!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EDIP_JustoBazantKaxiras_1998_Si__MO_958932894036_002 Supported species : Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 116.623182258 Forces: 1 8.49108234e-02 4.75334141e-01 9.62950201e-01 2 -5.77099396e+00 8.14177978e-01 -1.24050300e+01 3 5.71830505e-01 -1.57169189e+01 -6.32666593e+00 4 -1.47359106e+01 -4.48036177e+00 9.03752107e-01 5 -5.99405936e+00 -9.39262467e+00 -1.30717538e+01 6 1.76640260e+01 -1.96093421e+00 -2.01752108e+01 7 6.29911452e+00 -2.24097181e+01 -1.95489295e-01 8 -3.32287739e+00 -3.57388111e+00 -6.68640865e+00 9 -1.65437251e+01 -8.85539660e+00 -1.82999198e+01 10 9.21929393e+00 1.27556434e+01 -1.16526709e+01 11 -1.52276966e+01 -4.10097213e+00 -1.12745930e+00 12 -2.25139924e+01 1.73647603e+01 -4.51460361e+00 13 1.05346487e+01 -5.34856313e+00 -2.06688932e+01 14 -1.47629556e+00 7.97568638e+00 -4.89224449e+00 15 2.82361538e+01 8.69912158e+00 -8.33783856e+00 16 7.31240928e+00 2.22644244e+01 5.15601540e+00 17 -1.15846736e+01 -8.31558210e+00 -8.18814523e+00 18 -1.96715331e+00 1.52098034e+00 2.32963290e-01 19 9.89842501e-01 -9.76509773e+00 1.39553697e+01 20 -1.55387737e+01 2.89688307e+00 8.19064754e+00 21 3.32973046e-01 -1.32621587e+01 6.98795569e+00 22 2.09945856e+01 4.18926556e+00 5.37058201e+00 23 4.27269686e+00 1.43916679e-01 4.12385855e+00 24 3.72408749e+00 -6.44816631e+00 3.10136347e+01 25 -2.76542935e+01 1.37227098e-01 4.14067912e+00 26 -3.96142344e+00 1.80237305e+01 -1.84622120e+00 27 -2.99551610e+00 -1.03292195e+01 1.54023830e+01 28 -1.17496633e+01 8.46214526e+00 6.91349747e+00 29 1.65996015e+01 -1.82617412e+00 7.54408015e+00 30 1.52730368e+01 1.07021437e+01 -1.46479999e+00 31 1.33404647e+01 -7.79464927e+00 1.66563791e+01 32 5.58737190e+00 1.71549779e+01 1.22986066e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 703.509458526 Forces: 1 -5.70492641e+00 -2.32849765e+01 -1.84360507e+01 2 -1.86364751e+01 2.63881658e+01 1.64115392e+01 3 2.46403157e+01 1.21847319e+01 -2.34904843e+01 4 1.31416403e+01 -1.88659895e+01 5.87143690e-01 5 3.72332313e+00 1.74120687e+01 -2.15918050e+01 6 2.57024122e+01 -1.54709565e+01 -3.26064711e+01 7 -2.20259555e+01 -2.26361159e+01 -1.83305957e+01 8 -2.27433736e+01 6.67637052e-01 2.15415300e+00 9 -1.68761313e+01 1.85390143e+01 -2.07324152e+01 10 -1.58309141e+01 -2.02818132e+01 1.65879175e+01 11 -1.10611821e+01 -2.86445052e+01 1.05064254e+01 12 -3.60524520e+01 2.26680610e+01 -2.00449444e+01 13 2.69106121e+01 -1.69618389e+01 -4.16128353e+00 14 1.72191904e+01 -1.96392019e+00 -1.30208340e+01 15 1.46514030e+01 2.77585850e+01 -1.55798016e+01 16 2.12534014e+01 1.02660191e+01 3.02071793e+01 17 2.22377073e+01 1.58041906e+01 2.38977730e+01 18 -6.04939049e+00 2.34981972e+01 -2.43901120e+01 19 2.78217045e+01 2.73650381e+00 1.10867268e+01 20 -2.34157280e+01 2.54938845e+01 -4.34110797e+00 21 -2.30014727e+01 2.47373869e+01 2.73820901e+01 22 -8.16294691e+00 3.55765172e+01 2.42618586e+01 23 -1.90135683e+01 -1.70121357e+01 1.98266949e+01 24 1.59402101e+01 -1.29912384e+01 2.51619410e+01 25 -1.54322806e+01 -2.12489469e+01 1.17737527e+01 26 -3.13666224e+00 -2.09942148e+01 7.91810582e+00 27 -1.93354431e-01 -4.42835161e+00 -1.34285586e+01 28 -1.35073405e+01 -2.36724411e+01 -2.51314564e+00 29 2.10030321e+01 -2.63223470e+01 5.67723221e+00 30 1.87298825e+01 -2.13599728e+01 7.73725955e+00 31 -2.05071283e+00 2.21936686e+01 1.35698008e+01 32 9.92003223e+00 1.02151323e+01 -2.20799838e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==12942== Memcheck, a memory error detector ==12942== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==12942== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==12942== Command: python runner2.py EDIP_JustoBazantKaxiras_1998_Si__MO_958932894036_002 ==12942== ==12942== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==12942== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==12942== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==12942== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==12942== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==12942== by 0x4010732: call_init (dl-init.c:72) ==12942== by 0x4010732: _dl_init (dl-init.c:119) ==12942== by 0x40151FE: dl_open_worker (dl-open.c:522) ==12942== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==12942== by 0x40147C9: _dl_open (dl-open.c:605) ==12942== by 0x544CF95: dlopen_doit (dlopen.c:66) ==12942== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==12942== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==12942== by 0x544D734: _dlerror_run (dlerror.c:162) ==12942== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==12942== ==12942== ==12942== HEAP SUMMARY: ==12942== in use at exit: 4,421,559 bytes in 3,926 blocks ==12942== total heap usage: 112,126 allocs, 108,200 frees, 57,616,880 bytes allocated ==12942== ==12942== LEAK SUMMARY: ==12942== definitely lost: 0 bytes in 0 blocks ==12942== indirectly lost: 0 bytes in 0 blocks ==12942== possibly lost: 182,191 bytes in 111 blocks ==12942== still reachable: 4,239,368 bytes in 3,815 blocks ==12942== suppressed: 0 bytes in 0 blocks ==12942== Rerun with --leak-check=full to see details of leaked memory ==12942== ==12942== For counts of detected and suppressed errors, rerun with: -v ==12942== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2509 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.