!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_BorovikovMendelevKing_2016_CuZr__MO_097471813275_000 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 = 4.07838931615 Forces: 1 -1.15086591e+01 -1.62740838e+01 -2.38793077e+01 2 -5.35919521e+00 9.24547587e+00 -5.22175555e+00 3 1.59950482e+01 -9.02729000e+00 1.42679259e+01 4 -8.27440252e+00 2.04778568e+01 1.03817985e+01 5 5.31871674e-01 -1.47751244e+01 1.86172493e+00 6 7.31716471e+00 6.01977468e+00 -4.05151984e+00 7 -2.10607350e+00 -4.32396937e+01 -4.51101103e+01 8 -5.58392309e+00 -9.89805201e+00 -3.63203403e+00 9 1.05112524e+00 -1.38113954e+01 -1.48749834e+01 10 -6.66345866e+00 7.98285603e+00 -1.32934072e+01 11 -6.47855250e+00 -6.97935762e+00 -1.14649710e+00 12 -6.98419583e+00 1.35701733e+01 1.29367856e+01 13 -1.78781399e+01 -1.57867164e+01 -4.22955604e+01 14 7.53133191e+00 1.73714974e+01 -1.27830974e+01 15 3.39684396e+01 -1.76965456e+01 2.68026763e+01 16 2.00774075e+00 2.67406217e+01 1.65844599e+01 17 -1.54618444e+01 -2.39535265e+01 -2.79269499e+01 18 2.99625809e+00 7.28555343e+00 -7.76384204e+00 19 1.17502900e+01 -8.79442897e+00 1.18296389e+01 20 -5.11218080e+00 2.34084258e+01 2.33308866e+01 21 -7.99403538e+00 -4.49622815e+00 -8.76167786e-01 22 1.35186739e+01 4.21767546e+01 4.52925917e+01 23 3.26379410e+00 -2.03478271e-01 4.38205875e+00 24 4.56601710e+00 3.55218195e-02 6.09183798e+00 25 -9.64545038e+00 -8.91935728e+00 -1.07232730e+01 26 -3.45416950e+00 1.33733505e+01 -8.63384153e+00 27 2.43997388e+01 -3.65613143e+01 1.62537968e+01 28 -3.45308188e+01 3.51051460e+01 4.73090961e+00 29 -4.55755353e+00 -4.36707489e+00 6.42234087e+00 30 4.76752332e+00 9.64763755e+00 1.35122839e+00 31 1.08409041e+01 -7.64339462e+00 9.58881829e+00 32 7.08673159e+00 9.98641646e+00 1.01028683e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 77.1599094761 Forces: 1 -2.49965582e+00 -1.30766501e+01 -2.36646496e+01 2 -1.43633610e+01 6.20635704e+00 1.41746811e+01 3 1.80902129e+01 -6.41370490e+00 1.56164423e+01 4 3.16217471e-01 2.66843374e+01 7.53945977e+00 5 4.69386430e+00 -6.34615019e+00 2.16026184e+00 6 -2.72340705e+00 1.56699569e+01 1.20011410e+00 7 -1.14759135e+01 -4.43130782e+01 -4.34159868e+01 8 -6.92312673e+00 -1.08292158e+01 -3.46377000e+00 9 -1.42319922e+01 -2.25399932e+01 1.09966172e+01 10 -1.21687531e+01 3.51276924e+00 -6.87087852e+00 11 -7.08707169e+00 -8.48420701e+00 -8.63615024e-01 12 1.07266915e+02 -3.30928848e+00 6.79637296e+01 13 -1.74045259e+01 -1.91009345e+01 -4.09533667e+01 14 -1.04720117e+02 2.78758147e+01 -6.77778038e+01 15 3.09715054e+01 -2.11613466e+01 2.83494021e+01 16 1.01674043e+00 2.67244995e+01 1.77302518e+01 17 1.41342209e+01 -3.92311580e+01 -2.87455965e+01 18 4.69585810e+00 7.94034665e+00 -8.35999272e+00 19 1.52966925e+01 2.39544774e+00 1.34609178e+01 20 6.33787239e+00 3.57274256e+01 2.44727074e+01 21 -9.82842057e+00 1.57427999e-02 -6.31719624e-02 22 -9.70113285e+00 6.20162343e+01 3.58185837e+01 23 -1.55715504e+01 -1.58723188e+01 6.02979917e+00 24 1.49474832e+01 4.03866627e+00 -1.30294677e+01 25 -6.27793647e+00 -1.14688560e+01 -1.16387590e+01 26 -2.07683374e+00 8.39703007e+00 -1.33815062e+01 27 4.05029275e+01 -3.85598948e+01 -6.57989859e+00 28 -3.87346348e+01 3.26039467e+01 3.80560461e-01 29 -4.66384566e+00 -5.93868489e+00 7.43430821e+00 30 1.88631118e+00 6.60485996e+00 1.25412083e+00 31 9.26728085e+00 -8.60119601e+00 9.82821705e+00 32 1.10281763e+01 8.83324292e+00 4.39828867e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Zr (Configuration in file "config-F-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 343.24179857 Forces: 1 -1.79343690e+01 -3.81093106e+01 -4.13218815e+01 2 1.57079665e+01 -6.41114762e+00 -4.71151811e+01 3 -4.17098513e+01 -5.69444945e+01 4.08620482e+01 4 -4.81651193e+01 1.56625447e+01 -1.70073362e+01 5 3.64341111e+01 -3.43300951e+01 -9.63814834e+01 6 3.79148770e+01 -2.97448943e+00 -5.96241957e+01 7 5.02680695e+01 -6.66171340e+01 2.40696310e+01 8 -3.31656821e+01 3.75697874e+01 9.96708368e+00 9 -4.51147720e+01 2.00456895e+01 -2.40591176e+01 10 -3.26873085e+01 4.48996916e+01 -4.66289800e+01 11 6.24775607e+00 -1.57923325e+01 5.19433182e+00 12 -3.91524801e+01 4.47450965e+01 -1.04246108e+01 13 1.74120004e+01 -2.70435063e+01 -5.19095882e+01 14 3.46718868e+01 3.16880938e+01 -1.96815821e+01 15 4.08777473e+01 1.14070207e+01 1.66577203e+01 16 5.44879930e+00 4.48706370e+01 2.59273441e+01 17 -5.76989336e+01 -5.78236711e+01 4.25176924e+01 18 3.97030581e+01 1.31384620e+01 2.11431525e+01 19 -2.56218258e+01 -2.60682357e+01 2.60126770e+01 20 -2.23095413e+01 -1.79966330e+01 3.21359668e+01 21 9.96855992e+00 -4.30254176e+01 -1.85877379e+01 22 4.33514973e+01 3.80217145e+00 -1.02867899e+01 23 2.77902053e+01 -3.19418100e+01 2.81416789e+01 24 -1.03858236e+01 2.46548859e+01 5.10843785e+01 25 -5.54175199e+01 1.27342589e+01 1.56987802e+01 26 7.79919666e+00 6.38015922e+01 -3.79324547e+01 27 -9.04456091e+00 -3.50274232e+01 7.27350651e+01 28 -4.03177078e+01 2.86286099e+01 1.90383449e+01 29 1.98075362e+01 -5.84606114e+00 -1.96533723e+01 30 2.09059041e+01 2.27922963e+01 7.36794541e+00 31 5.26771640e+01 -6.14977917e+00 2.36634464e+01 32 1.17391595e+01 5.16607032e+01 3.83970240e+01 MIXED STRUCTURE (pbc=False)-- Species = Cu Zr (Configuration in file "config-F-CuZr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 294.146820518 Forces: 1 -2.71527356e+01 -1.88016710e+01 -2.10535669e+01 2 2.67273167e+01 -5.45166466e+01 -1.03317056e+02 3 2.57078430e+01 -6.89158772e+01 3.95072851e+00 4 -1.06929699e+02 -2.32450937e+01 -1.00820132e+01 5 -5.37209986e+00 -1.58360252e+01 -1.37533950e+01 6 6.34656403e+01 -5.50237587e+01 -5.89796031e+01 7 6.37612998e+00 -9.69698368e+00 2.07664180e+00 8 2.41384346e+01 -1.14763212e+02 -5.69152154e+01 9 -6.71728344e+01 3.51905580e+01 -6.64605596e+01 10 8.52468634e+00 2.11867352e+01 -1.12492381e+01 11 -1.56586374e+01 7.83016182e+01 -2.65150991e+01 12 -2.25732942e+01 1.72327556e+01 1.09027385e+00 13 -4.63340288e+01 1.26478376e+01 -7.83301493e+01 14 1.77720058e+01 2.14527412e+01 -5.83615677e+00 15 8.42818670e+01 6.06816578e+01 3.84294316e+01 16 8.75851479e+00 4.03752072e+01 -1.49505844e+01 17 -2.35399362e+01 -4.17689923e+01 1.13613679e+01 18 3.22576246e+01 -9.11637393e+01 8.40738620e+01 19 -1.02449208e+01 -2.04003526e+01 1.44964399e+01 20 -2.17540381e+01 -2.34722547e+01 3.85701670e+01 21 -2.10944767e+01 -2.64967936e+01 -1.88166724e+01 22 5.01938125e+01 -2.85290742e+00 -1.76750561e+01 23 2.73701346e+01 -3.98616399e+01 4.41831282e+01 24 5.69943550e+00 2.67507223e+00 2.89606436e+01 25 -1.18351337e+02 4.59302348e+01 4.93014131e-01 26 -1.61147635e+01 7.87626897e+01 -4.27832802e+00 27 -3.45482662e+01 -3.04762303e+01 4.60846106e+01 28 -2.08679709e+01 3.04842474e+01 2.97718101e+01 29 5.55394341e+01 6.92103590e+01 6.95242040e+01 30 2.95683730e+01 3.82696457e+01 8.16773125e+00 31 3.92162964e+01 9.93421850e+00 3.51059179e+01 32 5.21114895e+01 7.49566000e+01 5.18727205e+01 MIXED STRUCTURE (pbc=True)-- Species = Cu Zr (Configuration in file "config-T-CuZr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1470.06716703 Forces: 1 -1.72528401e+00 7.50980944e+01 -3.81901692e+01 2 1.86025960e+01 -3.10623426e+01 -2.11665151e+01 3 8.37407278e+01 -8.74914915e+01 2.92388096e+00 4 -5.02699260e+01 -4.10403043e+01 -3.60462881e+01 5 -1.93918970e+01 -3.71353230e+01 2.43932211e+01 6 5.04034899e+01 -1.01384400e+02 -8.25408552e+01 7 -7.69432692e+01 1.56270411e+01 -5.61169746e+00 8 -1.58879011e+01 -1.45471629e+02 -7.13079067e+01 9 -2.32099668e+01 -5.69691005e+01 1.52975324e+01 10 3.39113120e+01 5.07191003e+01 6.25113901e+00 11 -4.49115184e+00 4.51855635e+01 -3.86857824e+01 12 -3.65547135e+00 5.78698502e+00 -4.02875101e+01 13 -6.41538720e+01 -3.01982580e+01 -4.67922904e+00 14 8.31704729e+00 9.22318325e+01 4.49649369e+01 15 3.20521465e+01 1.40344917e+02 1.16909963e+02 16 1.91629301e+00 6.23263691e+01 1.86641315e+00 17 -3.65474315e+01 3.25437636e+01 5.92147963e+00 18 9.34290950e+01 -1.23486594e+02 7.18501489e+01 19 -1.67740720e+01 -2.44803140e+01 -2.92473608e+00 20 1.02647832e+02 -9.15912900e+01 8.08709353e+01 21 -4.87849892e+01 -1.88057342e+01 -3.67679867e+01 22 -4.78929704e+01 -1.44691567e+01 -4.18107457e+01 23 3.37723154e+00 -3.43162767e+01 1.29387493e+01 24 -2.46155591e+01 -5.04396550e+01 -3.11063633e+01 25 -1.44296218e+02 6.31078793e+01 -1.06729294e+02 26 5.02050535e+01 3.88076343e+01 -2.48831609e+01 27 -1.49277446e+01 -3.78235870e+01 1.74655408e+00 28 9.99223813e+00 1.07931179e+02 8.02985707e+01 29 6.33161963e+01 7.68735579e+01 6.13449883e+01 30 -3.48841228e+01 3.38757054e+00 1.12903998e+02 31 -3.34011971e+01 -1.28323589e+01 -4.04997267e+01 32 1.09941785e+02 1.29026329e+02 -1.72445439e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==30850== Memcheck, a memory error detector ==30850== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==30850== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==30850== Command: python runner2.py EAM_Dynamo_BorovikovMendelevKing_2016_CuZr__MO_097471813275_000 ==30850== ==30850== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==30850== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==30850== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30850== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30850== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30850== by 0x4010732: call_init (dl-init.c:72) ==30850== by 0x4010732: _dl_init (dl-init.c:119) ==30850== by 0x40151FE: dl_open_worker (dl-open.c:522) ==30850== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==30850== by 0x40147C9: _dl_open (dl-open.c:605) ==30850== by 0x544CF95: dlopen_doit (dlopen.c:66) ==30850== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==30850== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==30850== by 0x544D734: _dlerror_run (dlerror.c:162) ==30850== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==30850== ==30850== ==30850== HEAP SUMMARY: ==30850== in use at exit: 40,115,672 bytes in 4,274 blocks ==30850== total heap usage: 198,820 allocs, 194,546 frees, 114,208,110 bytes allocated ==30850== ==30850== LEAK SUMMARY: ==30850== definitely lost: 0 bytes in 0 blocks ==30850== indirectly lost: 0 bytes in 0 blocks ==30850== possibly lost: 183,295 bytes in 113 blocks ==30850== still reachable: 39,932,377 bytes in 4,161 blocks ==30850== suppressed: 0 bytes in 0 blocks ==30850== Rerun with --leak-check=full to see details of leaked memory ==30850== ==30850== For counts of detected and suppressed errors, rerun with: -v ==30850== 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.