Enter a model name: === Verification check vc-memory-leak start (2022-11-29 20:32:22) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Sim_LAMMPS_SMTBQ_SallesPolitanoAmzallag_2016_Al__SM_404097633924_000 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 = 97.00065493354583 Forces: 1 -5.70048871e+00 -1.01788367e+01 -1.05623667e+01 2 -9.71816626e+00 1.45643635e+01 -1.44715871e+01 3 -1.55269598e+00 -1.54479365e+01 -1.62108525e+00 4 -9.22604778e+00 4.47888618e+00 4.83810106e+00 5 1.41172604e+01 -2.28475052e+01 -5.66314983e+00 6 5.89100782e+00 1.16345122e+00 -9.19656981e+00 7 9.03115220e+00 -3.20844841e+01 -2.77778298e+01 8 -9.17523627e+00 -1.15702204e+01 -5.51320528e+00 9 -1.23089292e+01 -1.62826126e+01 -2.83919260e+01 10 -1.45033046e+00 2.47013799e+01 -2.48217255e+01 11 -4.94742879e+00 -1.65874715e+01 9.79930762e+00 12 -1.80737458e+01 2.35090654e+01 1.23776482e+01 13 -4.09369238e+00 -1.22980374e+01 -4.72029267e+01 14 1.01251282e+01 1.22350863e+01 -8.51658290e+00 15 4.25372140e+01 -4.70119289e+00 9.45721947e+00 16 5.22697258e+00 3.49368768e+01 1.45391206e+01 17 -1.41262819e+01 -6.95219389e+00 -4.70820881e+00 18 -7.54726748e+00 8.77790527e+00 7.16956949e+00 19 5.75540254e+00 -1.21001259e+01 9.62424797e+00 20 -6.54965329e+00 8.42370613e+00 7.70139805e+00 21 -1.01320665e+01 -1.56307770e+01 9.78330049e+00 22 2.33823676e+01 2.29073532e+01 2.21855065e+01 23 5.29880225e+00 -2.61635627e+00 8.70123543e+00 24 3.01259248e+00 4.72517822e-01 8.99203352e+00 25 -1.37287183e+01 -3.89849531e+00 9.31415099e+00 26 -8.49150008e+00 2.25904886e+01 -9.54713106e+00 27 8.71155304e+00 -3.24380741e+01 1.30571744e+01 28 -2.87728128e+01 2.33864800e+01 5.56035338e+00 29 -7.04949196e+00 -1.05578885e+01 8.90721390e+00 30 1.16353694e+01 1.68335416e+01 1.51979044e+00 31 1.81855979e+01 -1.00661351e+01 1.56631929e+01 32 9.73413345e+00 1.72772414e+01 1.88037303e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 97.00065493354583 Forces: 1 -5.70048871e+00 -1.01788367e+01 -1.05623667e+01 2 -9.71816626e+00 1.45643635e+01 -1.44715871e+01 3 -1.55269598e+00 -1.54479365e+01 -1.62108525e+00 4 -9.22604778e+00 4.47888618e+00 4.83810106e+00 5 1.41172604e+01 -2.28475052e+01 -5.66314983e+00 6 5.89100782e+00 1.16345122e+00 -9.19656981e+00 7 9.03115220e+00 -3.20844841e+01 -2.77778298e+01 8 -9.17523627e+00 -1.15702204e+01 -5.51320528e+00 9 -1.23089292e+01 -1.62826126e+01 -2.83919260e+01 10 -1.45033046e+00 2.47013799e+01 -2.48217255e+01 11 -4.94742879e+00 -1.65874715e+01 9.79930762e+00 12 -1.80737458e+01 2.35090654e+01 1.23776482e+01 13 -4.09369238e+00 -1.22980374e+01 -4.72029267e+01 14 1.01251282e+01 1.22350863e+01 -8.51658290e+00 15 4.25372140e+01 -4.70119289e+00 9.45721947e+00 16 5.22697258e+00 3.49368768e+01 1.45391206e+01 17 -1.41262819e+01 -6.95219389e+00 -4.70820881e+00 18 -7.54726748e+00 8.77790527e+00 7.16956949e+00 19 5.75540254e+00 -1.21001259e+01 9.62424797e+00 20 -6.54965329e+00 8.42370613e+00 7.70139805e+00 21 -1.01320665e+01 -1.56307770e+01 9.78330049e+00 22 2.33823676e+01 2.29073532e+01 2.21855065e+01 23 5.29880225e+00 -2.61635627e+00 8.70123543e+00 24 3.01259248e+00 4.72517822e-01 8.99203352e+00 25 -1.37287183e+01 -3.89849531e+00 9.31415099e+00 26 -8.49150008e+00 2.25904886e+01 -9.54713106e+00 27 8.71155304e+00 -3.24380741e+01 1.30571744e+01 28 -2.87728128e+01 2.33864800e+01 5.56035338e+00 29 -7.04949196e+00 -1.05578885e+01 8.90721390e+00 30 1.16353694e+01 1.68335416e+01 1.51979044e+00 31 1.81855979e+01 -1.00661351e+01 1.56631929e+01 32 9.73413345e+00 1.72772414e+01 1.88037303e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==170599== Memcheck, a memory error detector ==170599== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==170599== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==170599== Command: python runner2.py Sim_LAMMPS_SMTBQ_SallesPolitanoAmzallag_2016_Al__SM_404097633924_000 ==170599== ==170946== Warning: invalid file descriptor 255988 in syscall close() ==170946== Warning: invalid file descriptor 255989 in syscall close() ==170946== Warning: invalid file descriptor 255990 in syscall close() ==170946== Warning: invalid file descriptor 255991 in syscall close() ==170946== Use --log-fd= to select an alternative log fd. ==170946== Warning: invalid file descriptor 255992 in syscall close() ==170946== Warning: invalid file descriptor 255993 in syscall close() -------------------------------------------------------------------------- By default, for Open MPI 4.0 and later, infiniband ports on a device are not used by default. The intent is to use UCX for these devices. You can override this policy by setting the btl_openib_allow_ib MCA parameter to true. Local host: c401-004 Local adapter: hfi1_0 Local port: 1 -------------------------------------------------------------------------- ==170599== Conditional jump or move depends on uninitialised value(s) ==170599== at 0x1397E97B: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==170599== by 0x115E4C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x1396B527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==170599== by 0x115A1670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==170599== by 0x115A56714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==170599== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==170599== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==170599== by 0x114DF3A4F: lammps_open (in /usr/local/lib/liblammps.so.0) ==170599== by 0x5A7EFF4: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==170599== by 0x5A7E409: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==170599== by 0x8C02305: _ctypes_callproc (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==170599== by 0x8C02AE6: ??? (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==170599== -------------------------------------------------------------------------- WARNING: There is at least non-excluded one OpenFabrics device found, but there are no active ports detected (or Open MPI was unable to use them). This is most certainly not what you wanted. Check your cables, subnet manager configuration, etc. The openib BTL will be ignored for this job. Local host: c401-004 -------------------------------------------------------------------------- ==170599== Syscall param rt_sigaction(act->sa_mask) points to uninitialised byte(s) ==170599== at 0x4893166: __libc_sigaction (sigaction.c:58) ==170599== by 0x224D5B4F: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==170599== by 0x224DB890: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==170599== by 0x224DC47A: psm2_ep_open (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==170599== by 0x2253730D: ompi_mtl_psm2_module_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==170599== by 0x22537764: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==170599== by 0x115A3AC53: ompi_mtl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==170599== by 0x13974E4D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pml_cm.so) ==170599== by 0x115A49673: mca_pml_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==170599== by 0x115A56789: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==170599== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==170599== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==170599== Address 0x1ffeffd9a8 is on thread 1's stack ==170599== in frame #0, created by __libc_sigaction (sigaction.c:43) ==170599== ==170599== Syscall param rt_sigaction(act->sa_mask) points to uninitialised byte(s) ==170599== at 0x4893166: __libc_sigaction (sigaction.c:58) ==170599== by 0x224D5B63: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==170599== by 0x224DB890: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==170599== by 0x224DC47A: psm2_ep_open (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==170599== by 0x2253730D: ompi_mtl_psm2_module_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==170599== by 0x22537764: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==170599== by 0x115A3AC53: ompi_mtl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==170599== by 0x13974E4D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pml_cm.so) ==170599== by 0x115A49673: mca_pml_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==170599== by 0x115A56789: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==170599== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==170599== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==170599== Address 0x1ffeffd9a8 is on thread 1's stack ==170599== in frame #0, created by __libc_sigaction (sigaction.c:43) ==170599== ==170599== Conditional jump or move depends on uninitialised value(s) ==170599== at 0x115E06E84: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x1395B4B2: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==170599== by 0x115E5CFA4: mca_rcache_base_mem_cb (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E072FB: opal_mem_hooks_release_hook (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E5775A: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x4881F9B: _nl_unload_locale (loadlocale.c:298) ==170599== by 0x49E84BD: _nl_locale_subfreeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x49E73A6: free_mem (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x49E8B21: __libc_freeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x48311C6: _vgnU_freeres (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_core-amd64-linux.so) ==170599== by 0x48969C1: __run_exit_handlers (exit.c:132) ==170599== ==170599== Use of uninitialised value of size 8 ==170599== at 0x115E06EAD: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x1395B4B2: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==170599== by 0x115E5CFA4: mca_rcache_base_mem_cb (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E072FB: opal_mem_hooks_release_hook (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E5775A: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x4881F9B: _nl_unload_locale (loadlocale.c:298) ==170599== by 0x49E84BD: _nl_locale_subfreeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x49E73A6: free_mem (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x49E8B21: __libc_freeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x48311C6: _vgnU_freeres (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_core-amd64-linux.so) ==170599== by 0x48969C1: __run_exit_handlers (exit.c:132) ==170599== ==170599== Use of uninitialised value of size 8 ==170599== at 0x115E06EB4: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x1395B4B2: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==170599== by 0x115E5CFA4: mca_rcache_base_mem_cb (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E072FB: opal_mem_hooks_release_hook (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E5775A: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x4881F9B: _nl_unload_locale (loadlocale.c:298) ==170599== by 0x49E84BD: _nl_locale_subfreeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x49E73A6: free_mem (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x49E8B21: __libc_freeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x48311C6: _vgnU_freeres (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_core-amd64-linux.so) ==170599== by 0x48969C1: __run_exit_handlers (exit.c:132) ==170599== ==170599== Use of uninitialised value of size 8 ==170599== at 0x115E06ED3: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x1395B4B2: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==170599== by 0x115E5CFA4: mca_rcache_base_mem_cb (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E072FB: opal_mem_hooks_release_hook (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E5775A: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x4881F9B: _nl_unload_locale (loadlocale.c:298) ==170599== by 0x49E84BD: _nl_locale_subfreeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x49E73A6: free_mem (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x49E8B21: __libc_freeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x48311C6: _vgnU_freeres (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_core-amd64-linux.so) ==170599== by 0x48969C1: __run_exit_handlers (exit.c:132) ==170599== ==170599== Conditional jump or move depends on uninitialised value(s) ==170599== at 0x115E06F09: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x1395B4B2: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==170599== by 0x115E5CFA4: mca_rcache_base_mem_cb (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E072FB: opal_mem_hooks_release_hook (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x115E5775A: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==170599== by 0x49E8B21: __libc_freeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==170599== by 0x48311C6: _vgnU_freeres (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_core-amd64-linux.so) ==170599== by 0x48969C1: __run_exit_handlers (exit.c:132) ==170599== by 0x4896A5F: exit (exit.c:139) ==170599== by 0x4874089: (below main) (libc-start.c:342) ==170599== ==170599== ==170599== HEAP SUMMARY: ==170599== in use at exit: 53,189,730 bytes in 18,085 blocks ==170599== total heap usage: 3,782,084 allocs, 3,763,999 frees, 1,089,818,993 bytes allocated ==170599== ==170599== LEAK SUMMARY: ==170599== definitely lost: 16,469,224 bytes in 113 blocks ==170599== indirectly lost: 7,560,993 bytes in 20 blocks ==170599== possibly lost: 1,022,744 bytes in 111 blocks ==170599== still reachable: 28,136,737 bytes in 17,840 blocks ==170599== of which reachable via heuristic: ==170599== stdstring : 38 bytes in 1 blocks ==170599== suppressed: 32 bytes in 1 blocks ==170599== Rerun with --leak-check=full to see details of leaked memory ==170599== ==170599== Use --track-origins=yes to see where uninitialised values come from ==170599== For lists of detected and suppressed errors, rerun with: -s ==170599== ERROR SUMMARY: 12 errors from 8 contexts (suppressed: 8207 from 610) ================================================================================ 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" (Search for the word "lost" in the file to identify memory leaks.) Grade: F Comment: Memory leak detected. === Verification check vc-memory-leak end (2022-11-29 20:47:44) ===