!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_QuinticClampedSpline_ErcolessiAdams_1994_Al__MO_450093727396_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 = 93.14438092712905 Forces: 1 -5.61765477e+00 -6.61600686e+00 -6.88675454e+00 2 -1.45070898e+00 1.95419608e+00 -1.08564453e+01 3 3.17415962e+00 -1.02687377e+01 -1.35595508e+00 4 -9.34910809e+00 9.58544378e-02 3.59077766e+00 5 -1.86148954e+00 -1.24549349e+01 -8.84083785e+00 6 9.49413062e+00 2.94524644e+00 -1.17091954e+01 7 9.80744141e+00 -1.10571104e+01 9.82843338e-01 8 -3.93797236e+00 -4.26161613e+00 1.97126607e+00 9 -7.72788115e+00 -2.95031753e+00 -1.52696457e+01 10 1.37292595e+00 1.35300388e+01 -1.12215626e+01 11 -3.61178023e+00 -6.91198448e+00 3.54861208e+00 12 -1.20536581e+01 1.21980190e+01 3.71554987e+00 13 -6.84842015e-02 -2.89295526e+00 -1.68337950e+01 14 1.13629493e+01 1.02051088e+01 -9.15100495e+00 15 1.57023696e+01 -5.00488064e+00 2.32857210e-01 16 -7.88144847e-01 1.70064610e+01 2.46429322e+00 17 -1.52584524e+01 -7.85088855e+00 -3.76187299e+00 18 2.89282127e+00 7.43889293e+00 -2.25065668e-01 19 5.71338521e+00 -1.26572261e+01 9.74219734e+00 20 -7.73346765e+00 7.75642479e+00 8.54939140e+00 21 -5.61739070e+00 -1.13081039e+01 2.29069868e+00 22 1.30271147e+01 6.64324358e+00 2.32075793e+00 23 5.79938664e+00 -4.36250382e+00 8.46570200e+00 24 -1.39808069e+00 1.51596675e+00 7.37559327e+00 25 -1.19203197e+01 -4.83480839e+00 3.42543762e+00 26 1.03838381e+00 1.64754330e+01 -6.02496553e+00 27 -2.01009479e+00 -9.39652857e+00 9.76173736e+00 28 -9.15963398e+00 5.68506861e+00 5.49325855e+00 29 -3.10915809e+00 -8.30857721e+00 5.94269594e+00 30 1.00308022e+01 1.23363614e+01 1.88719475e-01 31 1.06428403e+01 -5.32992193e+00 8.96080068e+00 32 2.61476964e+00 1.06807867e+01 1.31139109e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 93.14438092712905 Forces: 1 -5.61765477e+00 -6.61600686e+00 -6.88675454e+00 2 -1.45070898e+00 1.95419608e+00 -1.08564453e+01 3 3.17415962e+00 -1.02687377e+01 -1.35595508e+00 4 -9.34910809e+00 9.58544378e-02 3.59077766e+00 5 -1.86148954e+00 -1.24549349e+01 -8.84083785e+00 6 9.49413062e+00 2.94524644e+00 -1.17091954e+01 7 9.80744141e+00 -1.10571104e+01 9.82843338e-01 8 -3.93797236e+00 -4.26161613e+00 1.97126607e+00 9 -7.72788115e+00 -2.95031753e+00 -1.52696457e+01 10 1.37292595e+00 1.35300388e+01 -1.12215626e+01 11 -3.61178023e+00 -6.91198448e+00 3.54861208e+00 12 -1.20536581e+01 1.21980190e+01 3.71554987e+00 13 -6.84842015e-02 -2.89295526e+00 -1.68337950e+01 14 1.13629493e+01 1.02051088e+01 -9.15100495e+00 15 1.57023696e+01 -5.00488064e+00 2.32857210e-01 16 -7.88144847e-01 1.70064610e+01 2.46429322e+00 17 -1.52584524e+01 -7.85088855e+00 -3.76187299e+00 18 2.89282127e+00 7.43889293e+00 -2.25065668e-01 19 5.71338521e+00 -1.26572261e+01 9.74219734e+00 20 -7.73346765e+00 7.75642479e+00 8.54939140e+00 21 -5.61739070e+00 -1.13081039e+01 2.29069868e+00 22 1.30271147e+01 6.64324358e+00 2.32075793e+00 23 5.79938664e+00 -4.36250382e+00 8.46570200e+00 24 -1.39808069e+00 1.51596675e+00 7.37559327e+00 25 -1.19203197e+01 -4.83480839e+00 3.42543762e+00 26 1.03838381e+00 1.64754330e+01 -6.02496553e+00 27 -2.01009479e+00 -9.39652857e+00 9.76173736e+00 28 -9.15963398e+00 5.68506861e+00 5.49325855e+00 29 -3.10915809e+00 -8.30857721e+00 5.94269594e+00 30 1.00308022e+01 1.23363614e+01 1.88719475e-01 31 1.06428403e+01 -5.32992193e+00 8.96080068e+00 32 2.61476964e+00 1.06807867e+01 1.31139109e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==3284539== Memcheck, a memory error detector ==3284539== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3284539== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==3284539== Command: python runner2.py EAM_QuinticClampedSpline_ErcolessiAdams_1994_Al__MO_450093727396_003 ==3284539== ==3284539== Invalid read of size 8 ==3284539== at 0x40286A0: strncmp (strcmp.S:170) ==3284539== by 0x400668D: is_dst (dl-load.c:216) ==3284539== by 0x400810E: _dl_dst_count (dl-load.c:253) ==3284539== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==3284539== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==3284539== by 0x4008602: decompose_rpath (dl-load.c:654) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:696) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:677) ==3284539== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==3284539== by 0x4003494: openaux (dl-deps.c:64) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==3284539== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x400DF99: dl_open_worker (dl-open.c:782) ==3284539== Address 0x64cd481 is 1 bytes inside a block of size 8 alloc'd ==3284539== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3284539== by 0x40271DF: malloc (rtld-malloc.h:56) ==3284539== by 0x40271DF: strdup (strdup.c:42) ==3284539== by 0x4008594: decompose_rpath (dl-load.c:629) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:696) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:677) ==3284539== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==3284539== by 0x4003494: openaux (dl-deps.c:64) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==3284539== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x400DF99: dl_open_worker (dl-open.c:782) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x400E34D: _dl_open (dl-open.c:883) ==3284539== ==3284539== Invalid read of size 8 ==3284539== at 0x40286A8: strncmp (strcmp.S:172) ==3284539== by 0x400668D: is_dst (dl-load.c:216) ==3284539== by 0x400810E: _dl_dst_count (dl-load.c:253) ==3284539== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==3284539== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==3284539== by 0x4008602: decompose_rpath (dl-load.c:654) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:696) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:677) ==3284539== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==3284539== by 0x4003494: openaux (dl-deps.c:64) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==3284539== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x400DF99: dl_open_worker (dl-open.c:782) ==3284539== Address 0x64cd489 is 1 bytes after a block of size 8 alloc'd ==3284539== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3284539== by 0x40271DF: malloc (rtld-malloc.h:56) ==3284539== by 0x40271DF: strdup (strdup.c:42) ==3284539== by 0x4008594: decompose_rpath (dl-load.c:629) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:696) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:677) ==3284539== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==3284539== by 0x4003494: openaux (dl-deps.c:64) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==3284539== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x400DF99: dl_open_worker (dl-open.c:782) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x400E34D: _dl_open (dl-open.c:883) ==3284539== ==3284539== Invalid read of size 8 ==3284539== at 0x40286A0: strncmp (strcmp.S:170) ==3284539== by 0x400668D: is_dst (dl-load.c:216) ==3284539== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==3284539== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==3284539== by 0x4008602: decompose_rpath (dl-load.c:654) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:696) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:677) ==3284539== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==3284539== by 0x4003494: openaux (dl-deps.c:64) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==3284539== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x400DF99: dl_open_worker (dl-open.c:782) ==3284539== Address 0x64cd481 is 1 bytes inside a block of size 8 alloc'd ==3284539== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3284539== by 0x40271DF: malloc (rtld-malloc.h:56) ==3284539== by 0x40271DF: strdup (strdup.c:42) ==3284539== by 0x4008594: decompose_rpath (dl-load.c:629) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:696) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:677) ==3284539== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==3284539== by 0x4003494: openaux (dl-deps.c:64) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==3284539== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x400DF99: dl_open_worker (dl-open.c:782) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x400E34D: _dl_open (dl-open.c:883) ==3284539== ==3284539== Invalid read of size 8 ==3284539== at 0x40286A8: strncmp (strcmp.S:172) ==3284539== by 0x400668D: is_dst (dl-load.c:216) ==3284539== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==3284539== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==3284539== by 0x4008602: decompose_rpath (dl-load.c:654) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:696) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:677) ==3284539== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==3284539== by 0x4003494: openaux (dl-deps.c:64) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==3284539== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x400DF99: dl_open_worker (dl-open.c:782) ==3284539== Address 0x64cd489 is 1 bytes after a block of size 8 alloc'd ==3284539== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==3284539== by 0x40271DF: malloc (rtld-malloc.h:56) ==3284539== by 0x40271DF: strdup (strdup.c:42) ==3284539== by 0x4008594: decompose_rpath (dl-load.c:629) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:696) ==3284539== by 0x400A8C8: cache_rpath (dl-load.c:677) ==3284539== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==3284539== by 0x4003494: openaux (dl-deps.c:64) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==3284539== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x400DF99: dl_open_worker (dl-open.c:782) ==3284539== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==3284539== by 0x400E34D: _dl_open (dl-open.c:883) ==3284539== ==3284539== ==3284539== HEAP SUMMARY: ==3284539== in use at exit: 3,734,006 bytes in 5,931 blocks ==3284539== total heap usage: 83,818 allocs, 77,887 frees, 321,460,616 bytes allocated ==3284539== ==3284539== LEAK SUMMARY: ==3284539== definitely lost: 0 bytes in 0 blocks ==3284539== indirectly lost: 0 bytes in 0 blocks ==3284539== possibly lost: 158,559 bytes in 109 blocks ==3284539== still reachable: 3,575,447 bytes in 5,822 blocks ==3284539== of which reachable via heuristic: ==3284539== stdstring : 4,256 bytes in 48 blocks ==3284539== suppressed: 0 bytes in 0 blocks ==3284539== Rerun with --leak-check=full to see details of leaked memory ==3284539== ==3284539== For lists of detected and suppressed errors, rerun with: -s ==3284539== 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.