!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_HoytGarvinWebb_2003_PbCu__MO_119135752160_005 Supported species : Cu Pb random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = -4.09416597674 Forces: 1 -2.52771901e+00 -6.00296094e+00 -6.34255388e+00 2 -8.67600184e+00 1.41796920e+01 -6.22068092e+00 3 2.78633727e+00 -7.65987142e+00 -1.71295177e+00 4 -4.69136417e+00 5.01824278e+00 2.10540394e+00 5 8.74445645e+00 -1.64720425e+01 -1.29173801e+00 6 4.08363575e+00 2.08913587e+00 -6.65436425e+00 7 3.43690523e+00 -2.11269959e+01 -1.83505241e+01 8 -9.81051696e+00 -9.70698727e+00 3.87989637e+00 9 -3.09696057e+00 -6.41619983e+00 -7.52254362e+00 10 -4.39087552e+00 8.91087938e+00 -1.16284975e+01 11 2.12285752e+00 -8.85861824e+00 -1.18993503e+01 12 -6.07786988e+00 9.30348048e+00 1.83030681e+00 13 -9.33117086e+00 -6.89281104e+00 -3.09923303e+01 14 5.02150274e+00 6.81535706e+00 -3.99494370e+00 15 2.84067001e+01 -1.55652517e+00 1.12313861e+01 16 4.97215063e+00 2.19409034e+01 9.55401204e+00 17 -1.23456292e+01 -7.57836512e+00 -2.84852849e+00 18 7.39747942e+00 8.17046580e+00 2.11061889e+00 19 4.16724041e+00 -8.82439508e+00 5.53970027e+00 20 -4.22236046e+00 5.77165766e+00 5.69621653e+00 21 -1.08660547e+01 -6.29338215e+00 4.34319438e+00 22 1.26730057e+01 1.84481791e+01 1.44246341e+01 23 3.33759521e+00 -8.34205517e-01 6.42914682e+00 24 2.45518127e+00 2.85970582e+00 2.48522550e+00 25 -1.73755907e+01 -3.25714733e+00 9.76293769e+00 26 -4.35579045e+00 1.60314340e+01 -5.23154503e+00 27 8.93987942e+00 -2.40618715e+01 8.15038940e+00 28 -1.96335252e+01 1.69713093e+01 3.39345407e+00 29 -2.29101197e+00 -1.09245350e+01 5.62630933e+00 30 5.54745386e+00 1.11032997e+01 -4.89830093e+00 31 9.55520182e+00 -1.14690525e+01 1.18315132e+01 32 6.04485869e+00 1.03222240e+01 1.11945073e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 44.0002799774 Forces: 1 1.53725016e+01 -1.23794189e+01 2.25997730e+00 2 -2.91654580e+01 1.17434416e+01 2.72320591e+01 3 2.35950179e+00 1.26829467e+00 -5.71404574e-01 4 7.97279509e+00 9.18920308e+00 -4.27603363e+00 5 1.58803617e+01 -4.73596656e+00 1.46661377e+00 6 -1.61569713e+01 2.34219670e+01 1.94940206e+01 7 -3.14705902e+00 -2.13490651e+01 -1.80562161e+01 8 -9.53307424e+00 -9.79488583e+00 3.57483066e+00 9 -1.09593343e+01 -1.67715207e+01 1.57223943e+01 10 -1.15017149e+01 -2.64549488e+00 -4.85189217e+00 11 1.87333568e+00 -8.33133118e+00 -1.21159026e+01 12 3.04500059e+00 3.91616042e+00 8.20541521e+00 13 -8.59010073e+00 -8.18203313e+00 -2.59252758e+01 14 -7.73732413e+00 5.24643185e+00 -9.36528965e+00 15 2.35157959e+01 -1.60106616e+00 1.08545552e+01 16 6.36581072e+00 1.70433069e+01 9.88101983e+00 17 4.82994698e+00 -1.48481955e+01 -1.80949631e+00 18 7.57524435e+00 7.80983131e+00 2.28544288e+00 19 3.75867175e+00 6.13883314e-01 4.72615447e+00 20 1.14891979e+01 1.82496568e+01 -2.53480078e+00 21 -1.12684241e+01 -7.68375715e-01 4.25233875e+00 22 -4.93949937e+00 2.73660569e+01 1.75132339e+01 23 -1.19655801e+01 -2.28480800e+01 -2.06757525e+01 24 2.38920336e+01 8.38501876e+00 -3.09075907e+01 25 -1.29014972e+01 -4.74296069e+00 9.46425416e+00 26 -3.49255095e+00 6.49904042e+00 -7.09123579e+00 27 1.85566206e+01 -2.41842148e+01 -8.99890219e+00 28 -2.02039848e+01 2.04963153e+01 -5.16312425e+00 29 -2.08050830e+00 -1.04294125e+01 5.67504864e+00 30 2.91106042e-02 6.07904879e+00 -4.57948287e+00 31 8.05979800e+00 -1.24062368e+01 1.05477781e+01 32 9.06735448e+00 8.69060125e+00 3.76726312e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Pb (Configuration in file "config-F-Pb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 300.738945322 Forces: 1 -2.13728705e+01 -1.88978383e+01 -2.36180276e+01 2 -6.73640830e+00 2.06307846e+00 -1.87123179e+01 3 -7.36520911e-01 -1.62478008e+01 5.04088177e+00 4 -1.13427916e+01 3.17142522e+00 3.86647803e+00 5 5.85050902e-01 -1.78541341e+01 -1.51760406e+01 6 1.83881598e+01 -8.23296199e+00 -1.48589081e+01 7 1.59280826e+01 -1.51957754e+01 2.16041718e+00 8 -1.89042849e+00 9.15992651e-01 8.72187011e+00 9 -1.44062344e+01 -3.58072944e+00 -1.19522353e+01 10 3.78597885e+00 1.09372513e+01 -9.76922587e+00 11 3.91439176e+00 2.10797062e+00 -1.21654071e+00 12 -1.45188654e+01 1.45812317e+01 3.81603895e-01 13 -1.74878772e+01 -6.40798501e+00 -1.06841972e+01 14 4.23016047e+01 5.52366104e+01 -5.16131833e+01 15 1.33672038e+01 -7.23347565e+00 1.94346961e+01 16 -1.16697496e+01 1.18221122e+01 6.97275692e+00 17 -8.74890366e+00 -9.34037188e+00 7.40348717e+00 18 -8.57708071e+00 -7.67140117e+00 4.16008607e-01 19 -4.66603371e+00 -1.30716602e+01 1.09703169e+01 20 -1.18625574e+01 -4.85193840e+00 1.13999201e+01 21 1.80364915e+00 -1.60774146e+01 2.19005965e-01 22 1.63734649e+01 8.85828390e-01 -3.75950533e+00 23 9.57291212e+00 -9.85035726e+00 1.14063644e+01 24 2.01290782e+00 -1.34797354e+00 2.12495391e+01 25 -1.93193247e+01 -5.86712353e+00 -1.39350259e+00 26 8.10433666e+00 1.62610087e+01 -4.36368619e+00 27 1.72416895e+00 9.94956463e-01 2.00577776e+01 28 -1.15277291e+01 1.47004500e+01 1.64769345e+01 29 5.75651861e+00 9.29772941e+00 -5.47646922e+00 30 1.02584265e+01 6.67571281e+00 3.40038066e+00 31 1.18368074e+01 3.66987344e+00 9.96423281e+00 32 -8.50288764e-01 8.40770963e+00 1.30511683e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pb (Configuration in file "config-T-Pb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 523.993134393 Forces: 1 5.06112770e+00 5.41009877e+00 -3.36112562e+00 2 -1.09368820e+01 1.03428798e-01 -4.84663305e+00 3 -4.70345278e+00 -1.46928922e+00 1.32426019e+00 4 2.50115543e+00 6.08196821e-02 -1.76818364e+00 5 -4.46209963e+00 -6.15373806e+00 -5.43818250e+00 6 7.64922370e+00 -2.28395163e+00 2.03242281e+00 7 3.14921304e+00 7.31480711e-01 -2.40504722e-01 8 -2.19759847e+00 3.43076433e+00 8.38042813e+00 9 4.45478233e+00 -3.88143184e+00 8.50165095e-01 10 8.76356181e+00 2.39600180e-01 2.89882358e+00 11 5.41735417e+00 1.64946423e+00 -1.06198681e+00 12 2.78064922e-05 -8.49715783e-01 -5.60732556e-02 13 -9.12149450e+00 1.10673703e+01 -6.81670278e-01 14 -3.26076276e+00 -7.80407519e-02 -1.87662192e+00 15 7.61967921e-01 3.37580044e+00 1.05517563e+01 16 -6.18163457e+00 -1.12173858e+01 -2.64789455e+00 17 7.57456173e+00 1.32914061e-01 2.38096122e+00 18 -7.40370665e+00 -6.33376206e+00 -3.84999136e+00 19 -4.10544357e+00 3.21222076e+00 2.88547680e+00 20 8.47414564e+00 -5.60457416e+00 4.47689346e+00 21 -4.54838482e+00 2.58371304e+00 8.98953127e-01 22 -1.58795585e+00 5.54921335e+00 -5.10176649e+00 23 4.18469754e+00 -5.57319514e+00 1.44181212e+00 24 -1.38987864e+00 1.50890728e-01 6.17407554e-01 25 -6.49980327e+00 -5.65495133e+00 -6.67602469e+00 26 9.10707512e+00 4.38465636e+00 -7.54490833e+00 27 4.87637756e+00 -6.41669980e-01 9.18573496e+00 28 -5.97616322e+00 8.04985268e+00 4.15837814e+00 29 5.49005958e+00 9.42016768e+00 -9.15326993e+00 30 1.37877883e+00 -1.05344988e+01 2.32566312e+00 31 -4.78846562e+00 6.09298189e+00 -3.52558527e+00 32 -1.68038360e+00 -5.36923349e+00 3.42128585e+00 MIXED STRUCTURE (pbc=False)-- Species = Cu Pb (Configuration in file "config-F-CuPb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 160.137893894 Forces: 1 -1.20325245e+00 -2.94218677e+00 -4.10091381e+00 2 -1.26467453e+01 -2.68883847e+00 -1.74319910e+01 3 -2.14700396e+00 -1.18044543e+01 -1.96130533e-01 4 -7.91856768e+00 4.50108813e+00 -3.81855976e+00 5 1.14707891e+00 -6.43506803e+00 -8.62314289e+00 6 9.01347222e+00 -1.01712991e+00 -1.46925145e+01 7 6.38292708e+00 -8.00330875e+00 5.50304833e+00 8 5.17049674e-01 -1.94212582e+01 3.75559820e+00 9 -4.57665754e+00 -6.68763270e+00 -6.52072405e+00 10 -4.43556127e+00 7.44728509e+00 -1.24391036e+01 11 -2.12642020e+01 -9.49037325e+00 -5.73076838e-01 12 -4.13356018e+00 7.55808147e+00 -3.28130676e+00 13 -1.25457707e+00 -2.29784484e+00 -3.38284742e+01 14 7.77509887e+00 8.74849490e+00 -6.30501727e+00 15 2.74942583e+01 -4.09156066e+00 8.35151936e+00 16 4.73785385e+00 3.30555607e+01 6.32733687e+00 17 -3.46473539e+01 -1.50998885e+01 -2.52861211e+01 18 1.30918856e+01 7.27601788e+00 -7.31062960e+00 19 2.13241187e+01 -1.38446065e+01 3.48375203e+01 20 -1.21555052e+01 -7.39730524e+00 1.88583131e+01 21 1.85403468e+00 -1.84137727e+01 -6.23327776e+00 22 1.49273604e+01 -8.45604286e+00 -1.86484803e+01 23 1.27852281e+01 -2.09491854e+01 1.31447023e+01 24 -2.28561702e+01 -4.77178591e+01 1.51114965e+01 25 -1.87111964e+01 -1.21499699e+01 -2.47459513e+01 26 -1.75484767e+01 1.64507920e+01 -5.03584651e+01 27 1.61841635e+00 -6.55003712e+01 1.55773402e+01 28 -8.31280315e+01 6.58982770e+01 4.41221937e+01 29 -5.38468884e+00 -3.66369399e+01 -5.08704895e+01 30 3.62155407e+01 1.17866198e+01 -4.53016959e+01 31 5.64256300e+01 -4.30802271e+01 1.42941616e+01 32 3.87015967e+01 2.01403607e+02 1.60682836e+02 MIXED STRUCTURE (pbc=True)-- Species = Cu Pb (Configuration in file "config-T-CuPb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 233.546100364 Forces: 1 3.69112930e+00 5.68472394e+00 -1.54435295e+00 2 -1.50480817e+01 -3.44140049e+00 -9.91898574e+00 3 -4.27719926e+00 3.12032831e+00 1.83080495e+00 4 3.00723029e+00 6.63666610e+00 -9.67230983e-01 5 1.31830666e+00 8.49863891e+00 -1.86496884e+00 6 6.51025103e+00 -3.46815408e+00 2.73125118e+00 7 -4.06900417e+00 -7.25837241e+00 4.88346620e+00 8 -8.98175991e-01 -1.46351946e+01 1.02985486e+01 9 1.48596513e+01 -1.55637344e+01 1.80350090e-01 10 -6.64593619e+00 -4.58075825e+00 -9.02933884e+00 11 -2.01070114e+01 -8.45108584e+00 4.33958422e+00 12 3.04278835e+00 2.17795592e+00 4.95141357e+00 13 -2.87666255e+00 -7.95129548e-01 -2.74422765e+01 14 -5.91722651e+00 1.24829510e+01 4.39357881e+00 15 1.82182469e+01 -3.80567139e+00 1.34286159e+01 16 9.45355377e+00 2.18925751e+01 1.34183362e+01 17 -2.95080432e+01 -5.52177448e+00 -2.57143708e+01 18 1.42112337e+01 1.17595792e+01 -5.38054912e+00 19 2.11321648e+01 1.99283705e+00 3.34642177e+01 20 3.26129257e+00 -6.02329490e-01 1.61665915e+01 21 2.13633623e+00 8.19706887e+00 -3.96482027e+00 22 3.00347002e+00 -9.89990215e+00 -1.65655011e+01 23 1.10129722e+00 1.56897234e+00 3.50848824e-01 24 -2.12702069e+01 -1.69166078e+01 1.04411351e+01 25 -2.55266640e+00 4.92667285e+00 -1.25978143e+01 26 9.76761508e-01 2.43712875e+00 -1.20587373e+01 27 5.06264909e+00 -1.17372146e+01 1.57428957e+01 28 -6.59726491e+00 6.68911185e-01 1.01258701e+00 29 -7.88645221e-01 5.22362591e+00 -1.00306151e+01 30 3.89861316e+00 1.84941831e+00 -4.21759593e+00 31 1.16981103e+01 1.17448977e+01 3.73802587e+00 32 -6.02696183e+00 -4.18562173e+00 -7.50937702e-02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==501== Memcheck, a memory error detector ==501== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==501== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==501== Command: python runner2.py EAM_Dynamo_HoytGarvinWebb_2003_PbCu__MO_119135752160_005 ==501== ==501== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==501== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==501== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==501== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==501== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==501== by 0x4010732: call_init (dl-init.c:72) ==501== by 0x4010732: _dl_init (dl-init.c:119) ==501== by 0x40151FE: dl_open_worker (dl-open.c:522) ==501== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==501== by 0x40147C9: _dl_open (dl-open.c:605) ==501== by 0x544CF95: dlopen_doit (dlopen.c:66) ==501== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==501== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==501== by 0x544D734: _dlerror_run (dlerror.c:162) ==501== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==501== ==501== ==501== HEAP SUMMARY: ==501== in use at exit: 7,136,541 bytes in 4,275 blocks ==501== total heap usage: 193,085 allocs, 188,810 frees, 77,181,544 bytes allocated ==501== ==501== LEAK SUMMARY: ==501== definitely lost: 0 bytes in 0 blocks ==501== indirectly lost: 0 bytes in 0 blocks ==501== possibly lost: 182,735 bytes in 112 blocks ==501== still reachable: 6,953,806 bytes in 4,163 blocks ==501== suppressed: 0 bytes in 0 blocks ==501== Rerun with --leak-check=full to see details of leaked memory ==501== ==501== For counts of detected and suppressed errors, rerun with: -v ==501== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2527 from 174) ================================================================================ 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.