Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:25:00) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Morse_Shifted_GirifalcoWeizer_1959LowCutoff_Pb__MO_534638645497_002 Supported species : Pb random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Pb (Configuration in file "config-F-Pb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 959.516888453 Forces: 1 -2.57128495e+01 -5.92802231e+01 -5.10036269e+01 2 -1.54828498e+01 1.23957415e+01 -5.77300323e+01 3 2.14404799e+01 -5.72037046e+01 -1.96585797e+01 4 -4.68613386e+01 3.54760995e+01 2.87043779e+01 5 9.91563301e+00 -6.78593976e+01 -3.18709685e+01 6 4.15180697e+01 6.89556429e+00 -4.79524063e+01 7 4.07616999e+01 -9.20569137e+01 -5.79213383e+01 8 -3.54797188e+01 -3.72275406e+01 1.36200953e+01 9 -5.68959531e+01 2.81999172e-01 -7.03758539e+01 10 -2.06127583e+01 8.68920749e+01 -7.56987904e+01 11 -2.62595367e+01 -4.68954517e+01 3.78667353e+01 12 -4.81595381e+01 6.33142328e+01 -1.76836235e+01 13 -1.75980100e-01 -2.51222005e+01 -1.42488503e+02 14 4.17180374e+01 4.63375288e+01 -3.68616915e+01 15 1.25143268e+02 -1.91473027e+01 1.91871766e+01 16 9.96381007e+00 1.10765481e+02 3.63530098e+01 17 -7.03688727e+01 -3.57950531e+01 5.33636917e+00 18 1.94588569e+01 4.19534842e+01 6.72415645e+00 19 5.61110925e+00 -5.49925046e+01 3.73645596e+01 20 -3.64350666e+01 1.85441525e+01 3.48042734e+01 21 -3.41778870e+01 -5.65890675e+01 1.46146149e+01 22 7.59277350e+01 6.03114063e+01 4.83908071e+01 23 3.81090255e+01 -2.11788332e+01 4.01203963e+01 24 -5.02274202e+00 2.45958822e+01 4.17880793e+01 25 -5.10307449e+01 -4.49481860e+01 1.38788227e+01 26 -1.45420180e+01 8.23787785e+01 -2.47738196e+01 27 2.51953023e+01 -9.01970426e+01 6.04041442e+01 28 -8.61140959e+01 7.22062651e+01 3.38573073e+01 29 -2.35404818e+01 -4.82731621e+01 2.54762807e+01 30 5.00449697e+01 6.27062442e+01 1.33672890e+01 31 6.12864478e+01 -2.66792049e+01 5.48688430e+01 32 3.07779870e+01 5.83908532e+01 6.72918955e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pb (Configuration in file "config-T-Pb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1505.1137404 Forces: 1 6.36387162e+01 -7.65834079e+01 1.09012790e+01 2 -5.10241605e+01 2.63662894e+01 2.91451588e+01 3 2.12705088e+01 1.58473156e+01 -1.54558395e+01 4 4.02901695e+01 5.67973432e+01 4.24105170e+01 5 2.27038100e+01 -1.82293561e+01 3.51351689e+00 6 -7.07293160e+01 7.90803081e+01 1.87908744e+01 7 -1.92082050e+01 -6.14998321e+01 -5.71941603e+01 8 -4.09402144e+01 -3.56358184e+01 1.82369343e+01 9 -6.70395375e+01 -4.36580874e+01 3.44626986e+01 10 -3.56548030e+01 4.13201073e+01 -2.45987656e+01 11 -2.51436309e+01 -5.03270225e+01 4.53886037e+01 12 1.49545757e+01 1.26244901e+01 -3.36032268e+01 13 1.92193642e+00 -3.63614244e+01 -1.01220294e+02 14 -5.43680557e+00 1.28945268e+01 -2.91550321e+01 15 8.26864563e+01 -2.25444572e+01 2.00687485e+01 16 1.53576042e+01 6.15340312e+01 4.17584854e+01 17 2.70225743e+01 -3.32421397e+01 1.71062830e+01 18 2.60790832e+01 4.48553737e+01 5.07224232e+00 19 8.58904975e+00 1.10592692e+01 1.38629909e+01 20 5.41069140e+01 7.88059775e+01 -3.01013947e+01 21 -3.77948950e+01 -4.04167115e+00 1.67146114e+01 22 -6.77003613e+00 1.04813254e+02 5.26915140e+01 23 -4.87664076e+01 -8.70486960e+01 -5.00431649e+01 24 2.88607139e+01 3.85426468e+01 -6.26231687e+01 25 -5.93764904e+00 -5.88590955e+01 1.39425495e+01 26 -7.57092051e+00 1.50938337e+01 -3.24908413e+01 27 5.85926851e+01 -9.79375438e+01 -3.09883341e+01 28 -7.93175009e+01 6.48688046e+01 -1.82560862e+01 29 -2.44160880e+01 -5.08477454e+01 2.53994185e+01 30 -1.79289764e+01 1.47373678e+01 3.69242736e+01 31 3.26847123e+01 -3.37185231e+01 2.83959497e+01 32 4.49196366e+01 3.12938822e+01 1.09436591e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==19629== Memcheck, a memory error detector ==19629== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==19629== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==19629== Command: python runner2.py Morse_Shifted_GirifalcoWeizer_1959LowCutoff_Pb__MO_534638645497_002 ==19629== ==19629== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==19629== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==19629== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==19629== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==19629== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==19629== by 0x4010732: call_init (dl-init.c:72) ==19629== by 0x4010732: _dl_init (dl-init.c:119) ==19629== by 0x40151FE: dl_open_worker (dl-open.c:522) ==19629== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==19629== by 0x40147C9: _dl_open (dl-open.c:605) ==19629== by 0x544CF95: dlopen_doit (dlopen.c:66) ==19629== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==19629== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==19629== by 0x544D734: _dlerror_run (dlerror.c:162) ==19629== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==19629== ==19629== ==19629== HEAP SUMMARY: ==19629== in use at exit: 4,607,714 bytes in 3,908 blocks ==19629== total heap usage: 119,207 allocs, 115,299 frees, 58,513,773 bytes allocated ==19629== ==19629== LEAK SUMMARY: ==19629== definitely lost: 0 bytes in 0 blocks ==19629== indirectly lost: 0 bytes in 0 blocks ==19629== possibly lost: 182,191 bytes in 111 blocks ==19629== still reachable: 4,425,523 bytes in 3,797 blocks ==19629== suppressed: 0 bytes in 0 blocks ==19629== Rerun with --leak-check=full to see details of leaked memory ==19629== ==19629== For counts of detected and suppressed errors, rerun with: -v ==19629== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2503 from 173) ================================================================================ 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 06:25:26) ===