Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:19:22) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouWadleyJohnson_2001_Cu__MO_380822813353_000 Supported species : Cu random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = -20.5770833426 Forces: 1 -2.00136265e+00 -4.20296484e+00 -4.50478848e+00 2 -5.39537617e+00 7.48807914e+00 -6.18126839e+00 3 2.07966045e+00 -5.98893989e+00 -1.17488187e+00 4 -4.20341443e+00 3.28343102e+00 1.51513447e+00 5 6.48713476e+00 -1.08896831e+01 -1.40691162e+00 6 2.31127157e+00 9.32163464e-01 -3.89414626e+00 7 3.01141762e+00 -1.48546643e+01 -1.30957127e+01 8 -6.96327945e+00 -7.54992931e+00 2.38847377e+00 9 -7.43268695e+00 -1.65984883e+00 -7.68068811e+00 10 -3.77440803e+00 1.14950166e+01 -1.05309809e+01 11 -3.89061099e+00 -8.55338422e+00 7.52407582e+00 12 -4.58467492e+00 8.99197983e+00 -4.35809979e+00 13 -1.86798202e+00 -4.76305463e+00 -2.39492295e+01 14 3.96142220e+00 5.12071982e+00 -3.12977513e+00 15 2.10413325e+01 -9.79381754e-01 7.11625265e+00 16 2.95243151e+00 1.64479969e+01 7.90807347e+00 17 -8.95813539e+00 -5.53703297e+00 -1.97350007e+00 18 5.53527820e+00 7.33006737e+00 4.06598075e-01 19 2.99165898e+00 -6.53013592e+00 4.16341606e+00 20 -3.34243934e+00 4.13533538e+00 4.37317355e+00 21 -7.46380122e+00 -4.96903283e+00 3.04691648e+00 22 9.65711249e+00 1.21934067e+01 9.96421663e+00 23 2.35730180e+00 -5.96919050e-01 4.65907164e+00 24 1.88292444e+00 1.93768200e+00 2.31735559e+00 25 -4.80533773e+00 -7.64957406e+00 4.98334791e+00 26 -2.96801390e+00 1.05007419e+01 -4.64341118e+00 27 5.65897314e+00 -1.63250238e+01 6.49938126e+00 28 -1.35734763e+01 1.15467964e+01 2.69042860e+00 29 -4.46691475e+00 -8.02806809e+00 3.00681704e+00 30 4.48056262e+00 8.07761100e+00 -3.01218902e+00 31 7.01922978e+00 -7.86596112e+00 8.56440439e+00 32 4.26420220e+00 7.46257120e+00 8.40844562e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 21.2487567223 Forces: 1 1.00771454e+01 -1.08545529e+01 2.38408994e+00 2 -2.04146383e+01 6.53404695e+00 1.90146951e+01 3 2.40143755e+00 2.08509064e+00 -5.85014137e-01 4 6.91374032e+00 7.07230024e+00 -1.77648317e+00 5 1.22614708e+01 -2.54594528e+00 8.91065666e-01 6 -1.23213561e+01 1.62849278e+01 9.54521849e+00 7 -2.86361294e+00 -1.53391439e+01 -1.36120498e+01 8 -7.54075548e+00 -7.44168345e+00 2.69518390e+00 9 -1.34483954e+01 -9.37743141e+00 8.86926805e+00 10 -8.73326686e+00 3.55334205e+00 -5.20819047e+00 11 -3.77316121e+00 -9.00446808e+00 8.38046684e+00 12 -5.06298984e-01 5.22310779e+00 -4.84376893e+00 13 -1.14703493e+00 -6.36301476e+00 -2.01147960e+01 14 -1.63558577e+00 3.62165788e+00 -4.53739216e+00 15 1.70473460e+01 -1.34012700e+00 6.89135188e+00 16 4.35298350e+00 1.22069770e+01 8.82428151e+00 17 3.46459778e+00 -9.67492231e+00 -8.01288380e-01 18 6.57791143e+00 7.89268134e+00 2.81559997e-01 19 3.10607352e+00 7.57081027e-01 3.06077203e+00 20 8.98692989e+00 1.37474461e+01 -2.98969385e+00 21 -8.43693542e+00 -1.35396158e-01 3.09945107e+00 22 -3.49551311e+00 1.97856050e+01 1.27279499e+01 23 -1.05522091e+01 -1.51719894e+01 -9.34431434e+00 24 1.80592688e+01 6.33781905e+00 -2.30553237e+01 25 -8.07560526e-01 -9.58096709e+00 4.95925979e+00 26 -2.08036306e+00 2.89278905e+00 -6.53134808e+00 27 1.26019966e+01 -1.79873905e+01 -6.88174368e+00 28 -1.50215498e+01 1.39575351e+01 -3.18057864e+00 29 -4.57505501e+00 -8.35786420e+00 2.98873232e+00 30 -1.64395844e+00 4.05750338e+00 -1.18930204e+00 31 5.79562418e+00 -9.07803483e+00 7.48620470e+00 32 7.35072458e+00 6.24302084e+00 2.55173626e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==10809== Memcheck, a memory error detector ==10809== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==10809== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==10809== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001_Cu__MO_380822813353_000 ==10809== ==10809== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==10809== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==10809== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==10809== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==10809== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==10809== by 0x4010732: call_init (dl-init.c:72) ==10809== by 0x4010732: _dl_init (dl-init.c:119) ==10809== by 0x40151FE: dl_open_worker (dl-open.c:522) ==10809== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==10809== by 0x40147C9: _dl_open (dl-open.c:605) ==10809== by 0x544CF95: dlopen_doit (dlopen.c:66) ==10809== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==10809== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==10809== by 0x544D734: _dlerror_run (dlerror.c:162) ==10809== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==10809== ==10809== ==10809== HEAP SUMMARY: ==10809== in use at exit: 10,240,293 bytes in 3,961 blocks ==10809== total heap usage: 122,314 allocs, 118,353 frees, 64,861,181 bytes allocated ==10809== ==10809== LEAK SUMMARY: ==10809== definitely lost: 0 bytes in 0 blocks ==10809== indirectly lost: 0 bytes in 0 blocks ==10809== possibly lost: 182,191 bytes in 111 blocks ==10809== still reachable: 10,058,102 bytes in 3,850 blocks ==10809== suppressed: 0 bytes in 0 blocks ==10809== Rerun with --leak-check=full to see details of leaked memory ==10809== ==10809== For counts of detected and suppressed errors, rerun with: -v ==10809== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2504 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 06:19:50) ===