Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:15:33) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_2015_NiCo__MO_010613863288_000 Supported species : Co Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Co (Configuration in file "config-F-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = 390.165255335 Forces: 1 -6.50233145e+01 -1.90447847e+02 -2.57368362e+02 2 -3.55070304e-02 3.59428680e+01 -3.01002415e+01 3 9.57556389e+01 -1.03150389e+02 6.69210704e+01 4 -6.92611163e+01 2.72365788e+02 1.93337433e+02 5 7.53139395e-01 -3.60499030e+01 -2.30384180e+01 6 7.84069621e+00 7.63661174e+00 -1.63731427e+01 7 -2.20301279e+01 -2.58361452e+02 -2.71491580e+02 8 -8.73822557e+01 -9.67733186e+01 1.38206043e+01 9 -1.52094001e+00 -6.24409740e+00 -4.99533772e+00 10 -5.54190571e+01 2.39556462e+01 -6.54123307e+01 11 -2.01218425e+02 -1.04411073e+02 -1.23697318e+02 12 -3.05025703e+00 1.13454160e+01 -2.58363728e-01 13 -1.35966886e+02 -6.30569394e+01 -2.63517852e+02 14 3.42314662e+01 3.70065214e+01 -1.33637568e+01 15 2.51813226e+02 3.32019767e+01 1.41532500e+02 16 8.53044231e+01 2.41967521e+02 2.02781485e+01 17 -4.13069279e+01 -1.29516938e+02 -1.38993610e+02 18 6.45539797e+01 -3.69968906e+01 8.39154215e+00 19 2.09861804e+01 -2.18242417e+01 1.71584743e+01 20 -1.15193265e+01 1.21408509e+02 1.40096634e+02 21 -1.08112275e+02 -5.21486650e+01 -1.08963703e+01 22 1.46717039e+02 2.62291973e+02 2.16753511e+02 23 5.28660769e+01 -1.08259774e+01 8.70146884e+01 24 -1.06669895e+01 3.11878467e+01 2.17667597e+01 25 -6.75355836e+01 4.24080537e+01 -9.27333537e+00 26 -7.82344597e+01 2.04518204e+02 -8.71589852e+01 27 1.63180073e+02 -3.12031033e+02 6.09629465e+01 28 -2.21733225e+02 1.98291480e+02 6.15398571e+01 29 1.86815676e+02 -1.44702639e+02 2.02677729e+02 30 1.20427710e+01 2.64982444e+01 1.39786831e+01 31 2.87156406e+01 -2.36506297e+01 4.13593759e+00 32 2.84406473e+01 4.01653750e+01 4.55724840e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Co (Configuration in file "config-T-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = 513.471317902 Forces: 1 3.89836508e+01 -2.71709541e+02 -2.39608675e+02 2 -7.29598071e+00 3.46001706e+01 -1.96159056e+01 3 1.09614568e+02 -6.73279561e+01 7.36807639e+01 4 -2.81901234e+01 2.77186754e+02 1.96886423e+02 5 1.68456642e+01 2.87987378e+00 -2.96064754e+01 6 -1.14728952e+02 1.23014603e+02 3.72530988e+01 7 -3.99906138e+01 -2.56901823e+02 -2.75582677e+02 8 -8.62856165e+01 -9.74507197e+01 1.31702459e+01 9 -4.76187985e+00 -8.59833704e+01 7.95534085e+01 10 -7.53525291e+01 -3.44142959e+00 -6.07809697e+01 11 -2.01510087e+02 -1.03282748e+02 -1.24426709e+02 12 1.13550695e+02 -3.48541606e+00 -1.17296480e+02 13 -1.33870319e+02 -6.74757594e+01 -2.54508572e+02 14 1.51814772e+01 4.56203689e+01 -1.56554071e+01 15 2.47628168e+02 3.11321077e+01 1.40330774e+02 16 8.55711137e+01 2.23626827e+02 3.11283829e+01 17 2.68466113e+02 -4.25693946e+02 -6.10629191e+01 18 6.42754154e+01 -3.79502175e+01 8.63096635e+00 19 1.98900483e+01 2.16218995e+01 3.74020404e+01 20 2.98990826e+02 3.00219005e+02 1.34465929e+02 21 -1.07384939e+02 -5.04392953e+01 -9.45043973e+00 22 -1.58786668e+02 5.57315179e+02 1.13992995e+02 23 -2.65741842e+02 -2.17680804e+02 4.38778411e+01 24 -3.74055871e+00 3.07433377e+01 1.15527750e+01 25 -6.20529190e+01 4.10828409e+01 -8.24351443e+00 26 -7.12312252e+01 1.72270592e+02 -1.09505186e+02 27 1.68635406e+02 -3.11783191e+02 5.20420724e+01 28 -2.18568082e+02 2.58803496e+02 -1.64383708e+01 29 1.87350391e+02 -1.43181979e+02 2.03077968e+02 30 -1.18488583e+02 8.42089892e+00 1.44700400e+02 31 2.62735712e+01 -2.62636099e+01 -3.30044191e-01 32 3.67238096e+01 4.15138526e+01 2.03662629e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -72.7400114567 Forces: 1 -2.14418174e+00 -1.27157418e+00 -1.54034051e+00 2 -2.11779849e+00 6.20432473e-01 -5.86512771e+00 3 3.18708533e+00 -4.92443316e+00 7.67888507e-01 4 -5.91925852e+00 1.81686993e+00 -2.66469683e+00 5 -1.84499706e-01 -3.32459694e+00 -3.11417869e+00 6 5.05089276e+00 1.19703959e+00 -3.65950295e+00 7 9.09944816e-01 -1.92470338e+00 1.56195420e+00 8 -1.07968672e+00 -6.11076109e+00 1.85568615e+00 9 -3.75842709e+00 -2.61313512e+00 4.53891364e-01 10 3.20747367e+00 3.03191714e+00 -1.26206653e+00 11 -4.05759864e+00 3.68172326e+00 1.62855986e+00 12 -2.65892400e+00 7.93787377e-01 -1.39319422e+00 13 1.43459687e+00 2.66044465e+00 -7.39898439e+00 14 8.02532746e-01 3.10359925e-01 -1.07668065e+00 15 6.71050879e+00 2.73641926e+00 -2.09682861e+00 16 -3.42661910e+00 4.55779523e+00 -2.44119006e+00 17 -2.04450379e+00 -2.90668828e+00 2.64281837e+00 18 3.04057962e+00 -1.08503260e+00 -4.23506123e-01 19 -4.26745191e-01 -3.87265197e+00 2.70116536e+00 20 -3.59824002e+00 -9.45083883e-01 4.02250531e+00 21 -1.38219473e+00 -2.66517803e+00 -2.40838771e+00 22 5.48385115e+00 -3.12456030e+00 1.57666726e+00 23 3.78694167e+00 -2.70777523e+00 1.52800993e+00 24 -1.82100353e+00 1.29910164e+00 3.70329143e+00 25 -4.60325040e+00 3.88352331e+00 -1.54685907e+00 26 2.49687816e+00 2.91017993e+00 -7.19498080e-01 27 1.33522625e+00 -2.93157732e+00 3.26949468e+00 28 -3.28701573e+00 1.72428100e+00 2.44419342e+00 29 -3.46648361e+00 1.05001998e+00 1.77040750e+00 30 3.55323808e+00 3.20459790e+00 2.52380422e+00 31 4.01052784e+00 7.82095944e-01 2.87340041e+00 32 9.66153253e-01 4.14716294e+00 2.28730417e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -55.141527544 Forces: 1 1.53650410e+00 2.38468842e+00 -5.02511250e+00 2 -9.89753052e-01 2.23127455e+00 1.36293463e-01 3 4.89732286e+00 -1.29812037e+00 -1.09272231e+00 4 -2.18849229e-01 2.13757220e+00 -4.01109080e+00 5 2.68775572e-01 -5.20819735e+00 2.99973664e+00 6 2.91480223e+00 3.62393506e-01 1.27424719e-01 7 -5.86696420e+00 3.02718145e+00 7.22541947e-01 8 -1.12177864e+00 -5.87095973e+00 1.60528641e+00 9 5.35542018e-01 -2.81195373e+00 4.90881014e+00 10 3.58424107e+00 2.62517842e+00 6.15664587e+00 11 -3.84224583e+00 3.54631977e+00 1.89730094e+00 12 1.61194739e+00 -7.95878919e+00 -1.10624871e+00 13 2.91846781e-01 2.97294039e+00 -3.87981326e+00 14 -4.67401400e+00 -1.13649221e+00 -1.38853850e+00 15 3.84205024e+00 3.68442886e+00 -3.86237556e+00 16 -3.86958789e+00 1.72488077e+00 -4.07829611e+00 17 -7.43253133e-01 2.91575768e+00 5.34946072e+00 18 2.92241617e+00 -1.11049407e+00 -3.05572078e-01 19 -5.14198056e-01 -2.77209181e+00 -8.47181296e-01 20 -2.32969973e+00 -3.02234085e+00 -1.29123225e-01 21 -1.78714535e+00 4.58948459e+00 -1.35498168e+00 22 -2.22116541e+00 -5.20379681e+00 2.32323033e+00 23 3.78550930e+00 -3.33617880e-01 2.50285412e+00 24 -1.12787545e+00 2.02523547e+00 -2.71985637e+00 25 1.19607631e+00 6.84448993e+00 4.38247444e-01 26 3.23218903e+00 -2.40744830e+00 3.23115901e-01 27 2.39218763e+00 -4.17661011e+00 -2.08342924e+00 28 -5.02098116e+00 7.81838346e-01 -2.18328007e+00 29 -3.57439462e+00 1.15344222e+00 1.81800547e+00 30 2.01054039e+00 -3.38338100e+00 3.37897982e+00 31 4.16673109e-01 2.01129823e+00 -2.03857017e+00 32 2.46328156e+00 1.67588862e+00 1.41825794e+00 MIXED STRUCTURE (pbc=False)-- Species = Co Ni (Configuration in file "config-F-CoNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 763.923526335 Forces: 1 -1.92310921e+00 -7.91308130e-01 -8.09970180e-01 2 -1.78071577e+01 2.40573419e+02 -3.08968186e+02 3 -1.80549147e+02 -4.47719962e+02 4.33636021e+02 4 -2.67595687e+01 -1.18923115e+02 -1.37491195e+02 5 7.75175835e+01 -2.85780480e+01 -1.41330252e+02 6 6.04484375e+00 4.43254133e-01 -5.41412051e+00 7 2.61929523e+00 -1.17831139e+01 -2.79567243e+00 8 -1.84509980e+01 -9.44026436e+01 1.20696036e+02 9 -7.92687124e+01 -1.78645189e+01 -9.87119377e+01 10 5.90478791e-01 1.00827854e+02 -1.02466677e+02 11 8.89681732e+01 -7.09143071e+01 1.15551775e+02 12 -2.86195729e+02 2.45859126e+02 -2.95955461e+02 13 2.23522053e+01 1.69807625e+02 -2.61536249e+02 14 5.26171736e+00 5.44009819e+00 -1.53872064e+00 15 4.09736151e+02 1.00894960e+02 -1.40157044e+02 16 1.22573361e+02 8.04429847e+01 -8.23842092e+01 17 -9.29535655e+01 -1.39552926e+02 5.24261533e-01 18 -9.29105321e+01 2.68766991e+02 -4.03324267e+02 19 2.17126630e+02 -5.90729605e+02 2.29621971e+02 20 -3.24272061e+02 2.17905034e+02 5.18366693e+01 21 1.20202803e+02 -2.96594283e+02 -1.31606272e+02 22 2.34565799e+02 -2.07114239e+02 2.81841643e+01 23 1.50284140e+00 -6.05608115e-01 9.67510909e-01 24 6.83679649e+02 -2.74635385e+02 3.79295233e+02 25 -8.76758398e+01 -1.28430754e+02 3.12322933e+02 26 1.63963813e+02 4.01761211e+01 2.45530896e+02 27 -5.17708303e+02 7.69205126e+02 -5.84915219e+01 28 8.83720966e-01 2.11500262e+01 2.59399624e+01 29 -4.48130786e+02 1.34957744e+02 1.87503722e+02 30 1.76024032e+01 3.72038521e+01 -9.03997934e+00 31 1.79100625e+01 -1.87875228e+01 3.88179052e+01 32 -1.84960214e+01 1.37731253e+01 1.15926727e+01 MIXED STRUCTURE (pbc=True)-- Species = Co Ni (Configuration in file "config-T-CoNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 971.303608299 Forces: 1 2.03530938e+01 -1.06838263e+02 1.49727681e+02 2 -7.17451636e+01 2.32479690e+02 -2.17649526e+02 3 -2.15068381e+02 -3.92535625e+02 4.28042869e+02 4 -7.57039532e+00 -1.17360414e+02 -1.38922859e+02 5 7.79778625e+01 -4.43684767e+01 -1.18364951e+02 6 -1.01083935e+00 -1.61689931e+00 -9.67242066e+00 7 3.45045823e+00 -1.00250443e+01 -3.35440208e+00 8 -1.80863337e+01 -9.37304791e+01 1.20682275e+02 9 -4.69132850e+01 -1.89837442e-01 -3.95511539e+01 10 1.77297919e+01 9.15836225e+01 -7.25681665e+01 11 8.81219261e+01 -7.03016116e+01 1.14751944e+02 12 -2.84156948e+02 -1.05619258e+02 -5.65234861e+02 13 2.24075785e+01 1.65847374e+02 -2.51162290e+02 14 3.93166749e+01 -6.20432120e+01 1.18398923e+02 15 4.01752456e+02 1.01730383e+02 -1.44902747e+02 16 1.57533402e+02 2.64683858e+01 -7.82563843e+01 17 -1.08638680e+02 3.06762390e+02 2.10261807e+02 18 -9.34638907e+01 2.67846579e+02 -4.02999793e+02 19 2.54731711e+02 -5.37974977e+02 2.28809696e+02 20 -3.01804986e+02 3.38743408e+02 -1.05742336e+02 21 1.19895993e+02 -2.94055641e+02 -1.32994870e+02 22 2.18131963e+02 -2.14069248e+02 3.49387219e+01 23 2.94906987e+01 1.45027109e+02 -7.88547714e+01 24 7.37260722e+02 -2.45932680e+02 2.71628732e+02 25 2.64823857e+02 -3.03619334e+02 1.76638350e+02 26 2.07685679e+02 -1.81345350e+01 2.39410568e+02 27 -5.18141997e+02 7.69344192e+02 -6.12972845e+01 28 -4.30485787e+01 -7.21666876e+01 1.69170616e+01 29 -4.47463804e+02 1.35647392e+02 1.88217432e+02 30 -2.44258235e+02 2.25770196e+02 3.14353870e+01 31 -1.27427083e+02 -3.47310127e+01 1.31453178e+02 32 -1.31865266e+02 -8.19374855e+01 -3.97858092e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==5872== Memcheck, a memory error detector ==5872== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==5872== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==5872== Command: python runner2.py EAM_Dynamo_PunYamakovMishin_2015_NiCo__MO_010613863288_000 ==5872== ==5872== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==5872== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==5872== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5872== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5872== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5872== by 0x4010732: call_init (dl-init.c:72) ==5872== by 0x4010732: _dl_init (dl-init.c:119) ==5872== by 0x40151FE: dl_open_worker (dl-open.c:522) ==5872== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==5872== by 0x40147C9: _dl_open (dl-open.c:605) ==5872== by 0x544CF95: dlopen_doit (dlopen.c:66) ==5872== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==5872== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==5872== by 0x544D734: _dlerror_run (dlerror.c:162) ==5872== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==5872== ==5872== ==5872== HEAP SUMMARY: ==5872== in use at exit: 39,230,353 bytes in 4,274 blocks ==5872== total heap usage: 198,835 allocs, 194,561 frees, 113,050,057 bytes allocated ==5872== ==5872== LEAK SUMMARY: ==5872== definitely lost: 0 bytes in 0 blocks ==5872== indirectly lost: 0 bytes in 0 blocks ==5872== possibly lost: 182,735 bytes in 112 blocks ==5872== still reachable: 39,047,618 bytes in 4,162 blocks ==5872== suppressed: 0 bytes in 0 blocks ==5872== Rerun with --leak-check=full to see details of leaked memory ==5872== ==5872== For counts of detected and suppressed errors, rerun with: -v ==5872== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2522 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. === Verification check vc-memory-leak end (2018-12-15 06:16:14) ===