!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_003 Supported species : Ar random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ar (Configuration in file "config-F-Ar.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6542.92915433 Forces: 1 -6.74871151e+02 -1.94901415e+03 -2.62498451e+03 2 -5.45300096e+00 3.49778983e+02 -3.33964212e+02 3 1.17318564e+03 -1.04095440e+03 3.94788014e+02 4 -6.28070827e+02 2.80598002e+03 2.03634643e+03 5 1.31368267e+01 -3.90874887e+02 -2.53059450e+02 6 1.05380254e+02 6.63936483e+01 -1.93191211e+02 7 -2.97042635e+02 -2.56988613e+03 -2.64334452e+03 8 -8.88037690e+02 -9.23592529e+02 2.02971906e+02 9 -2.86323802e+01 -1.25884430e+02 -1.70638600e+02 10 -5.54288390e+02 2.69627339e+02 -6.85405872e+02 11 -7.91173069e+02 -8.51247209e+02 -2.14597395e+01 12 -2.19420952e+02 6.15719067e+02 -2.96050830e+02 13 -1.36553930e+03 -6.20015777e+02 -2.68205921e+03 14 3.65200283e+02 3.90930686e+02 -1.55825952e+02 15 2.54585631e+03 4.85009974e+02 1.57945288e+03 16 7.91048276e+02 1.71070077e+03 1.10662879e+03 17 -5.08776951e+02 -2.22993916e+02 2.41685153e+02 18 -2.94469669e+00 9.18896783e+03 -8.67582546e+03 19 2.90966324e+02 -9.18524320e+03 8.72126973e+03 20 -2.19190319e+02 1.26648068e+02 1.53161030e+02 21 -7.28783123e+02 -4.76147158e+02 -4.14326150e+01 22 1.37022080e+03 2.63919880e+03 2.04014618e+03 23 1.15562899e+03 -5.90178139e+02 8.43599370e+02 24 -7.77341489e+02 5.83236499e+02 2.84434432e+02 25 -3.74138389e+02 -6.26614318e+02 5.58173411e+02 26 2.62964313e+01 6.59485099e+02 -4.25791099e+02 27 2.37468518e+03 -3.07025096e+03 5.51188303e+02 28 -3.01481280e+03 2.58280314e+03 5.36408366e+00 29 -1.19273225e+03 -1.18390453e+03 -1.66262931e+03 30 5.77647731e+02 7.06447235e+02 -2.11513232e+02 31 1.38692873e+03 -5.27767995e+02 1.10162802e+03 32 9.50676480e+01 1.17364258e+03 1.25633811e+03 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ar (Configuration in file "config-T-Ar.xyz") ----------------------------------------------------------------------------------------------------- Energy = 8143.00860694 Forces: 1 3.82370461e+02 -2.79859787e+03 -2.39026650e+03 2 -5.68859067e+01 3.55319594e+02 -2.37144471e+02 3 1.22691852e+03 -7.51572151e+02 4.82920002e+02 4 -1.84817405e+02 2.86809378e+03 2.08042808e+03 5 1.65805180e+02 1.87043766e+01 -2.89773916e+02 6 -1.14104238e+03 1.10580863e+03 2.17348695e+02 7 -5.96249264e+02 -2.53367419e+03 -2.73024328e+03 8 -8.89291688e+02 -9.23200892e+02 2.03801297e+02 9 -2.40975918e+02 -6.12980560e+02 6.05832879e+02 10 -7.40782744e+02 2.01894857e+01 -5.66768036e+02 11 -7.91004264e+02 -8.51863588e+02 -2.09335687e+01 12 -6.54375721e+01 3.97935641e+02 -2.34402353e+02 13 -1.35416912e+03 -6.73962815e+02 -2.56455110e+03 14 1.01361475e+02 4.69151374e+02 -2.31566728e+02 15 2.43717287e+03 4.31886564e+02 1.57896993e+03 16 7.83626654e+02 1.48960707e+03 1.20874753e+03 17 3.30109105e+02 -8.53957476e+02 3.67609190e+02 18 4.04795145e-01 9.19306812e+03 -8.67602304e+03 19 3.02442441e+02 -8.84036569e+03 8.86288692e+03 20 1.10074420e+03 9.21130429e+02 5.44945129e+01 21 -9.20409875e+02 -1.28177383e+02 -1.10698468e-01 22 5.94468003e+02 3.37369364e+03 2.08960468e+03 23 -9.80746861e+01 -1.50312990e+03 2.16031075e+02 24 -7.72450280e+02 5.94014414e+02 1.38762777e+02 25 -3.15209381e+02 -6.29404725e+02 5.66505190e+02 26 5.62536590e+01 3.22080482e+02 -5.85148371e+02 27 2.66752470e+03 -3.10491430e+03 1.41983357e+02 28 -2.94833007e+03 2.91114051e+03 -4.58260011e+02 29 -1.19326616e+03 -1.18778761e+03 -1.66298142e+03 30 6.59558786e+02 3.31483285e+02 -1.85205014e+02 31 1.33727706e+03 -5.65367419e+02 1.03019380e+03 32 1.62358802e+02 1.15564917e+03 9.87258579e+02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==15506== Memcheck, a memory error detector ==15506== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==15506== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==15506== Command: python runner2.py LJ_Shifted_Bernardes_1958MedCutoff_Ar__MO_126566794224_003 ==15506== ==15506== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==15506== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==15506== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==15506== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==15506== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==15506== by 0x4010732: call_init (dl-init.c:72) ==15506== by 0x4010732: _dl_init (dl-init.c:119) ==15506== by 0x40151FE: dl_open_worker (dl-open.c:522) ==15506== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==15506== by 0x40147C9: _dl_open (dl-open.c:605) ==15506== by 0x544CF95: dlopen_doit (dlopen.c:66) ==15506== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==15506== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==15506== by 0x544D734: _dlerror_run (dlerror.c:162) ==15506== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==15506== ==15506== ==15506== HEAP SUMMARY: ==15506== in use at exit: 5,248,335 bytes in 3,908 blocks ==15506== total heap usage: 139,777 allocs, 135,869 frees, 60,898,117 bytes allocated ==15506== ==15506== LEAK SUMMARY: ==15506== definitely lost: 0 bytes in 0 blocks ==15506== indirectly lost: 0 bytes in 0 blocks ==15506== possibly lost: 182,191 bytes in 111 blocks ==15506== still reachable: 5,066,144 bytes in 3,797 blocks ==15506== suppressed: 0 bytes in 0 blocks ==15506== Rerun with --leak-check=full to see details of leaked memory ==15506== ==15506== For counts of detected and suppressed errors, rerun with: -v ==15506== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2507 from 172) ================================================================================ 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.