!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_FarkasJones_1996_NbTiAl__MO_042691367780_000 Supported species : Al Nb Ti 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 = 202.102679595 Forces: 1 -7.75358799e+00 -1.80474993e+01 -1.88696906e+01 2 -1.11749379e+01 1.25208680e+01 -1.63010010e+01 3 8.78664485e+00 -2.18788864e+01 -1.12781538e+01 4 -1.32947639e+01 1.08137431e+01 8.29708199e+00 5 8.11107789e+00 -2.72960606e+01 -8.00891925e+00 6 1.00011090e+01 5.45681262e+00 -1.24045891e+01 7 1.82059448e+01 -5.72330157e+01 -5.18656052e+01 8 -3.04812724e+01 -2.15657009e+01 -7.70985077e+00 9 -2.62486561e+01 -1.47195541e+01 -3.87528668e+01 10 -9.71485046e+00 4.36346660e+01 -4.27838511e+01 11 -5.84512497e+00 -3.35134640e+01 2.47732606e+01 12 -2.17705945e+01 3.55597678e+01 4.93743172e-01 13 -9.10887183e+00 -2.69000839e+01 -8.14637443e+01 14 1.58732084e+01 2.06318244e+01 -1.34884311e+01 15 7.26847040e+01 -1.41107623e+01 1.51299005e+01 16 9.93221021e+00 5.84825730e+01 2.84419321e+01 17 -3.08019973e+01 -1.62611114e+01 -8.53159884e+00 18 7.40662096e+00 2.37072994e+01 1.30753051e+00 19 1.50234294e+01 -2.19184640e+01 1.91280636e+01 20 -1.24938497e+01 1.58425566e+01 1.55997550e+01 21 -2.65681548e+01 -1.85776024e+01 1.85045547e+01 22 4.10388407e+01 4.39397111e+01 4.50361194e+01 23 7.40302008e+00 -2.54128785e+00 1.22100111e+01 24 1.12474679e+01 -1.14765679e+01 1.16327049e+01 25 -1.86023073e+01 -1.69267168e+01 2.37027943e+01 26 -1.49039184e+01 3.77588502e+01 -1.93689700e+01 27 1.22731596e+01 -5.46185127e+01 2.00681016e+01 28 -5.26087467e+01 4.38611867e+01 8.41499824e+00 29 -1.67985237e+01 -1.81175198e+01 1.45526901e+01 30 1.81529593e+01 2.92691562e+01 8.16418559e+00 31 3.33644236e+01 -1.68175117e+01 2.38045418e+01 32 1.86653375e+01 3.10413066e+01 3.15653028e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 354.437626486 Forces: 1 3.51373146e+01 -3.08353893e+01 9.64259193e+00 2 -5.20276008e+01 -1.07032476e+01 6.14246212e+01 3 8.18982578e+00 5.11553628e+00 -7.75494926e+00 4 2.72371667e+01 2.15841263e+01 -2.85541170e+00 5 1.78422110e+01 -1.08522591e+00 -6.18864191e+00 6 -4.34935634e+01 4.17162391e+01 4.95121621e+00 7 -2.31965892e+00 -5.12066053e+01 -5.08010014e+01 8 -2.98696370e+01 -2.14621203e+01 -7.79698555e+00 9 -4.32804254e+01 -4.07381627e+01 2.50520442e+01 10 -2.26298381e+01 2.48653529e+01 -2.16023907e+01 11 -5.99536693e+00 -3.19265547e+01 2.41177153e+01 12 1.14103016e+01 1.73796786e+01 1.08698894e+01 13 -6.86433140e+00 -2.83702251e+01 -6.31228063e+01 14 -1.91001955e+01 8.93579785e+00 -2.17551238e+01 15 5.63230385e+01 -1.40193601e+01 1.40117964e+01 16 1.21437575e+01 4.19120126e+01 2.97634913e+01 17 1.93596719e+01 -3.15219889e+01 -9.83655550e+00 18 7.53158940e+00 2.31625835e+01 1.17279585e+00 19 1.58483866e+01 6.55702194e+00 1.76506080e+01 20 2.36819165e+01 4.44714606e+01 -1.39039606e+01 21 -2.69118301e+01 -1.89856131e+00 1.84231372e+01 22 -7.27499759e+00 6.65097675e+01 5.20684196e+01 23 -3.31557946e+01 -3.20783578e+01 -1.02247825e+01 24 5.47863470e+01 1.49556404e+01 -6.19436491e+01 25 -3.11123614e+00 -2.20463148e+01 2.33328111e+01 26 -1.17622068e+01 9.02559656e+00 -2.44523822e+01 27 3.67970658e+01 -5.44101816e+01 -2.67319900e+01 28 -5.17222150e+01 4.58124480e+01 -1.86362063e+01 29 -1.64507767e+01 -1.70805046e+01 1.43503058e+01 30 -2.81736341e+00 1.20191309e+01 1.50838276e+01 31 2.73565164e+01 -1.84386559e+01 1.68469562e+01 32 2.51419286e+01 2.37990630e+01 8.84460975e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Nb (Configuration in file "config-F-Nb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 149.467157847 Forces: 1 -1.58430097e+01 -1.69852661e+01 -1.76126670e+01 2 4.11628061e+01 -8.68911383e+00 -5.37206549e+01 3 2.19182487e+01 -4.12599524e+01 -1.24205381e+01 4 -5.63068669e+01 2.71097098e+00 3.92984389e+01 5 -2.60091475e+00 -8.52133669e+00 -1.05520898e+01 6 1.76780805e+01 -1.28705933e+01 -3.66442717e+01 7 7.42783823e+01 3.30817695e+00 -1.41939603e+01 8 6.47762129e+00 1.99885984e+01 1.64942001e+01 9 -3.24235479e+01 1.55421418e+01 -2.70759352e+01 10 -3.23283374e+01 5.18578730e+01 -5.35528849e+01 11 2.57186564e+01 -1.92750420e+01 -8.90480831e+00 12 -3.06005492e+01 2.86526777e+01 -5.86792017e+00 13 3.11579426e+01 -3.50251984e+01 -3.30365786e+01 14 1.73918288e+01 1.34573977e+01 -7.40468436e+00 15 1.25332273e+01 -7.74537321e+01 7.99978152e+01 16 2.67856191e+01 4.71037578e+01 7.21049730e+00 17 -3.00857557e+01 -1.30423563e+01 1.32990576e+01 18 1.73588569e+01 3.38548159e+01 -3.34333667e+01 19 1.39299491e+01 -7.55056154e+01 2.80789240e+01 20 -4.67370968e+01 2.10397419e+01 3.30185947e+01 21 -3.73424658e+01 -3.40924835e+01 4.00501423e+01 22 -4.30148579e+01 8.57916245e+01 -9.00141955e+01 23 2.05876796e+01 -8.52980305e+00 1.16862889e+00 24 -2.10546570e+01 -2.33234072e+01 1.10668795e+01 25 -5.65785941e+01 -1.94245359e+01 3.22714605e+01 26 -1.82112590e+01 4.16252766e+01 -3.10959676e+01 27 1.32809174e+00 -2.59047017e+01 3.61147258e+01 28 -2.49826082e+01 2.22936688e+01 2.00284901e+01 29 2.06998231e+01 -4.67759548e+01 1.66560818e+01 30 1.70477045e+01 2.76914153e+01 1.29119919e+01 31 4.23869580e+01 2.54209211e+01 4.97152766e+00 32 3.96690443e+01 2.63400345e+01 4.28930670e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ti (Configuration in file "config-F-Ti.xyz") ----------------------------------------------------------------------------------------------------- Energy = 52.0847369235 Forces: 1 -7.37527049e+00 -1.06734971e+01 -1.56317964e+01 2 6.92701086e+00 -4.20963877e+00 -1.43015779e+01 3 7.44414807e+00 -2.03820507e+01 6.99578344e-01 4 -1.88531987e+01 8.36366657e+00 3.27382511e+00 5 -1.46819888e+00 -1.02558346e+01 -9.47045751e+00 6 1.20755388e+01 -1.04624111e+01 -1.73487031e+01 7 2.07681582e+01 -1.88846145e+01 -2.98709132e+00 8 -8.02503833e+00 3.37311152e+00 -1.04719020e+01 9 -2.24810787e+01 -4.86269472e+00 -2.44705025e+01 10 7.00742036e+00 2.17567316e+01 -2.15223348e+01 11 1.87786012e+01 -1.49506888e+01 1.32468499e+01 12 -2.81937047e+01 2.89814145e+01 3.11154272e+00 13 -6.92492719e+00 2.84993733e+00 -1.63097001e+01 14 8.97372208e+00 8.82070353e+00 -5.98269350e+00 15 2.00200176e+01 8.26746690e+00 6.33856364e+00 16 3.66655362e+00 1.37331737e+01 8.84054963e+00 17 -9.08293510e+00 -6.36143701e+00 9.39597595e+00 18 -1.75089613e+01 -8.05575730e+00 3.25866131e+00 19 -7.56574110e+00 -1.29603523e+01 7.67650350e+00 20 -1.08026260e+01 -5.12039289e+00 7.23000268e+00 21 -3.42419275e+00 -2.07697029e+01 7.88990557e+00 22 1.79466753e+01 -7.17358985e-01 5.44478266e+00 23 6.77782661e+00 -7.21792862e+00 6.08796823e+00 24 4.74389743e+00 5.90584916e+00 1.53099286e+01 25 -1.98830451e+01 -5.95055825e+00 5.54630038e+00 26 3.87157272e+00 2.03394727e+01 -9.63873664e+00 27 3.67289778e+00 -4.35527304e+00 1.83029061e+01 28 -9.97636093e+00 8.40370189e+00 9.04803115e+00 29 9.47832608e+00 1.93722665e+01 1.95324632e+00 30 9.43474119e+00 4.32674002e+00 -3.06454243e+00 31 7.97884684e+00 4.86457724e+00 8.76366504e+00 32 1.99932459e+00 6.83137865e+00 9.78125133e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ti (Configuration in file "config-T-Ti.xyz") ----------------------------------------------------------------------------------------------------- Energy = 224.753814221 Forces: 1 -8.80089892e+00 -3.94455534e+00 -6.16220821e+00 2 3.21278091e+00 -1.09336187e+00 1.02447454e+01 3 9.85728699e+00 -3.84145021e+00 3.72148211e+00 4 -5.60525987e+00 8.61742259e+00 3.63128549e+00 5 -1.21656315e+00 2.82282275e+00 3.22215995e+00 6 8.02915396e+00 -1.20898256e+01 2.59222792e+00 7 1.14792491e+01 -9.23978229e+00 -7.31852074e+00 8 -9.40724914e+00 4.98128814e+00 -9.22421180e+00 9 -1.22424210e+01 -6.12990617e-01 -7.70281617e+00 10 6.58227292e+00 7.69411210e+00 -1.36288898e+01 11 2.02827189e+01 -1.58544053e+01 1.46909516e+01 12 -2.38201147e+01 1.83796243e+01 5.24991551e+00 13 -7.44408610e+00 6.10420841e+00 -1.70758265e+00 14 8.30159355e+00 5.40601526e-01 1.64194063e+00 15 2.59227503e+00 8.29047469e+00 7.61024592e+00 16 1.60612982e+00 -3.07445318e+00 1.15657980e+01 17 5.75422496e+00 1.96296823e+00 8.47163532e+00 18 -1.74643905e+01 -8.19661736e+00 2.55693746e+00 19 -8.42625245e+00 -6.91811522e+00 -8.63400338e+00 20 2.18973457e+00 -1.37105611e+01 -1.02279952e+01 21 -7.07763616e+00 -6.05939182e+00 2.97342378e+00 22 7.24588389e+00 1.37866668e+00 3.64959603e+00 23 8.92178106e+00 4.81079825e+00 8.20985872e-01 24 2.54711401e+00 3.90162160e+00 -9.81560266e+00 25 -6.24763324e+00 -4.78677004e+00 3.06323624e+00 26 5.00661442e+00 9.09581665e+00 -9.36838209e+00 27 5.79665386e+00 -3.05283858e+00 4.38078198e+00 28 -4.77225012e+00 2.18052986e+00 2.53181916e+00 29 9.14698863e+00 1.93669676e+01 1.65674892e+00 30 3.56609119e+00 -1.08911897e+01 -5.40816737e+00 31 -5.60287248e+00 1.25849148e+01 -5.76792357e+00 32 -3.99092000e+00 -9.34653002e+00 6.90386316e-01 MIXED STRUCTURE (pbc=False)-- Species = Al Nb Ti (Configuration in file "config-F-AlNbTi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 32.0633863384 Forces: 1 2.01087806e+01 2.63916974e+01 6.50606778e+00 2 -2.27515772e+01 -6.66223607e+00 -3.00607218e+01 3 1.23977304e+01 -3.27400201e+01 1.10214411e+01 4 -2.95937044e+01 4.06539965e+00 2.58901476e+00 5 3.69478960e+00 -2.00336996e+01 -1.71363162e+01 6 1.30665243e+01 3.02487357e+00 -2.34511286e+01 7 1.83670111e+01 -3.12299798e+01 -8.08089503e+00 8 -5.38894188e+00 2.36817312e+00 4.35102929e+00 9 -1.29317184e+01 6.96644216e+00 -1.55373052e+01 10 1.08884505e+01 1.29033642e+01 -2.65481342e+01 11 -9.88999780e+00 -2.35419452e+01 3.14786376e+01 12 1.75813290e+01 3.30029036e+01 -3.75304461e+01 13 -3.43472606e+01 -9.49252018e-01 -1.90932208e+01 14 1.70451141e+01 1.93865912e+01 -1.01941974e+01 15 1.73921131e+01 6.38469850e+00 9.13136642e+00 16 5.80887387e+00 2.09426561e+01 5.42881359e+00 17 -1.59618112e+01 -1.20160324e+01 -9.00860998e+00 18 -2.20189373e+01 -2.37016244e+01 -1.95719585e+00 19 -8.98577745e+00 -2.95477579e+01 7.59834818e+00 20 -1.79665308e+01 6.56185917e+00 1.51178588e+01 21 -1.04641044e+01 -3.19769574e+01 -4.23218078e+00 22 2.57672088e+01 2.00915930e+01 3.05312266e+01 23 8.05434097e+00 -4.32477951e+00 7.80529321e+00 24 1.99579545e+01 2.66063172e+01 3.30572880e+00 25 -5.55950033e+00 -2.58439918e+01 3.42454857e+01 26 2.07052244e+00 -3.42880522e+01 -2.01781238e+01 27 -3.00575314e+00 5.40057469e+00 2.60317432e+01 28 -1.12918921e+01 9.74129642e+00 7.26391349e+00 29 -1.81932677e-01 5.89209439e+01 -6.75487895e-01 30 5.57596452e+00 9.83476399e+00 -2.66497405e+00 31 3.07995149e+00 -3.25165318e+00 6.53033573e+00 32 9.48278036e+00 7.51383353e+00 1.74126335e+01 MIXED STRUCTURE (pbc=True)-- Species = Al Nb Ti (Configuration in file "config-T-AlNbTi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3175.91575879 Forces: 1 -1.64759875e+03 -2.88346210e+04 -6.24226496e+03 2 1.55104171e+04 1.34030810e+04 2.19850244e+03 3 1.42223122e+03 -9.46555383e+01 2.09106127e+03 4 -6.21131040e+02 4.92337015e+03 6.33354122e+03 5 -2.18386074e+03 -7.89652002e+02 2.20513319e+03 6 -1.09731931e+04 1.45975264e+04 3.69316633e+03 7 -1.27818074e+03 -2.59830513e+01 1.56922722e+03 8 -3.87210877e+01 1.17338956e+02 1.97284869e+02 9 -1.14103918e+01 5.62649726e+02 1.47117089e+01 10 1.76415106e+02 -2.10247918e+02 3.77929902e+01 11 3.21354573e+01 -1.15853029e+01 8.03733729e+01 12 6.03244014e+01 -1.10619745e+03 1.10895821e+03 13 -7.02487512e+01 9.75796558e+01 1.24310109e+02 14 -1.50633210e+03 -3.30885708e+03 1.34772747e+03 15 -8.15477339e+01 9.14362999e+01 9.56366624e+01 16 8.37116420e+01 -9.67127596e+01 8.87625294e+01 17 8.19779926e+01 -3.21109891e+01 -3.50026957e+02 18 -2.51848160e+02 1.62330390e+02 -5.10776001e+02 19 4.17109061e+02 -9.30909172e+01 -5.42119969e+02 20 1.46104583e+02 4.79253624e+03 -4.46259736e+03 21 -3.05770881e+02 -5.93672274e+01 -6.61505309e+02 22 5.51355782e+00 4.40212178e+02 -5.22946027e+02 23 3.91271626e+02 -4.47467833e+03 -6.24125394e+03 24 6.84357264e+02 6.69540749e+02 -4.91703577e+02 25 -8.17079662e+00 -1.28576007e+02 4.17006074e+01 26 -1.85859756e+01 3.40321708e+01 -1.95685063e+01 27 -3.30218092e+01 3.74317338e+02 -1.24492574e+02 28 8.11011862e+01 -4.85124602e+02 -3.23506333e+02 29 7.75604381e+01 5.03913544e+01 -1.45131201e+02 30 -4.37543635e+01 -3.17129908e+02 -3.45334851e+02 31 -4.17027632e+01 4.98496210e+01 -4.83430609e+01 32 -5.51513536e+01 -2.97602151e+02 -1.96319589e+02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==31373== Memcheck, a memory error detector ==31373== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==31373== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==31373== Command: python runner2.py EAM_Dynamo_FarkasJones_1996_NbTiAl__MO_042691367780_000 ==31373== ==31373== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==31373== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==31373== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==31373== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==31373== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==31373== by 0x4010732: call_init (dl-init.c:72) ==31373== by 0x4010732: _dl_init (dl-init.c:119) ==31373== by 0x40151FE: dl_open_worker (dl-open.c:522) ==31373== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==31373== by 0x40147C9: _dl_open (dl-open.c:605) ==31373== by 0x544CF95: dlopen_doit (dlopen.c:66) ==31373== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==31373== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==31373== by 0x544D734: _dlerror_run (dlerror.c:162) ==31373== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==31373== ==31373== ==31373== HEAP SUMMARY: ==31373== in use at exit: 49,732,402 bytes in 4,434 blocks ==31373== total heap usage: 233,833 allocs, 229,399 frees, 132,468,562 bytes allocated ==31373== ==31373== LEAK SUMMARY: ==31373== definitely lost: 0 bytes in 0 blocks ==31373== indirectly lost: 0 bytes in 0 blocks ==31373== possibly lost: 183,295 bytes in 113 blocks ==31373== still reachable: 49,549,107 bytes in 4,321 blocks ==31373== suppressed: 0 bytes in 0 blocks ==31373== Rerun with --leak-check=full to see details of leaked memory ==31373== ==31373== For counts of detected and suppressed errors, rerun with: -v ==31373== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2538 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.