!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhangAshcraftMendelev_2016_NiNb__MO_047308317761_000 Supported species : Nb Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Nb (Configuration in file "config-F-Nb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1477.03370475 Forces: 1 -6.71946869e+01 -7.17544509e+01 -7.27447973e+01 2 -9.03773856e+01 -1.07853583e+02 -2.53127766e+02 3 -8.31592385e+01 -2.44445171e+02 -7.42461554e+01 4 -2.26309449e+02 -6.03287852e+01 -5.94847276e+01 5 2.01005189e+01 -1.81854319e+02 -1.34034986e+02 6 1.24711880e+02 -7.09313155e+01 -1.50900240e+02 7 1.68041080e+02 -2.77046484e+02 -8.18138936e+01 8 2.32011092e+02 -3.93848894e+02 -2.33665294e+02 9 -1.51126632e+02 -6.88086251e+00 -1.94349753e+02 10 -8.30961085e+01 2.14749896e+02 -2.27692351e+02 11 -4.23025647e+02 1.03300356e+02 -2.75267931e+02 12 -1.77450133e+02 1.46760553e+02 -2.71429478e+01 13 1.08214594e+02 7.47634767e+01 -5.19771761e+02 14 1.28338883e+02 1.26904334e+02 -1.14707452e+02 15 5.34015138e+02 1.14725145e+02 -1.09445410e+02 16 8.33417656e+01 5.50920175e+02 -8.97504544e+01 17 -1.40234030e+02 -1.12576603e+02 7.88394607e+00 18 -2.50488646e+02 -2.39420207e+02 2.27048578e+02 19 -1.42817536e+01 -1.42151517e+02 1.26000149e+02 20 -1.10653171e+02 -8.05976134e+00 1.13565178e+02 21 5.96776212e+01 -2.76859742e+02 1.09657490e+02 22 2.95958211e+02 -8.24552016e+01 1.40539771e+02 23 6.83321709e+01 -6.52647084e+01 7.76755476e+01 24 3.85754821e+01 -8.00692859e+01 2.38575490e+02 25 -3.50904106e+02 7.91078296e+01 1.01322204e+02 26 -1.50942208e+02 3.65894909e+02 1.42249540e+02 27 -9.92196946e+01 -9.27011177e+00 2.69283156e+02 28 -1.09133220e+02 9.11489912e+01 9.20732485e+01 29 2.30471268e+02 2.05033514e+02 4.32687054e+02 30 1.96039784e+02 1.82320434e+02 7.95014331e+01 31 1.95303388e+02 2.63041728e+01 2.27686499e+02 32 4.44632323e+01 1.49137215e+02 2.32396638e+02 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = 16.3894189045 Forces: 1 -4.58104294e+00 3.15170134e-01 -5.55275080e+00 2 4.59978626e-01 -1.17200690e+01 -1.21877712e+01 3 -9.40695265e+00 -7.38037265e+00 -2.19345413e+01 4 -6.03019659e+00 -2.52620716e+01 2.40303828e+01 5 6.39673460e-01 -1.92053479e+00 -5.06811418e-01 6 5.56335549e+00 -5.30483109e+00 -1.75745471e+00 7 2.57238070e+00 -1.04473669e+01 -1.05981670e+01 8 6.42182528e+01 -1.74808064e+01 -4.55904621e+01 9 -1.07632837e+01 1.36526115e+01 -4.31864779e+01 10 -3.64499310e-01 4.41631548e+00 -7.97602827e+00 11 -4.02259880e+00 7.31193967e+00 -5.93191829e+00 12 -1.35448558e+01 2.17471022e+01 1.31434811e+01 13 -2.95237200e+01 -1.43915845e+01 -3.20660720e+01 14 3.63901658e+01 5.85791209e+01 -5.10039665e+01 15 2.21215271e+01 -7.02346909e+01 4.41274687e+01 16 -1.53526472e+01 3.26003916e+01 1.07340722e+01 17 -1.24206002e+01 -5.57491062e-02 1.02268502e+01 18 -5.76734615e+01 -2.07662303e+01 5.64096222e+01 19 -1.38411946e+00 -2.14190883e-01 5.14628618e-03 20 -8.90174484e+00 -2.53032116e+01 3.00230697e+01 21 2.42781710e+01 -1.17887372e+00 2.04842316e+01 22 9.02480307e+00 1.69564781e+01 -1.14325393e+01 23 2.93227705e+00 -2.02448304e+01 1.59139850e+01 24 -1.61601402e+01 -3.28547446e+01 2.54373286e+01 25 -2.20889325e+01 2.76800338e+01 -3.67113572e+01 26 -5.53823189e-01 1.15742889e+01 -6.30143728e+00 27 -1.51144491e+01 2.68710604e+00 4.50279794e+01 28 -1.13802340e-01 7.89033952e-01 6.22068709e-01 29 -2.48025318e+01 1.01750259e+01 -8.19152584e+01 30 9.33033098e+00 2.82176003e+01 1.89598868e+01 31 8.33358282e+01 1.00147210e+01 5.10187239e+01 32 -8.06334223e+00 1.80432190e+01 8.48871646e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = 70.3458226083 Forces: 1 -1.99282368e+01 1.90662184e+01 1.92444462e+00 2 -6.63115785e+00 -1.20303677e+01 -4.88731990e-01 3 -1.44441988e+01 1.68437792e+01 -3.91687932e+01 4 -2.99779581e-02 -2.42638561e+01 2.09781226e+01 5 2.30633077e+01 1.65251868e+01 2.50873201e+01 6 1.51111566e+01 1.60497924e+00 4.45797933e+01 7 -2.31234353e+01 -1.00538807e+01 -3.23805697e+01 8 6.49784825e+01 -1.99675167e+01 -4.60050346e+01 9 -6.73132592e-01 1.50654222e+01 -3.87695270e+01 10 1.01420438e+01 -2.22690340e+01 4.32809694e+00 11 -5.66985393e+00 8.13993545e+00 -6.26397506e+00 12 -1.12182421e+01 1.78314039e+01 1.52224237e+01 13 -3.38342640e+01 -1.41183785e+01 1.28493368e+01 14 3.71480245e+01 6.34383264e+01 -4.27386439e+01 15 1.55671291e+01 -6.83508123e+01 4.83358626e+01 16 -1.20904696e+01 2.22420742e+01 1.74442883e+01 17 2.59632135e+01 -1.57865744e+01 2.82126698e+01 18 -5.92321079e+01 -2.26521969e+01 5.68962687e+01 19 -2.12020321e+01 1.20551832e+01 -3.70550962e+01 20 6.83599349e+00 -2.76527347e+01 1.88081243e+01 21 4.30638673e+01 2.33367557e+01 1.82252211e+01 22 -1.10002133e+01 2.59484631e+01 -9.91844895e+00 23 2.15126599e+00 -4.13968391e+01 -5.74520271e+00 24 -3.19978067e+01 -4.81371613e+01 -1.24138693e+01 25 -2.04185965e+01 2.90647499e+01 -3.66659511e+01 26 -1.66471918e+01 -2.95458364e+01 1.59852503e+01 27 -1.78791667e+01 3.26403545e+00 3.92538767e+01 28 -6.32439683e+00 2.79369169e+00 -1.14796060e+01 29 -2.48957950e+01 1.08983515e+01 -8.34908194e+01 30 9.61982350e+00 2.84360127e+01 2.04688623e+01 31 9.14127346e+01 1.34789021e+01 3.22274980e+01 32 -7.81676683e+00 2.61917177e+01 -1.82431912e+01 MIXED STRUCTURE (pbc=False)-- Species = Nb Ni (Configuration in file "config-F-NbNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 146.044014448 Forces: 1 -7.09265741e+01 -8.67015227e+00 -4.26631717e+01 2 2.09737471e-01 -1.10218043e+01 -6.12185895e+01 3 4.87188092e+01 -5.58458074e+01 2.84075055e+01 4 -7.53043269e+01 -5.36037755e+01 -3.67614367e+01 5 -2.20270452e+01 -1.82316982e+01 -4.60120914e+01 6 2.83961065e+01 2.13926641e+01 -1.37671925e+01 7 4.02086054e+01 -3.84489038e+01 7.52091287e+00 8 3.56180719e+01 -3.43333590e+01 -1.07996913e+02 9 -1.25616203e+01 -1.05020049e+01 -3.20939773e+01 10 -3.97475217e+00 1.84484706e+01 -1.83112410e+01 11 -2.15445643e+00 6.42356771e+01 -3.25960765e+01 12 -2.72920009e+01 4.50970631e+01 5.06713479e+00 13 7.39882302e+00 6.69889423e-01 -1.78287507e+01 14 5.90600309e+01 1.42717856e+01 -6.04201818e+01 15 3.83908004e+01 3.96786520e+00 -2.17505017e+01 16 -4.73412214e+01 3.63987343e+01 3.23113381e+01 17 -1.09355285e+01 -2.28644603e+01 -2.51979338e+00 18 -4.69124169e+01 -4.67735702e+01 4.93489954e+01 19 -5.82603269e+00 -3.17264858e+01 2.10709363e+01 20 -2.46964929e+01 -5.77616344e+00 3.80442743e+01 21 -5.10807186e+00 -7.96074147e+01 2.68764999e+01 22 7.80287976e+01 -1.77079937e+01 -4.46827617e+00 23 1.22325181e+01 -2.48961384e+01 3.17829859e+01 24 7.39339537e+00 -1.84072072e+01 5.71148649e+01 25 -7.43581050e+01 3.39957507e+01 2.63007545e+01 26 3.58647288e+01 3.38809648e+01 -4.09060018e+01 27 -2.60296153e+01 1.56102108e+01 6.29973432e+01 28 -5.11399810e+01 7.88196853e+00 5.04815381e+01 29 4.63360617e+01 8.96656768e+01 2.93766013e+01 30 2.77940526e+01 2.91639144e+01 4.11773433e+00 31 3.10420726e+01 1.64510672e+01 3.64598453e+01 32 9.89563021e+00 4.72852365e+01 3.20349299e+01 MIXED STRUCTURE (pbc=True)-- Species = Nb Ni (Configuration in file "config-T-NbNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6673.94388022 Forces: 1 -3.65581211e+01 1.27684671e+02 -6.80688949e+01 2 1.26858371e+01 1.06944236e+02 -6.18553393e+01 3 2.87013346e+01 1.81775832e+02 2.25250528e+02 4 1.78784130e+02 4.28827111e+01 -2.40625758e+02 5 -1.77413828e+02 1.85576899e+02 -5.24278137e+01 6 3.91986290e+00 2.02222278e+02 -7.89402675e-01 7 7.05872100e+01 3.81072394e+02 1.25597046e+02 8 -7.88816303e+01 9.94761552e+01 -1.51112858e+02 9 4.27476139e+01 -1.40706467e+02 -4.34174117e+01 10 -3.73846131e+01 -2.63280344e+02 -3.47774920e+01 11 1.32747639e+02 3.25412350e+01 -7.09697420e+01 12 2.59657403e+02 -1.43209880e+02 -1.25125450e+01 13 -1.82834375e+01 -1.42459579e+02 6.03295280e+01 14 9.96563357e+01 -4.23931990e+02 -3.52558817e+02 15 -7.56480659e+01 -1.28956699e+02 -1.12072299e+02 16 -4.36306721e+02 -3.65975891e+02 1.89010915e+02 17 2.07126584e+02 2.53051408e+01 -7.60604636e+00 18 2.83580620e+01 -5.33791815e+00 3.99179169e+01 19 -9.42137831e+00 1.66148197e+02 -1.45916576e+02 20 2.36705831e+02 1.34356412e+02 2.70785669e+02 21 -1.97271926e+02 -2.11034377e+01 5.45228979e+01 22 -1.62615061e+02 1.22919333e+02 -9.03128313e+00 23 -3.84927774e+01 9.16209183e+01 1.34684474e+01 24 -8.95693826e+01 5.20152096e+01 8.03613193e+01 25 2.15218650e+02 8.82941842e+01 2.99066287e+01 26 2.06809406e+02 -1.72452952e+01 -9.84417390e+01 27 4.14450158e+01 -1.32478823e+02 7.48722012e+01 28 5.21846882e+01 -7.93370460e+01 1.74555565e+02 29 -2.48639251e+02 5.52379242e+01 -4.69675169e+01 30 -7.93354975e+01 -1.22304436e+02 7.20349757e+01 31 -6.03450266e+01 1.89053233e+01 1.64312123e+02 32 -7.11688858e+01 -1.28651248e+02 -6.57742268e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==7680== Memcheck, a memory error detector ==7680== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==7680== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==7680== Command: python runner2.py EAM_Dynamo_ZhangAshcraftMendelev_2016_NiNb__MO_047308317761_000 ==7680== ==7680== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==7680== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==7680== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7680== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7680== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==7680== by 0x4010732: call_init (dl-init.c:72) ==7680== by 0x4010732: _dl_init (dl-init.c:119) ==7680== by 0x40151FE: dl_open_worker (dl-open.c:522) ==7680== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7680== by 0x40147C9: _dl_open (dl-open.c:605) ==7680== by 0x544CF95: dlopen_doit (dlopen.c:66) ==7680== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==7680== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==7680== by 0x544D734: _dlerror_run (dlerror.c:162) ==7680== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==7680== ==7680== ==7680== HEAP SUMMARY: ==7680== in use at exit: 39,893,152 bytes in 4,274 blocks ==7680== total heap usage: 193,714 allocs, 189,440 frees, 113,615,207 bytes allocated ==7680== ==7680== LEAK SUMMARY: ==7680== definitely lost: 0 bytes in 0 blocks ==7680== indirectly lost: 0 bytes in 0 blocks ==7680== possibly lost: 183,295 bytes in 113 blocks ==7680== still reachable: 39,709,857 bytes in 4,161 blocks ==7680== suppressed: 0 bytes in 0 blocks ==7680== Rerun with --leak-check=full to see details of leaked memory ==7680== ==7680== For counts of detected and suppressed errors, rerun with: -v ==7680== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2521 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.