!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_BonnyGrigorev1Terentyev_2017_W__MO_234187151804_000 Supported species : Re W random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Re (Configuration in file "config-F-Re.xyz") ----------------------------------------------------------------------------------------------------- Energy = 240.935061726 Forces: 1 -1.19663426e+01 -4.34775299e+01 -3.48542812e+01 2 -1.50641802e+01 2.33055294e+01 -2.61967412e+01 3 1.24571542e+01 -2.42276809e+01 -4.41322409e+00 4 -2.05172565e+01 3.37481844e+01 3.18635617e+01 5 7.03471532e+00 -4.51128991e+01 -1.52019378e+01 6 2.24698525e+01 8.51830616e+00 -2.58266701e+01 7 1.28582376e+01 -8.21504982e+01 -6.62786247e+01 8 -2.98047272e+01 -2.73136048e+01 9.63990244e+00 9 -1.96933755e+01 -4.37485273e+01 -4.99074620e+01 10 3.93774029e+01 4.51309652e+01 -4.46436333e+01 11 -2.23349002e+01 -3.52161399e+01 -1.75882256e+01 12 -5.68309824e+01 3.65960135e+01 4.55904298e+01 13 -3.79355299e+01 -1.37372383e+01 -1.07336056e+02 14 2.05764554e+01 2.72166531e+01 -1.78366692e+01 15 9.57749813e+01 -1.23050889e+01 3.23770985e+01 16 7.96014066e+00 7.57423360e+01 1.55954127e+01 17 -4.40388070e+01 -2.37821831e+01 -1.43429194e+01 18 1.71282847e+01 2.36599326e+01 -1.26087823e+01 19 1.36998875e+01 -3.99206993e+01 2.87222162e+01 20 -2.33418194e+01 1.99446867e+01 2.92736856e+01 21 -2.90539057e+01 -2.85870291e+01 1.09639614e+01 22 5.55767396e+01 6.77697847e+01 6.48022644e+01 23 1.43196909e+01 -7.40353036e+00 1.87489086e+01 24 6.27066884e+00 1.03020511e+01 2.01862125e+01 25 -6.79965170e+01 -3.53220392e+01 -1.99317326e+01 26 1.83275234e+01 7.45354206e+01 -2.19223888e+01 27 5.86879663e+01 -9.24590537e+01 4.84321481e+01 28 -9.01475959e+01 7.85043530e+01 3.40108865e+01 29 -1.02347276e+01 -2.57593073e+01 2.32250975e+01 30 2.43879255e+01 3.76454503e+01 5.65220107e+00 31 3.81548488e+01 -2.02587687e+01 3.06744661e+01 32 1.38981915e+01 3.81621512e+01 2.91308953e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Re (Configuration in file "config-T-Re.xyz") ----------------------------------------------------------------------------------------------------- Energy = 617.539401815 Forces: 1 5.30426248e+01 -5.17781452e+01 1.69464142e+00 2 -8.30018035e+01 2.35385503e+01 7.59157009e+01 3 7.88826073e+00 2.05037778e+01 2.61676126e+00 4 3.41521021e+01 4.89158295e+01 4.10573303e+01 5 1.48208485e+01 -2.52891974e+01 -2.36833335e+00 6 -6.48235577e+01 6.04957101e+01 -8.37920244e+00 7 -1.74401711e+01 -7.11743341e+01 -6.55871202e+01 8 -3.15267498e+01 -2.69700432e+01 1.08628847e+01 9 -4.16672128e+01 -7.80758804e+01 3.29663288e+01 10 3.91417008e+01 2.62680806e+01 -1.54913906e+01 11 -2.23507598e+01 -3.58015342e+01 -1.74799757e+01 12 8.78034914e+00 7.99716107e+00 7.90343927e+01 13 -3.47839569e+01 -1.98335155e+01 -8.31275983e+01 14 -5.37496699e+01 1.22197117e+01 -3.65910555e+01 15 7.54440442e+01 -1.22236405e+01 3.54881324e+01 16 1.43279380e+01 4.68508436e+01 1.90321760e+01 17 1.85371395e+01 -3.66155498e+01 -1.56054830e+01 18 1.96205870e+01 2.42471412e+01 -1.25782416e+01 19 1.68474636e+01 1.25720806e+00 2.01959517e+01 20 1.83439917e+01 5.29317473e+01 -9.84841727e+00 21 -3.32353805e+01 -4.83757408e+00 1.40871740e+01 22 2.87698382e+00 1.02385025e+02 5.96326622e+01 23 -3.58678615e+01 -4.20962672e+01 -1.76656272e+01 24 7.44576916e+01 2.41690437e+01 -8.72232551e+01 25 -4.38832971e+01 -4.22242508e+01 -2.00582771e+01 26 2.42393095e+01 3.05344620e+01 -2.68689445e+01 27 9.39614342e+01 -9.75231403e+01 -1.88389868e+01 28 -9.00949938e+01 7.72598612e+01 -1.06384917e+01 29 -1.02947577e+01 -2.61840976e+01 2.32077313e+01 30 2.61578435e+00 1.01974261e+01 4.89867454e+00 31 2.36681186e+01 -2.52019405e+01 2.12134036e+01 32 1.99538001e+01 2.60575316e+01 6.44645442e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = W (Configuration in file "config-F-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 124.873641351 Forces: 1 -1.82782238e+01 -2.29282111e+01 -2.17545208e+01 2 2.32882868e+01 -2.28498768e+01 -3.27685463e+01 3 1.86823823e+01 -5.70028621e+01 -1.84496906e+01 4 -4.36766727e+01 1.61668254e+01 -1.25943316e+01 5 -5.66858162e+01 -2.54247715e+01 -5.62938851e+01 6 3.19916255e+01 1.01185399e+01 -1.63967741e+01 7 6.35067507e+01 -2.32248758e+01 5.01731374e+01 8 2.87526668e+01 5.54148035e+01 -7.79145370e+01 9 -5.54456236e+01 1.45541803e+01 -3.53933549e+01 10 1.39401314e+01 1.95630539e+01 -2.18320635e+01 11 4.11033662e+01 2.50015602e+01 2.56684060e+01 12 -1.83688605e+01 9.55587183e+00 9.97768625e+00 13 -1.11852972e+01 6.83391112e+00 -1.34077613e+01 14 1.80769292e+01 1.50939385e+01 -1.35663595e+01 15 3.49197937e+01 -1.92128278e+01 -1.21558788e+01 16 -2.76607677e+01 2.70690316e+01 -6.44005722e-02 17 -3.13039636e+01 -3.41083576e+01 9.54062935e+00 18 -2.86587998e+01 2.06428224e+01 4.82776907e+01 19 1.70678408e+01 -1.83468783e+01 9.12101640e+00 20 -1.78767328e+01 2.57841311e+01 2.24959309e+01 21 1.05662513e+01 -8.25688538e+01 6.21725533e+01 22 3.61697132e+01 3.41595810e+01 -4.80953433e+01 23 1.30759480e+01 -5.84477993e+01 5.20390881e+01 24 -2.19207869e+01 -2.49969173e+00 3.36628027e+01 25 -2.88838227e+01 1.39480847e+01 8.65959668e+00 26 1.06398167e+01 2.44263282e+01 -1.62888462e+01 27 4.43157858e+00 -1.91264852e+01 3.08797618e+01 28 -2.91322234e+01 1.53800206e+01 1.21860215e+01 29 -1.30110828e+01 1.10954705e+01 -1.49604429e+01 30 1.27175245e+01 1.85148772e+01 2.87523431e+00 31 4.57533862e+01 -1.90970608e+01 2.00652601e+01 32 -2.25953180e+01 4.15155199e+01 1.41419211e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = W (Configuration in file "config-T-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 385.216977478 Forces: 1 -6.41959094e+00 -1.53468838e+01 1.68129353e+01 2 1.47488159e+01 -1.70590350e+01 -1.19591401e+01 3 2.58904473e+01 -2.59039948e+01 -2.65012017e+01 4 -3.30372258e+01 1.39902612e+01 -1.62643666e+01 5 -6.32162387e+01 -9.06549298e+00 -3.20739090e+01 6 1.59392755e+01 2.65788835e+01 3.73493733e+01 7 3.69002885e+01 8.77369178e+00 4.22055633e+01 8 3.15411550e+01 5.27035360e+01 -7.86841082e+01 9 -4.07967173e+01 1.40301906e+01 -2.20519152e+01 10 1.39306952e+01 5.35360192e+00 5.17325949e+00 11 3.94536955e+01 2.62472250e+01 2.31617797e+01 12 3.44774006e+00 -2.50056752e+01 2.58880831e+00 13 -2.02926956e+01 1.20563740e+01 3.93919967e+01 14 3.07202573e+01 1.18902808e+02 1.52235727e+02 15 1.38552873e+01 -1.70441185e+01 -1.52616197e+01 16 -3.55114363e+01 3.46352784e+00 6.38197301e+00 17 3.52076844e+01 -3.03706781e+01 -8.38396732e+00 18 -3.00039280e+01 2.09068252e+01 4.93138229e+01 19 3.26117465e+01 -1.92923039e+00 -2.16045812e+01 20 9.24952072e+01 7.19804092e+01 2.23084256e+01 21 1.51624676e+01 -6.84526586e+01 6.21266748e+01 22 -5.07779226e+01 7.31904657e+01 -7.02814619e+01 23 -6.22435358e+01 -1.01095575e+02 3.49477567e+01 24 -3.29748209e+01 -2.06920505e+01 -2.55608787e+01 25 -7.14368709e+00 1.61512916e+01 1.47416029e+01 26 1.25208810e+01 -1.10371542e+01 -8.37081626e+00 27 3.38680537e+00 -2.07093769e+01 9.35142620e+00 28 4.19571014e+01 1.24123571e+01 1.79570693e+01 29 -1.11665042e+01 1.13599857e+01 -1.62160365e+01 30 -4.12226885e+01 -8.91601113e+00 -2.03836282e+01 31 2.37098366e+01 -1.54120292e+02 -1.33278473e+02 32 -4.86723957e+01 3.86467926e+01 -2.91720906e+01 MIXED STRUCTURE (pbc=False)-- Species = Re W (Configuration in file "config-F-ReW.xyz") ----------------------------------------------------------------------------------------------------- Energy = 159.426093642 Forces: 1 -1.22175613e+01 -1.37035821e+01 -2.56622825e+01 2 1.27417290e+01 -1.86106354e+01 -2.53582646e+01 3 2.30593324e+01 -2.53793613e+01 6.89844619e+00 4 -4.77898824e+01 1.36942308e+01 -2.18746450e+01 5 1.92266378e-01 -1.07649681e+01 -9.50922266e+00 6 1.79859413e+01 -5.74201405e+00 -2.30928158e+01 7 2.66853610e+01 -2.91890333e+01 -2.03464831e+01 8 -4.39868871e+01 -9.98231646e+00 -2.76020141e+01 9 -3.79335422e+01 1.60942826e+01 -1.83501005e+01 10 -1.37712624e+01 1.59556436e+01 -2.34206199e+01 11 5.80030066e+01 2.14249127e+00 -6.66849870e+01 12 -2.43919267e+01 1.87944852e+01 -1.10766351e+01 13 2.46885517e+00 1.25631216e+01 -1.96551803e+01 14 1.02953587e+01 9.06635173e+00 -9.28292657e+00 15 3.68225105e+01 2.01365707e+01 -6.82023303e+00 16 1.22455242e+01 2.29294110e+01 1.28528693e+01 17 -5.56789439e+01 -7.67585681e+01 -7.12269466e+00 18 4.33418323e+01 2.52698680e+01 2.37776971e+00 19 6.12477891e+01 -6.71617367e+01 2.80726248e+01 20 -7.53867109e+01 6.57309518e+01 4.03060010e+01 21 -3.36916250e+01 -5.47549089e+01 -6.83376203e+00 22 6.84961762e+01 2.57561848e+01 1.82823081e+01 23 7.63555050e+01 -8.41218121e+01 3.99847581e+01 24 -6.76679634e+01 6.52905634e+01 2.68608227e+01 25 -9.20781029e+01 -2.39431427e+01 4.23520324e+01 26 2.03023158e+01 4.88680497e+01 1.60157000e+01 27 2.87467748e+01 5.10980273e+00 3.91901131e+01 28 -1.23124479e+01 1.38011508e+01 1.25294803e+01 29 -4.25112157e+00 4.94867372e+00 5.51478874e+00 30 1.83578858e+01 2.91949675e+01 -1.24470629e+01 31 1.91772143e+01 -7.65608647e+00 2.38165043e+01 32 -1.53674007e+01 1.24213648e+01 2.00857113e+01 MIXED STRUCTURE (pbc=True)-- Species = Re W (Configuration in file "config-T-ReW.xyz") ----------------------------------------------------------------------------------------------------- Energy = 380.575202177 Forces: 1 -8.36834968e+01 -2.74475725e+01 6.22486506e+01 2 2.32534366e+01 -6.05867607e+00 1.65811792e+01 3 1.06440880e+01 4.43283480e+00 9.82832367e+00 4 4.19230126e+01 6.20172381e+01 -2.93498534e+01 5 1.22454383e+01 1.68150430e+01 2.69988414e-01 6 8.91059579e+00 -3.64174295e+00 1.26173777e+00 7 -5.74867065e+01 -5.21161174e+01 -2.46237623e+01 8 -4.36765330e+01 -8.96037332e+00 -2.89830187e+01 9 -2.51124367e+01 1.49308142e+01 -5.59870562e+00 10 -1.86767754e+01 -2.07388104e+01 -1.09628670e+01 11 5.89198215e+01 2.07986759e+00 -6.74154219e+01 12 -7.68422307e+00 -1.62507288e+00 -1.32281722e+01 13 6.44784029e-01 9.92091055e+00 -1.18415468e+01 14 1.14166362e+01 -8.10316081e+00 -7.89317938e+00 15 1.77076519e+01 1.83586292e+01 -4.90602457e+00 16 1.59216452e+01 -8.67866091e+00 2.11499014e+01 17 -1.71154498e+01 -6.16118181e+01 1.28136655e+00 18 4.23836932e+01 2.54064443e+01 1.89257613e+00 19 1.26430561e+02 -3.96076382e+01 -7.35914685e+01 20 -7.16367976e+01 6.46191607e+01 1.42986955e+01 21 -3.67490494e+01 -3.62305865e+01 -5.96479058e+00 22 3.95591575e+01 3.19258521e+01 2.15740288e+01 23 6.60178330e+01 -7.00489289e+01 3.76292821e+01 24 -6.92076724e+01 6.78064475e+01 6.46554530e+00 25 -7.44517311e+01 -2.49510927e+01 4.11377526e+01 26 1.94256744e+01 3.95630607e+01 1.66092769e+01 27 2.95143418e+01 1.18949279e+01 1.51159939e+01 28 1.41463298e+01 9.03736658e+00 1.27575090e+01 29 -3.25434026e+00 7.02834861e+00 8.75801019e+00 30 -6.85968317e+00 3.71805812e+00 -1.33828429e+01 31 -6.20541928e+00 -1.25912402e+01 1.18424472e+01 32 -1.72643866e+01 -7.14351210e+00 -2.96061115e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==30201== Memcheck, a memory error detector ==30201== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==30201== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==30201== Command: python runner2.py EAM_Dynamo_BonnyGrigorev1Terentyev_2017_W__MO_234187151804_000 ==30201== ==30201== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==30201== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==30201== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30201== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30201== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30201== by 0x4010732: call_init (dl-init.c:72) ==30201== by 0x4010732: _dl_init (dl-init.c:119) ==30201== by 0x40151FE: dl_open_worker (dl-open.c:522) ==30201== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==30201== by 0x40147C9: _dl_open (dl-open.c:605) ==30201== by 0x544CF95: dlopen_doit (dlopen.c:66) ==30201== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==30201== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==30201== by 0x544D734: _dlerror_run (dlerror.c:162) ==30201== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==30201== ==30201== ==30201== HEAP SUMMARY: ==30201== in use at exit: 22,242,393 bytes in 4,274 blocks ==30201== total heap usage: 192,866 allocs, 188,592 frees, 93,853,114 bytes allocated ==30201== ==30201== LEAK SUMMARY: ==30201== definitely lost: 0 bytes in 0 blocks ==30201== indirectly lost: 0 bytes in 0 blocks ==30201== possibly lost: 182,735 bytes in 112 blocks ==30201== still reachable: 22,059,658 bytes in 4,162 blocks ==30201== suppressed: 0 bytes in 0 blocks ==30201== Rerun with --leak-check=full to see details of leaked memory ==30201== ==30201== For counts of detected and suppressed errors, rerun with: -v ==30201== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2530 from 173) ================================================================================ 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.