Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:18:15) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouWadleyJohnson_2001NISTretabulation_Ag__MO_505250810900_000 Supported species : Ag random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ag (Configuration in file "config-F-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 225.069373819 Forces: 1 -8.79972746e+00 -1.63190337e+01 -1.68902641e+01 2 -1.59165232e+01 2.44729576e+01 -2.21040707e+01 3 -2.22503404e+00 -2.37162948e+01 -2.55003975e+00 4 -1.36746791e+01 7.69179448e+00 8.04860116e+00 5 2.31020914e+01 -3.65502560e+01 -8.15602079e+00 6 8.97117565e+00 2.00794928e+00 -1.41619436e+01 7 1.32736150e+01 -5.14552019e+01 -4.55278667e+01 8 -1.51044312e+01 -1.79064924e+01 -8.53497653e+00 9 -1.88298417e+01 -2.66744376e+01 -4.50907039e+01 10 -2.28379021e+00 3.83966331e+01 -3.90079660e+01 11 -7.01684096e+00 -2.64150115e+01 1.61634230e+01 12 -2.81983654e+01 3.74377746e+01 2.04712818e+01 13 -7.86688298e+00 -2.00218182e+01 -7.46907422e+01 14 1.57656604e+01 1.92573000e+01 -1.32726313e+01 15 6.69935371e+01 -7.68823014e+00 1.63025334e+01 16 8.40268528e+00 5.41575373e+01 2.38858341e+01 17 -2.20996828e+01 -1.08166464e+01 -7.87505218e+00 18 -1.15078785e+01 1.43928080e+01 1.10855800e+01 19 9.52626797e+00 -1.88957633e+01 1.48690670e+01 20 -1.02111320e+01 1.36333925e+01 1.21807016e+01 21 -1.66908859e+01 -2.38599994e+01 1.52396037e+01 22 3.65355512e+01 3.79642023e+01 3.61049616e+01 23 8.48180150e+00 -4.16141430e+00 1.38368824e+01 24 4.68783129e+00 1.02780755e+00 1.34461667e+01 25 -2.07773551e+01 -6.21457076e+00 1.45740877e+01 26 -1.32897436e+01 3.47670298e+01 -1.56717784e+01 27 1.57695744e+01 -5.32523657e+01 1.98205622e+01 28 -4.69866786e+01 3.84827245e+01 8.50992857e+00 29 -1.16726519e+01 -1.68158591e+01 1.32145532e+01 30 1.76960877e+01 2.62116018e+01 2.15130803e+00 31 2.85051962e+01 -1.62021890e+01 2.44048366e+01 32 1.54410496e+01 2.70640714e+01 2.92241433e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ag (Configuration in file "config-T-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 448.233946516 Forces: 1 3.31516078e+01 -2.18094506e+01 8.09106962e+00 2 -5.43825151e+01 1.87211695e+01 4.21886639e+01 3 -5.55658362e+00 1.52546952e+00 1.55138998e+00 4 2.47661867e+01 1.82295824e+01 -1.54632898e+00 5 3.89915459e+01 -3.70778529e+00 -6.98678215e-01 6 -4.10729219e+01 4.21795909e+01 1.25525183e+01 7 -7.30623934e+00 -4.69937702e+01 -4.54506112e+01 8 -1.66572766e+01 -1.76569076e+01 -7.94467999e+00 9 -3.31022819e+01 -5.14314880e+01 1.08153098e+01 10 -1.70951093e+01 8.91379668e+00 -1.98523177e+01 11 -6.73777578e+00 -2.71685985e+01 1.79143689e+01 12 1.79643867e+01 1.58868615e+01 4.83941736e+01 13 -6.24889789e+00 -2.39468270e+01 -5.88674869e+01 14 -3.91789804e+01 1.28311676e+01 -2.87901748e+01 15 5.13521153e+01 -7.70376235e+00 1.70121354e+01 16 1.24325643e+01 3.69385900e+01 2.63785866e+01 17 2.36156105e+01 -2.39358754e+01 -1.07700950e+01 18 -1.11836007e+01 1.50974083e+01 1.07792683e+01 19 1.00931545e+01 8.20139014e+00 8.63982765e+00 20 2.90405915e+01 4.51239560e+01 -1.47546513e+01 21 -1.84580570e+01 -5.58076383e+00 1.61050912e+01 22 -6.23113164e+00 6.03568912e+01 4.40941454e+01 23 -3.55268556e+01 -4.00760528e+01 -1.53985721e+01 24 4.57115800e+01 1.41205191e+01 -5.08592360e+01 25 -4.87426247e+00 -1.15463762e+01 1.46392378e+01 26 -1.05670785e+01 7.54929073e+00 -2.08315593e+01 27 3.77869772e+01 -5.67460472e+01 -2.49216393e+01 28 -4.74611100e+01 4.04705999e+01 -1.80092371e+01 29 -1.18456604e+01 -1.73870981e+01 1.31226310e+01 30 3.52327366e+00 8.67180053e+00 2.67953692e+00 31 2.17439283e+01 -1.89763109e+01 1.62999032e+01 32 2.33128158e+01 1.98490298e+01 7.43741026e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==9223== Memcheck, a memory error detector ==9223== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==9223== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==9223== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Ag__MO_505250810900_000 ==9223== ==9223== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==9223== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==9223== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9223== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9223== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==9223== by 0x4010732: call_init (dl-init.c:72) ==9223== by 0x4010732: _dl_init (dl-init.c:119) ==9223== by 0x40151FE: dl_open_worker (dl-open.c:522) ==9223== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==9223== by 0x40147C9: _dl_open (dl-open.c:605) ==9223== by 0x544CF95: dlopen_doit (dlopen.c:66) ==9223== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==9223== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==9223== by 0x544D734: _dlerror_run (dlerror.c:162) ==9223== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==9223== ==9223== ==9223== HEAP SUMMARY: ==9223== in use at exit: 5,937,437 bytes in 3,960 blocks ==9223== total heap usage: 116,125 allocs, 112,165 frees, 59,485,115 bytes allocated ==9223== ==9223== LEAK SUMMARY: ==9223== definitely lost: 0 bytes in 0 blocks ==9223== indirectly lost: 0 bytes in 0 blocks ==9223== possibly lost: 182,191 bytes in 111 blocks ==9223== still reachable: 5,755,246 bytes in 3,849 blocks ==9223== suppressed: 0 bytes in 0 blocks ==9223== Rerun with --leak-check=full to see details of leaked memory ==9223== ==9223== For counts of detected and suppressed errors, rerun with: -v ==9223== 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. === Verification check vc-memory-leak end (2018-12-15 06:18:40) ===