!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZopeMishin_2003_TiAl__MO_117656786760_005 Supported species : Al Ti 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 = -27.7618627263 Forces: 1 -1.95102235e+00 -2.10367455e+00 -2.58474764e+00 2 -9.11778666e-01 1.82615433e+00 -4.42878314e+00 3 1.04169293e+00 -3.85492443e+00 2.39685208e-01 4 -3.60410402e+00 1.62802838e+00 1.10020841e+00 5 1.72868322e+00 -4.65210007e+00 -1.70390030e+00 6 2.13735692e+00 1.19157728e+00 -2.86000863e+00 7 2.26438493e+00 -5.69590869e+00 -3.64019368e+00 8 -2.58157331e+00 -1.48317624e+00 -1.22253431e-01 9 -4.21016633e+00 -1.94649450e+00 -5.46388593e+00 10 -2.26194055e-01 6.80741597e+00 -5.76808795e+00 11 -3.06451685e+00 -5.34254040e+00 3.00956732e+00 12 -4.85335713e+00 3.99260654e+00 1.42215607e+00 13 4.35882577e+00 -2.36008174e+00 -7.88017433e+00 14 1.50620664e+00 1.36039940e+00 -1.61009779e+00 15 6.52350190e+00 -8.02393243e-01 -3.02882034e+00 16 1.97884757e+00 7.83158175e+00 3.54283489e+00 17 -4.87295708e+00 -2.79864193e+00 -1.16118723e+00 18 1.44411728e+00 3.10726800e+00 -1.65853606e+00 19 1.22118972e+00 -4.86536165e+00 3.53999874e+00 20 -3.06528649e+00 2.45759298e+00 3.08063302e+00 21 -2.16638596e+00 -4.59034466e+00 8.74776452e-01 22 6.04507752e+00 3.21536982e+00 2.88000549e+00 23 1.83070930e+00 -8.43757254e-01 2.77002608e+00 24 8.60009609e-01 1.72533860e+00 3.48156091e+00 25 -4.57703937e+00 -3.11642224e+00 -1.15142717e+00 26 1.43727964e+00 6.22311225e+00 -2.22180172e+00 27 1.75383512e+00 -5.59125167e+00 4.96581859e+00 28 -5.80198240e+00 4.12926208e+00 2.99282550e+00 29 -2.95782871e+00 -2.40906294e+00 2.65386131e+00 30 3.44719721e+00 5.43477806e+00 4.22421385e-01 31 3.79912715e+00 -2.53667900e+00 4.45851657e+00 32 1.46615031e+00 4.06232977e+00 3.84900938e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 107.224373923 Forces: 1 2.94896670e+00 -1.88875362e+00 1.28265035e+00 2 -3.17608116e+00 2.16461410e+00 2.65615051e+00 3 -1.46726726e-01 1.86789496e+00 5.60616162e-01 4 2.54146586e+00 2.84181494e+00 -4.66264910e-01 5 3.13396486e+00 -1.04876423e+00 5.45472097e-01 6 -3.30661211e+00 4.92807482e+00 7.44512840e-01 7 -2.46026572e+00 -4.08217298e+00 -3.51605739e+00 8 -2.44864360e+00 -1.77896279e+00 -2.89519443e-01 9 -4.27887063e+00 -4.01792628e+00 1.06823603e+00 10 -8.95340989e-01 2.95320341e+00 -1.98688928e+00 11 -3.51301605e+00 -4.94543392e+00 2.57455525e+00 12 -7.65734812e-01 9.25075510e-01 1.37741097e+00 13 5.05866844e+00 -2.71850932e+00 -3.94134794e+00 14 -2.40554173e+00 -1.05400304e-02 -1.25454067e+00 15 3.02917825e+00 -2.49954783e-01 -2.86354785e+00 16 2.59856700e+00 3.92262571e+00 3.68558537e+00 17 1.06572808e+00 -2.41886131e+00 -8.78839856e-01 18 1.41014075e+00 2.75298245e+00 -1.36571202e+00 19 5.29023300e-01 -3.85747160e-01 9.23215854e-01 20 2.50241304e+00 4.95983078e+00 -1.16153827e+00 21 -2.01244062e+00 -9.45059586e-01 1.77316620e+00 22 1.49965053e-01 4.80226219e+00 3.43443471e+00 23 -4.48652073e+00 -4.03049733e+00 -6.28231542e-01 24 3.71724080e+00 2.30912781e+00 -3.98874944e+00 25 -2.59514083e-01 -3.47402320e+00 -8.36160306e-01 26 1.95689805e+00 7.13337018e-01 -2.05532326e+00 27 2.47160826e+00 -5.55741632e+00 -1.58956594e+00 28 -4.87508134e+00 3.21760424e+00 -2.45176693e-01 29 -2.40802824e+00 -2.11503141e+00 2.83977409e+00 30 2.77634448e-01 1.91314925e+00 8.98772304e-01 31 1.26700196e+00 -2.54468533e+00 2.45588897e+00 32 2.77995370e+00 1.94074242e+00 2.47023119e-01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ti (Configuration in file "config-F-Ti.xyz") ----------------------------------------------------------------------------------------------------- Energy = 49.4693057222 Forces: 1 -5.32958692e+00 -7.23097207e+00 -8.45263557e+00 2 -7.65603487e+00 -3.88515521e+00 -2.83650106e+01 3 8.98720198e+00 -2.67581950e+01 -1.40259644e+01 4 -2.40529105e+01 2.34893049e+01 -1.90438549e+01 5 -2.58479397e+00 -1.12629140e+01 -1.23633845e+01 6 1.43633317e+01 -8.06429669e+00 -1.49905646e+01 7 1.87289200e+01 -5.01924383e+00 -9.08848823e+00 8 1.66180146e+01 -9.82479167e+00 8.44203786e+00 9 -4.45792685e+00 -9.03047685e-01 -4.47201689e+00 10 -1.22187637e+00 4.41009562e+00 -6.84629221e+00 11 -3.12068343e+01 1.23528921e+01 5.56990275e+00 12 -7.34262096e+00 5.59195467e+00 -2.12112971e+00 13 -5.79057005e+00 9.15315919e+00 -3.47851852e+01 14 3.61539429e+00 4.50821850e+00 -4.41819231e+00 15 2.47295243e+01 9.51526266e+00 1.94857444e+01 16 1.43104478e+01 1.44674259e+01 -1.35604054e+01 17 -2.72363779e+01 -3.82043337e+01 2.12607347e+01 18 1.95556616e+01 2.53933512e+01 -4.23925688e+00 19 8.77438397e+00 -2.28634972e+01 2.45429293e+01 20 -1.97199181e+01 7.23602025e+00 1.44628725e+01 21 -1.03275049e+01 -1.51606859e+01 1.24160154e+01 22 1.55687462e+01 9.94827901e+00 -1.05783311e+01 23 1.39078798e+01 -2.35024338e+01 1.02138003e+01 24 -1.61803031e+01 1.48228011e+01 1.37075878e+01 25 -8.37488517e+00 1.48570488e+00 -3.17408412e+00 26 -1.22532800e+01 1.13560567e+01 1.83932322e+01 27 1.12301443e+01 -7.72052173e+00 7.60127261e+00 28 -9.84314166e+00 1.21089521e+01 3.28333460e+00 29 1.24852730e+01 6.05870758e+00 2.27175810e+01 30 1.34816195e+01 6.09106985e+00 -1.06064612e+01 31 1.23403828e+01 -5.37545286e+00 5.17173934e+00 32 -1.51183603e+01 7.78628501e+00 1.38624732e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ti (Configuration in file "config-T-Ti.xyz") ----------------------------------------------------------------------------------------------------- Energy = 372.840114274 Forces: 1 4.12467316e+00 -1.67029769e+01 2.36015010e+01 2 -5.33117239e+00 -3.79886237e+00 -1.89194208e+01 3 3.73221455e+00 -6.02256993e-01 -2.43993360e+01 4 -4.82482599e+00 2.82377528e+01 -1.74796072e+01 5 -2.79873752e+01 -5.40218589e+00 2.37989883e+01 6 1.59964741e+00 -1.79408594e+01 1.59247351e+01 7 2.93872916e+00 -4.31014373e+00 -9.95633638e+00 8 1.51249398e+01 -6.50872876e+00 9.80924472e+00 9 3.82586942e+01 -8.58346751e+00 4.39662308e+01 10 7.83588013e+00 6.74083560e+00 1.53619133e+01 11 -2.88142770e+01 1.21913043e+01 8.14783237e+00 12 -1.94040356e+00 -3.29003775e+00 9.41059726e-01 13 -8.03627114e+00 1.34773757e+01 -2.00362641e+01 14 1.78222674e+01 -6.45424339e+00 2.94141877e+01 15 1.22975473e+01 8.82301338e+00 2.24910461e+01 16 1.49904128e+01 -4.09256510e+00 -1.72862505e+01 17 -1.85347287e+01 -3.07767993e+01 2.25858794e+01 18 1.64331342e+01 2.63536437e+01 -5.62133134e+00 19 1.20217988e+01 -1.53501858e+01 9.20824712e+00 20 1.19678890e+01 2.44490869e+01 -7.68171436e+00 21 -1.88343269e+01 2.73647474e+01 8.03170544e+00 22 -4.10483076e+00 1.01826716e+01 -1.95012795e+01 23 1.14750076e+01 -1.78505295e+01 -2.24116407e+01 24 -2.80564630e+01 2.04376817e+01 -2.03158871e+01 25 -6.09952737e-01 2.44968500e+00 -3.94570760e+00 26 -1.62852066e+01 -1.85906289e+01 2.75737200e+01 27 1.50523309e+01 -1.31673792e+01 -1.08760080e+01 28 -4.26197010e-01 2.77930983e+01 -2.41279918e+01 29 1.17167873e+01 6.05502669e+00 1.82986707e+01 30 2.78661236e+01 -2.99338958e+01 -9.59165250e-01 31 -3.47756999e+01 -6.73423379e+00 -4.18049910e+01 32 -2.66963462e+01 -4.46594276e+00 -1.38320301e+01 MIXED STRUCTURE (pbc=False)-- Species = Al Ti (Configuration in file "config-F-AlTi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 536.189592323 Forces: 1 -8.27325869e+01 -5.09490952e+01 -8.14714925e+01 2 1.10287646e+00 -1.35513775e+01 -6.27063636e+01 3 4.92074423e+01 -1.51549702e+01 6.03349893e+01 4 -3.98728895e+01 1.26003137e+02 -2.01785352e+02 5 3.01557023e+01 -3.50206598e+01 -3.85539210e+01 6 1.09755218e+01 2.44761593e+01 -2.68857793e+01 7 6.52113135e+00 -2.35076699e+01 2.17761997e+01 8 6.78530460e+01 -1.80457909e+02 -2.00653236e+02 9 -1.80259616e+01 3.01681312e+00 -7.37419858e+00 10 -6.77358958e+01 1.01191524e+02 -8.57895149e+00 11 -1.13464317e+02 2.52243487e+02 -2.58063209e-01 12 -2.26601804e+02 7.73246587e+01 -1.93189551e+02 13 1.10394106e+02 -1.15216429e+02 -7.16699015e+01 14 1.50865880e+01 3.78903679e+01 -5.92634180e+01 15 3.35296296e+01 -5.59980382e+01 4.27026720e+01 16 -1.09637033e+02 4.54251530e+01 -5.57655881e+01 17 -5.86839144e+01 -1.95539193e+02 1.88938960e+02 18 -7.44130248e+01 -1.90337811e+02 1.01125505e+02 19 1.64804067e+02 -1.71538413e+02 2.75823623e+01 20 -2.00516034e+02 1.42493271e+02 1.12130613e+01 21 4.11794477e+01 -8.83079073e+01 4.38177856e+01 22 6.97060384e+01 -3.50118644e-01 3.16442356e+01 23 6.81626384e+00 -6.56634417e+00 1.52138848e+00 24 -3.98010340e+01 -6.98615478e+01 2.96067814e+01 25 -3.86561270e+01 7.60312856e+01 4.68570603e+01 26 1.65906543e+02 -4.78096834e+01 1.93207690e+02 27 -1.03761621e+01 2.54264926e+01 3.97578218e+01 28 -9.44975500e+00 5.82712267e+00 2.17338031e+00 29 1.32535892e+02 2.53655753e+02 3.24701169e+01 30 8.85240613e+01 1.11369194e+01 9.40097692e+01 31 7.31297450e+01 5.22533432e+01 5.41539348e+00 32 2.25384364e+01 2.57716790e+01 3.40006443e+01 MIXED STRUCTURE (pbc=True)-- Species = Al Ti (Configuration in file "config-T-AlTi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 881.133886782 Forces: 1 -1.70833592e+01 -8.13032993e+01 -8.25631107e+01 2 1.76547726e+01 -1.41332714e+01 -9.53936261e+00 3 4.67316738e+01 4.13521712e+00 6.62097242e+01 4 -1.17046907e+01 1.33440116e+02 -2.06329229e+02 5 5.57214280e+01 -3.60532138e+01 5.25107121e+00 6 -7.77450468e+01 1.48246790e+02 7.39583468e+01 7 -5.19422175e-01 9.54857464e+01 -7.22698493e+01 8 6.45887084e+01 -1.82252294e+02 -2.00293703e+02 9 -7.47201658e+00 -1.65097642e+01 1.28453745e+02 10 -7.21323257e+01 9.09136090e+01 1.27076878e+00 11 -1.13818002e+02 2.51549968e+02 -6.87740005e-01 12 -1.95730379e+02 4.90214275e+00 -1.90765507e+02 13 1.08521614e+02 -1.07014802e+02 -4.08681540e+01 14 -6.54299957e+00 3.81214802e+01 -1.33023467e+01 15 2.24781262e+01 -4.91335676e+01 4.17620666e+01 16 -1.07019249e+02 3.81483201e+01 -5.53500719e+01 17 -5.61491866e+01 -1.59051261e+02 2.16325785e+02 18 -7.45976011e+01 -1.92543450e+02 1.01964758e+02 19 1.50920558e+02 -1.54770830e+02 -2.14022796e+01 20 -2.03664816e+02 7.41271667e+01 -7.85368908e+01 21 -1.24396928e+01 -5.02509187e-02 3.89456780e+01 22 5.63532098e+01 1.56662943e-01 3.74543180e+01 23 1.43252653e+01 -7.27802227e+01 -9.71776695e+01 24 -3.99774273e+01 -6.42601093e+01 1.55527837e+01 25 -3.34286510e+01 7.45865716e+01 5.04615865e+01 26 1.65086475e+02 -5.09586056e+01 1.93272140e+02 27 -1.08679784e+01 2.82532361e+01 3.51714305e+00 28 1.54360567e+01 8.07203178e+01 -9.14673778e+01 29 1.32470343e+02 2.53825056e+02 3.36857488e+01 30 1.08152971e+02 -1.83943052e+02 1.91632212e+02 31 5.90517226e+01 3.57086304e+01 -5.17501404e+01 32 2.33999191e+01 1.24369625e+01 1.25855579e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==11347== Memcheck, a memory error detector ==11347== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==11347== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==11347== Command: python runner2.py EAM_Dynamo_ZopeMishin_2003_TiAl__MO_117656786760_005 ==11347== ==11347== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==11347== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==11347== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11347== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11347== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11347== by 0x4010732: call_init (dl-init.c:72) ==11347== by 0x4010732: _dl_init (dl-init.c:119) ==11347== by 0x40151FE: dl_open_worker (dl-open.c:522) ==11347== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==11347== by 0x40147C9: _dl_open (dl-open.c:605) ==11347== by 0x544CF95: dlopen_doit (dlopen.c:66) ==11347== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==11347== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==11347== by 0x544D734: _dlerror_run (dlerror.c:162) ==11347== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==11347== ==11347== ==11347== HEAP SUMMARY: ==11347== in use at exit: 39,242,369 bytes in 4,274 blocks ==11347== total heap usage: 198,995 allocs, 194,721 frees, 113,066,400 bytes allocated ==11347== ==11347== LEAK SUMMARY: ==11347== definitely lost: 0 bytes in 0 blocks ==11347== indirectly lost: 0 bytes in 0 blocks ==11347== possibly lost: 182,735 bytes in 112 blocks ==11347== still reachable: 39,059,634 bytes in 4,162 blocks ==11347== suppressed: 0 bytes in 0 blocks ==11347== Rerun with --leak-check=full to see details of leaked memory ==11347== ==11347== For counts of detected and suppressed errors, rerun with: -v ==11347== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2515 from 171) ================================================================================ 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.