Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:11:12) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_JacobsenNorskovPuska_1987_Al__MO_411692133366_000 Supported species : Al 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 = -56.8432771683 Forces: 1 -9.39911457e-01 -2.24824855e+00 -2.41204098e+00 2 -1.75852998e+00 3.38818858e+00 -5.37736993e-01 3 2.03400698e+00 -3.34070008e+00 -2.10446172e+00 4 -1.90075955e+00 1.66942597e+00 1.21461398e+00 5 1.36234488e+00 -3.67374684e+00 -2.95307248e-01 6 1.31493707e+00 1.37515258e+00 -1.31538846e+00 7 1.97369141e+00 -8.09243806e+00 -7.99737886e+00 8 -4.58679586e+00 -1.59094048e+00 -3.24707055e-01 9 -2.56635290e+00 -4.24743450e+00 -3.63785863e+00 10 3.01095231e+00 3.89889229e+00 -3.20463192e+00 11 7.08863529e+00 -2.35848235e+00 -5.78878255e+00 12 -3.97230018e+00 4.06250108e+00 2.34231487e+00 13 -4.37430220e+00 -3.33258680e+00 -8.85936042e+00 14 1.62110739e+00 2.21993539e+00 -1.21585274e+00 15 8.23768943e+00 -1.97974261e+00 2.65523267e+00 16 -2.86879476e-01 5.83701813e+00 2.14046328e+00 17 -3.90007886e+00 -1.87288990e+00 -1.23792517e+00 18 1.03809808e+00 3.12963967e+00 1.48360151e+00 19 1.73105123e+00 -2.68777585e+00 2.16504519e+00 20 -1.03091263e+00 2.47980822e+00 1.44034599e+00 21 -3.83662069e+00 -2.94270673e+00 1.78889916e+00 22 4.65912385e+00 7.43676014e+00 6.16272615e+00 23 7.83410785e-01 -2.29367451e-01 1.52822928e+00 24 8.65933040e-01 8.70942231e-01 1.63059718e+00 25 -7.64149875e+00 -1.73536927e+00 5.53753689e+00 26 -1.30661878e+00 5.27424806e+00 -2.97744776e+00 27 3.43443072e+00 -9.45191241e+00 3.02037926e+00 28 -7.06795592e+00 6.36390233e+00 1.47293618e+00 29 -2.14506205e+00 -2.97980462e+00 3.78868364e-01 30 1.67576573e+00 3.43415738e+00 2.78803767e-01 31 4.08335203e+00 -2.91159852e+00 2.83654206e+00 32 2.40004907e+00 4.23517298e+00 3.83174473e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = -65.9757916659 Forces: 1 2.75709152e+00 -3.52939538e+00 6.97221657e-01 2 -4.77992396e+00 3.06679617e+00 4.79320324e+00 3 1.04025109e+00 -7.59421451e-01 -1.38972433e+00 4 1.68249263e+00 2.21564947e+00 -1.40146177e-01 5 2.20657114e+00 -2.68406889e+00 1.11334390e+00 6 -3.51090267e+00 4.95655145e+00 1.98060542e+00 7 6.82879962e-01 -4.98497340e+00 -5.01545538e+00 8 -2.42620840e+00 -1.79527627e+00 -4.65791096e-01 9 -3.24474444e+00 -4.52413076e+00 2.91503795e+00 10 8.26440208e-01 9.06109459e-01 -8.89614191e-01 11 5.07955609e+00 -6.11699466e-01 -5.45193823e+00 12 2.77444124e-01 1.00745269e+00 2.52575785e+00 13 -3.26250132e+00 -2.55301817e+00 -5.19707004e+00 14 -1.58847163e+00 1.15640103e+00 -1.99675505e+00 15 5.65030599e+00 -1.09736067e+00 1.80527920e+00 16 1.42342190e-01 3.43477022e+00 1.33153682e+00 17 1.32608344e+00 -3.11632527e+00 -1.15043310e+00 18 7.54410278e-02 2.33004330e+00 1.69858926e+00 19 4.54041981e-01 -4.43233453e-01 1.32199876e+00 20 3.20209164e+00 5.47947402e+00 -1.80139422e+00 21 -2.34662961e+00 -7.78064651e-01 1.02868440e+00 22 -1.02967200e+00 6.21247466e+00 4.35316323e+00 23 -3.11340800e+00 -5.03487931e+00 -2.08094063e+00 24 3.75158495e+00 2.08541481e+00 -3.54414330e+00 25 -4.91424372e+00 -9.50990068e-01 5.05111390e+00 26 -1.60639225e+00 6.62583427e-01 -1.89445327e+00 27 3.78405972e+00 -4.76343864e+00 -2.01232887e+00 28 -4.00288521e+00 4.40964088e+00 -1.68318795e+00 29 -1.87888128e+00 -1.61386800e+00 1.92362014e-01 30 1.75621885e-02 1.53367599e+00 4.12520911e-01 31 3.66861786e+00 -2.63554166e+00 2.27123700e+00 32 1.08000674e+00 2.41864792e+00 1.22172035e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==731== Memcheck, a memory error detector ==731== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==731== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==731== Command: python runner2.py EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_000 ==731== ==731== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==731== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==731== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==731== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==731== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==731== by 0x4010732: call_init (dl-init.c:72) ==731== by 0x4010732: _dl_init (dl-init.c:119) ==731== by 0x40151FE: dl_open_worker (dl-open.c:522) ==731== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==731== by 0x40147C9: _dl_open (dl-open.c:605) ==731== by 0x544CF95: dlopen_doit (dlopen.c:66) ==731== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==731== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==731== by 0x544D734: _dlerror_run (dlerror.c:162) ==731== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==731== ==731== ==731== HEAP SUMMARY: ==731== in use at exit: 5,106,240 bytes in 3,968 blocks ==731== total heap usage: 116,318 allocs, 112,350 frees, 62,970,960 bytes allocated ==731== ==731== LEAK SUMMARY: ==731== definitely lost: 0 bytes in 0 blocks ==731== indirectly lost: 0 bytes in 0 blocks ==731== possibly lost: 182,751 bytes in 112 blocks ==731== still reachable: 4,923,489 bytes in 3,856 blocks ==731== suppressed: 0 bytes in 0 blocks ==731== Rerun with --leak-check=full to see details of leaked memory ==731== ==731== For counts of detected and suppressed errors, rerun with: -v ==731== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2519 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. === Verification check vc-memory-leak end (2018-12-15 06:11:38) ===