!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouZimmermanWong_2008_PdH__MO_114797992931_000 Supported species : H Pd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = H (Configuration in file "config-F-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -4.65050506943 Forces: 1 -2.22831369e+00 -1.75005271e+00 -3.09282775e+00 2 -2.87252470e+00 6.43207878e+00 -1.71813391e+00 3 1.02185488e+00 -2.16772728e+00 3.48039122e+00 4 -2.53684169e+00 2.32316295e+00 9.87862377e-02 5 5.21970861e+00 -5.54347782e+00 -8.37165676e-01 6 5.98364009e-01 5.43485227e-01 -1.00331226e+00 7 6.94453033e-01 -8.59550380e+00 -9.37387309e+00 8 -4.93803286e+00 -3.60842919e+00 -5.15831663e-02 9 -8.90514388e-01 -2.58484395e+00 -2.56778306e+00 10 -1.75138600e+00 2.98855180e+00 -4.24747978e+00 11 7.91283803e-03 -2.86894544e+00 -2.59317470e+00 12 -1.63031798e+00 2.74172463e+00 1.30999403e+00 13 -4.52596665e+00 -4.11516778e+00 -1.18062141e+01 14 1.54867878e+00 2.29830296e+00 -1.27070115e+00 15 1.08677008e+01 -2.22568177e+00 3.52219055e+00 16 1.64721865e+00 8.27075331e+00 4.22283419e+00 17 -3.82474432e+00 -3.04936704e+00 -1.96655139e+00 18 4.51036499e+00 2.52397886e+00 7.25126503e-01 19 2.06113159e+00 -2.22688048e+00 1.78079418e+00 20 -1.13200744e+00 2.33512203e+00 1.85613200e+00 21 -4.00682538e+00 -2.99475975e+00 9.80802813e-01 22 5.05900870e+00 8.10555347e+00 6.86803525e+00 23 1.15019437e+00 -4.81414030e-01 1.48537053e+00 24 -9.04500374e-01 2.23714644e+00 1.18625163e+00 25 -4.82775796e+00 -1.23119109e+00 2.29516048e+00 26 -1.88968724e+00 5.24459267e+00 -2.35922647e+00 27 5.07311249e+00 -1.08408753e+01 1.78751979e+00 28 -7.79870790e+00 6.98529486e+00 1.41997080e+00 29 -1.71619361e+00 -3.24388549e+00 2.60499985e+00 30 1.58779546e+00 3.35750451e+00 1.25263285e+00 31 3.94902644e+00 -2.37421910e+00 2.48330549e+00 32 2.47779655e+00 3.51516953e+00 3.52772815e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = H (Configuration in file "config-T-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -15.231278272 Forces: 1 1.62894409e+00 -3.16474728e+00 2.16485303e-01 2 -4.41102366e+00 6.68631450e+00 9.92347635e-01 3 6.89760002e-01 1.68212608e+00 5.24273281e+00 4 -1.04946157e+00 2.79659763e+00 -1.27494542e+00 5 8.34357384e+00 -1.48496434e+00 -6.95177228e-01 6 -3.26753901e+00 6.19455540e+00 4.78643722e+00 7 -5.00319079e-01 -8.32354580e+00 -1.02603398e+01 8 -4.72523204e+00 -3.85451185e+00 -2.91477083e-01 9 -4.81549422e+00 -9.11638109e+00 8.68917995e+00 10 -4.13131282e+00 -2.05804927e+00 -3.05115027e+00 11 -3.05091740e-01 -2.68795534e+00 -2.83428010e+00 12 2.25408067e+00 9.54486341e-01 3.25034597e+00 13 -4.15596610e+00 -4.70513077e+00 -1.10019775e+01 14 -3.63074458e+00 2.26948888e+00 -3.71989644e+00 15 1.04349953e+01 -2.53559751e+00 3.25771255e+00 16 2.31224522e+00 7.54008728e+00 4.41412374e+00 17 2.97637387e+00 -7.43565384e+00 -1.73272214e+00 18 4.54442636e+00 2.25332963e+00 9.53743765e-01 19 1.73544821e+00 8.05392157e-01 2.03884869e+00 20 6.41589545e+00 9.18683161e+00 -7.61590790e-01 21 -3.99936253e+00 -1.89517175e+00 1.45401668e+00 22 -3.84923661e-01 1.25730729e+01 6.54968214e+00 23 -6.86850584e+00 -1.00623534e+01 -3.01891151e+00 24 5.20076995e-01 2.63122739e+00 -2.03613608e+00 25 -3.83897579e+00 -1.83756614e+00 2.60570833e+00 26 -1.89969596e+00 3.07205364e+00 -3.68960099e+00 27 9.29127103e+00 -1.11166027e+01 -4.81418680e+00 28 -9.55506546e+00 1.14516845e+01 -4.77302325e+00 29 -1.46951640e+00 -3.07256175e+00 2.90092470e+00 30 -3.40973589e-01 2.11040343e+00 2.78409881e+00 31 4.10911936e+00 -2.38449430e+00 2.52634201e+00 32 4.09299363e+00 3.52763576e+00 1.29268512e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Pd (Configuration in file "config-F-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 26.1789217767 Forces: 1 -4.10647845e+00 -3.58238679e+00 -3.80168265e+00 2 -7.06164608e+00 -1.08962431e+00 -1.08140240e+01 3 -6.32944587e+00 -1.41272157e+01 -5.24516075e+00 4 -9.30474543e+00 -1.05371664e+00 -3.59770008e+00 5 -1.89021042e+00 -9.42867492e+00 -8.85765236e+00 6 1.02338822e+01 2.76534252e+00 -9.30939046e+00 7 8.45898713e+00 -9.82674570e+00 4.09572734e+00 8 7.45519353e-01 -7.50405301e+00 -1.10493391e+01 9 -4.69064637e+00 -2.83973565e+00 -3.33976190e+00 10 2.40361800e+00 5.34102385e+00 -7.41968784e+00 11 -1.02143330e+01 6.50120580e+00 -2.81346572e+00 12 -4.44547295e+00 6.88872293e+00 1.97997397e+00 13 1.71287191e+00 4.27358745e+00 -1.92183963e+01 14 3.76469718e+00 3.01628560e+00 -4.60822129e+00 15 2.11307925e+01 3.75957905e+00 -4.52367666e+00 16 -3.04922326e+00 1.75561881e+01 1.11102897e+00 17 -5.17093495e+00 -6.45738682e+00 1.45878073e+00 18 -1.23465548e+01 8.06781452e-01 4.23724896e+00 19 -5.06272661e+00 -8.13221162e+00 9.28185037e+00 20 -5.80150865e+00 6.40976309e-01 6.03231616e+00 21 4.66971566e+00 -2.22694322e+01 2.16618344e+00 22 2.36207892e+01 -5.84424690e+00 4.49484323e+00 23 3.13836747e+00 -2.65315046e+00 2.65960011e+00 24 5.54381438e-01 3.51649361e-01 1.86380834e+01 25 -9.64265906e+00 2.32409340e+00 1.54838047e+00 26 -6.79387001e-01 1.11378169e+01 -9.44833737e+00 27 -3.10986933e+00 -6.45162533e+00 1.22958700e+01 28 -8.95524377e+00 4.43739461e+00 5.96045287e+00 29 -2.27359538e+00 1.26022356e+01 7.42879351e+00 30 5.71311024e+00 6.89448608e+00 4.44235876e-01 31 8.62552554e+00 3.17212252e+00 1.16501909e+01 32 9.36242351e+00 8.79071457e+00 8.56293626e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pd (Configuration in file "config-T-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 313.664183526 Forces: 1 6.78343063e+00 5.57918830e-01 3.06267647e+00 2 -8.61206410e+00 9.99571211e+00 1.08977381e+01 3 1.59482475e-01 -9.65766084e-01 -6.11831610e+00 4 1.07338077e+01 3.16806478e+00 3.40459462e+00 5 -4.64423455e+00 -3.09740374e+00 8.17286861e+00 6 -5.89522755e+00 1.56444403e+01 -3.47348160e+00 7 -2.08961156e+00 -1.28688336e+00 1.60087832e+01 8 -2.06765530e+00 -4.79593653e+00 -9.91468652e+00 9 1.48961087e+00 -3.34581698e+00 7.35471732e+00 10 4.00654804e+00 -2.05372872e+00 1.63331649e+01 11 -8.83519773e+00 4.63678724e+00 -3.08032911e-01 12 7.85292176e-01 -8.01134977e+00 4.69985164e+00 13 5.18600407e+00 1.26893617e+00 -9.79775326e+00 14 9.98336760e-01 -1.78898376e+01 -3.15043484e+00 15 7.90588492e+00 5.95373320e+00 -4.64971555e+00 16 -8.77195214e+00 6.22606801e+00 5.32996744e+00 17 -1.97650590e+00 1.00027494e+01 -4.41491844e+00 18 -1.01595600e+01 4.02053525e+00 1.81439634e+00 19 -5.12275108e+00 6.83657387e+00 -2.10082906e+00 20 7.38862799e+00 3.85065060e+00 -6.05379673e+00 21 8.01193081e+00 -1.27893527e+01 -2.71918965e+00 22 1.18566545e+01 -5.56350877e+00 2.77618605e+00 23 -1.62873005e+00 -4.96194557e+00 -1.48354737e+01 24 -1.96670882e-01 8.99284529e+00 -8.51566499e-01 25 1.00142687e+01 -9.76712393e-01 -4.45499217e+00 26 2.43758853e+00 -8.11273041e+00 -1.74814557e+01 27 -1.13272645e+00 -1.55982379e+01 -4.11358364e+00 28 -9.28006583e+00 -4.37112741e+00 1.87718103e+00 29 -7.16986238e+00 1.20861273e+01 5.79358203e+00 30 -1.06517047e+01 3.44144369e+00 -1.08868474e+00 31 -8.50904281e+00 4.22158663e+00 1.21924414e+01 32 1.89860948e+01 -7.08383472e+00 -4.19123806e+00 MIXED STRUCTURE (pbc=False)-- Species = H Pd (Configuration in file "config-F-HPd.xyz") ----------------------------------------------------------------------------------------------------- Energy = -45.3355857689 Forces: 1 1.48523857e+00 -3.83930245e+00 -2.98092013e+00 2 -5.82413013e-01 -3.65488216e+00 -6.61482827e+00 3 -1.32327380e+00 -1.47125571e+00 -1.12584531e+00 4 -3.64313313e+00 6.01180866e+00 -1.36485388e+00 5 -1.35532787e+00 1.68825238e-01 1.97637857e+00 6 2.59361660e+00 -1.20164651e+00 1.16115806e+00 7 -6.36520803e-01 1.03389811e+00 -1.07559544e-01 8 3.74560930e+00 -3.18878958e+00 2.85559924e+00 9 -6.30720538e+00 2.22487617e+00 -5.31385972e+00 10 -2.67414708e+00 1.39542812e+00 -1.19234614e+00 11 4.45509127e+00 3.32253683e+00 2.03073907e+00 12 6.64461125e-01 -1.78602425e+00 1.06757027e+00 13 -3.08575438e+00 -4.24570547e+00 -1.88276449e+00 14 2.37812115e+00 1.05736688e+00 -3.90987882e-03 15 3.77229087e+00 1.34641931e+00 -2.15785480e+00 16 5.15351288e-01 2.26091479e+00 4.53147687e+00 17 -8.34384065e-01 8.09918308e-01 -3.85961922e-01 18 3.40745209e+00 6.73515179e-01 -3.26556093e+00 19 1.35109887e+00 -8.67174579e+00 2.82055040e+00 20 -5.01263146e+00 1.67796469e+00 1.22521749e+00 21 9.19491836e-01 5.13759217e-01 2.00590878e+00 22 8.38809757e-01 3.06774747e+00 -3.78320140e+00 23 1.27117416e+00 -2.76155579e+00 1.10314756e+00 24 3.29146653e+00 7.19258725e-01 2.84550475e+00 25 -4.34831411e+00 -2.75534485e+00 3.88498488e+00 26 9.32603322e-01 3.67526084e+00 -1.12902705e+00 27 -1.07527372e+00 6.54363795e+00 3.77448277e-01 28 1.98401226e-01 -7.51610684e-01 8.81781217e-01 29 -1.56861181e+00 -3.36872437e+00 -4.18362213e-01 30 2.90834410e+00 3.00392467e+00 -3.22980853e+00 31 1.84917914e-01 -3.74465717e+00 1.24301579e+00 32 -2.46654937e+00 1.93418365e+00 4.94618299e+00 MIXED STRUCTURE (pbc=True)-- Species = H Pd (Configuration in file "config-T-HPd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 7.62778946124 Forces: 1 1.75614341e+00 -7.75521404e+00 6.04390578e+00 2 -3.35024406e-01 -2.94628558e+00 -6.44726478e+00 3 -3.13099104e-01 -1.82105638e+00 -4.08403612e-01 4 7.03299970e-01 8.29282163e+00 5.52382434e+00 5 3.13973807e-01 -1.39394400e+00 1.08961733e+01 6 -5.61720832e+00 8.79473821e+00 7.37866813e+00 7 -5.08637953e-01 -3.53492518e-02 -4.40278405e-01 8 3.62564307e+00 -2.93738670e+00 4.04713449e+00 9 -6.20647836e+00 1.47996360e+00 -4.19706084e+00 10 -2.78139176e+00 -4.14502607e+00 1.19308660e+00 11 4.88614371e+00 3.27378498e+00 2.69732290e+00 12 -1.01791185e+00 -3.43575174e+00 5.82628507e+00 13 -1.12641044e+00 -2.55166569e+00 3.14195611e+00 14 4.16354180e+00 1.31430101e-01 -2.41904244e+00 15 3.49355347e+00 1.60033577e+00 -5.35658831e-01 16 7.89246169e-01 2.40167815e+00 8.04777742e+00 17 -4.38300897e+00 4.74778163e+00 -1.19709403e+00 18 5.78991733e+00 2.28588160e+00 -5.18117343e+00 19 4.43977531e+00 -1.09833881e+01 -6.09388913e+00 20 5.34370074e+00 1.04676406e+01 -4.78950506e+00 21 4.70856599e+00 4.01631134e+00 3.51376204e-01 22 -5.23456945e+00 7.15067626e+00 -1.19869359e+01 23 -3.66250725e+00 -1.75047315e+01 -6.94115083e+00 24 -3.32646973e-01 4.07431886e+00 -6.69197514e+00 25 -3.31258681e+00 -3.29157926e+00 3.14839353e+00 26 1.66728785e+00 -3.89370580e+00 -1.72211309e+00 27 -4.29871913e+00 5.48009540e+00 -5.28105262e+00 28 2.28674491e-01 6.99206314e-01 1.66302586e+00 29 -1.62407059e+00 -3.85742824e+00 -4.25781489e-01 30 1.56101217e+00 3.04108728e+00 -3.32047660e+00 31 -1.26065835e+00 -2.88553278e+00 1.81029838e+00 32 -1.45554958e+00 1.50029344e+00 6.30962805e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==11027== Memcheck, a memory error detector ==11027== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==11027== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==11027== Command: python runner2.py EAM_Dynamo_ZhouZimmermanWong_2008_PdH__MO_114797992931_000 ==11027== ==11027== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==11027== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==11027== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11027== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11027== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11027== by 0x4010732: call_init (dl-init.c:72) ==11027== by 0x4010732: _dl_init (dl-init.c:119) ==11027== by 0x40151FE: dl_open_worker (dl-open.c:522) ==11027== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==11027== by 0x40147C9: _dl_open (dl-open.c:605) ==11027== by 0x544CF95: dlopen_doit (dlopen.c:66) ==11027== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==11027== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==11027== by 0x544D734: _dlerror_run (dlerror.c:162) ==11027== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==11027== ==11027== ==11027== HEAP SUMMARY: ==11027== in use at exit: 7,118,457 bytes in 4,275 blocks ==11027== total heap usage: 192,977 allocs, 188,702 frees, 77,160,107 bytes allocated ==11027== ==11027== LEAK SUMMARY: ==11027== definitely lost: 0 bytes in 0 blocks ==11027== indirectly lost: 0 bytes in 0 blocks ==11027== possibly lost: 182,735 bytes in 112 blocks ==11027== still reachable: 6,935,722 bytes in 4,163 blocks ==11027== suppressed: 0 bytes in 0 blocks ==11027== Rerun with --leak-check=full to see details of leaked memory ==11027== ==11027== For counts of detected and suppressed errors, rerun with: -v ==11027== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2525 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.