!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_OBrienBarrPrice_2018_PtAu__MO_946831081299_000 Supported species : Au Pt random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Au (Configuration in file "config-F-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 629.075133576 Forces: 1 -4.05683235e+01 -4.29428759e+01 -6.40547927e+01 2 -3.35669736e+01 4.26703898e+01 -4.95220903e+01 3 1.26113028e+01 -4.27704330e+01 3.55704139e+01 4 -3.33387901e+01 3.47439702e+01 2.33519390e+01 5 3.76594648e+01 -7.62573757e+01 -2.89368847e+01 6 3.43807654e+01 1.36044211e+01 -4.01666630e+01 7 2.26604036e+01 -1.72491381e+02 -1.63130103e+02 8 -1.29381034e+02 -1.19823725e+02 1.70849987e+01 9 -7.37837240e+01 -1.26947354e+01 -7.55168711e+01 10 -3.94932716e+01 1.07433038e+02 -1.05904357e+02 11 -2.45154662e+01 -7.91232352e+01 7.94095516e+01 12 -4.33312019e+01 9.80604517e+01 -5.77711053e+01 13 -2.98795990e+01 -2.85117807e+01 -2.31043937e+02 14 3.36736936e+01 3.57273296e+01 -1.74163581e+01 15 2.43515590e+02 6.66883242e+01 7.81067560e+01 16 5.05702901e+01 1.32584186e+02 8.97793952e+01 17 -6.27132750e+01 -4.54859397e+01 -3.21454968e+01 18 3.17896755e+01 3.80116429e+01 -8.76553149e+00 19 2.57907672e+01 -6.13878237e+01 3.83503381e+01 20 -3.04139451e+01 3.61188910e+01 3.86221157e+01 21 -6.56539518e+01 -4.62978353e+01 4.36275689e+01 22 1.03239284e+02 1.45621674e+02 1.34203988e+02 23 1.94886189e+01 -1.03676539e+01 3.91049130e+01 24 1.93295618e+01 1.52999748e+01 2.45897952e+01 25 -3.25764310e+01 -8.70348107e+01 6.16486910e+01 26 -3.03683522e+01 9.10459976e+01 -4.82241250e+01 27 9.61036219e+01 -1.96234154e+02 5.55269063e+01 28 -1.74509290e+02 1.53343286e+02 2.53677255e+01 29 -4.06147420e+01 -5.95809860e+01 1.41137278e+01 30 4.01366649e+01 7.59820893e+01 -4.34939915e+01 31 6.93457032e+01 -7.93981201e+01 8.87543491e+01 32 4.44129633e+01 7.34671992e+01 7.88791339e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Pt (Configuration in file "config-F-Pt.xyz") ----------------------------------------------------------------------------------------------------- Energy = -113.888701206 Forces: 1 -1.44526755e+00 -2.49947030e+00 -2.87195066e+00 2 3.14529009e+00 -2.85725619e+00 -7.35794313e+00 3 1.98936762e+00 -8.32253324e+00 -3.14355593e+00 4 -7.35804138e+00 2.39720210e+00 1.15765320e+00 5 1.26021013e+00 -2.47053120e+00 -2.42239301e+00 6 3.21888769e+00 -1.97916531e+00 -2.44342130e+00 7 2.70565705e+00 -2.82121347e+00 -1.58869970e+00 8 2.13260129e+00 1.52626722e+00 -6.70417034e+00 9 -7.91255279e+00 2.23913347e+00 -5.12725889e+00 10 -1.48917608e+00 5.73762857e+00 -7.77409182e+00 11 2.22787884e+00 -2.02375199e+00 2.76310415e+00 12 -3.81609453e+00 3.23269710e+00 2.04171144e-01 13 -3.21696531e+00 -1.50109258e+00 -5.86507533e+00 14 3.51175155e+00 3.51080830e+00 -1.61840106e+00 15 6.13009782e+00 2.71392152e+00 -1.05594530e+00 16 4.69736921e+00 5.93921656e+00 1.40695335e+00 17 -5.11832967e+00 -4.45233411e+00 2.61200571e+00 18 -2.96548881e-02 -3.80795172e+00 3.48130234e+00 19 2.02294490e+00 -3.53496168e+00 3.29905714e+00 20 -4.24658835e+00 5.72221487e-01 3.53061751e+00 21 -1.08922188e+00 -7.56745196e+00 2.26113149e+00 22 9.55220299e+00 -1.30460342e+00 2.18065037e+00 23 2.02206860e+00 -2.33041485e+00 2.36518396e+00 24 -3.54003751e+00 -3.51251877e+00 6.68263232e+00 25 -1.07715833e+01 2.66282625e+00 -8.56587527e-01 26 -3.04979768e+00 7.69818305e+00 2.35713294e+00 27 1.10531937e+00 7.95242594e-01 8.70331727e+00 28 -9.30506039e-01 1.26570203e+00 5.51545426e-01 29 4.69026798e-01 1.71360057e+00 -1.62761686e+00 30 4.11956084e+00 3.13428068e+00 -1.52783895e+00 31 4.86991617e+00 2.27899139e+00 3.15998064e+00 32 -1.16633396e+00 3.56732791e+00 5.26851082e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pt (Configuration in file "config-T-Pt.xyz") ----------------------------------------------------------------------------------------------------- Energy = -83.106900063 Forces: 1 4.37927546e+00 -5.85445793e+00 3.74174760e+00 2 5.00486719e+00 -3.87760713e+00 1.54150332e-01 3 2.00552825e+00 -8.56073200e-01 -3.85634206e+00 4 7.47910292e+00 8.43910547e+00 4.66265594e+00 5 2.15583085e+00 -1.60341167e+00 1.77189584e+00 6 -5.68244564e+00 -5.45448565e+00 2.65614299e+00 7 -1.07004774e+01 -4.96864242e+00 -1.70641582e+00 8 1.22693425e+00 2.59813736e+00 -6.12227784e+00 9 -1.05464315e+00 3.89888692e+00 1.24501203e+00 10 -7.31191112e-01 5.36731549e+00 -4.32975182e+00 11 3.50441622e+00 -3.20826865e+00 3.92625578e+00 12 3.45217436e+00 -2.50017724e+00 1.44696455e-01 13 -9.27584035e+00 5.13088857e-02 4.05307658e+00 14 -3.75848056e+00 5.97961469e+00 -3.46067682e-01 15 -1.77344972e+00 2.38020473e+00 2.35890551e-02 16 6.05204531e+00 -1.62547398e+00 8.26854969e-01 17 -1.10007038e+00 3.09429535e+00 5.23763557e+00 18 7.92559958e-01 -3.14483446e+00 2.73940862e+00 19 2.74400408e+00 -7.34873225e-01 8.24096387e-01 20 2.18220710e+00 7.48288480e+00 -5.61945756e+00 21 -3.35785487e+00 3.29140597e+00 1.31683751e+00 22 4.18914586e+00 -4.52768585e-01 2.21626312e+00 23 -6.74637275e+00 -1.81321216e-01 2.47134327e+00 24 -6.60191896e+00 -4.06399741e+00 -3.09711903e+00 25 -5.11809812e+00 2.39915070e+00 -1.15650568e+00 26 -1.56502595e+00 -1.59354769e+00 2.40113363e+00 27 4.54553486e+00 4.46431733e-01 -7.25974462e-01 28 5.40337894e+00 -1.55238710e+00 -1.50861863e+00 29 -2.98632211e-01 6.53097743e-01 -2.75569097e+00 30 1.83367043e+00 -5.59322305e+00 -5.17032176e+00 31 3.31999427e+00 3.02962127e+00 -9.46128818e+00 32 -2.50616911e+00 -1.84591050e+00 5.44303583e+00 MIXED STRUCTURE (pbc=False)-- Species = Au Pt (Configuration in file "config-F-AuPt.xyz") ----------------------------------------------------------------------------------------------------- Energy = 21.3889537454 Forces: 1 -5.70014695e+00 -5.99868559e+00 -3.72364869e+00 2 -4.30482418e+00 2.05223032e+00 -1.85241857e+01 3 -6.49000529e+00 -1.71088479e+01 -5.30961327e+00 4 -1.51533753e+01 -8.07763016e+00 3.21007875e+00 5 -3.17057121e+00 -1.55638852e+01 -1.49883600e+01 6 2.12227617e+01 5.23875618e-01 -2.26488241e+01 7 1.94211869e+01 -1.91903853e+01 5.20835955e+00 8 -4.25417757e+00 -5.54663855e+00 9.13064004e+00 9 -1.39215911e+01 3.24600349e+00 -1.65807768e+01 10 -7.98454791e+00 1.49209668e+01 -1.64346983e+01 11 -6.40337827e+00 -5.29922938e+00 -9.91179018e+00 12 -1.04352946e+01 1.20048082e+01 -3.08607557e+00 13 -4.36117179e+00 -2.34252545e-01 -2.83635913e+01 14 1.18512360e+01 8.91462636e+00 -7.59942666e+00 15 2.25438958e+01 1.97711504e+00 5.05613922e+00 16 6.92436402e+00 2.41779102e+01 4.89579579e+00 17 -8.20659172e+00 -1.12428785e+01 -2.23751694e+00 18 -5.58155273e+00 -2.73602754e+00 5.17636645e+00 19 -6.34178767e+00 -1.53225870e+01 1.00968734e+01 20 -1.23382935e+01 3.60642053e+00 1.27684808e+01 21 3.67243134e+00 -1.67165268e+01 3.00302560e+00 22 1.92604615e+01 4.67706915e+00 -4.49979081e+00 23 8.08413760e+00 -1.47675740e+01 1.00095148e+01 24 9.82660773e-01 3.54349599e+00 2.10605685e+01 25 -1.96948220e+01 -3.73164761e+00 4.93483226e+00 26 -4.39042135e+00 2.99533577e+01 5.80719439e+00 27 -1.30016993e+01 -7.16658907e+00 2.21453974e+01 28 -7.51145199e+00 7.42133527e+00 6.29238432e+00 29 1.03461455e+01 -3.21248245e+00 -5.26777078e+00 30 1.46719339e+01 1.43788847e+01 -1.89749783e+00 31 1.58631271e+01 -2.54986135e+00 1.37785648e+01 32 4.40136222e+00 2.30676293e+01 1.84993508e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==5236== Memcheck, a memory error detector ==5236== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==5236== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==5236== Command: python runner2.py EAM_Dynamo_OBrienBarrPrice_2018_PtAu__MO_946831081299_000 ==5236== ==5236== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==5236== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==5236== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5236== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5236== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==5236== by 0x4010732: call_init (dl-init.c:72) ==5236== by 0x4010732: _dl_init (dl-init.c:119) ==5236== by 0x40151FE: dl_open_worker (dl-open.c:522) ==5236== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==5236== by 0x40147C9: _dl_open (dl-open.c:605) ==5236== by 0x544CF95: dlopen_doit (dlopen.c:66) ==5236== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==5236== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==5236== by 0x544D734: _dlerror_run (dlerror.c:162) ==5236== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==5236== ==5236== ==5236== HEAP SUMMARY: ==5236== in use at exit: 22,223,623 bytes in 4,275 blocks ==5236== total heap usage: 188,620 allocs, 184,345 frees, 98,318,445 bytes allocated ==5236== ==5236== LEAK SUMMARY: ==5236== definitely lost: 0 bytes in 0 blocks ==5236== indirectly lost: 0 bytes in 0 blocks ==5236== possibly lost: 182,135 bytes in 111 blocks ==5236== still reachable: 22,041,488 bytes in 4,164 blocks ==5236== suppressed: 0 bytes in 0 blocks ==5236== Rerun with --leak-check=full to see details of leaked memory ==5236== ==5236== For counts of detected and suppressed errors, rerun with: -v ==5236== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2539 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.