775189e+02 24 -7.66446002e+02 5.75061654e+02 2.80447701e+02 25 -3.68894336e+02 -6.17831475e+02 5.50349859e+02 26 2.59278514e+01 6.50241527e+02 -4.19823064e+02 27 2.34140077e+03 -3.02721726e+03 5.43462657e+02 28 -2.97255614e+03 2.54660168e+03 5.28889880e+00 29 -1.17601450e+03 -1.16731051e+03 -1.63932532e+03 30 5.69551220e+02 6.96545426e+02 -2.08548589e+02 31 1.36748905e+03 -5.20370616e+02 1.08618722e+03 32 9.37351470e+01 1.15719240e+03 1.23872884e+03 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ar (Configuration in file "config-T-Ar.xyz") ----------------------------------------------------------------------------------------------------- Energy = 8028.53823178 Forces: 1 3.77010998e+02 -2.75937172e+03 -2.35676367e+03 2 -5.60885564e+01 3.50339296e+02 -2.33820527e+02 3 1.20972156e+03 -7.41037895e+02 4.76151218e+02 4 -1.82226941e+02 2.82789355e+03 2.05126805e+03 5 1.63481197e+02 1.84421640e+01 -2.85712307e+02 6 -1.12504910e+03 1.09030917e+03 2.14302257e+02 7 -5.87892050e+02 -2.49816133e+03 -2.69197523e+03 8 -8.76827011e+02 -9.10260950e+02 2.00944728e+02 9 -2.37598318e+02 -6.04388807e+02 5.97341318e+02 10 -7.30399612e+02 1.99065245e+01 -5.58823989e+02 11 -7.79917240e+02 -8.39923566e+02 -2.06401452e+01 12 -6.45203955e+01 3.92358045e+02 -2.31116883e+02 13 -1.33518861e+03 -6.64516284e+02 -2.52860541e+03 14 9.99407242e+01 4.62575606e+02 -2.28321027e+02 15 2.40301259e+03 4.25833083e+02 1.55683855e+03 16 7.72643026e+02 1.46872823e+03 1.19180530e+03 17 3.25482170e+02 -8.41988139e+02 3.62456617e+02 18 3.99095392e-01 9.06421485e+03 -8.55441687e+03 19 2.98203280e+02 -8.71645606e+03 8.73866157e+03 20 1.08531580e+03 9.08219505e+02 5.37306952e+01 21 -9.07509054e+02 -1.26380827e+02 -1.09141664e-01 22 5.86135783e+02 3.32640675e+03 2.06031601e+03 23 -9.67000273e+01 -1.48206146e+03 2.13003066e+02 24 -7.61623326e+02 5.85688488e+02 1.36817854e+02 25 -3.10791312e+02 -6.20582750e+02 5.58564801e+02 26 5.54651794e+01 3.17566100e+02 -5.76946699e+02 27 2.63013574e+03 -3.06139471e+03 1.39993282e+02 28 -2.90700524e+03 2.87033697e+03 -4.51836889e+02 29 -1.17654090e+03 -1.17113911e+03 -1.63967247e+03 30 6.50314165e+02 3.26837108e+02 -1.82609160e+02 31 1.31853331e+03 -5.57442986e+02 1.01575423e+03 32 1.60083088e+02 1.13945115e+03 9.73420876e+02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==15910== Memcheck, a memory error detector ==15910== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==15910== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==15910== Command: python runner2.py LJ_Truncated_Nguyen_2005_Ar__MO_398194508715_001 ==15910== ==15910== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==15910== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==15910== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==15910== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==15910== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==15910== by 0x4010732: call_init (dl-init.c:72) ==15910== by 0x4010732: _dl_init (dl-init.c:119) ==15910== by 0x40151FE: dl_open_worker (dl-open.c:522) ==15910== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==15910== by 0x40147C9: _dl_open (dl-open.c:605) ==15910== by 0x544CF95: dlopen_doit (dlopen.c:66) ==15910== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==15910== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==15910== by 0x544D734: _dlerror_run (dlerror.c:162) ==15910== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==15910== ==15910== ==15910== HEAP SUMMARY: ==15910== in use at exit: 5,661,833 bytes in 3,908 blocks ==15910== total heap usage: 154,466 allocs, 150,558 frees, 62,479,025 bytes allocated ==15910== ==15910== LEAK SUMMARY: ==15910== definitely lost: 0 bytes in 0 blocks ==15910== indirectly lost: 0 bytes in 0 blocks ==15910== possibly lost: 182,191 bytes in 111 blocks ==15910== still reachable: 5,479,642 bytes in 3,797 blocks ==15910== suppressed: 0 bytes in 0 blocks ==15910== Rerun with --leak-check=full to see details of leaked memory ==15910== ==15910== For counts of detected and suppressed errors, rerun with: -v ==15910== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2506 from 172) ================================================================================ 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 06:22:52) ===