!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Shifted_Bernardes_1958MedCutoff_Ne__MO_160637895352_003 Supported species : Ne random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ne (Configuration in file "config-F-Ne.xyz") ----------------------------------------------------------------------------------------------------- Energy = 138.456687846 Forces: 1 -1.46475282e+01 -4.29443283e+01 -5.77193888e+01 2 -1.54363398e-01 7.56773256e+00 -7.02042987e+00 3 2.57037788e+01 -2.25890183e+01 8.64920569e+00 4 -1.35373659e+01 6.17850255e+01 4.50029444e+01 5 2.67273353e-01 -8.29859232e+00 -5.36478444e+00 6 2.12902820e+00 1.45254384e+00 -3.99314972e+00 7 -6.94669128e+00 -5.65649754e+01 -5.84429716e+01 8 -1.94875927e+01 -2.02836719e+01 4.38046359e+00 9 -5.14222386e-01 -2.71551329e+00 -3.54858072e+00 10 -1.20899397e+01 5.68038461e+00 -1.48263789e+01 11 -1.72404067e+01 -1.86483483e+01 -4.64197952e-01 12 -4.63924462e+00 1.33077767e+01 -6.50500556e+00 13 -3.02176791e+01 -1.35438265e+01 -5.87670920e+01 14 7.83311157e+00 8.39398426e+00 -3.26135587e+00 15 5.58162644e+01 1.07197185e+01 3.49046800e+01 16 1.74098162e+01 3.72792984e+01 2.43552317e+01 17 -1.08663763e+01 -4.67787216e+00 5.24425638e+00 18 -1.95482782e-01 2.04012036e+02 -1.92743897e+02 19 6.43810224e+00 -2.03814258e+02 1.93576559e+02 20 -4.59208892e+00 2.70107981e+00 3.17466285e+00 21 -1.59291563e+01 -1.01454520e+01 -8.92022131e-01 22 2.99669217e+01 5.82459994e+01 4.51921560e+01 23 2.51962348e+01 -1.28580156e+01 1.82876660e+01 24 -1.70691854e+01 1.27302308e+01 5.99810169e+00 25 -7.95595026e+00 -1.36448087e+01 1.21995579e+01 26 6.34445162e-01 1.41107400e+01 -9.26905762e+00 27 5.27131019e+01 -6.76862628e+01 1.18802101e+01 28 -6.64569392e+01 5.70241447e+01 -7.07494633e-02 29 -2.62850707e+01 -2.58746638e+01 -3.67223441e+01 30 1.24260283e+01 1.52137721e+01 -4.64200482e+00 31 3.02757739e+01 -1.15067870e+01 2.40468790e+01 32 2.01540331e+00 2.55719274e+01 2.73608364e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ne (Configuration in file "config-T-Ne.xyz") ----------------------------------------------------------------------------------------------------- Energy = 169.56608494 Forces: 1 8.42817352e+00 -6.16709055e+01 -5.27019381e+01 2 -1.26567705e+00 7.66112682e+00 -5.08547114e+00 3 2.68505408e+01 -1.65195536e+01 1.05381385e+01 4 -4.14511463e+00 6.30930609e+01 4.59769175e+01 5 3.59663400e+00 4.07460251e-01 -6.24150084e+00 6 -2.50478852e+01 2.42149438e+01 4.80710902e+00 7 -1.32358839e+01 -5.59154170e+01 -6.03441313e+01 8 -1.94861797e+01 -2.02893382e+01 4.37690561e+00 9 -5.27982384e+00 -1.32936236e+01 1.32534315e+01 10 -1.61609484e+01 3.90948567e-01 -1.23958442e+01 11 -1.72469917e+01 -1.86399982e+01 -4.71786255e-01 12 -1.46080126e+00 8.76240698e+00 -5.15955715e+00 13 -2.99553208e+01 -1.46667023e+01 -5.63841786e+01 14 2.22743183e+00 1.01502928e+01 -4.98327040e+00 15 5.36415815e+01 9.61572071e+00 3.48720298e+01 16 1.72630950e+01 3.26681355e+01 2.65487468e+01 17 7.27795755e+00 -1.86654290e+01 7.97970248e+00 18 -1.58843066e-01 2.04057219e+02 -1.92729730e+02 19 6.65162954e+00 -1.96500371e+02 1.96748424e+02 20 2.41969680e+01 2.00894010e+01 1.20136020e+00 21 -2.00794756e+01 -2.79141053e+00 1.09203371e-02 22 1.32122717e+01 7.42983948e+01 4.62664620e+01 23 -2.18106063e+00 -3.29447724e+01 4.65718637e+00 24 -1.69415313e+01 1.29343087e+01 3.03901006e+00 25 -6.83950624e+00 -1.36827267e+01 1.23808519e+01 26 1.25245862e+00 6.98490677e+00 -1.27273426e+01 27 5.90675226e+01 -6.83864457e+01 3.14394637e+00 28 -6.50980781e+01 6.42903708e+01 -1.01039691e+01 29 -2.62796844e+01 -2.59173401e+01 -3.67107920e+01 30 1.43743958e+01 7.25343080e+00 -4.11303824e+00 31 2.93303497e+01 -1.22743279e+01 2.26517088e+01 32 3.49179575e+00 2.52862334e+01 2.16996986e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==15709== Memcheck, a memory error detector ==15709== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==15709== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==15709== Command: python runner2.py LJ_Shifted_Bernardes_1958MedCutoff_Ne__MO_160637895352_003 ==15709== ==15709== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==15709== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==15709== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==15709== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==15709== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==15709== by 0x4010732: call_init (dl-init.c:72) ==15709== by 0x4010732: _dl_init (dl-init.c:119) ==15709== by 0x40151FE: dl_open_worker (dl-open.c:522) ==15709== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==15709== by 0x40147C9: _dl_open (dl-open.c:605) ==15709== by 0x544CF95: dlopen_doit (dlopen.c:66) ==15709== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==15709== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==15709== by 0x544D734: _dlerror_run (dlerror.c:162) ==15709== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==15709== ==15709== ==15709== HEAP SUMMARY: ==15709== in use at exit: 4,856,351 bytes in 3,907 blocks ==15709== total heap usage: 126,733 allocs, 122,826 frees, 59,226,126 bytes allocated ==15709== ==15709== LEAK SUMMARY: ==15709== definitely lost: 0 bytes in 0 blocks ==15709== indirectly lost: 0 bytes in 0 blocks ==15709== possibly lost: 182,191 bytes in 111 blocks ==15709== still reachable: 4,674,160 bytes in 3,796 blocks ==15709== suppressed: 0 bytes in 0 blocks ==15709== Rerun with --leak-check=full to see details of leaked memory ==15709== ==15709== For counts of detected and suppressed errors, rerun with: -v ==15709== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2510 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.