!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 and Daniel S. Karls ----------------------------------------------------------------------------------------------------- Results for KIM Model : EAM_CubicNaturalSpline_ErcolessiAdams_1994_Al__MO_800509458712_003 Supported species : Al random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 93.14435632747295 Forces: 1 -5.61765030e+00 -6.61600400e+00 -6.88675255e+00 2 -1.45070884e+00 1.95419695e+00 -1.08564443e+01 3 3.17538582e+00 -1.02688580e+01 -1.35714909e+00 4 -9.34911324e+00 9.58280637e-02 3.59079726e+00 5 -1.86177773e+00 -1.24549842e+01 -8.84110878e+00 6 9.49445660e+00 2.94639446e+00 -1.17112115e+01 7 9.80740364e+00 -1.10582083e+01 9.85127471e-01 8 -3.93797966e+00 -4.26303848e+00 1.96955043e+00 9 -7.72771117e+00 -2.95032315e+00 -1.52694619e+01 10 1.37355820e+00 1.35291458e+01 -1.12204963e+01 11 -3.61014377e+00 -6.91109125e+00 3.54648532e+00 12 -1.20536566e+01 1.21980177e+01 3.71555129e+00 13 -7.01443042e-02 -2.89298117e+00 -1.68327156e+01 14 1.13628213e+01 1.02048805e+01 -9.15086696e+00 15 1.57023932e+01 -5.00475506e+00 2.32716959e-01 16 -7.88581586e-01 1.70066991e+01 2.46379870e+00 17 -1.52601380e+01 -7.85150928e+00 -3.76099423e+00 18 2.89342121e+00 7.44096601e+00 -2.26797801e-01 19 5.71160597e+00 -1.26574891e+01 9.74428572e+00 20 -7.73191122e+00 7.75522222e+00 8.54951026e+00 21 -5.61772430e+00 -1.13083928e+01 2.29074423e+00 22 1.30274346e+01 6.64336928e+00 2.32100491e+00 23 5.79939933e+00 -4.36233929e+00 8.46541413e+00 24 -1.39808147e+00 1.51596861e+00 7.37559384e+00 25 -1.19201844e+01 -4.83469735e+00 3.42549060e+00 26 1.03823746e+00 1.64753364e+01 -6.02502002e+00 27 -2.01009580e+00 -9.39653021e+00 9.76173744e+00 28 -9.15963853e+00 5.68506818e+00 5.49326174e+00 29 -3.10918044e+00 -8.30747144e+00 5.94397038e+00 30 1.00307607e+01 1.23363341e+01 1.88727988e-01 31 1.06428410e+01 -5.32992163e+00 8.96080049e+00 32 2.61470223e+00 1.06811675e+01 1.31144498e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 93.14435632747295 Forces: 1 -5.61765030e+00 -6.61600400e+00 -6.88675255e+00 2 -1.45070884e+00 1.95419695e+00 -1.08564443e+01 3 3.17538582e+00 -1.02688580e+01 -1.35714909e+00 4 -9.34911324e+00 9.58280637e-02 3.59079726e+00 5 -1.86177773e+00 -1.24549842e+01 -8.84110878e+00 6 9.49445660e+00 2.94639446e+00 -1.17112115e+01 7 9.80740364e+00 -1.10582083e+01 9.85127471e-01 8 -3.93797966e+00 -4.26303848e+00 1.96955043e+00 9 -7.72771117e+00 -2.95032315e+00 -1.52694619e+01 10 1.37355820e+00 1.35291458e+01 -1.12204963e+01 11 -3.61014377e+00 -6.91109125e+00 3.54648532e+00 12 -1.20536566e+01 1.21980177e+01 3.71555129e+00 13 -7.01443042e-02 -2.89298117e+00 -1.68327156e+01 14 1.13628213e+01 1.02048805e+01 -9.15086696e+00 15 1.57023932e+01 -5.00475506e+00 2.32716959e-01 16 -7.88581586e-01 1.70066991e+01 2.46379870e+00 17 -1.52601380e+01 -7.85150928e+00 -3.76099423e+00 18 2.89342121e+00 7.44096601e+00 -2.26797801e-01 19 5.71160597e+00 -1.26574891e+01 9.74428572e+00 20 -7.73191122e+00 7.75522222e+00 8.54951026e+00 21 -5.61772430e+00 -1.13083928e+01 2.29074423e+00 22 1.30274346e+01 6.64336928e+00 2.32100491e+00 23 5.79939933e+00 -4.36233929e+00 8.46541413e+00 24 -1.39808147e+00 1.51596861e+00 7.37559384e+00 25 -1.19201844e+01 -4.83469735e+00 3.42549060e+00 26 1.03823746e+00 1.64753364e+01 -6.02502002e+00 27 -2.01009580e+00 -9.39653021e+00 9.76173744e+00 28 -9.15963853e+00 5.68506818e+00 5.49326174e+00 29 -3.10918044e+00 -8.30747144e+00 5.94397038e+00 30 1.00307607e+01 1.23363341e+01 1.88727988e-01 31 1.06428410e+01 -5.32992163e+00 8.96080049e+00 32 2.61470223e+00 1.06811675e+01 1.31144498e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1951787== Memcheck, a memory error detector ==1951787== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1951787== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==1951787== Command: python runner2.py EAM_CubicNaturalSpline_ErcolessiAdams_1994_Al__MO_800509458712_003 ==1951787== ==1951787== Invalid read of size 8 ==1951787== at 0x40286A0: strncmp (strcmp.S:170) ==1951787== by 0x400668D: is_dst (dl-load.c:216) ==1951787== by 0x400810E: _dl_dst_count (dl-load.c:253) ==1951787== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==1951787== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==1951787== by 0x4008602: decompose_rpath (dl-load.c:654) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1951787== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1951787== by 0x4003494: openaux (dl-deps.c:64) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1951787== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1951787== Address 0x56cc881 is 1 bytes inside a block of size 8 alloc'd ==1951787== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1951787== by 0x40271DF: malloc (rtld-malloc.h:56) ==1951787== by 0x40271DF: strdup (strdup.c:42) ==1951787== by 0x4008594: decompose_rpath (dl-load.c:629) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1951787== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1951787== by 0x4003494: openaux (dl-deps.c:64) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1951787== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x400E34D: _dl_open (dl-open.c:883) ==1951787== ==1951787== Invalid read of size 8 ==1951787== at 0x40286A8: strncmp (strcmp.S:172) ==1951787== by 0x400668D: is_dst (dl-load.c:216) ==1951787== by 0x400810E: _dl_dst_count (dl-load.c:253) ==1951787== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==1951787== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==1951787== by 0x4008602: decompose_rpath (dl-load.c:654) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1951787== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1951787== by 0x4003494: openaux (dl-deps.c:64) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1951787== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1951787== Address 0x56cc889 is 1 bytes after a block of size 8 alloc'd ==1951787== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1951787== by 0x40271DF: malloc (rtld-malloc.h:56) ==1951787== by 0x40271DF: strdup (strdup.c:42) ==1951787== by 0x4008594: decompose_rpath (dl-load.c:629) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1951787== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1951787== by 0x4003494: openaux (dl-deps.c:64) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1951787== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x400E34D: _dl_open (dl-open.c:883) ==1951787== ==1951787== Invalid read of size 8 ==1951787== at 0x40286A0: strncmp (strcmp.S:170) ==1951787== by 0x400668D: is_dst (dl-load.c:216) ==1951787== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==1951787== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==1951787== by 0x4008602: decompose_rpath (dl-load.c:654) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1951787== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1951787== by 0x4003494: openaux (dl-deps.c:64) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1951787== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1951787== Address 0x56cc881 is 1 bytes inside a block of size 8 alloc'd ==1951787== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1951787== by 0x40271DF: malloc (rtld-malloc.h:56) ==1951787== by 0x40271DF: strdup (strdup.c:42) ==1951787== by 0x4008594: decompose_rpath (dl-load.c:629) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1951787== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1951787== by 0x4003494: openaux (dl-deps.c:64) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1951787== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x400E34D: _dl_open (dl-open.c:883) ==1951787== ==1951787== Invalid read of size 8 ==1951787== at 0x40286A8: strncmp (strcmp.S:172) ==1951787== by 0x400668D: is_dst (dl-load.c:216) ==1951787== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==1951787== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==1951787== by 0x4008602: decompose_rpath (dl-load.c:654) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1951787== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1951787== by 0x4003494: openaux (dl-deps.c:64) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1951787== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1951787== Address 0x56cc889 is 1 bytes after a block of size 8 alloc'd ==1951787== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1951787== by 0x40271DF: malloc (rtld-malloc.h:56) ==1951787== by 0x40271DF: strdup (strdup.c:42) ==1951787== by 0x4008594: decompose_rpath (dl-load.c:629) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1951787== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1951787== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1951787== by 0x4003494: openaux (dl-deps.c:64) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1951787== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1951787== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1951787== by 0x400E34D: _dl_open (dl-open.c:883) ==1951787== ==1951787== ==1951787== HEAP SUMMARY: ==1951787== in use at exit: 3,734,006 bytes in 5,931 blocks ==1951787== total heap usage: 83,618 allocs, 77,687 frees, 287,989,364 bytes allocated ==1951787== ==1951787== LEAK SUMMARY: ==1951787== definitely lost: 0 bytes in 0 blocks ==1951787== indirectly lost: 0 bytes in 0 blocks ==1951787== possibly lost: 158,559 bytes in 109 blocks ==1951787== still reachable: 3,575,447 bytes in 5,822 blocks ==1951787== of which reachable via heuristic: ==1951787== stdstring : 4,256 bytes in 48 blocks ==1951787== suppressed: 0 bytes in 0 blocks ==1951787== Rerun with --leak-check=full to see details of leaked memory ==1951787== ==1951787== For lists of detected and suppressed errors, rerun with: -s ==1951787== ERROR SUMMARY: 8 errors from 4 contexts (suppressed: 0 from 0) ================================================================================ 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.