!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_VailheFarkas_1997_CoAl__MO_284963179498_005 Supported species : Al Co 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 = 187.461915615 Forces: 1 -7.94269241e+00 -1.83468112e+01 -1.92410299e+01 2 -1.35828419e+01 1.64573134e+01 -1.48382759e+01 3 9.24612465e+00 -1.97551696e+01 -1.02771106e+01 4 -1.15563077e+01 1.17367345e+01 9.04980666e+00 5 7.41521188e+00 -3.00943900e+01 -9.12932592e+00 6 1.34055115e+01 4.75951838e+00 -1.54370793e+01 7 1.47717910e+01 -5.18775245e+01 -4.70709825e+01 8 -2.47464463e+01 -2.05142168e+01 1.13197088e+01 9 -1.53980390e+01 -1.65220836e+01 -2.95394304e+01 10 -8.98448905e+00 3.18123156e+01 -3.56025984e+01 11 8.73339342e-01 -2.58427434e+01 8.91569504e-01 12 -2.05878716e+01 3.46281767e+01 4.39926011e-01 13 -1.73810105e+01 -1.76245078e+01 -7.62663247e+01 14 1.51421172e+01 1.98837234e+01 -1.30032317e+01 15 6.47598457e+01 -1.44219775e+01 1.92102977e+01 16 1.06735351e+01 5.27364834e+01 2.58898765e+01 17 -2.96340928e+01 -1.51285548e+01 -9.19078355e+00 18 8.89382499e+00 2.28667646e+01 -4.68158492e-01 19 1.53851346e+01 -2.16527919e+01 1.87005966e+01 20 -1.22446529e+01 1.64855782e+01 1.52945103e+01 21 -2.61719205e+01 -1.54838149e+01 1.57111698e+01 22 3.28295342e+01 4.54803700e+01 3.96300916e+01 23 7.55551531e+00 -2.58804606e+00 1.22703502e+01 24 1.10164099e+01 -1.03672048e+01 1.05334358e+01 25 -2.48224835e+01 -1.56923061e+01 2.99843687e+01 26 -1.29621995e+01 3.49657165e+01 -1.87536840e+01 27 1.36886535e+01 -5.39328750e+01 1.71532691e+01 28 -5.17990224e+01 4.33327689e+01 8.02312778e+00 29 -1.38629855e+01 -2.59888274e+01 5.83709548e+00 30 1.67233335e+01 2.79157033e+01 7.21910377e+00 31 3.18332461e+01 -1.69492007e+01 2.21833906e+01 32 1.74639270e+01 2.97218791e+01 2.94763205e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 231.171619907 Forces: 1 3.10995014e+01 -2.80543073e+01 8.83376235e+00 2 -5.11149958e+01 -7.75038962e+00 5.70272667e+01 3 6.62200508e+00 3.53091890e+00 -7.10870757e+00 4 2.37799434e+01 1.88198470e+01 -2.74432262e+00 5 1.54686888e+01 -4.87187878e+00 -6.56927950e+00 6 -3.52629516e+01 3.56217244e+01 2.38490516e+00 7 -3.08263902e+00 -4.46658645e+01 -4.38468847e+01 8 -2.14001733e+01 -2.12392290e+01 8.65804608e+00 9 -2.97348243e+01 -3.68735779e+01 3.05885728e+01 10 -2.11385078e+01 1.31018131e+01 -1.53159068e+01 11 -1.66414183e+00 -2.16924450e+01 -1.95483765e+00 12 1.03409666e+01 1.54894052e+01 8.79166523e+00 13 -1.38261287e+01 -1.62394178e+01 -5.88144683e+01 14 -1.69826046e+01 7.92375627e+00 -1.84724407e+01 15 5.03961500e+01 -1.12735729e+01 1.65388265e+01 16 1.24248743e+01 3.83014863e+01 2.44665438e+01 17 1.79230536e+01 -2.80103590e+01 -8.99579124e+00 18 6.51237267e+00 1.87845167e+01 6.21895174e-01 19 1.31567719e+01 4.90851797e+00 1.59245681e+01 20 2.15981431e+01 3.87259870e+01 -1.24131326e+01 21 -2.33820919e+01 -1.33305127e+00 1.47398670e+01 22 -1.09262118e+01 6.09674489e+01 4.32767762e+01 23 -2.86125703e+01 -2.90012516e+01 -8.91509681e+00 24 4.99896592e+01 1.50872939e+01 -5.64777473e+01 25 -1.16715184e+01 -1.74151038e+01 2.71126866e+01 26 -1.03517124e+01 8.92509253e+00 -2.04920357e+01 27 3.43883780e+01 -4.81622004e+01 -2.32588713e+01 28 -4.60738882e+01 4.22551363e+01 -1.63980394e+01 29 -1.15454027e+01 -2.18616855e+01 7.16466074e+00 30 -2.50220824e+00 1.09290225e+01 1.22839386e+01 31 2.42745405e+01 -1.58156372e+01 1.50841206e+01 32 2.12975223e+01 2.08880046e+01 8.27946071e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Co (Configuration in file "config-F-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = -78.5965728485 Forces: 1 -2.29111535e+00 -2.07656124e+00 -2.12400594e+00 2 2.38257588e-01 -1.20942075e+00 -8.53578064e+00 3 3.14971402e+00 -5.54670394e+00 -3.67881792e-01 4 -6.37924211e+00 2.31555050e+00 4.34383551e+00 5 -1.54882514e+00 -3.30110047e+00 -2.83464796e+00 6 4.90082206e+00 -5.43663252e-01 -5.25291575e+00 7 6.61059905e+00 -3.41942657e+00 -2.31417008e+00 8 -1.03728893e+00 -5.18656595e-01 6.32035594e+00 9 -3.97019633e+00 1.46443152e+00 -2.89930900e+00 10 -2.09138946e+00 5.35248296e+00 -6.59410301e+00 11 -2.07340927e+00 -5.29595181e+00 4.44838593e-01 12 -2.78019627e+00 2.07256529e+00 5.62593702e-01 13 2.93088330e+00 1.57784927e-01 -5.46854944e+00 14 2.10584427e+00 7.54433705e-01 -4.43882538e-01 15 6.36820809e+00 5.01574977e+00 -6.67481428e+00 16 5.78554156e+00 5.98108402e+00 -1.24495932e+00 17 -3.84441560e+00 -1.43469257e+00 1.53008959e+00 18 2.98642050e+00 -7.82674171e-01 -4.24684302e+00 19 3.21362562e+00 -6.38305294e+00 1.30865551e+00 20 -4.89329463e+00 3.13575944e+00 3.83895486e+00 21 -3.99537586e+00 -1.96603026e+00 3.92428413e+00 22 4.45615028e+00 -7.72142210e+00 6.05899971e+00 23 1.71318969e+00 -1.49745037e+00 -5.60365852e-01 24 -4.16314667e+00 -3.27252382e+00 2.31932654e+00 25 -4.60600013e+00 -3.09328702e+00 -2.30258063e+00 26 -2.38489245e+00 7.08780328e+00 3.06448254e+00 27 -3.14935757e+00 -3.95892912e+00 4.37093489e+00 28 -1.00654318e+00 3.35011007e+00 4.08914228e+00 29 -5.01901378e+00 1.53953684e+00 1.97408086e+00 30 1.61617055e+00 4.09199367e+00 2.11886573e+00 31 4.88677596e+00 4.42916247e+00 3.67992969e+00 32 4.27150021e+00 5.27309852e+00 1.91543916e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Co (Configuration in file "config-T-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = -25.1898189825 Forces: 1 -1.40048462e+00 -1.21912598e+01 9.38188510e+00 2 2.15692936e+00 -2.37761980e+00 -3.73588810e+00 3 4.60236355e+00 1.60658986e-01 -9.27213209e-01 4 -1.24330912e+00 4.56937478e-01 5.14950634e+00 5 -7.55680888e+00 1.85636411e-01 6.69320432e+00 6 -1.69410778e+00 -4.49915504e+00 3.94444154e+00 7 1.03380236e-01 1.96230219e+00 -7.58822093e+00 8 -1.40243476e+00 -7.08353422e-01 7.50099808e+00 9 3.54757107e+00 7.62884599e+00 1.82790668e+00 10 -8.06616740e+00 1.08936725e+01 2.41105487e+00 11 -2.39036077e+00 -7.18986441e+00 1.12888179e+00 12 2.42029468e+00 -1.23695972e+00 -5.69185662e+00 13 7.15938581e+00 -2.14426304e+00 9.18815956e+00 14 2.12006190e+00 -3.12063033e+00 2.99096814e+00 15 1.32686896e+00 5.52839747e+00 -6.76198501e+00 16 6.37316820e+00 9.21458103e-01 -3.78242596e+00 17 4.90981269e+00 3.07775659e+00 7.39509262e+00 18 3.19267636e+00 -8.39592041e-01 -5.04627509e+00 19 4.17508756e+00 -4.31155739e+00 -1.26278502e-02 20 -1.93671300e+00 6.97081331e+00 -1.18768037e+01 21 -2.05285477e+00 5.64427765e+00 6.43528280e+00 22 2.64905346e+00 -7.76544395e+00 8.07023863e+00 23 2.04305051e+00 -3.49212478e-01 -9.57112172e+00 24 -6.71501963e+00 -2.84345437e+00 -5.93065826e+00 25 2.25898275e+00 -6.68233680e+00 9.82342479e-02 26 -5.23575079e+00 1.62796735e+00 4.12804365e+00 27 -7.87797307e+00 -8.33092501e+00 -1.20327740e+01 28 1.80252230e+00 4.94308763e+00 2.46155890e+00 29 -5.76461403e+00 1.68956459e+00 2.14413434e+00 30 -7.42542360e+00 7.14786653e-01 5.76734839e+00 31 3.86421545e+00 5.46888654e+00 -6.69086667e+00 32 6.05659736e+00 6.71557808e+00 -7.06822293e+00 MIXED STRUCTURE (pbc=False)-- Species = Al Co (Configuration in file "config-F-AlCo.xyz") ----------------------------------------------------------------------------------------------------- Energy = -20.8970697543 Forces: 1 -1.74443803e+00 -1.65810896e+00 -1.71958459e+00 2 6.07003593e-01 -2.06427574e+00 -1.04572620e+01 3 -6.65499680e+00 -1.03648816e+01 -1.26764744e+01 4 -8.82500128e+00 -1.25856694e+01 -2.09285860e+01 5 3.75555036e+00 -2.71813322e+00 -3.01403118e+00 6 8.09240401e+00 -6.20010212e+00 -5.86695901e+00 7 3.22076567e+00 -5.22316095e+00 -5.46105351e+00 8 -7.13577348e-01 4.91959948e+00 -6.81918676e-01 9 -3.90593373e+00 5.41871733e-01 -1.57840374e+00 10 -8.66705798e-01 8.13554887e+00 -6.76039569e+00 11 9.15693025e+00 -1.93783776e+01 -2.70162779e+01 12 -5.07374020e+00 1.92338725e+00 5.37686102e-01 13 -1.77692826e+00 4.17940585e+00 -6.61385822e+00 14 5.22109373e+00 7.99951911e+00 -7.94848191e+00 15 4.26273072e+00 -7.68084768e+00 6.59886663e+00 16 -5.10515594e+00 5.43372759e+00 2.11622987e+00 17 -8.17375631e+00 -1.08072676e+01 9.12390713e+00 18 5.68229921e+00 -6.69047666e+00 -1.02591544e+01 19 -1.18205624e+01 -3.86274773e+00 2.05614407e+01 20 -9.46472973e+00 -5.05108011e+00 8.74029989e+00 21 2.06003763e+01 -7.64379807e+00 -3.28323267e+00 22 4.96728873e+00 4.66882025e+00 -7.09294499e-01 23 1.74477314e+00 -2.57700243e+00 2.58198603e+00 24 2.00039476e+00 2.54336771e-01 7.09574982e+00 25 -1.92657524e+01 1.47909376e+01 1.78270751e+01 26 4.51975576e+00 3.49081453e+01 2.18085429e+01 27 4.59227389e+00 9.73094113e+00 1.08377479e+01 28 -4.95852911e+00 2.96538707e+00 7.94905298e+00 29 -9.15610084e+00 -1.08555002e+01 2.79950626e+00 30 1.75116368e+01 1.18366830e+01 -8.37455142e-01 31 4.19895821e+00 -6.47251987e-01 4.39407000e+00 32 -2.62832685e+00 3.72037104e+00 2.84026213e+00 MIXED STRUCTURE (pbc=True)-- Species = Al Co (Configuration in file "config-T-AlCo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 8.59221371383 Forces: 1 -5.95073286e-01 6.92021783e-01 -2.17989879e-01 2 7.00880339e-01 -1.92847680e+00 -3.06823451e+00 3 8.84381377e-01 2.06602539e+01 -5.24457035e+00 4 -1.81493448e+00 -1.15997350e+01 -1.61090189e+01 5 3.87285064e+00 -9.53162547e-01 7.10741318e-01 6 6.68036821e-01 -7.44939893e+00 -2.85310055e+00 7 -1.16211977e+00 -2.05806797e+00 -7.48498496e+00 8 -2.26037410e+00 4.64293965e+00 -6.81844489e-01 9 1.83015255e+00 3.29467591e+00 6.73708960e+00 10 6.16507077e+00 -9.14246039e+00 1.26466639e+01 11 8.16908447e+00 -1.81410622e+01 -2.46401130e+01 12 1.66314051e+00 -1.28151163e+00 5.09746330e-01 13 -3.88029252e+00 1.92337843e+00 -1.28897764e+00 14 3.95110196e+00 1.00498199e+01 -9.58511078e+00 15 6.66018471e-01 -1.14313589e+01 8.76468195e+00 16 -4.85490588e+00 -7.93720225e-01 1.99412750e+00 17 1.81613358e+00 5.21905279e+00 7.14039933e+00 18 4.48959871e+00 -8.22528180e+00 -1.33894282e+01 19 -3.49411180e-01 8.98580308e+00 8.29857775e+00 20 -3.44506051e+00 -9.80790140e+00 2.19452451e+00 21 1.92426908e+01 1.56942377e+00 -2.70057273e-01 22 -1.63182091e+00 4.75011816e+00 -2.75246585e+00 23 -1.46148637e+00 -1.74818439e+00 4.91021638e+00 24 2.03495112e+00 -7.76295809e-03 4.09665091e+00 25 -5.62094831e+00 5.57213405e+00 1.53828218e+01 26 -1.21982523e-02 9.04335777e+00 2.88162452e+01 27 7.27899847e+00 1.37621953e+01 4.76198916e+00 28 -2.26319725e+01 -1.21620713e+01 -1.70781697e+01 29 -9.26031766e+00 -9.93506526e+00 1.19527633e+00 30 2.22476473e+00 7.93824940e+00 -3.03337561e+00 31 -2.31366894e+00 4.62298666e+00 8.16457308e-01 32 -4.36327066e+00 3.93881109e+00 -1.27876768e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==6895== Memcheck, a memory error detector ==6895== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==6895== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==6895== Command: python runner2.py EAM_Dynamo_VailheFarkas_1997_CoAl__MO_284963179498_005 ==6895== ==6895== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==6895== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==6895== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6895== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6895== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6895== by 0x4010732: call_init (dl-init.c:72) ==6895== by 0x4010732: _dl_init (dl-init.c:119) ==6895== by 0x40151FE: dl_open_worker (dl-open.c:522) ==6895== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6895== by 0x40147C9: _dl_open (dl-open.c:605) ==6895== by 0x544CF95: dlopen_doit (dlopen.c:66) ==6895== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6895== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==6895== by 0x544D734: _dlerror_run (dlerror.c:162) ==6895== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==6895== ==6895== ==6895== HEAP SUMMARY: ==6895== in use at exit: 15,527,441 bytes in 4,274 blocks ==6895== total heap usage: 192,866 allocs, 188,592 frees, 86,433,986 bytes allocated ==6895== ==6895== LEAK SUMMARY: ==6895== definitely lost: 0 bytes in 0 blocks ==6895== indirectly lost: 0 bytes in 0 blocks ==6895== possibly lost: 182,735 bytes in 112 blocks ==6895== still reachable: 15,344,706 bytes in 4,162 blocks ==6895== suppressed: 0 bytes in 0 blocks ==6895== Rerun with --leak-check=full to see details of leaked memory ==6895== ==6895== For counts of detected and suppressed errors, rerun with: -v ==6895== 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.