!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Pair_Johnson_Fe__MO_857282754307_003 Supported species : Fe random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 82.6941705699 Forces: 1 -3.80908795e+00 -6.29520228e+00 -7.12168776e+00 2 -1.01336537e+01 1.76615186e+01 -6.73233820e+00 3 3.70867684e+00 -7.88176803e+00 -1.16277620e+00 4 -5.11624040e+00 4.97923677e+00 2.35331111e+00 5 1.22200902e+01 -1.89179786e+01 -1.29645682e+00 6 3.57567104e+00 1.62926280e+00 -6.51034153e+00 7 1.12922647e+00 -2.63661608e+01 -2.45464775e+01 8 -9.80847927e+00 -1.05596711e+01 2.23608438e+00 9 -5.61970473e+00 -1.82346704e+01 -1.39485451e+01 10 1.58750235e+01 1.31481501e+01 -1.17615763e+01 11 2.52044198e+00 -8.07351621e+00 -1.38239899e+01 12 -1.78274519e+01 1.26487620e+01 1.52914226e+01 13 -1.50353593e+01 -7.22134974e+00 -3.58537459e+01 14 6.01893169e+00 8.55669628e+00 -5.68989410e+00 15 2.96534330e+01 -1.02074901e+01 9.86639346e+00 16 -1.17752440e+00 2.28819846e+01 1.87146278e+00 17 -1.31209406e+01 -7.01421739e+00 -3.74201887e+00 18 6.55269009e+00 6.78886116e+00 1.73068129e+00 19 4.28639764e+00 -1.15251152e+01 6.42504207e+00 20 -4.97688842e+00 7.65695120e+00 6.32661148e+00 21 -1.14811455e+01 -6.85083612e+00 4.95327575e+00 22 1.63057844e+01 2.50028008e+01 1.91950327e+01 23 3.27567941e+00 -1.38493771e+00 7.24467846e+00 24 4.41804846e+00 3.43149690e+00 3.51705023e+00 25 -1.87309489e+01 -3.22936014e-02 8.45417538e+00 26 -1.14831155e+01 1.86610581e+01 -6.16839202e+00 27 1.56760173e+01 -2.90572446e+01 7.55049336e+00 28 -2.54918531e+01 2.33230935e+01 3.57312774e+00 29 5.00861472e-02 -1.49306829e+01 6.24211736e+00 30 8.64922029e+00 1.36531240e+01 7.55140331e+00 31 1.06415285e+01 -5.78987965e+00 7.34363208e+00 32 9.25544683e+00 1.03200176e+01 1.66322446e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 143.881281043 Forces: 1 1.63391112e+01 -1.09097491e+01 2.89380862e+00 2 -4.75781675e+01 1.35152271e+01 5.03535975e+01 3 1.46243967e+00 2.57316067e+00 2.10210489e+00 4 1.02349720e+01 9.21087992e+00 -3.33594250e+00 5 1.71323221e+01 -1.36895993e+01 1.35029418e+00 6 -2.19806363e+01 2.92774908e+01 1.94021591e+01 7 -7.55357100e+00 -2.45864018e+01 -2.66704246e+01 8 -9.86363815e+00 -1.06369993e+01 1.98068221e+00 9 -1.48252704e+01 -3.00462085e+01 1.31936518e+01 10 1.41385991e+01 6.29168737e+00 -4.22745960e+00 11 2.02962322e+00 -7.58341348e+00 -1.42950323e+01 12 4.88209042e+00 4.32250436e+00 2.50789195e+01 13 -1.33560905e+01 -9.14982769e+00 -3.03499237e+01 14 -1.98423563e+01 7.61148738e+00 -1.60336481e+01 15 2.48582206e+01 -9.70455235e+00 9.84118317e+00 16 1.45746826e+00 1.69487812e+01 2.73837039e+00 17 8.16135853e+00 -1.70208187e+01 -2.31183735e+00 18 6.62022620e+00 6.32384558e+00 2.33739516e+00 19 2.96535876e+00 -2.28092043e+00 3.62625206e+00 20 2.31989942e+01 2.89982034e+01 -3.52649433e+00 21 -9.68082028e+00 7.60630306e-01 6.64885992e+00 22 -2.85863988e+00 3.56071708e+01 2.19789533e+01 23 -2.46848148e+01 -3.67047530e+01 -2.11042747e+01 24 4.28296416e+01 1.19249227e+01 -5.32017111e+01 25 -1.36087463e+01 -1.89318134e+00 9.56725667e+00 26 -1.20853264e+01 8.30665205e+00 -7.31559389e+00 27 2.77810917e+01 -3.04026950e+01 -1.32997369e+01 28 -2.95714964e+01 2.72018607e+01 -1.11250963e+01 29 5.45637773e-01 -1.45270906e+01 6.30751557e+00 30 2.09689985e+00 7.05765844e+00 1.04419906e+01 31 9.11129126e+00 -6.21284590e+00 6.02677370e+00 32 1.16442277e+01 9.41689365e+00 1.09274070e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2269== Memcheck, a memory error detector ==2269== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2269== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==2269== Command: python runner2.py Pair_Johnson_Fe__MO_857282754307_003 ==2269== ==2269== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==2269== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==2269== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2269== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2269== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2269== by 0x4010732: call_init (dl-init.c:72) ==2269== by 0x4010732: _dl_init (dl-init.c:119) ==2269== by 0x40151FE: dl_open_worker (dl-open.c:522) ==2269== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2269== by 0x40147C9: _dl_open (dl-open.c:605) ==2269== by 0x544CF95: dlopen_doit (dlopen.c:66) ==2269== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2269== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==2269== by 0x544D734: _dlerror_run (dlerror.c:162) ==2269== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==2269== ==2269== ==2269== HEAP SUMMARY: ==2269== in use at exit: 4,416,098 bytes in 3,879 blocks ==2269== total heap usage: 108,338 allocs, 104,459 frees, 56,892,506 bytes allocated ==2269== ==2269== LEAK SUMMARY: ==2269== definitely lost: 0 bytes in 0 blocks ==2269== indirectly lost: 0 bytes in 0 blocks ==2269== possibly lost: 182,191 bytes in 111 blocks ==2269== still reachable: 4,233,907 bytes in 3,768 blocks ==2269== suppressed: 0 bytes in 0 blocks ==2269== Rerun with --leak-check=full to see details of leaked memory ==2269== ==2269== For counts of detected and suppressed errors, rerun with: -v ==2269== 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.