Enter a model name: === Verification check vc-memory-leak start (2023-04-28 14:23:03) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ManzanoMoeiniMarinelli_2012_CaSiOH__SM_714124634215_000 Supported species : Ca H O Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ca (Configuration in file "config-F-Ca.xyz") ----------------------------------------------------------------------------------------------------- Energy = 431.86240007141157 Forces: 1 -1.78595864e+01 -1.62013939e+01 -2.12799170e+01 2 -8.97788833e+00 6.74199223e+00 -3.07161220e+01 3 -1.34407041e+00 -2.72546901e+01 7.05863705e+00 4 -2.26754547e+01 9.53982036e+00 6.66945157e+00 5 8.99652847e+00 -3.11951889e+01 -1.82634566e+01 6 2.04493096e+01 1.39318976e+00 -2.34857521e+01 7 1.88514475e+01 -3.49595891e+01 -1.68154222e+01 8 -2.43779632e+00 -1.12083542e+01 4.00467191e+00 9 -1.90354201e+01 -4.73700271e+00 -3.26803732e+01 10 -1.78184373e+01 4.10426387e+01 -3.97765716e+01 11 -2.05856523e+01 -1.36834085e+01 1.29401037e+01 12 -2.12986395e+01 2.37902130e+01 7.82147030e+00 13 4.69106890e+00 -1.57950069e+01 -5.56681213e+01 14 2.09810316e+01 2.39012132e+01 -1.91087611e+01 15 5.13304791e+01 -8.55281641e+00 1.15244152e+01 16 8.06854380e+00 4.53796328e+01 2.35272631e+01 17 -2.16419029e+01 -1.54011816e+01 -3.15652462e+00 18 -4.08748677e+00 4.31318258e+00 6.22059338e+00 19 4.23016592e+00 -2.24379746e+01 1.62008939e+01 20 -1.61027130e+01 6.58574883e+00 1.65334712e+01 21 -1.03548507e+01 -2.64656920e+01 9.06557070e+00 22 3.19577388e+01 2.03931992e+01 1.49822733e+01 23 1.34032018e+01 -8.42184776e+00 1.88572379e+01 24 2.34043981e+00 8.47393224e-01 2.05057765e+01 25 -2.88538138e+01 -1.18695797e+01 -1.55569131e+01 26 -7.34008814e+00 3.69551423e+01 -1.04456379e+01 27 7.79408842e+00 -2.69169990e+01 3.19558880e+01 28 -3.29102494e+01 3.10036820e+01 1.97247766e+01 29 -7.01712590e-02 -1.54087004e+01 6.42896628e+00 30 2.24162430e+01 2.44148712e+01 -1.79639648e+00 31 2.61542696e+01 -1.15398867e+01 2.47558151e+01 32 1.17296650e+01 2.57473930e+01 2.99726936e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ca (Configuration in file "config-T-Ca.xyz") ----------------------------------------------------------------------------------------------------- Energy = 431.86240007141157 Forces: 1 -1.78595864e+01 -1.62013939e+01 -2.12799170e+01 2 -8.97788833e+00 6.74199223e+00 -3.07161220e+01 3 -1.34407041e+00 -2.72546901e+01 7.05863705e+00 4 -2.26754547e+01 9.53982036e+00 6.66945157e+00 5 8.99652847e+00 -3.11951889e+01 -1.82634566e+01 6 2.04493096e+01 1.39318976e+00 -2.34857521e+01 7 1.88514475e+01 -3.49595891e+01 -1.68154222e+01 8 -2.43779632e+00 -1.12083542e+01 4.00467191e+00 9 -1.90354201e+01 -4.73700271e+00 -3.26803732e+01 10 -1.78184373e+01 4.10426387e+01 -3.97765716e+01 11 -2.05856523e+01 -1.36834085e+01 1.29401037e+01 12 -2.12986395e+01 2.37902130e+01 7.82147030e+00 13 4.69106890e+00 -1.57950069e+01 -5.56681213e+01 14 2.09810316e+01 2.39012132e+01 -1.91087611e+01 15 5.13304791e+01 -8.55281641e+00 1.15244152e+01 16 8.06854380e+00 4.53796328e+01 2.35272631e+01 17 -2.16419029e+01 -1.54011816e+01 -3.15652462e+00 18 -4.08748677e+00 4.31318258e+00 6.22059338e+00 19 4.23016592e+00 -2.24379746e+01 1.62008939e+01 20 -1.61027130e+01 6.58574883e+00 1.65334712e+01 21 -1.03548507e+01 -2.64656920e+01 9.06557070e+00 22 3.19577388e+01 2.03931992e+01 1.49822733e+01 23 1.34032018e+01 -8.42184776e+00 1.88572379e+01 24 2.34043981e+00 8.47393224e-01 2.05057765e+01 25 -2.88538138e+01 -1.18695797e+01 -1.55569131e+01 26 -7.34008814e+00 3.69551423e+01 -1.04456379e+01 27 7.79408842e+00 -2.69169990e+01 3.19558880e+01 28 -3.29102494e+01 3.10036820e+01 1.97247766e+01 29 -7.01712590e-02 -1.54087004e+01 6.42896628e+00 30 2.24162430e+01 2.44148712e+01 -1.79639648e+00 31 2.61542696e+01 -1.15398867e+01 2.47558151e+01 32 1.17296650e+01 2.57473930e+01 2.99726936e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = H (Configuration in file "config-F-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -1.5800372932481186 Forces: 1 -9.90874493e-03 -5.54209955e-02 -5.03965854e-02 2 7.99204027e-01 9.91511469e-01 -3.15700320e-01 3 3.17997165e-03 7.71656211e-02 1.96665845e-01 4 -1.38937232e-01 2.60116747e-01 -1.00702736e-01 5 1.50682892e-01 1.31046493e-01 -5.83785582e-02 6 -2.93025434e-01 -3.09613533e-01 5.40866202e-01 7 -1.83521705e+00 1.78231544e+00 5.85467662e-01 8 2.12105604e+00 -1.75674547e+00 -1.11633801e+00 9 7.84881500e-02 -1.94048958e-01 2.88240829e-01 10 -3.00000752e-01 -1.64841795e+00 1.69274804e+00 11 2.34181614e-01 1.58498479e+00 -1.94852688e+00 12 -2.05572280e-01 1.09068974e-01 -8.47186635e-03 13 -7.45672199e-01 -9.49690478e-01 1.51206849e-01 14 5.21373664e-04 1.66644954e-02 -1.18305984e-02 15 5.89585709e-02 3.17143250e-02 -7.51853252e-02 16 -2.24112540e-02 3.45168983e-02 9.16737201e-02 17 -2.57545986e-02 -2.11653895e-02 2.40347246e-02 18 1.24788961e-02 -1.36759306e-01 -1.92560304e-01 19 5.85155835e-03 -5.11913582e-02 1.59388347e-02 20 -1.06879515e-01 1.54707610e+00 -1.47068137e+00 21 3.61360845e+00 2.63908790e-01 2.46310996e+00 22 -3.59540923e-04 -7.40133923e-02 4.13699606e-03 23 -3.55966860e+00 -2.80894727e-01 -2.51841890e+00 24 -4.08302497e-02 -2.71101262e-03 1.11766735e-01 25 1.24112903e+00 -1.30615713e+00 2.51198038e+00 26 1.89721065e-01 1.78404500e-01 1.42118022e-02 27 -1.22522490e+00 -3.19909331e-01 -9.45501347e-01 28 -2.15430140e-02 2.80391249e-02 1.66589549e-02 29 -8.06716649e-02 1.34899113e-01 8.32185856e-02 30 -1.77269162e+00 -2.19642260e-01 1.39623571e+00 31 1.13096925e-01 -2.08428621e-03 1.51245705e-01 32 1.76221009e+00 1.57032695e-01 -1.52671474e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = H (Configuration in file "config-T-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -1.5800372932481186 Forces: 1 -9.90874493e-03 -5.54209955e-02 -5.03965854e-02 2 7.99204027e-01 9.91511469e-01 -3.15700320e-01 3 3.17997165e-03 7.71656211e-02 1.96665845e-01 4 -1.38937232e-01 2.60116747e-01 -1.00702736e-01 5 1.50682892e-01 1.31046493e-01 -5.83785582e-02 6 -2.93025434e-01 -3.09613533e-01 5.40866202e-01 7 -1.83521705e+00 1.78231544e+00 5.85467662e-01 8 2.12105604e+00 -1.75674547e+00 -1.11633801e+00 9 7.84881500e-02 -1.94048958e-01 2.88240829e-01 10 -3.00000752e-01 -1.64841795e+00 1.69274804e+00 11 2.34181614e-01 1.58498479e+00 -1.94852688e+00 12 -2.05572280e-01 1.09068974e-01 -8.47186635e-03 13 -7.45672199e-01 -9.49690478e-01 1.51206849e-01 14 5.21373664e-04 1.66644954e-02 -1.18305984e-02 15 5.89585709e-02 3.17143250e-02 -7.51853252e-02 16 -2.24112540e-02 3.45168983e-02 9.16737201e-02 17 -2.57545986e-02 -2.11653895e-02 2.40347246e-02 18 1.24788961e-02 -1.36759306e-01 -1.92560304e-01 19 5.85155835e-03 -5.11913582e-02 1.59388347e-02 20 -1.06879515e-01 1.54707610e+00 -1.47068137e+00 21 3.61360845e+00 2.63908790e-01 2.46310996e+00 22 -3.59540923e-04 -7.40133923e-02 4.13699606e-03 23 -3.55966860e+00 -2.80894727e-01 -2.51841890e+00 24 -4.08302497e-02 -2.71101262e-03 1.11766735e-01 25 1.24112903e+00 -1.30615713e+00 2.51198038e+00 26 1.89721065e-01 1.78404500e-01 1.42118022e-02 27 -1.22522490e+00 -3.19909331e-01 -9.45501347e-01 28 -2.15430140e-02 2.80391249e-02 1.66589549e-02 29 -8.06716649e-02 1.34899113e-01 8.32185856e-02 30 -1.77269162e+00 -2.19642260e-01 1.39623571e+00 31 1.13096925e-01 -2.08428621e-03 1.51245705e-01 32 1.76221009e+00 1.57032695e-01 -1.52671474e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = O (Configuration in file "config-F-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 33.4655815901566 Forces: 1 -7.90372953e-01 1.88136716e+00 7.63668874e-01 2 -1.49097990e+00 1.86882800e+00 -3.58743401e+00 3 -9.98074136e-01 -5.39823263e+00 -4.93450908e-01 4 -4.22938047e+00 -2.26564697e+00 -4.03253278e+00 5 1.06383634e+00 -2.79058636e+00 -4.06730050e-01 6 1.84891487e+00 1.31363076e+00 -6.86100823e-01 7 3.10715334e+00 -1.52555762e+00 -2.43618612e+00 8 -2.21173110e+00 1.56425366e+00 -6.06486403e+00 9 1.61062810e+00 -6.06398607e-02 -7.42619425e-01 10 -3.94645616e+00 -2.94925942e-02 1.38920344e-01 11 -4.57146568e+00 1.08651258e+00 3.14640866e+00 12 -1.22466797e+00 1.96111001e+00 -1.59836722e+00 13 9.82723723e-01 -1.13594576e+00 -7.26196256e+00 14 -1.02332864e+00 -3.60623548e-01 -8.32815417e-01 15 4.58213569e+00 5.85373353e-01 3.14185072e+00 16 2.79138347e+00 7.25000778e+00 -1.07262233e+00 17 -1.61672004e+00 -1.44441460e+00 8.58368302e-01 18 -7.22071881e-01 -8.57609320e-01 1.10153296e+00 19 2.51387395e-01 -8.40285188e-01 7.14059796e-01 20 -1.47839567e+00 -4.65238346e-01 1.48908930e+00 21 1.80926558e-01 -4.10043946e+00 4.37951111e+00 22 3.23942585e+00 -3.68884461e+00 1.08465202e+00 23 2.88837616e+00 4.13328656e-01 7.38849991e-01 24 -2.14323074e+00 -5.28464049e-01 4.15940099e+00 25 -2.39242242e+00 2.25702302e+00 -3.79248109e-01 26 2.90762065e-01 4.27991089e-01 -9.72941145e-01 27 7.11563219e-01 5.40409227e+00 4.28538474e+00 28 -4.84626789e-01 -4.42731018e-01 4.73745577e-01 29 2.11043707e+00 -1.48628319e+00 7.15377765e-01 30 2.94612586e+00 -1.56064137e+00 2.64582260e+00 31 1.73668034e+00 4.06239056e+00 -1.51964604e+00 32 -1.01853550e+00 -1.09423240e+00 2.25087721e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = O (Configuration in file "config-T-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 33.4655815901566 Forces: 1 -7.90372953e-01 1.88136716e+00 7.63668874e-01 2 -1.49097990e+00 1.86882800e+00 -3.58743401e+00 3 -9.98074136e-01 -5.39823263e+00 -4.93450908e-01 4 -4.22938047e+00 -2.26564697e+00 -4.03253278e+00 5 1.06383634e+00 -2.79058636e+00 -4.06730050e-01 6 1.84891487e+00 1.31363076e+00 -6.86100823e-01 7 3.10715334e+00 -1.52555762e+00 -2.43618612e+00 8 -2.21173110e+00 1.56425366e+00 -6.06486403e+00 9 1.61062810e+00 -6.06398607e-02 -7.42619425e-01 10 -3.94645616e+00 -2.94925942e-02 1.38920344e-01 11 -4.57146568e+00 1.08651258e+00 3.14640866e+00 12 -1.22466797e+00 1.96111001e+00 -1.59836722e+00 13 9.82723723e-01 -1.13594576e+00 -7.26196256e+00 14 -1.02332864e+00 -3.60623548e-01 -8.32815417e-01 15 4.58213569e+00 5.85373353e-01 3.14185072e+00 16 2.79138347e+00 7.25000778e+00 -1.07262233e+00 17 -1.61672004e+00 -1.44441460e+00 8.58368302e-01 18 -7.22071881e-01 -8.57609320e-01 1.10153296e+00 19 2.51387395e-01 -8.40285188e-01 7.14059796e-01 20 -1.47839567e+00 -4.65238346e-01 1.48908930e+00 21 1.80926558e-01 -4.10043946e+00 4.37951111e+00 22 3.23942585e+00 -3.68884461e+00 1.08465202e+00 23 2.88837616e+00 4.13328656e-01 7.38849991e-01 24 -2.14323074e+00 -5.28464049e-01 4.15940099e+00 25 -2.39242242e+00 2.25702302e+00 -3.79248109e-01 26 2.90762065e-01 4.27991089e-01 -9.72941145e-01 27 7.11563219e-01 5.40409227e+00 4.28538474e+00 28 -4.84626789e-01 -4.42731018e-01 4.73745577e-01 29 2.11043707e+00 -1.48628319e+00 7.15377765e-01 30 2.94612586e+00 -1.56064137e+00 2.64582260e+00 31 1.73668034e+00 4.06239056e+00 -1.51964604e+00 32 -1.01853550e+00 -1.09423240e+00 2.25087721e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 30.30170015219408 Forces: 1 -1.42513411e+01 -9.21990694e+00 -1.00236062e+01 2 1.30856824e+01 5.34702606e+00 -1.43187256e+01 3 2.91038207e+00 -1.42578694e+01 8.12258950e+00 4 -1.69209126e+01 1.34535977e+01 1.28622453e+01 5 5.46072709e+00 -7.85476928e+00 -1.00768593e+01 6 1.19854707e+01 -5.35355658e+00 -1.06628867e+01 7 9.86865290e+00 -7.72118197e+00 7.39411725e+00 8 -8.25594732e+00 -4.03659446e+00 6.18780645e+00 9 -1.17711865e+01 1.08907470e+01 -1.25781700e+01 10 -6.97800114e-01 3.69726972e+00 -3.85666794e+00 11 1.48221236e+01 -1.10562350e+01 -1.34662832e+01 12 -1.95143500e+01 -4.14639864e+00 -3.44632836e+00 13 -9.65939343e+00 9.45566296e+00 -8.41875515e+00 14 4.82686085e+00 2.47998756e+00 -4.31033017e+00 15 1.44388603e+01 5.54044651e+00 -3.00246204e-02 16 2.05055956e+00 1.46563549e+01 1.88355004e+00 17 -6.97185582e+00 -6.51002055e+00 -9.81062898e-01 18 3.20508851e-01 5.87656607e+00 -9.92589520e+00 19 7.88774797e+00 -1.53578409e+01 1.62174983e+01 20 -7.08975912e+00 8.84420913e+00 5.77247850e+00 21 -1.44507239e-01 -9.41370209e+00 2.82537652e+00 22 7.58473159e+01 -5.26676542e+00 -5.63050365e+01 23 -3.07953650e-01 5.31804390e-01 1.08870052e+00 24 -7.71646543e+01 -5.35897631e-01 5.66213345e+01 25 -2.00416605e+01 -1.39512467e+01 -5.70297107e+00 26 8.25660842e+00 1.92967101e+01 2.92420482e+00 27 1.55890083e+01 -4.13730848e+00 1.91313884e+01 28 -7.12503528e+00 8.87887226e+00 7.91772414e+00 29 2.31283714e+00 6.37424830e+00 9.09366529e-01 30 1.88004092e+00 2.29236553e+00 1.38338927e-01 31 1.58824621e+01 -6.05380330e+00 7.66523351e+00 32 -7.50949222e+00 7.25722919e+00 6.44164968e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 30.30170015219408 Forces: 1 -1.42513411e+01 -9.21990694e+00 -1.00236062e+01 2 1.30856824e+01 5.34702606e+00 -1.43187256e+01 3 2.91038207e+00 -1.42578694e+01 8.12258950e+00 4 -1.69209126e+01 1.34535977e+01 1.28622453e+01 5 5.46072709e+00 -7.85476928e+00 -1.00768593e+01 6 1.19854707e+01 -5.35355658e+00 -1.06628867e+01 7 9.86865290e+00 -7.72118197e+00 7.39411725e+00 8 -8.25594732e+00 -4.03659446e+00 6.18780645e+00 9 -1.17711865e+01 1.08907470e+01 -1.25781700e+01 10 -6.97800114e-01 3.69726972e+00 -3.85666794e+00 11 1.48221236e+01 -1.10562350e+01 -1.34662832e+01 12 -1.95143500e+01 -4.14639864e+00 -3.44632836e+00 13 -9.65939343e+00 9.45566296e+00 -8.41875515e+00 14 4.82686085e+00 2.47998756e+00 -4.31033017e+00 15 1.44388603e+01 5.54044651e+00 -3.00246204e-02 16 2.05055956e+00 1.46563549e+01 1.88355004e+00 17 -6.97185582e+00 -6.51002055e+00 -9.81062898e-01 18 3.20508851e-01 5.87656607e+00 -9.92589520e+00 19 7.88774797e+00 -1.53578409e+01 1.62174983e+01 20 -7.08975912e+00 8.84420913e+00 5.77247850e+00 21 -1.44507239e-01 -9.41370209e+00 2.82537652e+00 22 7.58473159e+01 -5.26676542e+00 -5.63050365e+01 23 -3.07953650e-01 5.31804390e-01 1.08870052e+00 24 -7.71646543e+01 -5.35897631e-01 5.66213345e+01 25 -2.00416605e+01 -1.39512467e+01 -5.70297107e+00 26 8.25660842e+00 1.92967101e+01 2.92420482e+00 27 1.55890083e+01 -4.13730848e+00 1.91313884e+01 28 -7.12503528e+00 8.87887226e+00 7.91772414e+00 29 2.31283714e+00 6.37424830e+00 9.09366529e-01 30 1.88004092e+00 2.29236553e+00 1.38338927e-01 31 1.58824621e+01 -6.05380330e+00 7.66523351e+00 32 -7.50949222e+00 7.25722919e+00 6.44164968e+00 MIXED STRUCTURE (pbc=False)-- Species = Ca H O Si (Configuration in file "config-F-CaHOSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = -14.849569138305654 Forces: 1 -7.18473759e+00 -5.90854737e+00 -2.67456332e+00 2 8.55889986e+00 -8.37399831e+00 -7.57119647e+00 3 1.18698274e+01 7.56907249e-01 -8.74574198e+00 4 -5.09407741e+00 2.71297995e+00 5.16024538e+00 5 8.13948594e-01 -1.96915741e+00 1.79417666e-01 6 2.82539704e+00 2.99911060e+00 -2.70333154e+00 7 4.82117707e+00 -5.16966451e+00 -2.44820687e+00 8 -3.37714304e+00 4.44102376e+00 5.55345064e-01 9 -1.73996393e+01 8.87782376e-01 -1.41887440e+01 10 -7.36283302e+00 1.53585814e+00 -1.09430570e+01 11 2.10788916e+00 -1.03391056e+01 1.00512458e+01 12 -6.83275541e+00 5.42127209e+00 4.93419109e+00 13 1.58045742e+01 -9.60501373e-01 -9.42734699e+00 14 8.61579513e+00 1.70206472e+00 -5.08524957e+00 15 1.06975934e+00 -1.81090379e+00 -3.20243432e-01 16 3.08041891e+00 7.77277884e+00 9.66241342e+00 17 -1.29930174e+01 -6.01173158e+00 5.45040860e+00 18 -2.06232798e+00 -2.33671080e-01 -5.12791579e+00 19 -8.95822656e-01 -2.66914978e+00 2.32707484e+00 20 -3.70564560e-01 1.71927780e+00 2.14528494e+00 21 -3.10979711e+00 -8.12877167e+00 1.59632656e-01 22 6.93450946e+00 2.36802540e+00 -6.22274834e+00 23 4.80057392e+00 -6.23239506e+00 2.16932512e+00 24 -5.52193052e+00 1.09016553e+01 7.79024428e+00 25 -1.92192772e+00 -8.78470050e-01 -1.87936477e+00 26 1.74035958e+01 9.89342343e+00 -3.75873038e+00 27 -6.82196524e-01 1.50466312e+00 1.06280280e+01 28 -2.09774738e+01 4.75423230e+00 1.53888174e+01 29 3.17514377e+00 -7.31941518e+00 4.69960233e-01 30 6.60860412e-01 1.02291960e+01 -7.47160179e+00 31 2.83133693e+00 -7.15725063e+00 8.90911805e+00 32 4.12537011e-01 3.56248222e+00 2.58728976e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==3718415== Memcheck, a memory error detector ==3718415== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3718415== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==3718415== Command: python runner2.py Sim_LAMMPS_ReaxFF_ManzanoMoeiniMarinelli_2012_CaSiOH__SM_714124634215_000 ==3718415== ==3718415== Conditional jump or move depends on uninitialised value(s) ==3718415== at 0x699E467: NpyIter_GetInnerFixedStrideArray (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==3718415== by 0x6A9AACC: execute_ufunc_loop (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==3718415== by 0x6AA3C47: ufunc_generic_fastcall (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==3718415== by 0x5F3C40: ??? (in /usr/bin/python3.8) ==3718415== by 0x5F3F04: PyObject_CallFunctionObjArgs (in /usr/bin/python3.8) ==3718415== by 0x69B0AA5: array_add (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==3718415== by 0x50F85E: PyNumber_Add (in /usr/bin/python3.8) ==3718415== by 0x56C1D8: _PyEval_EvalFrameDefault (in /usr/bin/python3.8) ==3718415== by 0x5F6835: _PyFunction_Vectorcall (in /usr/bin/python3.8) ==3718415== by 0x56BBDE: _PyEval_EvalFrameDefault (in /usr/bin/python3.8) ==3718415== by 0x569CE9: _PyEval_EvalCodeWithName (in /usr/bin/python3.8) ==3718415== by 0x5F6A12: _PyFunction_Vectorcall (in /usr/bin/python3.8) ==3718415== ==3721406== Warning: invalid file descriptor 1024 in syscall close() ==3721406== Warning: invalid file descriptor 1025 in syscall close() ==3721406== Warning: invalid file descriptor 1026 in syscall close() ==3721406== Warning: invalid file descriptor 1027 in syscall close() ==3721406== Use --log-fd= to select an alternative log fd. ==3721406== Warning: invalid file descriptor 1028 in syscall close() ==3721406== 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: c002 Local adapter: mlx5_0 Local port: 1 -------------------------------------------------------------------------- ==3718415== Conditional jump or move depends on uninitialised value(s) ==3718415== at 0x1891197B: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_openib.so) ==3718415== by 0xC7229C8: mca_btl_base_select (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0x139F5527: mca_bml_r2_component_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_bml_r2.so) ==3718415== by 0xC34170A: mca_bml_base_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==3718415== by 0xC381714: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==3718415== by 0xC325072: PMPI_Init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.40.20.3) ==3718415== by 0x9678915: lammps_mpi_init (in /usr/local/lib/liblammps.so.0) ==3718415== by 0x967894F: lammps_open (in /usr/local/lib/liblammps.so.0) ==3718415== by 0x57CC5FF4: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==3718415== by 0x57CC5409: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.7.1.0) ==3718415== by 0x57CAF305: _ctypes_callproc (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==3718415== by 0x57CAFAE6: ??? (in /usr/lib/python3.8/lib-dynload/_ctypes.cpython-38-x86_64-linux-gnu.so) ==3718415== -------------------------------------------------------------------------- WARNING: There is at least non-excluded one OpenFabrics device found, but there are no active ports detected (or Open MPI was unable to use them). This is most certainly not what you wanted. Check your cables, subnet manager configuration, etc. The openib BTL will be ignored for this job. Local host: c002 -------------------------------------------------------------------------- ==3718415== Conditional jump or move depends on uninitialised value(s) ==3718415== at 0x699E467: NpyIter_GetInnerFixedStrideArray (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==3718415== by 0x6A9AACC: execute_ufunc_loop (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==3718415== by 0x6AA3C47: ufunc_generic_fastcall (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==3718415== by 0x504DFD: ??? (in /usr/bin/python3.8) ==3718415== by 0x56BBDE: _PyEval_EvalFrameDefault (in /usr/bin/python3.8) ==3718415== by 0x569CE9: _PyEval_EvalCodeWithName (in /usr/bin/python3.8) ==3718415== by 0x5F6A12: _PyFunction_Vectorcall (in /usr/bin/python3.8) ==3718415== by 0x5F5C01: PyObject_Call (in /usr/bin/python3.8) ==3718415== by 0x56D1FB: _PyEval_EvalFrameDefault (in /usr/bin/python3.8) ==3718415== by 0x569CE9: _PyEval_EvalCodeWithName (in /usr/bin/python3.8) ==3718415== by 0x5F6A12: _PyFunction_Vectorcall (in /usr/bin/python3.8) ==3718415== by 0x5F5C01: PyObject_Call (in /usr/bin/python3.8) ==3718415== ==3718415== Conditional jump or move depends on uninitialised value(s) ==3718415== at 0xC6DCE84: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC732E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0x139E54B2: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==3718415== by 0xC732FA4: mca_rcache_base_mem_cb (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC6DD2FB: opal_mem_hooks_release_hook (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC72D75A: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0x4881F9B: _nl_unload_locale (loadlocale.c:298) ==3718415== by 0x49E84BD: _nl_locale_subfreeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x49E73A6: free_mem (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x49E8B21: __libc_freeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x48311C6: _vgnU_freeres (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_core-amd64-linux.so) ==3718415== by 0x48969C1: __run_exit_handlers (exit.c:132) ==3718415== ==3718415== Use of uninitialised value of size 8 ==3718415== at 0xC6DCEAD: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC732E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0x139E54B2: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==3718415== by 0xC732FA4: mca_rcache_base_mem_cb (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC6DD2FB: opal_mem_hooks_release_hook (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC72D75A: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0x4881F9B: _nl_unload_locale (loadlocale.c:298) ==3718415== by 0x49E84BD: _nl_locale_subfreeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x49E73A6: free_mem (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x49E8B21: __libc_freeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x48311C6: _vgnU_freeres (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_core-amd64-linux.so) ==3718415== by 0x48969C1: __run_exit_handlers (exit.c:132) ==3718415== ==3718415== Use of uninitialised value of size 8 ==3718415== at 0xC6DCEB4: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC732E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0x139E54B2: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==3718415== by 0xC732FA4: mca_rcache_base_mem_cb (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC6DD2FB: opal_mem_hooks_release_hook (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC72D75A: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0x4881F9B: _nl_unload_locale (loadlocale.c:298) ==3718415== by 0x49E84BD: _nl_locale_subfreeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x49E73A6: free_mem (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x49E8B21: __libc_freeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x48311C6: _vgnU_freeres (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_core-amd64-linux.so) ==3718415== by 0x48969C1: __run_exit_handlers (exit.c:132) ==3718415== ==3718415== Use of uninitialised value of size 8 ==3718415== at 0xC6DCED3: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC732E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0x139E54B2: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==3718415== by 0xC732FA4: mca_rcache_base_mem_cb (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC6DD2FB: opal_mem_hooks_release_hook (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC72D75A: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0x4881F9B: _nl_unload_locale (loadlocale.c:298) ==3718415== by 0x49E84BD: _nl_locale_subfreeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x49E73A6: free_mem (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x49E8B21: __libc_freeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x48311C6: _vgnU_freeres (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_core-amd64-linux.so) ==3718415== by 0x48969C1: __run_exit_handlers (exit.c:132) ==3718415== ==3718415== Conditional jump or move depends on uninitialised value(s) ==3718415== at 0xC6DCF09: opal_interval_tree_traverse (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC732E59: mca_rcache_base_vma_tree_iterate (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0x139E54B2: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_rcache_grdma.so) ==3718415== by 0xC732FA4: mca_rcache_base_mem_cb (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC6DD2FB: opal_mem_hooks_release_hook (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0xC72D75A: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.40.20.3) ==3718415== by 0x49E8B21: __libc_freeres (in /usr/lib/x86_64-linux-gnu/libc-2.31.so) ==3718415== by 0x48311C6: _vgnU_freeres (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_core-amd64-linux.so) ==3718415== by 0x48969C1: __run_exit_handlers (exit.c:132) ==3718415== by 0x4896A5F: exit (exit.c:139) ==3718415== by 0x4874089: (below main) (libc-start.c:342) ==3718415== ==3718415== ==3718415== HEAP SUMMARY: ==3718415== in use at exit: 29,632,762 bytes in 19,954 blocks ==3718415== total heap usage: 257,734 allocs, 237,780 frees, 334,286,182 bytes allocated ==3718415== ==3718415== LEAK SUMMARY: ==3718415== definitely lost: 11,864 bytes in 34 blocks ==3718415== indirectly lost: 609 bytes in 13 blocks ==3718415== possibly lost: 879,232 bytes in 136 blocks ==3718415== still reachable: 28,741,025 bytes in 19,770 blocks ==3718415== of which reachable via heuristic: ==3718415== stdstring : 38 bytes in 1 blocks ==3718415== suppressed: 32 bytes in 1 blocks ==3718415== Rerun with --leak-check=full to see details of leaked memory ==3718415== ==3718415== Use --track-origins=yes to see where uninitialised values come from ==3718415== For lists of detected and suppressed errors, rerun with: -s ==3718415== ERROR SUMMARY: 119 errors from 8 contexts (suppressed: 19156 from 656) ================================================================================ 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 (2023-04-28 14:24:49) ===