!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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.