Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:19:32) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZopeMishin_2003_Al__MO_664470114311_005 Supported species : Al random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = -27.7618627325 Forces: 1 -1.95102485e+00 -2.10367614e+00 -2.58474938e+00 2 -9.11778305e-01 1.82615395e+00 -4.42878341e+00 3 1.04169289e+00 -3.85492454e+00 2.39685025e-01 4 -3.60410345e+00 1.62802809e+00 1.10020801e+00 5 1.72868324e+00 -4.65210113e+00 -1.70390202e+00 6 2.13735717e+00 1.19157729e+00 -2.86000879e+00 7 2.26438538e+00 -5.69590762e+00 -3.64019376e+00 8 -2.58157300e+00 -1.48317705e+00 -1.22254109e-01 9 -4.21016704e+00 -1.94649383e+00 -5.46388605e+00 10 -2.26193676e-01 6.80741526e+00 -5.76808686e+00 11 -3.06451581e+00 -5.34253948e+00 3.00956686e+00 12 -4.85335735e+00 3.99260640e+00 1.42215516e+00 13 4.35882543e+00 -2.36008288e+00 -7.88017455e+00 14 1.50620768e+00 1.36040053e+00 -1.61009906e+00 15 6.52350258e+00 -8.02393101e-01 -3.02882114e+00 16 1.97884683e+00 7.83158229e+00 3.54283466e+00 17 -4.87295734e+00 -2.79864212e+00 -1.16118702e+00 18 1.44411713e+00 3.10726771e+00 -1.65853585e+00 19 1.22118947e+00 -4.86536234e+00 3.53999910e+00 20 -3.06528731e+00 2.45759273e+00 3.08063355e+00 21 -2.16638609e+00 -4.59034522e+00 8.74777070e-01 22 6.04507757e+00 3.21536892e+00 2.88000471e+00 23 1.83071099e+00 -8.43758939e-01 2.77002775e+00 24 8.60009764e-01 1.72533832e+00 3.48156089e+00 25 -4.57703996e+00 -3.11642259e+00 -1.15142756e+00 26 1.43727943e+00 6.22311398e+00 -2.22180191e+00 27 1.75383447e+00 -5.59125170e+00 4.96582014e+00 28 -5.80198412e+00 4.12926352e+00 2.99282678e+00 29 -2.95782763e+00 -2.40906237e+00 2.65386174e+00 30 3.44719762e+00 5.43477872e+00 4.22421506e-01 31 3.79912700e+00 -2.53667889e+00 4.45851642e+00 32 1.46615128e+00 4.06233222e+00 3.84901211e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 107.224377973 Forces: 1 2.94896633e+00 -1.88875384e+00 1.28265152e+00 2 -3.17623831e+00 2.16461386e+00 2.65633916e+00 3 -1.46726510e-01 1.86789464e+00 5.60615873e-01 4 2.54146641e+00 2.84181448e+00 -4.66265630e-01 5 3.13396446e+00 -1.04876387e+00 5.45471753e-01 6 -3.30661187e+00 4.92807554e+00 7.44512562e-01 7 -2.46026538e+00 -4.08217177e+00 -3.51605709e+00 8 -2.44864371e+00 -1.77896344e+00 -2.89519297e-01 9 -4.27887038e+00 -4.01792577e+00 1.06823544e+00 10 -8.95340832e-01 2.95320394e+00 -1.98688907e+00 11 -3.51301471e+00 -4.94543305e+00 2.57455532e+00 12 -7.65734724e-01 9.25074821e-01 1.37741078e+00 13 5.05866780e+00 -2.71851063e+00 -3.94134828e+00 14 -2.40554174e+00 -1.05401791e-02 -1.25454109e+00 15 3.02917843e+00 -2.49955104e-01 -2.86354808e+00 16 2.59856607e+00 3.92262566e+00 3.68558581e+00 17 1.06572791e+00 -2.41886111e+00 -8.78840150e-01 18 1.41014095e+00 2.75298253e+00 -1.36571177e+00 19 5.29023165e-01 -3.85746845e-01 9.23216421e-01 20 2.50241282e+00 4.95983168e+00 -1.16153839e+00 21 -2.01244115e+00 -9.45059565e-01 1.77316670e+00 22 1.49964685e-01 4.80226167e+00 3.43443485e+00 23 -4.48652086e+00 -4.03049806e+00 -6.28231701e-01 24 3.71739846e+00 2.30912749e+00 -3.98893844e+00 25 -2.59514603e-01 -3.47402354e+00 -8.36160756e-01 26 1.95689801e+00 7.13337219e-01 -2.05532441e+00 27 2.47160786e+00 -5.55741699e+00 -1.58956445e+00 28 -4.87508139e+00 3.21760435e+00 -2.45176753e-01 29 -2.40802748e+00 -2.11503141e+00 2.83977452e+00 30 2.77634584e-01 1.91315014e+00 8.98772800e-01 31 1.26700165e+00 -2.54468529e+00 2.45588894e+00 32 2.77995405e+00 1.94074246e+00 2.47022906e-01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==11114== Memcheck, a memory error detector ==11114== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==11114== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==11114== Command: python runner2.py EAM_Dynamo_ZopeMishin_2003_Al__MO_664470114311_005 ==11114== ==11114== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==11114== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==11114== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11114== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11114== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11114== by 0x4010732: call_init (dl-init.c:72) ==11114== by 0x4010732: _dl_init (dl-init.c:119) ==11114== by 0x40151FE: dl_open_worker (dl-open.c:522) ==11114== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==11114== by 0x40147C9: _dl_open (dl-open.c:605) ==11114== by 0x544CF95: dlopen_doit (dlopen.c:66) ==11114== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==11114== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==11114== by 0x544D734: _dlerror_run (dlerror.c:162) ==11114== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==11114== ==11114== ==11114== HEAP SUMMARY: ==11114== in use at exit: 10,038,787 bytes in 3,961 blocks ==11114== total heap usage: 116,125 allocs, 112,164 frees, 64,097,443 bytes allocated ==11114== ==11114== LEAK SUMMARY: ==11114== definitely lost: 0 bytes in 0 blocks ==11114== indirectly lost: 0 bytes in 0 blocks ==11114== possibly lost: 182,191 bytes in 111 blocks ==11114== still reachable: 9,856,596 bytes in 3,850 blocks ==11114== suppressed: 0 bytes in 0 blocks ==11114== Rerun with --leak-check=full to see details of leaked memory ==11114== ==11114== For counts of detected and suppressed errors, rerun with: -v ==11114== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2505 from 170) ================================================================================ 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 06:20:01) ===