Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:27:41) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 = 20781.882816362555 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 = 20781.882816362555 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 ================================================================================ VALGRIND OUTPUT ================================================================================ ==30275== Memcheck, a memory error detector ==30275== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==30275== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==30275== Command: python runner2.py LJ_Shifted_Bernardes_1958LowCutoff_Kr__MO_995724792024_003 ==30275== ==32019== Warning: invalid file descriptor 1048564 in syscall close() ==32019== Warning: invalid file descriptor 1048565 in syscall close() ==32019== Warning: invalid file descriptor 1048566 in syscall close() ==32019== Warning: invalid file descriptor 1048567 in syscall close() ==32019== Use --log-fd= to select an alternative log fd. ==32019== Warning: invalid file descriptor 1048568 in syscall close() ==32019== Warning: invalid file descriptor 1048569 in syscall close() ==32021== Warning: invalid file descriptor 1048564 in syscall close() ==32021== Warning: invalid file descriptor 1048565 in syscall close() ==32021== Warning: invalid file descriptor 1048566 in syscall close() ==32021== Warning: invalid file descriptor 1048567 in syscall close() ==32021== Use --log-fd= to select an alternative log fd. ==32021== Warning: invalid file descriptor 1048568 in syscall close() ==32021== Warning: invalid file descriptor 1048569 in syscall close() ==32024== Warning: invalid file descriptor 1048564 in syscall close() ==32024== Warning: invalid file descriptor 1048565 in syscall close() ==32024== Warning: invalid file descriptor 1048566 in syscall close() ==32024== Warning: invalid file descriptor 1048567 in syscall close() ==32024== Use --log-fd= to select an alternative log fd. ==32024== Warning: invalid file descriptor 1048568 in syscall close() ==32024== Warning: invalid file descriptor 1048569 in syscall close() ==32026== Warning: invalid file descriptor 1048564 in syscall close() ==32026== Warning: invalid file descriptor 1048565 in syscall close() ==32026== Warning: invalid file descriptor 1048566 in syscall close() ==32026== Warning: invalid file descriptor 1048567 in syscall close() ==32026== Use --log-fd= to select an alternative log fd. ==32026== Warning: invalid file descriptor 1048568 in syscall close() ==32026== Warning: invalid file descriptor 1048569 in syscall close() ==32028== Warning: invalid file descriptor 1048564 in syscall close() ==32028== Warning: invalid file descriptor 1048565 in syscall close() ==32028== Warning: invalid file descriptor 1048566 in syscall close() ==32028== Warning: invalid file descriptor 1048567 in syscall close() ==32028== Use --log-fd= to select an alternative log fd. ==32028== Warning: invalid file descriptor 1048568 in syscall close() ==32028== Warning: invalid file descriptor 1048569 in syscall close() ==32029== Warning: invalid file descriptor 1048564 in syscall close() ==32029== Warning: invalid file descriptor 1048565 in syscall close() ==32029== Warning: invalid file descriptor 1048566 in syscall close() ==32029== Warning: invalid file descriptor 1048567 in syscall close() ==32029== Use --log-fd= to select an alternative log fd. ==32029== Warning: invalid file descriptor 1048568 in syscall close() ==32029== Warning: invalid file descriptor 1048569 in syscall close() ==30275== ==30275== HEAP SUMMARY: ==30275== in use at exit: 1,718,292 bytes in 1,321 blocks ==30275== total heap usage: 30,945 allocs, 29,624 frees, 38,087,104 bytes allocated ==30275== ==30275== LEAK SUMMARY: ==30275== definitely lost: 0 bytes in 0 blocks ==30275== indirectly lost: 0 bytes in 0 blocks ==30275== possibly lost: 178,943 bytes in 97 blocks ==30275== still reachable: 1,539,349 bytes in 1,224 blocks ==30275== suppressed: 0 bytes in 0 blocks ==30275== Rerun with --leak-check=full to see details of leaked memory ==30275== ==30275== For counts of detected and suppressed errors, rerun with: -v ==30275== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16342 from 602) ================================================================================ 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 (2019-08-08 23:28:03) ===