!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Morse_EIP_GuthikondaElliott_2011_AuCd__MO_703849496106_002 Supported species : Au Cd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Au (Configuration in file "config-F-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 315.671691135 Forces: 1 -9.88300445e+00 -1.92686907e+01 -2.05080765e+01 2 -9.50684927e+00 1.35007216e+01 -1.73817432e+01 3 1.28153470e+01 -3.39359441e+01 -1.55120911e+01 4 -2.34176335e+01 1.35239776e+01 1.66469809e+00 5 -2.09764550e+00 -3.15093419e+01 -9.07280350e+00 6 1.92561082e+01 1.17882080e+01 -2.07470515e+01 7 1.78735872e+01 -5.89141190e+01 -4.33333954e+01 8 -2.86397226e+01 -2.20146265e+01 -4.08250069e+00 9 -1.97850731e+01 -1.55693854e+01 -3.42063736e+01 10 -9.72052738e+00 3.78624054e+01 -4.04912038e+01 11 -7.59007161e+00 -2.67347482e+01 6.22586003e+00 12 -2.33968784e+01 3.28317122e+01 4.14182413e+00 13 -1.39673171e+01 -2.79799441e+01 -8.30143129e+01 14 1.83143193e+01 2.25316519e+01 -1.51347574e+01 15 7.66892036e+01 -8.99403357e+00 1.97823951e+01 16 1.12753806e+01 6.26778450e+01 2.73914854e+01 17 -3.70440661e+01 -2.34384350e+01 -5.67394804e+00 18 2.11920626e+01 2.87954558e+01 1.80041713e+01 19 9.17855509e+00 -2.73965066e+01 1.51082680e+01 20 -1.41027620e+01 1.67892651e+01 1.75905897e+01 21 -2.41890269e+01 -2.39192546e+01 1.63862198e+01 22 4.28526605e+01 4.68082258e+01 3.31892925e+01 23 1.05316420e+01 -6.38193119e+00 2.28484040e+01 24 5.68168575e+00 1.24259318e+01 1.13630092e+01 25 -2.80330872e+01 -1.18963417e+01 1.87419351e+01 26 -1.26678725e+01 4.15176631e+01 -1.80199531e+01 27 2.20376735e+01 -6.42692422e+01 2.42746805e+01 28 -5.49945541e+01 4.60480793e+01 1.14161040e+01 29 -1.60736965e+01 -2.34406026e+01 1.76893440e+01 30 1.97621336e+01 3.08377566e+01 -2.81069880e+00 31 3.02702590e+01 -2.29780324e+01 3.03967677e+01 32 1.73791707e+01 3.07022805e+01 3.37738609e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Au (Configuration in file "config-T-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 723.74349221 Forces: 1 1.31685042e+02 -7.12549220e+01 4.70179627e+01 2 -1.18224893e+02 1.68242884e+01 1.67112321e+02 3 9.50037151e+00 2.68634221e+01 -9.03723696e+00 4 5.90482175e+01 3.84326724e+01 -2.82089593e+01 5 1.96058441e+01 1.24480447e+01 9.07410215e+00 6 -1.51619139e+02 1.42926556e+02 1.97138486e+02 7 -2.86925937e+01 -5.08040736e+01 -4.25269299e+01 8 -2.93458157e+01 -2.31921751e+01 -4.78267712e+00 9 -5.45297140e+01 -7.15345360e+01 9.57760314e+01 10 -3.29307769e+01 3.06291148e+00 4.92490598e+00 11 -9.23819116e+00 -2.59482672e+01 5.68628276e+00 12 3.75337917e+01 -5.77983357e+00 3.17159026e+01 13 -9.12314424e+00 -3.72526004e+01 -5.07337164e+01 14 -5.34472829e+01 -6.28277004e-01 -3.86283025e+01 15 4.26651219e+01 -8.67417187e+00 1.81570813e+01 16 1.75045920e+01 2.63224197e+01 3.15557718e+01 17 6.41006843e+01 -5.67826709e+01 -2.03883542e+00 18 2.49377240e+01 2.74181870e+01 1.83449629e+01 19 1.01579625e+01 3.51410035e+01 6.68507772e+00 20 1.73247420e+02 1.32051798e+02 -4.12179077e+01 21 -2.63505009e+01 1.69928511e+01 1.86379341e+01 22 -6.04331263e+01 9.51609999e+01 5.18087943e+01 23 -1.61270742e+02 -1.55516581e+02 -2.12174965e+02 24 1.18290389e+02 2.84069050e+01 -1.73595869e+02 25 5.59651100e+00 -2.27279669e+01 1.78654181e+01 26 -6.80125239e+00 -1.92787898e+01 -2.78282785e+01 27 7.06920008e+01 -6.85622500e+01 -7.47333516e+01 28 -5.80644787e+01 5.63898083e+01 -4.24082815e+01 29 -1.45340863e+01 -2.23693432e+01 1.91136617e+01 30 -2.05907797e+01 -5.03543569e+00 7.61581969e+00 31 1.47648674e+01 -2.89219330e+01 1.52003844e+01 32 3.58659781e+01 1.58219593e+01 -1.55155896e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Cd (Configuration in file "config-F-Cd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 119.550377546 Forces: 1 -2.81127378e+00 -3.10964357e+00 -2.51774488e+00 2 -1.26666111e+01 1.35547223e+01 -1.84872876e+01 3 -1.38210621e+01 -2.03339374e+01 2.16495774e+00 4 -1.09059196e+01 -1.17574527e-01 1.36900642e+00 5 1.58134500e+01 -2.39939513e+01 -1.12632824e+01 6 4.04116964e+00 -1.31605753e+01 -1.94042414e+01 7 3.87868671e+00 -8.48551318e+00 -2.12589667e+00 8 1.10360282e+01 7.64397712e+00 1.57525354e+00 9 -3.04263888e+00 5.51654631e-01 -4.29379222e+00 10 -4.36078067e+00 7.66094358e+00 -4.78371125e+00 11 -2.54723498e+00 7.42257210e+00 -2.13466851e+00 12 -5.30191727e+00 6.15560050e+00 -4.37437975e+00 13 1.48746319e+00 -6.95551959e+00 -1.29230095e+01 14 5.81620069e+00 4.40322668e+00 -6.35955877e+00 15 1.01591224e+01 1.68024094e+01 7.65043607e+00 16 -5.12596285e+00 1.18617419e+01 -7.63320057e-01 17 -1.13260025e+01 -8.96293356e+00 -7.92281794e+00 18 -2.63222641e+00 1.21448229e+01 5.69382670e+00 19 2.62483820e+00 -1.37049330e+01 1.83778281e+01 20 -1.44822429e+01 1.08254057e+01 6.99724974e+00 21 1.01674656e+01 -1.65455181e+01 -3.66871817e+00 22 5.33452067e+00 1.91695401e-01 1.15892737e+01 23 7.18837277e+00 -3.48802683e+00 4.94857809e+00 24 8.24632284e+00 -5.59327764e+00 1.03011764e+01 25 -9.16908540e+00 -6.33612979e+00 2.76253083e+00 26 5.99136582e+00 9.27927322e+00 -3.05487828e+00 27 -5.64366748e+00 1.20228884e+01 4.57312175e+00 28 -4.18746746e+00 3.04742857e+00 6.62068067e+00 29 -1.58432592e+01 -1.69959126e+01 8.04534638e+00 30 2.69677397e+01 2.00958751e+01 5.11273401e+00 31 4.49383907e+00 1.39441176e+00 2.66029430e+00 32 6.20767082e-01 2.72479737e+00 3.63501296e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cd (Configuration in file "config-T-Cd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 245.112944053 Forces: 1 1.49937052e+01 5.12647646e+00 8.16312774e+00 2 -2.69837779e+01 1.11433638e+01 2.21778646e+01 3 -1.25111046e+01 -1.44767611e+01 8.62776389e-01 4 3.32987327e+01 -1.35101290e+01 9.22742291e+00 5 1.01941905e+01 -6.52428218e+00 2.97847577e+00 6 -2.66332918e+01 -2.52024277e+01 -4.87290361e+00 7 -1.94157956e+01 1.67139800e+01 -2.77048576e+00 8 1.13403919e+01 6.96711090e+00 2.15715329e+00 9 4.31612075e+01 2.14190375e+01 1.65319978e+01 10 -6.65861852e+00 -1.79525953e+00 3.10378357e+00 11 -2.70562691e+00 7.84765940e+00 -2.49370635e+00 12 2.15883589e+01 -1.32661190e+01 -9.43274526e+00 13 2.18558431e+00 2.80097961e+00 1.03295311e+01 14 1.74235776e+01 -1.34663848e+01 1.92712033e+01 15 -2.60961289e+01 2.86975448e+01 1.18135896e+01 16 -6.50128259e+00 1.65231553e+00 1.68710242e+00 17 4.55663446e+00 1.16411796e+01 -1.58075777e+01 18 -2.88414099e+00 1.23910111e+01 5.84967859e+00 19 5.25520627e+00 -3.05688255e+00 2.40049864e+00 20 -2.14478841e+00 3.74891021e+00 -1.02422319e+01 21 1.42862992e+01 1.49357718e+01 -1.99731469e+01 22 -6.05724290e+00 6.59655546e-01 1.44225250e+01 23 -7.95705008e+00 1.31794174e+01 -3.75340033e+00 24 2.57154332e+01 -6.08387423e+00 -2.79770806e+01 25 6.04302185e+00 -7.43762214e+00 3.59717493e+00 26 5.61908355e-01 -1.80993213e+01 -8.98618767e+00 27 -8.14223670e+00 1.26635243e+01 -8.59052079e+00 28 -2.75509709e-01 -2.45557614e+01 2.56841697e+00 29 -1.55693962e+01 -1.73392050e+01 8.19847961e+00 30 7.21274204e+00 9.22325991e+00 1.32036706e+01 31 -2.85023615e+01 7.76528896e+00 -3.27197556e+01 32 -1.87786405e+01 -2.37624570e+01 -1.09247302e+01 MIXED STRUCTURE (pbc=False)-- Species = Au Cd (Configuration in file "config-F-AuCd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 326.579488726 Forces: 1 -1.22657059e+01 -1.28514429e+01 -9.94298399e+00 2 3.61261006e+01 9.07659260e-01 -5.55037718e+01 3 -7.16044384e+00 -3.63540162e+01 5.21742098e+00 4 -5.94881964e+01 -1.46521548e+01 2.50645946e+01 5 -1.83671015e+01 -2.67511341e+01 -1.87427507e+01 6 3.30342538e+01 2.68231925e+01 -2.17937201e+01 7 3.26730133e+01 -5.96101515e+01 -3.43251345e+01 8 6.54990792e+01 -1.68574246e+00 -4.37057573e+01 9 -2.63027366e+01 -1.21199911e+01 -5.15431154e+01 10 1.26318394e+01 1.91930567e+01 -6.37494022e+00 11 2.49693168e+01 9.34935590e+00 -1.05865608e+01 12 -4.07971512e+01 8.80729155e+01 -6.37401447e+01 13 -1.14329721e+01 8.23403810e+00 -2.92557184e+01 14 9.28112518e+00 8.47303544e+00 -1.04698127e+01 15 2.86590341e+01 -1.37863740e+01 9.91601900e+00 16 -2.10387517e+01 2.47125709e+01 -1.02076504e+01 17 -9.88704627e+00 -1.15877323e+01 -5.49548388e+00 18 -5.82581031e+01 -3.06462439e+01 5.12695624e+01 19 1.36344690e+00 -1.05850975e+01 7.33963648e+00 20 -4.55223234e+01 -2.39784969e+01 1.84829093e+01 21 -1.10614520e+01 -2.61856545e+01 1.42743892e+01 22 1.29746954e+01 4.58387057e+01 4.09076310e+01 23 6.48147551e+00 -5.31279155e+00 9.05520828e+00 24 2.62580577e+01 -3.81775192e+01 4.34397498e+01 25 -6.37863609e+01 -6.59366210e+01 6.31827845e+01 26 5.23763273e+01 4.79706305e+01 2.77322900e+01 27 -8.59573561e+00 4.54808933e+01 2.85608572e+01 28 -9.73721461e+00 1.44956054e+01 1.99463564e+01 29 2.96818703e+01 2.79278932e+01 -2.63409408e+01 30 1.68512279e+01 9.44710057e+00 1.12004349e+01 31 1.24243872e+01 -8.87311808e-01 8.52813949e+00 32 2.41604453e+00 1.41818227e+01 1.39105021e+01 MIXED STRUCTURE (pbc=True)-- Species = Au Cd (Configuration in file "config-T-AuCd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 547.844930155 Forces: 1 5.55433218e+01 -1.60862643e+01 5.00340115e+01 2 4.11707700e+01 -1.32774449e+00 -2.49317343e+01 3 -8.23915410e+00 8.44952804e+00 1.80834797e+01 4 -1.32087247e+01 4.36070016e+00 2.20669724e+01 5 -8.07189480e+00 -1.26905541e+00 3.49144758e+01 6 2.91070885e+00 5.87196354e+01 1.51938487e+01 7 1.42395726e+00 -5.19825708e+01 -3.34017115e+01 8 6.59079209e+01 -2.15914790e+00 -4.41619548e+01 9 2.47915194e+01 -3.44376633e+01 -3.40826580e+01 10 -4.79358833e+00 -2.72193324e+01 -1.18045544e+00 11 2.49234211e+01 9.82262419e+00 -1.15751189e+01 12 -2.18946502e+01 8.30402938e+01 -5.84358161e+01 13 -7.10081119e+00 1.51558327e+01 -4.92859284e+00 14 -4.34389729e+01 2.09664364e+01 -3.68223564e+00 15 -2.95659171e+01 -2.12815252e+01 -1.29461387e+01 16 -2.04245336e+01 -2.28667389e+01 -2.50366973e+01 17 3.20812576e+01 5.80397670e+01 -5.24589546e+01 18 -5.92738510e+01 -3.22063683e+01 5.23702148e+01 19 -1.45634611e+01 1.85722366e+01 -2.38102365e+01 20 -1.99364392e+01 -3.10153885e+01 -1.73118722e+01 21 -1.67290826e+01 1.12630259e+01 2.98238500e+01 22 1.46434118e+00 4.66490088e+01 4.10575833e+01 23 -6.13871706e+01 -5.59592608e+00 -5.85524557e+01 24 2.30741913e+01 -3.69193517e+01 1.16153449e+01 25 2.21240213e+01 -8.80610408e+01 5.69516634e+01 26 5.26890097e+01 2.87591385e+01 3.19246729e+01 27 -4.82845140e+00 4.52101940e+01 1.15747877e+01 28 7.25947212e+01 -4.94016087e+01 7.78719344e+01 29 3.05712880e+01 2.89518362e+01 -2.52496226e+01 30 -8.33446448e+01 1.02448713e+01 -3.30384624e+01 31 -5.25658588e+01 -8.35733429e+00 2.43995809e+01 32 1.80967568e+01 -1.80180679e+01 -1.30977027e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==16302== Memcheck, a memory error detector ==16302== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==16302== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==16302== Command: python runner2.py Morse_EIP_GuthikondaElliott_2011_AuCd__MO_703849496106_002 ==16302== ==16302== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==16302== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==16302== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==16302== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==16302== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==16302== by 0x4010732: call_init (dl-init.c:72) ==16302== by 0x4010732: _dl_init (dl-init.c:119) ==16302== by 0x40151FE: dl_open_worker (dl-open.c:522) ==16302== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==16302== by 0x40147C9: _dl_open (dl-open.c:605) ==16302== by 0x544CF95: dlopen_doit (dlopen.c:66) ==16302== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==16302== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==16302== by 0x544D734: _dlerror_run (dlerror.c:162) ==16302== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==16302== ==16302== ==16302== HEAP SUMMARY: ==16302== in use at exit: 12,484,706 bytes in 4,273 blocks ==16302== total heap usage: 462,552 allocs, 458,279 frees, 111,167,184 bytes allocated ==16302== ==16302== LEAK SUMMARY: ==16302== definitely lost: 0 bytes in 0 blocks ==16302== indirectly lost: 0 bytes in 0 blocks ==16302== possibly lost: 182,735 bytes in 112 blocks ==16302== still reachable: 12,301,971 bytes in 4,161 blocks ==16302== suppressed: 0 bytes in 0 blocks ==16302== Rerun with --leak-check=full to see details of leaked memory ==16302== ==16302== For counts of detected and suppressed errors, rerun with: -v ==16302== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2529 from 172) ================================================================================ 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.