Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:12:22) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MendelevAckland_2007_Zr__MO_537826574817_000 Supported species : Zr random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Zr (Configuration in file "config-F-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 593.566456623 Forces: 1 -3.58473891e+01 -3.98030330e+01 -4.69479102e+01 2 -1.97717982e+01 2.38112923e+01 -6.05019582e+01 3 -6.26608585e+00 -5.57182159e+01 3.05685862e+01 4 -5.15663426e+01 1.39343138e+01 1.03987412e+01 5 3.59506388e+01 -6.40789813e+01 -3.93282814e+01 6 2.89523899e+01 6.55711695e+00 -4.03258075e+01 7 3.85531501e+01 -9.30627691e+01 -5.53867691e+01 8 -3.54494241e+01 -5.46742413e+01 -1.45603487e+01 9 -4.43489144e+01 -5.06385219e+00 -5.65586471e+01 10 -2.77256224e+01 8.05658719e+01 -6.96605845e+01 11 -3.61218556e+01 -3.25114342e+01 2.47380701e+00 12 -5.20161981e+01 6.83463792e+01 -1.92032142e+01 13 1.65951591e+01 -2.80728507e+01 -1.30497785e+02 14 3.50894920e+01 3.86095803e+01 -3.13290832e+01 15 1.24988127e+02 -4.79775668e+00 -2.02645175e+01 16 2.29973605e+01 1.16372755e+02 2.86044788e+01 17 -6.48154716e+01 -4.70793605e+01 -2.49782246e+01 18 2.82993050e+01 1.46617692e+01 4.07854398e+00 19 2.43903748e+01 -5.65609041e+01 4.53343292e+01 20 -3.86389313e+01 2.97763316e+01 4.95113560e+01 21 -3.77869522e+01 -6.37631823e+01 1.48029101e+01 22 8.70258550e+01 4.54134860e+01 5.28745617e+01 23 4.19185048e+01 -2.48413128e+01 3.67676667e+01 24 -1.43813010e+01 2.33038385e+01 4.20429551e+01 25 -7.03261047e+01 -2.79437614e+01 3.62985902e+01 26 -1.14397701e+01 8.14027780e+01 -8.41919707e+00 27 2.07059341e+01 -8.09470261e+01 5.77677860e+01 28 -7.74837632e+01 6.39246281e+01 3.16638750e+01 29 -2.58366910e+01 -1.97877123e+01 3.30689845e+01 30 5.39683719e+01 6.52570312e+01 2.58943798e+00 31 6.56799752e+01 -2.73450041e+01 7.61843379e+01 32 2.47079771e+01 5.41142262e+01 6.29313808e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zr (Configuration in file "config-T-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 2431.31014731 Forces: 1 7.50198685e+01 -5.84389565e+01 1.21751472e+01 2 -3.08854400e+01 5.70680678e+01 5.71301512e+00 3 -8.69031626e-01 4.24753620e+01 5.93742920e+01 4 4.27988001e+01 4.98525325e+01 6.95672459e+00 5 5.96658453e+01 5.01079534e+00 -1.18293630e+01 6 -9.01074993e+01 1.08144338e+02 5.59739076e+01 7 -2.87407229e+01 -6.64483182e+01 -4.98006300e+01 8 -6.44701651e+01 -4.27631567e+01 2.79928530e+00 9 -6.08371102e+01 -6.42008538e+01 3.26684215e+01 10 -3.78909341e+01 1.01549715e+01 -3.29638806e+01 11 -2.21198973e+01 -6.19715219e+01 2.34534834e+01 12 -3.07242146e+00 2.09218423e+01 -1.63680552e+01 13 1.98386278e+01 -6.66774699e+01 -9.75293814e+01 14 -2.43045915e+01 -1.12494507e+00 -3.39141157e+01 15 7.92323154e+01 -1.55498444e+01 -1.72948566e+01 16 3.30353262e+01 5.75226031e+01 5.56292497e+01 17 2.63584676e+01 -3.73031914e+01 -3.06143735e+01 18 6.15544365e+01 4.08411596e+01 -6.28573229e+00 19 4.26750735e+01 1.50965014e+01 1.27329528e+01 20 4.48236579e+01 1.16283692e+02 -8.24100326e+00 21 -5.63536057e+01 4.34066080e+00 1.69337274e+01 22 1.03748115e+00 1.05862995e+02 6.18771232e+01 23 -5.93919091e+01 -8.95519067e+01 -6.88924773e+01 24 -1.89286647e+00 5.87172900e+01 -5.48477538e+01 25 -2.22370723e+01 -6.46642551e+01 3.86238983e+01 26 2.63532955e+00 1.35648475e+01 -2.79073763e+01 27 6.22211651e+01 -1.17371573e+02 -3.92959146e+01 28 -8.07216152e+01 4.07906512e+01 -1.19997673e+01 29 -4.74400970e+01 -4.52927523e+01 3.25512031e+01 30 -1.09416367e+01 1.20762084e+01 2.56610758e+01 31 3.92685536e+01 -5.07825767e+01 5.97380469e+01 32 5.21116675e+01 2.34168031e+01 4.92312693e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2098== Memcheck, a memory error detector ==2098== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2098== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==2098== Command: python runner2.py EAM_Dynamo_MendelevAckland_2007_Zr__MO_537826574817_000 ==2098== ==2098== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==2098== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==2098== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2098== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2098== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2098== by 0x4010732: call_init (dl-init.c:72) ==2098== by 0x4010732: _dl_init (dl-init.c:119) ==2098== by 0x40151FE: dl_open_worker (dl-open.c:522) ==2098== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2098== by 0x40147C9: _dl_open (dl-open.c:605) ==2098== by 0x544CF95: dlopen_doit (dlopen.c:66) ==2098== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2098== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==2098== by 0x544D734: _dlerror_run (dlerror.c:162) ==2098== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==2098== ==2098== ==2098== HEAP SUMMARY: ==2098== in use at exit: 10,115,857 bytes in 3,961 blocks ==2098== total heap usage: 118,702 allocs, 114,741 frees, 64,317,363 bytes allocated ==2098== ==2098== LEAK SUMMARY: ==2098== definitely lost: 0 bytes in 0 blocks ==2098== indirectly lost: 0 bytes in 0 blocks ==2098== possibly lost: 182,191 bytes in 111 blocks ==2098== still reachable: 9,933,666 bytes in 3,850 blocks ==2098== suppressed: 0 bytes in 0 blocks ==2098== Rerun with --leak-check=full to see details of leaked memory ==2098== ==2098== For counts of detected and suppressed errors, rerun with: -v ==2098== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2503 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 06:12:53) ===