!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Xe__MO_849320763277_003 Supported species : Xe random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Xe (Configuration in file "config-F-Xe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 84329.8626392 Forces: 1 -8.65010024e+03 -2.48969600e+04 -3.35475393e+04 2 -6.51660370e+01 4.48640273e+03 -4.31048601e+03 3 1.50055977e+04 -1.33428708e+04 5.04957194e+03 4 -8.06263366e+03 3.58494117e+04 2.59949173e+04 5 1.70723472e+02 -5.03429349e+03 -3.26032603e+03 6 1.37146511e+03 8.49481808e+02 -2.50245410e+03 7 -3.74172868e+03 -3.28358790e+04 -3.37401899e+04 8 -1.13543212e+04 -1.18068402e+04 2.60483979e+03 9 -3.81068390e+02 -1.61570540e+03 -2.20749151e+03 10 -7.09672247e+03 3.47845860e+03 -8.79166521e+03 11 -1.01317788e+04 -1.08881103e+04 -2.75264146e+02 12 -2.82856947e+03 7.89926254e+03 -3.78417319e+03 13 -1.74265682e+04 -7.93558989e+03 -3.43041702e+04 14 4.69316495e+03 5.02264499e+03 -2.01313268e+03 15 3.25577001e+04 6.19123902e+03 2.01625863e+04 16 1.01075843e+04 2.19070705e+04 1.41399069e+04 17 -6.54433528e+03 -2.87947498e+03 3.09795135e+03 18 -2.04713192e+01 1.17178445e+05 -1.10618460e+05 19 3.71329882e+03 -1.17146056e+05 1.11221111e+05 20 -2.83114664e+03 1.62956381e+03 1.98276299e+03 21 -9.32647312e+03 -6.12777584e+03 -5.32009122e+02 22 1.75328301e+04 3.37010981e+04 2.60296076e+04 23 1.47971723e+04 -7.55816462e+03 1.08156432e+04 24 -9.93756152e+03 7.46618746e+03 3.66872751e+03 25 -4.81706933e+03 -8.02571038e+03 7.14319748e+03 26 3.28689519e+02 8.47951977e+03 -5.45391470e+03 27 3.02833928e+04 -3.92149609e+04 7.07568697e+03 28 -3.85078113e+04 3.29779674e+04 9.33249360e+01 29 -1.52355180e+04 -1.51510938e+04 -2.12270666e+04 30 7.41856471e+03 9.07045742e+03 -2.70431964e+03 31 1.77540424e+04 -6.75779071e+03 1.41020409e+04 32 1.22481735e+03 1.50300655e+04 1.60907864e+04 MONOATOMIC STRUCTURE (pbc=True)-- Species = Xe (Configuration in file "config-T-Xe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 105317.711511 Forces: 1 4.88404636e+03 -3.57487369e+04 -3.05289647e+04 2 -7.25057614e+02 4.56094327e+03 -3.04765793e+03 3 1.56968672e+04 -9.60599619e+03 6.18233334e+03 4 -2.35131559e+03 3.66508101e+04 2.65576691e+04 5 2.12545877e+03 2.39544188e+02 -3.72042415e+03 6 -1.45881237e+04 1.41454709e+04 2.77406911e+03 7 -7.60367508e+03 -3.23538284e+04 -3.48520240e+04 8 -1.13741499e+04 -1.17999589e+04 2.61830026e+03 9 -3.08217058e+03 -7.85821631e+03 7.75151370e+03 10 -9.48403437e+03 2.64979526e+02 -7.25207748e+03 11 -1.01282668e+04 -1.08988616e+04 -2.66024181e+02 12 -8.33420281e+02 5.08402393e+03 -2.99497362e+03 13 -1.72828755e+04 -8.63335110e+03 -3.27760302e+04 14 1.29558497e+03 6.01754090e+03 -2.97369001e+03 15 3.11404760e+04 5.50390253e+03 2.01593068e+04 16 1.00105733e+04 1.90486072e+04 1.54518083e+04 17 4.21628014e+03 -1.09283296e+04 4.71165867e+03 18 2.71925111e+01 1.17236749e+05 -1.10623415e+05 19 3.86505887e+03 -1.12703119e+05 1.13023384e+05 20 1.40684899e+04 1.17937682e+04 6.96037718e+02 21 -1.17837825e+04 -1.64166501e+03 -3.16791050e+00 22 7.57886913e+03 4.31008742e+04 2.66634249e+04 23 -1.25018033e+03 -1.92241474e+04 2.77310465e+03 24 -9.87768955e+03 7.60824907e+03 1.77500001e+03 25 -4.04041146e+03 -8.06444805e+03 7.24992621e+03 26 7.16888651e+02 4.12897040e+03 -7.49651845e+03 27 3.40370235e+04 -3.96660990e+04 1.81167886e+03 28 -3.76446347e+04 3.71680317e+04 -5.85299028e+03 29 -1.52445892e+04 -1.52063227e+04 -2.12340989e+04 30 8.44606183e+03 4.24102977e+03 -2.36160050e+03 31 1.71002783e+04 -7.24608649e+03 1.31660561e+04 32 2.08522775e+03 1.47856719e+04 1.26183850e+04 ================================================================================ VALGRIND OUTPUT ================================================================================ ==15772== Memcheck, a memory error detector ==15772== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==15772== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==15772== Command: python runner2.py LJ_Shifted_Bernardes_1958MedCutoff_Xe__MO_849320763277_003 ==15772== ==15772== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==15772== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==15772== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==15772== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==15772== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==15772== by 0x4010732: call_init (dl-init.c:72) ==15772== by 0x4010732: _dl_init (dl-init.c:119) ==15772== by 0x40151FE: dl_open_worker (dl-open.c:522) ==15772== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==15772== by 0x40147C9: _dl_open (dl-open.c:605) ==15772== by 0x544CF95: dlopen_doit (dlopen.c:66) ==15772== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==15772== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==15772== by 0x544D734: _dlerror_run (dlerror.c:162) ==15772== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==15772== ==15772== ==15772== HEAP SUMMARY: ==15772== in use at exit: 5,729,527 bytes in 3,908 blocks ==15772== total heap usage: 154,859 allocs, 150,951 frees, 63,609,133 bytes allocated ==15772== ==15772== LEAK SUMMARY: ==15772== definitely lost: 0 bytes in 0 blocks ==15772== indirectly lost: 0 bytes in 0 blocks ==15772== possibly lost: 182,191 bytes in 111 blocks ==15772== still reachable: 5,547,336 bytes in 3,797 blocks ==15772== suppressed: 0 bytes in 0 blocks ==15772== Rerun with --leak-check=full to see details of leaked memory ==15772== ==15772== For counts of detected and suppressed errors, rerun with: -v ==15772== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2508 from 174) ================================================================================ 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.