!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_WilliamsMishinHamilton_2006_Ag__MO_131620013077_005 Supported species : Ag random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ag (Configuration in file "config-F-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 195.308221552 Forces: 1 -7.72174221e+00 -1.67216810e+01 -1.43947267e+01 2 -5.59014268e+00 7.23724229e+00 -1.60199933e+01 3 5.51173130e+00 -1.56913911e+01 -2.85696781e+00 4 -1.46711888e+01 8.10855696e+00 6.85938594e+00 5 2.02289700e+00 -2.15819623e+01 -9.49821529e+00 6 1.28915238e+01 2.57425946e+00 -1.51896482e+01 7 1.30103478e+01 -2.58537092e+01 -1.40884739e+01 8 -1.09954124e+01 -1.07617967e+01 4.58639407e+00 9 -1.06593494e+01 -1.47908050e+01 -2.38453263e+01 10 1.27899021e+01 2.21251289e+01 -1.80382749e+01 11 1.80839984e+00 -1.33477444e+01 -9.36558561e+00 12 -2.42026856e+01 2.14185199e+01 1.05598923e+01 13 -8.98405977e+00 -5.48383734e+00 -4.02714425e+01 14 1.22771926e+01 1.50460211e+01 -1.26466570e+01 15 3.70568133e+01 -8.06706906e+00 5.13744702e+00 16 -1.40644053e+00 3.62932543e+01 2.98611435e+00 17 -2.37455716e+01 -1.47715531e+01 -5.48472711e+00 18 8.79221068e+00 1.03652431e+01 -1.85667993e+00 19 8.67568494e+00 -1.76878275e+01 1.51892361e+01 20 -1.29392843e+01 9.76914866e+00 1.52265307e+01 21 -1.19564704e+01 -1.50770600e+01 6.92384565e+00 22 2.23365767e+01 1.72218050e+01 1.24692233e+01 23 7.45910203e+00 -4.29809436e+00 1.26062924e+01 24 1.43070875e+00 -4.49416690e+00 1.14673643e+01 25 -2.96069252e+01 -1.92421513e+00 1.38808374e+01 26 -6.23809440e+00 2.92320700e+01 -5.88376647e+00 27 4.45562200e-01 -2.21159941e+01 1.65314391e+01 28 -2.35898570e+01 1.76347828e+01 7.67520782e+00 29 4.21105801e-01 -1.44321625e+01 8.08816132e+00 30 1.56264268e+01 1.76432971e+01 3.25283235e+00 31 2.08593811e+01 -7.09320951e+00 1.53966533e+01 32 8.89165744e+00 1.95249498e+01 2.06036276e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ag (Configuration in file "config-T-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 392.053533151 Forces: 1 1.59711515e+01 -1.33316187e+01 3.14145609e+00 2 -1.47344357e+01 3.32509958e+00 1.25507414e+01 3 4.62523473e+00 5.70084603e+00 9.75285080e-01 4 1.20142235e+01 1.41959345e+01 9.82717355e+00 5 3.96798156e+00 -7.37397188e+00 -3.28512385e+00 6 -2.07978421e+01 2.08431001e+01 1.41126539e+00 7 -3.09881480e+00 -1.61695456e+01 -1.20222666e+01 8 -1.24042288e+01 -1.05007829e+01 5.70600107e+00 9 -1.18707331e+01 -2.66587182e+01 5.54836184e+00 10 1.29115666e+01 1.05591889e+01 -1.55080426e+00 11 2.02811104e+00 -1.36707361e+01 -9.07971855e+00 12 -1.14965172e+00 6.44761180e+00 1.94216586e+01 13 -7.02245358e+00 -6.61873643e+00 -2.34419811e+01 14 -1.26402458e+01 5.64437616e+00 -1.39918784e+01 15 2.11136846e+01 -7.89640800e+00 6.09214177e+00 16 -1.94597831e-01 2.00948427e+01 4.17803877e+00 17 4.57345125e+00 -1.62673474e+01 -6.67287595e+00 18 1.19137206e+01 1.06528815e+01 -2.03031934e+00 19 8.79426374e+00 3.09300493e+00 6.24270184e+00 20 1.26254312e+01 2.54667569e+01 -4.89679027e+00 21 -1.22481732e+01 1.89051104e+00 8.02636848e+00 22 -2.70555075e+00 2.75625701e+01 1.12253458e+01 23 -2.03749807e+01 -2.08062004e+01 -9.52979809e+00 24 1.19705645e+01 2.59228675e+00 -1.80031091e+01 25 -1.55008828e+01 -5.27393415e+00 1.35562381e+01 26 -3.83924859e+00 7.83675802e+00 -7.93044711e+00 27 9.80903880e+00 -2.48490136e+01 -1.03810869e+01 28 -2.21655646e+01 1.25648689e+01 -1.16335804e+01 29 4.62626964e-01 -1.46060472e+01 8.03038073e+00 30 2.99850822e+00 2.61075645e+00 5.48382183e+00 31 1.27026830e+01 -8.68262780e+00 6.46932670e+00 32 1.22651624e+01 1.16242940e+01 6.56347286e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==6898== Memcheck, a memory error detector ==6898== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==6898== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==6898== Command: python runner2.py EAM_Dynamo_WilliamsMishinHamilton_2006_Ag__MO_131620013077_005 ==6898== ==6898== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==6898== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==6898== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6898== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6898== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6898== by 0x4010732: call_init (dl-init.c:72) ==6898== by 0x4010732: _dl_init (dl-init.c:119) ==6898== by 0x40151FE: dl_open_worker (dl-open.c:522) ==6898== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6898== by 0x40147C9: _dl_open (dl-open.c:605) ==6898== by 0x544CF95: dlopen_doit (dlopen.c:66) ==6898== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6898== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==6898== by 0x544D734: _dlerror_run (dlerror.c:162) ==6898== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==6898== ==6898== ==6898== HEAP SUMMARY: ==6898== in use at exit: 9,988,787 bytes in 3,961 blocks ==6898== total heap usage: 114,514 allocs, 110,553 frees, 63,909,475 bytes allocated ==6898== ==6898== LEAK SUMMARY: ==6898== definitely lost: 0 bytes in 0 blocks ==6898== indirectly lost: 0 bytes in 0 blocks ==6898== possibly lost: 182,191 bytes in 111 blocks ==6898== still reachable: 9,806,596 bytes in 3,850 blocks ==6898== suppressed: 0 bytes in 0 blocks ==6898== Rerun with --leak-check=full to see details of leaked memory ==6898== ==6898== For counts of detected and suppressed errors, rerun with: -v ==6898== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2501 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.