!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_PunMishin_2009_NiAl__MO_751354403791_005 Supported species : Al Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 15.7488164843 Forces: 1 -3.32162158e+00 -2.71299971e+00 -3.36275367e+00 2 1.54871177e+00 -1.27660892e+00 -6.91169707e+00 3 2.36517643e+00 -6.00636379e+00 5.90552478e-01 4 -6.54962057e+00 2.23909845e+00 -1.91217239e-01 5 -1.06656288e+00 -4.38847395e+00 -3.37430506e+00 6 3.91511222e+00 1.32338286e+00 -3.92406625e+00 7 3.38281461e+00 -3.63218136e+00 -2.44533319e-01 8 -1.00222346e+00 -2.00451238e+00 1.11383455e+00 9 -4.44345872e+00 -3.71814364e-01 -5.60228672e+00 10 5.99657294e-01 6.29311274e+00 -4.91647983e+00 11 -2.64053171e+00 -2.60777671e+00 -4.18958185e-01 12 -5.78210713e+00 4.78440184e+00 1.07239303e+00 13 2.13438526e+00 -1.63800170e+00 -7.32135650e+00 14 4.45056666e+00 3.92477505e+00 -4.84225718e+00 15 6.95307966e+00 -1.92040864e+00 -6.87302186e-01 16 -2.10717441e+00 8.77559528e+00 -6.59958163e-01 17 -5.81740358e+00 -4.53392533e+00 1.98384203e-01 18 1.68181039e+00 5.03822886e-01 -5.29388452e-01 19 2.36383451e+00 -5.91260590e+00 3.58786898e+00 20 -4.53291479e+00 2.10375111e+00 5.28771958e+00 21 -2.22324012e+00 -4.54991933e+00 8.40257014e-01 22 5.67890486e+00 1.04095695e+00 5.70113066e-01 23 2.61351822e+00 -1.90940790e+00 4.18526159e+00 24 9.64955590e-01 -8.50095605e-01 4.75954611e+00 25 -6.20728140e+00 -1.12678777e+00 -7.12280631e-01 26 5.08469181e-01 7.22826008e+00 -1.14053196e+00 27 -1.09940780e+00 -1.37664061e+00 6.09638415e+00 28 -4.54191000e+00 3.00072398e+00 3.47790970e+00 29 3.69219636e-01 -3.17290458e+00 1.97507413e+00 30 5.34550408e+00 5.09108764e+00 1.76371831e+00 31 4.76341003e+00 -9.09565313e-01 4.24297627e+00 32 1.69632772e+00 4.59202499e+00 5.07737926e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 81.9827351121 Forces: 1 1.41812009e+00 4.77296480e-01 3.62953953e-01 2 1.64579507e+00 -1.26082865e+00 3.26578613e-01 3 1.62423960e+00 2.14732831e+00 1.68239528e+00 4 3.20303366e-01 2.70987753e+00 -1.79462727e-01 5 -8.58387017e-01 1.09911216e+00 -3.99480611e-01 6 -1.21746561e+00 2.96323526e+00 -6.18729141e-01 7 -2.56044374e+00 1.36049607e+00 3.81531062e-01 8 -1.02426110e+00 -2.70730762e+00 1.23276603e+00 9 -2.65715839e+00 -1.38727846e+00 -4.35067432e-01 10 7.32030725e-01 2.31202887e+00 2.42717918e-01 11 -2.71578050e+00 -2.51424437e+00 2.99013278e-02 12 -3.36444221e-01 -1.35350318e-01 4.44821635e-01 13 2.46169695e+00 -1.89115162e+00 -1.54758730e+00 14 1.23181277e+00 -8.31701438e-01 -2.08692676e+00 15 2.75784152e+00 -2.24408720e+00 -5.78310319e-02 16 -1.47371132e+00 1.81795112e+00 -4.66905726e-01 17 4.11796808e-01 -1.21619910e+00 3.00278582e-01 18 3.02107354e+00 5.84151243e-01 -1.29363116e-01 19 2.07345749e+00 -2.49819323e-01 -1.46227737e+00 20 -4.56570847e-01 2.65704902e+00 4.02620957e-01 21 -3.50559362e+00 1.64943635e+00 1.98773680e+00 22 -1.15672824e+00 2.25219332e+00 2.97638101e-01 23 -3.00770109e+00 -1.09921969e+00 -5.19634638e-01 24 1.21376960e+00 2.74806691e-01 -2.71266909e+00 25 -6.46297993e-01 -1.74917879e+00 -4.81108773e-01 26 1.12214713e+00 1.02309875e+00 -5.02564214e-01 27 -6.30126360e-01 -1.56951082e+00 -1.10384781e-01 28 -2.10643724e+00 -8.79453636e-01 2.84250616e-01 29 4.90109578e-01 -3.06337947e+00 2.14224397e+00 30 6.33706428e-01 -3.45435686e-01 2.34391243e+00 31 3.77583050e-01 -1.65477451e+00 3.90905753e-01 32 2.81762355e+00 1.47085952e+00 -1.14326032e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -60.1994404349 Forces: 1 -4.55689524e+00 -4.73911382e+00 -5.34661339e+00 2 3.30506869e+00 4.74719160e+00 -7.03792159e+00 3 3.31595876e+00 -7.93472804e+00 3.22578844e+00 4 -6.92709389e+00 4.50226203e+00 1.03005610e+00 5 -1.53184109e+00 -3.63654562e+00 -3.67033592e+00 6 3.24638982e+00 3.03657158e+00 -5.40072294e+00 7 5.05293909e+00 -3.93319612e+00 2.74038258e+00 8 4.01325085e-01 3.49766326e+00 3.02011222e+00 9 -2.11257630e+00 -1.50916749e+00 -3.11352536e+00 10 -3.64164318e+00 5.78822550e+00 -4.01567986e+00 11 3.33602760e+00 -1.95874112e+00 -7.19199358e-01 12 -4.89151539e+00 4.97743048e+00 -8.39784188e-01 13 3.80353495e-01 -6.07065443e+00 -4.31231345e+00 14 4.27676707e+00 2.27319567e+00 -3.81166823e+00 15 4.68312219e+00 -4.19226123e-01 -2.09778467e+00 16 -8.00324048e-01 4.74319542e+00 5.24234749e+00 17 -3.16358335e+00 -3.37191974e+00 3.25008777e+00 18 2.58591518e+00 -6.81443840e-02 2.74225034e+00 19 -1.25854242e+00 -8.48182136e-01 8.01618650e-01 20 -3.06398548e+00 -2.51465080e+00 2.64076870e+00 21 -2.53445345e+00 -3.95493316e+00 -2.43330276e+00 22 5.01432678e+00 -2.64647645e+00 -1.52618017e+00 23 2.74979139e+00 -2.51082678e+00 3.17031639e+00 24 -3.73851890e+00 1.19212554e+00 5.16205951e+00 25 -5.86986471e+00 -2.25427919e+00 2.40087949e+00 26 3.61580510e+00 5.44784886e+00 -3.27358845e+00 27 3.93892593e+00 -2.64063396e+00 5.09694433e+00 28 -3.96233286e+00 3.60439269e+00 2.43155156e+00 29 -4.48656249e+00 -1.99337316e+00 -3.11419982e+00 30 3.42092996e+00 4.56745723e+00 -6.84271524e-01 31 4.16415457e+00 3.47169209e-01 5.05801734e+00 32 -9.48067918e-01 4.28006346e+00 3.38391081e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -52.0964569739 Forces: 1 -1.99740073e+00 -5.90697903e+00 -4.24153254e+00 2 3.68846893e+00 4.32954793e+00 -4.40331756e+00 3 2.98765241e+00 -6.32738563e+00 3.74121287e+00 4 -7.28686177e-01 2.68696375e+00 8.83228438e-01 5 -1.95126815e+00 5.08828458e+00 2.05997132e+00 6 9.14287535e-01 4.01621572e+00 -4.14778155e+00 7 1.60636134e+00 -1.47863273e+00 2.24006715e+00 8 4.97248690e-01 3.38476427e+00 2.91841042e+00 9 -2.54125848e+00 -1.27670975e+00 2.83428409e+00 10 -5.47432962e+00 2.66142794e+00 1.16102052e+00 11 3.57183739e+00 -1.52262986e+00 -7.76762463e-01 12 -9.69887682e-02 6.12137207e+00 -2.84423592e+00 13 9.56040626e-01 -6.64600260e+00 -2.30516372e+00 14 7.02818861e+00 2.06565121e-01 1.32120195e+00 15 -2.68913523e+00 -1.69745428e+00 -2.05372579e+00 16 -1.35416233e+00 7.63198322e-01 6.11311027e+00 17 5.58381554e-01 -2.15018673e+00 3.13694231e+00 18 2.27845399e+00 -3.18871795e-01 2.88301891e+00 19 -3.56309590e+00 5.20819758e+00 -2.54070498e+00 20 -1.20644687e+00 -4.67464104e+00 5.41819043e-01 21 -4.53094583e+00 9.22677396e-01 -3.43515212e+00 22 -4.92250988e-01 -1.95086914e+00 -8.70723289e-01 23 6.97891515e+00 3.48495795e+00 6.33813682e-01 24 -4.65877503e+00 1.56654033e+00 2.49111913e+00 25 -1.51506957e+00 -1.06527821e+00 4.08664549e+00 26 2.80235345e+00 4.47460616e+00 -3.69664633e+00 27 5.08411101e+00 -4.17283568e+00 -7.26846326e-01 28 -4.97765866e+00 2.95410447e+00 2.14850285e-01 29 -4.28163220e+00 -1.88143561e+00 -2.89881400e+00 30 3.30504877e+00 -1.19889006e+00 2.60368693e-01 31 2.24148276e+00 -1.93451947e+00 -4.00575378e-02 32 -2.43972770e+00 -3.66610197e+00 -2.53962045e+00 MIXED STRUCTURE (pbc=False)-- Species = Al Ni (Configuration in file "config-F-AlNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 0.59352743589 Forces: 1 -6.25534169e+00 -3.15877325e+01 -3.61635733e+01 2 5.50505559e-01 -4.59088119e-01 -7.43308581e+00 3 4.72843677e+00 -5.52298251e+00 -4.06470931e-01 4 -1.82399389e+00 2.87605919e+01 3.31946941e+01 5 7.64742978e-01 -3.41725779e+00 -1.76597415e+00 6 6.76110750e+01 -5.28382376e+01 1.58489580e+01 7 4.93144236e-01 -2.19408458e+00 1.00217359e+00 8 5.54580117e-01 -4.43507989e+00 2.71583314e+00 9 -5.59783923e+00 -8.13800691e-02 -3.75425028e+00 10 1.63125729e+00 5.12416042e+00 -4.39556071e+00 11 -1.14220405e+00 1.09098085e+00 2.21174506e+00 12 -1.30311115e+02 -1.92141265e+01 -1.34535853e+02 13 -6.13675701e+01 5.41317973e+01 -2.43161585e+01 14 1.82600580e+01 2.64088236e+00 -1.41350901e+01 15 8.47389970e+00 -2.22541991e+00 -5.29953195e+00 16 -1.99248376e+01 4.32593599e+00 9.04404646e+00 17 -3.38533496e+00 -1.12294282e+01 -6.05991605e+00 18 -1.53396079e+00 3.36158790e+00 -1.29480416e+00 19 -1.47240772e-01 -5.37345059e+00 5.64832245e+00 20 -4.78958708e+00 8.87338257e+00 9.55057267e+00 21 8.70574614e+00 -8.61891405e+01 -3.76036438e+01 22 9.70375786e+00 -9.40330591e+00 -2.31958579e+00 23 5.38184820e+00 -1.87388827e+00 4.50965869e+00 24 -7.47402711e+00 8.04260118e+01 3.85111500e+01 25 -4.15132671e+00 -1.30682739e-01 1.69015022e+00 26 1.30454077e+02 2.65754834e+01 1.34037037e+02 27 1.50259922e-01 2.12466655e+00 4.13806607e+00 28 -2.55772382e+00 2.36392992e+00 3.73752420e+00 29 -4.65163912e+01 -7.14510499e+01 -2.00289782e+01 30 4.59464234e+01 8.66710769e+01 1.19459188e+01 31 4.94205574e+00 -1.79699783e+00 8.07366720e+00 32 -1.13733738e+01 2.95284560e+00 1.36529591e+01 MIXED STRUCTURE (pbc=True)-- Species = Al Ni (Configuration in file "config-T-AlNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 28.939654163 Forces: 1 -1.04177755e+00 -3.04461093e+01 -3.70802431e+01 2 1.74288692e+00 3.81271310e-01 -1.68414966e+00 3 5.29743554e+00 -1.38885948e+00 -2.14716151e+00 4 5.79311212e+00 3.07824630e+01 3.30813989e+01 5 1.38027212e+00 -1.79577280e+00 2.70971612e+00 6 6.29770085e+01 -5.30321249e+01 1.62889299e+01 7 -4.80753024e+00 -2.72676019e-01 4.41684142e+00 8 -3.20959154e-01 -4.61607649e+00 2.57847090e+00 9 -3.39793533e+00 -3.45230130e-01 -8.46158824e-01 10 7.78166929e-01 4.28124971e+00 2.42826521e+00 11 -2.19729147e+00 5.12320536e-01 1.52483144e+00 12 -1.26840997e+02 -2.37032876e+01 -1.34143099e+02 13 -6.01844113e+01 5.41728432e+01 -2.12150544e+01 14 1.27195449e+01 -2.00677780e-03 -1.72402679e+01 15 -5.68898503e+00 2.55534160e+00 -1.37495762e+01 16 -2.07731191e+01 2.21897681e+00 9.40706886e+00 17 -1.01793740e+00 -6.56824387e+00 -6.28743938e+00 18 -1.78134316e+00 2.81417024e+00 -1.28512737e+00 19 -2.72223340e+00 -2.57851727e+00 8.70056694e-01 20 -7.66080072e-01 9.66107999e+00 7.17634926e+00 21 8.73117455e+00 -6.95545756e+01 -4.71379230e+01 22 4.27348142e+00 -9.14450882e+00 -1.85741363e+00 23 7.71117030e-01 -5.08327385e+00 4.19199457e+00 24 -7.20996083e+00 8.00763820e+01 3.65549862e+01 25 1.46305994e+01 -5.50554339e+00 7.23732862e+00 26 1.30268322e+02 2.19514035e+01 1.34210506e+02 27 2.72993612e-02 2.22498045e+00 -2.43170228e+00 28 -2.86428635e+00 1.53868883e+00 1.80593649e+00 29 -4.63348156e+01 -7.09295884e+01 -1.97483461e+01 30 4.55621920e+01 8.40406485e+01 1.17029954e+01 31 2.68049197e+00 3.97663039e-01 9.00887187e+00 32 -9.68344117e+00 -1.26430879e+01 2.16591141e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==5532== Memcheck, a memory error detector ==5532== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==5532== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==5532== Command: python runner2.py EAM_Dynamo_PunMishin_2009_NiAl__MO_751354403791_005 ==5532== ==5532== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==5532== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==5532== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5532== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5532== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5532== by 0x4010732: call_init (dl-init.c:72) ==5532== by 0x4010732: _dl_init (dl-init.c:119) ==5532== by 0x40151FE: dl_open_worker (dl-open.c:522) ==5532== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==5532== by 0x40147C9: _dl_open (dl-open.c:605) ==5532== by 0x544CF95: dlopen_doit (dlopen.c:66) ==5532== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==5532== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==5532== by 0x544D734: _dlerror_run (dlerror.c:162) ==5532== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==5532== ==5532== ==5532== HEAP SUMMARY: ==5532== in use at exit: 39,192,313 bytes in 4,273 blocks ==5532== total heap usage: 197,919 allocs, 193,646 frees, 112,984,770 bytes allocated ==5532== ==5532== LEAK SUMMARY: ==5532== definitely lost: 0 bytes in 0 blocks ==5532== indirectly lost: 0 bytes in 0 blocks ==5532== possibly lost: 182,735 bytes in 112 blocks ==5532== still reachable: 39,009,578 bytes in 4,161 blocks ==5532== suppressed: 0 bytes in 0 blocks ==5532== Rerun with --leak-check=full to see details of leaked memory ==5532== ==5532== For counts of detected and suppressed errors, rerun with: -v ==5532== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2520 from 172) ================================================================================ 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.