!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_IMD_BrommerBoissieuEuchner_2009_MgZn__MO_710767216198_003 Supported species : Mg Zn random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mg (Configuration in file "config-F-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 196.937023752 Forces: 1 -1.29857972e+03 -2.39314563e+03 -2.76829050e+03 2 -1.22550307e+03 1.28348565e+03 -1.75983415e+03 3 1.54992856e+03 -3.02925180e+03 -1.40127015e+03 4 -1.51553727e+03 1.87889841e+03 1.21496394e+03 5 2.05759621e+02 -3.46823452e+03 -1.43508548e+03 6 1.49374111e+03 1.42858702e+03 -1.76508475e+03 7 3.63995217e+03 -3.89736143e+03 -1.32774829e+03 8 -2.96477679e+03 -2.83539407e+03 -1.59752610e+03 9 -3.17004546e+03 -2.57160991e+03 -4.87485091e+03 10 -5.78621035e+02 6.09781409e+03 -4.13847446e+03 11 -2.15786508e+03 -3.94869840e+03 3.66034084e+03 12 -2.82960797e+03 4.02036705e+03 1.19506193e+03 13 1.72785572e+03 -3.07633379e+03 -6.00647616e+03 14 2.59231275e+03 3.35122038e+03 -2.19044198e+03 15 6.72600488e+03 -3.37166673e+03 -9.71750782e+02 16 3.78542210e+02 6.93665563e+03 6.70879507e+02 17 -4.66917095e+03 -2.32066256e+03 -1.65076435e+03 18 7.18158830e+02 3.15482182e+03 1.35789264e+03 19 1.84852129e+03 -4.03761252e+03 2.14509412e+03 20 -1.44820295e+03 2.88063690e+03 2.14221394e+03 21 -3.71427726e+03 -2.68525076e+03 1.20577072e+03 22 4.20292607e+03 3.06748599e+03 1.29362329e+03 23 1.20791584e+03 -5.55241904e+02 2.69069600e+03 24 2.08626551e+03 2.66581489e+02 1.21676577e+03 25 -2.90731682e+03 -3.00176975e+03 7.81877722e+02 26 -1.79950928e+03 5.93079935e+03 -2.94600038e+03 27 -6.59685473e+02 -3.29646481e+03 3.18778761e+03 28 -3.17695826e+03 2.38234874e+03 1.98412033e+03 29 -2.00427885e+03 -3.46212527e+03 2.14064154e+03 30 2.44857887e+03 3.81422896e+03 1.02331227e+03 31 4.03064700e+03 -2.51298631e+03 2.72256082e+03 32 1.26282581e+03 3.96987869e+03 4.19999544e+03 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mg (Configuration in file "config-T-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 286.126121659 Forces: 1 3.91544838e+03 -2.98865219e+03 1.16756815e+03 2 -1.54463153e+03 1.67919800e+03 1.36923140e+03 3 1.60793712e+03 1.39270264e+03 -6.37111644e+02 4 4.06424952e+03 3.55221613e+03 6.99246257e+02 5 1.81928038e+03 6.35883612e+01 -1.48355991e+03 6 -4.56008536e+03 4.18234350e+03 -2.68614006e+02 7 2.88737542e+02 -3.49069726e+03 -1.87509471e+03 8 -2.98128931e+03 -2.82892424e+03 -1.58084010e+03 9 -4.19816578e+03 -4.97370720e+03 -8.38273261e+02 10 -3.06856213e+03 4.16787701e+03 -8.73511284e+02 11 -2.15017464e+03 -3.96205214e+03 3.66939296e+03 12 9.79776551e+02 1.60492624e+03 1.07139426e+03 13 2.03750006e+03 -4.04434197e+03 -4.01502006e+03 14 -1.47085932e+03 1.76841030e+03 -3.01134804e+03 15 5.03449517e+03 -3.51711350e+03 -8.64072371e+02 16 9.50777895e+02 4.64451120e+03 1.59255060e+03 17 8.66862799e+02 -2.79011051e+03 -2.42214154e+03 18 7.36846684e+02 3.16289207e+03 1.35462780e+03 19 2.26111658e+03 1.83838585e+02 2.39599745e+03 20 2.57090379e+03 6.12256909e+03 -1.94534143e+03 21 -3.82170564e+03 -6.41740712e+02 1.29928858e+03 22 2.75395789e+02 4.54140224e+03 2.22827944e+03 23 -4.04944773e+03 -2.89139024e+03 3.26400776e+02 24 2.98424954e+03 1.24824919e+03 -1.42427819e+03 25 -1.10961464e+03 -4.21107081e+03 9.86527922e+02 26 -1.55725461e+03 2.04037548e+03 -3.79828679e+03 27 1.08369283e+03 -4.25520782e+03 -8.16681011e+02 28 -4.08860528e+03 1.80539731e+03 -2.14288223e+02 29 -2.01653508e+03 -3.47355300e+03 2.12797364e+03 30 -1.30212048e+03 1.29109579e+03 2.96094512e+03 31 3.53190400e+03 -2.95138843e+03 2.32903997e+03 32 2.90987690e+03 3.56835689e+03 4.89998244e+02 MONOATOMIC STRUCTURE (pbc=False)-- Species = Zn (Configuration in file "config-F-Zn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 247.608522849 Forces: 1 -1.55165402e+03 -1.94258021e+03 -2.93940161e+01 2 2.38921022e+03 4.85269737e+02 -9.57220505e+02 3 -7.34906972e+02 -2.99139340e+02 -3.77655044e+02 4 -2.41421346e+03 -1.52266067e+03 1.16478363e+03 5 -4.02230032e+02 -9.95825307e+02 -7.82907260e+02 6 2.85115100e+03 -7.26693709e+02 -2.62411871e+03 7 1.58341097e+03 -4.49072718e+02 -1.08601620e+03 8 -2.17267471e+03 9.25198779e+02 1.27067409e+03 9 -1.23537736e+03 1.09425930e+03 -8.67905137e+02 10 -1.23045972e+03 1.80900680e+03 -2.73189707e+02 11 2.44945475e+03 1.14019785e+03 -9.07237422e+01 12 -1.04265816e+03 9.64139029e+02 -1.13053623e+03 13 -4.69502065e+01 -1.60432992e+03 -1.73037288e+03 14 1.36576748e+03 1.84212425e+03 -2.98464855e+03 15 2.82115931e+03 -2.17915320e+03 2.83664974e+03 16 -3.05152117e+03 3.14148212e+03 2.51982440e+02 17 -2.77736862e+01 -1.43565833e+01 1.85504556e+01 18 -6.07891495e+02 1.95291145e+02 -1.72812614e+03 19 4.61587293e+00 -1.25146834e+03 9.35172399e+02 20 -8.08965044e+02 -1.19778408e+03 1.35913287e+03 21 -2.66028121e+03 -2.90542120e+03 1.09615047e+03 22 3.63662088e+03 8.28511600e+02 -3.23230186e+03 23 6.71450490e+02 -1.48081854e+03 2.02688794e+03 24 -2.33000779e+03 -1.63783700e+03 2.63783593e+03 25 -7.68398202e+02 -1.11000537e+03 -2.11135805e+03 26 8.96071779e+02 1.03385495e+03 -5.50664801e+02 27 1.06499810e+03 -6.63239507e+02 1.12382493e+03 28 -1.99896033e+03 2.99458704e+03 2.32640104e+03 29 -1.74482678e+03 -1.67286169e+03 -1.08975548e+03 30 1.43148388e+03 1.05848102e+03 3.65907580e+02 31 4.27716342e+03 1.90330463e+03 2.18412626e+03 32 -6.12807814e+02 2.23753911e+03 2.04881455e+03 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zn (Configuration in file "config-T-Zn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 307.667397425 Forces: 1 -1.05303427e+03 -1.81329666e+03 -4.07390988e+02 2 2.46669750e+03 9.25823589e+01 -3.08161045e+02 3 -6.80625590e+02 1.63041127e+03 -2.49112112e+03 4 -2.25054404e+03 -1.50461143e+03 1.20514173e+03 5 -8.59931148e+02 -9.11371824e+02 1.37873738e+02 6 2.55963974e+03 -8.62464227e+02 -2.60557849e+03 7 -3.62978281e+02 1.63823122e+03 -4.92638656e+03 8 -2.20939102e+03 9.51016498e+02 1.31492503e+03 9 -1.23100673e+03 1.76380084e+03 5.72184768e+02 10 -1.21908278e+03 3.49749436e+03 1.95594170e+03 11 2.48743804e+03 1.11436939e+03 -5.38957458e+01 12 -3.79586068e+02 5.13282988e+02 -1.46046992e+03 13 8.63098052e+02 -2.13993152e+03 2.77668829e+02 14 2.99994515e+03 2.07775255e+03 -7.06149023e+02 15 2.34039028e+03 -2.38492262e+03 2.84969053e+03 16 -3.02643818e+03 2.62961391e+03 1.66126213e+02 17 3.22219958e+03 1.94516439e+03 2.17841718e+03 18 -5.73948004e+02 2.26433322e+02 -1.78284046e+03 19 -5.13618748e+01 -1.73005208e+02 1.74949653e+03 20 8.51475961e+02 -2.73272465e+03 6.97845044e+02 21 -4.50593175e+03 -5.56388300e+02 9.43453643e+02 22 2.95611468e+03 7.57001672e+02 -3.67544357e+03 23 1.58630737e+03 -2.31353637e+02 1.90976051e+03 24 -2.34149250e+03 -1.69888163e+03 2.43824590e+03 25 -5.15898812e+02 -1.10342888e+03 -2.20699181e+03 26 7.95601821e+02 -1.93493510e+03 5.47882216e+02 27 5.85648852e+02 -1.78740762e+03 -2.92724241e+03 28 -2.15606495e+03 2.89609695e+03 2.02477661e+03 29 -1.79809924e+03 -1.72124626e+03 -1.13176837e+03 30 1.25829064e+03 -4.72950421e+03 2.33687857e+03 31 2.81225543e+03 2.71930933e+03 2.09478276e+03 32 -2.56968786e+03 1.83291271e+03 -7.17651996e+02 MIXED STRUCTURE (pbc=False)-- Species = Mg Zn (Configuration in file "config-F-MgZn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 155.780424086 Forces: 1 -5.75621136e+00 -9.15223285e+00 -9.63927440e+00 2 -2.36794539e+03 5.13199008e+02 -1.82510650e+03 3 -1.79020349e+03 -1.52678051e+03 -1.46575367e+03 4 -2.02697131e+03 -6.86355860e+02 -6.38226643e+03 5 2.45990094e+03 -2.32629031e+03 -1.62714000e+03 6 2.48090086e+03 -5.04356029e+02 -2.81376664e+03 7 4.13182664e+03 -4.12689121e+02 -2.90148551e+03 8 -6.00579514e+03 -3.28118333e+03 -5.77315745e+02 9 -6.00136374e+03 -3.07659689e+03 -3.87089255e+03 10 -1.27033186e+03 7.48071989e+03 -4.31286264e+03 11 2.64882305e+03 -1.52380705e+03 7.56259029e+03 12 -4.16583204e+03 3.03075834e+03 -1.81969348e+03 13 3.67721028e+03 -2.73374840e+03 -1.12449284e+03 14 2.32688202e+03 4.07670959e+03 -3.96711290e+03 15 5.40009514e+03 -1.86202192e+03 6.34503760e+02 16 -2.51826102e+03 5.01935844e+03 -2.49505992e+03 17 -1.97562516e+03 -7.84504884e+03 2.41936372e+03 18 5.60878881e+03 7.41135964e+02 -1.52616833e+03 19 -1.60552774e+03 -2.20042013e+03 1.05528875e+03 20 -4.01018118e+03 -2.47351363e+03 2.60276806e+03 21 -2.67441534e+03 -2.40444394e+03 3.72338349e+03 22 5.60785078e+03 -1.70925937e+03 2.09150095e+03 23 1.24779854e+03 -6.30438251e+02 6.13472253e+02 24 -1.91452220e+03 -1.53377880e+03 1.23499939e+03 25 -3.47265678e+03 4.65398160e+03 5.23512752e+02 26 5.19116728e+03 1.20298919e+03 9.76824544e+02 27 4.66023247e+03 3.23066235e+03 2.70635631e+03 28 -3.76955432e+03 2.39691922e+03 3.47991765e+03 29 -7.87204547e+03 -2.65439680e+03 -2.22488978e+01 30 2.93616978e+03 2.53821387e+03 5.01837796e+02 31 5.81514571e+03 2.30215049e+03 3.64225225e+03 32 -7.45803920e+02 2.20748348e+03 2.97243337e+03 MIXED STRUCTURE (pbc=True)-- Species = Mg Zn (Configuration in file "config-T-MgZn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 228.834201122 Forces: 1 2.23551884e+03 7.07750638e+03 -3.10035747e+03 2 -3.66295723e+03 8.64004621e+02 4.19678145e+03 3 -1.14729099e+03 4.10079794e+03 -4.61189991e+03 4 1.27175613e+03 3.15475273e+02 -5.72727866e+03 5 2.78847692e+03 2.90840890e+02 5.60919757e+03 6 7.94370545e+02 -1.49103039e+03 -3.17172936e+03 7 -2.33414078e+03 2.25192506e+03 -3.47043491e+03 8 -6.04130926e+03 -3.25817695e+03 -5.60246168e+02 9 -3.28331442e+03 -3.58289212e+03 -8.61389066e+02 10 -4.71265170e+03 5.35779826e+03 2.99087776e+02 11 2.67266919e+03 -1.53642134e+03 7.61513944e+03 12 1.59231482e+03 -2.94105394e+03 1.70480930e+03 13 4.02835695e+03 -2.92657518e+03 2.14204950e+03 14 -2.80150637e+03 -6.18520858e+02 -2.16874637e+03 15 -8.17822970e+02 -1.96239023e+03 -1.61611389e+03 16 -1.02129757e+03 -8.24369491e+02 -4.78582586e+03 17 -5.74810630e+02 -1.76657195e+03 4.98933229e+03 18 5.66720171e+03 7.80531723e+02 -1.55184313e+03 19 -4.78556071e+03 8.71193492e+02 -3.29898396e+03 20 -4.00246425e+03 -2.80585952e+03 1.85524463e+03 21 -5.89101262e+03 4.83436345e+03 4.15115706e+03 22 9.15483338e+02 -4.44312555e+03 3.17051529e+03 23 1.43285426e+03 4.63052659e+03 -1.46491156e+03 24 -4.99767839e+02 -6.18451626e+01 -3.37273527e+03 25 3.93237479e+03 5.98523645e+03 3.02938809e+03 26 5.67830722e+03 -6.26148111e+03 3.83098648e+03 27 4.51618308e+03 2.35738049e+03 -2.89311642e+03 28 1.44008062e+03 1.22521597e+03 2.69304722e+03 29 -7.88384535e+03 -2.66483160e+03 -3.15409937e+01 30 1.95614947e+03 -1.16617606e+03 -1.51477348e+03 31 4.57477877e+03 1.27795081e+03 2.86008938e+03 32 3.96287603e+03 -3.90942594e+03 -3.94489901e+03 ================================================================================ VALGRIND OUTPUT ================================================================================ ==11500== Memcheck, a memory error detector ==11500== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==11500== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==11500== Command: python runner2.py EAM_IMD_BrommerBoissieuEuchner_2009_MgZn__MO_710767216198_003 ==11500== ==11500== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==11500== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==11500== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11500== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11500== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11500== by 0x4010732: call_init (dl-init.c:72) ==11500== by 0x4010732: _dl_init (dl-init.c:119) ==11500== by 0x40151FE: dl_open_worker (dl-open.c:522) ==11500== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==11500== by 0x40147C9: _dl_open (dl-open.c:605) ==11500== by 0x544CF95: dlopen_doit (dlopen.c:66) ==11500== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==11500== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==11500== by 0x544D734: _dlerror_run (dlerror.c:162) ==11500== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==11500== ==11500== ==11500== HEAP SUMMARY: ==11500== in use at exit: 9,708,360 bytes in 4,201 blocks ==11500== total heap usage: 229,222 allocs, 225,021 frees, 94,620,944 bytes allocated ==11500== ==11500== LEAK SUMMARY: ==11500== definitely lost: 0 bytes in 0 blocks ==11500== indirectly lost: 0 bytes in 0 blocks ==11500== possibly lost: 182,735 bytes in 112 blocks ==11500== still reachable: 9,525,625 bytes in 4,089 blocks ==11500== suppressed: 0 bytes in 0 blocks ==11500== Rerun with --leak-check=full to see details of leaked memory ==11500== ==11500== For counts of detected and suppressed errors, rerun with: -v ==11500== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2530 from 173) ================================================================================ 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.