!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_BonnyCastinBullens_2013_FeW__MO_737567242631_000 Supported species : Fe W random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -12.9527205198 Forces: 1 -5.87390505e+00 -4.84725584e+00 -8.96036531e+00 2 -9.51453664e+00 1.81155168e+01 -5.95879083e+00 3 9.44585508e+00 -8.06745995e+00 -1.11574291e+00 4 -6.44851549e+00 4.99687439e+00 2.42348447e+00 5 1.12301562e+01 -1.88081719e+01 1.99660501e+00 6 2.20036414e+00 1.52072897e+00 -2.88523803e+00 7 1.54555860e+00 -2.80440210e+01 -3.27455228e+01 8 -1.10151711e+01 -8.67682853e+00 -9.12130990e+00 9 -2.83012154e+00 -4.89971014e+00 -8.22294561e+00 10 -6.36218390e+00 8.28876469e+00 -1.44713706e+01 11 -1.92942481e+00 -7.84689189e+00 -5.03094529e-03 12 -5.78101278e+00 1.08945057e+01 1.76584798e+00 13 -1.40928841e+01 -1.23163327e+01 -3.86032105e+01 14 6.99241990e+00 1.16790911e+01 -8.64130726e+00 15 3.02632570e+01 -1.30592957e+01 1.62195600e+01 16 1.62651103e+00 2.22182786e+01 1.75475705e+01 17 -1.61418815e+01 -2.23090250e+00 -5.73058553e+00 18 1.58347484e+00 4.25906315e+00 2.13663464e+00 19 1.37563803e+01 -1.00153907e+01 1.04492599e+01 20 -5.48634829e+00 9.23915736e+00 3.89304480e+00 21 -1.12801483e+01 -9.97084690e+00 8.01847653e+00 22 2.00728561e+01 2.29259782e+01 2.27547088e+01 23 9.70757114e+00 -5.27105871e+00 5.26362631e+00 24 -8.39078336e+00 6.29691079e+00 3.76629100e+00 25 -8.58804679e+00 -6.52143864e+00 6.14567984e+00 26 1.43759992e+00 1.20868384e+01 -7.17963245e+00 27 2.19335343e+01 -3.65076645e+01 7.82346708e+00 28 -3.21540754e+01 2.72412502e+01 3.55139704e+00 29 -7.45086726e+00 2.08132702e+00 9.99799198e+00 30 5.71752038e+00 9.73752321e+00 5.72126280e+00 31 1.03391007e+01 -4.54757038e+00 6.76153373e+00 32 5.48774660e+00 1.00490313e+01 7.40461028e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 7.32803645352 Forces: 1 1.20281342e+00 -7.42646771e+00 -1.31413807e+00 2 -1.58620506e+01 1.86429134e+01 3.97769245e+00 3 1.17896065e+01 2.68014038e+00 8.13217190e-01 4 -1.96192660e+00 5.53292829e+00 3.72387310e-01 5 1.80651174e+01 -6.80894713e+00 3.30902903e+00 6 -3.99727337e+00 2.42998207e+01 2.87164285e+01 7 -2.46824946e+00 -2.36408366e+01 -3.34254799e+01 8 -1.03368844e+01 -8.95542607e+00 -9.55531989e+00 9 -6.27985644e+00 -1.60122129e+01 8.12513826e+00 10 -1.39880201e+01 -3.80356449e+00 -8.18048520e+00 11 -2.25701120e+00 -6.99172920e+00 -5.30657523e-01 12 2.18870513e+01 -6.76112839e-01 1.45809678e+01 13 -1.32908698e+01 -1.31735044e+01 -3.44283539e+01 14 -2.36500739e+01 1.26111254e+01 -2.48141576e+01 15 2.61350023e+01 -1.38834214e+01 1.60630534e+01 16 2.25371252e+00 1.87954690e+01 1.76660166e+01 17 2.16778719e+00 -1.41625836e+01 -2.97332332e+00 18 1.37931846e+00 3.96239033e+00 2.50938165e+00 19 1.70380302e+01 2.08602814e+00 8.01477426e+00 20 1.57800044e+01 2.40794077e+01 -3.10839681e+00 21 -1.13454048e+01 -5.94418105e+00 9.00498407e+00 22 3.01752571e+00 3.63254772e+01 2.01052483e+01 23 -1.01671152e+01 -3.71819912e+01 -2.11412899e+01 24 -4.78095537e+00 8.04233148e+00 -1.09433064e+01 25 -5.08810049e+00 -7.14188060e+00 6.79271572e+00 26 2.80744796e+00 5.15350204e+00 -8.28690695e+00 27 2.64927823e+01 -3.69665913e+01 -5.93064934e-01 28 -3.52365474e+01 2.77099875e+01 -6.56478301e+00 29 -6.86167904e+00 2.53390503e+00 1.01121405e+01 30 1.00896886e+00 5.14933076e+00 8.72270592e+00 31 8.71360635e+00 -4.10879552e+00 5.27852331e+00 32 7.83324354e+00 9.27348871e+00 1.69525914e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = W (Configuration in file "config-F-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 930.454365031 Forces: 1 -7.85863490e+01 -6.55683228e+01 -1.07939598e+02 2 3.55361870e+01 7.35005801e+00 -1.79797394e+02 3 1.38034805e+02 -2.16372489e+02 5.18440857e+01 4 -2.09884506e+02 1.34624084e+02 1.10531786e+02 5 -4.87939426e+00 -3.78579241e+01 -5.05718108e+01 6 4.29456224e+01 7.77784444e+01 -8.40005078e+01 7 1.37089760e+02 -1.08151738e+02 -8.67775150e+01 8 9.74598762e+01 -4.81766224e+00 -2.77851947e+01 9 -1.30171506e+02 -3.21952706e+02 -2.60792179e+02 10 5.78900550e+01 1.49665196e+02 -1.15631020e+02 11 -2.14381822e+02 7.65742226e+01 -1.85970468e+02 12 -8.69509546e+01 3.15741272e+02 2.96015969e+02 13 1.00176945e+02 -4.61113330e+01 -7.50194584e+01 14 4.12635146e+01 3.35801767e+01 -6.51115870e+01 15 4.51818434e+01 -7.16751940e+01 1.75904773e+00 16 -2.72943925e+01 7.32512141e+01 -1.83219426e+01 17 -1.11049807e+02 -4.90257515e+01 -5.62200406e+01 18 -3.74016781e+01 -1.77515855e+02 -1.16550940e+01 19 8.77247155e+01 -5.21722963e+01 1.15859390e+02 20 -1.63755962e+02 -8.49462440e+00 1.53541366e+02 21 -2.15379405e+02 -1.91160396e+02 1.16931760e+02 22 2.35248116e+02 1.29858144e+02 -1.45732405e+02 23 6.65369193e+01 -1.37405164e+02 1.00220905e+02 24 -1.59136936e+02 6.45456772e+01 2.05954048e+02 25 -1.36146512e+02 -4.60474786e+01 -8.58431035e+01 26 3.37667711e+01 1.25679932e+02 1.55613595e+01 27 1.15654962e+02 -3.82454723e+01 1.19827021e+02 28 -9.26463030e+01 1.00689043e+02 4.63292151e+01 29 3.24693726e+02 1.77292005e+02 1.30533779e+02 30 1.05528505e+02 3.85950896e+01 -3.70848747e+01 31 7.57775771e+01 2.68111851e+01 3.01894660e+01 32 -7.28443716e+01 4.05386625e+01 9.91549938e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = W (Configuration in file "config-T-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1650.48431392 Forces: 1 -4.97613021e+01 9.80846029e+00 -1.23701246e+01 2 6.69854590e+01 9.85719858e+00 -1.19318690e+02 3 1.39610243e+02 -1.57107441e+02 3.33969667e+01 4 -1.10662424e+02 1.37722119e+02 1.64974611e+02 5 -6.71466835e+01 4.46294220e+01 1.18561783e+02 6 -7.05181963e+01 1.72679735e+02 -2.65831279e+01 7 1.88977624e+02 1.44134480e+01 -8.54173836e+01 8 9.82309322e+01 -5.55960779e+00 -2.88392491e+01 9 4.67603634e+01 -3.79481480e+02 -2.39795127e+02 10 1.17504607e+02 9.63116599e+01 2.21666527e+02 11 -2.14996257e+02 7.81269698e+01 -1.86919717e+02 12 2.17343482e+01 3.13056296e+02 3.33563338e+02 13 1.32995861e+02 -6.48938704e+01 7.96978881e+00 14 -1.08403159e+02 1.18994754e+02 4.63962822e+01 15 -9.78884147e+01 -1.13955796e+02 5.11150246e+01 16 -1.28557010e+02 -1.35311269e+02 -8.93853725e+01 17 -1.79225475e+02 1.15249760e+02 -7.50778463e+01 18 -3.87356209e+01 -1.78181649e+02 -1.11582513e+01 19 1.81475876e+02 1.54889549e+02 -4.22602245e+01 20 -1.45758887e+02 -3.10023472e+01 8.45041926e+01 21 -2.63554960e+02 2.18714844e+01 1.61327421e+02 22 2.18350601e+02 1.31393783e+02 -1.46692973e+02 23 1.67800706e+02 -3.26774440e+01 -5.19957451e+01 24 -1.62769519e+02 7.31156873e+01 1.67821307e+02 25 -5.62406275e+01 -6.05450892e+01 -9.64114395e+01 26 1.25115801e+02 -4.41245792e+01 -1.17879134e+01 27 1.00103596e+02 -1.77036575e+02 -1.39299408e+02 28 -1.70020431e+02 -2.16147254e+01 -3.51606507e+01 29 3.25554200e+02 1.78200817e+02 1.31410815e+02 30 1.08974786e+02 -6.65138799e+01 -3.47985626e+01 31 -2.33407970e+01 -6.97083636e+01 -5.67506445e+01 32 -1.52595240e+02 -1.32607027e+02 -3.26856064e+01 MIXED STRUCTURE (pbc=False)-- Species = Fe W (Configuration in file "config-F-FeW.xyz") ----------------------------------------------------------------------------------------------------- Energy = 451.612323525 Forces: 1 -4.01256215e+01 -5.16028557e+01 -5.70321863e+01 2 9.47919317e+01 -1.85751010e+02 -2.00783390e+02 3 4.04543545e+01 -5.81146288e+01 1.24005023e+01 4 -1.36483193e+02 -2.47822706e+01 2.04563052e+01 5 1.96175082e+01 -3.31364232e+01 -1.44256946e+01 6 1.40007016e+02 -1.53772834e+02 -8.24323131e+01 7 3.49143723e+00 -2.27171963e+01 3.57774159e+00 8 8.85272602e+01 -1.89821254e+02 -7.24194600e+01 9 -1.77778101e+02 9.35422760e+01 -1.39167236e+02 10 -5.92079010e+00 3.15043032e+01 -2.50682335e+01 11 3.89332965e+01 2.27417710e+02 1.52203479e+02 12 -1.83236979e+01 9.76264930e+00 -1.18449631e+01 13 -1.34853536e+02 5.23760772e+01 -8.46011446e+01 14 4.90623061e+01 4.83270791e+01 1.08248179e+00 15 4.69762684e+01 1.08375737e+02 1.03644018e+02 16 2.65561937e+01 2.76605590e+01 2.17201105e+01 17 -1.83963356e+01 -5.48241666e+01 2.61679471e+01 18 5.05768501e+01 -8.60562075e+01 5.20388146e+01 19 5.27269348e+00 -7.16566426e+00 5.18039717e+00 20 -1.41625078e+01 -9.34894214e+00 3.60944350e+01 21 -3.57956765e+01 -2.28315871e+01 -1.12758059e+01 22 4.22454052e+01 4.82901235e+01 -1.06373863e+02 23 1.94976961e+01 -9.29206070e+01 9.80816783e+01 24 -2.77734651e+01 -1.49234302e+01 1.32452728e+01 25 -1.68466210e+02 4.66309004e+01 2.66654375e+01 26 3.71971047e+01 9.21617737e+01 -2.95911379e+01 27 -7.63420701e+01 -9.43671208e+01 1.13472922e+01 28 -2.56796240e+01 2.16876941e+01 4.85327643e+01 29 3.47031060e+01 1.35884970e+02 1.04907448e+02 30 6.64954895e+00 3.26558848e+01 -3.08561154e+01 31 3.81070553e+01 1.81114844e+01 5.50603785e+01 32 9.74337954e+01 1.07746977e+02 7.34650393e+01 MIXED STRUCTURE (pbc=True)-- Species = Fe W (Configuration in file "config-T-FeW.xyz") ----------------------------------------------------------------------------------------------------- Energy = 767.557953012 Forces: 1 2.12834820e+01 -8.26999822e+01 -5.17907095e+01 2 8.98807047e+01 -1.77077631e+02 -1.80973328e+02 3 4.42915917e+01 -4.35598858e+01 2.56426248e+00 4 -6.15058927e+01 -2.60078393e+01 -7.24451412e+00 5 3.58175786e+01 -2.55162177e+01 9.80540086e+00 6 5.46149284e+01 -1.48500580e+02 -4.26539420e+01 7 -2.42636711e+01 -2.63835794e+01 8.18029028e+00 8 8.93033082e+01 -1.90923909e+02 -7.33739643e+01 9 -1.01802692e+02 8.38481847e+01 -1.13211952e+02 10 -8.43476957e+01 4.23368206e+01 5.52552063e+01 11 3.78353426e+01 2.28655675e+02 1.50511103e+02 12 -1.63394808e+01 -5.36535970e+01 -7.03349939e+01 13 -1.28379578e+02 1.38158541e+01 1.56430644e+02 14 2.20341219e+01 8.78559107e+01 3.58344264e+01 15 3.60548320e+01 1.15672546e+02 1.03028997e+02 16 2.60059681e+01 2.72994331e+01 2.48491979e+01 17 -1.71023154e+01 1.46004260e+02 3.10619898e+01 18 5.04790908e+01 -8.64656062e+01 5.43570666e+01 19 -7.28864331e+00 -5.78446903e+00 -2.53132219e+01 20 1.64091909e+01 -4.69549575e+00 2.54245768e+01 21 -4.30742873e+01 -5.80989501e+00 -1.39189254e+01 22 -5.89642465e+01 6.20774590e+01 -6.27347803e+01 23 -2.78452142e+01 3.53674955e+00 1.85617745e+02 24 -4.80658632e+01 -9.22938768e+01 -9.39225776e+01 25 -1.13563375e+02 5.44146358e+01 -7.26138714e-01 26 1.64744577e+02 -4.48535609e+01 -2.41871264e+01 27 -7.88084206e+01 -9.43253660e+01 -3.47265079e+00 28 6.09263400e+00 2.13886181e+01 5.85900478e+01 29 3.46606867e+01 1.36004993e+02 1.05356842e+02 30 -8.58351224e+01 -1.28947638e+02 -9.17776589e+01 31 2.70910357e+01 1.82464620e+01 -4.52682392e+01 32 1.40587425e+02 1.96341528e+02 -1.05963073e+02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==30037== Memcheck, a memory error detector ==30037== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==30037== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==30037== Command: python runner2.py EAM_Dynamo_BonnyCastinBullens_2013_FeW__MO_737567242631_000 ==30037== ==30037== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==30037== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==30037== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30037== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30037== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30037== by 0x4010732: call_init (dl-init.c:72) ==30037== by 0x4010732: _dl_init (dl-init.c:119) ==30037== by 0x40151FE: dl_open_worker (dl-open.c:522) ==30037== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==30037== by 0x40147C9: _dl_open (dl-open.c:605) ==30037== by 0x544CF95: dlopen_doit (dlopen.c:66) ==30037== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==30037== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==30037== by 0x544D734: _dlerror_run (dlerror.c:162) ==30037== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==30037== ==30037== ==30037== HEAP SUMMARY: ==30037== in use at exit: 22,236,789 bytes in 4,275 blocks ==30037== total heap usage: 193,087 allocs, 188,812 frees, 93,877,327 bytes allocated ==30037== ==30037== LEAK SUMMARY: ==30037== definitely lost: 0 bytes in 0 blocks ==30037== indirectly lost: 0 bytes in 0 blocks ==30037== possibly lost: 182,735 bytes in 112 blocks ==30037== still reachable: 22,054,054 bytes in 4,163 blocks ==30037== suppressed: 0 bytes in 0 blocks ==30037== Rerun with --leak-check=full to see details of leaked memory ==30037== ==30037== For counts of detected and suppressed errors, rerun with: -v ==30037== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2526 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.