Enter a model name: === Verification check vc-memory-leak start (2025-07-10 13:15:48) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Buckingham_PotashnikovBoyarchenkovNekrasov_2011_PuUO__SM_422015835006_000 Supported species : O Pu U random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = O (Configuration in file "config-F-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3882.871751311781 Forces: 1 -2.52900335e+01 -3.75160947e+01 -3.34128050e+01 2 -1.06188259e+01 -6.00783167e+00 -4.06398204e+01 3 -9.91801908e+00 -4.30815466e+01 -1.51281851e+01 4 -3.88725798e+01 5.38968383e+00 -3.26296585e-01 5 9.92210248e+00 -3.90762033e+01 -2.76977733e+01 6 3.05946509e+01 -1.17563327e+01 -3.29277553e+01 7 3.08515710e+01 -6.01871308e+01 -5.34113958e+01 8 7.31169208e-01 -2.25525937e+01 -6.85501281e+00 9 -2.51319874e+01 -6.47549836e-01 -4.53735944e+01 10 -1.75271236e+01 3.65544969e+01 -4.94963761e+01 11 -1.49299222e+01 6.94179127e+00 -1.06343742e+01 12 -3.66008309e+01 3.86291396e+01 7.19100874e-01 13 -7.41637997e+01 -1.20907899e+01 -1.62979001e+02 14 2.94734437e+01 3.43707804e+01 -2.76848977e+01 15 1.36851175e+02 2.58749379e+01 1.01627828e+02 16 1.59052172e+01 4.54008336e+01 9.99941630e+00 17 -4.21834080e+01 -3.24803780e+01 4.30090929e-01 18 -5.75749018e+00 2.84978202e+00 6.55996971e+00 19 -1.87179142e+00 -4.47691585e+01 3.83065251e+01 20 -3.18866986e+01 -2.18074371e-02 3.39457272e+01 21 -6.71295841e+00 -4.47212287e+01 2.79658733e+01 22 5.86195571e+01 2.24194384e+01 3.69891860e+01 23 2.71634754e+01 -1.89912875e+01 3.18912885e+01 24 7.51764702e+00 -6.73524354e+00 3.92561735e+01 25 -3.97126687e+01 8.72487429e+00 7.51870875e+00 26 -1.15089462e+01 4.36361851e+01 -5.25954960e-01 27 1.17853360e+01 -2.83178213e+01 3.96515120e+01 28 -5.90245224e+01 5.35072187e+01 2.52933175e+01 29 -7.06709886e+00 7.12999717e+00 6.99664162e+00 30 3.74501777e+01 3.97932947e+01 7.26137682e+00 31 4.64911992e+01 1.73342941e+00 5.17857473e+01 32 1.54219828e+01 3.59971151e+01 4.08947596e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = O (Configuration in file "config-T-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 2951.3847014761777 Forces: 1 -2.51736646e+01 -3.74164796e+01 -3.33106744e+01 2 -1.05916738e+01 -5.96596553e+00 -4.05218556e+01 3 -9.86994330e+00 -4.29658263e+01 -1.50988669e+01 4 -3.87504249e+01 5.42138277e+00 -2.68064837e-01 5 9.89368887e+00 -3.89670804e+01 -2.75989776e+01 6 3.04826011e+01 -1.17082162e+01 -3.28123413e+01 7 3.07521185e+01 -6.00912724e+01 -5.33844692e+01 8 6.89387572e-01 -2.25279056e+01 -6.82551765e+00 9 -2.50354306e+01 -6.89307370e-01 -4.52569448e+01 10 -1.74999442e+01 3.64416485e+01 -4.93951958e+01 11 -1.48933932e+01 6.91683268e+00 -1.05930935e+01 12 -3.64886577e+01 3.85218856e+01 7.80543236e-01 13 -7.42227875e+01 -1.21266383e+01 -1.62883779e+02 14 2.93595521e+01 3.42572754e+01 -2.75846195e+01 15 1.36751251e+02 2.58317177e+01 1.01672219e+02 16 1.58800104e+01 4.52951296e+01 1.00424528e+01 17 -4.20659496e+01 -3.23731121e+01 3.88451731e-01 18 -5.71593780e+00 2.90792632e+00 6.52370420e+00 19 -1.82584255e+00 -4.46548098e+01 3.82046804e+01 20 -3.17728284e+01 2.79054783e-02 3.38304475e+01 21 -6.77080789e+00 -4.46103381e+01 2.79234724e+01 22 5.84960046e+01 2.24674677e+01 3.69629996e+01 23 2.70460646e+01 -1.88958304e+01 3.17768715e+01 24 7.50644250e+00 -6.69850305e+00 3.91324470e+01 25 -3.96126546e+01 8.68243971e+00 7.49048959e+00 26 -1.14815846e+01 4.35254709e+01 -5.68680852e-01 27 1.18341497e+01 -2.83697916e+01 3.95361015e+01 28 -5.89219095e+01 5.34037196e+01 2.51795602e+01 29 -7.11827286e+00 7.08832688e+00 6.96387859e+00 30 3.73336720e+01 3.96846072e+01 7.23086519e+00 31 4.63912653e+01 1.69082531e+00 5.16852668e+01 32 1.53954996e+01 3.58965156e+01 4.07786297e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Pu (Configuration in file "config-F-Pu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 15443.920890649919 Forces: 1 -8.45368975e+01 -9.56316936e+01 -1.01459655e+02 2 -6.26193833e+01 -4.92848094e+01 -1.64497717e+02 3 -3.44800598e+01 -1.59912761e+02 -3.78694432e+01 4 -1.75268054e+02 -3.98709106e+01 -4.32983538e+01 5 2.57573548e+01 -1.29010711e+02 -1.20562831e+02 6 1.28327183e+02 -4.11073786e+01 -1.26112906e+02 7 1.23320882e+02 -1.31529622e+02 -3.34822507e+01 8 6.60080285e+01 -6.83796847e+01 -4.97887104e+01 9 -1.28484514e+02 3.57480802e+01 -1.27900946e+02 10 -2.91111024e+01 1.26058854e+02 -1.22386693e+02 11 -4.72287089e+01 7.02628167e+01 -3.78042491e+01 12 -1.28341603e+02 1.22725071e+02 -2.85013904e+01 13 5.04283718e+01 5.34560925e+01 -1.80684105e+02 14 9.98316816e+01 1.10273567e+02 -9.68772244e+01 15 1.59938087e+02 2.82656969e+01 -6.35285735e+01 16 4.35549424e+01 1.64725661e+02 -4.82194090e+01 17 -1.28945789e+02 -1.34549060e+02 3.28301276e+01 18 -5.77858912e+01 -5.14921984e+01 6.61542402e+01 19 -3.43290055e+01 -1.40128441e+02 1.14800197e+02 20 -1.27750628e+02 -4.67872836e+01 1.27498684e+02 21 5.07768002e+01 -1.44557642e+02 4.24523970e+01 22 1.64518372e+02 -3.68261679e+01 3.69995643e+01 23 9.83837913e+01 -8.61517888e+01 1.05693301e+02 24 3.77386998e+01 -3.57574660e+01 1.54870912e+02 25 -1.60321153e+02 5.92901282e+01 5.18315519e+01 26 -5.29423652e+01 1.61341774e+02 4.04140229e+01 27 -4.12020403e+01 4.62513820e+01 1.58147807e+02 28 -8.74202739e+01 8.52465989e+01 8.43339543e+01 29 6.35201877e+01 3.68040279e+01 6.54549303e+01 30 1.30962249e+02 1.31669031e+02 4.08530498e+01 31 1.23768964e+02 3.30472991e+01 1.36869283e+02 32 1.39318743e+01 1.25811537e+02 1.23770435e+02 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pu (Configuration in file "config-T-Pu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 11718.160839461854 Forces: 1 -8.41349100e+01 -9.51745236e+01 -1.00976496e+02 2 -6.24818068e+01 -4.91846737e+01 -1.64088431e+02 3 -3.43140323e+01 -1.59490873e+02 -3.77686273e+01 4 -1.74805454e+02 -3.97342472e+01 -4.31406470e+01 5 2.56369112e+01 -1.28546984e+02 -1.20095362e+02 6 1.27899576e+02 -4.09077799e+01 -1.25667778e+02 7 1.22923222e+02 -1.31119325e+02 -3.33533110e+01 8 6.59139243e+01 -6.82624894e+01 -4.96084911e+01 9 -1.28053571e+02 3.56008622e+01 -1.27447974e+02 10 -2.89510130e+01 1.25630655e+02 -1.21909732e+02 11 -4.71316114e+01 7.01652707e+01 -3.76986840e+01 12 -1.27877838e+02 1.22312234e+02 -2.83487274e+01 13 5.03314776e+01 5.33575467e+01 -1.80228735e+02 14 9.93960864e+01 1.09794594e+02 -9.65056107e+01 15 1.59542417e+02 2.81191813e+01 -6.33426585e+01 16 4.33676011e+01 1.64304358e+02 -4.81229536e+01 17 -1.28523200e+02 -1.34064349e+02 3.27408843e+01 18 -5.76163372e+01 -5.13858842e+01 6.60463174e+01 19 -3.41904817e+01 -1.39672830e+02 1.14375611e+02 20 -1.27357368e+02 -4.66078793e+01 1.27027895e+02 21 5.06050896e+01 -1.44164851e+02 4.23014632e+01 22 1.64015733e+02 -3.66714766e+01 3.68431857e+01 23 9.79277574e+01 -8.57569622e+01 1.05206556e+02 24 3.76324061e+01 -3.55666572e+01 1.54418221e+02 25 -1.59923867e+02 5.91434559e+01 5.17064948e+01 26 -5.28573789e+01 1.60922916e+02 4.03142456e+01 27 -4.10112780e+01 4.61646769e+01 1.57671522e+02 28 -8.69495528e+01 8.47906695e+01 8.38532656e+01 29 6.33084880e+01 3.66239693e+01 6.53142068e+01 30 1.30501562e+02 1.31191850e+02 4.06817031e+01 31 1.23346297e+02 3.28757049e+01 1.36471963e+02 32 1.38311515e+01 1.25313842e+02 1.23330685e+02 MONOATOMIC STRUCTURE (pbc=False)-- Species = U (Configuration in file "config-F-U.xyz") ----------------------------------------------------------------------------------------------------- Energy = 15336.754286789854 Forces: 1 -9.35246460e+01 -1.02589488e+02 -9.74179696e+01 2 -4.07602959e+01 -4.32925925e+01 -1.40916074e+02 3 -2.66104870e+01 -1.57214198e+02 -3.82277773e+01 4 -1.57862394e+02 -5.19792018e+01 -4.61886481e+01 5 3.73539712e+01 -1.16551434e+02 -1.28043149e+02 6 1.27961251e+02 -3.49867051e+01 -1.29570768e+02 7 1.17753766e+02 -1.23139196e+02 -3.08024678e+01 8 3.15263542e+01 -5.03263723e+01 -5.74271867e+01 9 -1.20279238e+02 3.68919823e+01 -1.29020751e+02 10 -4.43395362e+01 1.34870856e+02 -1.16889009e+02 11 -4.56069821e+01 4.43620976e+01 -5.24796347e+01 12 -1.28598657e+02 1.22256459e+02 -3.71082962e+01 13 2.90919215e+01 4.54212052e+01 -1.66228830e+02 14 1.19771587e+02 9.83364894e+01 -9.54570669e+01 15 1.42868807e+02 1.85850522e+01 -3.21624273e+01 16 5.02917756e+01 1.56499367e+02 -4.29373370e+01 17 -1.34559595e+02 -1.31220361e+02 2.50734967e+01 18 -4.88162344e+01 -4.37390541e+01 6.42314141e+01 19 -3.27882242e+01 -1.33998156e+02 1.22060470e+02 20 -1.15509897e+02 -2.65939641e+01 1.38228613e+02 21 4.96269701e+01 -1.50941321e+02 4.15330497e+01 22 1.52833650e+02 -3.87093575e+01 3.42515726e+01 23 1.03424653e+02 -9.10144936e+01 1.05143059e+02 24 3.48295109e+01 -3.64693818e+01 1.39546543e+02 25 -1.68414919e+02 4.61692080e+01 3.81227447e+01 26 -4.35749683e+01 1.71125779e+02 2.45384090e+01 27 -3.93520128e+01 2.27599374e+01 1.58624777e+02 28 -1.06558864e+02 9.86653412e+01 1.05556259e+02 29 5.36949461e+01 4.28106683e+01 4.83729082e+01 30 1.30878861e+02 1.21096627e+02 3.19601829e+01 31 1.20247998e+02 3.60278997e+01 1.27464916e+02 32 4.50009274e+01 1.36886307e+02 1.36168978e+02 MONOATOMIC STRUCTURE (pbc=True)-- Species = U (Configuration in file "config-T-U.xyz") ----------------------------------------------------------------------------------------------------- Energy = 11611.079478941665 Forces: 1 -9.31174008e+01 -1.02155975e+02 -9.69267572e+01 2 -4.05501462e+01 -4.31229783e+01 -1.40455572e+02 3 -2.65058228e+01 -1.56744532e+02 -3.81230178e+01 4 -1.57451938e+02 -5.18266605e+01 -4.60999878e+01 5 3.71909185e+01 -1.16116503e+02 -1.27577612e+02 6 1.27536040e+02 -3.48917672e+01 -1.29136768e+02 7 1.17361519e+02 -1.22689079e+02 -3.06555955e+01 8 3.14275113e+01 -5.01909390e+01 -5.72244029e+01 9 -1.19870868e+02 3.67833930e+01 -1.28535146e+02 10 -4.41953842e+01 1.34450063e+02 -1.16496319e+02 11 -4.54488829e+01 4.42108082e+01 -5.23713286e+01 12 -1.28116907e+02 1.21785643e+02 -3.69821584e+01 13 2.89661945e+01 4.52212537e+01 -1.65728594e+02 14 1.19301745e+02 9.79404630e+01 -9.50631649e+01 15 1.42475968e+02 1.84899415e+01 -3.20160919e+01 16 5.01074971e+01 1.56080990e+02 -4.27895951e+01 17 -1.34125617e+02 -1.30755940e+02 2.49271210e+01 18 -4.86001598e+01 -4.35891495e+01 6.40555122e+01 19 -3.26156586e+01 -1.33529637e+02 1.21675827e+02 20 -1.15086599e+02 -2.64447734e+01 1.37739191e+02 21 4.94649596e+01 -1.50454052e+02 4.13412226e+01 22 1.52346531e+02 -3.86034928e+01 3.40688681e+01 23 1.02978015e+02 -9.06105615e+01 1.04687712e+02 24 3.46842771e+01 -3.62975754e+01 1.39146506e+02 25 -1.67988787e+02 4.60105240e+01 3.80304614e+01 26 -4.34355090e+01 1.70664161e+02 2.43927431e+01 27 -3.92278487e+01 2.25689005e+01 1.58194230e+02 28 -1.06152085e+02 9.82268222e+01 1.05112107e+02 29 5.35692144e+01 4.26110922e+01 4.82336606e+01 30 1.30394173e+02 1.20673701e+02 3.17975900e+01 31 1.19768189e+02 3.58609454e+01 1.27040638e+02 32 4.49168615e+01 1.36444914e+02 1.35738721e+02 MIXED STRUCTURE (pbc=False)-- Species = O Pu U (Configuration in file "config-F-OPuU.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3895.4199969543156 Forces: 1 -3.63394246e+01 -1.43280283e+01 3.12105319e+01 2 2.78282237e+01 8.61742514e+01 3.07371995e+01 3 -4.12548012e+00 -1.24081305e+02 -8.57549249e+01 4 -1.09496627e+02 -2.75155847e+01 -6.27455226e+01 5 9.01812013e+00 6.40913360e+00 2.92883167e+01 6 6.86936976e+01 -2.15090772e+01 -5.99726103e+01 7 -2.40630265e+01 1.21073450e+01 2.88876424e+01 8 6.93688217e+01 -2.79994227e+01 -7.12279399e+01 9 -7.16783019e+01 -2.04253464e+01 -1.14928075e+02 10 -1.57696443e+00 8.29757434e+01 -9.00696809e+01 11 -4.89487824e+00 -1.63212371e+01 -3.05579319e+01 12 -1.05225146e+02 8.08135650e+01 -3.81541821e+00 13 6.45763320e+01 -3.35903271e+00 -9.29848039e+01 14 -2.88403129e+01 2.70154671e+01 -2.28812237e+01 15 -4.37353300e+01 -5.06377461e+01 5.16244881e+01 16 8.67979223e+01 8.16520501e+01 -2.55695028e+01 17 -1.01670009e+02 -1.12666765e+02 3.21065246e+01 18 5.37933541e+00 1.92328622e+00 4.44569576e+01 19 1.74012347e+01 1.27345974e+01 -2.16199137e+01 20 -7.69234623e+01 6.58258208e+00 1.04774030e+02 21 6.30134604e+01 -1.10412877e+02 3.86124672e+00 22 -3.35492343e+01 2.20056175e+01 -1.19687789e+01 23 7.73428918e+01 -8.73678390e+01 4.56219380e+01 24 1.71241678e+01 -1.72847580e+01 8.84854403e+01 25 2.28021373e+01 -4.79004046e+00 8.34257652e+00 26 3.88912630e+00 8.47155263e+01 4.84719392e+01 27 -6.37828660e+00 3.57604436e-01 -2.92161871e+01 28 -5.06816385e+01 4.01566727e+01 5.96190826e+01 29 7.46280285e+01 2.16760936e+01 -2.72831231e+00 30 -3.57557583e+01 -1.83289165e+01 7.52061128e+00 31 9.84369501e+01 2.28646983e+01 4.20744849e+01 32 2.86334319e+01 6.68637427e+01 6.89578163e+01 MIXED STRUCTURE (pbc=True)-- Species = O Pu U (Configuration in file "config-T-OPuU.xyz") ----------------------------------------------------------------------------------------------------- Energy = -719.6672777407275 Forces: 1 -4.93933286e+01 -3.96451016e+01 6.72416411e+00 2 2.70810300e+01 7.74144973e+01 1.62233288e+01 3 -9.34668877e-01 -1.35354428e+01 -5.85287665e+01 4 -6.48181524e+01 1.69695304e+01 -3.14228191e+01 5 1.94306809e+01 -2.15793280e+01 3.65038332e+00 6 8.92642453e+00 -1.29540480e+01 2.02968008e+01 7 -4.94510874e-02 -5.79896311e+00 1.55589455e+01 8 4.34758073e+01 1.73432719e+01 -3.88034177e+01 9 -2.55355768e+01 -1.37079642e+01 -2.95154541e+01 10 -1.11807204e+00 2.80900463e+01 -2.67253762e+01 11 8.80459688e+00 -2.51776294e+01 -4.03172493e+00 12 -7.95459328e+01 1.85312376e+01 -4.76777984e+00 13 1.58473591e+01 -1.25922755e+01 1.39023357e+00 14 4.36020388e+00 3.48037695e+01 -4.46336889e+01 15 -5.34640796e+00 -4.53981892e+01 3.33103388e+01 16 5.89355606e+01 1.46282646e+01 -1.49008857e+01 17 -6.64590575e+01 -3.00356808e+01 1.13305556e+01 18 1.80142650e+01 5.08984303e+01 2.76576808e+01 19 1.17329963e+01 -3.00360002e+01 -3.32896290e+01 20 -1.06450414e+01 2.14216635e+01 4.10990578e+01 21 5.54357193e+01 -1.90020324e+01 9.38512014e+00 22 4.63589509e-01 9.80552549e+00 -9.89181170e+00 23 1.28005673e+01 -4.22397008e+01 2.35865782e+01 24 -2.33604692e+01 -3.94312861e+00 2.47544823e+01 25 3.84566950e+00 -2.31886502e+00 1.99160684e+01 26 3.53882926e+00 -2.45992850e+01 3.57385901e+01 27 -6.09232971e+00 8.71851927e+00 -2.23982405e+00 28 -2.04913844e+01 -5.18654462e+00 1.16746201e+01 29 3.01926835e+01 3.88916244e-01 -1.56067462e+01 30 -1.61292512e+00 5.92293747e+00 1.19552490e+01 31 2.21493666e+01 1.94428991e+01 -7.00454447e+00 32 1.03674483e+01 2.33706703e+01 7.11027108e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1677355== Memcheck, a memory error detector ==1677355== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1677355== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==1677355== Command: python runner2.py Sim_LAMMPS_Buckingham_PotashnikovBoyarchenkovNekrasov_2011_PuUO__SM_422015835006_000 ==1677355== ==1677355== Invalid read of size 8 ==1677355== at 0x40286A0: strncmp (strcmp.S:170) ==1677355== by 0x400668D: is_dst (dl-load.c:216) ==1677355== by 0x400810E: _dl_dst_count (dl-load.c:253) ==1677355== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==1677355== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==1677355== by 0x4008602: decompose_rpath (dl-load.c:654) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1677355== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1677355== by 0x4003494: openaux (dl-deps.c:64) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1677355== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1677355== Address 0x4c5f9c1 is 1 bytes inside a block of size 8 alloc'd ==1677355== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1677355== by 0x40271DF: malloc (rtld-malloc.h:56) ==1677355== by 0x40271DF: strdup (strdup.c:42) ==1677355== by 0x4008594: decompose_rpath (dl-load.c:629) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1677355== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1677355== by 0x4003494: openaux (dl-deps.c:64) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1677355== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x400E34D: _dl_open (dl-open.c:883) ==1677355== ==1677355== Invalid read of size 8 ==1677355== at 0x40286A8: strncmp (strcmp.S:172) ==1677355== by 0x400668D: is_dst (dl-load.c:216) ==1677355== by 0x400810E: _dl_dst_count (dl-load.c:253) ==1677355== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==1677355== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==1677355== by 0x4008602: decompose_rpath (dl-load.c:654) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1677355== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1677355== by 0x4003494: openaux (dl-deps.c:64) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1677355== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1677355== Address 0x4c5f9c9 is 1 bytes after a block of size 8 alloc'd ==1677355== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1677355== by 0x40271DF: malloc (rtld-malloc.h:56) ==1677355== by 0x40271DF: strdup (strdup.c:42) ==1677355== by 0x4008594: decompose_rpath (dl-load.c:629) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1677355== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1677355== by 0x4003494: openaux (dl-deps.c:64) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1677355== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x400E34D: _dl_open (dl-open.c:883) ==1677355== ==1677355== Invalid read of size 8 ==1677355== at 0x40286A0: strncmp (strcmp.S:170) ==1677355== by 0x400668D: is_dst (dl-load.c:216) ==1677355== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==1677355== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==1677355== by 0x4008602: decompose_rpath (dl-load.c:654) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1677355== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1677355== by 0x4003494: openaux (dl-deps.c:64) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1677355== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1677355== Address 0x4c5f9c1 is 1 bytes inside a block of size 8 alloc'd ==1677355== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1677355== by 0x40271DF: malloc (rtld-malloc.h:56) ==1677355== by 0x40271DF: strdup (strdup.c:42) ==1677355== by 0x4008594: decompose_rpath (dl-load.c:629) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1677355== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1677355== by 0x4003494: openaux (dl-deps.c:64) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1677355== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x400E34D: _dl_open (dl-open.c:883) ==1677355== ==1677355== Invalid read of size 8 ==1677355== at 0x40286A8: strncmp (strcmp.S:172) ==1677355== by 0x400668D: is_dst (dl-load.c:216) ==1677355== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==1677355== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==1677355== by 0x4008602: decompose_rpath (dl-load.c:654) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1677355== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1677355== by 0x4003494: openaux (dl-deps.c:64) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1677355== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1677355== Address 0x4c5f9c9 is 1 bytes after a block of size 8 alloc'd ==1677355== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==1677355== by 0x40271DF: malloc (rtld-malloc.h:56) ==1677355== by 0x40271DF: strdup (strdup.c:42) ==1677355== by 0x4008594: decompose_rpath (dl-load.c:629) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:696) ==1677355== by 0x400A8C8: cache_rpath (dl-load.c:677) ==1677355== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==1677355== by 0x4003494: openaux (dl-deps.c:64) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==1677355== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x400DF99: dl_open_worker (dl-open.c:782) ==1677355== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==1677355== by 0x400E34D: _dl_open (dl-open.c:883) ==1677355== ==1677355== Syscall param socketcall.getsockopt(optlen) points to uninitialised byte(s) ==1677355== at 0x4ABB5EE: getsockopt_syscall (getsockopt.c:29) ==1677355== by 0x4ABB5EE: getsockopt (getsockopt.c:94) ==1677355== by 0x91A9157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1677355== by 0x91B0A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1677355== by 0x91B7DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1677355== by 0x90B73C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1677355== by 0x904BE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1677355== by 0x7CA60E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1677355== by 0x7C1134CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1677355== by 0x7BAC9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1677355== by 0x7BA62C21: PMPI_Init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1677355== by 0x7AC44495: lammps_mpi_init (in /usr/local/lib/python3.10/dist-packages/lammps/liblammps.so) ==1677355== by 0x7AC444CF: lammps_open (in /usr/local/lib/python3.10/dist-packages/lammps/liblammps.so) ==1677355== Address 0x1ffeffd39c is on thread 1's stack ==1677355== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1677355== ==1677355== Syscall param socketcall.getsockopt(optlen_out) points to uninitialised byte(s) ==1677355== at 0x4ABB5EE: getsockopt_syscall (getsockopt.c:29) ==1677355== by 0x4ABB5EE: getsockopt (getsockopt.c:94) ==1677355== by 0x91A9157: pmix_ptl_base_set_timeout (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1677355== by 0x91B0A1A: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1677355== by 0x91B7DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1677355== by 0x90B73C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1677355== by 0x904BE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1677355== by 0x7CA60E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1677355== by 0x7C1134CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1677355== by 0x7BAC9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1677355== by 0x7BA62C21: PMPI_Init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1677355== by 0x7AC44495: lammps_mpi_init (in /usr/local/lib/python3.10/dist-packages/lammps/liblammps.so) ==1677355== by 0x7AC444CF: lammps_open (in /usr/local/lib/python3.10/dist-packages/lammps/liblammps.so) ==1677355== Address 0x1ffeffd39c is on thread 1's stack ==1677355== in frame #2, created by pmix_ptl_base_make_connection (???:) ==1677355== ==1677355== Syscall param setsockopt(optlen) contains uninitialised byte(s) ==1677355== at 0x4ABBACE: setsockopt_syscall (setsockopt.c:29) ==1677355== by 0x4ABBACE: setsockopt (setsockopt.c:95) ==1677355== by 0x91B0BA9: pmix_ptl_base_make_connection (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1677355== by 0x91B7DF3: ??? (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1677355== by 0x90B73C1: PMIx_Init (in /usr/lib/x86_64-linux-gnu/pmix2/lib/libpmix.so.2.5.2) ==1677355== by 0x904BE4A: ext3x_client_init (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext3x.so) ==1677355== by 0x7CA60E6D: ??? (in /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_singleton.so) ==1677355== by 0x7C1134CB: orte_init (in /usr/lib/x86_64-linux-gnu/libopen-rte.so.40.30.2) ==1677355== by 0x7BAC9418: ompi_mpi_init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1677355== by 0x7BA62C21: PMPI_Init (in /usr/lib/x86_64-linux-gnu/libmpi.so.40.30.2) ==1677355== by 0x7AC44495: lammps_mpi_init (in /usr/local/lib/python3.10/dist-packages/lammps/liblammps.so) ==1677355== by 0x7AC444CF: lammps_open (in /usr/local/lib/python3.10/dist-packages/lammps/liblammps.so) ==1677355== by 0x87E6E2D: ??? (in /usr/lib/x86_64-linux-gnu/libffi.so.8.1.0) ==1677355== hwloc x86 backend cannot work under Valgrind, disabling. May be reenabled by dumping CPUIDs with hwloc-gather-cpuid and reloading them under Valgrind with HWLOC_CPUID_PATH. ==1677355== ==1677355== HEAP SUMMARY: ==1677355== in use at exit: 6,872,397 bytes in 18,810 blocks ==1677355== total heap usage: 309,706 allocs, 290,896 frees, 4,017,908,697 bytes allocated ==1677355== ==1677355== LEAK SUMMARY: ==1677355== definitely lost: 730 bytes in 7 blocks ==1677355== indirectly lost: 79 bytes in 2 blocks ==1677355== possibly lost: 159,971 bytes in 114 blocks ==1677355== still reachable: 6,711,617 bytes in 18,687 blocks ==1677355== of which reachable via heuristic: ==1677355== stdstring : 4,256 bytes in 48 blocks ==1677355== suppressed: 0 bytes in 0 blocks ==1677355== Rerun with --leak-check=full to see details of leaked memory ==1677355== ==1677355== Use --track-origins=yes to see where uninitialised values come from ==1677355== For lists of detected and suppressed errors, rerun with: -s ==1677355== ERROR SUMMARY: 11 errors from 7 contexts (suppressed: 0 from 0) ================================================================================ 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 (2025-07-10 13:16:57) ===