Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:27:06) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_BereSerra_2006_GaN__MO_861114678890_000 Supported species : Ga N random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ga (Configuration in file "config-F-Ga.xyz") ----------------------------------------------------------------------------------------------------- Energy = 165.965103206 Forces: 1 -9.12719721e+00 -1.43469553e+01 -1.70804404e+01 2 -4.13740951e+00 6.67197950e+00 -2.15952055e+01 3 8.00819492e+00 -1.62486274e+01 1.05495622e+00 4 -1.80812096e+01 1.28320921e+01 5.45103634e+00 5 7.37243887e+00 -1.98357730e+01 -4.40444577e+00 6 1.24261108e+01 -4.66171939e+00 -1.51654014e+01 7 8.34284429e+00 -2.68884228e+01 -1.96428184e+01 8 -9.74890423e+00 -1.99694007e+01 -3.87146154e+00 9 -1.20066410e+01 -7.38451771e+00 -1.80988040e+01 10 -1.97528519e+00 2.26662689e+01 -2.88769284e+01 11 -2.40525814e+01 -2.07984921e+01 2.03919612e+00 12 -2.41659878e+01 1.44685231e+01 5.67292678e+00 13 7.12653710e+00 1.94100031e+00 -4.19011868e+01 14 9.35851883e+00 8.91792618e+00 -8.41854404e+00 15 4.31999802e+01 3.84146650e+00 -1.13963117e+01 16 9.27034333e+00 4.16330286e+01 -1.54110875e+00 17 -1.60601170e+01 -8.91135372e+00 3.39003084e+00 18 1.65479733e+00 -2.48306749e+00 -1.94774131e+00 19 3.00814025e-01 -1.58502403e+01 1.13428932e+01 20 -1.18505855e+01 3.20560471e+00 1.06107223e+01 21 -7.48645310e+00 -1.96011641e+01 5.80575906e+00 22 2.84315104e+01 8.35974477e+00 1.66455916e+01 23 6.28387108e+00 -2.67231291e+00 9.35206994e+00 24 4.42319377e+00 4.10911791e+00 1.37006429e+01 25 -2.18503754e+01 -2.48567102e+00 -7.09280870e+00 26 -7.50158612e+00 2.99651622e+01 9.67930384e+00 27 1.43018330e+00 -1.57030087e+01 2.50192117e+01 28 -2.17775213e+01 1.67275439e+01 1.13797663e+01 29 -3.61397892e+00 -1.07581899e+01 2.32486130e+01 30 2.11323517e+01 2.19296715e+01 3.31549337e+00 31 1.62042095e+01 -4.90703709e+00 2.34922136e+01 32 8.46993375e+00 1.62368236e+01 1.98327795e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ga (Configuration in file "config-T-Ga.xyz") ----------------------------------------------------------------------------------------------------- Energy = 408.545441924 Forces: 1 -2.02728455e+00 -8.02755183e+00 -2.36079043e+00 2 -1.24464667e+01 1.49638283e+01 1.75561155e+01 3 7.74890681e+00 1.11209014e+01 8.60261068e+00 4 1.48126881e+01 1.80923921e+01 1.20329621e+01 5 1.56808221e+01 -2.86777461e+00 9.14705850e+00 6 -1.08574332e+01 1.34164903e+01 -1.15534358e+01 7 -2.22420323e+01 -1.75163256e+01 -1.46932779e+01 8 -1.87863796e+01 -1.79717860e+01 2.16061951e+00 9 -6.28224045e+00 -1.35197662e+01 6.94122444e+00 10 6.62533792e+00 4.22825911e+00 -8.71273054e+00 11 -2.26287979e+01 -2.36856649e+01 4.29684559e+00 12 -8.27391633e+00 -6.77843521e+00 1.31126419e+01 13 1.18941235e+01 -2.68003662e+00 -2.07047791e+01 14 -1.37098624e+01 6.32428677e+00 -1.36511845e+01 15 2.37402133e+01 5.85243842e+00 -7.32991817e+00 16 1.09846274e+01 1.97186262e+01 2.55174122e+00 17 1.44059352e+01 -1.06023154e+01 5.38341996e+00 18 8.21766618e+00 -2.64908346e-01 -5.68633410e+00 19 8.80752672e-01 4.54364057e+00 -8.38690466e+00 20 1.16245007e+01 1.71169263e+01 -1.17126419e+01 21 -1.13904631e+01 1.18377394e+00 8.20225848e+00 22 1.68739886e+00 2.34384730e+01 1.38659873e+01 23 -2.82027809e+01 -1.78078616e+01 2.27784820e+00 24 2.07156370e+01 4.02643142e+00 -2.71354495e+01 25 -3.84345818e-01 -5.61142573e+00 -8.09115040e+00 26 -8.22335002e-01 1.02638443e+01 6.07644688e+00 27 6.94353582e+00 -2.27121906e+01 -4.72945564e+00 28 -2.57682899e+01 6.09768207e+00 -1.12311147e+01 29 -4.94145795e+00 -1.36763476e+01 2.27397381e+01 30 1.28968112e+01 2.31949700e+00 3.93039943e+00 31 2.67608294e+00 -2.69274375e+00 1.28169627e+01 32 1.72290466e+01 3.70764268e+00 4.28428680e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = N (Configuration in file "config-F-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -19.148173773 Forces: 1 2.82014563e+00 1.66098802e+00 2.06116494e+00 2 -1.92028252e+00 -1.92436476e+00 3.81045382e+00 3 -2.36213280e+00 2.67818300e+00 -3.00827136e+00 4 2.29550477e+00 -9.86089076e-01 -2.95729965e+00 5 2.28331447e+00 9.64729913e-01 1.33937702e+00 6 -9.65242207e-01 2.50971773e-01 2.21878366e+00 7 -1.44769092e+00 5.53483663e-01 -1.77109241e+00 8 -2.70200125e+00 2.70340256e+00 5.52097898e-01 9 2.79740267e-01 -1.14294939e+00 1.19640488e+00 10 8.28715789e-01 -1.39873587e+00 5.99926485e-01 11 1.09592373e+00 8.91764537e-01 -1.52598424e-01 12 2.00437876e+00 -1.01421623e+00 7.38214374e-01 13 3.61364509e-01 1.18589301e+00 1.13714455e+00 14 -1.62930071e+00 -1.12979045e+00 3.69485224e-01 15 -1.66140603e+00 -6.12095979e-01 4.71594795e-01 16 -6.65881793e-01 -2.92612945e+00 2.93321547e+00 17 4.29821228e-01 1.43812859e+00 1.17634729e+00 18 2.28543605e+00 -6.70818643e-01 -1.13235466e-01 19 1.34851933e+00 1.32913488e+00 -1.32238630e+00 20 9.16642656e-01 -1.43851424e+00 -2.26655022e+00 21 3.66986977e-01 2.94794399e+00 2.63711711e+00 22 -2.04397798e+00 -1.07633223e+00 2.04984130e+00 23 -1.35717906e+00 1.84052374e+00 -2.16682827e+00 24 2.40553646e-01 1.14598048e+00 -2.13250645e+00 25 1.24311074e+00 1.73866372e+00 1.41822050e+00 26 -7.65580771e-01 -2.49030836e+00 8.35529056e-01 27 1.63971845e+00 1.92092634e+00 -2.39337219e+00 28 1.84648273e+00 -1.42082344e+00 -2.41919850e+00 29 1.61507061e+00 7.56406478e-01 -2.99928391e-01 30 -2.26273685e+00 -1.98462293e+00 -1.31143079e+00 31 -3.59516119e+00 -1.78624300e-01 -2.45393689e+00 32 -5.22856264e-01 -3.61270935e+00 -7.76283055e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = N (Configuration in file "config-T-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -27.1633991068 Forces: 1 4.15147758e+00 1.39372378e+00 6.44867372e-01 2 -1.90696138e+00 -2.86497057e+00 9.40048567e-01 3 -2.52567457e+00 6.80791013e-01 -3.76285901e+00 4 -1.27048572e+00 1.14909535e-01 -3.59630570e+00 5 2.83328127e+00 -1.66359971e+00 1.44804229e+00 6 1.71923664e+00 3.96220811e-01 2.94617395e+00 7 8.75616492e-03 -1.27403978e+00 7.36858250e-01 8 -2.69611121e+00 2.60920289e+00 6.42042055e-01 9 -1.05062644e+00 -7.19143869e-01 -1.90543275e+00 10 -4.21063647e-01 4.21539607e-01 5.84390367e-02 11 1.10965496e+00 8.76793449e-01 -1.20001123e-01 12 -7.38612688e-01 -8.91086307e-01 1.41732864e+00 13 -1.70313684e+00 -9.85714073e-01 8.12459688e-01 14 1.36482178e+00 -2.03272297e-01 1.51114576e+00 15 1.52506530e+00 -5.94240311e-01 -1.31267530e-01 16 -5.61548032e-01 -1.94293307e+00 1.96015446e+00 17 -3.16460218e+00 1.05376547e+00 6.09763074e-01 18 2.29811658e+00 -6.71708470e-01 -1.23968185e-01 19 -4.52993178e-01 2.29767155e+00 1.96152056e+00 20 1.20249830e-01 -2.36793780e-01 8.79786401e-02 21 -2.26598675e-01 2.46085484e+00 2.42514227e+00 22 3.01039694e-01 -1.06359496e+00 1.98583871e+00 23 -1.13808515e+00 -8.30071077e-01 -3.08073673e+00 24 8.45168527e-02 1.09691613e+00 -1.94727390e+00 25 1.11811888e+00 1.77478149e+00 1.28678941e+00 26 -2.67750763e-01 -1.86389990e+00 9.22809258e-01 27 1.63943529e+00 1.89203822e+00 -6.90855897e-01 28 2.08099656e+00 -2.88363424e+00 -8.30990498e-02 29 1.56774735e+00 7.32998105e-01 -2.90893937e-01 30 -4.59178211e-01 9.20827362e-01 -2.18782397e+00 31 -2.53105690e+00 -7.28157405e-01 -1.82908454e+00 32 -8.08029160e-01 6.93825557e-01 -2.64779969e+00 MIXED STRUCTURE (pbc=False)-- Species = Ga N (Configuration in file "config-F-GaN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 49.6206461053 Forces: 1 -7.47436706e+00 -9.02504470e+00 -1.97306114e+01 2 5.16387835e+00 3.47237205e+00 -9.27521790e+00 3 1.77881116e+01 -2.94516771e+01 -1.30421323e+01 4 -2.99005434e+01 2.54215639e+01 -2.56303566e+01 5 -4.31215259e+00 -1.17879458e+01 -7.26685275e+00 6 1.78535509e+01 -2.86055976e+00 -1.57723014e+01 7 7.52349915e+00 -8.81089643e+00 9.00048941e-02 8 -1.67147561e+01 -1.21033628e+01 -6.55622389e+00 9 -3.04824301e+00 -3.79713251e+00 -3.28382190e+00 10 3.58020736e+00 4.30838575e+00 -6.53594248e+00 11 7.15868598e+00 5.76783774e+00 -3.06208414e+00 12 -5.51920964e+00 8.72242168e+00 3.89683809e+00 13 -8.67505922e+00 4.91933085e+00 -1.58614114e+01 14 2.62074104e+00 6.41544568e+00 -3.31036443e+00 15 2.13481307e+01 2.13634398e+01 -8.54647325e+00 16 -2.19162423e+00 3.95145854e+00 2.44915597e+00 17 -3.13865717e+01 -2.60529397e+01 2.69667460e+01 18 1.19492345e+01 9.97768849e+00 4.52481010e+00 19 -6.81010293e+00 -1.38920950e+01 1.74379247e+01 20 -7.71156496e+00 3.73660242e+00 9.76472733e+00 21 1.07894694e+01 -2.61309888e+01 -4.25070986e-01 22 3.37935518e+01 -1.08744384e+01 9.93931610e+00 23 2.67665050e+00 -4.74919346e+00 4.52088821e+00 24 2.36439710e+00 -7.55575292e+00 2.37408031e+01 25 -8.32955852e+00 9.61401414e+00 4.75819338e+00 26 -1.59397887e-01 2.51742508e+00 -2.10359777e+00 27 -1.64823545e+01 1.29777369e+01 1.12225949e+01 28 2.46011048e-01 -1.27641374e-01 1.80567129e-01 29 -1.35867172e+01 1.86445297e+01 -2.02853852e+00 30 2.37838821e+00 4.69194922e+00 4.05552736e-01 31 1.58021634e+01 9.48571717e+00 1.71955285e+01 32 -7.34448145e-01 1.12317498e+01 5.33735001e+00 MIXED STRUCTURE (pbc=True)-- Species = Ga N (Configuration in file "config-T-GaN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 166.068012995 Forces: 1 -2.51364740e+00 1.80679000e+00 -4.00240114e+01 2 -1.23223998e+00 2.97090341e+00 1.15581084e+01 3 3.26289714e+01 -1.11251363e+01 -2.48766741e+00 4 1.59234511e+00 3.60832977e+01 -2.37298483e+01 5 7.48663125e+00 -1.18618797e+00 -4.09987306e+00 6 4.99240147e+00 4.68959116e+00 -2.23581860e+01 7 -2.23143682e+01 -2.33364879e+01 -3.27598602e+00 8 -2.02372671e+01 -1.13963837e+01 -6.12030290e+00 9 -1.63736552e+00 -5.86163822e-01 -9.25306886e+00 10 2.24229527e+00 -6.70797827e+00 -6.08642383e+00 11 8.38465717e+00 3.67332491e+00 -2.10426634e+00 12 -1.09300560e+01 -3.00842531e+01 -4.86325014e+00 13 3.22680812e-01 2.94796571e+00 7.90763335e+00 14 8.72239132e+00 4.85215451e+00 -8.83325329e+00 15 -8.56731773e-01 2.30225295e+01 -4.53778217e+00 16 -1.22380662e+00 -6.81964693e+00 1.17808848e+01 17 -1.06351166e+01 -2.69592675e+01 3.09141913e+01 18 2.03644446e+01 1.06881826e+01 2.76940807e+00 19 -1.10398115e+01 -7.44979370e+00 5.38241708e+00 20 9.13898278e+00 2.09451639e+01 2.52495424e+01 21 1.04687032e+01 -1.37048984e+01 4.68690442e+00 22 -8.55124569e+00 7.77061929e+00 1.45703113e+01 23 -8.06463289e+00 -1.95527309e+01 1.62532147e+01 24 4.64486948e-01 -7.08442674e+00 2.02279139e+00 25 5.85465698e+00 2.06566440e+01 8.35630827e+00 26 1.76066799e+00 -1.44298242e+01 -9.54531382e-01 27 -2.40932092e+01 4.60478641e+00 -4.65670659e+00 28 -1.18128595e+01 -4.42679987e+00 -2.73046327e+00 29 -1.45265931e+01 1.86408939e+01 -5.27947273e+00 30 1.99789520e+00 -2.27618084e+00 3.01773786e+00 31 2.09958124e+01 1.46911372e+01 1.33891594e+01 32 1.22509271e+01 9.08217592e+00 -6.46351895e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2656== Memcheck, a memory error detector ==2656== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2656== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==2656== Command: python runner2.py SW_BereSerra_2006_GaN__MO_861114678890_000 ==2656== ==2656== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==2656== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==2656== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2656== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2656== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2656== by 0x4010732: call_init (dl-init.c:72) ==2656== by 0x4010732: _dl_init (dl-init.c:119) ==2656== by 0x40151FE: dl_open_worker (dl-open.c:522) ==2656== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2656== by 0x40147C9: _dl_open (dl-open.c:605) ==2656== by 0x544CF95: dlopen_doit (dlopen.c:66) ==2656== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2656== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==2656== by 0x544D734: _dlerror_run (dlerror.c:162) ==2656== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==2656== ==2656== ==2656== HEAP SUMMARY: ==2656== in use at exit: 4,518,077 bytes in 4,313 blocks ==2656== total heap usage: 186,385 allocs, 182,072 frees, 73,914,162 bytes allocated ==2656== ==2656== LEAK SUMMARY: ==2656== definitely lost: 0 bytes in 0 blocks ==2656== indirectly lost: 0 bytes in 0 blocks ==2656== possibly lost: 182,735 bytes in 112 blocks ==2656== still reachable: 4,335,342 bytes in 4,201 blocks ==2656== suppressed: 0 bytes in 0 blocks ==2656== Rerun with --leak-check=full to see details of leaked memory ==2656== ==2656== For counts of detected and suppressed errors, rerun with: -v ==2656== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2522 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. === Verification check vc-memory-leak end (2018-12-15 06:27:38) ===