Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:09:04) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_CaiYe_1996_AlCu__MO_942551040047_005 Supported species : Al Cu 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 = 97.2190813432 Forces: 1 -5.58966704e+00 -1.04817941e+01 -1.11343262e+01 2 -5.32504680e+00 6.85589984e+00 -9.96877996e+00 3 6.03048692e+00 -8.00083596e+00 -1.99059784e+00 4 -8.13994485e+00 7.30387795e+00 5.53614888e+00 5 -1.00906108e+00 -1.75314086e+01 -5.55833992e+00 6 1.07237913e+01 6.08857525e+00 -1.16281403e+01 7 1.05321703e+01 -3.21462558e+01 -2.31956564e+01 8 -1.71689076e+01 -1.27533518e+01 -1.57791151e+00 9 -9.52333758e+00 -1.52957497e+01 -2.43264305e+01 10 -2.31346495e+00 2.15247197e+01 -2.33986341e+01 11 -8.78004657e+00 -1.62155603e+01 8.34011218e+00 12 -1.61971825e+01 1.91435734e+01 1.41080085e+01 13 -6.79467205e+00 -1.48719950e+01 -4.57595206e+01 14 1.02438718e+01 1.25352882e+01 -9.52865001e+00 15 4.04217017e+01 -1.15639583e+01 5.03939522e+00 16 4.04599078e+00 3.48987182e+01 1.34699889e+01 17 -2.22767232e+01 -1.51686582e+01 -6.72969523e+00 18 1.54152458e+01 1.97330032e+01 -1.84414168e+01 19 7.13791933e+00 -2.48314374e+01 1.55327535e+01 20 -1.76405505e+01 8.37350213e+00 1.99151487e+01 21 -1.40182501e+01 -1.27682675e+01 7.22232650e+00 22 2.38069932e+01 2.32661934e+01 2.36032223e+01 23 5.97254819e+00 -2.88166027e+00 8.13735539e+00 24 6.47648894e+00 5.66468460e+00 9.62778656e+00 25 -1.70277784e+01 -5.00082679e+00 -5.59052740e+00 26 -6.52988576e+00 2.42940034e+01 -1.05500840e+01 27 1.36136226e+01 -3.29874103e+01 1.79907446e+01 28 -2.98697298e+01 2.66836963e+01 9.07868630e+00 29 -8.17315653e+00 -1.24755271e+01 1.07844385e+01 30 1.31658412e+01 1.92769661e+01 9.59874027e+00 31 1.83934102e+01 -7.90597193e+00 1.29347249e+01 32 1.03973230e+01 1.72379674e+01 1.84591296e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 236.418383888 Forces: 1 3.31390082e+01 -1.82915378e+01 7.14575977e+00 2 -2.89514973e+01 9.02150457e+00 3.04344269e+01 3 4.38323661e+00 8.14842709e+00 4.86551512e-01 4 1.50980231e+01 1.46258166e+01 -2.14512488e+00 5 4.07588242e+00 -5.25358388e+00 7.79685957e-01 6 -3.09441906e+01 3.82911038e+01 9.63577187e+00 7 -3.22460118e+00 -2.69223140e+01 -2.34172572e+01 8 -1.77583016e+01 -1.27603552e+01 -1.42495407e+00 9 -1.82744024e+01 -3.08501024e+01 1.11578927e+01 10 -8.35847940e+00 1.14262142e+01 -1.04108502e+01 11 -8.82706746e+00 -1.62755753e+01 8.58640622e+00 12 1.22010655e+01 5.60817673e+00 2.70989688e+01 13 -5.94366224e+00 -1.77925286e+01 -3.60872730e+01 14 -1.97463279e+01 4.51802020e+00 -1.68353762e+01 15 3.16014914e+01 -1.14736202e+01 5.77812702e+00 16 5.54668532e+00 2.40124379e+01 1.48974395e+01 17 6.39953104e+00 -2.31230605e+01 -7.72878999e+00 18 1.68381435e+01 1.99238657e+01 -1.89349066e+01 19 7.82271361e+00 -7.20231295e+00 1.26528173e+01 20 2.52462384e+00 2.65409155e+01 3.32824271e+00 21 -1.43399509e+01 -1.69574380e+00 8.03370673e+00 22 -4.95929310e+00 3.67496896e+01 2.78106995e+01 23 -1.70153277e+01 -2.55455955e+01 -1.83991033e+01 24 3.09518469e+01 1.03755704e+01 -3.12993530e+01 25 -7.23942303e+00 -8.30352166e+00 -4.77744827e+00 26 -4.72638373e+00 6.80627460e+00 -1.35259631e+01 27 2.70196455e+01 -3.46336696e+01 -9.64641148e+00 28 -2.97191906e+01 2.66764483e+01 -8.44794678e+00 29 -8.12118355e+00 -1.25111060e+01 1.08354570e+01 30 2.91824478e+00 7.99570778e+00 1.13930681e+01 31 1.30191589e+01 -1.01263011e+01 8.67787711e+00 32 1.46099822e+01 1.20407556e+01 4.34785938e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 39.3261824305 Forces: 1 -4.31589218e+00 -1.05857742e+01 -4.04876777e+00 2 1.75233477e+01 -4.23828594e+00 -2.15254477e+01 3 -2.70621280e+01 -2.97082948e+01 -1.57083560e+01 4 -2.20072953e+01 -4.75620035e+00 1.91176616e+01 5 -1.75559946e+00 -1.66336302e+01 -2.74871216e+01 6 8.74903437e+00 -2.49720102e+01 -3.11651408e+01 7 1.28872895e+01 -8.99356149e+00 6.89114553e+00 8 4.90655804e+00 2.96788901e+01 6.43584318e+00 9 -1.44325214e+01 1.37946121e+01 -1.49847192e+01 10 -1.46661288e+01 1.47563306e+01 -1.91989605e+01 11 6.70608408e+00 -6.03033717e+00 7.25257850e+00 12 -9.99104177e+00 8.73224412e+00 2.57937018e+00 13 1.12073289e+00 -1.01891126e+01 -1.62857049e+01 14 6.33450437e+00 1.35524873e+01 -9.07114200e+00 15 5.92501687e+00 1.89942856e+01 2.77273359e+01 16 1.66604698e+01 1.11518915e+01 2.19396632e+01 17 -1.07374500e+01 -4.49346681e+01 -2.86238805e+01 18 9.56328092e+00 1.09852084e+01 6.10576563e+00 19 -1.59058547e+00 -4.17940450e+00 4.32590535e+00 20 -7.85625954e+00 2.94938910e+01 3.86662519e+01 21 2.27505399e+01 -7.22975686e+00 2.48246706e+01 22 1.89069641e+01 -1.30309889e+01 6.58859927e-02 23 7.29683339e-02 -3.87689220e-01 5.28178683e-02 24 -5.58320217e+00 -7.51870399e+00 7.59187661e+00 25 -1.28634079e+01 5.76265388e+00 -6.43334899e+00 26 7.25629077e+00 3.91968941e+00 -7.74487189e+00 27 9.23993767e+00 3.13858920e+00 1.21328472e+01 28 -9.76231218e+00 4.45598589e+00 9.02514655e+00 29 -2.52849495e+01 2.05182192e+00 -4.21144535e+00 30 1.96248688e+01 1.35419015e+01 -1.49189575e+01 31 1.18674227e+01 -3.17151542e+00 1.20356434e+01 32 -1.21865372e+01 1.25494514e+01 1.46374554e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 62.4533166713 Forces: 1 2.99332391e+00 1.17410101e+00 -9.31384931e+00 2 1.67251220e+01 -5.67687743e+00 -1.08685957e+01 3 -2.74822816e+01 -2.06534728e+01 -1.54924227e+01 4 -1.47148571e+01 -5.62831349e+00 2.06804876e+01 5 7.72892715e+00 -1.03436417e+01 -1.40558179e+01 6 -2.77305657e+00 -3.17138815e+01 -2.62897602e+01 7 3.83411738e+00 -4.57905592e+00 1.27602048e+01 8 5.08361456e+00 2.93567123e+01 5.99435432e+00 9 -1.83476469e-01 1.39280212e+01 -1.26471776e+01 10 -1.38158724e+01 4.34122869e+00 -1.65062439e+01 11 6.49665457e+00 -5.92014317e+00 6.96042554e+00 12 -4.22465940e-01 2.07043171e+00 1.68121595e+01 13 -3.84216143e+00 -7.84834567e+00 -2.53315747e+00 14 -4.62794622e+00 1.37473195e+01 -1.04227702e+01 15 -6.59709895e-01 1.96203880e+01 3.17707673e+01 16 1.82323199e+01 4.89666477e+00 2.13228931e+01 17 -5.22753688e+00 -4.09845553e+01 -3.61839317e+01 18 9.18503973e+00 1.06982149e+01 6.20923383e+00 19 -9.37383982e+00 2.10084302e+00 -9.60581036e+00 20 1.13143910e-01 3.32683038e+01 3.50565982e+01 21 2.52930193e+01 -2.41849570e+00 2.27059023e+01 22 1.11285214e+01 -1.12696122e+01 -2.63943640e+00 23 -1.01709019e+01 -9.73467081e-01 4.60890677e+00 24 -5.26994433e+00 -9.81246927e+00 2.18125751e+00 25 -1.01660590e+01 6.86415770e+00 -6.25962203e+00 26 4.77596368e+00 -6.49882561e+00 -6.44754257e+00 27 9.15008509e+00 6.08271246e+00 -1.20699105e+00 28 -8.02053852e+00 -1.08812502e+00 7.96491302e+00 29 -2.48876225e+01 2.36711179e+00 -4.10328180e+00 30 1.80792639e+01 1.29521729e+01 -1.55183646e+01 31 1.41257554e+01 -3.65584779e+00 -4.84861575e+00 32 -1.13066012e+01 5.59674592e+00 9.91528730e+00 MIXED STRUCTURE (pbc=False)-- Species = Al Cu (Configuration in file "config-F-AlCu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 73.8954251771 Forces: 1 -7.65058756e+00 -8.62619867e+00 -1.54288798e+00 2 5.96637745e+00 5.09489328e+00 -1.47815382e+01 3 -1.11562219e+01 -3.32943705e+01 -8.51793869e+00 4 -3.76028666e+01 -1.09544606e+01 -2.48899856e+00 5 2.20334758e+00 -5.94841013e+00 -1.82967672e+01 6 4.05996997e+00 -1.81544077e+00 -3.05744720e+00 7 2.89223546e+01 -9.83584214e+00 -2.77087116e+01 8 1.96885738e+01 1.05144468e+01 -1.15218977e+01 9 -1.21245585e+01 8.14941741e+00 -1.64574808e+01 10 2.35313550e+00 5.62692552e+00 -5.89958644e+00 11 1.44265769e+01 2.77516201e+01 -1.78581459e+00 12 -5.02185320e+00 4.89599310e+00 3.84630394e+00 13 -1.99006672e+01 -1.81034622e+01 -1.62598998e+01 14 2.27178761e+01 1.59287384e+01 -1.45444998e+01 15 2.27778065e+01 -2.42887900e+01 -6.98753294e+00 16 -2.10317079e+01 2.36036130e+01 3.86309582e+00 17 -1.94676784e+01 -1.69439777e+01 -2.70717018e+00 18 1.20105168e+01 7.61995825e+00 2.69708709e+01 19 1.37916489e+01 -2.56801459e+01 1.00338113e+01 20 -2.42349989e+01 1.91596415e+01 1.05307139e+01 21 -2.71777736e+01 -2.93212505e+01 9.18503970e+00 22 2.56187556e+01 2.03681053e+01 5.37663747e+00 23 2.00943103e+01 -1.67090510e+01 1.60581404e+01 24 -1.06431944e+01 1.29787381e+01 1.70155385e+01 25 -1.17516349e+01 -5.61457945e+00 -4.16893095e+00 26 5.39995563e+00 1.32125367e+01 -6.47117165e+00 27 -5.26838759e+00 -4.72597322e+00 1.30847889e+01 28 -4.95266836e+00 7.62561808e+00 1.25226954e+01 29 -7.63020879e+00 2.09597491e+00 -4.20723361e+00 30 1.42323336e+01 2.12030628e+01 1.55261996e+01 31 2.08803007e+01 -1.31786301e+01 1.27225683e+01 32 -9.52883210e+00 1.92112996e+01 1.06691037e+01 MIXED STRUCTURE (pbc=True)-- Species = Al Cu (Configuration in file "config-T-AlCu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 117.985394518 Forces: 1 -1.94696843e+01 8.12851256e+00 -5.94272859e-01 2 9.81267780e+00 8.85245936e+00 5.04034488e-01 3 -9.59295361e+00 -2.45090853e+01 -6.58940476e+00 4 -3.33894033e+01 -1.26877663e+01 -2.63375394e+00 5 3.43908955e+00 -9.55979406e-01 -1.29864548e+01 6 -1.53365429e+00 -1.35508201e+01 4.00290701e+00 7 2.60518888e+01 4.28050850e+00 -3.13859215e+01 8 1.99448088e+01 1.02237803e+01 -1.17788732e+01 9 3.61559000e+00 8.69911708e+00 -1.37974227e+01 10 1.20129804e+01 -1.13385671e+01 -1.73361685e+00 11 1.41672643e+01 2.80663864e+01 -2.02854994e+00 12 9.54235867e-01 -4.97954249e+00 4.10589975e+00 13 -2.46215500e+01 -2.46960824e+01 6.43747868e-01 14 2.44351860e+01 2.15907487e+01 1.92925090e+00 15 1.14771735e+01 -2.41714289e+01 -5.46775975e+00 16 -2.30776232e+01 4.36165422e+00 -2.92228367e+00 17 -1.14592363e+01 -1.05750179e+01 2.15618252e+00 18 1.18625403e+01 7.79515957e+00 2.69249435e+01 19 1.68915858e+01 -2.09394747e+01 2.59812848e+00 20 -2.66800345e+01 1.97342416e+01 -2.40122972e-01 21 -3.45788727e+01 -2.89447673e+00 1.37006760e+01 22 1.97080925e+01 2.25362311e+01 5.75248781e+00 23 2.37410461e+01 -3.54751814e-01 1.84568140e+01 24 -1.08942565e+01 1.46634881e+01 1.08553657e+01 25 -7.09310990e-01 -9.22569557e+00 -2.49332046e+00 26 3.29835533e+00 1.22340273e+00 -6.10646264e+00 27 -5.60046765e+00 -4.24157581e+00 1.01590401e+01 28 -4.27818987e+00 3.34496610e+00 4.17370054e+00 29 -7.16668852e+00 2.07738852e+00 -4.07553266e+00 30 1.56299276e+01 -5.00175179e-01 1.37539267e+01 31 1.78959864e+01 -1.49101833e+01 -7.36324229e+00 32 -2.18865034e+01 1.49525780e+01 -7.52011040e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==30980== Memcheck, a memory error detector ==30980== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==30980== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==30980== Command: python runner2.py EAM_Dynamo_CaiYe_1996_AlCu__MO_942551040047_005 ==30980== ==30980== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==30980== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==30980== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30980== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30980== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30980== by 0x4010732: call_init (dl-init.c:72) ==30980== by 0x4010732: _dl_init (dl-init.c:119) ==30980== by 0x40151FE: dl_open_worker (dl-open.c:522) ==30980== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==30980== by 0x40147C9: _dl_open (dl-open.c:605) ==30980== by 0x544CF95: dlopen_doit (dlopen.c:66) ==30980== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==30980== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==30980== by 0x544D734: _dlerror_run (dlerror.c:162) ==30980== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==30980== ==30980== ==30980== HEAP SUMMARY: ==30980== in use at exit: 14,440,357 bytes in 4,274 blocks ==30980== total heap usage: 198,995 allocs, 194,721 frees, 85,672,185 bytes allocated ==30980== ==30980== LEAK SUMMARY: ==30980== definitely lost: 0 bytes in 0 blocks ==30980== indirectly lost: 0 bytes in 0 blocks ==30980== possibly lost: 182,735 bytes in 112 blocks ==30980== still reachable: 14,257,622 bytes in 4,162 blocks ==30980== suppressed: 0 bytes in 0 blocks ==30980== Rerun with --leak-check=full to see details of leaked memory ==30980== ==30980== For counts of detected and suppressed errors, rerun with: -v ==30980== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2520 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. === Verification check vc-memory-leak end (2018-12-15 06:09:40) ===