Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:17:55) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouJohnsonWadley_2004_Ta__MO_130046220009_005 Supported species : Ta random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ta (Configuration in file "config-F-Ta.xyz") ----------------------------------------------------------------------------------------------------- Energy = 12.2620905001 Forces: 1 -6.40193922e+00 -1.26364508e+01 -1.31357225e+01 2 -1.37975597e+01 2.24813273e+01 -1.64867930e+01 3 -2.50308101e+00 -2.04884028e+01 -2.38629493e+00 4 -1.13218710e+01 5.17063881e+00 6.13453791e+00 5 2.02461779e+01 -2.93281157e+01 -7.05461938e+00 6 6.69863349e+00 1.29019896e+00 -1.24302468e+01 7 1.38251813e+01 -4.59551666e+01 -4.01204929e+01 8 -2.98177019e+01 -2.99757617e+01 -1.16161616e+01 9 -1.32745118e+01 -2.03917296e+01 -3.23645958e+01 10 -3.70321727e+00 2.83400209e+01 -3.20002617e+01 11 -5.76428780e+00 -2.00837894e+01 1.74531807e+00 12 -2.17010112e+01 2.96722593e+01 1.42563245e+01 13 -5.99214085e+00 -1.46523506e+01 -5.94044249e+01 14 1.11536646e+01 1.07468814e+01 -5.64109167e+00 15 6.75303401e+01 1.73519587e+01 5.45755665e+00 16 1.57507752e+01 4.58531119e+01 1.87585753e+01 17 -1.76795902e+01 -8.55613913e+00 -6.10466364e+00 18 -1.38458611e+01 1.06848326e+01 1.30815886e+01 19 7.77359805e+00 -1.50915268e+01 1.25753227e+01 20 -7.70031007e+00 1.10619320e+01 8.78332581e+00 21 -1.43548284e+01 -2.13652619e+01 1.41027412e+01 22 3.36212554e+01 2.92310331e+01 3.57150941e+01 23 5.61431464e+00 -2.84150202e+00 1.04627877e+01 24 4.02942295e+00 7.35553185e-01 1.11684516e+01 25 -2.32797856e+01 -6.56958135e+00 1.75682305e+01 26 -1.18150608e+01 3.16513381e+01 -1.23778165e+01 27 1.16597947e+01 -4.54103913e+01 1.79170126e+01 28 -3.75611995e+01 3.10579055e+01 6.49375668e+00 29 -7.80230738e+00 -9.37734852e+00 1.54264997e+01 30 1.31918789e+01 1.79046985e+01 -3.70363277e+00 31 2.40920919e+01 -1.43750546e+01 2.05190031e+01 32 1.31291354e+01 2.38648827e+01 2.46606913e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ta (Configuration in file "config-T-Ta.xyz") ----------------------------------------------------------------------------------------------------- Energy = 211.934357073 Forces: 1 2.92588268e+01 -2.00909518e+01 6.70046959e+00 2 -4.60915819e+01 1.96283685e+01 3.69232048e+01 3 -4.56277109e+00 2.37598034e+00 1.16496899e+00 4 2.76546840e+01 1.20701277e+01 -1.93589165e+00 5 3.55454305e+01 -2.68421693e+00 -1.21745995e+00 6 -3.55586497e+01 3.64099908e+01 8.97733219e+00 7 -5.24286868e+00 -4.38401917e+01 -4.09067368e+01 8 -3.17332688e+01 -2.97741021e+01 -1.05927754e+01 9 -2.65955497e+01 -4.27445701e+01 1.38493853e+01 10 -1.65352541e+01 4.01871737e+00 -1.56637762e+01 11 -5.16327312e+00 -2.12967781e+01 3.20277079e+00 12 9.70496234e+00 1.22713394e+01 3.81156306e+01 13 -4.85809582e+00 -1.90756812e+01 -4.51411737e+01 14 -3.04046741e+01 6.28270155e+00 -1.96291530e+01 15 5.10080961e+01 2.18210910e+01 5.76881080e+00 16 1.93765897e+01 3.04803300e+01 2.20343012e+01 17 2.12400225e+01 -2.08434468e+01 -9.80183318e+00 18 -1.29346504e+01 1.21936684e+01 1.22766522e+01 19 8.69010477e+00 6.95476196e+00 8.08071656e+00 20 2.47956317e+01 3.98001670e+01 -1.34844496e+01 21 -1.62413808e+01 -5.33905800e+00 1.49713628e+01 22 -3.81199391e+00 5.03372769e+01 4.36839772e+01 23 -3.21244074e+01 -3.52201046e+01 -1.23382636e+01 24 3.89216427e+01 1.13645766e+01 -4.21794311e+01 25 -9.77071384e+00 -1.12918126e+01 1.79348237e+01 26 -9.41449863e+00 7.66078107e+00 -1.78765581e+01 27 3.16174226e+01 -5.03622917e+01 -2.08853851e+01 28 -4.07184793e+01 3.46671454e+01 -1.50110390e+01 29 -8.41302297e+00 -1.06037222e+01 1.49435978e+01 30 1.89179393e+00 3.33573699e+00 -2.52225026e+00 31 1.90246536e+01 -1.74870846e+01 1.43600262e+01 32 2.14452732e+01 1.89812515e+01 6.19814569e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==8830== Memcheck, a memory error detector ==8830== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==8830== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==8830== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004_Ta__MO_130046220009_005 ==8830== ==8830== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==8830== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==8830== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==8830== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==8830== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==8830== by 0x4010732: call_init (dl-init.c:72) ==8830== by 0x4010732: _dl_init (dl-init.c:119) ==8830== by 0x40151FE: dl_open_worker (dl-open.c:522) ==8830== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==8830== by 0x40147C9: _dl_open (dl-open.c:605) ==8830== by 0x544CF95: dlopen_doit (dlopen.c:66) ==8830== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==8830== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==8830== by 0x544D734: _dlerror_run (dlerror.c:162) ==8830== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==8830== ==8830== ==8830== HEAP SUMMARY: ==8830== in use at exit: 5,884,646 bytes in 3,968 blocks ==8830== total heap usage: 115,282 allocs, 111,314 frees, 61,557,837 bytes allocated ==8830== ==8830== LEAK SUMMARY: ==8830== definitely lost: 0 bytes in 0 blocks ==8830== indirectly lost: 0 bytes in 0 blocks ==8830== possibly lost: 182,751 bytes in 112 blocks ==8830== still reachable: 5,701,895 bytes in 3,856 blocks ==8830== suppressed: 0 bytes in 0 blocks ==8830== Rerun with --leak-check=full to see details of leaked memory ==8830== ==8830== For counts of detected and suppressed errors, rerun with: -v ==8830== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2519 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. === Verification check vc-memory-leak end (2018-12-15 06:18:20) ===