Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:13:30) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MendelevKramerBecker_2008_Cu__MO_945691923444_005 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 = 14.9708950253 Forces: 1 -1.50365592e+01 -3.28249892e+01 -4.98012788e+01 2 -1.01072693e+01 1.18333987e+01 -5.79918595e+00 3 2.68449671e+01 -2.45359376e+01 1.58707244e+01 4 -1.62833756e+01 5.37497401e+01 3.25490184e+01 5 9.01637971e+00 -1.42964097e+01 -1.83378502e+00 6 2.37795726e+00 3.75168424e-01 -2.82605924e+00 7 4.40397607e+00 -3.88874863e+01 -4.74969519e+01 8 -2.98557760e+01 -2.62087943e+01 1.02699711e+00 9 -7.20142522e+00 -2.09189575e+01 -2.78376807e+01 10 -3.01899888e+00 1.47114689e+01 -1.75567223e+01 11 -2.30345553e+01 -1.61215472e+01 5.62855305e+00 12 -5.50473395e+00 1.91901256e+01 2.02314755e+01 13 -1.97794968e+01 -8.91142928e+00 -6.26072021e+01 14 9.68301429e+00 8.98440781e+00 -3.11700007e+00 15 7.03548956e+01 1.55481179e+01 1.69720475e+01 16 1.59654158e+01 4.69670337e+01 1.14758936e+01 17 -7.45326611e+00 -2.70885065e+01 -2.84891144e+01 18 4.70803376e+00 2.68328401e+00 4.64587378e-01 19 2.93561937e+00 -3.45860916e+00 3.37949420e+00 20 -1.62104801e+00 2.49897764e+01 2.93868586e+01 21 -2.26632354e+01 -1.04768551e+01 9.16651525e+00 22 2.23143898e+01 3.26088113e+01 2.59917334e+01 23 9.24277030e+00 -8.39041752e-01 1.71858043e+01 24 -8.57181634e-01 1.55555456e+00 2.19728319e+00 25 -3.28302119e+00 -4.75298525e+00 3.57374873e+00 26 -2.47136223e+01 1.73887108e+01 -1.08232675e+01 27 2.90849529e+01 -4.28987851e+01 1.25452825e+01 28 -3.99685167e+01 3.71390743e+01 -6.80583344e+00 29 -3.24171490e+00 -2.44220500e+01 3.09675727e+01 30 3.05913115e+00 4.23774068e+00 2.07739723e+00 31 2.07644874e+00 1.35922668e-01 1.81549387e+00 32 2.15558447e+01 4.54404801e+00 2.24876006e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 86.2155545031 Forces: 1 9.05746261e+00 -5.13812399e+01 -4.68680509e+01 2 -1.10617534e+01 1.23183898e+01 -2.89044296e+00 3 2.72263769e+01 -1.92023408e+01 1.74134407e+01 4 -8.98340791e+00 5.47716950e+01 3.39033974e+01 5 1.26474517e+01 -8.21198936e+00 -1.21187260e+00 6 -2.38699919e+01 2.86580225e+01 1.16917371e+01 7 1.77074028e+00 -3.78964877e+01 -4.82409616e+01 8 -3.05152443e+01 -2.59833826e+01 1.17838034e+00 9 -2.80371856e+01 -2.62973700e+01 1.32556683e+01 10 -6.88884771e+00 9.39819239e+00 -1.52494551e+01 11 -2.29889757e+01 -1.67884088e+01 5.98204193e+00 12 -4.46002886e+00 1.61355626e+01 2.07966978e+01 13 -1.95498845e+01 -1.01822477e+01 -6.03890966e+01 14 8.19605250e+00 9.63818828e+00 -3.69006225e+00 15 6.77797889e+01 1.49475468e+01 1.66376989e+01 16 1.56966858e+01 4.40341616e+01 1.20922476e+01 17 4.14976507e+01 -7.23093746e+01 -1.82153768e+01 18 6.24767679e+00 3.28858124e+00 3.96308164e-01 19 2.59692974e+00 2.40644988e+00 4.45180822e+00 20 5.11609346e+01 5.47802110e+01 3.01621849e+01 21 -2.31711857e+01 -6.75812311e+00 9.92816337e+00 22 -2.58287384e+01 7.77009133e+01 9.28620193e+00 23 -4.54347026e+01 -3.90188547e+01 3.99089033e+00 24 -1.74756301e-01 2.49894238e+00 -1.21970582e+00 25 6.09411319e-01 -5.15275301e+00 3.85071001e+00 26 -2.44432186e+01 1.24441508e+01 -1.31989467e+01 27 5.19175920e+01 -4.78365067e+01 -1.87757231e+01 28 -4.27182986e+01 4.22706897e+01 -1.86294218e+01 29 -3.59728543e+00 -2.48202057e+01 3.09180721e+01 30 1.26723424e+00 2.79372745e+00 2.67982307e+00 31 8.21147365e-01 4.24087469e-01 1.08845869e+00 32 2.32303702e+01 3.32977234e+00 1.88751857e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==3115== Memcheck, a memory error detector ==3115== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3115== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==3115== Command: python runner2.py EAM_Dynamo_MendelevKramerBecker_2008_Cu__MO_945691923444_005 ==3115== ==3115== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==3115== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==3115== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==3115== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==3115== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==3115== by 0x4010732: call_init (dl-init.c:72) ==3115== by 0x4010732: _dl_init (dl-init.c:119) ==3115== by 0x40151FE: dl_open_worker (dl-open.c:522) ==3115== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==3115== by 0x40147C9: _dl_open (dl-open.c:605) ==3115== by 0x544CF95: dlopen_doit (dlopen.c:66) ==3115== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==3115== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==3115== by 0x544D734: _dlerror_run (dlerror.c:162) ==3115== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==3115== ==3115== ==3115== HEAP SUMMARY: ==3115== in use at exit: 9,981,223 bytes in 3,960 blocks ==3115== total heap usage: 114,226 allocs, 110,266 frees, 63,893,941 bytes allocated ==3115== ==3115== LEAK SUMMARY: ==3115== definitely lost: 0 bytes in 0 blocks ==3115== indirectly lost: 0 bytes in 0 blocks ==3115== possibly lost: 182,191 bytes in 111 blocks ==3115== still reachable: 9,799,032 bytes in 3,849 blocks ==3115== suppressed: 0 bytes in 0 blocks ==3115== Rerun with --leak-check=full to see details of leaked memory ==3115== ==3115== For counts of detected and suppressed errors, rerun with: -v ==3115== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2509 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. === Verification check vc-memory-leak end (2018-12-15 06:13:59) ===