Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:10:22) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_FortiniMendelevBuldyrev_2008_Ru__MO_114077951467_005 Supported species : Ru random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ru (Configuration in file "config-F-Ru.xyz") ----------------------------------------------------------------------------------------------------- Energy = 177.34809626 Forces: 1 -1.72362659e+01 -5.42895921e+01 -5.68673410e+01 2 -4.93881708e+01 2.70528504e+00 -7.89783001e+01 3 2.20372507e+01 -5.61497427e+01 -2.51829744e+01 4 -5.23375214e+01 2.47601188e+01 2.26373644e+01 5 2.06086122e+01 -8.85819525e+01 -2.51617679e+01 6 4.27030890e+01 -1.97162915e+01 -4.97530715e+01 7 6.09501391e+01 -1.21934867e+02 -6.50803245e+01 8 2.82076642e+01 -1.81275404e+02 -4.87587822e+01 9 -4.18654664e+01 7.63465245e-01 -5.31001647e+01 10 -3.87692416e+01 6.19855808e+01 -8.31729595e+01 11 -1.42229947e+02 2.51224623e+01 -6.11950084e+01 12 -4.00627131e+01 3.74245534e+01 -1.37544584e+00 13 -1.00676598e+01 2.97298822e+01 -2.15085185e+02 14 2.33401152e+01 3.01340870e+01 -2.55014358e+01 15 2.13002293e+02 7.06689552e+01 6.75938001e+00 16 3.17733818e+01 1.51489385e+02 2.90044005e+00 17 -6.42052042e+01 -1.42419313e+01 3.77465932e+01 18 -5.66821985e+01 -5.40575969e+01 6.01056610e+01 19 -5.12623889e+00 -2.21811342e+01 1.97830213e+01 20 -1.44689584e+01 -5.14936337e-01 1.50729702e+01 21 -1.18107024e+01 -6.54934288e+01 4.54772323e+01 22 9.84643722e+01 4.53547788e-01 7.48531348e+01 23 1.27910689e+01 -1.00097214e+01 1.47774342e+01 24 1.45939906e+00 -2.63551983e+01 5.97495785e+01 25 -8.44400577e+01 9.39070996e+00 2.80103485e+01 26 -4.30057231e+01 1.02148987e+02 1.99373182e+01 27 5.19519935e+01 -8.70953117e+01 4.55616084e+01 28 -9.48494352e+01 9.43877954e+01 2.03129354e+01 29 2.80635514e+01 6.72976904e+01 1.49273052e+02 30 5.27059899e+01 6.16184212e+01 5.89302546e+00 31 7.38495542e+01 -1.40150790e+01 8.87050785e+01 32 4.63702913e+00 4.58312612e+01 7.16565843e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ru (Configuration in file "config-T-Ru.xyz") ----------------------------------------------------------------------------------------------------- Energy = 4247.43080244 Forces: 1 2.84059708e+01 -8.89855232e+01 -2.47206226e+02 2 6.41789190e+01 -3.78616161e+01 -1.34622737e+02 3 3.26489963e+02 1.34500571e+02 1.87809639e+02 4 2.51255394e+02 1.75640907e+02 2.41294608e+02 5 1.72306572e+02 1.20605677e+02 -1.00458298e+02 6 -2.49814428e+02 -8.43176496e+01 -2.86237043e+02 7 -2.34576398e+02 -2.48522939e+02 -2.87856988e+01 8 -3.08116635e+02 -2.99027198e+02 1.81218475e+02 9 -7.80913814e+01 -1.62340903e+02 6.28407060e+01 10 6.86734290e+01 1.32480019e+02 -1.23385035e+02 11 -1.06608918e+02 -2.10127073e+02 2.22843648e+02 12 -2.74035922e+01 -6.74104434e+01 2.45177270e+02 13 -1.29337045e+02 -6.86687276e+01 -4.25903035e+02 14 -2.19695149e+02 1.24156070e+02 -2.14503792e+02 15 2.88708060e+02 1.16202401e+02 2.57793963e+02 16 7.95497036e+01 3.07883179e+02 1.90990367e+02 17 1.46819415e+02 -7.58685827e+01 2.86879491e+02 18 1.17502647e+02 2.39873452e+01 1.11502759e+02 19 1.87457347e+02 2.30050188e+02 -1.17219341e+02 20 9.66188038e+01 -4.11358938e+01 -2.71859477e+02 21 -1.66360943e+02 5.42532163e+01 1.69437192e+02 22 -7.48785614e+01 1.95622281e+02 3.73453191e+02 23 -1.82691266e+02 -3.15213617e+01 -9.33094505e+01 24 -7.59520771e+01 -1.05528465e+02 -2.30674146e+02 25 -3.60313010e+01 -1.38773381e+02 5.23854580e+01 26 4.01208795e+01 1.32668447e+02 -1.42725784e+01 27 3.02489759e+02 -3.54500337e+02 -3.35005807e+02 28 -3.19869878e+02 2.27234371e+02 -2.29311680e+02 29 -8.56711473e+01 -1.12528682e+02 2.91631729e+02 30 -3.82297629e+01 5.04179060e+01 1.17428514e+02 31 -1.61193069e+01 -2.81165881e+01 -4.88129557e+01 32 1.78870927e+02 1.29532787e+02 -9.11197109e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==32231== Memcheck, a memory error detector ==32231== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==32231== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==32231== Command: python runner2.py EAM_Dynamo_FortiniMendelevBuldyrev_2008_Ru__MO_114077951467_005 ==32231== ==32231== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==32231== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==32231== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==32231== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==32231== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==32231== by 0x4010732: call_init (dl-init.c:72) ==32231== by 0x4010732: _dl_init (dl-init.c:119) ==32231== by 0x40151FE: dl_open_worker (dl-open.c:522) ==32231== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==32231== by 0x40147C9: _dl_open (dl-open.c:605) ==32231== by 0x544CF95: dlopen_doit (dlopen.c:66) ==32231== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==32231== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==32231== by 0x544D734: _dlerror_run (dlerror.c:162) ==32231== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==32231== ==32231== ==32231== HEAP SUMMARY: ==32231== in use at exit: 10,030,937 bytes in 3,960 blocks ==32231== total heap usage: 116,077 allocs, 112,117 frees, 64,089,003 bytes allocated ==32231== ==32231== LEAK SUMMARY: ==32231== definitely lost: 0 bytes in 0 blocks ==32231== indirectly lost: 0 bytes in 0 blocks ==32231== possibly lost: 182,191 bytes in 111 blocks ==32231== still reachable: 9,848,746 bytes in 3,849 blocks ==32231== suppressed: 0 bytes in 0 blocks ==32231== Rerun with --leak-check=full to see details of leaked memory ==32231== ==32231== For counts of detected and suppressed errors, rerun with: -v ==32231== 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 06:10:53) ===