!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_2004_Ti__MO_723456820410_006 Supported species : Ti random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ti (Configuration in file "config-F-Ti.xyz") ----------------------------------------------------------------------------------------------------- Energy = 241.60808192766675 Forces: 1 -1.03855670e+01 -1.93270250e+01 -2.05699637e+01 2 -9.52389946e+00 1.25127619e+01 -1.84917637e+01 3 1.11376813e+01 -1.48690560e+01 -3.47193645e+00 4 -1.51577856e+01 1.35769711e+01 1.02773579e+01 5 -2.01768989e+00 -3.20960198e+01 -1.01715492e+01 6 1.98547247e+01 1.12024300e+01 -2.15116819e+01 7 1.90526180e+01 -5.82928010e+01 -4.16873414e+01 8 -3.10981857e+01 -2.30320276e+01 -2.61314836e+00 9 -1.73438601e+01 -2.77292836e+01 -4.42800825e+01 10 -4.11016344e+00 3.91070884e+01 -4.24405313e+01 11 -1.59274354e+01 -2.94836522e+01 1.50932296e+01 12 -2.95682472e+01 3.48727182e+01 2.56382659e+01 13 -1.23887868e+01 -2.70277397e+01 -8.30755331e+01 14 1.89066627e+01 2.30035919e+01 -1.76677680e+01 15 7.33306554e+01 -2.11668789e+01 9.14719664e+00 16 7.04723187e+00 6.34352164e+01 2.43638327e+01 17 -4.04811983e+01 -2.75692075e+01 -1.22007535e+01 18 2.79144524e+01 3.57157340e+01 -3.34347926e+01 19 1.29776118e+01 -4.51444521e+01 2.81890963e+01 20 -3.21699860e+01 1.52912760e+01 3.62368471e+01 21 -2.56109845e+01 -2.33813852e+01 1.26198820e+01 22 4.33556363e+01 4.22162340e+01 4.24600485e+01 23 1.12600800e+01 -5.42538824e+00 1.53464493e+01 24 1.17068920e+01 1.04404443e+01 1.78571811e+01 25 -3.10752336e+01 -9.06121082e+00 -1.01011995e+01 26 -1.17995462e+01 4.42123058e+01 -1.90224486e+01 27 2.46875727e+01 -5.96321139e+01 3.27356844e+01 28 -5.42190321e+01 4.83284449e+01 1.64330979e+01 29 -1.48335673e+01 -2.27430418e+01 1.95554445e+01 30 2.41938837e+01 3.51832484e+01 1.75103906e+01 31 3.35303250e+01 -1.44216747e+01 2.37073554e+01 32 1.87551407e+01 3.13044929e+01 3.35691341e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ti (Configuration in file "config-T-Ti.xyz") ----------------------------------------------------------------------------------------------------- Energy = 241.60808192766675 Forces: 1 -1.03855670e+01 -1.93270250e+01 -2.05699637e+01 2 -9.52389946e+00 1.25127619e+01 -1.84917637e+01 3 1.11376813e+01 -1.48690560e+01 -3.47193645e+00 4 -1.51577856e+01 1.35769711e+01 1.02773579e+01 5 -2.01768989e+00 -3.20960198e+01 -1.01715492e+01 6 1.98547247e+01 1.12024300e+01 -2.15116819e+01 7 1.90526180e+01 -5.82928010e+01 -4.16873414e+01 8 -3.10981857e+01 -2.30320276e+01 -2.61314836e+00 9 -1.73438601e+01 -2.77292836e+01 -4.42800825e+01 10 -4.11016344e+00 3.91070884e+01 -4.24405313e+01 11 -1.59274354e+01 -2.94836522e+01 1.50932296e+01 12 -2.95682472e+01 3.48727182e+01 2.56382659e+01 13 -1.23887868e+01 -2.70277397e+01 -8.30755331e+01 14 1.89066627e+01 2.30035919e+01 -1.76677680e+01 15 7.33306554e+01 -2.11668789e+01 9.14719664e+00 16 7.04723187e+00 6.34352164e+01 2.43638327e+01 17 -4.04811983e+01 -2.75692075e+01 -1.22007535e+01 18 2.79144524e+01 3.57157340e+01 -3.34347926e+01 19 1.29776118e+01 -4.51444521e+01 2.81890963e+01 20 -3.21699860e+01 1.52912760e+01 3.62368471e+01 21 -2.56109845e+01 -2.33813852e+01 1.26198820e+01 22 4.33556363e+01 4.22162340e+01 4.24600485e+01 23 1.12600800e+01 -5.42538824e+00 1.53464493e+01 24 1.17068920e+01 1.04404443e+01 1.78571811e+01 25 -3.10752336e+01 -9.06121082e+00 -1.01011995e+01 26 -1.17995462e+01 4.42123058e+01 -1.90224486e+01 27 2.46875727e+01 -5.96321139e+01 3.27356844e+01 28 -5.42190321e+01 4.83284449e+01 1.64330979e+01 29 -1.48335673e+01 -2.27430418e+01 1.95554445e+01 30 2.41938837e+01 3.51832484e+01 1.75103906e+01 31 3.35303250e+01 -1.44216747e+01 2.37073554e+01 32 1.87551407e+01 3.13044929e+01 3.35691341e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==398338== Memcheck, a memory error detector ==398338== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==398338== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==398338== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004_Ti__MO_723456820410_006 ==398338== ==398338== Invalid read of size 8 ==398338== at 0x40286A0: strncmp (strcmp.S:170) ==398338== by 0x400668D: is_dst (dl-load.c:216) ==398338== by 0x400810E: _dl_dst_count (dl-load.c:253) ==398338== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==398338== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==398338== by 0x4008602: decompose_rpath (dl-load.c:654) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:696) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:677) ==398338== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==398338== by 0x4003494: openaux (dl-deps.c:64) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==398338== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x400DF99: dl_open_worker (dl-open.c:782) ==398338== Address 0x64cd2c1 is 1 bytes inside a block of size 8 alloc'd ==398338== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==398338== by 0x40271DF: malloc (rtld-malloc.h:56) ==398338== by 0x40271DF: strdup (strdup.c:42) ==398338== by 0x4008594: decompose_rpath (dl-load.c:629) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:696) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:677) ==398338== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==398338== by 0x4003494: openaux (dl-deps.c:64) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==398338== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x400DF99: dl_open_worker (dl-open.c:782) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x400E34D: _dl_open (dl-open.c:883) ==398338== ==398338== Invalid read of size 8 ==398338== at 0x40286A8: strncmp (strcmp.S:172) ==398338== by 0x400668D: is_dst (dl-load.c:216) ==398338== by 0x400810E: _dl_dst_count (dl-load.c:253) ==398338== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==398338== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==398338== by 0x4008602: decompose_rpath (dl-load.c:654) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:696) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:677) ==398338== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==398338== by 0x4003494: openaux (dl-deps.c:64) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==398338== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x400DF99: dl_open_worker (dl-open.c:782) ==398338== Address 0x64cd2c9 is 1 bytes after a block of size 8 alloc'd ==398338== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==398338== by 0x40271DF: malloc (rtld-malloc.h:56) ==398338== by 0x40271DF: strdup (strdup.c:42) ==398338== by 0x4008594: decompose_rpath (dl-load.c:629) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:696) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:677) ==398338== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==398338== by 0x4003494: openaux (dl-deps.c:64) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==398338== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x400DF99: dl_open_worker (dl-open.c:782) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x400E34D: _dl_open (dl-open.c:883) ==398338== ==398338== Invalid read of size 8 ==398338== at 0x40286A0: strncmp (strcmp.S:170) ==398338== by 0x400668D: is_dst (dl-load.c:216) ==398338== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==398338== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==398338== by 0x4008602: decompose_rpath (dl-load.c:654) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:696) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:677) ==398338== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==398338== by 0x4003494: openaux (dl-deps.c:64) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==398338== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x400DF99: dl_open_worker (dl-open.c:782) ==398338== Address 0x64cd2c1 is 1 bytes inside a block of size 8 alloc'd ==398338== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==398338== by 0x40271DF: malloc (rtld-malloc.h:56) ==398338== by 0x40271DF: strdup (strdup.c:42) ==398338== by 0x4008594: decompose_rpath (dl-load.c:629) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:696) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:677) ==398338== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==398338== by 0x4003494: openaux (dl-deps.c:64) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==398338== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x400DF99: dl_open_worker (dl-open.c:782) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x400E34D: _dl_open (dl-open.c:883) ==398338== ==398338== Invalid read of size 8 ==398338== at 0x40286A8: strncmp (strcmp.S:172) ==398338== by 0x400668D: is_dst (dl-load.c:216) ==398338== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==398338== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==398338== by 0x4008602: decompose_rpath (dl-load.c:654) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:696) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:677) ==398338== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==398338== by 0x4003494: openaux (dl-deps.c:64) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==398338== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x400DF99: dl_open_worker (dl-open.c:782) ==398338== Address 0x64cd2c9 is 1 bytes after a block of size 8 alloc'd ==398338== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==398338== by 0x40271DF: malloc (rtld-malloc.h:56) ==398338== by 0x40271DF: strdup (strdup.c:42) ==398338== by 0x4008594: decompose_rpath (dl-load.c:629) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:696) ==398338== by 0x400A8C8: cache_rpath (dl-load.c:677) ==398338== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==398338== by 0x4003494: openaux (dl-deps.c:64) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==398338== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x400DF99: dl_open_worker (dl-open.c:782) ==398338== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==398338== by 0x400E34D: _dl_open (dl-open.c:883) ==398338== ==398338== ==398338== HEAP SUMMARY: ==398338== in use at exit: 3,734,006 bytes in 5,931 blocks ==398338== total heap usage: 83,564 allocs, 77,633 frees, 322,287,932 bytes allocated ==398338== ==398338== LEAK SUMMARY: ==398338== definitely lost: 0 bytes in 0 blocks ==398338== indirectly lost: 0 bytes in 0 blocks ==398338== possibly lost: 158,559 bytes in 109 blocks ==398338== still reachable: 3,575,447 bytes in 5,822 blocks ==398338== of which reachable via heuristic: ==398338== stdstring : 4,256 bytes in 48 blocks ==398338== suppressed: 0 bytes in 0 blocks ==398338== Rerun with --leak-check=full to see details of leaked memory ==398338== ==398338== For lists of detected and suppressed errors, rerun with: -s ==398338== 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.