Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:16:10) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EAM_Dynamo_SmirnovaStarikov_U__MO_649864794085_000 Supported species : U random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = U (Configuration in file "config-F-U.xyz") ----------------------------------------------------------------------------------------------------- Energy = -89.5794135839 Forces: 1 -2.66871059e+00 -4.64552786e+00 -6.25627766e+00 2 -4.81189137e+00 8.50183519e+00 -3.73326638e+00 3 3.80515810e+00 -6.07128798e+00 3.78206583e+00 4 -5.67192934e+00 6.82185844e+00 3.46553468e+00 5 7.94987010e+00 -6.46184068e+00 -1.26835246e+00 6 6.66257361e-02 2.53667316e-01 -1.87675783e-01 7 2.01510665e+00 -7.50871638e+00 -7.66206417e+00 8 -3.37234172e+00 -4.33957716e+00 -2.48475559e+00 9 -9.17425936e-01 1.51726210e-01 -8.72744205e-01 10 -2.30213864e+00 2.10659031e+00 -2.82140759e+00 11 9.13694305e-02 -1.59578056e+00 -4.46062599e+00 12 8.45649220e-02 4.77992648e-01 7.36809493e-02 13 -3.61877057e+00 -3.98619961e+00 -9.91887086e+00 14 1.37099940e+00 1.00186046e+00 -5.68030049e-01 15 9.93727685e+00 3.28658606e-01 1.81037835e+00 16 1.23050159e+00 8.04528160e+00 1.73801480e+00 17 -2.31372552e+00 -3.85595383e+00 -2.09224394e+00 18 2.04750745e+00 -3.12254227e-01 2.32390170e+00 19 5.35349010e-01 -5.92608544e-01 9.70764615e-01 20 -1.98255393e-01 3.28124462e+00 3.04480221e+00 21 -3.79231981e+00 -2.84655181e+00 5.08464436e-01 22 5.62008190e+00 6.55347774e+00 6.70086086e+00 23 6.99770131e-01 -4.65968904e-01 2.26310767e+00 24 1.11603937e-01 1.30915073e-01 9.94398769e-01 25 -6.58150695e+00 7.63148087e-02 2.89019127e+00 26 -2.06144836e+00 5.16826731e+00 -8.25751761e-01 27 2.94828728e+00 -6.90016359e+00 2.76161481e+00 28 -5.10530154e+00 4.22031531e+00 6.74561146e-02 29 -3.85557645e-01 -1.17235813e+00 5.04962435e+00 30 2.02022613e+00 2.43594093e+00 2.80173085e-01 31 1.87088895e+00 -1.30934532e+00 1.64992404e+00 32 1.39613578e+00 2.50818801e+00 2.77710788e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = U (Configuration in file "config-T-U.xyz") ----------------------------------------------------------------------------------------------------- Energy = -88.2812132144 Forces: 1 5.37594227e-04 -6.98209630e+00 -7.05216987e+00 2 -5.07709067e+00 9.82420639e+00 -2.58964847e+00 3 4.92704918e+00 -3.18993914e+00 5.30269557e+00 4 -2.07085385e+00 8.52453755e+00 3.01632160e+00 5 8.21738427e+00 -6.81349639e+00 -1.06207206e+00 6 -2.47721643e+00 5.61295519e+00 2.15761980e+00 7 -1.31333410e+00 -8.65003309e+00 -8.80370644e+00 8 -4.17581026e+00 -3.66657700e+00 -2.34027462e+00 9 -4.55825318e+00 -3.17394025e+00 2.69306916e+00 10 -1.42207793e+00 2.44624751e+00 -2.21739728e+00 11 1.04499409e+00 -1.97690863e+00 -3.86241339e+00 12 -8.03963427e-02 7.53738511e-01 2.14159812e+00 13 -4.72131910e+00 -5.80050444e+00 -7.68743235e+00 14 5.72365878e-01 2.61365483e+00 -1.93092861e+00 15 7.54090658e+00 -9.12261799e-01 2.16595088e+00 16 1.87410178e+00 5.58286533e+00 2.16898367e+00 17 7.46047647e+00 -1.34322930e+01 -2.64987117e+00 18 3.25187279e+00 5.63877796e-01 1.39529626e+00 19 1.25631670e+00 4.36824135e-01 2.10623560e+00 20 8.63838503e+00 1.11178272e+01 4.67274454e+00 21 -5.19431440e+00 -3.95268738e-01 -6.16254282e-02 22 -3.70585531e+00 1.68031941e+01 4.73034471e+00 23 -7.75943876e+00 -9.46355335e+00 2.28920652e+00 24 -2.37632197e-01 2.09708565e+00 -3.46071223e-01 25 -4.84397475e+00 -9.05059308e-01 3.22534987e+00 26 -2.05297051e+00 2.42239199e+00 -2.87025291e+00 27 6.30368582e+00 -9.40676273e+00 -2.19542044e+00 28 -7.79886536e+00 5.82596631e+00 -5.38387744e-02 29 -8.16869731e-01 -1.30158705e+00 4.02772276e+00 30 2.15699065e+00 1.21468187e+00 9.56986916e-01 31 2.76119473e+00 -3.03519774e+00 1.32680780e+00 32 2.30001130e+00 3.26542458e+00 1.34618927e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==6521== Memcheck, a memory error detector ==6521== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==6521== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==6521== Command: python runner2.py EAM_Dynamo_SmirnovaStarikov_U__MO_649864794085_000 ==6521== ==6521== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==6521== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==6521== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6521== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6521== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6521== by 0x4010732: call_init (dl-init.c:72) ==6521== by 0x4010732: _dl_init (dl-init.c:119) ==6521== by 0x40151FE: dl_open_worker (dl-open.c:522) ==6521== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6521== by 0x40147C9: _dl_open (dl-open.c:605) ==6521== by 0x544CF95: dlopen_doit (dlopen.c:66) ==6521== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6521== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==6521== by 0x544D734: _dlerror_run (dlerror.c:162) ==6521== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==6521== ==6521== ==6521== HEAP SUMMARY: ==6521== in use at exit: 7,106,164 bytes in 3,968 blocks ==6521== total heap usage: 117,102 allocs, 113,134 frees, 69,602,184 bytes allocated ==6521== ==6521== LEAK SUMMARY: ==6521== definitely lost: 0 bytes in 0 blocks ==6521== indirectly lost: 0 bytes in 0 blocks ==6521== possibly lost: 182,751 bytes in 112 blocks ==6521== still reachable: 6,923,413 bytes in 3,856 blocks ==6521== suppressed: 0 bytes in 0 blocks ==6521== Rerun with --leak-check=full to see details of leaked memory ==6521== ==6521== For counts of detected and suppressed errors, rerun with: -v ==6521== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2527 from 171) ================================================================================ 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. === Verification check vc-memory-leak end (2018-12-15 06:16:36) ===