!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_NicholAckland_2016_Na__MO_048172193005_000 Supported species : Na random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Na (Configuration in file "config-F-Na.xyz") ----------------------------------------------------------------------------------------------------- Energy = 143.943917604 Forces: 1 -3.99676753e+00 -1.08609065e+01 -8.94809175e+00 2 -3.50249228e+00 2.52455145e+00 -9.06845421e+00 3 2.32857943e+00 -7.58253052e+00 -2.42051323e+00 4 -6.80226025e+00 6.37450537e+00 6.12595956e+00 5 2.29199683e+00 -1.15035392e+01 -5.00126849e+00 6 6.65299469e+00 7.41595605e-01 -8.07844176e+00 7 6.30810554e+00 -1.77245430e+01 -1.25174021e+01 8 -1.12766278e+01 -1.11514491e+01 2.13721633e+00 9 -9.84835104e+00 5.24512459e-02 -1.19356011e+01 10 -4.12486886e+00 1.48067272e+01 -1.34081498e+01 11 -4.46240580e+00 -8.55864253e+00 7.29558682e+00 12 -7.99152977e+00 1.20723561e+01 -4.65096436e+00 13 9.10679645e-04 -2.53532796e+00 -2.55245719e+01 14 6.45567939e+00 6.28892856e+00 -4.09429326e+00 15 2.56223302e+01 5.23126338e+00 5.02863156e+00 16 5.35030855e+00 1.82980498e+01 7.43660430e+00 17 -1.12952652e+01 -6.21117601e+00 -9.38767975e-01 18 2.84822673e+00 6.90925703e+00 -3.85774012e+00 19 1.99273122e+00 -1.13288079e+01 7.42966656e+00 20 -7.37875472e+00 3.24615170e+00 6.88299867e+00 21 -6.35220579e+00 -8.19683916e+00 4.68104632e+00 22 1.31389488e+01 1.12622356e+01 1.13328211e+01 23 3.92817109e+00 -2.34420232e+00 6.70784785e+00 24 3.93354456e+00 1.36035093e+00 7.09172534e+00 25 -7.86877119e+00 -8.54203547e+00 4.81695806e+00 26 -3.40278697e+00 1.37536059e+01 -4.27389423e+00 27 4.93267336e+00 -1.61751421e+01 9.35429207e+00 28 -1.66079982e+01 1.39078387e+01 5.04145708e+00 29 -3.77181469e+00 -7.09874220e+00 3.49052888e+00 30 7.71445692e+00 1.05798186e+01 -3.30276551e+00 31 9.84593763e+00 -7.75189273e+00 1.15345734e+01 32 5.33730450e+00 1.01560896e+01 1.16330059e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Na (Configuration in file "config-T-Na.xyz") ----------------------------------------------------------------------------------------------------- Energy = 267.432801037 Forces: 1 1.21904544e+01 -1.53534589e+01 1.91025335e+00 2 -1.77608260e+01 1.45837221e+00 1.98584926e+01 3 2.59802665e+00 4.27649679e+00 -1.45202061e+00 4 8.91674258e+00 9.33730053e+00 8.76835871e+00 5 5.18668020e+00 -2.08764093e+00 -1.18271525e+00 6 -1.61974720e+01 1.50801816e+01 3.25647711e+00 7 -2.18357771e+00 -1.41490172e+01 -1.18069393e+01 8 -1.24169191e+01 -1.06490789e+01 3.18757027e+00 9 -1.29342427e+01 -7.86468371e+00 7.66345668e+00 10 -7.03093099e+00 7.13163651e+00 -5.08716898e+00 11 -3.96267140e+00 -9.14303394e+00 8.60734263e+00 12 -1.40016907e+00 4.12209219e+00 -4.91025266e+00 13 1.69403642e-01 -4.45526832e+00 -1.86816589e+01 14 -1.41809498e+00 9.99285736e-01 -2.96049860e+00 15 1.88106957e+01 5.77975337e+00 5.66802091e+00 16 5.90999833e+00 1.05488699e+01 8.80870197e+00 17 5.24866704e+00 -7.60279624e+00 -1.31930523e-01 18 3.99762034e+00 7.64926317e+00 -4.60762796e+00 19 2.75262990e+00 -5.33851579e-01 4.19769174e+00 20 9.37670219e+00 1.52004516e+01 -3.90183353e+00 21 -7.23775567e+00 2.71150296e-01 4.17856317e+00 22 -1.08405119e+00 1.99123326e+01 1.10797756e+01 23 -1.25676998e+01 -1.58617592e+01 -9.42975555e+00 24 1.92319517e+01 5.53314378e+00 -2.21090796e+01 25 -9.66199623e-01 -1.07445055e+01 3.99965477e+00 26 -1.93066209e+00 2.76008845e+00 -6.19473953e+00 27 1.20317943e+01 -1.73606580e+01 -6.74985140e+00 28 -1.46223803e+01 1.33445808e+01 -3.18542338e+00 29 -4.10479121e+00 -7.72258841e+00 3.13405642e+00 30 -1.66292593e+00 3.00478116e+00 -1.64318668e+00 31 5.52873407e+00 -9.14430004e+00 7.28703437e+00 32 7.53126864e+00 6.26286005e+00 2.42923221e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==4901== Memcheck, a memory error detector ==4901== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==4901== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==4901== Command: python runner2.py EAM_Dynamo_NicholAckland_2016_Na__MO_048172193005_000 ==4901== ==4901== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==4901== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==4901== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==4901== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==4901== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==4901== by 0x4010732: call_init (dl-init.c:72) ==4901== by 0x4010732: _dl_init (dl-init.c:119) ==4901== by 0x40151FE: dl_open_worker (dl-open.c:522) ==4901== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==4901== by 0x40147C9: _dl_open (dl-open.c:605) ==4901== by 0x544CF95: dlopen_doit (dlopen.c:66) ==4901== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==4901== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==4901== by 0x544D734: _dlerror_run (dlerror.c:162) ==4901== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==4901== ==4901== ==4901== HEAP SUMMARY: ==4901== in use at exit: 9,972,509 bytes in 3,960 blocks ==4901== total heap usage: 114,082 allocs, 110,122 frees, 63,880,803 bytes allocated ==4901== ==4901== LEAK SUMMARY: ==4901== definitely lost: 0 bytes in 0 blocks ==4901== indirectly lost: 0 bytes in 0 blocks ==4901== possibly lost: 182,191 bytes in 111 blocks ==4901== still reachable: 9,790,318 bytes in 3,849 blocks ==4901== suppressed: 0 bytes in 0 blocks ==4901== Rerun with --leak-check=full to see details of leaked memory ==4901== ==4901== For counts of detected and suppressed errors, rerun with: -v ==4901== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2509 from 171) ================================================================================ 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.