Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:17:26) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouJohnsonWadley_2004_Fe__MO_650279905230_005 Supported species : Fe 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 = 27.8371680501 Forces: 1 -9.49475310e+00 -8.48907551e+00 -1.64123279e+01 2 -9.41252476e+00 1.28779058e+01 -6.16049694e+00 3 1.87105665e+01 -1.68993675e+01 -4.64615036e+00 4 -1.43712229e+01 1.04489229e+01 -2.46639611e+00 5 2.29201173e+00 -2.03936162e+01 -6.74700218e-01 6 1.21783359e+01 7.46936851e+00 -1.13969106e+01 7 2.74632489e+00 -4.20892857e+01 -3.89905908e+01 8 -1.27406536e+01 -9.84225358e+00 7.55168350e+00 9 -6.86948399e+00 -1.26462162e+01 -1.81460022e+01 10 -7.23325232e+00 1.71040494e+01 -2.24537841e+01 11 5.61140977e+00 -1.44789232e+01 -4.29433466e+00 12 -1.17700799e+01 2.16639800e+01 2.68738362e+00 13 -1.68727706e+01 -1.81906778e+01 -5.89522007e+01 14 9.18525568e+00 1.53707432e+01 -1.21012776e+01 15 4.79957262e+01 -1.83084931e+01 2.12426764e+01 16 1.77479044e+00 4.10938309e+01 2.16420418e+01 17 -2.48006994e+01 -1.36860402e+01 6.10368293e-01 18 1.93235609e+01 1.62333781e+01 6.20478435e+00 19 8.65320745e+00 -1.07741529e+01 9.12371746e+00 20 -6.43264777e+00 9.12574358e+00 9.21302830e+00 21 -1.64172750e+01 -1.03492197e+01 9.93648531e+00 22 2.29673718e+01 3.91252981e+01 2.77000857e+01 23 5.54845482e+00 -3.89377327e+00 1.04083995e+01 24 -2.90141692e+00 3.90860420e+00 3.24413393e+00 25 -1.96557385e+01 -4.87193082e+00 2.37653300e+01 26 -9.33919639e+00 2.02807682e+01 -1.19465127e+01 27 2.29693974e+01 -4.98734628e+01 9.89047073e+00 28 -4.08585308e+01 3.48627540e+01 3.08050169e+00 29 -8.81524134e+00 -1.78934696e+01 5.09837504e+00 30 8.90161114e+00 1.81589064e+01 5.32008729e+00 31 1.77472132e+01 -1.19357326e+01 1.47767368e+01 32 1.13802497e+01 1.68914375e+01 1.71453951e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 101.464729085 Forces: 1 1.66323859e+01 -1.92324790e+01 -2.40568129e+00 2 -2.67667351e+01 1.19918384e+01 1.95313974e+01 3 2.31313971e+01 -1.39092381e+00 -5.93123928e-01 4 -6.65840420e+00 1.27795101e+01 -7.19224801e+00 5 9.25572375e+00 -1.25884839e+01 3.91503628e+00 6 -2.12791985e+01 4.58718741e+01 5.44969872e+01 7 -3.22244561e+00 -3.96647167e+01 -4.08370706e+01 8 -1.21874849e+01 -1.02039007e+01 7.14587421e+00 9 -2.38307261e+01 -3.14998083e+01 2.64979577e+01 10 -1.55304941e+01 9.06864394e+00 -1.08705640e+01 11 5.20105097e+00 -1.40015774e+01 -4.96197963e+00 12 7.67182615e+00 6.61835593e+00 1.44986240e+01 13 -1.55183440e+01 -2.05967458e+01 -5.30537699e+01 14 -1.59017764e+01 1.37900522e+01 -2.59562030e+01 15 4.08051873e+01 -2.07009383e+01 2.07115274e+01 16 2.18074717e+00 3.83439155e+01 2.17232519e+01 17 5.28661756e+00 -3.13828298e+01 2.77599186e+00 18 1.95820695e+01 1.57537695e+01 6.69132988e+00 19 8.18372523e+00 4.41484125e+00 1.04434223e+01 20 6.59930802e+01 5.66056848e+01 -3.00205351e+00 21 -1.67439096e+01 -3.64217345e+00 1.10250706e+01 22 -3.13959140e+00 5.91981326e+01 2.54149819e+01 23 -5.90013104e+01 -6.99148680e+01 -5.35988374e+01 24 1.39396130e+01 1.07517010e+01 -2.55359950e+01 25 -1.37539662e+01 -7.38670807e+00 2.38733913e+01 26 -8.18396177e+00 7.85720056e+00 -1.71129284e+01 27 4.24014346e+01 -4.99776549e+01 -2.16416397e+01 28 -4.51831735e+01 4.38835026e+01 -1.43533458e+01 29 -8.43362205e+00 -1.75331683e+01 5.25859518e+00 30 2.10032503e+00 1.10972184e+01 8.09256382e+00 31 1.64757166e+01 -1.27028765e+01 1.32638178e+01 32 1.64942437e+01 1.43936119e+01 5.75561968e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==8259== Memcheck, a memory error detector ==8259== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==8259== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==8259== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004_Fe__MO_650279905230_005 ==8259== ==8259== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==8259== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==8259== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==8259== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==8259== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==8259== by 0x4010732: call_init (dl-init.c:72) ==8259== by 0x4010732: _dl_init (dl-init.c:119) ==8259== by 0x40151FE: dl_open_worker (dl-open.c:522) ==8259== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==8259== by 0x40147C9: _dl_open (dl-open.c:605) ==8259== by 0x544CF95: dlopen_doit (dlopen.c:66) ==8259== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==8259== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==8259== by 0x544D734: _dlerror_run (dlerror.c:162) ==8259== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==8259== ==8259== ==8259== HEAP SUMMARY: ==8259== in use at exit: 5,877,173 bytes in 3,961 blocks ==8259== total heap usage: 114,082 allocs, 110,121 frees, 59,272,769 bytes allocated ==8259== ==8259== LEAK SUMMARY: ==8259== definitely lost: 0 bytes in 0 blocks ==8259== indirectly lost: 0 bytes in 0 blocks ==8259== possibly lost: 182,191 bytes in 111 blocks ==8259== still reachable: 5,694,982 bytes in 3,850 blocks ==8259== suppressed: 0 bytes in 0 blocks ==8259== Rerun with --leak-check=full to see details of leaked memory ==8259== ==8259== For counts of detected and suppressed errors, rerun with: -v ==8259== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2508 from 175) ================================================================================ 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 06:17:52) ===