Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:22:40) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : MFF_MistriotisFlytzanisFarantos_1989_Si__MO_080526771943_001 Supported species : Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1054.77501109 Forces: 1 -3.12091109e+01 -2.99539225e+01 -3.35660591e+01 2 -3.12681178e+01 -4.23720668e+01 -1.38223538e+02 3 -5.63112017e+01 -1.51101875e+02 -2.76344187e+01 4 -1.13231299e+02 -2.31355525e+01 -2.67651123e+01 5 1.43150346e+01 -8.00818442e+01 -6.91628958e+01 6 6.25703704e+01 -3.32330438e+01 -7.98569502e+01 7 7.41304047e+01 -1.05690158e+02 -4.20119164e+01 8 5.14482464e+01 -7.99848149e+01 -5.82147358e+01 9 -7.11496077e+01 1.19505388e+01 -8.55990420e+01 10 -3.61349991e+01 8.90636999e+01 -9.46253362e+01 11 -1.19697798e+02 -5.22971545e+00 -7.65497929e+01 12 -8.57031678e+01 6.92517620e+01 -1.77692301e+01 13 4.68983987e+01 3.83727126e+01 -1.94061909e+02 14 4.97356226e+01 3.84751694e+01 -4.11560403e+01 15 1.98206149e+02 5.28085543e+01 -4.22738258e+01 16 3.24128519e+01 2.04778858e+02 -3.78227657e+01 17 -5.67396598e+01 -4.74894906e+01 8.08288001e+00 18 -6.92119148e+01 -8.22244711e+01 6.87521326e+01 19 -1.94624064e+00 -5.76047913e+01 5.64900205e+01 20 -5.09502914e+01 -7.98513075e+00 5.41834908e+01 21 2.81503513e+01 -1.29172035e+02 5.68543353e+01 22 1.40905393e+02 -4.35810020e+01 4.40055885e+01 23 2.07065986e+01 -2.13914342e+01 3.14646431e+01 24 2.52560671e+01 -4.17120783e+01 1.36537740e+02 25 -1.59860325e+02 3.29891540e+01 4.02412546e+01 26 -4.99855917e+01 1.59771730e+02 6.27143842e+01 27 -5.63345085e+01 1.10194013e+01 1.32848216e+02 28 -4.36580465e+01 3.04458456e+01 2.91126171e+01 29 7.83930296e+01 8.23652540e+01 1.06181161e+02 30 1.01720494e+02 8.24994607e+01 3.71423356e+01 31 8.79638159e+01 1.48180819e+01 1.06610070e+02 32 2.05790518e+01 6.33332031e+01 9.40726990e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 5110.57069764 Forces: 1 -6.30901918e+00 6.60519764e+01 -1.29643931e+01 2 3.40315591e+01 -1.11384261e+01 -5.74357147e+01 3 3.80120239e+01 -3.39164749e+00 -5.27542724e+01 4 4.97195808e+01 2.05092920e+01 2.00631522e+01 5 -6.36649048e+01 4.17916525e+01 -9.51941896e-01 6 1.54940653e+01 1.03727645e+00 -6.53678357e+01 7 -6.47054121e+01 5.27285796e+01 2.49039734e+01 8 -5.39160315e+01 -3.32572091e+01 2.49781372e+01 9 -2.19322206e+01 -3.45924598e+01 -1.84687086e+01 10 3.64505977e+01 2.40243364e+01 2.99413401e+00 11 -7.22069906e+01 -8.40062197e+01 1.95468414e+01 12 -2.38180873e+00 -1.67549625e+01 1.39506615e+01 13 8.14899246e+00 1.74011844e+01 -7.32877080e+01 14 1.85206072e+01 -8.45101457e+01 -2.38425426e+01 15 4.89638464e+01 4.19207872e+01 -6.19297827e+00 16 -5.99498382e-01 7.32220365e+01 -2.47892284e+00 17 3.65103716e+01 6.04691320e+01 1.58416833e+01 18 1.32331431e+01 1.47268499e+00 -5.58484580e+00 19 8.59342870e+01 9.97486348e+01 -2.98581284e+01 20 6.49109806e+01 1.14484933e+01 6.68990466e+00 21 -3.05499766e+01 2.94417954e+01 2.28815779e+01 22 -4.92318719e+01 4.62521247e+01 2.38483723e+01 23 -5.16109790e+01 1.26990592e+01 2.70429078e+01 24 -1.67999284e+01 -1.34868735e+01 2.74808693e+01 25 -3.70238428e+01 -6.90345705e+01 1.34100318e+01 26 3.25241829e+01 1.53800991e+01 5.14120780e+01 27 -7.23082499e+01 -3.46449362e+01 -3.45330407e+01 28 -3.14165688e+01 -1.37596352e+02 -3.98732756e+01 29 2.74735882e+01 1.42695760e+01 8.81202930e+01 30 3.79078351e+01 -7.27934769e+01 5.28594145e+01 31 -2.94784500e+01 -1.85203428e+01 1.91930136e+01 32 5.63000920e+01 -1.61410984e+01 -3.16227374e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==16177== Memcheck, a memory error detector ==16177== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==16177== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==16177== Command: python runner2.py MFF_MistriotisFlytzanisFarantos_1989_Si__MO_080526771943_001 ==16177== ==16177== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==16177== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==16177== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==16177== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==16177== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==16177== by 0x4010732: call_init (dl-init.c:72) ==16177== by 0x4010732: _dl_init (dl-init.c:119) ==16177== by 0x40151FE: dl_open_worker (dl-open.c:522) ==16177== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==16177== by 0x40147C9: _dl_open (dl-open.c:605) ==16177== by 0x544CF95: dlopen_doit (dlopen.c:66) ==16177== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==16177== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==16177== by 0x544D734: _dlerror_run (dlerror.c:162) ==16177== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==16177== ==16177== ==16177== HEAP SUMMARY: ==16177== in use at exit: 4,428,834 bytes in 3,917 blocks ==16177== total heap usage: 796,156 allocs, 792,239 frees, 74,005,410 bytes allocated ==16177== ==16177== LEAK SUMMARY: ==16177== definitely lost: 0 bytes in 0 blocks ==16177== indirectly lost: 0 bytes in 0 blocks ==16177== possibly lost: 182,191 bytes in 111 blocks ==16177== still reachable: 4,246,643 bytes in 3,806 blocks ==16177== suppressed: 0 bytes in 0 blocks ==16177== Rerun with --leak-check=full to see details of leaked memory ==16177== ==16177== For counts of detected and suppressed errors, rerun with: -v ==16177== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2509 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. === Verification check vc-memory-leak end (2018-12-15 06:23:16) ===