!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_AngeloMoodyBaskes_1995_Ni__MO_800536961967_004 Supported species : Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -42.00849191199364 Forces: 1 -1.85572421e+00 -3.71061380e+00 -4.06581506e+00 2 -3.13974889e+00 5.84165993e+00 -4.55808674e+00 3 1.96723664e+00 -3.00160157e+00 1.35557157e+00 4 -2.60463166e+00 3.25761000e+00 3.17152550e+00 5 5.53311063e+00 -7.78685170e+00 -2.10489741e+00 6 8.70956158e-01 1.17213903e+00 -2.70704168e+00 7 4.76026764e+00 -1.10491609e+01 -9.43856133e+00 8 -7.32294674e+00 -5.28188470e+00 -4.96595476e-01 9 -5.24033207e+00 -4.77350142e+00 -8.46883175e+00 10 -2.21583857e+00 1.19567474e+01 -9.59713562e+00 11 -6.00282717e+00 -9.17261864e+00 6.60092984e+00 12 -5.53730461e+00 6.45422929e+00 3.16740135e+00 13 1.29770985e+00 -7.09025145e+00 -1.80630824e+01 14 2.92202131e+00 5.75638166e+00 -4.21386707e+00 15 1.47928532e+01 -5.97502784e+00 2.38958069e+00 16 2.82206776e+00 1.56195770e+01 5.66377487e+00 17 -8.17306096e+00 -4.07275612e+00 -3.26438820e+00 18 1.71142956e+00 8.33995446e+00 -9.00478716e+00 19 2.39032401e+00 -1.10501531e+01 6.33696612e+00 20 -5.01677491e+00 4.90861813e+00 5.43458895e+00 21 -6.18623630e+00 -5.98461483e+00 2.53389585e+00 22 8.99910464e+00 8.81288772e+00 7.31723840e+00 23 1.67338055e+00 -4.28527919e-01 2.68898019e+00 24 5.00604942e+00 3.63643918e+00 5.88738746e+00 25 -7.00788319e+00 -5.29774348e+00 -1.35124182e+00 26 -2.65656745e+00 1.11116133e+01 -5.19689914e+00 27 2.78647873e+00 -1.23610034e+01 7.89937686e+00 28 -9.14254876e+00 8.10913283e+00 3.84189285e+00 29 -1.99464740e+00 -6.43441032e+00 3.27482442e+00 30 4.62913863e+00 5.44779698e+00 1.94274669e+00 31 7.67131667e+00 -4.46292047e+00 5.10072277e+00 32 4.26362754e+00 7.50885477e+00 7.92382646e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -42.00849191199364 Forces: 1 -1.85572421e+00 -3.71061380e+00 -4.06581506e+00 2 -3.13974889e+00 5.84165993e+00 -4.55808674e+00 3 1.96723664e+00 -3.00160157e+00 1.35557157e+00 4 -2.60463166e+00 3.25761000e+00 3.17152550e+00 5 5.53311063e+00 -7.78685170e+00 -2.10489741e+00 6 8.70956158e-01 1.17213903e+00 -2.70704168e+00 7 4.76026764e+00 -1.10491609e+01 -9.43856133e+00 8 -7.32294674e+00 -5.28188470e+00 -4.96595476e-01 9 -5.24033207e+00 -4.77350142e+00 -8.46883175e+00 10 -2.21583857e+00 1.19567474e+01 -9.59713562e+00 11 -6.00282717e+00 -9.17261864e+00 6.60092984e+00 12 -5.53730461e+00 6.45422929e+00 3.16740135e+00 13 1.29770985e+00 -7.09025145e+00 -1.80630824e+01 14 2.92202131e+00 5.75638166e+00 -4.21386707e+00 15 1.47928532e+01 -5.97502784e+00 2.38958069e+00 16 2.82206776e+00 1.56195770e+01 5.66377487e+00 17 -8.17306096e+00 -4.07275612e+00 -3.26438820e+00 18 1.71142956e+00 8.33995446e+00 -9.00478716e+00 19 2.39032401e+00 -1.10501531e+01 6.33696612e+00 20 -5.01677491e+00 4.90861813e+00 5.43458895e+00 21 -6.18623630e+00 -5.98461483e+00 2.53389585e+00 22 8.99910464e+00 8.81288772e+00 7.31723840e+00 23 1.67338055e+00 -4.28527919e-01 2.68898019e+00 24 5.00604942e+00 3.63643918e+00 5.88738746e+00 25 -7.00788319e+00 -5.29774348e+00 -1.35124182e+00 26 -2.65656745e+00 1.11116133e+01 -5.19689914e+00 27 2.78647873e+00 -1.23610034e+01 7.89937686e+00 28 -9.14254876e+00 8.10913283e+00 3.84189285e+00 29 -1.99464740e+00 -6.43441032e+00 3.27482442e+00 30 4.62913863e+00 5.44779698e+00 1.94274669e+00 31 7.67131667e+00 -4.46292047e+00 5.10072277e+00 32 4.26362754e+00 7.50885477e+00 7.92382646e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==62440== Memcheck, a memory error detector ==62440== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==62440== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==62440== Command: python runner2.py EAM_CubicNaturalSpline_AngeloMoodyBaskes_1995_Ni__MO_800536961967_004 ==62440== ==62440== Invalid read of size 8 ==62440== at 0x40286A0: strncmp (strcmp.S:170) ==62440== by 0x400668D: is_dst (dl-load.c:216) ==62440== by 0x400810E: _dl_dst_count (dl-load.c:253) ==62440== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==62440== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==62440== by 0x4008602: decompose_rpath (dl-load.c:654) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:696) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:677) ==62440== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==62440== by 0x4003494: openaux (dl-deps.c:64) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==62440== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x400DF99: dl_open_worker (dl-open.c:782) ==62440== Address 0x56cc911 is 1 bytes inside a block of size 8 alloc'd ==62440== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==62440== by 0x40271DF: malloc (rtld-malloc.h:56) ==62440== by 0x40271DF: strdup (strdup.c:42) ==62440== by 0x4008594: decompose_rpath (dl-load.c:629) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:696) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:677) ==62440== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==62440== by 0x4003494: openaux (dl-deps.c:64) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==62440== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x400DF99: dl_open_worker (dl-open.c:782) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x400E34D: _dl_open (dl-open.c:883) ==62440== ==62440== Invalid read of size 8 ==62440== at 0x40286A8: strncmp (strcmp.S:172) ==62440== by 0x400668D: is_dst (dl-load.c:216) ==62440== by 0x400810E: _dl_dst_count (dl-load.c:253) ==62440== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==62440== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==62440== by 0x4008602: decompose_rpath (dl-load.c:654) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:696) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:677) ==62440== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==62440== by 0x4003494: openaux (dl-deps.c:64) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==62440== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x400DF99: dl_open_worker (dl-open.c:782) ==62440== Address 0x56cc919 is 1 bytes after a block of size 8 alloc'd ==62440== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==62440== by 0x40271DF: malloc (rtld-malloc.h:56) ==62440== by 0x40271DF: strdup (strdup.c:42) ==62440== by 0x4008594: decompose_rpath (dl-load.c:629) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:696) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:677) ==62440== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==62440== by 0x4003494: openaux (dl-deps.c:64) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==62440== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x400DF99: dl_open_worker (dl-open.c:782) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x400E34D: _dl_open (dl-open.c:883) ==62440== ==62440== Invalid read of size 8 ==62440== at 0x40286A0: strncmp (strcmp.S:170) ==62440== by 0x400668D: is_dst (dl-load.c:216) ==62440== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==62440== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==62440== by 0x4008602: decompose_rpath (dl-load.c:654) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:696) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:677) ==62440== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==62440== by 0x4003494: openaux (dl-deps.c:64) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==62440== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x400DF99: dl_open_worker (dl-open.c:782) ==62440== Address 0x56cc911 is 1 bytes inside a block of size 8 alloc'd ==62440== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==62440== by 0x40271DF: malloc (rtld-malloc.h:56) ==62440== by 0x40271DF: strdup (strdup.c:42) ==62440== by 0x4008594: decompose_rpath (dl-load.c:629) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:696) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:677) ==62440== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==62440== by 0x4003494: openaux (dl-deps.c:64) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==62440== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x400DF99: dl_open_worker (dl-open.c:782) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x400E34D: _dl_open (dl-open.c:883) ==62440== ==62440== Invalid read of size 8 ==62440== at 0x40286A8: strncmp (strcmp.S:172) ==62440== by 0x400668D: is_dst (dl-load.c:216) ==62440== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==62440== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==62440== by 0x4008602: decompose_rpath (dl-load.c:654) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:696) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:677) ==62440== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==62440== by 0x4003494: openaux (dl-deps.c:64) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==62440== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x400DF99: dl_open_worker (dl-open.c:782) ==62440== Address 0x56cc919 is 1 bytes after a block of size 8 alloc'd ==62440== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==62440== by 0x40271DF: malloc (rtld-malloc.h:56) ==62440== by 0x40271DF: strdup (strdup.c:42) ==62440== by 0x4008594: decompose_rpath (dl-load.c:629) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:696) ==62440== by 0x400A8C8: cache_rpath (dl-load.c:677) ==62440== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==62440== by 0x4003494: openaux (dl-deps.c:64) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==62440== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x400DF99: dl_open_worker (dl-open.c:782) ==62440== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==62440== by 0x400E34D: _dl_open (dl-open.c:883) ==62440== ==62440== ==62440== HEAP SUMMARY: ==62440== in use at exit: 3,734,006 bytes in 5,931 blocks ==62440== total heap usage: 83,653 allocs, 77,722 frees, 299,135,566 bytes allocated ==62440== ==62440== LEAK SUMMARY: ==62440== definitely lost: 0 bytes in 0 blocks ==62440== indirectly lost: 0 bytes in 0 blocks ==62440== possibly lost: 158,559 bytes in 109 blocks ==62440== still reachable: 3,575,447 bytes in 5,822 blocks ==62440== of which reachable via heuristic: ==62440== stdstring : 4,256 bytes in 48 blocks ==62440== suppressed: 0 bytes in 0 blocks ==62440== Rerun with --leak-check=full to see details of leaked memory ==62440== ==62440== For lists of detected and suppressed errors, rerun with: -s ==62440== 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.