Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:16:04) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_SmirnovaKuskinStarikov_2013_UMoXe__MO_679329885632_005 Supported species : Mo U Xe random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mo (Configuration in file "config-F-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 55.936140324 Forces: 1 -1.28862100e+01 -1.19688049e+01 -1.19762302e+01 2 -2.89413506e+00 5.69712013e+00 -2.80460552e+01 3 -2.45164391e+00 -3.00956201e+01 5.27485641e+00 4 -2.75918513e+01 -3.80561151e-01 -2.00261181e+00 5 3.64058082e+00 -2.01762715e+01 -1.88145871e+01 6 1.52052251e+01 3.68510616e+00 -1.78260510e+01 7 1.75354209e+01 -1.99980628e+01 1.65083465e+00 8 8.69149105e+00 -2.87993728e+00 -2.77774898e+00 9 -1.56163196e+01 1.86950221e+00 -1.47735538e+01 10 -6.47892367e+00 1.84685908e+01 -1.93305389e+01 11 -1.14841402e+01 4.36507553e+00 -7.58452647e+00 12 -1.68156272e+01 1.61127185e+01 -2.00960754e+00 13 6.93325389e+00 -2.78216926e+00 -2.59313415e+01 14 1.22187839e+01 9.77617232e+00 -9.51155966e+00 15 2.51645799e+01 4.46991444e+00 -6.08165115e+00 16 6.48419963e+00 2.93473933e+01 -3.67580863e+00 17 -1.42989468e+01 -1.88947289e+01 -7.17608694e-01 18 -1.34447582e+00 -6.96852185e+00 1.00395357e+01 19 -1.89845441e+00 -1.56944854e+01 1.73162576e+01 20 -1.64954848e+01 -1.65253033e+00 1.97918743e+01 21 -5.00831599e-01 -2.65237279e+01 -6.22394425e+00 22 2.55715084e+01 -1.95226930e+00 -2.67909974e+00 23 1.49304884e+01 -1.63229580e+01 1.55663439e+01 24 -6.34619631e+00 5.38080206e+00 2.55813626e+01 25 -2.79114252e+01 4.13160213e+00 -4.73818736e-01 26 -6.00209941e+00 2.75149866e+01 2.61334603e-01 27 1.48148153e+00 -1.87858418e+00 2.78986837e+01 28 -1.08482177e+01 1.04797540e+01 1.09321183e+01 29 5.69729374e+00 -2.28610482e+00 7.94621225e+00 30 1.88685792e+01 1.85181579e+01 -1.52520875e-01 31 1.70565134e+01 5.30162698e+00 1.88740058e+01 32 2.38558308e+00 1.53368147e+01 1.94554443e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = U (Configuration in file "config-F-U.xyz") ----------------------------------------------------------------------------------------------------- Energy = 139.372999723 Forces: 1 -1.00483256e+01 -1.49820352e+01 -3.66657030e+00 2 3.94327133e+01 -3.16209941e+01 -9.15667707e+00 3 -3.29403348e+01 -2.03461935e+01 -3.14801754e+01 4 -4.81255665e+01 -2.19943177e+01 -5.17393361e+01 5 -5.75967058e+00 -1.14496146e+01 -2.42505510e+01 6 1.68188389e+01 -1.87681102e+01 -3.68313180e+01 7 1.68118513e+01 -7.89764419e+00 1.00961330e+01 8 3.75928845e+00 8.41499799e+00 9.17687058e+00 9 -4.38099625e+01 3.96607010e+01 -1.70237269e+01 10 -1.56222081e+01 2.70579030e+01 -5.31604948e+00 11 3.23216539e+01 3.21012351e+00 -3.65986740e+01 12 -9.57670951e+00 1.43911284e+01 -6.53887019e+00 13 8.53428137e+00 -1.68120484e+01 -1.96225017e+01 14 1.94213610e+01 1.17923195e+01 -1.37169137e+01 15 2.08742896e+01 1.07310049e+01 2.53757912e+01 16 -9.71739594e+00 3.83951766e+01 -1.01227913e+01 17 -3.77986122e+01 -2.26380904e+01 -1.85636336e+01 18 5.19141972e+01 6.30451593e+00 2.73869471e+01 19 -4.89059231e+00 -1.58610464e+01 5.38844959e+01 20 -1.50105853e+01 2.60714400e+00 1.94247003e+01 21 4.90506939e+01 -2.20864614e+01 7.33179929e+00 22 1.68844088e+01 -3.26759690e+01 -3.64094171e+01 23 1.24737112e+01 -1.34601602e+01 9.63303703e+00 24 -1.26607942e+01 1.88890823e+01 1.72882160e+01 25 -5.54583232e+01 1.88534920e+01 4.50322970e+01 26 -2.08230993e+01 3.73310062e+01 -2.64914671e+01 27 -3.11312417e+01 -5.73788850e+01 2.48455237e+01 28 -1.86544500e+01 1.19548487e+01 9.20497598e+00 29 1.90232205e+01 -3.87423130e+01 1.03751445e+01 30 1.19848629e+01 1.54091542e+01 -3.03693178e+00 31 1.43351198e+00 2.81118471e+01 4.67617114e+01 32 5.12889875e+01 5.35994380e+01 3.47479618e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Xe (Configuration in file "config-F-Xe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 8146.21570018 Forces: 1 -1.71594364e+03 -2.99666589e+03 -3.13011471e+03 2 4.36846753e+02 -1.68220909e+03 -5.44073436e+02 3 3.09462922e+03 -8.72847852e+02 1.07631857e+03 4 -1.60840298e+03 3.70215859e+03 1.23165675e+03 5 2.84500399e+01 -4.12480350e+01 -5.49122951e+01 6 1.12044622e+03 -1.05802491e+03 -4.97138372e+02 7 1.85799985e+03 -2.26805273e+03 -3.60429517e+03 8 -1.30008408e+03 -6.01034780e+02 1.72957821e+02 9 -2.25481440e+03 -2.57369374e+02 -5.08029122e+02 10 2.08078226e+03 2.01874627e+03 -1.54491354e+03 11 -2.00402198e+03 -8.05713292e+02 1.91558702e+03 12 -1.27082884e+03 6.54716573e+02 1.10996491e+03 13 1.59109835e+03 1.15239564e+03 -2.31216179e+03 14 1.03468929e+01 1.22280752e+01 -9.17156401e+00 15 1.01071411e+03 1.52647817e+03 -4.38513402e+02 16 2.34462395e+03 1.38834564e+03 -2.05021042e+03 17 -9.91610792e+02 -1.15307118e+03 5.47084404e+02 18 8.60609339e+02 1.46272499e+03 -6.47473044e+01 19 -1.15300985e+01 -4.41779044e+02 5.62662392e+02 20 -2.09682723e+02 -2.96905669e+02 6.28479109e+02 21 -2.20560607e+03 -7.88728940e+02 1.58253637e+03 22 1.13239687e+03 1.61335052e+03 2.47924155e+03 23 1.65576312e+03 -1.73292350e+03 4.94122879e+02 24 -1.64173569e+03 1.69999332e+03 4.95123393e+01 25 -1.68004436e+02 -8.52176522e+01 -1.18751948e+02 26 -3.69547562e+03 1.92453147e+03 -1.12306476e+03 27 -5.78450452e+02 -3.74038859e+03 2.69532211e+03 28 -1.02478186e+03 8.21662838e+02 2.22042825e+02 29 2.79601615e+02 -1.55950571e+03 -1.41919013e+03 30 6.03628200e+02 1.47649021e+03 -8.46983945e+02 31 1.07173542e+03 -9.42955756e+02 1.71498684e+03 32 1.50130144e+03 1.87081970e+03 1.78379602e+03 MIXED STRUCTURE (pbc=False)-- Species = Mo U Xe (Configuration in file "config-F-MoUXe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1888.63661937 Forces: 1 -1.55046171e+02 -1.01391515e+03 -8.99463016e+02 2 3.49872694e+00 -1.77017703e+00 -2.59511540e+01 3 -4.03870585e+01 -2.48098511e+02 -2.26884183e+02 4 1.08518557e+02 1.00586834e+03 8.85806393e+02 5 -8.07881904e+02 -6.07614415e+01 -5.89346023e+02 6 1.65040895e+01 2.72799193e+01 -2.16457042e+01 7 8.22141668e+02 2.14145871e+00 5.74035241e+02 8 1.03175257e+01 -2.01568367e+02 -2.17055156e+02 9 -4.20456611e+02 -1.34991885e+02 -2.75009919e+02 10 8.81901356e+01 2.70195124e+02 -1.73828187e+02 11 2.17423273e+02 -1.34363369e+02 1.35437004e+01 12 -1.05855694e+02 4.77512195e+02 -2.12427185e+02 13 -5.56181907e+01 -2.82314063e+02 -2.38744992e+02 14 4.49214859e+01 3.46447910e+01 -6.07996784e+00 15 4.92392285e+02 2.10660907e+02 -2.35844020e+02 16 1.73206799e+02 3.66447301e+02 2.27218481e+02 17 -6.07265204e+01 -4.28651561e+01 -2.76890496e+00 18 -2.86119095e+02 -1.12736539e+02 5.27348576e+02 19 -1.17343175e+01 -9.41236697e+01 1.27947267e+02 20 -1.76076759e+01 3.12762670e+00 1.72048086e+01 21 5.51535203e+01 -9.49580540e+01 9.32543857e+00 22 2.39259465e+02 1.01427082e+03 -1.14793228e+03 23 -2.00110736e+02 -1.20622316e+03 9.93774938e+02 24 1.13976985e+01 -2.38762645e+02 2.51395567e+02 25 -8.98427210e+01 -2.00589507e+02 2.61200862e+02 26 -2.17650838e+02 2.44851424e+02 4.85021408e+01 27 -7.14748939e+01 -1.97471441e+01 1.13764749e+02 28 -1.29990043e+01 1.16705720e+01 1.80575200e+01 29 2.37511207e+02 -3.19060073e+01 -2.28160858e+02 30 -6.25586363e+01 1.27886525e+03 -9.37488993e+02 31 1.20129404e+02 -1.08004306e+03 1.12175194e+03 32 -2.44957734e+01 2.52202181e+02 2.47752916e+02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==6416== Memcheck, a memory error detector ==6416== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==6416== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==6416== Command: python runner2.py EAM_Dynamo_SmirnovaKuskinStarikov_2013_UMoXe__MO_679329885632_005 ==6416== ==6416== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==6416== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==6416== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6416== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6416== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6416== by 0x4010732: call_init (dl-init.c:72) ==6416== by 0x4010732: _dl_init (dl-init.c:119) ==6416== by 0x40151FE: dl_open_worker (dl-open.c:522) ==6416== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6416== by 0x40147C9: _dl_open (dl-open.c:605) ==6416== by 0x544CF95: dlopen_doit (dlopen.c:66) ==6416== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6416== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==6416== by 0x544D734: _dlerror_run (dlerror.c:162) ==6416== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==6416== ==6416== ==6416== HEAP SUMMARY: ==6416== in use at exit: 16,921,215 bytes in 4,422 blocks ==6416== total heap usage: 221,774 allocs, 217,352 frees, 100,590,315 bytes allocated ==6416== ==6416== LEAK SUMMARY: ==6416== definitely lost: 0 bytes in 0 blocks ==6416== indirectly lost: 0 bytes in 0 blocks ==6416== possibly lost: 181,615 bytes in 110 blocks ==6416== still reachable: 16,739,600 bytes in 4,312 blocks ==6416== suppressed: 0 bytes in 0 blocks ==6416== Rerun with --leak-check=full to see details of leaked memory ==6416== ==6416== For counts of detected and suppressed errors, rerun with: -v ==6416== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2558 from 173) ================================================================================ 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 06:16:40) ===