!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : SW_WangStroudMarkworth_1989_CdTe__MO_786496821446_000 Supported species : Cd Te random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Cd (Configuration in file "config-F-Cd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1351.14770745 Forces: 1 -3.50201280e+01 -3.62073486e+01 -3.89719924e+01 2 -2.63156903e+01 -3.67128867e+01 -1.00286437e+02 3 -1.66948066e+01 -8.85955919e+01 -2.48512104e+01 4 -8.67375207e+01 -1.25622712e+01 -1.40050996e+01 5 1.20687690e+01 -7.92781374e+01 -6.22532726e+01 6 4.94503101e+01 -1.51893261e+01 -6.14558552e+01 7 6.58734646e+01 -1.08720548e+02 -7.68843137e+01 8 3.15882687e+01 -8.00320883e+01 -4.08944953e+01 9 -5.95262727e+01 1.39886641e+01 -7.83486616e+01 10 -3.36300526e+01 8.60678034e+01 -9.18023241e+01 11 -6.54966169e+01 1.45113417e+01 -4.25593106e+01 12 -7.04370979e+01 5.80284525e+01 -2.05360219e+01 13 2.80747230e+01 1.59676704e+01 -1.40604339e+02 14 5.18558140e+01 5.07226591e+01 -4.62503727e+01 15 1.39900350e+02 2.80663486e+01 -2.01212964e+01 16 3.62336212e+01 1.29317027e+02 -2.42780748e+01 17 -6.17523484e+01 -4.73158741e+01 9.91359847e-03 18 -5.36101526e+01 -5.59509156e+01 5.39240703e+01 19 1.46084941e+01 -6.42045303e+01 4.46810015e+01 20 -4.98206121e+01 1.11927867e+01 5.34166814e+01 21 -1.59463345e+01 -9.57033152e+01 5.04176992e+01 22 1.19451292e+02 1.80578066e+01 5.90263374e+01 23 3.80712772e+01 -2.64985337e+01 5.34429939e+01 24 1.55362653e+01 -2.86792356e+01 9.61967548e+01 25 -1.13338683e+02 2.30491575e+01 3.30761192e+01 26 -4.96971242e+01 1.20974892e+02 3.74117072e+01 27 -1.77809736e+01 -1.94024059e+01 9.13295017e+01 28 -6.77426935e+01 5.67402342e+01 4.17352331e+01 29 3.14457212e+01 1.90535000e+01 6.98524000e+01 30 7.72162841e+01 6.98980249e+01 2.88478016e+01 31 8.04263735e+01 1.43364448e+01 8.10464045e+01 32 3.17460794e+01 6.50801959e+01 8.96884569e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cd (Configuration in file "config-T-Cd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3995.07735411 Forces: 1 3.39353169e+01 -7.45645355e-01 1.82345042e+01 2 -2.52948974e+01 -6.33509158e+00 2.16142404e+01 3 4.01129910e+01 4.57784377e+01 7.03025457e+00 4 4.87040505e+01 3.08357574e+01 9.35646391e+00 5 -3.17737252e+00 2.59681269e+01 -3.40338409e+01 6 -5.54115433e+01 5.26431609e+01 -7.51855460e+00 7 -8.05144209e+00 -3.41900747e+01 -6.44940797e+01 8 -4.40120095e+01 -3.69700320e+01 2.83121763e+00 9 -4.20166196e+01 -1.06525731e+01 3.33685067e+00 10 -3.14370383e+01 1.48656423e+01 -2.32555341e+01 11 -1.34626500e+01 -4.06443349e+01 2.17781126e+01 12 1.80583125e+01 -4.37440195e+01 5.48023922e+00 13 -4.54166336e+00 -2.85646866e+01 -7.56465689e+01 14 -2.64639861e+01 -2.67316806e+01 -5.10144929e+01 15 6.44836247e+01 -1.37841999e+01 2.33323500e+01 16 1.88925765e+01 1.57896729e+01 8.12488844e+00 17 4.45655471e+01 -6.71091186e+00 -1.13645440e+01 18 1.03956521e+01 1.22705874e+01 8.01196462e+00 19 9.75666925e+01 2.42655715e+01 1.97450995e+00 20 4.93296381e+01 1.15313114e+02 -1.26650580e+01 21 -9.82192036e+01 1.31317848e+01 3.50004049e+01 22 -1.49291678e+01 1.08440202e+02 6.17451909e+01 23 -7.05532960e+01 -3.91171595e+01 -7.20534221e+00 24 2.19126099e+01 5.05892196e+00 -4.67269885e+01 25 -1.28082348e+01 -2.04763130e+01 2.35579871e+01 26 -2.07137388e+01 8.80343859e+00 -4.68849512e+00 27 4.08953512e+01 -6.84700158e+01 -2.07713326e+01 28 -4.73692808e+01 -2.12356219e+01 4.07277293e+00 29 -1.39561197e+01 -3.57759565e+01 4.24215939e+01 30 -2.13581446e+01 -3.06578124e+01 3.88176374e+01 31 2.26212720e+01 -8.62124457e+00 2.16049165e+01 32 4.23027736e+01 2.62955473e-01 1.05873166e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Te (Configuration in file "config-F-Te.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1289.10608195 Forces: 1 -2.60090299e+01 -2.99902900e+01 -2.19582931e+01 2 -1.61684915e+01 -3.93048412e+01 -8.42742599e+01 3 -3.55540150e+01 -7.94130555e+01 -1.98476394e+01 4 -9.97022078e+01 -5.00381346e+01 -1.58560829e+01 5 -1.08422595e+00 -5.95420412e+01 -6.53509618e+01 6 1.01460673e+02 -6.90804102e+00 -1.10274190e+02 7 7.22398397e+01 -6.39689359e+01 -2.91325139e+01 8 -1.95779301e+00 -2.49488666e+01 -2.32745646e+01 9 -5.07462289e+01 1.52560241e+01 -5.24120348e+01 10 -1.51686641e+01 5.23676860e+01 -5.39572448e+01 11 -4.30454552e+01 3.16868990e+01 -5.69844393e+01 12 -7.32093308e+01 8.15191759e+01 -4.01359215e+01 13 1.24906657e+01 1.35243220e+01 -1.04872880e+02 14 4.66319753e+01 5.72286613e+01 -7.36710113e+01 15 1.30280114e+02 -7.79577776e+00 -1.55051202e+01 16 -2.73848529e+01 1.36250725e+02 -3.19858648e+01 17 -3.54017666e+01 -4.30469265e+01 1.39236126e+01 18 -5.93269739e+01 -7.60316325e+01 3.21577860e+01 19 -2.59342280e+01 -5.08716693e+01 4.36928591e+01 20 -5.85742221e+01 -3.53462160e+01 5.44898596e+01 21 -1.44597807e+01 -1.24194945e+02 2.31575800e+01 22 1.40085813e+02 -2.94328517e+01 1.34616828e+01 23 4.67869896e+01 -6.06234931e+01 6.48978560e+01 24 -2.31698304e+01 -5.30714893e+01 1.31329739e+02 25 -9.14482159e+01 -1.26242331e+01 6.77521822e+00 26 -1.06725409e+01 1.15876798e+02 6.26482982e+00 27 -2.05680522e+01 4.56877914e+00 1.08554423e+02 28 -6.29414432e+01 8.42389923e+01 8.41269008e+01 29 3.08446050e+01 4.94479545e+01 2.42748497e+01 30 5.91708245e+01 7.39732100e+01 1.91945614e+01 31 1.25998103e+02 5.77094183e+01 9.17760191e+01 32 2.65377470e+01 7.35047951e+01 8.14152453e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Te (Configuration in file "config-T-Te.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3814.34333957 Forces: 1 4.34351042e+01 2.94975483e+01 -8.24577183e+00 2 -4.16747120e+00 -5.53651223e+01 2.15570821e+01 3 -6.02635825e+01 6.85094941e+01 -1.64723459e+01 4 3.12310035e+01 -4.03635854e+01 -7.40937574e+00 5 -3.97773022e+01 -3.73505731e+00 2.22995954e+01 6 6.95638755e+01 2.74580123e+00 -4.88397659e+01 7 1.40739752e+01 2.88353180e+01 -6.48067228e+01 8 -8.53310524e+01 2.70914698e+01 1.76001506e+01 9 2.12994621e+01 -1.30236955e+01 2.56090948e+01 10 -1.08400941e+01 5.98400859e+01 4.80189019e+01 11 6.72415978e-02 -1.90504424e+01 -1.18969486e+01 12 2.60914246e+01 2.70149317e+01 -4.15500733e+01 13 2.01964411e+00 -2.95655763e+01 4.05784395e+01 14 4.50284431e+01 3.49544626e+01 -3.26084403e+01 15 5.30755329e+01 -7.36712877e+01 2.37946906e+01 16 -8.36427178e+01 3.15753147e+01 -5.67418784e+00 17 6.46879159e+01 5.41095247e+01 2.59463671e+01 18 -2.09917051e+01 -3.84060260e+01 -4.36180029e+01 19 -5.07502003e+01 5.90708168e+01 2.25086537e+01 20 5.00897112e+01 -4.89098189e+01 1.12977442e+01 21 -9.19334662e+01 7.81889472e+00 8.35994072e+00 22 7.34016639e+01 -1.51657672e+00 -3.37261894e+01 23 4.11340401e+01 8.16553413e+00 2.96833699e+01 24 -6.10078924e+01 -4.34914353e+01 3.36402420e+01 25 1.40730364e+01 -7.13277781e+01 -2.72204286e+01 26 -1.50344817e+01 1.03820604e+01 -3.48847996e+01 27 -2.51515264e+01 -4.98949462e+01 -3.71615069e+01 28 -3.46362475e+01 5.74204022e+01 4.65119188e+01 29 -3.12834876e+01 -3.30276510e+01 -3.49920156e+01 30 2.22924756e+01 -4.71703447e+01 3.75222658e+01 31 5.16303518e+01 3.48743114e+01 2.11984860e+01 32 -8.38367434e+00 2.66133732e+01 1.29796320e+01 MIXED STRUCTURE (pbc=False)-- Species = Cd Te (Configuration in file "config-F-CdTe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1374.68145574 Forces: 1 -3.99540241e+01 -4.31769611e+01 -3.85564840e+01 2 -1.69913657e+01 -3.60526280e+01 -1.19077221e+02 3 -2.12037972e+01 -1.03151536e+02 -2.05515150e+01 4 -1.05584331e+02 -4.62413338e+01 -2.48775632e+01 5 5.24654313e+00 -7.34251997e+01 -5.40248804e+01 6 5.41482277e+01 -1.55066258e+01 -6.95214827e+01 7 5.19251138e+01 -4.85439964e+01 -8.25480876e+00 8 5.38980338e+01 -6.51543053e+01 -6.24551593e+01 9 -6.43181656e+01 3.76629706e+01 -7.53927468e+01 10 -2.07908276e+01 4.72085497e+01 -6.19982224e+01 11 -4.60292805e+01 4.66213134e+01 -1.05144905e+02 12 -8.17940423e+01 9.19325144e+01 -3.82986443e+01 13 2.72989399e+01 1.81396945e+01 -1.18901960e+02 14 4.46666426e+01 3.68768331e+01 -3.49728986e+01 15 1.19195535e+02 1.76485377e+01 -2.85743367e+01 16 9.71370376e+00 1.11797199e+02 -3.05630143e+01 17 -6.80850695e+01 -6.99015025e+01 3.01154941e+01 18 -6.93859952e+01 -1.10268392e+02 4.98908740e+01 19 -2.11371883e+01 -6.34521897e+01 5.38352547e+01 20 -8.64540293e+01 -5.06925326e+01 7.94263148e+01 21 -8.34089169e+00 -9.48529999e+01 -1.23656043e+01 22 1.12372914e+02 -2.61807656e+01 2.15722785e+01 23 6.54317987e+01 -4.62526390e+01 7.89016087e+01 24 2.36788175e+01 -4.50221395e+01 1.18096981e+02 25 -1.24119187e+02 3.03086659e+01 2.09928654e+01 26 -2.55323554e+01 1.59043429e+02 3.82696696e+01 27 -2.73089817e+01 2.42353786e+01 1.17122063e+02 28 -4.69995328e+01 5.92944912e+01 5.72301734e+01 29 8.23453077e+01 5.01725607e+01 4.26958007e+01 30 8.57509899e+01 8.63659867e+01 2.29640345e+01 31 1.08995183e+02 3.73746362e+01 8.67020580e+01 32 2.93613142e+01 8.31929864e+01 8.57159765e+01 MIXED STRUCTURE (pbc=True)-- Species = Cd Te (Configuration in file "config-T-CdTe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3786.22183223 Forces: 1 3.64254841e+01 6.28865269e+00 -6.15359629e+01 2 8.13213716e-01 -3.01625381e+01 -1.81651376e+01 3 1.03220327e+01 -1.56581726e+01 2.33984140e+01 4 3.18199031e+01 -6.52619115e+01 1.88495818e+01 5 -3.19477706e+01 4.02600060e+01 -4.30035573e+01 6 2.38140522e+01 5.48482831e+00 -2.45397887e+00 7 -1.11186791e+00 7.17109063e+00 4.92724605e+01 8 -2.30682158e+01 -1.45632204e+01 -2.96800499e+00 9 3.63237788e+01 2.11553673e+01 -6.23775918e+01 10 -3.60779976e+01 2.80035030e+01 4.49274195e+01 11 2.89915596e+00 -1.21472344e+01 -4.89690501e+01 12 -5.88456888e-01 3.82868147e+01 -1.64424319e+01 13 -2.12019808e+01 -2.61002522e+01 -1.58360974e+01 14 1.57075363e+01 1.46728434e+01 -1.95212103e+01 15 -2.41381750e+01 6.96539017e+00 3.74285956e+01 16 -3.44401767e+01 1.28579262e+01 4.31431130e+01 17 1.77626329e+00 -2.85862945e+01 3.62459192e+01 18 -2.80380572e+01 -9.83498738e+01 2.56126709e+01 19 -3.86008989e+01 1.31409546e+01 -2.32086778e+01 20 3.24250561e+00 -7.53909757e+01 2.91842972e+01 21 -4.74835008e+01 9.38286998e+00 -3.37437465e+01 22 -2.24416626e+01 -4.93463963e+01 3.64380457e+01 23 7.04997359e+01 -6.22558565e+00 2.10919330e-01 24 -2.89049497e+01 -4.23981553e+01 -1.59171278e+01 25 2.07981724e+00 1.87187499e+01 1.16136950e+01 26 -1.29699747e+01 8.54469245e+01 4.03442620e+01 27 9.26928736e+00 -1.20788798e+01 2.00640502e+01 28 -3.04224265e+01 5.38051680e+01 -4.35769852e+01 29 3.41007571e+01 9.83954824e+00 -2.75066501e+01 30 1.83523743e+01 4.15582412e+01 3.44355066e+01 31 6.08066052e+01 1.33091911e+01 1.43703574e+01 32 2.31836088e+01 4.99214203e+01 -3.03130974e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2989== Memcheck, a memory error detector ==2989== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2989== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==2989== Command: python runner2.py SW_WangStroudMarkworth_1989_CdTe__MO_786496821446_000 ==2989== ==2989== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==2989== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==2989== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2989== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2989== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2989== by 0x4010732: call_init (dl-init.c:72) ==2989== by 0x4010732: _dl_init (dl-init.c:119) ==2989== by 0x40151FE: dl_open_worker (dl-open.c:522) ==2989== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2989== by 0x40147C9: _dl_open (dl-open.c:605) ==2989== by 0x544CF95: dlopen_doit (dlopen.c:66) ==2989== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2989== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==2989== by 0x544D734: _dlerror_run (dlerror.c:162) ==2989== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==2989== ==2989== ==2989== HEAP SUMMARY: ==2989== in use at exit: 4,581,409 bytes in 4,310 blocks ==2989== total heap usage: 188,927 allocs, 184,617 frees, 74,168,253 bytes allocated ==2989== ==2989== LEAK SUMMARY: ==2989== definitely lost: 0 bytes in 0 blocks ==2989== indirectly lost: 0 bytes in 0 blocks ==2989== possibly lost: 182,735 bytes in 112 blocks ==2989== still reachable: 4,398,674 bytes in 4,198 blocks ==2989== suppressed: 0 bytes in 0 blocks ==2989== Rerun with --leak-check=full to see details of leaked memory ==2989== ==2989== For counts of detected and suppressed errors, rerun with: -v ==2989== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2533 from 176) ================================================================================ 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.