Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:15:40) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Pun_2017_Au__MO_188701096956_000 Supported species : Au random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Au (Configuration in file "config-F-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1686.37186199 Forces: 1 -1.86598595e+02 -5.23295250e+02 -7.10621585e+02 2 -4.05241008e-01 1.00730546e+02 -9.51827391e+01 3 3.26554613e+02 -2.89549919e+02 1.10585369e+02 4 -1.75924801e+02 7.62426383e+02 5.47601638e+02 5 3.61625214e+00 -1.10821533e+02 -7.15456655e+01 6 2.94677659e+01 1.98181848e+01 -5.49020661e+01 7 -6.83260393e+01 -6.90601152e+02 -7.05849412e+02 8 -2.45349003e+02 -2.53337694e+02 5.88185653e+01 9 -7.15317667e+00 -3.69519383e+01 -4.78115530e+01 10 -1.54695333e+02 7.62096552e+01 -1.90980493e+02 11 -2.20253721e+02 -2.35313245e+02 -5.52982945e+00 12 -6.06367890e+01 1.72307511e+02 -8.11056189e+01 13 -3.67507227e+02 -1.74820577e+02 -7.33585414e+02 14 1.01893747e+02 1.09708187e+02 -4.32983969e+01 15 6.94246167e+02 1.31187429e+02 4.26340088e+02 16 2.17074522e+02 4.73629505e+02 3.05174071e+02 17 -1.44468261e+02 -6.33634893e+01 6.78316222e+01 18 6.29023174e+00 2.37546419e+03 -2.23891754e+03 19 7.74466775e+01 -2.37262473e+03 2.25044839e+03 20 -6.22423068e+01 3.72958249e+01 4.31759047e+01 21 -2.04846693e+02 -1.34405911e+02 -1.28500184e+01 22 3.70336552e+02 7.10659522e+02 5.39157774e+02 23 3.20339709e+02 -1.63096504e+02 2.35972646e+02 24 -2.14979652e+02 1.63722904e+02 7.95228235e+01 25 -1.05844289e+02 -1.76889043e+02 1.55817807e+02 26 7.40095288e+00 1.87149471e+02 -1.21380446e+02 27 6.27028304e+02 -8.28085781e+02 1.52357520e+02 28 -8.07183703e+02 6.88496700e+02 4.00853059e+00 29 -3.26766171e+02 -3.30939052e+02 -4.53368338e+02 30 1.61824942e+02 1.98973628e+02 -5.96666001e+01 31 3.82193176e+02 -1.49263467e+02 3.02852299e+02 32 2.74673887e+01 3.25579645e+02 3.46930663e+02 MONOATOMIC STRUCTURE (pbc=True)-- Species = Au (Configuration in file "config-T-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 2400.05247919 Forces: 1 1.04141178e+02 -7.59177907e+02 -6.45490670e+02 2 -1.68928619e+01 1.02650296e+02 -6.93332836e+01 3 3.42512658e+02 -2.07743298e+02 1.35140878e+02 4 -4.99572952e+01 7.81748628e+02 5.59684543e+02 5 4.68771907e+01 4.07433639e+00 -8.42189522e+01 6 -3.15089548e+02 3.07154945e+02 6.00168760e+01 7 -1.52575837e+02 -6.81868517e+02 -7.30825358e+02 8 -2.45646467e+02 -2.53692277e+02 5.71260297e+01 9 -6.78066007e+01 -1.74596482e+02 1.70533659e+02 10 -2.08679941e+02 6.30790099e+00 -1.58152336e+02 11 -2.21687947e+02 -2.36096432e+02 -5.79299339e+00 12 -1.65794547e+01 1.10491109e+02 -6.30316177e+01 13 -3.64057472e+02 -1.90499191e+02 -7.01838312e+02 14 2.80269282e+01 1.33281267e+02 -6.67470546e+01 15 6.64730792e+02 1.14429696e+02 4.26725752e+02 16 2.15490564e+02 4.12286400e+02 3.32517842e+02 17 9.04470108e+01 -2.37746046e+02 1.06074299e+02 18 6.09842970e+00 2.37699383e+03 -2.23780532e+03 19 8.10125627e+01 -2.27473219e+03 2.29186740e+03 20 3.01953778e+02 2.57157566e+02 1.64794084e+01 21 -2.58765077e+02 -3.68886990e+01 -2.41837489e+00 22 1.53567921e+02 9.14451385e+02 5.53575594e+02 23 -2.30523102e+01 -4.17744825e+02 6.25649319e+01 24 -2.13969528e+02 1.67833484e+02 3.70677073e+01 25 -9.01607897e+01 -1.76359064e+02 1.59104357e+02 26 1.55963907e+01 9.38184291e+01 -1.66433088e+02 27 7.09693593e+02 -8.38276481e+02 3.72629832e+01 28 -7.89015880e+02 7.81601653e+02 -1.23225452e+02 29 -3.26589742e+02 -3.32439708e+02 -4.53146460e+02 30 1.85181801e+02 9.30150946e+01 -5.04167287e+01 31 3.68296578e+02 -1.60446384e+02 2.84056417e+02 32 4.68993760e+01 3.21011489e+02 2.69077318e+02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==6019== Memcheck, a memory error detector ==6019== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==6019== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==6019== Command: python runner2.py EAM_Dynamo_Pun_2017_Au__MO_188701096956_000 ==6019== ==6019== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==6019== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==6019== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6019== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6019== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6019== by 0x4010732: call_init (dl-init.c:72) ==6019== by 0x4010732: _dl_init (dl-init.c:119) ==6019== by 0x40151FE: dl_open_worker (dl-open.c:522) ==6019== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6019== by 0x40147C9: _dl_open (dl-open.c:605) ==6019== by 0x544CF95: dlopen_doit (dlopen.c:66) ==6019== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6019== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==6019== by 0x544D734: _dlerror_run (dlerror.c:162) ==6019== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==6019== ==6019== ==6019== HEAP SUMMARY: ==6019== in use at exit: 9,988,805 bytes in 3,961 blocks ==6019== total heap usage: 114,456 allocs, 110,495 frees, 63,907,721 bytes allocated ==6019== ==6019== LEAK SUMMARY: ==6019== definitely lost: 0 bytes in 0 blocks ==6019== indirectly lost: 0 bytes in 0 blocks ==6019== possibly lost: 182,191 bytes in 111 blocks ==6019== still reachable: 9,806,614 bytes in 3,850 blocks ==6019== suppressed: 0 bytes in 0 blocks ==6019== Rerun with --leak-check=full to see details of leaked memory ==6019== ==6019== For counts of detected and suppressed errors, rerun with: -v ==6019== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2505 from 173) ================================================================================ 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. === Verification check vc-memory-leak end (2018-12-15 06:16:07) ===