Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:07:37) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_AdamsFoilesWolfer_1989Universal6_Pd__MO_169076431435_000 Supported species : Pd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Pd (Configuration in file "config-F-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 141.98386501 Forces: 1 -1.22094714e+01 -2.45038094e+01 -2.82604412e+01 2 -8.23368770e+00 1.46658582e+01 -2.14622516e+01 3 1.29210808e+01 -2.15952007e+01 -9.33882087e-02 4 -1.82026304e+01 2.25492063e+01 1.42702172e+01 5 1.52280739e+01 -2.83561179e+01 -5.15447127e+00 6 9.19502563e+00 -4.75402506e+00 -1.33357380e+01 7 1.45549826e+01 -4.70117767e+01 -4.27938916e+01 8 -3.23448042e+01 -2.88995539e+01 -2.59801741e+00 9 -2.00565770e+01 -9.71729072e+00 -3.17450668e+01 10 -6.93640368e+00 3.61833092e+01 -3.54890308e+01 11 -1.56480035e+01 -2.45864306e+01 1.71884880e+01 12 -2.04036947e+01 2.16912285e+01 9.65076972e+00 13 -4.14237685e+00 -1.22331180e+01 -7.01214571e+01 14 1.28377370e+01 1.38569363e+01 -8.53630139e+00 15 7.02689470e+01 1.07704832e+01 1.43464580e+01 16 1.29809172e+01 5.36713857e+01 2.07714707e+01 17 -3.33525990e+01 -1.87265968e+01 -4.50625478e+00 18 1.34362808e+01 1.77014717e+01 -7.48345912e+00 19 1.08108842e+01 -2.58604391e+01 1.84275071e+01 20 -1.55331609e+01 1.18412238e+01 1.82185132e+01 21 -1.76665901e+01 -2.06793892e+01 1.37655755e+01 22 3.78359092e+01 2.89382230e+01 3.10665810e+01 23 6.31189870e+00 -3.95515514e+00 1.38800092e+01 24 8.03446026e+00 4.80602430e+00 1.28050757e+01 25 -2.42021568e+01 -8.12656644e+00 -4.05649737e+00 26 -1.03362340e+01 3.65968499e+01 -1.32695758e+01 27 1.25757521e+01 -4.23892506e+01 2.64767815e+01 28 -3.97429697e+01 3.39256261e+01 1.26638108e+01 29 -1.14159475e+01 -1.51031077e+01 1.72842616e+01 30 1.73715473e+01 2.54433243e+01 -9.07483118e+00 31 2.32279238e+01 -2.08875579e+01 2.80978312e+01 32 1.28358868e+01 2.47442353e+01 2.90673231e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pd (Configuration in file "config-T-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 440.62701785 Forces: 1 1.18844937e+01 -3.36078444e+01 -1.26283592e+01 2 -6.47899342e+01 2.54737776e+01 7.71790629e+01 3 2.19212878e+01 6.82077093e+00 8.10275258e+00 4 2.59911532e+01 3.53884729e+01 2.96712719e+01 5 3.71402301e+01 -5.05853695e+00 7.88415496e+00 6 -3.75126489e+01 2.75864186e+01 3.53594205e+00 7 -8.29249489e+00 -4.68844125e+01 -4.41016564e+01 8 -3.61931624e+01 -2.77428709e+01 -6.07322871e-01 9 -3.26827269e+01 -3.73373236e+01 1.80276390e+01 10 -1.79186915e+01 9.48634735e+00 -1.63204179e+01 11 -1.27760009e+01 -2.78638794e+01 2.30116901e+01 12 -9.88661161e-02 -1.45203950e+00 3.30340395e+01 13 -6.06468931e+00 -1.98722766e+01 -5.37428932e+01 14 -2.42321690e+01 1.21154810e+01 -2.14489739e+01 15 5.56595954e+01 1.01965434e+01 1.96186567e+01 16 1.52203063e+01 3.78940875e+01 2.71616211e+01 17 5.43551318e+00 -3.34461876e+01 -1.23167841e+01 18 2.00743745e+01 2.24926832e+01 -1.14263210e+01 19 1.71883637e+01 -2.86062108e+00 1.19797962e+01 20 4.87826319e+01 5.77634524e+01 -5.50354710e+00 21 -2.38191327e+01 -2.17076649e+00 1.24559583e+01 22 7.91243753e-01 5.90898594e+01 2.88503976e+01 23 -6.43961594e+01 -5.20549688e+01 -6.41680481e+00 24 6.65827097e+01 1.49397940e+01 -8.77113073e+01 25 -8.82814332e+00 -1.51373595e+01 -6.47195782e+00 26 -6.35383188e+00 1.26027628e+01 -2.28950028e+01 27 3.98417148e+01 -5.45199301e+01 -1.94925018e+01 28 -4.56193614e+01 3.98723935e+01 -8.14718494e+00 29 -1.32728237e+01 -1.74928127e+01 1.52833445e+01 30 1.51890686e-01 1.34438037e+01 -1.50894888e+01 31 1.41569702e+01 -2.78081291e+01 2.09131639e+01 32 2.20283579e+01 2.01433110e+01 7.61103268e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==29500== Memcheck, a memory error detector ==29500== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==29500== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==29500== Command: python runner2.py EAM_Dynamo_AdamsFoilesWolfer_1989Universal6_Pd__MO_169076431435_000 ==29500== ==29500== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==29500== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==29500== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==29500== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==29500== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==29500== by 0x4010732: call_init (dl-init.c:72) ==29500== by 0x4010732: _dl_init (dl-init.c:119) ==29500== by 0x40151FE: dl_open_worker (dl-open.c:522) ==29500== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==29500== by 0x40147C9: _dl_open (dl-open.c:605) ==29500== by 0x544CF95: dlopen_doit (dlopen.c:66) ==29500== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==29500== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==29500== by 0x544D734: _dlerror_run (dlerror.c:162) ==29500== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==29500== ==29500== ==29500== HEAP SUMMARY: ==29500== in use at exit: 5,106,433 bytes in 3,962 blocks ==29500== total heap usage: 114,195 allocs, 110,233 frees, 58,437,102 bytes allocated ==29500== ==29500== LEAK SUMMARY: ==29500== definitely lost: 0 bytes in 0 blocks ==29500== indirectly lost: 0 bytes in 0 blocks ==29500== possibly lost: 182,191 bytes in 111 blocks ==29500== still reachable: 4,924,242 bytes in 3,851 blocks ==29500== suppressed: 0 bytes in 0 blocks ==29500== Rerun with --leak-check=full to see details of leaked memory ==29500== ==29500== For counts of detected and suppressed errors, rerun with: -v ==29500== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2504 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. === Verification check vc-memory-leak end (2018-12-15 06:08:07) ===