!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : LJ_Shifted_Bernardes_1958LowCutoff_Kr__MO_995724792024_003 Supported species : Kr random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Kr (Configuration in file "config-F-Kr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 20781.8828164 Forces: 1 -2.13678340e+03 -6.15913513e+03 -8.29748664e+03 2 -1.66011455e+01 1.10791498e+03 -1.06160584e+03 3 3.71011105e+03 -3.29595432e+03 1.24849391e+03 4 -1.99034493e+03 8.86802430e+03 6.43263838e+03 5 4.19231942e+01 -1.24100452e+03 -8.03593935e+02 6 3.36573228e+02 2.10003643e+02 -6.15371051e+02 7 -9.31283858e+02 -8.12226904e+03 -8.34962204e+03 8 -2.80777615e+03 -2.91990035e+03 6.43110394e+02 9 -9.26337410e+01 -3.98884597e+02 -5.43136287e+02 10 -1.75389453e+03 8.56862762e+02 -2.17105702e+03 11 -2.50375359e+03 -2.69204116e+03 -6.79749542e+01 12 -6.97003366e+02 1.95052664e+03 -9.35893257e+02 13 -4.31288996e+03 -1.96149716e+03 -8.48172102e+03 14 1.15802077e+03 1.23944407e+03 -4.95604215e+02 15 8.05037553e+03 1.53208386e+03 4.98937024e+03 16 2.50018383e+03 5.41367146e+03 3.49760718e+03 17 -1.61414454e+03 -7.09033996e+02 7.65250209e+02 18 -6.89676386e+00 2.90098499e+04 -2.73875463e+04 19 9.18993196e+02 -2.90002138e+04 2.75342667e+04 20 -6.97050573e+02 4.01874356e+02 4.87698695e+02 21 -2.30542319e+03 -1.51106643e+03 -1.31317857e+02 22 4.33421180e+03 8.33846925e+03 6.44270037e+03 23 3.65685611e+03 -1.86772970e+03 2.67141752e+03 24 -2.45758090e+03 1.84532904e+03 9.03812607e+02 25 -1.18763312e+03 -1.98316850e+03 1.76572873e+03 26 8.20850422e+01 2.09180935e+03 -1.34763456e+03 27 7.49712440e+03 -9.70170977e+03 1.74670634e+03 28 -9.52666202e+03 8.15986882e+03 2.04361297e+01 29 -3.76910303e+03 -3.74518845e+03 -5.25249575e+03 30 1.83100740e+03 2.23895645e+03 -6.68749304e+02 31 4.38810452e+03 -1.67006464e+03 3.48545919e+03 32 3.01888731e+02 3.71417272e+03 3.97611343e+03 MONOATOMIC STRUCTURE (pbc=True)-- Species = Kr (Configuration in file "config-T-Kr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 25917.070097 Forces: 1 1.20828289e+03 -8.84380109e+03 -7.55290178e+03 2 -1.79540353e+02 1.12595302e+03 -7.51984258e+02 3 3.88059948e+03 -2.37581199e+03 1.52797935e+03 4 -5.82702684e+02 9.06542909e+03 6.57189266e+03 5 5.25011181e+02 5.91941972e+01 -9.18366589e+02 6 -3.60756840e+03 3.49726946e+03 6.86516174e+02 7 -1.88241317e+03 -8.00509912e+03 -8.62448274e+03 8 -2.81227464e+03 -2.91839848e+03 6.46133903e+02 9 -7.62064911e+02 -1.94102040e+03 1.91626949e+03 10 -2.34394433e+03 6.47959491e+01 -1.79276109e+03 11 -2.50302982e+03 -2.69439363e+03 -6.59581803e+01 12 -2.06441814e+02 1.25763243e+03 -7.40838194e+02 13 -4.27717684e+03 -2.13319013e+03 -8.10657599e+03 14 3.20425295e+02 1.48602684e+03 -7.33976299e+02 15 7.70286315e+03 1.36298014e+03 4.98825069e+03 16 2.47642057e+03 4.71018471e+03 3.82135858e+03 17 1.04310606e+03 -2.70139270e+03 1.16390815e+03 18 4.37338494e+00 2.90236402e+04 -2.73885120e+04 19 9.55984704e+02 -2.79050978e+04 2.79808450e+04 20 3.47953887e+03 2.91470230e+03 1.72198134e+02 21 -2.91231537e+03 -4.05662676e+02 -5.96317189e-01 22 1.87649556e+03 1.06619904e+04 6.59928057e+03 23 -3.09558475e+02 -4.75331173e+03 6.84581974e+02 24 -2.44249028e+03 1.88000479e+03 4.38849193e+02 25 -9.98053413e+02 -1.99242178e+03 1.79209979e+03 26 1.77529464e+02 1.01987748e+03 -1.85220077e+03 27 8.42434211e+03 -9.81242308e+03 4.48399029e+02 28 -9.31461281e+03 9.19687225e+03 -1.44803636e+03 29 -3.77110619e+03 -3.75824999e+03 -5.25396477e+03 30 2.08720912e+03 1.04846016e+03 -5.84676979e+02 31 4.22845824e+03 -1.79000700e+03 3.25641981e+03 32 5.14653411e+02 3.65526820e+03 3.12084990e+03 ================================================================================ VALGRIND OUTPUT ================================================================================ ==14453== Memcheck, a memory error detector ==14453== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==14453== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==14453== Command: python runner2.py LJ_Shifted_Bernardes_1958LowCutoff_Kr__MO_995724792024_003 ==14453== ==14453== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==14453== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==14453== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==14453== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==14453== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==14453== by 0x4010732: call_init (dl-init.c:72) ==14453== by 0x4010732: _dl_init (dl-init.c:119) ==14453== by 0x40151FE: dl_open_worker (dl-open.c:522) ==14453== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==14453== by 0x40147C9: _dl_open (dl-open.c:605) ==14453== by 0x544CF95: dlopen_doit (dlopen.c:66) ==14453== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==14453== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==14453== by 0x544D734: _dlerror_run (dlerror.c:162) ==14453== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==14453== ==14453== ==14453== HEAP SUMMARY: ==14453== in use at exit: 4,772,919 bytes in 3,907 blocks ==14453== total heap usage: 124,773 allocs, 120,866 frees, 59,082,406 bytes allocated ==14453== ==14453== LEAK SUMMARY: ==14453== definitely lost: 0 bytes in 0 blocks ==14453== indirectly lost: 0 bytes in 0 blocks ==14453== possibly lost: 182,191 bytes in 111 blocks ==14453== still reachable: 4,590,728 bytes in 3,796 blocks ==14453== suppressed: 0 bytes in 0 blocks ==14453== Rerun with --leak-check=full to see details of leaked memory ==14453== ==14453== For counts of detected and suppressed errors, rerun with: -v ==14453== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2511 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.