Enter a model name: === Verification check vc-memory-leak start (2022-11-30 10:16:42) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ReaxFF_AryanpourVanDuinKubicki_2010_FeHO__SM_222964216001_001 Supported species : Fe H O random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -53.46792974566435 Forces: 1 -1.24095017e+00 -2.21604748e+00 -2.65807913e+00 2 -1.79872374e+00 4.86070811e+00 -3.00369522e+00 3 1.97115539e+00 -2.66152464e+00 2.54346988e-01 4 -2.07153432e+00 2.21815048e+00 1.76411760e+00 5 3.15137313e+00 -5.37920172e+00 -1.52603312e-01 6 1.44581885e+00 1.04875107e+00 -2.25365239e+00 7 1.09005710e+00 -7.15458621e+00 -6.33520071e+00 8 -4.99908363e+00 -2.19386610e+00 1.33845381e+00 9 -4.79043508e+00 -4.28179003e+00 -6.29143100e+00 10 4.22544088e+00 6.61402079e+00 -3.19756329e+00 11 4.80583242e-01 -5.29245576e+00 4.84111924e+00 12 -4.32784386e+00 4.79344263e+00 2.80160648e+00 13 -2.82251226e+00 -3.80425286e+00 -1.20793770e+01 14 3.03821961e+00 3.21426207e+00 -3.55830494e+00 15 1.12737699e+01 -6.02634571e+00 1.70477859e+00 16 -6.30592852e+00 1.07259291e+01 2.83938663e+00 17 -5.16889015e+00 -2.56654827e+00 -2.07825364e+00 18 2.52747790e+00 4.86028542e+00 -2.77977995e+00 19 2.34293810e+00 -4.94198696e+00 3.64406945e+00 20 -2.29801121e+00 3.86809127e+00 2.38305520e+00 21 -4.29723075e+00 -3.18286343e+00 1.21119648e+00 22 5.44164554e+00 7.07094108e+00 5.31051061e+00 23 1.01110536e+00 -5.13047224e-02 1.92559148e+00 24 1.43488551e+00 1.35170744e+00 1.52443477e+00 25 -1.75825607e+00 -2.93796586e+00 1.31118496e+00 26 -5.39579796e-01 5.01049184e+00 -5.59420092e+00 27 2.81078152e+00 -9.21673546e+00 3.67422277e+00 28 -7.26153698e+00 5.62293835e+00 1.45909601e+00 29 -3.30357078e+00 -5.29339890e+00 1.78278774e+00 30 4.19892754e+00 4.47878515e+00 3.37281159e+00 31 3.88975471e+00 -3.05302759e+00 2.16238344e+00 32 2.65015308e+00 4.51539695e+00 4.67698768e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -53.46792974566435 Forces: 1 -1.24095017e+00 -2.21604748e+00 -2.65807913e+00 2 -1.79872374e+00 4.86070811e+00 -3.00369522e+00 3 1.97115539e+00 -2.66152464e+00 2.54346988e-01 4 -2.07153432e+00 2.21815048e+00 1.76411760e+00 5 3.15137313e+00 -5.37920172e+00 -1.52603312e-01 6 1.44581885e+00 1.04875107e+00 -2.25365239e+00 7 1.09005710e+00 -7.15458621e+00 -6.33520071e+00 8 -4.99908363e+00 -2.19386610e+00 1.33845381e+00 9 -4.79043508e+00 -4.28179003e+00 -6.29143100e+00 10 4.22544088e+00 6.61402079e+00 -3.19756329e+00 11 4.80583242e-01 -5.29245576e+00 4.84111924e+00 12 -4.32784386e+00 4.79344263e+00 2.80160648e+00 13 -2.82251226e+00 -3.80425286e+00 -1.20793770e+01 14 3.03821961e+00 3.21426207e+00 -3.55830494e+00 15 1.12737699e+01 -6.02634571e+00 1.70477859e+00 16 -6.30592852e+00 1.07259291e+01 2.83938663e+00 17 -5.16889015e+00 -2.56654827e+00 -2.07825364e+00 18 2.52747790e+00 4.86028542e+00 -2.77977995e+00 19 2.34293810e+00 -4.94198696e+00 3.64406945e+00 20 -2.29801121e+00 3.86809127e+00 2.38305520e+00 21 -4.29723075e+00 -3.18286343e+00 1.21119648e+00 22 5.44164554e+00 7.07094108e+00 5.31051061e+00 23 1.01110536e+00 -5.13047224e-02 1.92559148e+00 24 1.43488551e+00 1.35170744e+00 1.52443477e+00 25 -1.75825607e+00 -2.93796586e+00 1.31118496e+00 26 -5.39579796e-01 5.01049184e+00 -5.59420092e+00 27 2.81078152e+00 -9.21673546e+00 3.67422277e+00 28 -7.26153698e+00 5.62293835e+00 1.45909601e+00 29 -3.30357078e+00 -5.29339890e+00 1.78278774e+00 30 4.19892754e+00 4.47878515e+00 3.37281159e+00 31 3.88975471e+00 -3.05302759e+00 2.16238344e+00 32 2.65015308e+00 4.51539695e+00 4.67698768e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = H (Configuration in file "config-F-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -3.4748007096718148 Forces: 1 9.54855581e-03 4.23567781e+00 3.84595391e+00 2 -3.42764849e-01 8.45864421e-01 -2.79539829e-01 3 2.43281223e+00 3.24241656e+00 -2.58408864e-01 4 -4.85904225e-01 -4.54533188e+00 -3.65896775e+00 5 -8.70139070e-02 1.69250084e-01 1.62282393e-01 6 -2.58872357e-02 3.01257542e-01 2.18594343e-01 7 7.92820720e-02 -1.02481832e-01 8.43137681e-02 8 -2.03775183e+00 -3.63738041e+00 2.27708895e-01 9 1.07938598e+00 -2.20647533e-01 3.25127373e-01 10 -5.31690500e-01 -8.09081346e-01 6.45911037e-01 11 -4.43130654e-01 6.48756819e-01 -9.55850199e-01 12 3.48122997e-01 7.37370049e-02 -2.11792328e-01 13 3.22927951e-02 -2.22803605e-02 -1.10933845e-01 14 1.90346753e-02 2.36572444e-02 -8.16566635e-03 15 -3.28513714e-01 -1.21638684e-01 2.87886183e-01 16 -1.94611043e-02 -2.25050729e-01 2.58988912e-01 17 1.13002345e+00 3.56081267e+00 3.14423294e+00 18 -3.29688379e+00 3.38079239e+00 1.50124535e+00 19 2.27168069e-02 -4.11383513e-02 4.32076334e-02 20 -1.25366804e+00 -3.63084005e+00 -3.06866306e+00 21 -1.06126778e-01 -2.33906241e-02 -1.19110638e-01 22 6.40672975e-02 3.18626926e-02 -4.80566042e-02 23 1.52874457e-03 -5.53318179e-02 5.74896826e-02 24 -5.82219798e-02 -4.19136641e-02 7.56522094e-02 25 3.43458810e+00 -3.24108814e+00 -1.18782200e+00 26 -7.81607526e-01 4.65360268e-02 5.74426767e-01 27 -6.63653020e-02 -9.36284592e-02 -1.62446700e-01 28 7.59035244e-01 7.03001415e-02 -6.65662571e-01 29 3.11257616e-01 5.80871050e-02 -8.15211989e-01 30 -8.95683298e-01 9.91107555e-02 1.40095996e+00 31 -5.16038805e-01 5.42267025e-01 -1.81342496e-02 32 1.55301697e+00 -5.19162414e-01 -1.28521507e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = H (Configuration in file "config-T-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -3.4748007096718148 Forces: 1 9.54855581e-03 4.23567781e+00 3.84595391e+00 2 -3.42764849e-01 8.45864421e-01 -2.79539829e-01 3 2.43281223e+00 3.24241656e+00 -2.58408864e-01 4 -4.85904225e-01 -4.54533188e+00 -3.65896775e+00 5 -8.70139070e-02 1.69250084e-01 1.62282393e-01 6 -2.58872357e-02 3.01257542e-01 2.18594343e-01 7 7.92820720e-02 -1.02481832e-01 8.43137681e-02 8 -2.03775183e+00 -3.63738041e+00 2.27708895e-01 9 1.07938598e+00 -2.20647533e-01 3.25127373e-01 10 -5.31690500e-01 -8.09081346e-01 6.45911037e-01 11 -4.43130654e-01 6.48756819e-01 -9.55850199e-01 12 3.48122997e-01 7.37370049e-02 -2.11792328e-01 13 3.22927951e-02 -2.22803605e-02 -1.10933845e-01 14 1.90346753e-02 2.36572444e-02 -8.16566635e-03 15 -3.28513714e-01 -1.21638684e-01 2.87886183e-01 16 -1.94611043e-02 -2.25050729e-01 2.58988912e-01 17 1.13002345e+00 3.56081267e+00 3.14423294e+00 18 -3.29688379e+00 3.38079239e+00 1.50124535e+00 19 2.27168069e-02 -4.11383513e-02 4.32076334e-02 20 -1.25366804e+00 -3.63084005e+00 -3.06866306e+00 21 -1.06126778e-01 -2.33906241e-02 -1.19110638e-01 22 6.40672975e-02 3.18626926e-02 -4.80566042e-02 23 1.52874457e-03 -5.53318179e-02 5.74896826e-02 24 -5.82219798e-02 -4.19136641e-02 7.56522094e-02 25 3.43458810e+00 -3.24108814e+00 -1.18782200e+00 26 -7.81607526e-01 4.65360268e-02 5.74426767e-01 27 -6.63653020e-02 -9.36284592e-02 -1.62446700e-01 28 7.59035244e-01 7.03001415e-02 -6.65662571e-01 29 3.11257616e-01 5.80871050e-02 -8.15211989e-01 30 -8.95683298e-01 9.91107555e-02 1.40095996e+00 31 -5.16038805e-01 5.42267025e-01 -1.81342496e-02 32 1.55301697e+00 -5.19162414e-01 -1.28521507e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = O (Configuration in file "config-F-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 28.40932553655284 Forces: 1 -4.07064013e-01 1.51089809e+00 1.48587665e+00 2 -2.10896499e+00 -2.90996877e+00 -6.98624133e+00 3 -8.99763199e-01 -2.42270633e+00 3.01797134e+00 4 -1.31374242e+00 -4.72397036e+00 -3.34820188e+00 5 2.57896481e+00 -3.84686083e-01 -3.83292679e+00 6 7.38024962e-01 -4.97724706e+00 -7.11796082e-02 7 2.09208680e+00 1.27777848e+00 -1.55839821e+00 8 7.68960786e-01 -7.52937027e+00 4.04726913e+00 9 -6.34028207e+00 1.08242411e+01 5.59456199e+00 10 1.84081217e+00 2.23917236e+00 -1.32645432e+00 11 1.96456167e+00 1.35662208e+00 1.03496584e+00 12 -2.73658096e+00 -4.44903134e+00 -6.56937950e+00 13 2.16414025e+00 1.04733104e+00 -3.97562881e+00 14 2.44549085e+00 5.46111541e+00 -1.86342679e+00 15 5.20444679e+00 -2.58745733e+00 -1.52126142e+00 16 -4.42077842e+00 4.27799280e+00 -1.68277545e+00 17 -1.17753828e+00 -9.01876038e-01 2.86594817e-01 18 -3.48166739e+00 -2.52600851e+00 3.11580096e+00 19 1.45646465e+00 1.26316505e-01 -2.65373649e+00 20 8.64585914e-01 1.31909802e+00 -3.06099781e-01 21 -1.37910438e+00 -3.71238450e+00 1.32977717e+00 22 1.95270553e+00 -6.77286689e-01 2.97266476e+00 23 -2.58925537e-01 5.05319942e-01 -5.70316655e-01 24 1.49499537e+00 -2.15636336e+00 3.09066654e+00 25 -3.17131493e+00 1.90174840e+00 2.55933131e+00 26 -1.05334583e+00 2.55646936e+00 1.82245189e+00 27 -1.57523885e+00 1.60607470e+00 3.96375503e+00 28 5.30594502e-01 -1.73836725e+00 -1.93527743e+00 29 1.65287088e+00 2.73896750e+00 1.91703465e+00 30 6.73230352e-01 -3.16223815e-01 4.19959898e+00 31 1.97065429e+00 2.34328956e+00 -2.27432932e+00 32 -6.92793183e-02 9.20512402e-01 3.73127299e-02 MONOATOMIC STRUCTURE (pbc=True)-- Species = O (Configuration in file "config-T-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 28.40932553655284 Forces: 1 -4.07064013e-01 1.51089809e+00 1.48587665e+00 2 -2.10896499e+00 -2.90996877e+00 -6.98624133e+00 3 -8.99763199e-01 -2.42270633e+00 3.01797134e+00 4 -1.31374242e+00 -4.72397036e+00 -3.34820188e+00 5 2.57896481e+00 -3.84686083e-01 -3.83292679e+00 6 7.38024962e-01 -4.97724706e+00 -7.11796082e-02 7 2.09208680e+00 1.27777848e+00 -1.55839821e+00 8 7.68960786e-01 -7.52937027e+00 4.04726913e+00 9 -6.34028207e+00 1.08242411e+01 5.59456199e+00 10 1.84081217e+00 2.23917236e+00 -1.32645432e+00 11 1.96456167e+00 1.35662208e+00 1.03496584e+00 12 -2.73658096e+00 -4.44903134e+00 -6.56937950e+00 13 2.16414025e+00 1.04733104e+00 -3.97562881e+00 14 2.44549085e+00 5.46111541e+00 -1.86342679e+00 15 5.20444679e+00 -2.58745733e+00 -1.52126142e+00 16 -4.42077842e+00 4.27799280e+00 -1.68277545e+00 17 -1.17753828e+00 -9.01876038e-01 2.86594817e-01 18 -3.48166739e+00 -2.52600851e+00 3.11580096e+00 19 1.45646465e+00 1.26316505e-01 -2.65373649e+00 20 8.64585914e-01 1.31909802e+00 -3.06099781e-01 21 -1.37910438e+00 -3.71238450e+00 1.32977717e+00 22 1.95270553e+00 -6.77286689e-01 2.97266476e+00 23 -2.58925537e-01 5.05319942e-01 -5.70316655e-01 24 1.49499537e+00 -2.15636336e+00 3.09066654e+00 25 -3.17131493e+00 1.90174840e+00 2.55933131e+00 26 -1.05334583e+00 2.55646936e+00 1.82245189e+00 27 -1.57523885e+00 1.60607470e+00 3.96375503e+00 28 5.30594502e-01 -1.73836725e+00 -1.93527743e+00 29 1.65287088e+00 2.73896750e+00 1.91703465e+00 30 6.73230352e-01 -3.16223815e-01 4.19959898e+00 31 1.97065429e+00 2.34328956e+00 -2.27432932e+00 32 -6.92793183e-02 9.20512402e-01 3.73127299e-02 MIXED STRUCTURE (pbc=False)-- Species = Fe H O (Configuration in file "config-F-FeHO.xyz") ----------------------------------------------------------------------------------------------------- Energy = -60.97262343534051 Forces: 1 2.24109793e-01 -3.41034807e+00 -3.79027981e+00 2 -2.74577974e+00 -7.63976561e+00 -3.94883585e+00 3 -9.91689565e-01 -1.59696482e+00 6.57152912e-01 4 2.60783972e-01 3.51202032e+00 2.45552868e+00 5 -2.64398478e+00 7.56544234e-01 -4.27027759e+00 6 2.63495013e+00 -2.00480360e+00 -7.29888836e-01 7 3.72955229e+00 -1.39012260e+00 3.72484419e+00 8 3.49180511e+00 -1.06774758e+00 3.33114390e+00 9 -5.65704967e+00 3.26816076e+00 -2.00322514e+00 10 6.84570782e-02 -7.15976361e-02 -1.79610575e-02 11 -2.95711285e+00 3.34431187e+00 2.12311361e+00 12 1.28437076e+00 -5.46978874e-01 -1.40608947e-01 13 5.95816399e+00 1.14260902e+01 -7.36774010e+00 14 -8.37143138e-01 -1.13146105e+00 -2.63778326e-01 15 2.18014463e+00 6.04583556e-01 1.66970728e-01 16 -8.01713599e-01 -4.71752402e-01 -1.30916622e-01 17 -8.30371982e-01 -7.23923137e-02 1.59808583e-01 18 -3.45902170e+00 -3.79103309e-01 1.72662786e+00 19 -1.81437097e+00 -2.34687768e+00 2.72351960e+00 20 4.72250565e-01 5.04244557e-01 4.33110616e-01 21 4.77316222e+00 -5.24162443e+00 4.24038491e-01 22 1.71909871e+00 3.47605520e-01 -1.30617047e-01 23 2.92915115e-02 -1.88161742e+00 -6.07028771e-01 24 3.87313708e-01 -8.94718947e-01 3.25735811e+00 25 -4.04113266e+00 -8.15223871e-01 4.25049127e-01 26 2.15692038e+00 2.90453542e+00 -2.64807516e+00 27 6.60659175e-02 2.54379298e+00 1.93186068e+00 28 -8.76862850e-01 -6.57407257e-01 2.01411478e+00 29 -2.58905907e+00 1.70520263e+00 -9.30241984e-01 30 -8.32111001e-02 -2.25108673e-01 1.91250442e-01 31 7.82081227e-01 1.52377807e+00 1.09297730e+00 32 1.09981683e-01 -5.95253954e-01 1.41005633e-01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1799501== Memcheck, a memory error detector ==1799501== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1799501== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1799501== Command: python runner2.py Sim_LAMMPS_ReaxFF_AryanpourVanDuinKubicki_2010_FeHO__SM_222964216001_001 ==1799501== ==1800933== Warning: invalid file descriptor 1024 in syscall close() ==1800933== Warning: invalid file descriptor 1025 in syscall close() ==1800933== Warning: invalid file descriptor 1026 in syscall close() ==1800933== Warning: invalid file descriptor 1027 in syscall close() ==1800933== Use --log-fd= to select an alternative log fd. ==1800933== Warning: invalid file descriptor 1028 in syscall close() ==1800933== Warning: invalid file descriptor 1029 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: c012 Local adapter: mlx5_0 Local port: 1 -------------------------------------------------------------------------- ==1799501== Conditional jump or move depends on uninitialised value(s) ==1799501== at 0xEB7897B: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==1799501== by 0x12DC3C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB65527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==1799501== by 0x12D80670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12D846714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12D7EA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12CBE3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==1799501== by 0x12CBE3A4F: lammps_open (in /usr/local/lib/liblammps.so.0) ==1799501== by 0x627EFF4: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==1799501== by 0x627E409: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==1799501== by 0x9402305: _ctypes_callproc (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==1799501== by 0x9402AE6: ??? (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==1799501== -------------------------------------------------------------------------- WARNING: There was an error initializing an OpenFabrics device. Local host: c012 Local device: mlx5_0 -------------------------------------------------------------------------- ==1799501== Conditional jump or move depends on uninitialised value(s) ==1799501== at 0x12DBF6E84: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0x12DC4CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB55B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==1799501== by 0x12DC4C957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB76356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==1799501== by 0xEB78D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==1799501== by 0x12DC3C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB65527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==1799501== by 0x12D80670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12D846714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12D7EA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12CBE3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==1799501== ==1799501== Use of uninitialised value of size 8 ==1799501== at 0x12DBF6EAD: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0x12DC4CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB55B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==1799501== by 0x12DC4C957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB76356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==1799501== by 0xEB78D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==1799501== by 0x12DC3C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB65527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==1799501== by 0x12D80670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12D846714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12D7EA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12CBE3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==1799501== ==1799501== Use of uninitialised value of size 8 ==1799501== at 0x12DBF6EB4: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0x12DC4CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB55B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==1799501== by 0x12DC4C957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB76356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==1799501== by 0xEB78D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==1799501== by 0x12DC3C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB65527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==1799501== by 0x12D80670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12D846714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12D7EA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12CBE3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==1799501== ==1799501== Use of uninitialised value of size 8 ==1799501== at 0x12DBF6ED3: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0x12DC4CE59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB55B59: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==1799501== by 0x12DC4C957: mca_rcache_base_module_destroy (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB76356: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==1799501== by 0xEB78D18: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==1799501== by 0x12DC3C9C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==1799501== by 0xEB65527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==1799501== by 0x12D80670A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12D846714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12D7EA072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==1799501== by 0x12CBE3A15: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==1799501== ==1799501== ==1799501== HEAP SUMMARY: ==1799501== in use at exit: 29,289,400 bytes in 19,945 blocks ==1799501== total heap usage: 212,437 allocs, 192,492 frees, 369,417,518 bytes allocated ==1799501== ==1799501== LEAK SUMMARY: ==1799501== definitely lost: 12,011 bytes in 36 blocks ==1799501== indirectly lost: 640 bytes in 16 blocks ==1799501== possibly lost: 541,040 bytes in 117 blocks ==1799501== still reachable: 28,735,677 bytes in 19,775 blocks ==1799501== of which reachable via heuristic: ==1799501== stdstring : 38 bytes in 1 blocks ==1799501== suppressed: 32 bytes in 1 blocks ==1799501== Rerun with --leak-check=full to see details of leaked memory ==1799501== ==1799501== Use --track-origins=yes to see where uninitialised values come from ==1799501== For lists of detected and suppressed errors, rerun with: -s ==1799501== ERROR SUMMARY: 5 errors from 5 contexts (suppressed: 8627 from 610) ================================================================================ 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. === Verification check vc-memory-leak end (2022-11-30 10:17:38) ===