!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MendelevHanSon_2007_VFe__MO_249706810527_005 Supported species : Fe V random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 2.22657662277 Forces: 1 -6.68799206e+00 -5.64227489e+00 -1.07530502e+01 2 -1.02041470e+01 1.73311835e+01 -7.43196802e+00 3 9.99579464e+00 -9.70314026e+00 1.08443310e+00 4 -6.46912330e+00 8.52716954e+00 3.71139156e+00 5 1.22253794e+01 -2.04890060e+01 1.82811748e+00 6 2.48538214e+00 1.26662660e+00 -3.45116028e+00 7 3.56813356e+00 -3.17841163e+01 -3.61701612e+01 8 -1.70948834e+01 -1.28520179e+01 -1.06697159e+01 9 -1.05435106e+01 -7.70330204e+00 -1.79527206e+01 10 -5.57265448e+00 1.79490587e+01 -1.98680004e+01 11 -4.37580084e+00 -1.48673723e+01 1.59872379e+01 12 -7.61873409e+00 1.03738713e+01 8.17146469e+00 13 -1.01846351e+01 -1.43964047e+01 -4.62127167e+01 14 5.48283443e+00 7.15860621e+00 -4.48896832e+00 15 4.08206068e+01 -2.49432196e+00 1.57724957e+01 16 4.98525496e+00 2.85614424e+01 1.81494230e+01 17 -1.44059263e+01 -9.59349488e+00 -5.78634264e+00 18 6.98087759e+00 1.05108370e+01 -3.12353756e+00 19 4.40677815e+00 -9.02097525e+00 8.16823894e+00 20 -3.35958126e+00 8.31073860e+00 1.07084809e+01 21 -1.55818090e+01 -1.06570212e+01 6.72885988e+00 22 2.41473776e+01 2.38901349e+01 2.56726704e+01 23 8.18455491e+00 -3.86161023e+00 9.07332927e+00 24 -5.58407893e+00 7.42655966e-01 4.98468635e+00 25 -8.44357817e+00 -8.26838515e+00 -8.63246028e+00 26 -4.48055251e+00 1.55019478e+01 -9.66953168e+00 27 2.18397297e+01 -3.74129726e+01 1.59662612e+01 28 -3.35529877e+01 3.17264080e+01 4.46142247e+00 29 -8.99728412e+00 1.10216989e+00 1.21605996e+01 30 5.70240279e+00 9.98434961e+00 -1.80168646e+00 31 1.43810193e+01 -6.12351642e+00 1.11361863e+01 32 7.95115289e+00 1.19327319e+01 1.22467218e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 51.0601104985 Forces: 1 3.54034907e+00 -9.43973559e+00 -4.43387023e+00 2 -1.58234550e+01 1.84599983e+01 1.22774904e+00 3 1.50606093e+01 1.99902889e+00 4.75569539e+00 4 3.89293355e-01 1.12497174e+01 6.19317033e-01 5 2.31298990e+01 -3.79454733e+00 3.09523901e+00 6 -6.82367886e+00 2.37210237e+01 2.71486170e+01 7 -1.38394335e+00 -3.37017506e+01 -4.22726127e+01 8 -1.95247423e+01 -1.25304288e+01 -1.13842398e+01 9 -2.82484866e+01 -2.01964998e+01 1.26085850e+01 10 -1.69357081e+01 6.55199373e+00 -1.35541820e+01 11 -4.29153858e+00 -1.73353001e+01 1.86213472e+01 12 6.09832890e+00 -6.91759748e-01 2.13162803e+01 13 -8.89450528e+00 -1.87586011e+01 -4.38621019e+01 14 -1.52264085e+01 7.98412801e+00 -1.75209301e+01 15 4.00409549e+01 -4.87261376e+00 1.72475025e+01 16 6.92749034e+00 2.67604671e+01 2.18137565e+01 17 3.68861028e+01 -5.10626526e+01 4.73831554e+00 18 8.97764831e+00 1.21270063e+01 -3.79009670e+00 19 5.19004367e+00 2.70601318e+00 9.13086197e+00 20 1.95277264e+01 2.50686902e+01 2.23236106e+00 21 -1.85442560e+01 -5.77724418e+00 8.10329961e+00 22 -2.60309164e+01 6.85364701e+01 1.66798411e+01 23 -1.02407989e+01 -3.38439747e+01 -1.04913264e+01 24 -6.19059372e+00 4.37749681e+00 -7.61859079e+00 25 -4.53920803e+00 -1.09711125e+01 -1.04547996e+01 26 -4.28238033e+00 7.17638805e+00 -1.56801837e+01 27 4.09031575e+01 -4.35829682e+01 -1.09493021e+01 28 -3.97130583e+01 3.74226955e+01 -2.72572375e+00 29 -9.28906719e+00 -1.09936482e-01 1.24482632e+01 30 1.55713733e+00 7.91766615e+00 -1.66194658e+00 31 1.32357792e+01 -6.73372411e+00 1.03529730e+01 32 1.45182253e+01 1.13440664e+01 4.25990186e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = V (Configuration in file "config-F-V.xyz") ----------------------------------------------------------------------------------------------------- Energy = -19.8875462359 Forces: 1 -5.32837829e+00 -7.30097266e+00 -2.75518222e+00 2 6.02354290e+00 2.04181519e+00 -5.74373230e+00 3 1.07352977e+00 -1.07025145e+01 -5.37616256e+00 4 -1.01520332e+01 4.70431700e+00 -3.45503807e+00 5 -5.73476981e+00 -1.07375612e+01 -9.72332135e+00 6 1.34124965e+01 -3.79047502e-02 -2.15934916e+01 7 3.01624406e+01 -3.46052585e+01 3.58704717e+00 8 -3.09601543e+01 1.26589990e+01 7.98519468e-02 9 -4.61856768e+00 4.93358663e+00 -1.33694202e+00 10 -6.62443292e-01 1.34879505e+00 -5.29120549e+00 11 -4.94497832e+00 1.32998392e+01 -1.55224417e+01 12 -4.06134028e+00 1.76594660e+00 8.29544112e-01 13 -1.37591530e+01 -3.53930312e+00 -1.70747673e+01 14 1.31864086e+01 1.44344650e+01 -7.96113353e+00 15 1.85959236e+01 7.45300582e+00 4.23870727e+00 16 -6.90261330e+00 8.24782288e+00 7.40042904e+00 17 -1.03662943e+01 -2.59333250e+01 -1.14672988e+01 18 -1.91244116e+00 -7.17057768e+00 1.03872921e+01 19 -4.57316926e-01 -6.51827276e+00 7.17287929e+00 20 -6.17485921e+00 1.89197582e+01 2.41308406e+01 21 -3.60946717e+00 -1.26293861e+01 5.20336768e-01 22 2.93897278e+01 -1.15968238e+01 3.90950026e+00 23 8.73889735e+00 -5.47530667e+00 5.07136048e+00 24 -5.98074478e+00 -3.71597869e+00 1.22701804e+01 25 -1.17358242e+01 6.19198652e-01 -4.87557772e+00 26 -2.52998956e+00 9.89610602e+00 -1.11605125e+01 27 1.38468062e+00 -8.53869573e+00 1.18842938e+01 28 -7.69295226e+00 5.60101263e+00 5.76113118e+00 29 -1.19649471e+01 1.92442080e+01 4.16702194e+00 30 6.97106378e+00 8.68821335e+00 3.41941761e+00 31 1.14746009e+01 7.53173176e+00 9.97348477e+00 32 9.13595569e+00 7.11306032e+00 8.53348848e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = V (Configuration in file "config-T-V.xyz") ----------------------------------------------------------------------------------------------------- Energy = 89.3744619857 Forces: 1 -7.07237391e-01 -1.71127114e+01 -7.78107242e-02 2 -2.56578135e-01 2.44379864e+01 2.95072602e+01 3 -4.52296818e+00 1.68843152e+00 -6.80872472e+00 4 2.58173505e+00 7.38149893e+00 -4.68853886e-01 5 2.95379255e+00 -1.03053029e+00 1.55372131e+01 6 1.97514458e+01 -1.76013313e+01 -1.13515280e+01 7 3.40412920e+01 -3.82829756e+01 1.85398763e+01 8 -4.19391027e+01 1.91475500e+01 1.12830222e+01 9 1.32521545e+01 9.88246351e+00 1.48796722e+01 10 -1.14888214e+01 -8.36455184e+00 1.09372099e+01 11 -7.65450927e+00 1.31609429e+01 -1.30330688e+01 12 6.77275373e+00 -1.62356195e+00 -7.13937798e-01 13 -5.18740628e+01 1.14275219e+01 1.97990175e+01 14 2.36710092e+01 1.93289887e+01 -8.51472843e+00 15 1.90676645e+01 1.09407847e+01 2.18520161e+01 16 -9.71368562e+00 -1.19336451e+01 2.04361840e+01 17 -1.52972413e+01 -2.65842030e+01 -1.59203207e+01 18 -9.75795195e-01 -4.12605340e+00 6.11212191e+00 19 -2.65631510e+01 9.00704720e+00 -2.39784481e+01 20 -1.40039127e+01 1.98631594e+01 3.88200008e+00 21 3.38842067e+00 -5.56120285e+00 -5.00782447e+00 22 2.73150395e+01 -1.09220267e+01 3.11269023e+00 23 1.77570242e+01 -8.05922229e+00 -3.49211131e-01 24 -1.30790631e+01 -6.64880923e+00 -1.72535044e+01 25 -5.98283127e+00 1.08579005e+00 -8.11059409e+00 26 -5.97641434e+00 -7.65133522e+00 -1.73712444e+01 27 -2.69679753e+00 -1.06985762e+01 1.12261049e-01 28 -1.19332998e+01 1.27072211e+01 -2.82696058e+00 29 -1.43226285e+01 2.30892592e+01 -4.03331525e+00 30 -1.28585765e+00 8.01163496e+00 9.33665404e+00 31 4.20975187e+01 1.66305130e+01 -4.25599242e+01 32 2.76241077e+01 -3.15900572e+01 -6.94719924e+00 MIXED STRUCTURE (pbc=False)-- Species = Fe V (Configuration in file "config-F-FeV.xyz") ----------------------------------------------------------------------------------------------------- Energy = 14.4714169052 Forces: 1 -7.13387820e+00 -1.62162281e+01 -1.17429873e+01 2 2.08291870e+01 -3.98903294e+00 -1.81274213e+01 3 9.18526786e+00 -6.54096419e+00 -2.68596004e-02 4 -1.93634783e+01 5.40459818e+00 1.96819331e+01 5 -1.88037441e+01 -2.80175370e+01 -1.01180362e+01 6 7.86810133e+01 -4.20213986e+01 -3.47949959e+01 7 2.56025997e+01 -3.66553553e+01 -1.14511465e+01 8 -5.48119902e+01 -2.01611047e-02 1.57944469e+01 9 -1.95561615e+01 -3.15170583e+00 -1.74056351e+01 10 1.76661643e+01 1.32151513e+01 -2.94910133e+01 11 2.88896770e+01 -4.08910686e+01 1.40952348e+01 12 -4.82382752e+01 4.79773723e+01 2.08463060e+01 13 -6.03534022e+01 3.96935425e+01 -4.60946878e+01 14 1.64442035e+01 1.36334787e+01 -1.94574702e+01 15 4.05995648e+01 2.11604647e+01 2.23446650e+01 16 -1.22293466e+01 3.27216977e+01 2.92639062e+00 17 -9.97675564e+00 -3.27143692e+00 1.13726967e-01 18 -4.39094227e+00 -8.29055332e+00 -1.33799031e+01 19 -5.02302694e+00 -5.47781154e+00 8.32589117e+00 20 -4.49805062e+00 4.15893361e+00 6.92572150e+00 21 -1.13964906e+01 -1.60842588e+01 -1.12424527e+01 22 3.18962033e+01 5.38125706e+00 2.67144718e+01 23 1.67691075e+01 -7.68648943e+00 1.79434891e+01 24 -1.55219067e+01 -6.44127851e+00 1.54473212e+01 25 -4.76083711e+00 -6.58008276e+00 4.16815794e+00 26 -6.54202972e+00 8.56437868e+00 -2.60299529e+00 27 -1.49484391e+01 -4.41671095e-01 1.24609767e+01 28 -1.14114360e-01 2.20956957e+00 3.24370202e+00 29 -1.50428113e+01 -1.95658640e+00 6.82303858e+00 30 1.56346515e+01 1.41384024e+01 2.55087673e+00 31 1.97494810e+01 1.22121128e+01 1.23259938e+01 32 1.07585597e+01 1.32626610e+01 1.32032604e+01 MIXED STRUCTURE (pbc=True)-- Species = Fe V (Configuration in file "config-T-FeV.xyz") ----------------------------------------------------------------------------------------------------- Energy = 216.056929552 Forces: 1 -7.08569844e+00 -2.11322225e+01 -1.37611329e+01 2 3.23662069e+01 -1.81620438e+01 1.69847350e+00 3 1.81937031e+01 3.58801710e+01 -5.13173377e+00 4 8.57567828e+00 9.72561401e-01 3.67036829e+01 5 -6.13123502e+01 -7.81896156e+01 8.21223767e+00 6 1.88899406e+02 -8.05169300e+01 6.64125847e+00 7 2.50442089e+01 -5.36333244e+01 -1.40569691e+01 8 -9.98706526e+01 -1.32700494e+01 7.22475763e+01 9 -2.05389248e+00 8.21003785e+00 -2.14496825e+01 10 1.08767363e+01 1.98412773e+01 -2.12333354e+01 11 4.47487787e+01 -6.06376474e+01 2.07393808e+01 12 -8.19259065e+01 5.03497193e+01 4.31651588e+01 13 -1.41320335e+02 1.42124606e+02 1.86624652e+01 14 3.89253338e+01 5.19946318e+01 -4.50592363e+00 15 4.76655856e+01 6.99650020e+01 8.54898537e+01 16 -1.62504176e+01 3.80930914e+01 7.89884187e+00 17 1.02579354e+01 -2.32838756e+00 9.52500059e+00 18 -9.28554808e+00 -7.70122330e+00 -1.87985979e+01 19 -3.56454474e+01 5.59623956e+01 4.73713465e+01 20 2.10285650e+01 -5.35159332e+00 -2.70441104e+01 21 1.05585769e+01 4.17123456e+00 -2.15475879e+01 22 2.89144209e+01 1.00837409e+01 2.65485172e+01 23 2.82950607e+01 -4.43705503e+01 -7.21666450e-01 24 -9.00687667e+01 -1.00015809e+02 -1.30905704e+02 25 2.86685362e+01 -2.72314839e+01 8.78402026e+00 26 -1.83389096e+01 -5.05689189e+01 -3.79971177e+01 27 -4.72051354e+01 -1.57382234e+01 -2.33966728e+01 28 -1.36905283e+00 7.67878009e+00 -5.07153489e+00 29 -2.64125765e+01 -1.05799310e+01 -9.99478751e+00 30 -2.45111193e+00 3.35732552e+01 1.28401746e+00 31 5.77139093e+01 4.54887979e+01 -4.20190922e+01 32 3.98631597e+01 1.50386513e+01 2.66381772e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2543== Memcheck, a memory error detector ==2543== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2543== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==2543== Command: python runner2.py EAM_Dynamo_MendelevHanSon_2007_VFe__MO_249706810527_005 ==2543== ==2543== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==2543== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==2543== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2543== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2543== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2543== by 0x4010732: call_init (dl-init.c:72) ==2543== by 0x4010732: _dl_init (dl-init.c:119) ==2543== by 0x40151FE: dl_open_worker (dl-open.c:522) ==2543== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2543== by 0x40147C9: _dl_open (dl-open.c:605) ==2543== by 0x544CF95: dlopen_doit (dlopen.c:66) ==2543== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2543== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==2543== by 0x544D734: _dlerror_run (dlerror.c:162) ==2543== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==2543== ==2543== ==2543== HEAP SUMMARY: ==2543== in use at exit: 39,677,093 bytes in 4,275 blocks ==2543== total heap usage: 192,977 allocs, 188,702 frees, 113,062,493 bytes allocated ==2543== ==2543== LEAK SUMMARY: ==2543== definitely lost: 0 bytes in 0 blocks ==2543== indirectly lost: 0 bytes in 0 blocks ==2543== possibly lost: 182,735 bytes in 112 blocks ==2543== still reachable: 39,494,358 bytes in 4,163 blocks ==2543== suppressed: 0 bytes in 0 blocks ==2543== Rerun with --leak-check=full to see details of leaked memory ==2543== ==2543== For counts of detected and suppressed errors, rerun with: -v ==2543== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2518 from 172) ================================================================================ 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.