!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Mg__MO_894868634445_000 Supported species : Mg random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mg (Configuration in file "config-F-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 424.381968833 Forces: 1 -1.32135101e+01 -2.38859518e+01 -2.47723982e+01 2 -2.24361000e+01 3.52731757e+01 -3.12705122e+01 3 -2.85709434e+00 -3.35768635e+01 -3.43828381e+00 4 -1.95260873e+01 1.13750854e+01 1.15855565e+01 5 3.29361435e+01 -5.22396397e+01 -1.16310174e+01 6 1.33734143e+01 2.75024613e+00 -2.07454491e+01 7 1.85036436e+01 -7.28330795e+01 -6.44928655e+01 8 -2.14858354e+01 -2.43334529e+01 -1.16580362e+01 9 -2.64771844e+01 -3.78773831e+01 -6.41153196e+01 10 -2.95294023e+00 5.39876963e+01 -5.49200058e+01 11 -8.93280755e+00 -3.69457993e+01 2.29523905e+01 12 -4.01457129e+01 5.34684697e+01 2.91208928e+01 13 -1.18600159e+01 -2.83648165e+01 -1.04235499e+02 14 2.28601053e+01 2.77946300e+01 -1.93440319e+01 15 9.32732726e+01 -1.11735626e+01 2.34486350e+01 16 1.16653292e+01 7.51083330e+01 3.38512865e+01 17 -3.19385870e+01 -1.59530857e+01 -1.13704358e+01 18 -1.56033243e+01 2.06822745e+01 1.51210037e+01 19 1.37727831e+01 -2.74771988e+01 2.14718701e+01 20 -1.53440770e+01 1.95513142e+01 1.81531058e+01 21 -2.37723572e+01 -3.36663722e+01 2.09866745e+01 22 5.16132315e+01 5.41366538e+01 5.07330749e+01 23 1.29102526e+01 -6.55046197e+00 2.06046363e+01 24 6.55047191e+00 1.64340353e+00 1.93059003e+01 25 -2.90097242e+01 -8.70069503e+00 2.03435139e+01 26 -1.83813472e+01 4.86611171e+01 -2.25013057e+01 27 2.31337963e+01 -7.56121915e+01 2.78188346e+01 28 -6.75495260e+01 5.54342156e+01 1.24512406e+01 29 -1.66720846e+01 -2.36065248e+01 1.75572273e+01 30 2.52710273e+01 3.73631864e+01 2.96040559e+00 31 4.05212258e+01 -2.28986827e+01 3.46780066e+01 32 2.17736187e+01 3.84659603e+01 4.13509047e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mg (Configuration in file "config-T-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 735.232183602 Forces: 1 4.62801385e+01 -3.07772767e+01 1.12154378e+01 2 -7.68788149e+01 2.62314242e+01 5.97735808e+01 3 -7.74261557e+00 1.69483782e+00 1.85315243e+00 4 3.42057612e+01 2.52631653e+01 -2.29449168e+00 5 5.44516919e+01 -5.51214545e+00 -7.27009292e-01 6 -5.72876642e+01 5.88657704e+01 1.80530728e+01 7 -1.01295485e+01 -6.57189762e+01 -6.38624934e+01 8 -2.29817173e+01 -2.43543203e+01 -1.11840152e+01 9 -4.58455845e+01 -7.14372239e+01 1.54906311e+01 10 -2.41105798e+01 1.19299506e+01 -2.77427598e+01 11 -9.08804911e+00 -3.73910675e+01 2.46434305e+01 12 2.57047159e+01 2.21603480e+01 6.75627724e+01 13 -9.36957237e+00 -3.31140995e+01 -8.19885814e+01 14 -5.49015820e+01 1.78560422e+01 -4.01639661e+01 15 7.15580538e+01 -1.05672939e+01 2.39401103e+01 16 1.72691071e+01 5.12257065e+01 3.66997345e+01 17 3.28879724e+01 -3.35073690e+01 -1.48469057e+01 18 -1.54343636e+01 2.09401217e+01 1.49824350e+01 19 1.38828190e+01 1.12048533e+01 1.22436039e+01 20 4.05713003e+01 6.24747968e+01 -2.03255798e+01 21 -2.55772261e+01 -7.86849185e+00 2.22528707e+01 22 -8.78651247e+00 8.43596362e+01 6.15960528e+01 23 -4.92320021e+01 -5.61511969e+01 -2.17197216e+01 24 6.43235790e+01 1.97772244e+01 -7.16160530e+01 25 -6.79819475e+00 -1.58598692e+01 2.00622834e+01 26 -1.46084119e+01 1.04742638e+01 -2.89440746e+01 27 5.34472252e+01 -7.89914910e+01 -3.45566729e+01 28 -6.62584329e+01 5.71562995e+01 -2.48840839e+01 29 -1.65480689e+01 -2.38588741e+01 1.77932758e+01 30 4.78116470e+00 1.21576793e+01 3.41598871e+00 31 3.02118797e+01 -2.63106233e+01 2.27829461e+01 32 3.20035324e+01 2.76481987e+01 1.04950295e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==9648== Memcheck, a memory error detector ==9648== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==9648== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==9648== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Mg__MO_894868634445_000 ==9648== ==9648== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==9648== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==9648== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9648== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9648== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9648== by 0x4010732: call_init (dl-init.c:72) ==9648== by 0x4010732: _dl_init (dl-init.c:119) ==9648== by 0x40151FE: dl_open_worker (dl-open.c:522) ==9648== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==9648== by 0x40147C9: _dl_open (dl-open.c:605) ==9648== by 0x544CF95: dlopen_doit (dlopen.c:66) ==9648== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==9648== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==9648== by 0x544D734: _dlerror_run (dlerror.c:162) ==9648== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==9648== ==9648== ==9648== HEAP SUMMARY: ==9648== in use at exit: 5,957,601 bytes in 3,961 blocks ==9648== total heap usage: 116,434 allocs, 112,473 frees, 59,579,335 bytes allocated ==9648== ==9648== LEAK SUMMARY: ==9648== definitely lost: 0 bytes in 0 blocks ==9648== indirectly lost: 0 bytes in 0 blocks ==9648== possibly lost: 182,191 bytes in 111 blocks ==9648== still reachable: 5,775,410 bytes in 3,850 blocks ==9648== suppressed: 0 bytes in 0 blocks ==9648== Rerun with --leak-check=full to see details of leaked memory ==9648== ==9648== For counts of detected and suppressed errors, rerun with: -v ==9648== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2510 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.