!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Ni__MO_110256178378_005 Supported species : Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -25.9142218284 Forces: 1 -3.48819532e+00 -5.94129948e+00 -6.28130315e+00 2 -8.26504674e+00 1.40156583e+01 -6.47974419e+00 3 4.69811750e+00 -5.12668803e+00 1.73345004e-02 4 -5.02689594e+00 4.93042459e+00 4.61644250e+00 5 9.48620752e+00 -1.62757593e+01 -5.92153880e-01 6 4.37036015e+00 7.55060808e-01 -5.97327594e+00 7 3.11438209e+00 -2.28370250e+01 -2.30726206e+01 8 -1.21773300e+01 -1.06572884e+01 5.10364996e+00 9 -5.22769332e+00 -6.33042411e+00 -1.03557267e+01 10 -4.36063915e+00 1.16926432e+01 -1.39452383e+01 11 -4.12856253e+00 -8.93906853e+00 4.12002784e+00 12 -5.95482455e+00 7.89676059e+00 4.59649607e+00 13 -8.90676340e+00 -7.29914083e+00 -3.42032081e+01 14 5.00381235e+00 6.88617853e+00 -4.18640808e+00 15 2.94036512e+01 -5.22968598e+00 9.57773451e+00 16 4.48543166e+00 2.31373616e+01 1.14408917e+01 17 -1.11507698e+01 -5.72405186e+00 -4.36442903e+00 18 6.53517446e+00 1.10657394e+01 -7.80397188e+00 19 6.36298877e+00 -1.11596878e+01 9.41107605e+00 20 -5.92679904e+00 6.08714636e+00 7.21975319e+00 21 -1.34280343e+01 -6.06740623e+00 1.93710570e+00 22 1.36076611e+01 2.02086260e+01 1.78283548e+01 23 5.13263248e+00 -4.82923265e-01 8.17014101e+00 24 -2.62515331e-02 -2.55231753e+00 3.55927730e+00 25 -9.95249888e+00 -6.53140782e+00 -3.13865102e+00 26 -4.26071378e+00 1.48450372e+01 -7.89420883e+00 27 1.22742811e+01 -2.62828602e+01 1.06027812e+01 28 -2.22736141e+01 2.06373861e+01 5.16922914e+00 29 -5.74848656e+00 -1.06543403e+01 3.40072399e+00 30 5.71139845e+00 1.01656201e+01 2.97743910e+00 31 1.32035059e+01 -5.23109845e+00 7.59783883e+00 32 6.91351425e+00 1.09988303e+01 1.09446425e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -16.263440435 Forces: 1 5.90742495e+00 -8.98991074e+00 -1.39595975e-01 2 -2.04149210e+01 9.33424764e+00 1.11844654e+01 3 4.20491829e+00 3.82980548e+00 1.25439785e+00 4 8.24417090e-01 6.43412048e+00 1.46349378e+00 5 1.64800473e+01 -4.13269167e+00 8.59568625e-01 6 -3.20649481e+00 1.33224927e+01 7.53655843e+00 7 -1.55983932e+00 -2.03739898e+01 -2.46513511e+01 8 -1.16183206e+01 -1.10047628e+01 4.69932177e+00 9 -1.45214921e+01 -1.74220695e+01 1.52727090e+01 10 -1.20340713e+01 9.63525115e-01 -6.59632298e+00 11 -4.67482949e+00 -8.44805447e+00 3.53670363e+00 12 5.97099639e+00 2.27324844e+00 8.93315081e+00 13 -7.87442324e+00 -7.62243805e+00 -2.87644980e+01 14 -8.20863127e+00 5.46400434e+00 -1.00103898e+01 15 2.66706450e+01 -6.28551045e+00 9.43748053e+00 16 6.00045978e+00 1.92765209e+01 1.15623737e+01 17 6.01459338e+00 -1.42145221e+01 -1.09079829e+00 18 6.23269045e+00 1.05514148e+01 -7.42531338e+00 19 5.71938429e+00 -1.25362368e+00 8.79416467e+00 20 2.97868837e+00 1.32417417e+01 -1.12181033e+00 21 -1.35896459e+01 -1.21352957e+00 2.52062057e+00 22 -1.78497716e+00 3.14641860e+01 1.66287550e+01 23 -2.97424622e+00 -1.28403238e+01 -2.51992001e+00 24 1.10635399e+01 3.74386457e+00 -1.51447877e+01 25 -5.71144257e+00 -8.26539093e+00 -2.60986711e+00 26 -3.48519066e+00 5.43707490e+00 -9.89780217e+00 27 2.29379818e+01 -2.66895897e+01 -7.82273814e+00 28 -2.50673197e+01 2.49792797e+01 -5.31242180e+00 29 -5.29350868e+00 -1.00961942e+01 3.81264599e+00 30 -9.83910400e-01 5.08889616e+00 5.80071455e+00 31 1.17566547e+01 -5.55974406e+00 6.49099976e+00 32 1.02408228e+01 9.00792248e+00 3.31949263e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==8651== Memcheck, a memory error detector ==8651== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==8651== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==8651== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004_Ni__MO_110256178378_005 ==8651== ==8651== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==8651== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==8651== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==8651== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==8651== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==8651== by 0x4010732: call_init (dl-init.c:72) ==8651== by 0x4010732: _dl_init (dl-init.c:119) ==8651== by 0x40151FE: dl_open_worker (dl-open.c:522) ==8651== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==8651== by 0x40147C9: _dl_open (dl-open.c:605) ==8651== by 0x544CF95: dlopen_doit (dlopen.c:66) ==8651== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==8651== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==8651== by 0x544D734: _dlerror_run (dlerror.c:162) ==8651== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==8651== ==8651== ==8651== HEAP SUMMARY: ==8651== in use at exit: 5,877,421 bytes in 3,961 blocks ==8651== total heap usage: 114,082 allocs, 110,121 frees, 59,273,017 bytes allocated ==8651== ==8651== LEAK SUMMARY: ==8651== definitely lost: 0 bytes in 0 blocks ==8651== indirectly lost: 0 bytes in 0 blocks ==8651== possibly lost: 182,191 bytes in 111 blocks ==8651== still reachable: 5,695,230 bytes in 3,850 blocks ==8651== suppressed: 0 bytes in 0 blocks ==8651== Rerun with --leak-check=full to see details of leaked memory ==8651== ==8651== For counts of detected and suppressed errors, rerun with: -v ==8651== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2508 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.