Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:18:26) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouWadleyJohnson_2001NISTretabulation_Cu__MO_759493141826_000 Supported species : Cu random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6.79529382312 Forces: 1 -2.77330438e+00 -6.21824697e+00 -6.63342124e+00 2 -8.09520852e+00 1.22987976e+01 -8.20333509e+00 3 7.40194608e-01 -8.46300657e+00 -1.43506474e+00 4 -4.02899510e+00 3.86142815e+00 3.90657679e+00 5 1.01418553e+01 -1.63245248e+01 -1.67039587e+00 6 3.00535725e+00 1.63556813e+00 -5.18982865e+00 7 3.75789945e+00 -2.17890633e+01 -2.02372122e+01 8 -7.75460204e+00 -8.89357285e+00 9.60550963e-01 9 -9.87088723e+00 -5.65714325e+00 -1.45102012e+01 10 -3.41367043e+00 1.63257739e+01 -1.58516951e+01 11 -2.29290887e+00 -1.27365745e+01 1.03561913e+01 12 -7.83209051e+00 1.34801585e+01 7.00816282e-02 13 -3.82456593e+00 -7.33117349e+00 -3.35003614e+01 14 5.31237306e+00 7.01771740e+00 -4.36122776e+00 15 2.85006824e+01 -3.91579049e+00 9.22239029e+00 16 3.69498459e+00 2.18083429e+01 1.16410011e+01 17 -8.64427081e+00 -3.50628579e+00 -3.54053948e+00 18 -2.88512709e+00 7.77074035e+00 3.17849308e+00 19 4.60958933e+00 -6.80892284e+00 5.21517361e+00 20 -2.96317825e+00 6.22599739e+00 3.98477672e+00 21 -8.10443048e+00 -8.21292529e+00 6.24425324e+00 22 1.33238429e+01 1.85747027e+01 1.61214990e+01 23 2.33365367e+00 -6.97985421e-01 4.35288376e+00 24 1.90659345e+00 8.46139017e-01 3.76993899e+00 25 -5.40146753e+00 -7.96653770e+00 9.86219051e+00 26 -5.40108676e+00 1.34104123e+01 -7.63865069e+00 27 8.49876888e+00 -2.52578137e+01 6.93392042e+00 28 -2.05003415e+01 1.70200400e+01 2.63162260e+00 29 -6.07154999e+00 -9.75578160e+00 3.18090670e+00 30 6.07016441e+00 1.02426247e+01 3.28093707e-01 31 1.14141231e+01 -7.81244282e+00 9.44139178e+00 32 6.54760303e+00 1.08293484e+01 1.13699973e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 38.6808355461 Forces: 1 1.55331070e+01 -1.34762948e+01 4.05481632e+00 2 -2.67838058e+01 8.63282648e+00 1.98674883e+01 3 2.53717289e-01 1.22490893e+00 -2.87538669e-01 4 1.05960746e+01 8.30887096e+00 -1.06728472e+00 5 1.75286613e+01 -3.56328388e+00 6.45960275e-01 6 -1.88277004e+01 2.00275787e+01 7.64459416e+00 7 -3.64251188e+00 -2.13103999e+01 -2.06934563e+01 8 -7.52146012e+00 -9.25755777e+00 5.95891217e-01 9 -1.78524307e+01 -1.60188317e+01 1.01026685e+01 10 -1.08359054e+01 4.40833953e+00 -8.51141206e+00 11 -2.91303388e+00 -1.22788775e+01 1.01191889e+01 12 3.18945025e+00 7.31547786e+00 4.91917482e+00 13 -2.99429656e+00 -8.32782627e+00 -2.83951794e+01 14 -8.01729026e+00 4.98997689e+00 -9.09958685e+00 15 2.31365146e+01 -3.74931695e+00 8.74947701e+00 16 5.26357511e+00 1.69218625e+01 1.20249199e+01 17 1.04169483e+01 -1.06850175e+01 -3.98331826e+00 18 -3.22417599e+00 7.03259693e+00 3.47968306e+00 19 4.41519582e+00 3.43457016e+00 3.89735289e+00 20 1.32916364e+01 2.02018336e+01 -6.25932820e+00 21 -8.47955864e+00 -2.37777121e+00 6.54246156e+00 22 -4.26516880e+00 2.80834064e+01 1.96193147e+01 23 -1.52557440e+01 -1.98163870e+01 -8.98922641e+00 24 2.15231021e+01 6.78332551e+00 -2.42097016e+01 25 -4.17106505e-01 -9.51404527e+00 9.80629508e+00 26 -4.52102469e+00 3.54380038e+00 -9.44009755e+00 27 1.83553037e+01 -2.56629262e+01 -1.12310029e+01 28 -2.18858799e+01 1.95511908e+01 -7.17036412e+00 29 -5.59928239e+00 -9.10107477e+00 3.70753064e+00 30 -3.83479313e-01 4.13356167e+00 2.62539265e+00 31 9.83748251e+00 -8.41840391e+00 7.57410317e+00 32 1.00790861e+01 8.96388723e+00 3.36118384e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==9534== Memcheck, a memory error detector ==9534== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==9534== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==9534== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Cu__MO_759493141826_000 ==9534== ==9534== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==9534== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==9534== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9534== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9534== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9534== by 0x4010732: call_init (dl-init.c:72) ==9534== by 0x4010732: _dl_init (dl-init.c:119) ==9534== by 0x40151FE: dl_open_worker (dl-open.c:522) ==9534== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==9534== by 0x40147C9: _dl_open (dl-open.c:605) ==9534== by 0x544CF95: dlopen_doit (dlopen.c:66) ==9534== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==9534== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==9534== by 0x544D734: _dlerror_run (dlerror.c:162) ==9534== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==9534== ==9534== ==9534== HEAP SUMMARY: ==9534== in use at exit: 5,878,453 bytes in 3,960 blocks ==9534== total heap usage: 114,082 allocs, 110,122 frees, 59,274,963 bytes allocated ==9534== ==9534== LEAK SUMMARY: ==9534== definitely lost: 0 bytes in 0 blocks ==9534== indirectly lost: 0 bytes in 0 blocks ==9534== possibly lost: 182,191 bytes in 111 blocks ==9534== still reachable: 5,696,262 bytes in 3,849 blocks ==9534== suppressed: 0 bytes in 0 blocks ==9534== Rerun with --leak-check=full to see details of leaked memory ==9534== ==9534== For counts of detected and suppressed errors, rerun with: -v ==9534== 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 06:18:51) ===