!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ADP_MishinMehlPapaconstantopoulos_2005_Ni__SM_477692857359_000 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 = -55.524053824940864 Forces: 1 -1.46451743e+00 -2.53023279e+00 -2.82294795e+00 2 -1.54547017e+00 1.71126970e+00 -3.74797877e+00 3 1.57347061e+00 -4.26303233e+00 3.54099690e-02 4 -3.47434538e+00 1.13841994e+00 5.91490761e-01 5 2.32759823e+00 -4.54328202e+00 -1.81194128e+00 6 9.27202849e-01 1.72483373e+00 -2.03545542e+00 7 3.16642896e+00 -6.06919049e+00 -3.65034611e+00 8 -3.09505790e+00 -3.23080977e+00 -1.31465496e+00 9 -4.20400382e+00 -2.89843065e+00 -6.05965239e+00 10 -1.94030374e-01 8.32431100e+00 -6.53000142e+00 11 -2.10937025e+00 -5.74836070e+00 3.06556698e+00 12 -4.59225751e+00 5.62532588e+00 1.37636027e+00 13 4.76829021e+00 -2.75158100e+00 -8.84191882e+00 14 9.67212166e-01 1.48670868e+00 -8.95108851e-01 15 7.57498420e+00 -1.35606514e+00 -3.40514614e+00 16 2.64491723e+00 8.61811364e+00 2.19946935e+00 17 -5.94111702e+00 -3.19612192e+00 -1.76944354e+00 18 1.47685640e+00 4.15737697e+00 4.75308655e-01 19 2.22988467e+00 -4.60933260e+00 3.56101995e+00 20 -2.01044220e+00 3.90630379e+00 2.63917947e+00 21 -3.79569444e+00 -4.60399593e+00 1.08418015e+00 22 6.03841896e+00 3.76747076e+00 3.55881287e+00 23 1.92391863e+00 -8.27487443e-01 2.56648756e+00 24 -2.35714111e-01 1.02363338e+00 2.20298107e+00 25 -3.68779031e+00 -1.99325700e+00 3.43920760e+00 26 -1.32600643e+00 6.54366415e+00 -2.51229348e+00 27 3.76002204e-02 -6.88848798e+00 3.96694757e+00 28 -4.68943948e+00 3.26593897e+00 1.78450897e+00 29 -3.37942103e+00 -3.96813888e+00 3.10986876e+00 30 2.96334442e+00 6.27215552e+00 3.57405532e-01 31 4.98885293e+00 -2.87979978e+00 4.16597513e+00 32 2.13569716e+00 4.79208028e+00 5.21670850e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -55.524053824940864 Forces: 1 -1.46451743e+00 -2.53023279e+00 -2.82294795e+00 2 -1.54547017e+00 1.71126970e+00 -3.74797877e+00 3 1.57347061e+00 -4.26303233e+00 3.54099690e-02 4 -3.47434538e+00 1.13841994e+00 5.91490761e-01 5 2.32759823e+00 -4.54328202e+00 -1.81194128e+00 6 9.27202849e-01 1.72483373e+00 -2.03545542e+00 7 3.16642896e+00 -6.06919049e+00 -3.65034611e+00 8 -3.09505790e+00 -3.23080977e+00 -1.31465496e+00 9 -4.20400382e+00 -2.89843065e+00 -6.05965239e+00 10 -1.94030374e-01 8.32431100e+00 -6.53000142e+00 11 -2.10937025e+00 -5.74836070e+00 3.06556698e+00 12 -4.59225751e+00 5.62532588e+00 1.37636027e+00 13 4.76829021e+00 -2.75158100e+00 -8.84191882e+00 14 9.67212166e-01 1.48670868e+00 -8.95108851e-01 15 7.57498420e+00 -1.35606514e+00 -3.40514614e+00 16 2.64491723e+00 8.61811364e+00 2.19946935e+00 17 -5.94111702e+00 -3.19612192e+00 -1.76944354e+00 18 1.47685640e+00 4.15737697e+00 4.75308655e-01 19 2.22988467e+00 -4.60933260e+00 3.56101995e+00 20 -2.01044220e+00 3.90630379e+00 2.63917947e+00 21 -3.79569444e+00 -4.60399593e+00 1.08418015e+00 22 6.03841896e+00 3.76747076e+00 3.55881287e+00 23 1.92391863e+00 -8.27487443e-01 2.56648756e+00 24 -2.35714111e-01 1.02363338e+00 2.20298107e+00 25 -3.68779031e+00 -1.99325700e+00 3.43920760e+00 26 -1.32600643e+00 6.54366415e+00 -2.51229348e+00 27 3.76002204e-02 -6.88848798e+00 3.96694757e+00 28 -4.68943948e+00 3.26593897e+00 1.78450897e+00 29 -3.37942103e+00 -3.96813888e+00 3.10986876e+00 30 2.96334442e+00 6.27215552e+00 3.57405532e-01 31 4.98885293e+00 -2.87979978e+00 4.16597513e+00 32 2.13569716e+00 4.79208028e+00 5.21670850e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==253608== Memcheck, a memory error detector ==253608== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==253608== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==253608== Command: python runner2.py Sim_LAMMPS_ADP_MishinMehlPapaconstantopoulos_2005_Ni__SM_477692857359_000 ==253608== ==254467== Warning: invalid file descriptor 255988 in syscall close() ==254467== Warning: invalid file descriptor 255989 in syscall close() ==254467== Warning: invalid file descriptor 255990 in syscall close() ==254467== Warning: invalid file descriptor 255991 in syscall close() ==254467== Use --log-fd= to select an alternative log fd. ==254467== Warning: invalid file descriptor 255992 in syscall close() ==254467== 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: c401-061 Local adapter: hfi1_0 Local port: 1 -------------------------------------------------------------------------- ==253608== Conditional jump or move depends on uninitialised value(s) ==253608== at 0x55D3897B: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==253608== by 0x112169C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D25527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==253608== by 0x8DDA70A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8E1A714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8DBE072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x528C4165: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==253608== by 0x528C419F: lammps_open (in /usr/local/lib/liblammps.so.0) ==253608== by 0x57FF7FF4: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==253608== by 0x57FF7409: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==253608== by 0x20B79A305: _ctypes_callproc (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==253608== by 0x20B79AAE6: ??? (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==253608== -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: c401-061 Local device: hfi1_0 -------------------------------------------------------------------------- ==253608== Conditional jump or move depends on uninitialised value(s) ==253608== at 0x111D0E84: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x11226E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D15B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==253608== by 0x11226957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D36356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==253608== by 0x55D38D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==253608== by 0x112169C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D25527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==253608== by 0x8DDA70A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8E1A714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8DBE072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x528C4165: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==253608== ==253608== Use of uninitialised value of size 8 ==253608== at 0x111D0EAD: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x11226E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D15B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==253608== by 0x11226957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D36356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==253608== by 0x55D38D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==253608== by 0x112169C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D25527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==253608== by 0x8DDA70A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8E1A714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8DBE072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x528C4165: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==253608== ==253608== Use of uninitialised value of size 8 ==253608== at 0x111D0EB4: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x11226E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D15B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==253608== by 0x11226957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D36356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==253608== by 0x55D38D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==253608== by 0x112169C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D25527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==253608== by 0x8DDA70A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8E1A714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8DBE072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x528C4165: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==253608== ==253608== Use of uninitialised value of size 8 ==253608== at 0x111D0ED3: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x11226E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D15B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==253608== by 0x11226957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D36356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==253608== by 0x55D38D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==253608== by 0x112169C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==253608== by 0x55D25527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==253608== by 0x8DDA70A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8E1A714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8DBE072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x528C4165: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==253608== ==253608== Syscall param rt_sigaction(act->sa_mask) points to uninitialised byte(s) ==253608== at 0x4893166: __libc_sigaction (sigaction.c:58) ==253608== by 0x560BDB4F: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==253608== by 0x560C3890: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==253608== by 0x560C447A: psm2_ep_open (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==253608== by 0x5614430D: ompi_mtl_psm2_module_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==253608== by 0x56144764: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==253608== by 0x8DFEC53: ompi_mtl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x55D2EE4D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pml_cm.so) ==253608== by 0x8E0D673: mca_pml_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8E1A789: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8DBE072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x528C4165: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==253608== Address 0x1ffeffd9a8 is on thread 1's stack ==253608== in frame #0, created by __libc_sigaction (sigaction.c:43) ==253608== ==253608== Syscall param rt_sigaction(act->sa_mask) points to uninitialised byte(s) ==253608== at 0x4893166: __libc_sigaction (sigaction.c:58) ==253608== by 0x560BDB63: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==253608== by 0x560C3890: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==253608== by 0x560C447A: psm2_ep_open (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==253608== by 0x5614430D: ompi_mtl_psm2_module_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==253608== by 0x56144764: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==253608== by 0x8DFEC53: ompi_mtl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x55D2EE4D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pml_cm.so) ==253608== by 0x8E0D673: mca_pml_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8E1A789: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x8DBE072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==253608== by 0x528C4165: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==253608== Address 0x1ffeffd9a8 is on thread 1's stack ==253608== in frame #0, created by __libc_sigaction (sigaction.c:43) ==253608== ==253608== ==253608== HEAP SUMMARY: ==253608== in use at exit: 28,130,164 bytes in 17,850 blocks ==253608== total heap usage: 750,305 allocs, 732,455 frees, 157,323,193 bytes allocated ==253608== ==253608== LEAK SUMMARY: ==253608== definitely lost: 11,787 bytes in 37 blocks ==253608== indirectly lost: 121 bytes in 7 blocks ==253608== possibly lost: 184,788 bytes in 102 blocks ==253608== still reachable: 27,933,436 bytes in 17,703 blocks ==253608== suppressed: 32 bytes in 1 blocks ==253608== Rerun with --leak-check=full to see details of leaked memory ==253608== ==253608== Use --track-origins=yes to see where uninitialised values come from ==253608== For lists of detected and suppressed errors, rerun with: -s ==253608== ERROR SUMMARY: 7 errors from 7 contexts (suppressed: 19489 from 634) ================================================================================ 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. ERROR: Unable to perform verification check. Message = Failed to run valgrind; check that it is installed.