!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_HybridOverlay_BelandLuOsetskiy_2016_CoNi__SM_445377835613_000 Supported species : Co Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Co (Configuration in file "config-F-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = 96.54069965684405 Forces: 1 -8.27669768e+00 -1.26687536e+01 -1.48320475e+01 2 -1.25585000e+01 2.67069249e+01 -8.61902963e+00 3 1.01664473e+01 -2.23985903e+01 -5.91833196e+00 4 -1.99873772e+01 1.01401079e+01 9.46996344e-01 5 1.90851001e+01 -2.75779314e+01 -1.69522261e+00 6 4.68176048e+00 5.00959122e+00 -8.86172002e+00 7 7.93050892e+00 -4.37938998e+01 -4.12923034e+01 8 -2.35346615e+01 -2.05041189e+01 -8.41292415e+00 9 -1.40715500e+01 -1.51482665e+01 -2.26442391e+01 10 -7.96462330e+00 3.01480501e+01 -2.80011288e+01 11 -2.24176495e+00 -1.73600865e+01 4.45686131e+00 12 -1.29842397e+01 2.26516535e+01 2.14138576e+00 13 -1.18901975e+01 -2.36349521e+01 -6.06674742e+01 14 1.28809636e+01 1.88965177e+01 -1.05473431e+01 15 5.56183910e+01 -1.42659682e+01 1.41250557e+01 16 1.07503031e+01 4.62076093e+01 1.61909922e+01 17 -2.44392086e+01 -1.16035822e+01 -1.03212305e+01 18 9.75290360e+00 1.55435940e+01 1.76599420e+01 19 1.69988540e+01 -1.35165349e+01 1.15141100e+01 20 -7.53593676e+00 1.76442063e+01 1.14711285e+01 21 -2.58901981e+01 -1.63370847e+01 1.01733204e+01 22 3.42664498e+01 3.90679683e+01 3.15888317e+01 23 5.84022812e+00 -1.79138026e+00 1.28552317e+01 24 6.62365460e-01 -5.47856492e+00 9.32078956e+00 25 -2.22627378e+01 -1.61215789e+01 1.58778653e+01 26 -1.03130458e+01 3.22277687e+01 -1.29345954e+01 27 1.67440880e+01 -5.00998014e+01 1.63798901e+01 28 -3.90403518e+01 3.35667108e+01 5.97527931e+00 29 -1.12271065e+01 -1.47008078e+01 1.07816005e+01 30 1.14169765e+01 2.34917206e+01 -1.02018834e-01 31 2.47673906e+01 -1.68721480e+01 1.99781102e+01 32 1.26554666e+01 2.25716269e+01 2.34122186e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Co (Configuration in file "config-T-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = 96.54069965684405 Forces: 1 -8.27669768e+00 -1.26687536e+01 -1.48320475e+01 2 -1.25585000e+01 2.67069249e+01 -8.61902963e+00 3 1.01664473e+01 -2.23985903e+01 -5.91833196e+00 4 -1.99873772e+01 1.01401079e+01 9.46996344e-01 5 1.90851001e+01 -2.75779314e+01 -1.69522261e+00 6 4.68176048e+00 5.00959122e+00 -8.86172002e+00 7 7.93050892e+00 -4.37938998e+01 -4.12923034e+01 8 -2.35346615e+01 -2.05041189e+01 -8.41292415e+00 9 -1.40715500e+01 -1.51482665e+01 -2.26442391e+01 10 -7.96462330e+00 3.01480501e+01 -2.80011288e+01 11 -2.24176495e+00 -1.73600865e+01 4.45686131e+00 12 -1.29842397e+01 2.26516535e+01 2.14138576e+00 13 -1.18901975e+01 -2.36349521e+01 -6.06674742e+01 14 1.28809636e+01 1.88965177e+01 -1.05473431e+01 15 5.56183910e+01 -1.42659682e+01 1.41250557e+01 16 1.07503031e+01 4.62076093e+01 1.61909922e+01 17 -2.44392086e+01 -1.16035822e+01 -1.03212305e+01 18 9.75290360e+00 1.55435940e+01 1.76599420e+01 19 1.69988540e+01 -1.35165349e+01 1.15141100e+01 20 -7.53593676e+00 1.76442063e+01 1.14711285e+01 21 -2.58901981e+01 -1.63370847e+01 1.01733204e+01 22 3.42664498e+01 3.90679683e+01 3.15888317e+01 23 5.84022812e+00 -1.79138026e+00 1.28552317e+01 24 6.62365460e-01 -5.47856492e+00 9.32078956e+00 25 -2.22627378e+01 -1.61215789e+01 1.58778653e+01 26 -1.03130458e+01 3.22277687e+01 -1.29345954e+01 27 1.67440880e+01 -5.00998014e+01 1.63798901e+01 28 -3.90403518e+01 3.35667108e+01 5.97527931e+00 29 -1.12271065e+01 -1.47008078e+01 1.07816005e+01 30 1.14169765e+01 2.34917206e+01 -1.02018834e-01 31 2.47673906e+01 -1.68721480e+01 1.99781102e+01 32 1.26554666e+01 2.25716269e+01 2.34122186e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -18.657874002985714 Forces: 1 -1.66536510e+01 -1.33228087e+01 -7.81675481e-01 2 1.31226847e+00 3.84384361e+00 -7.82520342e+00 3 -4.31156754e+00 -4.70584424e+01 -4.01518994e+01 4 -4.03266751e+00 -6.87959076e+00 -9.53339826e+00 5 3.18501799e+00 -6.93926975e+00 -3.18991585e+00 6 6.44649901e+00 -4.55762971e-01 -2.11074534e+00 7 2.03868798e+01 -3.58650383e+00 -2.65866717e+01 8 1.54230252e+01 5.09293576e+00 -3.47736417e+00 9 -5.26903881e+00 -2.12323600e+00 -2.44667827e+00 10 7.68969820e-01 1.25435037e+01 -9.85586981e+00 11 -2.13301365e+01 -1.21879746e+00 2.76034662e+01 12 -4.84809416e+00 3.69042604e+00 -3.09884797e+00 13 2.94502363e+01 9.24093025e+00 -2.32079505e+01 14 1.09031216e+00 6.70667069e-01 -3.10083608e+00 15 1.35264633e+00 -6.74088335e+00 -5.98945633e+00 16 1.47395331e+00 3.80017438e+00 1.52677720e+00 17 -2.71036604e+01 -1.09788039e+01 -2.20760519e+01 18 -6.50132678e+00 4.06304749e+01 5.01661521e+01 19 2.87270559e+01 -1.13618916e+00 2.44721126e+01 20 -5.95692737e+00 5.27053972e+00 5.17807910e+00 21 -2.71115714e+01 -1.51725063e+01 2.51974045e+01 22 1.11157835e+01 1.48940291e+01 2.47704846e-01 23 1.01615831e+00 -3.65346523e-01 2.04246083e+00 24 1.58922894e+01 -1.84954407e+01 6.71900607e+00 25 -1.99756415e+00 6.06074693e+00 7.38505509e+00 26 -3.10783001e+01 2.81700065e+01 -9.80705305e+00 27 -5.02839775e+01 -1.47894392e+00 3.46294731e+01 28 -4.34056092e-01 1.83750465e+00 2.35851559e+00 29 5.39554128e+01 -2.70889103e+01 -4.58648888e+01 30 3.17951050e+00 6.19631480e+00 5.10225085e+00 31 1.48362784e+00 2.27322804e-01 1.69949849e+00 32 1.06528928e+01 2.08720157e+01 2.47765497e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -18.657874002985714 Forces: 1 -1.66536510e+01 -1.33228087e+01 -7.81675481e-01 2 1.31226847e+00 3.84384361e+00 -7.82520342e+00 3 -4.31156754e+00 -4.70584424e+01 -4.01518994e+01 4 -4.03266751e+00 -6.87959076e+00 -9.53339826e+00 5 3.18501799e+00 -6.93926975e+00 -3.18991585e+00 6 6.44649901e+00 -4.55762971e-01 -2.11074534e+00 7 2.03868798e+01 -3.58650383e+00 -2.65866717e+01 8 1.54230252e+01 5.09293576e+00 -3.47736417e+00 9 -5.26903881e+00 -2.12323600e+00 -2.44667827e+00 10 7.68969820e-01 1.25435037e+01 -9.85586981e+00 11 -2.13301365e+01 -1.21879746e+00 2.76034662e+01 12 -4.84809416e+00 3.69042604e+00 -3.09884797e+00 13 2.94502363e+01 9.24093025e+00 -2.32079505e+01 14 1.09031216e+00 6.70667069e-01 -3.10083608e+00 15 1.35264633e+00 -6.74088335e+00 -5.98945633e+00 16 1.47395331e+00 3.80017438e+00 1.52677720e+00 17 -2.71036604e+01 -1.09788039e+01 -2.20760519e+01 18 -6.50132678e+00 4.06304749e+01 5.01661521e+01 19 2.87270559e+01 -1.13618916e+00 2.44721126e+01 20 -5.95692737e+00 5.27053972e+00 5.17807910e+00 21 -2.71115714e+01 -1.51725063e+01 2.51974045e+01 22 1.11157835e+01 1.48940291e+01 2.47704846e-01 23 1.01615831e+00 -3.65346523e-01 2.04246083e+00 24 1.58922894e+01 -1.84954407e+01 6.71900607e+00 25 -1.99756415e+00 6.06074693e+00 7.38505509e+00 26 -3.10783001e+01 2.81700065e+01 -9.80705305e+00 27 -5.02839775e+01 -1.47894392e+00 3.46294731e+01 28 -4.34056092e-01 1.83750465e+00 2.35851559e+00 29 5.39554128e+01 -2.70889103e+01 -4.58648888e+01 30 3.17951050e+00 6.19631480e+00 5.10225085e+00 31 1.48362784e+00 2.27322804e-01 1.69949849e+00 32 1.06528928e+01 2.08720157e+01 2.47765497e+01 MIXED STRUCTURE (pbc=False)-- Species = Co Ni (Configuration in file "config-F-CoNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 36.089187550833586 Forces: 1 -3.94067181e+01 -7.06936398e+00 -2.92480936e+01 2 2.04877883e+01 -2.15257606e+01 -2.71302501e+01 3 3.84706666e+01 -1.66061209e+01 2.54848567e+01 4 -3.42539193e+01 -9.65180301e+00 -9.27350131e+00 5 -1.19110005e+01 -6.89605559e+00 -1.11554726e+01 6 7.32473092e+00 8.61484875e+00 -5.54376573e+00 7 1.47416803e+01 -6.13266853e+00 3.01282659e+00 8 1.07772324e+01 -1.91440892e+01 1.98413949e+01 9 -2.98113628e+01 2.22079235e+01 -1.81334589e+01 10 -1.59077659e+01 8.02381154e+00 -3.54055031e+01 11 3.84572842e+01 -1.65393554e+01 -8.33762558e+00 12 -3.81758019e+01 2.95844814e+01 3.25078091e-01 13 1.32510203e+01 1.06138587e+01 -2.58700766e+01 14 5.38808348e+00 8.87820037e-01 -3.30509022e+00 15 1.04837377e+01 8.54498127e+00 -3.82533370e+00 16 2.26217189e+01 1.04971434e+01 2.77466785e+01 17 -2.96955004e+01 -3.68205603e+01 -2.45150336e+00 18 2.64332685e+01 1.57472086e+01 4.92344732e-01 19 7.70780050e+00 -1.15799298e+01 2.12520335e+01 20 -1.10432773e+01 7.14647912e+00 2.41570917e+01 21 -5.79913213e+00 -1.63486761e+01 -1.37046930e+01 22 1.24636298e+01 -8.34235239e+00 -5.41929330e+00 23 1.24833747e+01 -7.37524791e+00 1.12895536e+01 24 -1.14578199e+01 1.42508927e+01 1.14659736e+01 25 -1.74767782e+01 1.77070613e+01 2.47849706e+01 26 5.99204060e+00 1.31639288e+01 5.82593543e+00 27 2.88959217e+00 -7.22886930e+00 4.63157303e+00 28 -9.02983885e+00 4.52345292e+00 6.54626568e+00 29 -1.39470514e+01 1.05797045e+00 -9.12026161e+00 30 8.76254745e+00 1.17666084e+01 -5.94046773e+00 31 5.79919070e+00 4.25986274e-01 2.32334606e+01 32 3.38057910e+00 6.49639595e+00 3.77435324e+00 MIXED STRUCTURE (pbc=True)-- Species = Co Ni (Configuration in file "config-T-CoNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 28.423780597148273 Forces: 1 -2.70888380e+01 -8.72991968e+00 -3.20182174e+01 2 2.04234232e+01 -2.18570601e+01 -2.55362558e+01 3 3.24690949e+01 1.38640278e+00 2.98904671e+01 4 -1.42360732e+01 -9.39074634e+00 -1.99984302e+01 5 -1.51681143e+01 1.29207122e+01 -1.26104841e+01 6 -2.39697898e+00 2.01140383e+01 1.66105681e+00 7 7.75825545e+00 -1.73086541e+00 7.85766160e+00 8 1.06834949e+01 -1.88229008e+01 1.96541926e+01 9 -2.70724955e+01 2.35668122e+01 -1.76312594e+01 10 -1.17706007e+01 -2.22369682e+00 -3.30330955e+01 11 3.74008253e+01 -1.63237956e+01 -9.37973003e+00 12 -3.20539876e+01 2.14491445e+01 5.30250173e+00 13 1.70227446e+01 9.93690641e+00 -1.84260405e+01 14 1.82268329e-01 -5.36282436e+00 -1.13477512e+01 15 4.39729668e+00 1.14931269e+01 -4.37824705e+00 16 2.09291694e+01 -1.25767500e+01 3.75327992e+01 17 -2.19580998e+01 -3.64650842e+01 -3.34296390e-01 18 2.50263079e+01 1.40696861e+01 -2.61281589e-02 19 5.55334671e+00 -6.08849108e+00 2.29246152e+01 20 5.45810936e+00 6.68893931e+00 3.29831790e+01 21 -1.55619117e+00 -2.14748534e+00 -2.28250246e+01 22 -2.80479302e+01 -8.55778967e+00 -2.53088738e+00 23 1.94457870e+01 -1.29267590e+01 -7.66890330e+00 24 -1.10657367e+01 1.35124464e+01 1.14863514e+01 25 -4.31336760e+00 2.11412601e+01 2.31242327e+01 26 7.25485835e+00 6.59952000e+00 5.01076017e+00 27 -2.57908890e+00 -7.26830372e+00 -5.57390617e+00 28 -2.59469188e+00 2.30602869e+00 1.25773492e+01 29 -1.26123267e+01 1.50119166e+00 -9.34544138e+00 30 -6.56438837e+00 1.07382727e+01 -1.40969587e+01 31 5.21291204e+00 2.32232321e+00 2.25535303e+01 32 1.86101531e+00 -9.27433946e+00 1.42023603e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==220607== Memcheck, a memory error detector ==220607== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==220607== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==220607== Command: python runner2.py Sim_LAMMPS_HybridOverlay_BelandLuOsetskiy_2016_CoNi__SM_445377835613_000 ==220607== ==222800== Warning: invalid file descriptor 255988 in syscall close() ==222800== Warning: invalid file descriptor 255989 in syscall close() ==222800== Warning: invalid file descriptor 255990 in syscall close() ==222800== Warning: invalid file descriptor 255991 in syscall close() ==222800== Use --log-fd= to select an alternative log fd. ==222800== Warning: invalid file descriptor 255992 in syscall close() ==222800== 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: c449-074 Local adapter: hfi1_0 Local port: 1 -------------------------------------------------------------------------- ==220607== Conditional jump or move depends on uninitialised value(s) ==220607== at 0x138C797B: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==220607== by 0x11B3099C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138B4527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==220607== by 0x11AEE470A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AF24714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AEC8072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11A36B5A5: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==220607== by 0x11A36B5DF: lammps_open (in /usr/local/lib/liblammps.so.0) ==220607== by 0x8D22FF4: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==220607== by 0x8D22409: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==220607== by 0x8D0C315: _ctypes_callproc (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==220607== by 0x8D0CAF6: ??? (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==220607== -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: c449-074 Local device: hfi1_0 -------------------------------------------------------------------------- ==220607== Conditional jump or move depends on uninitialised value(s) ==220607== at 0x11B2C3E84: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x11B319E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138A4B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==220607== by 0x11B319957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138C5356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==220607== by 0x138C7D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==220607== by 0x11B3099C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138B4527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==220607== by 0x11AEE470A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AF24714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AEC8072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11A36B5A5: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==220607== ==220607== Use of uninitialised value of size 8 ==220607== at 0x11B2C3EAD: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x11B319E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138A4B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==220607== by 0x11B319957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138C5356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==220607== by 0x138C7D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==220607== by 0x11B3099C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138B4527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==220607== by 0x11AEE470A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AF24714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AEC8072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11A36B5A5: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==220607== ==220607== Use of uninitialised value of size 8 ==220607== at 0x11B2C3EB4: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x11B319E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138A4B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==220607== by 0x11B319957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138C5356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==220607== by 0x138C7D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==220607== by 0x11B3099C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138B4527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==220607== by 0x11AEE470A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AF24714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AEC8072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11A36B5A5: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==220607== ==220607== Use of uninitialised value of size 8 ==220607== at 0x11B2C3ED3: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x11B319E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138A4B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==220607== by 0x11B319957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138C5356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==220607== by 0x138C7D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==220607== by 0x11B3099C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==220607== by 0x138B4527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==220607== by 0x11AEE470A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AF24714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AEC8072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11A36B5A5: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==220607== ==220607== Syscall param rt_sigaction(act->sa_mask) points to uninitialised byte(s) ==220607== at 0x48962E6: __libc_sigaction (sigaction.c:58) ==220607== by 0x1C01CB4F: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==220607== by 0x1C022890: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==220607== by 0x1C02347A: psm2_ep_open (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==220607== by 0x1C07E30D: ompi_mtl_psm2_module_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==220607== by 0x1C07E764: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==220607== by 0x11AF08C53: ompi_mtl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x138BDE4D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pml_cm.so) ==220607== by 0x11AF17673: mca_pml_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AF24789: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AEC8072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11A36B5A5: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==220607== Address 0x1ffeffd9a8 is on thread 1's stack ==220607== in frame #0, created by __libc_sigaction (sigaction.c:43) ==220607== ==220607== Syscall param rt_sigaction(act->sa_mask) points to uninitialised byte(s) ==220607== at 0x48962E6: __libc_sigaction (sigaction.c:58) ==220607== by 0x1C01CB63: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==220607== by 0x1C022890: ??? (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==220607== by 0x1C02347A: psm2_ep_open (in /usr/lib/x86_64-linux-gnu/libpsm2.so.2.1) ==220607== by 0x1C07E30D: ompi_mtl_psm2_module_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==220607== by 0x1C07E764: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_mtl_psm2.so) ==220607== by 0x11AF08C53: ompi_mtl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x138BDE4D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pml_cm.so) ==220607== by 0x11AF17673: mca_pml_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AF24789: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11AEC8072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==220607== by 0x11A36B5A5: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==220607== Address 0x1ffeffd9a8 is on thread 1's stack ==220607== in frame #0, created by __libc_sigaction (sigaction.c:43) ==220607== ==220607== ==220607== HEAP SUMMARY: ==220607== in use at exit: 28,258,771 bytes in 17,924 blocks ==220607== total heap usage: 863,789 allocs, 845,865 frees, 226,614,972 bytes allocated ==220607== ==220607== LEAK SUMMARY: ==220607== definitely lost: 9,035 bytes in 36 blocks ==220607== indirectly lost: 121 bytes in 7 blocks ==220607== possibly lost: 197,773 bytes in 107 blocks ==220607== still reachable: 28,051,810 bytes in 17,773 blocks ==220607== suppressed: 32 bytes in 1 blocks ==220607== Rerun with --leak-check=full to see details of leaked memory ==220607== ==220607== Use --track-origins=yes to see where uninitialised values come from ==220607== For lists of detected and suppressed errors, rerun with: -s ==220607== ERROR SUMMARY: 7 errors from 7 contexts (suppressed: 9922 from 588) ================================================================================ 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.