Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:15:25) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_PunYamakovMishin_2013_AlCo__MO_678952612413_000 Supported species : Al Co random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 15.748816484 Forces: 1 -3.32162199e+00 -2.71300023e+00 -3.36275383e+00 2 1.54871207e+00 -1.27660982e+00 -6.91169765e+00 3 2.36517606e+00 -6.00636464e+00 5.90553202e-01 4 -6.54962087e+00 2.23910015e+00 -1.91217463e-01 5 -1.06656256e+00 -4.38847396e+00 -3.37430556e+00 6 3.91511222e+00 1.32338239e+00 -3.92406613e+00 7 3.38281527e+00 -3.63218127e+00 -2.44533702e-01 8 -1.00222258e+00 -2.00451364e+00 1.11383409e+00 9 -4.44345893e+00 -3.71816170e-01 -5.60228727e+00 10 5.99657894e-01 6.29311272e+00 -4.91647929e+00 11 -2.64053314e+00 -2.60777589e+00 -4.18957555e-01 12 -5.78210754e+00 4.78440302e+00 1.07239430e+00 13 2.13438604e+00 -1.63800197e+00 -7.32135649e+00 14 4.45056715e+00 3.92477590e+00 -4.84225819e+00 15 6.95307838e+00 -1.92040836e+00 -6.87301117e-01 16 -2.10717474e+00 8.77559510e+00 -6.59957539e-01 17 -5.81740313e+00 -4.53392588e+00 1.98383034e-01 18 1.68181027e+00 5.03823555e-01 -5.29389044e-01 19 2.36383466e+00 -5.91260672e+00 3.58786943e+00 20 -4.53291514e+00 2.10375186e+00 5.28772038e+00 21 -2.22324160e+00 -4.54991930e+00 8.40256659e-01 22 5.67890564e+00 1.04095799e+00 5.70112364e-01 23 2.61351873e+00 -1.90940832e+00 4.18526229e+00 24 9.64954235e-01 -8.50093998e-01 4.75954576e+00 25 -6.20728022e+00 -1.12678807e+00 -7.12281380e-01 26 5.08469748e-01 7.22825913e+00 -1.14053229e+00 27 -1.09940743e+00 -1.37664178e+00 6.09638427e+00 28 -4.54190987e+00 3.00072388e+00 3.47790985e+00 29 3.69218618e-01 -3.17290396e+00 1.97507436e+00 30 5.34550452e+00 5.09108759e+00 1.76371820e+00 31 4.76341002e+00 -9.09565054e-01 4.24297631e+00 32 1.69632823e+00 4.59202574e+00 5.07737999e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 81.9827350575 Forces: 1 1.41811980e+00 4.77297634e-01 3.62954160e-01 2 1.64579544e+00 -1.26082999e+00 3.26578553e-01 3 1.62423892e+00 2.14732765e+00 1.68239555e+00 4 3.20304432e-01 2.70987924e+00 -1.79463952e-01 5 -8.58387801e-01 1.09911443e+00 -3.99481243e-01 6 -1.21746651e+00 2.96323369e+00 -6.18729900e-01 7 -2.56044289e+00 1.36049653e+00 3.81530294e-01 8 -1.02426048e+00 -2.70730889e+00 1.23276631e+00 9 -2.65715784e+00 -1.38728109e+00 -4.35066456e-01 10 7.32029857e-01 2.31203026e+00 2.42718765e-01 11 -2.71578206e+00 -2.51424385e+00 2.99025831e-02 12 -3.36445729e-01 -1.35350301e-01 4.44822240e-01 13 2.46169746e+00 -1.89115208e+00 -1.54758726e+00 14 1.23181239e+00 -8.31702811e-01 -2.08692928e+00 15 2.75783963e+00 -2.24408645e+00 -5.78294336e-02 16 -1.47371204e+00 1.81795081e+00 -4.66904901e-01 17 4.11797761e-01 -1.21619867e+00 3.00278562e-01 18 3.02107442e+00 5.84152061e-01 -1.29363794e-01 19 2.07345732e+00 -2.49819312e-01 -1.46227726e+00 20 -4.56570695e-01 2.65704996e+00 4.02619845e-01 21 -3.50559404e+00 1.64943453e+00 1.98773637e+00 22 -1.15672655e+00 2.25219378e+00 2.97639561e-01 23 -3.00770113e+00 -1.09922009e+00 -5.19633928e-01 24 1.21376961e+00 2.74807548e-01 -2.71266894e+00 25 -6.46295730e-01 -1.74917787e+00 -4.81109991e-01 26 1.12214779e+00 1.02309574e+00 -5.02564747e-01 27 -6.30125910e-01 -1.56951255e+00 -1.10386223e-01 28 -2.10643568e+00 -8.79452836e-01 2.84252544e-01 29 4.90107812e-01 -3.06337862e+00 2.14224401e+00 30 6.33705416e-01 -3.45435089e-01 2.34391177e+00 31 3.77582750e-01 -1.65477343e+00 3.90906849e-01 32 2.81762428e+00 1.47086007e+00 -1.14326065e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Co (Configuration in file "config-F-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1456.03179668 Forces: 1 -3.63983422e+01 -1.16324659e+02 -1.21564129e+02 2 1.93466316e+02 -9.21612052e+01 -8.11902413e+01 3 3.53778501e+01 -6.58561780e+01 -2.06228513e+01 4 -7.78416724e+01 7.80622464e+01 1.32210026e+02 5 -5.84262896e+02 -2.03686379e+02 -6.82780395e+02 6 6.06983392e+02 2.42990439e+02 -8.09884700e+02 7 1.28684658e+03 -9.26253794e+02 6.11509181e+02 8 -1.29191089e+03 8.38255076e+02 8.57377847e+02 9 -1.49771316e+02 1.08547288e+02 -2.48393746e+01 10 -1.63667951e+02 2.93050473e+01 -1.14262394e+02 11 1.07422487e+03 1.81331519e+02 -8.70072315e+02 12 -1.01344656e+01 1.97171134e+01 1.03176326e+00 13 -9.51586634e+02 -2.72883654e+03 -3.22276610e+02 14 1.44575651e+03 1.79738814e+03 -9.02235077e+02 15 3.30686357e+01 2.25024865e+01 -2.38565489e+00 16 -3.50054412e+02 9.57911165e+02 1.31428510e+03 17 -3.20990767e+01 -3.20649419e+01 1.42407660e+01 18 2.55635175e+01 3.37178777e+01 3.86375284e+01 19 2.94019735e+00 -3.94194254e+00 5.30872081e+00 20 -7.26667924e+00 -6.35149235e+00 7.64920994e-01 21 -7.76577907e+00 -3.31769625e+01 -3.55891804e+01 22 8.20812884e+02 1.89996781e+02 -7.83129669e+02 23 2.15243367e+01 -1.40227267e+01 1.85750280e+01 24 -8.36213214e+02 -2.40849762e+02 7.85790746e+02 25 -1.06951945e+03 -1.37007961e+02 9.31278148e+02 26 1.87145939e+02 -5.84476892e+01 -4.11687948e+02 27 1.13831659e+02 -3.44258063e+02 6.24225706e+01 28 -3.30435690e+02 4.21708622e+02 3.36156781e+02 29 -7.37696941e+00 -3.70453191e+01 -2.80065045e+01 30 1.32536813e+01 2.40096866e+01 -1.90257757e+01 31 2.20490377e+01 5.85815566e+01 6.71858933e+01 32 2.34600379e+01 3.62605748e+01 5.27777977e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Co (Configuration in file "config-T-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1570.48995913 Forces: 1 -2.37659902e+01 -1.25779071e+02 -1.06067090e+02 2 2.05003363e+02 -1.01286586e+02 -5.85744709e+01 3 3.45198824e+01 -6.54931148e+01 -2.07462260e+01 4 -7.38853179e+01 7.38853378e+01 1.30213845e+02 5 -6.08609320e+02 -1.63202515e+02 -6.63728450e+02 6 6.29334945e+02 2.44086238e+02 -7.47885624e+02 7 1.28012852e+03 -9.20995337e+02 6.16761823e+02 8 -1.29056969e+03 8.37105054e+02 8.56053995e+02 9 -1.85296287e+02 1.09267698e+02 4.42731337e+01 10 -1.63305747e+02 2.85172340e+01 -8.96872186e+01 11 1.07316036e+03 1.81414100e+02 -8.70863907e+02 12 2.90998431e+00 1.59153287e+01 -1.61378567e+01 13 -9.51139236e+02 -2.72756362e+03 -3.21908647e+02 14 1.45734361e+03 1.77161184e+03 -8.81192606e+02 15 1.24298962e+01 2.30542565e+01 -6.16812106e+00 16 -3.50811176e+02 9.49776775e+02 1.31751862e+03 17 -3.22190356e+01 -1.91212596e+01 1.24664824e+01 18 2.49241898e+01 3.24145795e+01 3.94023383e+01 19 5.61829348e+02 9.28647827e+02 5.03279981e+01 20 -2.22409645e+00 -1.30326580e+01 -3.18420200e+01 21 -6.45244038e+00 -2.58957183e+01 -3.92151646e+01 22 8.11259794e+02 1.92037031e+02 -7.88114680e+02 23 3.12124501e+01 -1.82159737e+01 -4.40974647e+00 24 -8.62610523e+02 -2.38438660e+02 7.25577586e+02 25 -1.05432032e+03 -1.35385519e+02 9.37233971e+02 26 1.88465632e+02 -7.42737079e+01 -4.19988489e+02 27 1.47495559e+02 -3.24257970e+02 -1.07999690e+01 28 -9.95008315e+02 -4.00576150e+02 3.06709660e+02 29 -6.21078992e+00 -3.56292907e+01 -2.68491994e+01 30 -1.19749725e+00 1.91416295e+01 -5.04146344e+00 31 2.47769215e+01 5.15099934e+01 4.62194332e+01 32 1.22831329e+02 -6.92377679e+01 2.64620614e+01 MIXED STRUCTURE (pbc=False)-- Species = Al Co (Configuration in file "config-F-AlCo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 585.220410049 Forces: 1 -7.26370243e+01 -5.45364004e+00 -6.75356259e+01 2 -1.68077626e+02 9.36444906e+01 -1.35610531e+02 3 1.25970845e+02 -7.85549512e+01 6.70364223e+01 4 -7.27524096e+01 2.12717155e+02 -1.57768354e+02 5 9.97432496e+01 -1.20016181e+02 -3.54634864e+01 6 1.43731318e+02 -1.69859004e+02 -1.97683654e+01 7 2.23659667e+00 -2.64419875e+01 -2.64714119e+01 8 4.87097128e+01 -3.59578154e+01 1.99128611e+02 9 -2.12569216e+02 -1.52719525e+02 3.43868682e+00 10 2.40401896e+02 1.89888574e+02 -6.11698976e+01 11 -3.98665260e+00 -9.64631669e+00 2.67560570e+01 12 -1.14916240e+01 5.86005481e+00 1.04172115e+01 13 -2.92592968e+02 3.43239112e+01 -1.08695757e+02 14 1.96621251e+02 2.36039786e+02 -3.33462059e+01 15 3.21182598e+02 -2.63475989e+02 -1.05334027e+02 16 -9.55895397e+01 3.51651381e+02 -3.55478703e+02 17 -1.02905593e+02 -2.96088486e+02 5.51516652e+01 18 1.81757103e+02 7.50241375e+01 -1.40056857e+02 19 2.35726183e+02 -3.59973826e+02 1.20504081e+02 20 -3.39086865e+02 3.78384929e+02 1.56559809e+02 21 3.67379044e+01 -5.16995882e+02 -3.47311218e+02 22 7.62439246e+01 -7.70519697e+01 -1.22773242e+02 23 4.99532819e+00 -1.47987645e+01 1.06014618e+01 24 -8.45318083e+01 2.63040717e+02 3.50155384e+02 25 -1.52234356e+01 -1.02361722e+01 -4.09823093e+01 26 -1.49541836e+02 3.22944784e+01 8.63688460e+01 27 -7.28778283e+01 8.79828408e+01 3.46261052e+01 28 -2.38975954e+00 4.29964067e+01 4.33149753e+01 29 -1.98898167e+02 -1.98615013e+02 3.93396984e+02 30 2.03754906e+02 8.75482441e+01 -3.74165647e+01 31 5.97937525e+01 2.27697427e+02 1.48091082e+02 32 -8.24542164e+01 1.67909891e+01 8.96351746e+01 MIXED STRUCTURE (pbc=True)-- Species = Al Co (Configuration in file "config-T-AlCo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 829.996332682 Forces: 1 -1.74098091e+02 1.33624786e+02 -4.80679638e+01 2 -1.68496799e+02 -4.15741523e+01 1.02462410e+02 3 1.27892590e+02 -7.36159910e+01 6.63401547e+01 4 1.28905343e+01 2.76323625e+02 -1.61874093e+02 5 1.83640639e+02 -9.10233794e+01 5.23470051e+01 6 1.56296487e+02 -3.38316959e+02 1.75031153e+02 7 -6.39993895e+01 4.00241417e+01 -1.22427429e+02 8 4.87797692e+01 -3.60723954e+01 1.99315895e+02 9 -1.32033280e+02 -1.86457891e+02 -7.21290257e+00 10 3.14881276e+02 2.84424239e+02 1.47167330e+02 11 -5.43783860e+00 -9.61346436e+00 2.69235043e+01 12 2.46555106e+00 -1.30132849e+02 1.20886801e+02 13 -4.10310696e+02 3.24398668e+01 3.21501756e+02 14 1.14179825e+02 2.78317257e+02 -3.11725721e+00 15 3.21075617e+02 -2.62056851e+02 -1.05421907e+02 16 -9.46939086e+01 3.51912121e+02 -3.55955334e+02 17 7.98714051e-01 -2.96041831e+02 5.60270880e+01 18 1.80406932e+02 7.54095979e+01 -1.39514727e+02 19 2.05102359e+02 -4.31524884e+02 -1.66292791e+02 20 -3.11673655e+02 3.89413163e+02 1.59971240e+02 21 -1.02717640e+01 -4.53586053e+02 -3.33512631e+02 22 -4.83986024e+00 -2.13810023e+01 -1.22534088e+02 23 -7.21111241e+00 -1.90388709e+00 4.39488883e+01 24 -8.34933426e+01 2.63785550e+02 3.25941794e+02 25 -1.24358915e+00 -5.85186289e-01 -4.07489483e+01 26 -1.49382957e+02 2.72220217e+01 8.64245209e+01 27 -1.28374051e+02 1.82078088e+02 -3.27221361e+02 28 -9.38338220e+01 3.48684558e+01 -3.02637443e+01 29 -1.99110607e+02 -1.98892881e+02 3.94473766e+02 30 1.69984076e+02 -1.87852140e+02 7.33508174e+00 31 2.71831181e+02 3.93652655e+02 -3.87173296e+02 32 -7.17207883e+01 -2.86376876e+00 6.52400855e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==5716== Memcheck, a memory error detector ==5716== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==5716== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==5716== Command: python runner2.py EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_000 ==5716== ==5716== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==5716== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==5716== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5716== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5716== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5716== by 0x4010732: call_init (dl-init.c:72) ==5716== by 0x4010732: _dl_init (dl-init.c:119) ==5716== by 0x40151FE: dl_open_worker (dl-open.c:522) ==5716== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==5716== by 0x40147C9: _dl_open (dl-open.c:605) ==5716== by 0x544CF95: dlopen_doit (dlopen.c:66) ==5716== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==5716== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==5716== by 0x544D734: _dlerror_run (dlerror.c:162) ==5716== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==5716== ==5716== ==5716== HEAP SUMMARY: ==5716== in use at exit: 39,228,625 bytes in 4,275 blocks ==5716== total heap usage: 198,866 allocs, 194,591 frees, 113,061,168 bytes allocated ==5716== ==5716== LEAK SUMMARY: ==5716== definitely lost: 0 bytes in 0 blocks ==5716== indirectly lost: 0 bytes in 0 blocks ==5716== possibly lost: 182,735 bytes in 112 blocks ==5716== still reachable: 39,045,890 bytes in 4,163 blocks ==5716== suppressed: 0 bytes in 0 blocks ==5716== Rerun with --leak-check=full to see details of leaked memory ==5716== ==5716== For counts of detected and suppressed errors, rerun with: -v ==5716== 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 06:16:06) ===