!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_1958LowCutoff_Ne__MO_466741694288_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 = 138.470443188 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 = 169.738219343 Forces: 1 8.42813120e+00 -6.16708695e+01 -5.27019990e+01 2 -1.26565238e+00 7.66118051e+00 -5.08542646e+00 3 2.68504570e+01 -1.65195051e+01 1.05380724e+01 4 -4.14519698e+00 6.30930664e+01 4.59767916e+01 5 3.59657183e+00 4.07434685e-01 -6.24143650e+00 6 -2.50477455e+01 2.42150305e+01 4.80708639e+00 7 -1.32359057e+01 -5.59154156e+01 -6.03440588e+01 8 -1.94861526e+01 -2.02892057e+01 4.37693534e+00 9 -5.27977467e+00 -1.32936256e+01 1.32533353e+01 10 -1.61608499e+01 3.90982641e-01 -1.23958163e+01 11 -1.72468804e+01 -1.86400272e+01 -4.71838777e-01 12 -1.46077779e+00 8.76243026e+00 -5.15953367e+00 13 -2.99553528e+01 -1.46667317e+01 -5.63841476e+01 14 2.22740364e+00 1.01502438e+01 -4.98335193e+00 15 5.36416094e+01 9.61557357e+00 3.48720940e+01 16 1.72629903e+01 3.26681564e+01 2.65487600e+01 17 7.27798422e+00 -1.86653777e+01 7.97964799e+00 18 -1.58889676e-01 2.04057110e+02 -1.92729696e+02 19 6.65158917e+00 -1.96500371e+02 1.96748376e+02 20 2.41969678e+01 2.00893602e+01 1.20136925e+00 21 -2.00794460e+01 -2.79145368e+00 1.09516817e-02 22 1.32123419e+01 7.42983436e+01 4.62663747e+01 23 -2.18103715e+00 -3.29446375e+01 4.65713087e+00 24 -1.69414586e+01 1.29343554e+01 3.03906205e+00 25 -6.83948687e+00 -1.36827748e+01 1.23808193e+01 26 1.25243498e+00 6.98489351e+00 -1.27272498e+01 27 5.90675982e+01 -6.83864346e+01 3.14398677e+00 28 -6.50980085e+01 6.42903616e+01 -1.01039094e+01 29 -2.62797347e+01 -2.59173379e+01 -3.67107287e+01 30 1.43743473e+01 7.25339893e+00 -4.11308490e+00 31 2.93302560e+01 -1.22743213e+01 2.26517198e+01 32 3.49166739e+00 2.52861676e+01 2.16997640e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==14728== Memcheck, a memory error detector ==14728== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==14728== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==14728== Command: python runner2.py LJ_Shifted_Bernardes_1958LowCutoff_Ne__MO_466741694288_003 ==14728== ==14728== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==14728== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==14728== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==14728== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==14728== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==14728== by 0x4010732: call_init (dl-init.c:72) ==14728== by 0x4010732: _dl_init (dl-init.c:119) ==14728== by 0x40151FE: dl_open_worker (dl-open.c:522) ==14728== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==14728== by 0x40147C9: _dl_open (dl-open.c:605) ==14728== by 0x544CF95: dlopen_doit (dlopen.c:66) ==14728== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==14728== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==14728== by 0x544D734: _dlerror_run (dlerror.c:162) ==14728== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==14728== ==14728== ==14728== HEAP SUMMARY: ==14728== in use at exit: 4,576,683 bytes in 3,908 blocks ==14728== total heap usage: 117,924 allocs, 114,016 frees, 58,104,553 bytes allocated ==14728== ==14728== LEAK SUMMARY: ==14728== definitely lost: 0 bytes in 0 blocks ==14728== indirectly lost: 0 bytes in 0 blocks ==14728== possibly lost: 182,191 bytes in 111 blocks ==14728== still reachable: 4,394,492 bytes in 3,797 blocks ==14728== suppressed: 0 bytes in 0 blocks ==14728== Rerun with --leak-check=full to see details of leaked memory ==14728== ==14728== For counts of detected and suppressed errors, rerun with: -v ==14728== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2508 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.