!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_Pd__MO_993644691224_001 Supported species : Pd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Pd (Configuration in file "config-F-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 169.6619418216767 Forces: 1 -6.80019334e+00 -2.78499358e+01 -2.18283806e+01 2 -7.68465195e+00 9.40018420e+00 -1.84477183e+01 3 1.05563859e+01 -2.25495873e+01 -1.18161909e+01 4 -1.54525832e+01 1.95642255e+01 1.68643545e+01 5 7.06096220e+00 -2.51822128e+01 -8.68685236e+00 6 1.05362893e+01 5.65895501e+00 -1.30019846e+01 7 1.59086712e+01 -4.97739384e+01 -4.10910084e+01 8 -1.42994964e+01 -1.06643514e+01 -7.59294847e+00 9 -1.79669591e+01 -2.18271907e+01 -4.47093148e+01 10 -3.42665038e+00 3.80725649e+01 -3.86603613e+01 11 -1.21422191e+01 -2.63405832e+01 1.92181972e+01 12 -2.64725129e+01 3.27679930e+01 2.22490767e+01 13 -4.41344611e+00 -3.01869936e+01 -7.23629565e+01 14 1.78869563e+01 2.55293851e+01 -2.28550770e+01 15 6.60139158e+01 -1.97157281e+01 2.38403149e+01 16 -2.44991633e+00 6.12628380e+01 2.40253936e+01 17 -2.86669656e+01 -1.24669653e+01 3.14704978e+00 18 6.05004113e+00 1.96080728e+01 3.85924573e+00 19 3.25611713e+00 -2.21853913e+01 1.21722628e+01 20 -1.20240766e+01 8.19522713e+00 1.02566453e+01 21 -1.90820654e+01 -2.06059050e+01 1.52150288e+01 22 3.72691058e+01 3.74713819e+01 3.26391425e+01 23 6.98713281e+00 -3.69006843e+00 1.42790717e+01 24 7.35386669e+00 4.28736425e+00 1.18194043e+01 25 -2.35599611e+01 -7.11407053e+00 -3.14757706e-01 26 -1.24886529e+01 3.65090239e+01 -1.45419238e+01 27 1.60838735e+01 -4.98789973e+01 2.35248802e+01 28 -4.44790276e+01 3.77446052e+01 1.01911543e+01 29 -1.13239106e+01 -1.89818367e+01 1.52946036e+01 30 1.89222326e+01 3.07615663e+01 -1.99941365e+00 31 2.48400733e+01 -2.36987296e+01 2.97400800e+01 32 1.40076650e+01 2.58790984e+01 2.95729825e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pd (Configuration in file "config-T-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 169.6619418216767 Forces: 1 -6.80019334e+00 -2.78499358e+01 -2.18283806e+01 2 -7.68465195e+00 9.40018420e+00 -1.84477183e+01 3 1.05563859e+01 -2.25495873e+01 -1.18161909e+01 4 -1.54525832e+01 1.95642255e+01 1.68643545e+01 5 7.06096220e+00 -2.51822128e+01 -8.68685236e+00 6 1.05362893e+01 5.65895501e+00 -1.30019846e+01 7 1.59086712e+01 -4.97739384e+01 -4.10910084e+01 8 -1.42994964e+01 -1.06643514e+01 -7.59294847e+00 9 -1.79669591e+01 -2.18271907e+01 -4.47093148e+01 10 -3.42665038e+00 3.80725649e+01 -3.86603613e+01 11 -1.21422191e+01 -2.63405832e+01 1.92181972e+01 12 -2.64725129e+01 3.27679930e+01 2.22490767e+01 13 -4.41344611e+00 -3.01869936e+01 -7.23629565e+01 14 1.78869563e+01 2.55293851e+01 -2.28550770e+01 15 6.60139158e+01 -1.97157281e+01 2.38403149e+01 16 -2.44991633e+00 6.12628380e+01 2.40253936e+01 17 -2.86669656e+01 -1.24669653e+01 3.14704978e+00 18 6.05004113e+00 1.96080728e+01 3.85924573e+00 19 3.25611713e+00 -2.21853913e+01 1.21722628e+01 20 -1.20240766e+01 8.19522713e+00 1.02566453e+01 21 -1.90820654e+01 -2.06059050e+01 1.52150288e+01 22 3.72691058e+01 3.74713819e+01 3.26391425e+01 23 6.98713281e+00 -3.69006843e+00 1.42790717e+01 24 7.35386669e+00 4.28736425e+00 1.18194043e+01 25 -2.35599611e+01 -7.11407053e+00 -3.14757706e-01 26 -1.24886529e+01 3.65090239e+01 -1.45419238e+01 27 1.60838735e+01 -4.98789973e+01 2.35248802e+01 28 -4.44790276e+01 3.77446052e+01 1.01911543e+01 29 -1.13239106e+01 -1.89818367e+01 1.52946036e+01 30 1.89222326e+01 3.07615663e+01 -1.99941365e+00 31 2.48400733e+01 -2.36987296e+01 2.97400800e+01 32 1.40076650e+01 2.58790984e+01 2.95729825e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2463055== Memcheck, a memory error detector ==2463055== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2463055== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==2463055== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_Pd__MO_993644691224_001 ==2463055== ==2463055== Invalid read of size 8 ==2463055== at 0x40286A0: strncmp (strcmp.S:170) ==2463055== by 0x400668D: is_dst (dl-load.c:216) ==2463055== by 0x400810E: _dl_dst_count (dl-load.c:253) ==2463055== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==2463055== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==2463055== by 0x4008602: decompose_rpath (dl-load.c:654) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:696) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:677) ==2463055== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==2463055== by 0x4003494: openaux (dl-deps.c:64) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==2463055== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x400DF99: dl_open_worker (dl-open.c:782) ==2463055== Address 0x5294651 is 1 bytes inside a block of size 8 alloc'd ==2463055== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2463055== by 0x40271DF: malloc (rtld-malloc.h:56) ==2463055== by 0x40271DF: strdup (strdup.c:42) ==2463055== by 0x4008594: decompose_rpath (dl-load.c:629) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:696) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:677) ==2463055== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==2463055== by 0x4003494: openaux (dl-deps.c:64) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==2463055== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x400DF99: dl_open_worker (dl-open.c:782) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x400E34D: _dl_open (dl-open.c:883) ==2463055== ==2463055== Invalid read of size 8 ==2463055== at 0x40286A8: strncmp (strcmp.S:172) ==2463055== by 0x400668D: is_dst (dl-load.c:216) ==2463055== by 0x400810E: _dl_dst_count (dl-load.c:253) ==2463055== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==2463055== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==2463055== by 0x4008602: decompose_rpath (dl-load.c:654) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:696) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:677) ==2463055== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==2463055== by 0x4003494: openaux (dl-deps.c:64) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==2463055== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x400DF99: dl_open_worker (dl-open.c:782) ==2463055== Address 0x5294659 is 1 bytes after a block of size 8 alloc'd ==2463055== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2463055== by 0x40271DF: malloc (rtld-malloc.h:56) ==2463055== by 0x40271DF: strdup (strdup.c:42) ==2463055== by 0x4008594: decompose_rpath (dl-load.c:629) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:696) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:677) ==2463055== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==2463055== by 0x4003494: openaux (dl-deps.c:64) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==2463055== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x400DF99: dl_open_worker (dl-open.c:782) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x400E34D: _dl_open (dl-open.c:883) ==2463055== ==2463055== Invalid read of size 8 ==2463055== at 0x40286A0: strncmp (strcmp.S:170) ==2463055== by 0x400668D: is_dst (dl-load.c:216) ==2463055== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==2463055== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==2463055== by 0x4008602: decompose_rpath (dl-load.c:654) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:696) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:677) ==2463055== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==2463055== by 0x4003494: openaux (dl-deps.c:64) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==2463055== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x400DF99: dl_open_worker (dl-open.c:782) ==2463055== Address 0x5294651 is 1 bytes inside a block of size 8 alloc'd ==2463055== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2463055== by 0x40271DF: malloc (rtld-malloc.h:56) ==2463055== by 0x40271DF: strdup (strdup.c:42) ==2463055== by 0x4008594: decompose_rpath (dl-load.c:629) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:696) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:677) ==2463055== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==2463055== by 0x4003494: openaux (dl-deps.c:64) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==2463055== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x400DF99: dl_open_worker (dl-open.c:782) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x400E34D: _dl_open (dl-open.c:883) ==2463055== ==2463055== Invalid read of size 8 ==2463055== at 0x40286A8: strncmp (strcmp.S:172) ==2463055== by 0x400668D: is_dst (dl-load.c:216) ==2463055== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==2463055== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==2463055== by 0x4008602: decompose_rpath (dl-load.c:654) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:696) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:677) ==2463055== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==2463055== by 0x4003494: openaux (dl-deps.c:64) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==2463055== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x400DF99: dl_open_worker (dl-open.c:782) ==2463055== Address 0x5294659 is 1 bytes after a block of size 8 alloc'd ==2463055== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==2463055== by 0x40271DF: malloc (rtld-malloc.h:56) ==2463055== by 0x40271DF: strdup (strdup.c:42) ==2463055== by 0x4008594: decompose_rpath (dl-load.c:629) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:696) ==2463055== by 0x400A8C8: cache_rpath (dl-load.c:677) ==2463055== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==2463055== by 0x4003494: openaux (dl-deps.c:64) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==2463055== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x400DF99: dl_open_worker (dl-open.c:782) ==2463055== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==2463055== by 0x400E34D: _dl_open (dl-open.c:883) ==2463055== ==2463055== ==2463055== HEAP SUMMARY: ==2463055== in use at exit: 3,734,006 bytes in 5,931 blocks ==2463055== total heap usage: 83,565 allocs, 77,634 frees, 290,819,006 bytes allocated ==2463055== ==2463055== LEAK SUMMARY: ==2463055== definitely lost: 0 bytes in 0 blocks ==2463055== indirectly lost: 0 bytes in 0 blocks ==2463055== possibly lost: 158,559 bytes in 109 blocks ==2463055== still reachable: 3,575,447 bytes in 5,822 blocks ==2463055== of which reachable via heuristic: ==2463055== stdstring : 4,256 bytes in 48 blocks ==2463055== suppressed: 0 bytes in 0 blocks ==2463055== Rerun with --leak-check=full to see details of leaked memory ==2463055== ==2463055== For lists of detected and suppressed errors, rerun with: -s ==2463055== ERROR SUMMARY: 4 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.