!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_TehranchiCurtin_2010_NiH__MO_535504325462_003 Supported species : H Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = H (Configuration in file "config-F-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -28.2865677697 Forces: 1 1.00675795e+00 1.76489279e+00 1.88266935e+00 2 6.88769462e-01 -1.52280136e+00 1.15127759e+00 3 -9.72376868e-01 1.67904632e+00 4.97540141e-01 4 1.41330322e+00 -9.64249229e-01 -9.41380366e-01 5 -5.79668687e-01 2.45608866e+00 6.51082381e-01 6 -1.15057212e+00 -7.27985625e-01 1.23301260e+00 7 -1.33678074e+00 2.45665654e+00 1.71339395e+00 8 1.53051597e+00 5.45789601e-01 3.84199251e-01 9 1.35855562e+00 1.04706319e+00 2.80849601e+00 10 5.20995948e-02 -2.07126619e+00 2.02616570e+00 11 -1.86249765e+00 1.25639141e+00 -2.77961659e-01 12 1.83512527e+00 -2.49373462e+00 -6.37143991e-01 13 7.68533835e-01 1.50240458e+00 2.57628416e+00 14 -1.29004210e+00 -1.61398545e+00 1.11716604e+00 15 -2.37994273e+00 1.42828851e+00 -1.02727590e-01 16 -1.40634850e-01 -2.05573103e+00 -8.82985148e-01 17 2.73736277e+00 1.53683120e+00 8.34665977e-01 18 -5.85548057e-01 -2.03207473e+00 5.62841284e-01 19 -1.05185201e+00 2.61870309e+00 -1.65636604e+00 20 1.34073437e+00 -1.67997503e+00 -1.69436752e+00 21 1.63157107e+00 1.76264828e+00 -5.11298327e-01 22 -2.20384759e+00 -2.26057659e+00 -1.13048649e+00 23 -1.03897100e+00 5.57319420e-01 -1.62159201e+00 24 -5.30746934e-01 -6.45143195e-01 -1.31613933e+00 25 2.02927776e+00 9.45256267e-01 -9.97781702e-01 26 4.92178016e-01 -2.32765155e+00 1.19908022e+00 27 -8.08336785e-01 2.88469937e+00 -1.46973482e+00 28 2.50675347e+00 -2.23342155e+00 -9.93812670e-01 29 1.02394767e+00 1.16302237e+00 -2.76656684e-01 30 -1.42796495e+00 -2.13006765e+00 -7.05052120e-01 31 -2.29646506e+00 1.09000280e+00 -1.47584476e+00 32 -7.59237901e-01 -1.93644058e+00 -1.94654343e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = H (Configuration in file "config-T-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -41.2472828318 Forces: 1 -1.37433764e+00 1.25938427e+00 -1.95838240e-01 2 2.02691387e+00 -9.09450325e-01 -1.96525876e+00 3 -4.63295309e-01 -3.94650234e-01 3.63398791e-01 4 -9.15814515e-01 -8.75586850e-01 -4.05695134e-03 5 -9.37199368e-01 3.26385948e-01 2.00307434e-01 6 1.51358486e+00 -1.93859609e+00 -6.01766174e-01 7 -2.44179847e-01 1.45028284e+00 1.55517524e+00 8 1.22576979e+00 7.59919304e-01 5.26988565e-01 9 1.25671506e+00 1.62027493e+00 -3.48647320e-01 10 9.92436552e-01 -4.04465490e-01 6.12481018e-01 11 -1.31704712e+00 9.96530412e-01 1.80002533e-01 12 -4.01376220e-01 -6.52396184e-01 -4.51504879e-01 13 5.98328442e-01 1.34256015e+00 1.64777545e+00 14 8.36347999e-01 -5.53295728e-01 1.08529827e+00 15 -1.76136684e+00 8.75751608e-01 -6.66386635e-02 16 -3.21742754e-01 -1.06005723e+00 -7.26208845e-01 17 -1.26741756e-01 1.25977062e+00 4.01205966e-01 18 -3.35187853e-01 -1.58819687e+00 2.09885205e-01 19 -5.29719697e-01 2.85276244e-01 -1.07530222e+00 20 -1.10957376e+00 -2.30426106e+00 4.14631063e-01 21 1.10388474e+00 2.92527508e-01 -8.19630028e-01 22 1.48991800e-01 -2.15690484e+00 -1.41281276e+00 23 1.53224465e+00 1.83441960e+00 6.16892745e-01 24 -1.89683648e+00 -9.64155977e-01 1.87730886e+00 25 1.02665489e+00 1.02768515e+00 -9.64359236e-01 26 4.05843389e-01 -3.54808300e-01 9.47114551e-01 27 -1.17057641e+00 2.08133639e+00 3.61857073e-01 28 1.65815482e+00 -1.48445201e+00 3.42634690e-01 29 9.38643853e-01 9.15450970e-01 -4.01949333e-01 30 1.46531669e-01 -6.83131762e-01 -9.38787219e-01 31 -1.64118145e+00 1.17608342e+00 -9.55217811e-01 32 -8.64869358e-01 -1.17923042e+00 -4.14979027e-01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -36.1106917582 Forces: 1 -3.07338251e+00 -2.66907108e+00 -4.01671233e+00 2 2.60965303e+00 9.44282157e-01 -9.01436292e+00 3 5.45445391e+00 -1.44114004e+01 -6.02039784e+00 4 -1.27914913e+01 8.71333005e+00 4.08648266e+00 5 2.95735832e+00 -7.35598600e+00 -6.16123184e+00 6 7.47832076e+00 -4.24696322e+00 -5.45305691e+00 7 8.54260631e+00 -1.08870006e+01 -4.25212077e+00 8 -4.81276337e+00 3.20114851e+00 -5.93300378e+00 9 -1.20450251e+01 -1.01491740e+00 -9.70321538e+00 10 2.15768535e-01 7.24416180e+00 -9.79576551e+00 11 9.22426449e+00 -4.90532352e+00 1.17165002e+01 12 -6.18633429e+00 1.23190004e+01 -3.11150243e+00 13 -4.15339089e+00 4.72693961e+00 -7.43403360e+00 14 3.03209857e+00 4.86095778e-01 -2.64842036e+00 15 1.06278782e+01 8.17993506e+00 -9.83477340e-01 16 1.05589188e+00 4.05839609e+00 6.53710573e+00 17 -7.61510845e+00 -6.90583575e+00 4.94229097e+00 18 -6.58856078e+00 1.28101882e+01 3.73073918e+00 19 4.07806150e+00 -8.49540684e+00 4.28073983e+00 20 -6.76671481e+00 7.22390303e+00 1.70015665e+00 21 2.55412179e+00 -1.38041579e+01 6.69933957e+00 22 9.78216470e+00 -9.28622928e-01 7.11636686e+00 23 1.17917670e+00 -1.09620613e+00 7.21029802e-01 24 2.89405737e+00 3.20366743e+00 6.78432671e+00 25 -3.30125846e+00 -8.47052376e+00 7.24364277e+00 26 -4.26537557e+00 8.59415072e+00 -1.15041688e+01 27 -5.51499168e+00 -1.14918793e+01 6.39444679e+00 28 -3.96240771e+00 2.48574876e+00 2.16033985e+00 29 -7.56959134e+00 5.70442021e+00 2.41767490e+00 30 1.89402639e+00 3.63216279e+00 -3.56938957e+00 31 6.10240850e+00 -4.08059797e+00 5.87211166e+00 32 8.96408530e+00 7.23636207e+00 7.19756519e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -39.9474120029 Forces: 1 -1.21618343e+00 -9.10026264e+00 7.25400408e+00 2 4.17302919e+00 3.92228957e+00 -3.09329807e-01 3 3.27814377e+00 -9.87216519e+00 -6.18540628e+00 4 -8.76664125e+00 8.05807589e+00 2.59402491e+00 5 5.58892687e+00 -3.60516414e+00 -9.16549753e-01 6 1.63622328e+00 7.33334590e-01 -2.28674456e+00 7 9.21463724e+00 -2.89243403e+00 -6.05011917e+00 8 -4.27625407e+00 2.99444927e+00 -6.42517428e+00 9 -1.17422711e+01 -7.60634905e-01 -6.29893840e+00 10 5.18012021e-01 6.61466821e+00 2.36648985e+00 11 8.66522889e+00 -4.40830051e+00 1.15400598e+01 12 -2.61353857e+00 9.09008124e+00 -7.35473747e+00 13 -3.58525263e+00 5.31102553e+00 -4.00481287e+00 14 2.54466276e+00 -2.83708031e+00 -6.11720340e-01 15 5.22695418e+00 5.99545768e+00 -2.82183914e+00 16 2.00214181e-01 -5.14833549e+00 5.87225865e+00 17 -5.81746057e+00 9.99896259e-01 4.66928348e+00 18 -7.23260100e+00 1.26715082e+01 3.98839185e+00 19 4.40709338e+00 -3.08301818e+00 -1.82037302e+00 20 -4.91583221e+00 1.11629385e+01 -9.77642693e+00 21 4.05994602e+00 -8.08988693e+00 6.96856551e+00 22 4.52348287e+00 -2.20585498e+00 9.03360190e+00 23 -2.73904497e+00 6.75969008e-01 -3.77568419e+00 24 2.94851846e+00 4.22892112e+00 -6.17185715e-01 25 4.11163668e+00 -7.55919052e+00 7.79324010e+00 26 -2.29223294e+00 -6.68781861e-01 -1.21604545e+01 27 -4.68291591e+00 -1.50598848e+01 -2.50805231e+00 28 -5.60721127e+00 -1.08804504e+00 1.35974759e+00 29 -7.32138842e+00 5.81714038e+00 2.66394401e+00 30 -3.88940602e+00 -1.43897963e+00 -4.43186586e-01 31 3.87563824e+00 -5.59106715e+00 4.30627376e+00 32 1.17258863e+01 5.13333096e+00 3.95684984e+00 MIXED STRUCTURE (pbc=False)-- Species = H Ni (Configuration in file "config-F-HNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = -53.6341816715 Forces: 1 1.10000904e+00 5.79763363e-01 4.39674777e-01 2 -2.11678317e-02 -3.92290061e-01 -4.63580614e-01 3 -2.65653026e-01 -4.23360451e-01 -4.48026639e-02 4 -3.40633551e-01 -3.21191062e-01 6.63039705e-02 5 -5.18768232e-01 9.00094872e-01 1.19830561e+00 6 4.02395727e+00 -5.93801599e+00 -1.34847667e+00 7 -1.68914589e-02 -6.92269443e-02 -2.01661683e-01 8 4.20991285e-01 1.62289296e-01 -3.64746906e-02 9 -1.57152428e-01 3.45866738e-01 -5.14767812e-01 10 6.11855548e-01 -1.09507708e+00 1.72196704e+00 11 2.27232766e-01 5.26632767e-01 2.54402838e-02 12 -1.35895004e-01 8.65599191e-02 -1.62698023e-01 13 -8.52035078e+00 1.45899238e+00 -6.50059244e+00 14 2.82860370e-02 1.55440153e-01 3.25018110e-02 15 1.23395873e+01 -2.23524215e+00 -5.91514262e+00 16 -4.52851549e+00 6.96625970e+00 -4.31065072e+00 17 -6.82455684e-02 3.81111671e-01 3.05586628e-01 18 -2.87753034e-01 2.85652617e-01 5.42162024e-01 19 -7.75960035e-02 8.99309041e-02 -5.88471644e-03 20 -4.79401370e-02 -1.43706565e+00 -4.40455235e-01 21 -7.39336322e+00 -3.91474262e+00 -4.94066306e-01 22 9.18253392e+00 1.30297443e+00 -1.27361148e+00 23 3.82442552e-01 -4.89653325e-01 1.49525689e+00 24 1.71125722e-01 -4.56503382e-01 -1.69268728e-01 25 -5.69992773e+00 -4.62924242e+00 -3.29662697e+00 26 3.07842361e+00 8.24203290e+00 -3.79795585e+00 27 3.09428282e+00 -3.40341155e+00 6.87118550e+00 28 -2.61112750e-01 2.11217400e-01 -2.40659570e-02 29 -1.26445620e+01 -5.89280287e+00 6.96607999e+00 30 6.40029968e+00 8.91552695e+00 9.22631209e+00 31 2.44897216e-01 7.57204746e-02 -5.18333173e-02 32 -3.20396444e-01 1.17590087e-02 1.61839884e-01 MIXED STRUCTURE (pbc=True)-- Species = H Ni (Configuration in file "config-T-HNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = -62.0069200937 Forces: 1 2.61834162e-01 2.82023377e+00 2.94773632e+00 2 1.00349686e-01 -1.84213315e-01 -1.49768933e-01 3 -5.86964914e-02 -3.65335924e-01 4.61805849e-02 4 -3.13441628e-02 -6.67299285e-02 3.99665191e-01 5 -7.14846388e+00 -7.19669610e-01 4.13509040e+00 6 2.70036845e+00 -4.17624068e+00 3.46842792e-01 7 8.81991426e-02 1.19299623e-03 1.86785919e-02 8 2.36689216e-01 2.96465433e-01 -1.92469395e-01 9 -9.10032494e-02 2.56753554e-02 -5.10221067e-01 10 8.27337612e-01 -2.71152574e+00 2.33775543e+00 11 3.45381612e-01 3.03991557e-01 1.62663412e-01 12 -1.21189754e-01 1.64908866e-02 -7.47629579e-02 13 -8.43355432e+00 2.10835997e+00 -7.65279880e+00 14 -6.80336715e-02 2.10728433e-01 1.19714272e-01 15 1.09016309e+01 -1.62468175e+00 -7.23822953e+00 16 -4.31906175e+00 6.00362636e+00 -3.73687783e+00 17 -2.76636676e-01 1.35597646e-01 2.77707198e-01 18 -2.23997147e-02 3.45006498e-01 4.24354131e-01 19 4.82631282e-02 -9.49099856e-05 2.92415799e-01 20 2.38544412e+00 2.78100922e-01 -1.15482196e+00 21 -9.30597836e+00 -3.59328475e+00 3.41641815e-01 22 8.87613433e+00 1.13975792e+00 -3.22168825e+00 23 6.09911001e+00 -4.09375021e+00 -3.63044794e+00 24 -6.95532159e-04 -2.07192656e-01 8.29744435e-02 25 -2.75078147e+00 -5.92882396e+00 -3.27549809e+00 26 3.26248314e+00 9.93997554e+00 -4.02039290e+00 27 4.59436167e+00 -5.02524344e+00 5.75312115e+00 28 -5.17148506e-01 3.72609067e-01 -8.68683618e-02 29 -1.24132801e+01 -5.56625824e+00 7.46743111e+00 30 5.05087565e+00 1.00179641e+01 9.66979061e+00 31 1.63958644e-01 5.24667653e-03 -1.85545060e-02 32 -3.84153878e-01 2.42021974e-01 1.39637292e-01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==6744== Memcheck, a memory error detector ==6744== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==6744== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==6744== Command: python runner2.py EAM_Dynamo_TehranchiCurtin_2010_NiH__MO_535504325462_003 ==6744== ==6744== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==6744== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==6744== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6744== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6744== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6744== by 0x4010732: call_init (dl-init.c:72) ==6744== by 0x4010732: _dl_init (dl-init.c:119) ==6744== by 0x40151FE: dl_open_worker (dl-open.c:522) ==6744== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6744== by 0x40147C9: _dl_open (dl-open.c:605) ==6744== by 0x544CF95: dlopen_doit (dlopen.c:66) ==6744== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6744== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==6744== by 0x544D734: _dlerror_run (dlerror.c:162) ==6744== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==6744== ==6744== ==6744== HEAP SUMMARY: ==6744== in use at exit: 8,809,705 bytes in 4,275 blocks ==6744== total heap usage: 192,977 allocs, 188,702 frees, 79,027,456 bytes allocated ==6744== ==6744== LEAK SUMMARY: ==6744== definitely lost: 0 bytes in 0 blocks ==6744== indirectly lost: 0 bytes in 0 blocks ==6744== possibly lost: 182,735 bytes in 112 blocks ==6744== still reachable: 8,626,970 bytes in 4,163 blocks ==6744== suppressed: 0 bytes in 0 blocks ==6744== Rerun with --leak-check=full to see details of leaked memory ==6744== ==6744== For counts of detected and suppressed errors, rerun with: -v ==6744== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2524 from 177) ================================================================================ 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.