Enter a model name: === Verification check vc-memory-leak start (2022-11-29 19:27:07) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Polymorphic_BereSerra_2006_GaN__SM_518345582208_000 Supported species : Ga N random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ga (Configuration in file "config-F-Ga.xyz") ----------------------------------------------------------------------------------------------------- Energy = 165.9651030478725 Forces: 1 -9.12720667e+00 -1.43469530e+01 -1.70804547e+01 2 -4.13741692e+00 6.67198605e+00 -2.15952057e+01 3 8.00820682e+00 -1.62486281e+01 1.05497408e+00 4 -1.80812125e+01 1.28320913e+01 5.45103738e+00 5 7.37244247e+00 -1.98357808e+01 -4.40444495e+00 6 1.24261090e+01 -4.66172080e+00 -1.51654013e+01 7 8.34281548e+00 -2.68883979e+01 -1.96428300e+01 8 -9.74887357e+00 -1.99694153e+01 -3.87147128e+00 9 -1.20066453e+01 -7.38452091e+00 -1.80988062e+01 10 -1.97526398e+00 2.26662725e+01 -2.88769414e+01 11 -2.40525718e+01 -2.07984810e+01 2.03919491e+00 12 -2.41660076e+01 1.44685195e+01 5.67293619e+00 13 7.12652366e+00 1.94099435e+00 -4.19012053e+01 14 9.35851105e+00 8.91791775e+00 -8.41854212e+00 15 4.31999893e+01 3.84146837e+00 -1.13962755e+01 16 9.27033930e+00 4.16330264e+01 -1.54109839e+00 17 -1.60601142e+01 -8.91135287e+00 3.39002987e+00 18 1.65479844e+00 -2.48307352e+00 -1.94773911e+00 19 3.00817341e-01 -1.58502317e+01 1.13428916e+01 20 -1.18505824e+01 3.20560365e+00 1.06107208e+01 21 -7.48645451e+00 -1.96011650e+01 5.80575692e+00 22 2.84315151e+01 8.35975317e+00 1.66456038e+01 23 6.28387216e+00 -2.67231390e+00 9.35207070e+00 24 4.42318427e+00 4.10911365e+00 1.37006402e+01 25 -2.18503817e+01 -2.48567542e+00 -7.09282056e+00 26 -7.50159799e+00 2.99651698e+01 9.67929957e+00 27 1.43018834e+00 -1.57030051e+01 2.50192205e+01 28 -2.17775164e+01 1.67275453e+01 1.13797685e+01 29 -3.61395753e+00 -1.07582007e+01 2.32486081e+01 30 2.11323535e+01 2.19296683e+01 3.31548729e+00 31 1.62041946e+01 -4.90703173e+00 2.34922076e+01 32 8.46994207e+00 1.62368175e+01 1.98327883e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ga (Configuration in file "config-T-Ga.xyz") ----------------------------------------------------------------------------------------------------- Energy = 165.9651030478725 Forces: 1 -9.12720667e+00 -1.43469530e+01 -1.70804547e+01 2 -4.13741692e+00 6.67198605e+00 -2.15952057e+01 3 8.00820682e+00 -1.62486281e+01 1.05497408e+00 4 -1.80812125e+01 1.28320913e+01 5.45103738e+00 5 7.37244247e+00 -1.98357808e+01 -4.40444495e+00 6 1.24261090e+01 -4.66172080e+00 -1.51654013e+01 7 8.34281548e+00 -2.68883979e+01 -1.96428300e+01 8 -9.74887357e+00 -1.99694153e+01 -3.87147128e+00 9 -1.20066453e+01 -7.38452091e+00 -1.80988062e+01 10 -1.97526398e+00 2.26662725e+01 -2.88769414e+01 11 -2.40525718e+01 -2.07984810e+01 2.03919491e+00 12 -2.41660076e+01 1.44685195e+01 5.67293619e+00 13 7.12652366e+00 1.94099435e+00 -4.19012053e+01 14 9.35851105e+00 8.91791775e+00 -8.41854212e+00 15 4.31999893e+01 3.84146837e+00 -1.13962755e+01 16 9.27033930e+00 4.16330264e+01 -1.54109839e+00 17 -1.60601142e+01 -8.91135287e+00 3.39002987e+00 18 1.65479844e+00 -2.48307352e+00 -1.94773911e+00 19 3.00817341e-01 -1.58502317e+01 1.13428916e+01 20 -1.18505824e+01 3.20560365e+00 1.06107208e+01 21 -7.48645451e+00 -1.96011650e+01 5.80575692e+00 22 2.84315151e+01 8.35975317e+00 1.66456038e+01 23 6.28387216e+00 -2.67231390e+00 9.35207070e+00 24 4.42318427e+00 4.10911365e+00 1.37006402e+01 25 -2.18503817e+01 -2.48567542e+00 -7.09282056e+00 26 -7.50159799e+00 2.99651698e+01 9.67929957e+00 27 1.43018834e+00 -1.57030051e+01 2.50192205e+01 28 -2.17775164e+01 1.67275453e+01 1.13797685e+01 29 -3.61395753e+00 -1.07582007e+01 2.32486081e+01 30 2.11323535e+01 2.19296683e+01 3.31548729e+00 31 1.62041946e+01 -4.90703173e+00 2.34922076e+01 32 8.46994207e+00 1.62368175e+01 1.98327883e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = N (Configuration in file "config-F-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -19.148173776947463 Forces: 1 2.82014635e+00 1.66098846e+00 2.06116540e+00 2 -1.92028296e+00 -1.92436448e+00 3.81045289e+00 3 -2.36213333e+00 2.67818246e+00 -3.00827109e+00 4 2.29550490e+00 -9.86089507e-01 -2.95729942e+00 5 2.28331424e+00 9.64729959e-01 1.33937683e+00 6 -9.65242184e-01 2.50971803e-01 2.21878367e+00 7 -1.44769070e+00 5.53483655e-01 -1.77109217e+00 8 -2.70200098e+00 2.70340226e+00 5.52098589e-01 9 2.79740149e-01 -1.14294925e+00 1.19640464e+00 10 8.28715733e-01 -1.39873596e+00 5.99926556e-01 11 1.09592380e+00 8.91766071e-01 -1.52598090e-01 12 2.00437883e+00 -1.01421622e+00 7.38214365e-01 13 3.61365013e-01 1.18589276e+00 1.13714432e+00 14 -1.62930096e+00 -1.12979060e+00 3.69485280e-01 15 -1.66140629e+00 -6.12095957e-01 4.71595015e-01 16 -6.65883082e-01 -2.92612976e+00 2.93321521e+00 17 4.29820984e-01 1.43812742e+00 1.17634644e+00 18 2.28543693e+00 -6.70819169e-01 -1.13236150e-01 19 1.34851924e+00 1.32913488e+00 -1.32238628e+00 20 9.16642870e-01 -1.43851696e+00 -2.26654646e+00 21 3.66986932e-01 2.94794363e+00 2.63711692e+00 22 -2.04397797e+00 -1.07633240e+00 2.04984137e+00 23 -1.35717906e+00 1.84052389e+00 -2.16682839e+00 24 2.40553490e-01 1.14598077e+00 -2.13250708e+00 25 1.24311005e+00 1.73864708e+00 1.41820133e+00 26 -7.65580489e-01 -2.49030849e+00 8.35528840e-01 27 1.63971872e+00 1.92092700e+00 -2.39337227e+00 28 1.84648310e+00 -1.42080299e+00 -2.41918196e+00 29 1.61507057e+00 7.56406121e-01 -2.99927920e-01 30 -2.26273663e+00 -1.98462313e+00 -1.31143059e+00 31 -3.59516099e+00 -1.78624323e-01 -2.45393675e+00 32 -5.22856276e-01 -3.61270905e+00 -7.76283033e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = N (Configuration in file "config-T-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -19.148173776947463 Forces: 1 2.82014635e+00 1.66098846e+00 2.06116540e+00 2 -1.92028296e+00 -1.92436448e+00 3.81045289e+00 3 -2.36213333e+00 2.67818246e+00 -3.00827109e+00 4 2.29550490e+00 -9.86089507e-01 -2.95729942e+00 5 2.28331424e+00 9.64729959e-01 1.33937683e+00 6 -9.65242184e-01 2.50971803e-01 2.21878367e+00 7 -1.44769070e+00 5.53483655e-01 -1.77109217e+00 8 -2.70200098e+00 2.70340226e+00 5.52098589e-01 9 2.79740149e-01 -1.14294925e+00 1.19640464e+00 10 8.28715733e-01 -1.39873596e+00 5.99926556e-01 11 1.09592380e+00 8.91766071e-01 -1.52598090e-01 12 2.00437883e+00 -1.01421622e+00 7.38214365e-01 13 3.61365013e-01 1.18589276e+00 1.13714432e+00 14 -1.62930096e+00 -1.12979060e+00 3.69485280e-01 15 -1.66140629e+00 -6.12095957e-01 4.71595015e-01 16 -6.65883082e-01 -2.92612976e+00 2.93321521e+00 17 4.29820984e-01 1.43812742e+00 1.17634644e+00 18 2.28543693e+00 -6.70819169e-01 -1.13236150e-01 19 1.34851924e+00 1.32913488e+00 -1.32238628e+00 20 9.16642870e-01 -1.43851696e+00 -2.26654646e+00 21 3.66986932e-01 2.94794363e+00 2.63711692e+00 22 -2.04397797e+00 -1.07633240e+00 2.04984137e+00 23 -1.35717906e+00 1.84052389e+00 -2.16682839e+00 24 2.40553490e-01 1.14598077e+00 -2.13250708e+00 25 1.24311005e+00 1.73864708e+00 1.41820133e+00 26 -7.65580489e-01 -2.49030849e+00 8.35528840e-01 27 1.63971872e+00 1.92092700e+00 -2.39337227e+00 28 1.84648310e+00 -1.42080299e+00 -2.41918196e+00 29 1.61507057e+00 7.56406121e-01 -2.99927920e-01 30 -2.26273663e+00 -1.98462313e+00 -1.31143059e+00 31 -3.59516099e+00 -1.78624323e-01 -2.45393675e+00 32 -5.22856276e-01 -3.61270905e+00 -7.76283033e-01 MIXED STRUCTURE (pbc=False)-- Species = Ga N (Configuration in file "config-F-GaN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 99.72009322003953 Forces: 1 -1.13710245e+01 -6.46657229e+00 -1.36937202e+01 2 -4.72196468e-01 1.62726605e+01 -1.32237192e+01 3 5.93510182e+00 -3.07136098e+01 -9.77297575e+00 4 -4.03209220e+01 1.02623142e+01 -1.48346201e+01 5 1.65500222e+01 -1.38241428e+01 -8.01525510e+00 6 1.05948929e+01 -9.83570290e+00 -8.40081758e+00 7 5.40896205e+00 -4.47497267e+00 -3.59539856e+00 8 6.30914049e+00 3.34214019e+00 -2.16762026e+00 9 -5.26200451e+00 1.25763702e-01 -9.81948854e+00 10 -8.39442823e+00 7.63072015e+00 -1.33541985e+01 11 -1.22857755e+01 -2.66345419e+01 -5.07975039e+00 12 -1.89109049e+01 1.16700157e+01 -9.29679788e+00 13 -5.02484223e+00 -9.78032022e+00 -3.11662156e+01 14 8.13457044e+00 6.80084213e+00 -6.69826835e+00 15 3.33120379e+01 -4.82445602e-01 8.70532209e+00 16 1.43006251e+01 4.69761982e+01 -1.34386839e+00 17 -2.81950478e+01 -3.70229798e+01 1.07709915e+01 18 1.29649455e+01 1.19223739e+01 -4.60654263e+00 19 -4.40210921e+00 -1.49106057e+01 2.38750516e+01 20 -1.23069400e+01 3.60046098e+00 1.54243378e+01 21 8.06235362e+00 -2.59791714e+01 -5.72176856e+00 22 2.10555956e+01 3.31007644e+01 -1.68900292e+01 23 9.31337677e+00 -3.13259910e+01 2.34600536e+01 24 3.97261381e+00 8.28003819e+00 2.63214967e+01 25 -2.99365302e+01 1.30977735e+01 1.55250215e+01 26 -6.61732463e+00 3.69289025e+01 7.90322769e+00 27 -5.89808872e+00 -3.29685268e+00 2.23724130e+01 28 -1.07925298e+00 4.24783471e-01 2.35767811e+00 29 2.33507482e+01 -6.91268718e+00 6.32475008e+00 30 1.63554452e+00 3.27151043e-01 4.70250693e+00 31 3.20607139e-03 -9.33458846e-02 -1.19538720e+00 32 9.57365488e+00 1.09910390e+01 1.11335913e+01 MIXED STRUCTURE (pbc=True)-- Species = Ga N (Configuration in file "config-T-GaN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 171.36726565745806 Forces: 1 -9.45143931e+00 -1.67974277e+01 -1.48303162e+01 2 -7.04525064e+00 2.77047128e+01 7.09098972e+00 3 4.01210974e+00 -7.06062037e+00 -9.11190976e+00 4 -1.77623699e+01 6.73989818e+00 -4.20738503e+00 5 2.67975475e+01 -1.59907312e+01 1.47716037e+01 6 -3.23439870e+00 -6.27415968e+00 -8.39590550e+00 7 -7.65273209e+00 -1.52962149e+01 -5.48604303e+00 8 4.72276102e+00 3.74433714e+00 -1.38937623e+00 9 8.69352403e+00 5.30056628e+00 -2.13628103e+01 10 -1.57621725e+01 -2.57995657e+00 -1.86705324e+01 11 -1.20253348e+01 -2.79206487e+01 -5.02143794e+00 12 -1.53952359e+01 8.29403454e+00 -1.18500067e+01 13 -5.95799285e+00 -7.24711448e+00 -2.68205881e+01 14 9.94228020e+00 9.75054185e+00 -1.07897839e+01 15 9.11735462e+00 1.81738627e+00 5.32254739e+00 16 1.96464573e+01 3.25548963e+01 5.23823562e+00 17 -1.71134720e+01 -3.26456115e+01 1.16274377e+01 18 1.69113283e+01 1.45461573e+01 -5.78673281e+00 19 -2.22093046e+01 -1.72232879e+01 9.91017711e+00 20 -5.19340390e-01 1.00102716e+01 2.02179268e+01 21 1.45427332e+01 -1.16972544e+01 -8.55928919e+00 22 -1.47156804e+00 3.68419263e+01 -1.33325315e+01 23 4.89588626e+00 -3.66044523e+01 1.88022073e+01 24 1.29448853e+01 2.14447940e+01 -1.57277366e+00 25 -1.42817687e+01 1.10497630e+01 1.84620754e+01 26 -2.58440321e+00 1.31011942e+01 8.58366372e+00 27 -7.57772194e+00 -3.80462293e+00 1.99695247e+01 28 -1.45507108e+00 1.91611444e+00 7.31249939e+00 29 2.34861492e+01 -6.94206489e+00 6.08261778e+00 30 -6.07742478e+00 5.92565015e+00 9.55684363e+00 31 -9.58368223e-02 1.93643328e+00 -8.78779411e-01 32 1.19598216e+01 -4.59451000e+00 5.11785161e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==42896== Memcheck, a memory error detector ==42896== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==42896== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==42896== Command: python runner2.py Sim_LAMMPS_Polymorphic_BereSerra_2006_GaN__SM_518345582208_000 ==42896== ==43396== Warning: invalid file descriptor 255988 in syscall close() ==43396== Warning: invalid file descriptor 255989 in syscall close() ==43396== Warning: invalid file descriptor 255990 in syscall close() ==43396== Warning: invalid file descriptor 255991 in syscall close() ==43396== Use --log-fd= to select an alternative log fd. ==43396== Warning: invalid file descriptor 255992 in syscall close() ==43396== 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 -------------------------------------------------------------------------- ==42896== Conditional jump or move depends on uninitialised value(s) ==42896== at 0x1157C97B: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==42896== by 0x115E4C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x11569527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==42896== by 0x115A1670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x115A56714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==42896== by 0x114DF3A4F: lammps_open (in /usr/local/lib/liblammps.so.0) ==42896== by 0x5A7EFF4: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==42896== by 0x5A7E409: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==42896== by 0x8C02305: _ctypes_callproc (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==42896== by 0x8C02AE6: ??? (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==42896== -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: c401-042 Local device: hfi1_0 -------------------------------------------------------------------------- ==42896== Conditional jump or move depends on uninitialised value(s) ==42896== at 0x115E06E84: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x11559B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==42896== by 0x115E5C957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x1157A356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==42896== by 0x1157CD18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==42896== by 0x115E4C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x11569527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==42896== by 0x115A1670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x115A56714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==42896== ==42896== Use of uninitialised value of size 8 ==42896== at 0x115E06EAD: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x11559B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==42896== by 0x115E5C957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x1157A356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==42896== by 0x1157CD18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==42896== by 0x115E4C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x11569527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==42896== by 0x115A1670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x115A56714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==42896== ==42896== Use of uninitialised value of size 8 ==42896== at 0x115E06EB4: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x11559B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==42896== by 0x115E5C957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x1157A356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==42896== by 0x1157CD18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==42896== by 0x115E4C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x11569527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==42896== by 0x115A1670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x115A56714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==42896== ==42896== Use of uninitialised value of size 8 ==42896== at 0x115E06ED3: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x115E5CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x11559B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==42896== by 0x115E5C957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x1157A356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==42896== by 0x1157CD18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==42896== by 0x115E4C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==42896== by 0x11569527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==42896== by 0x115A1670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x115A56714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==42896== ==42896== Syscall param rt_sigaction(act->sa_mask) points to uninitialised byte(s) ==42896== at 0x4893166: __libc_sigaction (sigaction.c:58) ==42896== by 0x19CD1B4F: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==42896== by 0x19CD7890: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==42896== by 0x19CD847A: psm2_ep_open (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==42896== by 0x19D3330D: ompi_mtl_psm2_module_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==42896== by 0x19D33764: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==42896== by 0x115A3AC53: ompi_mtl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x11572E4D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pml_cm.so) ==42896== by 0x115A49673: mca_pml_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x115A56789: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==42896== Address 0x1ffeffd9a8 is on thread 1's stack ==42896== in frame #0, created by __libc_sigaction (sigaction.c:43) ==42896== ==42896== Syscall param rt_sigaction(act->sa_mask) points to uninitialised byte(s) ==42896== at 0x4893166: __libc_sigaction (sigaction.c:58) ==42896== by 0x19CD1B63: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==42896== by 0x19CD7890: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==42896== by 0x19CD847A: psm2_ep_open (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==42896== by 0x19D3330D: ompi_mtl_psm2_module_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==42896== by 0x19D33764: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==42896== by 0x115A3AC53: ompi_mtl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x11572E4D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pml_cm.so) ==42896== by 0x115A49673: mca_pml_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x115A56789: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x1159FA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==42896== by 0x114DF3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==42896== Address 0x1ffeffd9a8 is on thread 1's stack ==42896== in frame #0, created by __libc_sigaction (sigaction.c:43) ==42896== ==42896== ==42896== HEAP SUMMARY: ==42896== in use at exit: 28,328,379 bytes in 17,987 blocks ==42896== total heap usage: 388,448 allocs, 370,461 frees, 193,891,781 bytes allocated ==42896== ==42896== LEAK SUMMARY: ==42896== definitely lost: 9,737 bytes in 36 blocks ==42896== indirectly lost: 121 bytes in 7 blocks ==42896== possibly lost: 185,272 bytes in 111 blocks ==42896== still reachable: 28,133,217 bytes in 17,832 blocks ==42896== of which reachable via heuristic: ==42896== stdstring : 38 bytes in 1 blocks ==42896== suppressed: 32 bytes in 1 blocks ==42896== Rerun with --leak-check=full to see details of leaked memory ==42896== ==42896== Use --track-origins=yes to see where uninitialised values come from ==42896== For lists of detected and suppressed errors, rerun with: -s ==42896== ERROR SUMMARY: 7 errors from 7 contexts (suppressed: 8723 from 619) ================================================================================ 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. === Verification check vc-memory-leak end (2022-11-29 19:31:32) ===