!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_StarikovKolotovaKuksin_2017_UMo__SM_682749584055_000 Supported species : Mo U random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mo (Configuration in file "config-F-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 29.62014300777277 Forces: 1 -7.19027694e+00 -6.66475472e+00 -7.90217137e+00 2 1.28304642e+00 -2.36589456e+00 -1.20959677e+01 3 4.68510730e-01 -9.46818547e+00 1.26472174e+00 4 -1.17806305e+01 4.88991608e-01 -6.86819822e-01 5 -4.49847595e+00 -8.79802147e+00 -5.43948636e+00 6 1.48849089e+01 7.40352215e-01 -1.64441244e+01 7 3.95607507e+00 -7.88070112e+00 3.79632129e+00 8 8.08033096e-01 -2.84283420e-01 3.26870570e+00 9 -7.06294374e+00 1.89064317e+00 -9.44293739e+00 10 -2.62536188e-01 7.94946055e+00 -6.02413515e+00 11 -3.73639958e+00 -5.34953968e+00 -3.32034744e+00 12 -9.38276021e+00 7.70812214e+00 9.96449584e-01 13 1.61457513e+00 7.94121043e-01 -8.45236902e+00 14 8.00327966e+00 7.83232937e+00 -7.29827663e+00 15 8.33548023e+00 1.21152887e-01 -1.48897615e+00 16 -2.50338689e+00 9.81043215e+00 -2.75264862e+00 17 -8.56828506e+00 -5.83033851e+00 1.98414421e-01 18 -8.37016225e-01 -3.95371526e-01 2.84826281e+00 19 -7.55311182e-01 -8.22671356e+00 7.27949596e+00 20 -6.12563680e+00 1.26332148e+00 6.26965905e+00 21 1.59431519e+00 -1.06677530e+01 1.43535273e+00 22 1.22115908e+01 -8.23737221e-01 1.53379581e+00 23 6.10706240e+00 -4.82126259e+00 5.80984347e+00 24 1.38185226e+00 -5.27875679e-01 8.97642078e+00 25 -6.44806055e+00 1.77897852e+00 -2.20116739e-01 26 2.12543858e+00 7.74747507e+00 2.83039678e-01 27 -4.08481263e+00 9.98066888e-01 1.07506800e+01 28 -5.79214248e+00 5.20675766e+00 5.30162689e+00 29 9.68099445e-01 2.54259321e+00 4.34370659e+00 30 8.33591095e+00 6.91477299e+00 2.46342498e-02 31 6.00009057e+00 1.19522673e+00 7.03335141e+00 32 9.50405533e-01 7.12163486e+00 1.01538946e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mo (Configuration in file "config-T-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 29.62014300777277 Forces: 1 -7.19027694e+00 -6.66475472e+00 -7.90217137e+00 2 1.28304642e+00 -2.36589456e+00 -1.20959677e+01 3 4.68510730e-01 -9.46818547e+00 1.26472174e+00 4 -1.17806305e+01 4.88991608e-01 -6.86819822e-01 5 -4.49847595e+00 -8.79802147e+00 -5.43948636e+00 6 1.48849089e+01 7.40352215e-01 -1.64441244e+01 7 3.95607507e+00 -7.88070112e+00 3.79632129e+00 8 8.08033096e-01 -2.84283420e-01 3.26870570e+00 9 -7.06294374e+00 1.89064317e+00 -9.44293739e+00 10 -2.62536188e-01 7.94946055e+00 -6.02413515e+00 11 -3.73639958e+00 -5.34953968e+00 -3.32034744e+00 12 -9.38276021e+00 7.70812214e+00 9.96449584e-01 13 1.61457513e+00 7.94121043e-01 -8.45236902e+00 14 8.00327966e+00 7.83232937e+00 -7.29827663e+00 15 8.33548023e+00 1.21152887e-01 -1.48897615e+00 16 -2.50338689e+00 9.81043215e+00 -2.75264862e+00 17 -8.56828506e+00 -5.83033851e+00 1.98414421e-01 18 -8.37016225e-01 -3.95371526e-01 2.84826281e+00 19 -7.55311182e-01 -8.22671356e+00 7.27949596e+00 20 -6.12563680e+00 1.26332148e+00 6.26965905e+00 21 1.59431519e+00 -1.06677530e+01 1.43535273e+00 22 1.22115908e+01 -8.23737221e-01 1.53379581e+00 23 6.10706240e+00 -4.82126259e+00 5.80984347e+00 24 1.38185226e+00 -5.27875679e-01 8.97642078e+00 25 -6.44806055e+00 1.77897852e+00 -2.20116739e-01 26 2.12543858e+00 7.74747507e+00 2.83039678e-01 27 -4.08481263e+00 9.98066888e-01 1.07506800e+01 28 -5.79214248e+00 5.20675766e+00 5.30162689e+00 29 9.68099445e-01 2.54259321e+00 4.34370659e+00 30 8.33591095e+00 6.91477299e+00 2.46342498e-02 31 6.00009057e+00 1.19522673e+00 7.03335141e+00 32 9.50405533e-01 7.12163486e+00 1.01538946e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = U (Configuration in file "config-F-U.xyz") ----------------------------------------------------------------------------------------------------- Energy = 433.7773768454393 Forces: 1 -5.57199272e+01 -5.46876527e+01 -5.83425963e+01 2 2.57707467e+01 -2.71017236e+01 -7.66109417e+01 3 3.33886876e+01 -5.93678196e+01 2.70636837e+01 4 -6.97149391e+01 2.03810054e+01 4.14702026e+01 5 1.25182298e+01 -6.28293976e+01 -6.10722631e+01 6 5.72740586e+01 -1.70309849e+01 -6.53613356e+01 7 4.92670189e+01 -5.34434184e+01 -1.22978964e+01 8 -4.04361653e+01 2.98850783e+01 2.29890500e+01 9 -8.99605003e+01 3.85834394e+01 -5.53025666e+01 10 -1.28652243e+01 6.39450983e+01 -2.77590403e+01 11 3.49976762e+01 3.09377188e+01 6.38705902e+01 12 -3.22845653e+01 1.69235636e+01 -2.62799988e+01 13 1.82331138e+01 1.57845236e+01 -3.77101861e+01 14 3.88151991e+01 3.68957344e+01 -4.59862765e+01 15 3.60605585e+01 -6.90986518e+00 4.04025209e+01 16 -2.66313309e+01 3.77256986e+01 6.28949564e+00 17 -3.37434567e+01 -4.07073109e+01 3.69997322e+01 18 -2.50524898e+01 2.62713479e+01 -4.85415673e+01 19 -2.11322538e+01 -5.95090053e+01 6.50654523e+01 20 -4.63324821e+01 -6.90103217e+00 5.73081577e+01 21 -2.30056963e+01 -1.08241353e+02 -4.81669348e+01 22 9.29929235e+01 5.99896589e+01 -4.58137877e+01 23 6.19596339e+01 -5.55509967e+01 4.95726859e+01 24 -1.25698940e+01 6.28021542e+01 1.10325257e+02 25 -3.70121950e+01 2.01138229e+01 -1.46097000e+01 26 6.47195608e+00 4.03515780e+01 -3.41080227e+01 27 -4.81233179e+01 -6.62452816e+01 6.11525792e+01 28 -3.49793010e+01 1.43645613e+01 3.96287665e+01 29 1.63135315e+01 -1.43259198e+01 -4.12515067e+01 30 2.94112698e+01 3.66956353e+01 -4.95399808e+00 31 5.08208719e+01 -1.99630790e+01 3.47130983e+01 32 4.52682629e+01 1.01164221e+02 4.73173471e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = U (Configuration in file "config-T-U.xyz") ----------------------------------------------------------------------------------------------------- Energy = 433.7773768454393 Forces: 1 -5.57199272e+01 -5.46876527e+01 -5.83425963e+01 2 2.57707467e+01 -2.71017236e+01 -7.66109417e+01 3 3.33886876e+01 -5.93678196e+01 2.70636837e+01 4 -6.97149391e+01 2.03810054e+01 4.14702026e+01 5 1.25182298e+01 -6.28293976e+01 -6.10722631e+01 6 5.72740586e+01 -1.70309849e+01 -6.53613356e+01 7 4.92670189e+01 -5.34434184e+01 -1.22978964e+01 8 -4.04361653e+01 2.98850783e+01 2.29890500e+01 9 -8.99605003e+01 3.85834394e+01 -5.53025666e+01 10 -1.28652243e+01 6.39450983e+01 -2.77590403e+01 11 3.49976762e+01 3.09377188e+01 6.38705902e+01 12 -3.22845653e+01 1.69235636e+01 -2.62799988e+01 13 1.82331138e+01 1.57845236e+01 -3.77101861e+01 14 3.88151991e+01 3.68957344e+01 -4.59862765e+01 15 3.60605585e+01 -6.90986518e+00 4.04025209e+01 16 -2.66313309e+01 3.77256986e+01 6.28949564e+00 17 -3.37434567e+01 -4.07073109e+01 3.69997322e+01 18 -2.50524898e+01 2.62713479e+01 -4.85415673e+01 19 -2.11322538e+01 -5.95090053e+01 6.50654523e+01 20 -4.63324821e+01 -6.90103217e+00 5.73081577e+01 21 -2.30056963e+01 -1.08241353e+02 -4.81669348e+01 22 9.29929235e+01 5.99896589e+01 -4.58137877e+01 23 6.19596339e+01 -5.55509967e+01 4.95726859e+01 24 -1.25698940e+01 6.28021542e+01 1.10325257e+02 25 -3.70121950e+01 2.01138229e+01 -1.46097000e+01 26 6.47195608e+00 4.03515780e+01 -3.41080227e+01 27 -4.81233179e+01 -6.62452816e+01 6.11525792e+01 28 -3.49793010e+01 1.43645613e+01 3.96287665e+01 29 1.63135315e+01 -1.43259198e+01 -4.12515067e+01 30 2.94112698e+01 3.66956353e+01 -4.95399808e+00 31 5.08208719e+01 -1.99630790e+01 3.47130983e+01 32 4.52682629e+01 1.01164221e+02 4.73173471e+01 MIXED STRUCTURE (pbc=False)-- Species = Mo U (Configuration in file "config-F-MoU.xyz") ----------------------------------------------------------------------------------------------------- Energy = 295.9110137553002 Forces: 1 -3.66364588e+01 -2.44549741e+01 -3.93080490e+01 2 1.37746872e+01 -8.49580370e+00 -6.81523061e+01 3 1.51226391e+01 -8.00995972e+01 -4.00714181e+01 4 -4.28561725e+01 1.33609972e+00 -9.17742114e+00 5 1.57130544e+01 -1.93134930e+01 -2.45250591e+01 6 7.08908774e+00 -1.06941871e-01 -1.82047128e+01 7 2.32298886e+01 -1.89745454e+01 -4.28784586e+00 8 3.58738036e+01 1.31101923e+01 -8.60958873e+00 9 -6.41767271e+01 1.46980952e+01 -3.81314812e+01 10 8.79202112e+00 1.84408845e+01 -1.63949979e+01 11 -6.72860809e+00 5.77981410e+01 1.79938638e+01 12 -2.20754539e+01 2.57802608e+01 1.16144420e+01 13 1.70707769e+01 4.08648875e+00 -2.03435063e+01 14 1.72140511e+01 2.77553269e+01 -3.66888427e+01 15 3.49275482e+01 -1.58689529e+01 6.56358713e+00 16 -1.87738186e+01 1.30309521e+01 7.11958084e+00 17 -7.82954688e+01 -4.87085116e+01 2.62886476e+01 18 1.03713206e+01 4.50550611e+01 4.16451544e+01 19 -2.66401707e+00 -3.03711079e+01 3.44132437e+01 20 -4.87335700e+01 -2.44549526e+01 3.45932082e+01 21 4.38411338e+01 -6.01849557e+01 1.90479096e+01 22 1.92166813e+01 2.99385593e+00 1.59899643e+01 23 8.42391498e+00 -5.45297808e+00 9.94632489e+00 24 1.54856961e+01 3.84543963e+00 2.50183413e+01 25 -2.76770020e+01 1.23559488e+01 -1.28994556e+01 26 4.04124072e+00 1.78200425e+01 -8.26102531e+00 27 4.35165433e+01 1.13013626e+01 3.97510703e+01 28 -1.89395750e+01 2.24855489e+01 8.33503239e+00 29 9.77816112e+00 1.00878432e+01 8.92069694e+00 30 8.56172759e+00 1.24018262e+01 7.69348639e+00 31 8.76078597e+00 -8.46023900e-02 1.02288951e+01 32 6.75210872e+00 2.21880464e+01 1.98922608e+01 MIXED STRUCTURE (pbc=True)-- Species = Mo U (Configuration in file "config-T-MoU.xyz") ----------------------------------------------------------------------------------------------------- Energy = 234.7691940440552 Forces: 1 -3.06997921e+01 -1.66317979e+01 -2.78089343e+01 2 3.38166134e+01 -3.30497070e+01 -8.38057239e+00 3 3.89046626e+01 -4.21632930e+01 -3.23979013e+01 4 -2.67798679e+01 2.19125641e+01 -6.25203612e+00 5 1.31272620e+01 4.07775924e+00 -5.40109458e+00 6 -5.84930958e+00 2.55934770e+00 -1.01318018e+01 7 -3.26769521e+01 2.70520006e+01 5.74177085e+00 8 3.96208635e+01 1.04407600e+01 -1.02722659e+01 9 -3.79461419e+01 1.41235955e+01 -1.31598124e+01 10 1.02976723e+01 -8.98034652e+00 -2.79261839e+00 11 2.67213576e+00 5.65391953e+01 2.15685917e+01 12 -4.59193297e+00 -5.32712134e+01 9.01801152e+00 13 2.80460436e+01 6.94853622e+00 -4.05675944e+00 14 9.66292343e+00 -1.33035053e+00 -3.48093939e+01 15 -1.50166096e+01 -3.03367178e+01 2.92598120e+01 16 -1.61466492e+01 -3.61299211e+00 1.08552536e+01 17 -4.83748627e+01 -7.47015949e+00 5.32995346e+01 18 1.45572232e+01 4.99437092e+01 4.81355853e+01 19 -2.89760485e+00 -6.84029836e+00 1.16581779e+01 20 -5.21813238e+01 -1.43459420e+01 -2.30220403e+01 21 4.82330134e+01 -3.50971128e+01 1.36458523e+01 22 1.85747956e+00 4.74521750e+00 8.79825149e+00 23 -2.71672943e+00 1.78522423e+00 1.96164524e+00 24 1.15955329e+01 1.19641967e+01 1.74953066e+01 25 -2.15873584e+01 9.43397479e+00 -1.42248883e+01 26 -1.10165157e+00 -2.08139857e+00 -8.16755488e+00 27 5.14952373e+01 2.88097923e+01 -3.53192808e+01 28 -6.33497449e-01 2.19334663e+01 -5.33692898e+00 29 7.58912186e+00 7.25919368e+00 1.27430572e+01 30 -1.22026579e+01 1.31370202e+00 8.17331861e+00 31 -1.64696095e+01 -9.71056272e+00 -6.53640158e+00 32 1.63967663e+01 -1.59203433e+01 -4.28388352e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==21408== Memcheck, a memory error detector ==21408== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==21408== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==21408== Command: python runner2.py Sim_LAMMPS_ADP_StarikovKolotovaKuksin_2017_UMo__SM_682749584055_000 ==21408== ==23104== Warning: invalid file descriptor 255988 in syscall close() ==23104== Warning: invalid file descriptor 255989 in syscall close() ==23104== Warning: invalid file descriptor 255990 in syscall close() ==23104== Warning: invalid file descriptor 255991 in syscall close() ==23104== Use --log-fd= to select an alternative log fd. ==23104== Warning: invalid file descriptor 255992 in syscall close() ==23104== 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: c401-042 Local adapter: hfi1_0 Local port: 1 -------------------------------------------------------------------------- ==21408== Conditional jump or move depends on uninitialised value(s) ==21408== at 0x1397E97B: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==21408== by 0x115E4C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1396B527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==21408== by 0x115A1670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x115A56714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==21408== by 0x114DF3A4F: lammps_open (in /usr/local/lib/liblammps.so.0) ==21408== by 0x5A7EFF4: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==21408== by 0x5A7E409: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==21408== by 0x8C02305: _ctypes_callproc (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==21408== by 0x8C02AE6: ??? (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==21408== -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: c401-042 Local device: hfi1_0 -------------------------------------------------------------------------- ==21408== Conditional jump or move depends on uninitialised value(s) ==21408== at 0x115E06E84: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1395BB59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==21408== by 0x115E5C957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1397C356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==21408== by 0x1397ED18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==21408== by 0x115E4C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1396B527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==21408== by 0x115A1670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x115A56714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==21408== ==21408== Use of uninitialised value of size 8 ==21408== at 0x115E06EAD: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1395BB59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==21408== by 0x115E5C957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1397C356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==21408== by 0x1397ED18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==21408== by 0x115E4C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1396B527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==21408== by 0x115A1670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x115A56714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==21408== ==21408== Use of uninitialised value of size 8 ==21408== at 0x115E06EB4: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1395BB59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==21408== by 0x115E5C957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1397C356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==21408== by 0x1397ED18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==21408== by 0x115E4C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1396B527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==21408== by 0x115A1670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x115A56714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==21408== ==21408== Use of uninitialised value of size 8 ==21408== at 0x115E06ED3: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1395BB59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==21408== by 0x115E5C957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1397C356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==21408== by 0x1397ED18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==21408== by 0x115E4C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==21408== by 0x1396B527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==21408== by 0x115A1670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x115A56714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==21408== ==21408== Syscall param rt_sigaction(act->sa_mask) points to uninitialised byte(s) ==21408== at 0x4893166: __libc_sigaction (sigaction.c:58) ==21408== by 0x208D7B4F: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==21408== by 0x208DD890: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==21408== by 0x208DE47A: psm2_ep_open (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==21408== by 0x2093930D: ompi_mtl_psm2_module_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==21408== by 0x20939764: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==21408== by 0x115A3AC53: ompi_mtl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x13974E4D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pml_cm.so) ==21408== by 0x115A49673: mca_pml_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x115A56789: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==21408== Address 0x1ffeffd9a8 is on thread 1's stack ==21408== in frame #0, created by __libc_sigaction (sigaction.c:43) ==21408== ==21408== Syscall param rt_sigaction(act->sa_mask) points to uninitialised byte(s) ==21408== at 0x4893166: __libc_sigaction (sigaction.c:58) ==21408== by 0x208D7B63: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==21408== by 0x208DD890: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==21408== by 0x208DE47A: psm2_ep_open (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==21408== by 0x2093930D: ompi_mtl_psm2_module_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==21408== by 0x20939764: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==21408== by 0x115A3AC53: ompi_mtl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x13974E4D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pml_cm.so) ==21408== by 0x115A49673: mca_pml_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x115A56789: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==21408== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==21408== Address 0x1ffeffd9a8 is on thread 1's stack ==21408== in frame #0, created by __libc_sigaction (sigaction.c:43) ==21408== ==21408== ==21408== HEAP SUMMARY: ==21408== in use at exit: 28,328,427 bytes in 17,987 blocks ==21408== total heap usage: 228,103 allocs, 210,116 frees, 165,040,019 bytes allocated ==21408== ==21408== LEAK SUMMARY: ==21408== definitely lost: 11,785 bytes in 37 blocks ==21408== indirectly lost: 121 bytes in 7 blocks ==21408== possibly lost: 183,224 bytes in 110 blocks ==21408== still reachable: 28,133,265 bytes in 17,832 blocks ==21408== of which reachable via heuristic: ==21408== stdstring : 38 bytes in 1 blocks ==21408== suppressed: 32 bytes in 1 blocks ==21408== Rerun with --leak-check=full to see details of leaked memory ==21408== ==21408== Use --track-origins=yes to see where uninitialised values come from ==21408== For lists of detected and suppressed errors, rerun with: -s ==21408== ERROR SUMMARY: 7 errors from 7 contexts (suppressed: 8588 from 601) ================================================================================ 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.