!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouWadleyJohnson_2001NISTretabulation_Fe__MO_681088298208_000 Supported species : Fe random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 27.8371862963 Forces: 1 -9.49544959e+00 -8.48901952e+00 -1.64131266e+01 2 -9.41234895e+00 1.28781113e+01 -6.16035338e+00 3 1.87109789e+01 -1.68993106e+01 -4.64533928e+00 4 -1.43713043e+01 1.04482451e+01 -2.46695692e+00 5 2.29217328e+00 -2.03934587e+01 -6.74614949e-01 6 1.21786311e+01 7.46926834e+00 -1.13979331e+01 7 2.74582515e+00 -4.20915269e+01 -3.89920143e+01 8 -1.27411279e+01 -9.84149925e+00 7.55216131e+00 9 -6.86982133e+00 -1.26460977e+01 -1.81460484e+01 10 -7.23346235e+00 1.71040474e+01 -2.24539052e+01 11 5.61112155e+00 -1.44789757e+01 -4.29392999e+00 12 -1.17699815e+01 2.16636195e+01 2.68734466e+00 13 -1.68736174e+01 -1.81899749e+01 -5.89522873e+01 14 9.18529299e+00 1.53707943e+01 -1.21013654e+01 15 4.79964370e+01 -1.83089030e+01 2.12437815e+01 16 1.77482005e+00 4.10935352e+01 2.16417717e+01 17 -2.48004426e+01 -1.36863648e+01 6.10308477e-01 18 1.93240880e+01 1.62334610e+01 6.20479260e+00 19 8.65264555e+00 -1.07740270e+01 9.12347268e+00 20 -6.43253904e+00 9.12579932e+00 9.21346037e+00 21 -1.64175828e+01 -1.03494798e+01 9.93674756e+00 22 2.29686054e+01 3.91272609e+01 2.77014324e+01 23 5.54852954e+00 -3.89414872e+00 1.04087949e+01 24 -2.90161689e+00 3.90888673e+00 3.24417057e+00 25 -1.96553044e+01 -4.87126728e+00 2.37650461e+01 26 -9.33936118e+00 2.02810541e+01 -1.19464658e+01 27 2.29684941e+01 -4.98733859e+01 9.89041810e+00 28 -4.08580324e+01 3.48622299e+01 3.08048870e+00 29 -8.81413249e+00 -1.78933179e+01 5.09949441e+00 30 8.90162259e+00 1.81589091e+01 5.31937024e+00 31 1.77459112e+01 -1.19359112e+01 1.47760598e+01 32 1.13809486e+01 1.68914467e+01 1.71452244e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 101.46474308 Forces: 1 1.66324955e+01 -1.92331535e+01 -2.40616559e+00 2 -2.67669660e+01 1.19921565e+01 1.95318601e+01 3 2.31318884e+01 -1.39056428e+00 -5.92268080e-01 4 -6.65850475e+00 1.27787965e+01 -7.19274771e+00 5 9.25637324e+00 -1.25876957e+01 3.91496731e+00 6 -2.12791324e+01 4.58719137e+01 5.44946379e+01 7 -3.22267425e+00 -3.96669288e+01 -4.08384237e+01 8 -1.21879619e+01 -1.02030085e+01 7.14641307e+00 9 -2.38308960e+01 -3.14991134e+01 2.64965387e+01 10 -1.55311642e+01 9.06776699e+00 -1.08711288e+01 11 5.20082019e+00 -1.40017357e+01 -4.96152050e+00 12 7.67209286e+00 6.61761632e+00 1.44990909e+01 13 -1.55193114e+01 -2.05959689e+01 -5.30543029e+01 14 -1.59022531e+01 1.37901802e+01 -2.59568662e+01 15 4.08065826e+01 -2.07013454e+01 2.07126034e+01 16 2.18059356e+00 3.83436624e+01 2.17231166e+01 17 5.28679373e+00 -3.13830585e+01 2.77587063e+00 18 1.95824032e+01 1.57537893e+01 6.69128576e+00 19 8.18302367e+00 4.41494631e+00 1.04433422e+01 20 6.59911984e+01 5.66045333e+01 -3.00166239e+00 21 -1.67446717e+01 -3.64197493e+00 1.10254871e+01 22 -3.13819814e+00 5.92000718e+01 2.54164994e+01 23 -5.89994234e+01 -6.99134618e+01 -5.35975791e+01 24 1.39395587e+01 1.07522032e+01 -2.55364608e+01 25 -1.37532473e+01 -7.38623491e+00 2.38732900e+01 26 -8.18416491e+00 7.85714419e+00 -1.71128514e+01 27 4.24000140e+01 -4.99771292e+01 -2.16411095e+01 28 -4.51825093e+01 4.38821911e+01 -1.43528436e+01 29 -8.43258492e+00 -1.75331597e+01 5.25987911e+00 30 2.10057492e+00 1.10969825e+01 8.09190818e+00 31 1.64746321e+01 -1.27027812e+01 1.32631659e+01 32 1.64946185e+01 1.43933600e+01 5.75597391e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==9625== Memcheck, a memory error detector ==9625== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==9625== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==9625== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Fe__MO_681088298208_000 ==9625== ==9625== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==9625== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==9625== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9625== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9625== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9625== by 0x4010732: call_init (dl-init.c:72) ==9625== by 0x4010732: _dl_init (dl-init.c:119) ==9625== by 0x40151FE: dl_open_worker (dl-open.c:522) ==9625== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==9625== by 0x40147C9: _dl_open (dl-open.c:605) ==9625== by 0x544CF95: dlopen_doit (dlopen.c:66) ==9625== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==9625== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==9625== by 0x544D734: _dlerror_run (dlerror.c:162) ==9625== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==9625== ==9625== ==9625== HEAP SUMMARY: ==9625== in use at exit: 5,876,277 bytes in 3,960 blocks ==9625== total heap usage: 114,082 allocs, 110,122 frees, 59,272,787 bytes allocated ==9625== ==9625== LEAK SUMMARY: ==9625== definitely lost: 0 bytes in 0 blocks ==9625== indirectly lost: 0 bytes in 0 blocks ==9625== possibly lost: 182,191 bytes in 111 blocks ==9625== still reachable: 5,694,086 bytes in 3,849 blocks ==9625== suppressed: 0 bytes in 0 blocks ==9625== Rerun with --leak-check=full to see details of leaked memory ==9625== ==9625== For counts of detected and suppressed errors, rerun with: -v ==9625== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2508 from 175) ================================================================================ 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.