!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_EAM_BonnyPasianotTerentyev_2011_FeCr__SM_237089298463_001 Supported species : Cr Fe random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Cr (Configuration in file "config-F-Cr.xyz") ----------------------------------------------------------------------------------------------------- Energy = -17.654016555510655 Forces: 1 -3.20326021e+00 -9.65045250e+00 -8.81927921e+00 2 -4.78239679e-01 3.05441970e+00 -5.48622565e+00 3 4.23672950e+00 -6.39351984e+00 1.51776138e+00 4 -6.47589136e+00 9.64556365e+00 6.39089038e+00 5 -3.36121835e+00 -8.68771024e+00 -4.33456259e+00 6 6.13146146e+00 4.23854552e+00 -6.05182401e+00 7 6.72915672e+00 -1.37285618e+01 -5.75577643e+00 8 -8.80465071e+00 -7.57178837e+00 9.36596656e-01 9 -5.72433458e+00 -3.33994121e+00 -8.41906760e+00 10 -5.10523199e+00 1.41947502e+01 -1.25675209e+01 11 -8.72826294e+00 -1.33988803e+01 4.76758559e+00 12 -6.92209084e+00 8.79472742e+00 -3.79230843e-01 13 6.88352017e+00 -8.53165091e+00 -2.50629981e+01 14 3.26783639e+00 4.15408001e+00 -2.91431903e+00 15 2.12949165e+01 3.57246353e-01 -3.93221858e+00 16 5.02546032e+00 2.18927258e+01 9.35083087e+00 17 -8.74446367e+00 -6.13497136e+00 -4.07220596e+00 18 5.08657117e+00 5.33326644e+00 -1.06738519e+00 19 4.24794492e+00 -5.88558363e+00 5.39912832e+00 20 -3.38396506e+00 5.26527684e+00 5.74438292e+00 21 -6.66992551e+00 -6.28981367e+00 3.23707633e+00 22 1.19204832e+01 8.20691249e+00 8.44944448e+00 23 2.72166620e+00 -1.48333248e+00 3.66750496e+00 24 -1.43574695e+00 2.09207685e+00 2.55881666e+00 25 -8.30070327e+00 -4.37202999e+00 6.23805982e+00 26 -1.87093891e+00 9.89602227e+00 -2.86980463e+00 27 2.17644907e+00 -1.28101685e+01 6.37330402e+00 28 -9.95037510e+00 7.00462518e+00 2.44867827e+00 29 -9.46069296e+00 -7.61120351e+00 6.29784521e+00 30 6.84486302e+00 9.44294423e+00 -1.26253953e+00 31 8.78127693e+00 -5.18372993e+00 1.08785151e+01 32 3.27165650e+00 7.50015517e+00 8.73853726e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cr (Configuration in file "config-T-Cr.xyz") ----------------------------------------------------------------------------------------------------- Energy = -17.654016555510655 Forces: 1 -3.20326021e+00 -9.65045250e+00 -8.81927921e+00 2 -4.78239679e-01 3.05441970e+00 -5.48622565e+00 3 4.23672950e+00 -6.39351984e+00 1.51776138e+00 4 -6.47589136e+00 9.64556365e+00 6.39089038e+00 5 -3.36121835e+00 -8.68771024e+00 -4.33456259e+00 6 6.13146146e+00 4.23854552e+00 -6.05182401e+00 7 6.72915672e+00 -1.37285618e+01 -5.75577643e+00 8 -8.80465071e+00 -7.57178837e+00 9.36596656e-01 9 -5.72433458e+00 -3.33994121e+00 -8.41906760e+00 10 -5.10523199e+00 1.41947502e+01 -1.25675209e+01 11 -8.72826294e+00 -1.33988803e+01 4.76758559e+00 12 -6.92209084e+00 8.79472742e+00 -3.79230843e-01 13 6.88352017e+00 -8.53165091e+00 -2.50629981e+01 14 3.26783639e+00 4.15408001e+00 -2.91431903e+00 15 2.12949165e+01 3.57246353e-01 -3.93221858e+00 16 5.02546032e+00 2.18927258e+01 9.35083087e+00 17 -8.74446367e+00 -6.13497136e+00 -4.07220596e+00 18 5.08657117e+00 5.33326644e+00 -1.06738519e+00 19 4.24794492e+00 -5.88558363e+00 5.39912832e+00 20 -3.38396506e+00 5.26527684e+00 5.74438292e+00 21 -6.66992551e+00 -6.28981367e+00 3.23707633e+00 22 1.19204832e+01 8.20691249e+00 8.44944448e+00 23 2.72166620e+00 -1.48333248e+00 3.66750496e+00 24 -1.43574695e+00 2.09207685e+00 2.55881666e+00 25 -8.30070327e+00 -4.37202999e+00 6.23805982e+00 26 -1.87093891e+00 9.89602227e+00 -2.86980463e+00 27 2.17644907e+00 -1.28101685e+01 6.37330402e+00 28 -9.95037510e+00 7.00462518e+00 2.44867827e+00 29 -9.46069296e+00 -7.61120351e+00 6.29784521e+00 30 6.84486302e+00 9.44294423e+00 -1.26253953e+00 31 8.78127693e+00 -5.18372993e+00 1.08785151e+01 32 3.27165650e+00 7.50015517e+00 8.73853726e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 27.538940452894625 Forces: 1 -2.09089438e+01 -1.57919215e+01 -2.60291361e+01 2 1.16239945e+01 -1.10769575e+01 -1.64003008e+01 3 4.04133674e+01 -2.85240442e+01 4.02636532e+00 4 -2.75988369e+01 4.04906821e+01 7.09016564e+00 5 7.12376606e-01 -6.19553122e+00 -4.65379408e+00 6 4.19530533e+01 -3.39506639e+01 -1.35156385e+01 7 2.87513306e+00 -1.36575707e+00 7.01406304e-01 8 7.44956819e-01 -6.72143075e+00 1.01358668e+01 9 -3.96590473e+01 1.08964716e+01 -2.43482108e+01 10 2.62865503e+00 9.07109728e+00 -4.53898876e+00 11 2.04077311e+01 8.08390697e+00 3.20080570e+01 12 -5.13297649e-01 2.57829332e-01 9.88167714e-01 13 -3.78991750e+01 3.41401635e+01 -8.98105169e+00 14 3.44388779e-01 4.51473279e+00 -2.94902608e+00 15 1.00822167e+01 3.08244134e+00 1.15484444e+01 16 -2.86064324e+00 1.28364250e+01 -9.01630657e+00 17 -7.71446006e+00 -1.88638565e+01 1.76023797e+01 18 -8.94737689e-01 1.49124584e+01 -1.26225930e+01 19 1.49368737e+01 -2.80168472e+01 1.46617683e+01 20 -1.70964046e+01 1.12576666e+01 1.84287846e+01 21 -2.06440279e+01 -5.31144378e+01 -2.52113383e+01 22 3.89602593e+01 2.54317785e+01 -3.84978664e+01 23 1.26662912e+01 -1.34433700e+01 1.26252924e+01 24 -1.68025295e+01 3.34198402e+01 5.34231584e+01 25 -8.67484601e+00 1.41785014e+01 -1.24603320e+01 26 -9.43340749e+00 7.73533557e+00 -1.11058635e+01 27 -6.30286842e+01 -7.86355139e+01 6.72141448e+00 28 -2.73893141e+00 1.19813336e-01 1.42941969e+00 29 5.72992476e-01 -1.22558995e+01 7.30162975e+00 30 3.08699389e+00 4.78346978e+00 -6.20588168e-01 31 4.98981861e+00 -1.99858375e+00 3.66746260e+00 32 6.94688702e+01 7.47422012e+01 8.59125168e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 27.538940452894625 Forces: 1 -2.09089438e+01 -1.57919215e+01 -2.60291361e+01 2 1.16239945e+01 -1.10769575e+01 -1.64003008e+01 3 4.04133674e+01 -2.85240442e+01 4.02636532e+00 4 -2.75988369e+01 4.04906821e+01 7.09016564e+00 5 7.12376606e-01 -6.19553122e+00 -4.65379408e+00 6 4.19530533e+01 -3.39506639e+01 -1.35156385e+01 7 2.87513306e+00 -1.36575707e+00 7.01406304e-01 8 7.44956819e-01 -6.72143075e+00 1.01358668e+01 9 -3.96590473e+01 1.08964716e+01 -2.43482108e+01 10 2.62865503e+00 9.07109728e+00 -4.53898876e+00 11 2.04077311e+01 8.08390697e+00 3.20080570e+01 12 -5.13297649e-01 2.57829332e-01 9.88167714e-01 13 -3.78991750e+01 3.41401635e+01 -8.98105169e+00 14 3.44388779e-01 4.51473279e+00 -2.94902608e+00 15 1.00822167e+01 3.08244134e+00 1.15484444e+01 16 -2.86064324e+00 1.28364250e+01 -9.01630657e+00 17 -7.71446006e+00 -1.88638565e+01 1.76023797e+01 18 -8.94737689e-01 1.49124584e+01 -1.26225930e+01 19 1.49368737e+01 -2.80168472e+01 1.46617683e+01 20 -1.70964046e+01 1.12576666e+01 1.84287846e+01 21 -2.06440279e+01 -5.31144378e+01 -2.52113383e+01 22 3.89602593e+01 2.54317785e+01 -3.84978664e+01 23 1.26662912e+01 -1.34433700e+01 1.26252924e+01 24 -1.68025295e+01 3.34198402e+01 5.34231584e+01 25 -8.67484601e+00 1.41785014e+01 -1.24603320e+01 26 -9.43340749e+00 7.73533557e+00 -1.11058635e+01 27 -6.30286842e+01 -7.86355139e+01 6.72141448e+00 28 -2.73893141e+00 1.19813336e-01 1.42941969e+00 29 5.72992476e-01 -1.22558995e+01 7.30162975e+00 30 3.08699389e+00 4.78346978e+00 -6.20588168e-01 31 4.98981861e+00 -1.99858375e+00 3.66746260e+00 32 6.94688702e+01 7.47422012e+01 8.59125168e+00 MIXED STRUCTURE (pbc=False)-- Species = Cr Fe (Configuration in file "config-F-CrFe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 69.1670910492295 Forces: 1 -3.42657129e+01 -5.37646347e+00 -2.83948173e+01 2 5.04016398e+01 -2.99679874e+01 -2.11739601e+01 3 4.63140283e+01 -2.37213360e+01 8.52758350e+00 4 -3.76320798e+01 -4.23912534e+01 6.43888291e+00 5 -1.42601988e+01 -1.99172514e+01 -7.65439541e+00 6 1.71617322e+01 1.13025845e+01 -8.03317549e+00 7 1.35595969e+01 -5.19525055e+00 -3.51365538e+00 8 9.15442572e+00 4.21837702e-01 7.99238789e-01 9 -5.75585119e+01 6.31462504e+01 -5.09403551e+01 10 -4.92226986e-01 4.22743391e+00 -8.08290629e+00 11 6.37006795e+01 -3.35093647e+01 -1.19714913e+01 12 -4.18478396e+01 4.74597599e+01 -1.10138154e+01 13 -1.75894039e+00 5.52409659e+00 -1.47531206e+01 14 6.03410866e+01 2.91474081e+00 -3.83815383e+01 15 1.26065843e+01 3.73910771e+00 7.83374940e+00 16 -5.45710159e+01 6.45693989e+00 3.91012408e+01 17 -5.82350950e+01 -4.14645402e+01 1.93538461e+01 18 4.83990883e+01 3.00994838e+01 1.91088718e+01 19 -1.34072389e+00 -2.06516858e+01 1.15272521e+01 20 -1.07591522e+01 -1.13590103e+01 2.45104942e+01 21 -1.77550171e+00 -2.00440931e+01 -2.10885757e+00 22 9.75902145e+00 -5.25843920e+00 -1.13924076e+01 23 2.14356866e+00 -1.72527181e+00 3.18417548e+00 24 3.62465872e+00 1.91117597e+01 1.57452337e+01 25 -2.98541308e+01 2.90539393e+01 2.71784753e+01 26 -2.64414057e-01 2.31983863e+01 7.06870066e+00 27 6.61418536e+01 -6.70779186e+01 1.50984449e+00 28 -6.94365020e+01 6.82077276e+01 1.07319508e+01 29 5.20051888e+00 -4.64767955e+00 -4.90175536e+00 30 2.41159640e+01 4.27781626e-01 -1.52691819e+01 31 8.94069200e-01 9.85880170e+00 1.59575582e+01 32 -1.94664702e+01 7.15691403e+00 1.90083350e+01 MIXED STRUCTURE (pbc=True)-- Species = Cr Fe (Configuration in file "config-T-CrFe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 113.66334552817986 Forces: 1 -3.05684915e+01 -1.16477627e+00 -2.89893035e+01 2 5.17187979e+01 -3.12786193e+01 -1.85898278e+01 3 4.30028769e+01 -7.51231744e+00 1.55500151e+01 4 -2.89725356e+01 -4.21564757e+01 2.39384905e+00 5 -4.17255088e+01 2.62816229e+01 -1.90352241e+01 6 9.47869583e+00 2.38192813e+01 5.53306222e+00 7 1.62160914e+01 2.72669823e+00 -2.31042136e+00 8 8.88323711e+00 1.76146881e+00 2.38054189e+00 9 -5.57131375e+01 6.44196697e+01 -4.95653755e+01 10 5.79980130e+00 -6.23305342e+00 -1.17496803e+01 11 6.47842442e+01 -3.42698636e+01 -1.00469031e+01 12 -4.34550519e+01 4.16726105e+01 -8.03201870e+00 13 -1.19909488e+00 5.96267807e+00 -1.15295644e+01 14 8.79621545e+01 -3.85627584e+01 -4.38256945e+01 15 6.00455385e+00 5.46216767e+00 8.22716578e+00 16 -5.96241532e+01 -1.32759372e+01 4.67834802e+01 17 -5.26724674e+01 -4.36657001e+01 2.09437173e+01 18 5.09463372e+01 3.06205630e+01 1.95742345e+01 19 -8.76108104e-01 -1.63022357e+01 1.22246404e+01 20 -8.62441464e-01 -1.10014389e+01 2.67525275e+01 21 -3.82469744e+00 9.06092214e+00 -1.84774344e+01 22 -1.87461160e+01 -1.39607168e+01 -1.00159680e+01 23 3.87270029e+00 -1.38481078e+01 -9.33482767e+00 24 2.60181756e+00 1.99259291e+01 1.43722781e+01 25 -1.19117910e+01 4.33206901e+01 2.60059176e+01 26 4.43044839e-01 1.71322863e+01 7.15775221e+00 27 6.77037790e+01 -6.78512634e+01 -6.61337695e+00 28 -7.58108264e+01 6.76944278e+01 4.16691082e+00 29 4.86052006e+00 -4.69661174e+00 -4.30032487e+00 30 2.76976560e+01 -8.31281805e+00 -1.42361107e+01 31 -1.54701756e+00 1.39543806e+01 1.51706826e+01 32 -2.44668689e+01 -1.97227023e+01 3.94152806e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==5187== Memcheck, a memory error detector ==5187== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==5187== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==5187== Command: python runner2.py Sim_LAMMPS_EAM_BonnyPasianotTerentyev_2011_FeCr__SM_237089298463_001 ==5187== ==5605== Warning: invalid file descriptor 4096 in syscall close() ==5605== Warning: invalid file descriptor 4097 in syscall close() ==5605== Warning: invalid file descriptor 4098 in syscall close() ==5605== Warning: invalid file descriptor 4099 in syscall close() ==5605== Use --log-fd= to select an alternative log fd. ==5605== Warning: invalid file descriptor 4100 in syscall close() ==5605== Warning: invalid file descriptor 4101 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: pd-compute-3-35 Local adapter: qib0 Local port: 1 -------------------------------------------------------------------------- ==5187== Conditional jump or move depends on uninitialised value(s) ==5187== at 0x10CD397B: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==5187== by 0x3042E9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CC0527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==5187== by 0x2FFF870A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x30038714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x2FFDC072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x2F47F5A5: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==5187== by 0x2F47F5DF: lammps_open (in /usr/local/lib/liblammps.so.0) ==5187== by 0x52BCFF4: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==5187== by 0x52BC409: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==5187== by 0x851B315: _ctypes_callproc (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==5187== by 0x851BAF6: ??? (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==5187== -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: pd-compute-3-35 Local device: qib0 -------------------------------------------------------------------------- ==5187== Conditional jump or move depends on uninitialised value(s) ==5187== at 0x303E8E84: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x3043EE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CB0B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==5187== by 0x3043E957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CD1356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==5187== by 0x10CD3D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==5187== by 0x3042E9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CC0527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==5187== by 0x2FFF870A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x30038714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x2FFDC072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x2F47F5A5: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==5187== ==5187== Use of uninitialised value of size 8 ==5187== at 0x303E8EAD: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x3043EE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CB0B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==5187== by 0x3043E957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CD1356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==5187== by 0x10CD3D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==5187== by 0x3042E9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CC0527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==5187== by 0x2FFF870A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x30038714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x2FFDC072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x2F47F5A5: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==5187== ==5187== Use of uninitialised value of size 8 ==5187== at 0x303E8EB4: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x3043EE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CB0B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==5187== by 0x3043E957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CD1356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==5187== by 0x10CD3D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==5187== by 0x3042E9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CC0527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==5187== by 0x2FFF870A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x30038714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x2FFDC072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x2F47F5A5: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==5187== ==5187== Use of uninitialised value of size 8 ==5187== at 0x303E8ED3: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x3043EE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CB0B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==5187== by 0x3043E957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CD1356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==5187== by 0x10CD3D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==5187== by 0x3042E9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==5187== by 0x10CC0527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==5187== by 0x2FFF870A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x30038714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x2FFDC072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==5187== by 0x2F47F5A5: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==5187== ==5187== ==5187== HEAP SUMMARY: ==5187== in use at exit: 7,307,711 bytes in 14,089 blocks ==5187== total heap usage: 7,342,406 allocs, 7,328,317 frees, 942,696,116 bytes allocated ==5187== ==5187== LEAK SUMMARY: ==5187== definitely lost: 11,713 bytes in 34 blocks ==5187== indirectly lost: 57 bytes in 6 blocks ==5187== possibly lost: 1,108,125 bytes in 371 blocks ==5187== still reachable: 6,187,784 bytes in 13,677 blocks ==5187== suppressed: 32 bytes in 1 blocks ==5187== Rerun with --leak-check=full to see details of leaked memory ==5187== ==5187== Use --track-origins=yes to see where uninitialised values come from ==5187== For lists of detected and suppressed errors, rerun with: -s ==5187== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 10042 from 580) ================================================================================ 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.