!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EDIP_BelkoGusakovDorozhkin_2010_Ge__MO_129433059219_001 Supported species : Ge random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ge (Configuration in file "config-F-Ge.xyz") ----------------------------------------------------------------------------------------------------- Energy = 313.101498704 Forces: 1 -9.56636227e+00 -1.14422155e+01 -9.26113141e+00 2 -7.17530462e+00 -1.12899959e+01 -3.81689916e+01 3 -1.30510700e+01 -3.55698957e+01 -8.86204363e-01 4 -1.64837570e+01 -2.07348377e+00 -7.21877847e+00 5 4.66284561e+00 -2.88113753e+01 -2.66580111e+01 6 1.42781574e+01 -1.55051006e-01 -1.69149752e+01 7 3.74223821e+01 -4.66339951e+01 -3.24440532e+00 8 -3.50929464e+00 -1.83909744e+01 -3.40061667e+01 9 -2.57003950e+01 -1.58621562e+00 -3.10630710e+01 10 -8.38102926e+00 3.86756408e+01 -4.22179775e+01 11 -8.03538613e+00 1.50386966e+01 -2.03434336e+01 12 -1.95978827e+01 1.60864288e+01 -2.65971799e+00 13 1.65759535e+00 1.67199701e+01 -3.44546124e+01 14 1.20628595e+01 7.94763891e+00 -1.17722704e+01 15 3.85572671e+01 1.00749830e+01 -1.52773824e+01 16 2.39223528e+01 3.28465857e+01 -1.64281564e+01 17 -2.37939407e+01 -8.24607659e+00 9.82968641e-01 18 -2.72690660e+01 -1.19789400e+01 3.16980612e+01 19 1.19591088e-01 -2.31651691e+01 1.15697739e+01 20 -1.47403741e+01 -2.81894213e+00 1.80865078e+01 21 1.32308374e+01 -3.31374527e+01 1.31049273e+01 22 3.35948967e+01 -1.25202815e+01 9.30514987e+00 23 6.94272672e+00 -8.18618879e+00 1.13153026e+01 24 -4.52796611e-01 -6.10772584e+00 3.62679076e+01 25 -4.79576295e+01 -9.28541286e+00 1.90179386e+01 26 -2.47048481e+01 4.74980412e+01 1.26021627e+01 27 -1.48860225e+01 6.71934110e+00 3.53978681e+01 28 -1.08164625e+01 1.08965071e+01 8.04539610e+00 29 6.01618397e+00 1.68544483e+01 1.27266449e+01 30 2.71389546e+01 3.39797646e+01 1.22352153e+01 31 4.27014709e+01 4.18525425e-01 4.44986569e+01 32 1.38135005e+01 1.76428202e+01 3.37208041e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ge (Configuration in file "config-T-Ge.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1544.23305602 Forces: 1 2.19537742e+01 9.01580621e+00 -2.18819237e+00 2 -7.17198053e+00 -5.54111644e+00 -1.85691125e+00 3 3.66269629e+01 2.21987935e+00 -2.75198883e-01 4 1.88973939e+01 1.59141431e+01 1.32842145e+01 5 3.47763704e+00 2.41894525e+01 -1.80340708e+01 6 -2.92125867e+01 1.31767801e+01 1.48323872e+01 7 2.32236640e+01 -3.88010470e+01 1.66891188e+01 8 -7.99114003e+00 -1.46925755e+01 -2.40412229e+01 9 -3.90927741e+01 -2.68055110e+01 1.53258653e+01 10 2.91850049e+00 2.67048089e+01 -2.30319045e+01 11 -1.11494514e+00 3.40690228e+00 1.24946245e+01 12 9.72272391e+00 -3.02702607e+01 4.34344330e+01 13 -4.23704975e+01 6.94032835e-01 -2.89195146e+01 14 -3.18141819e+01 5.38454398e+00 -1.15035729e+01 15 1.94022868e+01 -2.40689016e+01 2.02215285e+01 16 8.39797979e+00 1.53902844e+01 -6.41239542e+00 17 -6.83787280e+00 -1.28026923e+00 -1.06356580e+01 18 -2.40302822e+01 3.68975640e+00 2.49727720e+01 19 5.47822974e+01 1.52505821e+01 -1.31700048e+01 20 9.00227896e+00 5.60833738e-01 9.62187190e+00 21 1.33402677e+01 -2.00094279e+00 -1.95081722e+01 22 -1.24490672e+01 7.38033376e+00 9.34591897e+00 23 -1.33236759e+01 2.59597890e+00 -3.19740304e+01 24 1.18435041e+00 -1.47485710e+00 -1.18480301e+01 25 -2.31515244e+01 -3.14316029e+01 1.20929784e+01 26 -7.73446488e+00 2.54627897e+01 1.07791011e+00 27 4.54346321e+00 -2.90503148e+00 -1.32914174e+00 28 8.72141786e+00 1.06359113e-01 -1.31733017e+01 29 -1.00402004e+01 8.26657278e+00 1.03727184e+01 30 -2.24123281e+01 1.34448580e+01 1.15604855e+00 31 2.69428738e+01 -2.36875603e+01 2.89547832e+01 32 1.56096496e+01 1.01049777e+01 -1.59758508e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==12939== Memcheck, a memory error detector ==12939== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==12939== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==12939== Command: python runner2.py EDIP_BelkoGusakovDorozhkin_2010_Ge__MO_129433059219_001 ==12939== ==12939== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==12939== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==12939== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==12939== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==12939== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==12939== by 0x4010732: call_init (dl-init.c:72) ==12939== by 0x4010732: _dl_init (dl-init.c:119) ==12939== by 0x40151FE: dl_open_worker (dl-open.c:522) ==12939== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==12939== by 0x40147C9: _dl_open (dl-open.c:605) ==12939== by 0x544CF95: dlopen_doit (dlopen.c:66) ==12939== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==12939== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==12939== by 0x544D734: _dlerror_run (dlerror.c:162) ==12939== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==12939== ==12939== ==12939== HEAP SUMMARY: ==12939== in use at exit: 4,428,001 bytes in 3,925 blocks ==12939== total heap usage: 112,381 allocs, 108,456 frees, 57,644,122 bytes allocated ==12939== ==12939== LEAK SUMMARY: ==12939== definitely lost: 0 bytes in 0 blocks ==12939== indirectly lost: 0 bytes in 0 blocks ==12939== possibly lost: 182,191 bytes in 111 blocks ==12939== still reachable: 4,245,810 bytes in 3,814 blocks ==12939== suppressed: 0 bytes in 0 blocks ==12939== Rerun with --leak-check=full to see details of leaked memory ==12939== ==12939== For counts of detected and suppressed errors, rerun with: -v ==12939== 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.