!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MendelevKramerOtt_2009_CuZr__MO_600021860456_005 Supported species : Cu Zr 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 = 15.1572276552 Forces: 1 -1.50460337e+01 -3.28344906e+01 -4.98077255e+01 2 -1.01552882e+01 1.17693812e+01 -5.87650376e+00 3 2.68230513e+01 -2.45746998e+01 1.58637728e+01 4 -1.63292478e+01 5.37212258e+01 3.25373251e+01 5 9.01345196e+00 -1.43494240e+01 -1.86598107e+00 6 2.42422963e+00 3.45852714e-01 -2.87284432e+00 7 4.44795684e+00 -3.89600341e+01 -4.74886060e+01 8 -2.97982416e+01 -2.63830334e+01 9.63495546e-01 9 -7.24724014e+00 -2.09048749e+01 -2.78786621e+01 10 -3.04532532e+00 1.47783965e+01 -1.76163124e+01 11 -2.32212340e+01 -1.61007090e+01 5.55084468e+00 12 -5.55898814e+00 1.92265258e+01 2.02280466e+01 13 -1.97250424e+01 -8.85766306e+00 -6.27700566e+01 14 9.71546746e+00 9.01521770e+00 -3.14730071e+00 15 7.05367440e+01 1.55905930e+01 1.69361885e+01 16 1.59889144e+01 4.71549009e+01 1.14438321e+01 17 -7.46796308e+00 -2.71026345e+01 -2.84833976e+01 18 4.64586366e+00 2.62779447e+00 5.21394412e-01 19 2.93222478e+00 -3.47322854e+00 3.39279933e+00 20 -1.63281392e+00 2.49855100e+01 2.93994817e+01 21 -2.26552576e+01 -1.05188918e+01 9.19316506e+00 22 2.23728539e+01 3.25685462e+01 2.60284156e+01 23 9.25022978e+00 -8.49581809e-01 1.71981069e+01 24 -8.56927474e-01 1.52900035e+00 2.24586043e+00 25 -3.34073298e+00 -4.74042989e+00 3.60297119e+00 26 -2.47599312e+01 1.74707828e+01 -1.07621983e+01 27 2.90626343e+01 -4.28908187e+01 1.25845274e+01 28 -3.99796847e+01 3.71461007e+01 -6.79480173e+00 29 -3.18234188e+00 -2.43854448e+01 3.11682844e+01 30 3.11937449e+00 4.29402822e+00 2.09860200e+00 31 2.11502360e+00 1.32403302e-01 1.87256667e+00 32 2.15542741e+01 4.56969952e+00 2.25347096e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 91.1012746891 Forces: 1 9.10933951e+00 -5.15654174e+01 -4.71450986e+01 2 -1.11312592e+01 1.23145857e+01 -3.20307117e+00 3 2.73683363e+01 -1.91670533e+01 1.75622934e+01 4 -8.77766742e+00 5.50637565e+01 3.38006953e+01 5 1.26677373e+01 -8.11250521e+00 -1.51555548e+00 6 -2.39314885e+01 2.88016631e+01 1.14152663e+01 7 1.66582990e+00 -3.81923122e+01 -4.84419445e+01 8 -3.08158092e+01 -2.63500598e+01 1.19964098e+00 9 -2.83136041e+01 -2.65164390e+01 1.30575959e+01 10 -7.06344324e+00 9.66052647e+00 -1.56110992e+01 11 -2.34948464e+01 -1.71344800e+01 6.09707749e+00 12 -4.58415360e+00 1.61470316e+01 2.08911818e+01 13 -1.93903671e+01 -1.03536631e+01 -6.11839429e+01 14 8.35837206e+00 9.74268559e+00 -4.03528728e+00 15 6.83908470e+01 1.49752880e+01 1.66177896e+01 16 1.57311509e+01 4.45643988e+01 1.22535023e+01 17 4.18351380e+01 -7.27181522e+01 -1.81305481e+01 18 6.48911123e+00 3.37562840e+00 5.92730828e-01 19 2.75073080e+00 2.52856107e+00 4.51796282e+00 20 5.14695438e+01 5.51404291e+01 3.04216775e+01 21 -2.34850044e+01 -6.74478693e+00 1.02024688e+01 22 -2.59262591e+01 7.81140325e+01 9.50358686e+00 23 -4.57260507e+01 -3.92312253e+01 4.24438074e+00 24 -2.91890530e-01 2.55428885e+00 -1.23794087e+00 25 6.78195198e-01 -5.13618563e+00 4.05684804e+00 26 -2.46481162e+01 1.25622671e+01 -1.29978093e+01 27 5.19020437e+01 -4.81654140e+01 -1.89248481e+01 28 -4.29407255e+01 4.22415732e+01 -1.86512537e+01 29 -3.68398727e+00 -2.50676409e+01 3.16182406e+01 30 1.47028812e+00 2.78237662e+00 3.00907299e+00 31 8.60881448e-01 5.15338867e-01 1.21366381e+00 32 2.34571270e+01 3.37090363e+00 1.88027232e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Zr (Configuration in file "config-F-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 408.405187546 Forces: 1 -2.56023853e+01 -2.37901512e+01 -3.09126246e+01 2 -5.61721069e+00 -1.08354922e+01 -7.61792109e+01 3 1.34950594e+01 -7.61538461e+01 -2.44049203e+01 4 -8.19369370e+01 -1.69961092e+01 -1.65058222e+01 5 -1.26677916e+01 -5.17177466e+01 -4.83928226e+01 6 4.39451085e+01 1.25406950e+01 -4.92643029e+01 7 4.99948104e+01 -5.54348303e+01 -6.91786183e+00 8 2.94318141e+01 -2.02051112e+01 -3.42678664e+01 9 -4.28439831e+01 1.65300167e+01 -4.70124384e+01 10 -1.82304013e+01 4.92964502e+01 -4.68809880e+01 11 -1.19537551e+01 2.68065997e+01 -3.42219658e+01 12 -5.94922598e+01 5.09630392e+01 -1.54573561e+01 13 1.83115146e+01 -5.45343556e+00 -6.46810427e+01 14 2.88529349e+01 2.52992186e+01 -2.02984956e+01 15 6.75552618e+01 1.75893203e+01 -1.23781034e+01 16 2.30568495e+01 6.86240689e+01 -7.15893869e+00 17 -5.66063575e+01 -4.62526456e+01 1.95092607e+01 18 -2.11678957e+01 -3.00038732e+01 4.43672257e+01 19 -9.01742178e+00 -3.82673612e+01 4.20249405e+01 20 -3.84799281e+01 -1.52716034e+01 4.84801271e+01 21 -4.80339033e-01 -7.25597864e+01 5.60758842e+00 22 6.35357008e+01 1.02735234e+01 2.51315038e+01 23 2.56164668e+01 -2.78718444e+01 3.14737442e+01 24 1.66240083e+01 -7.95640192e+00 6.88066478e+01 25 -7.76524841e+01 1.44112973e+01 1.81327554e+01 26 -3.57417218e-02 6.99063295e+01 1.92176341e+01 27 -1.10306651e+01 -2.33154451e+00 6.71245115e+01 28 -3.71833572e+01 3.12397506e+01 3.29565421e+01 29 2.76704710e+01 1.99039644e+01 2.36116318e+01 30 4.69129463e+01 4.76193765e+01 -1.89702359e+00 31 4.40908869e+01 -1.08478577e+01 4.79337697e+01 32 1.09050807e+01 5.09459904e+01 4.24539011e+01 MIXED STRUCTURE (pbc=False)-- Species = Cu Zr (Configuration in file "config-F-CuZr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 108.949135084 Forces: 1 -1.45881519e+01 -1.02866000e+01 -1.32140471e+01 2 1.17164390e+00 1.61088853e+01 -4.57427248e+01 3 -1.22599358e+01 -7.54441897e+01 -1.53584052e+01 4 -7.17315801e+01 1.46457159e+01 -4.24969555e+01 5 -4.05474328e+00 -8.65281265e+00 -1.51878621e+01 6 2.63421132e+01 -2.20150678e+01 -3.54102911e+01 7 1.55160589e+01 -1.69288701e+01 2.98401941e+00 8 3.46648961e+01 1.45841585e+01 1.53937395e+01 9 -1.77392930e+01 -2.45235286e+01 -2.35700489e+01 10 1.90851449e+01 3.07764187e+01 -2.18717966e+01 11 2.62305601e+01 2.67821811e+01 -1.36969039e+01 12 -3.31671225e+01 2.01440285e+01 1.24485754e+01 13 -2.21241946e+01 -9.85135512e+00 -8.54765532e+00 14 1.67027919e+01 1.72287230e+01 -1.07577994e+01 15 4.12256856e+01 -4.78575434e+00 -1.47114786e+01 16 -3.94800967e+01 1.84387505e+01 -3.44936323e+01 17 -3.56607838e+01 -3.52670485e+01 2.80112103e+01 18 2.89597145e+01 2.50074959e+00 4.94373599e+01 19 -5.34139439e-02 -2.83372980e+00 2.90456399e+00 20 -6.92036068e+00 -8.47600738e+00 2.39241460e+01 21 1.57818974e+01 -7.97218324e+00 1.64686786e+01 22 3.70998848e+01 -5.28037026e+01 -3.87795331e+01 23 9.32196687e+00 -2.92957068e+01 8.70123428e+00 24 -1.35011194e+01 1.28811632e+01 1.04324903e+01 25 -3.48209678e+01 -2.78995199e+01 -2.38274542e+01 26 3.17716706e+01 3.85043226e+01 -1.27912379e+01 27 -1.39385727e+01 -2.32240443e+01 1.41420203e+01 28 -2.08578899e+01 3.38995648e+01 5.73208332e+01 29 -1.63667730e+01 1.30708272e+01 1.07446771e+01 30 3.39793169e+01 3.36897227e+01 4.94414958e+01 31 9.64466345e-01 4.35937790e+01 5.66192639e+01 32 1.84471873e+01 2.34111305e+01 1.14835181e+01 MIXED STRUCTURE (pbc=True)-- Species = Cu Zr (Configuration in file "config-T-CuZr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 930.118121907 Forces: 1 -4.30108853e+01 7.08327583e+01 5.30279679e+01 2 1.79669585e+01 2.46333659e+01 -3.88703003e+01 3 2.21918366e+00 -3.12039930e+01 -1.16280440e+01 4 -2.08550886e+01 1.28155233e+01 -4.97312029e+01 5 -1.48962241e+01 6.05320153e+01 2.57253676e+01 6 -6.25064497e+00 -4.98590817e+01 4.09880053e+01 7 -5.00550299e+01 2.38228374e+01 -5.35821812e+01 8 3.18298437e+01 2.00497471e+01 2.04681582e+01 9 3.17059956e+01 -4.79022207e+01 9.55395452e+01 10 4.02996769e+01 -9.88357954e+00 7.55396546e+01 11 4.00669162e+01 2.29355605e+01 -1.19870848e+01 12 1.02517686e+01 -1.45619438e+01 2.30535981e+01 13 -3.60799884e+01 -3.66942403e+01 1.68952716e+01 14 -2.58023216e+01 7.33945589e+00 5.14611061e+01 15 -8.10421651e+00 -3.07702343e+01 -4.94599444e+01 16 -4.91927297e+01 -1.87544446e+00 -4.09338956e+01 17 3.69478970e+01 -2.22083385e+01 4.81496626e+01 18 4.95223752e+01 7.54351497e+00 5.24944604e+01 19 3.19513000e+01 7.69370897e+01 -5.69196050e+01 20 1.01722932e+02 -8.64841728e+01 2.49825411e+01 21 2.73249166e+01 4.06758305e+01 1.21558835e+01 22 -4.39718634e+01 -8.77013047e+01 -9.25601611e+01 23 -8.09701984e+00 -2.27052092e+00 -7.30058684e-01 24 -3.94426299e+01 8.50410197e+00 -1.18221998e+01 25 1.15144698e+02 -1.13698340e+01 -1.02867419e+02 26 4.15231957e+01 -1.46422927e+01 -4.60622464e+01 27 4.06784912e+01 -6.91233252e+01 -3.88205227e+01 28 -1.14606935e+01 5.91611549e+01 -4.61103588e+01 29 -3.39098541e+01 8.12031162e+00 5.03784461e+00 30 -2.13330117e+01 3.15165806e+01 7.15358352e+01 31 -2.04675396e+02 8.49891819e+01 7.18453473e+01 32 -2.01855044e+00 -4.38585031e+01 -3.68150243e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==3376== Memcheck, a memory error detector ==3376== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3376== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==3376== Command: python runner2.py EAM_Dynamo_MendelevKramerOtt_2009_CuZr__MO_600021860456_005 ==3376== ==3376== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==3376== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==3376== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==3376== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==3376== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==3376== by 0x4010732: call_init (dl-init.c:72) ==3376== by 0x4010732: _dl_init (dl-init.c:119) ==3376== by 0x40151FE: dl_open_worker (dl-open.c:522) ==3376== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==3376== by 0x40147C9: _dl_open (dl-open.c:605) ==3376== by 0x544CF95: dlopen_doit (dlopen.c:66) ==3376== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==3376== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==3376== by 0x544D734: _dlerror_run (dlerror.c:162) ==3376== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==3376== ==3376== ==3376== HEAP SUMMARY: ==3376== in use at exit: 40,113,688 bytes in 4,274 blocks ==3376== total heap usage: 198,977 allocs, 194,703 frees, 114,228,432 bytes allocated ==3376== ==3376== LEAK SUMMARY: ==3376== definitely lost: 0 bytes in 0 blocks ==3376== indirectly lost: 0 bytes in 0 blocks ==3376== possibly lost: 183,295 bytes in 113 blocks ==3376== still reachable: 39,930,393 bytes in 4,161 blocks ==3376== suppressed: 0 bytes in 0 blocks ==3376== Rerun with --leak-check=full to see details of leaked memory ==3376== ==3376== For counts of detected and suppressed errors, rerun with: -v ==3376== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2520 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.