>> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/utils/PetscManager.py:47:initialize -- petsc(info) -- Initializing PETSc. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/meshio/MeshIO.py:45:read -- meshioascii(info) -- Reading finite-element mesh Creating new arrow section: orientation Creating new real section: coordinates Creating new int section: fault Creating new int section: end points Creating new int section: x_neg Creating new int section: x_pos Creating new NumberingFactory viewing Mesh 'Serial mesh' viewing Sieve :'mesh sieve' cap --> base: [0]: 2--(0)-->0 [0]: 3--(0)-->1 [0]: 3--(1)-->0 [0]: 4--(2)-->0 [0]: 4--(2)-->1 [0]: 5--(1)-->1 base --> cap: [0]: 0<--(0)--2 [0]: 0<--(1)--3 [0]: 0<--(2)--4 [0]: 1<--(0)--3 [0]: 1<--(1)--5 [0]: 1<--(2)--4 cap : [0]: [ <2, 0, 0, 0, 0> <3, 0, 0, 0, 0> <4, 0, 0, 0, 0> <5, 0, 0, 0, 0> ] base : [0]: [ <0,0, 0, 0, 0> <1,0, 0, 0, 0> ] viewing GeneralSection 'coordinates' Fields: 0 [0]: 2 dim 2 offset 0 -0.5 -0.5 [0]: 3 dim 2 offset 2 0.5 -0.5 [0]: 4 dim 2 offset 4 -0.5 0.5 [0]: 5 dim 2 offset 6 0.5 0.5 viewing Section end points : end points' [0]: 2 dim 1 offset 0 0 [0]: 5 dim 1 offset 1 0 viewing Section fault : fault' [0]: 3 dim 1 offset 0 0 [0]: 4 dim 1 offset 1 0 viewing Section x_neg : x_neg' [0]: 2 dim 1 offset 0 0 [0]: 4 dim 1 offset 1 0 viewing Section x_pos : x_pos' [0]: 3 dim 1 offset 0 0 [0]: 5 dim 1 offset 1 0 viewing UniformSection 'orientation' [0]: empty viewing a Sifter, comm = 1140850688, PETSC_COMM_SELF = 1140850689, commRank = 0 viewing Sifter: 'Send overlap for partition' cap --> base: [0]: empty cap: [0]: [ ] base: [0]: [ ] viewing a Sifter, comm = 1140850688, PETSC_COMM_SELF = 1140850689, commRank = 0 viewing Sifter: 'Receive overlap for partition' cap --> base: [0]: empty cap: [0]: [ ] base: [0]: [ ] Parameter file `User_Params' not found; using default parameters. WARNING: Vertex 1 has no neighbors WARNING: 2 vertices have no neighbors Partitioning step 1 too large for 1 processors. ERROR IN INPUT. [0]Got new tag 2147483513 [0]Got new tag 2147483512 [0]Got new tag 2147483513 [0]Got new tag 2147483512 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' viewing GeneralSection 'Serial Section' Fields: 0 [0]: 2 dim 2 offset 0 -0.5 -0.5 [0]: 3 dim 2 offset 2 0.5 -0.5 [0]: 4 dim 2 offset 4 -0.5 0.5 [0]: 5 dim 2 offset 6 0.5 0.5 [0]Got new tag 2147483519 [0]Got new tag 2147483511 [0]Got new tag 2147483511 [0]Got new tag 2147483510 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' viewing GeneralSection 'Parallel Section' Fields: 0 [0]: 2 dim 2 offset 0 -0.5 -0.5 [0]: 3 dim 2 offset 2 0.5 -0.5 [0]: 4 dim 2 offset 4 -0.5 0.5 [0]: 5 dim 2 offset 6 0.5 0.5 viewing Section end points : Serial Section' [0]: 2 dim 1 offset 0 0 [0]: 5 dim 1 offset 1 0 [0]Got new tag 2147483510 [0]Got new tag 2147483509 [0]Got new tag 2147483509 [0]Got new tag 2147483508 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' viewing Section : Parallel Section' [0]: 2 dim 1 offset 0 0 [0]: 5 dim 1 offset 1 0 viewing Section fault : Serial Section' [0]: 3 dim 1 offset 0 0 [0]: 4 dim 1 offset 1 0 [0]Got new tag 2147483508 [0]Got new tag 2147483507 [0]Got new tag 2147483507 [0]Got new tag 2147483506 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' viewing Section : Parallel Section' [0]: 3 dim 1 offset 0 0 [0]: 4 dim 1 offset 1 0 viewing Section x_neg : Serial Section' [0]: 2 dim 1 offset 0 0 [0]: 4 dim 1 offset 1 0 [0]Got new tag 2147483506 [0]Got new tag 2147483505 [0]Got new tag 2147483505 [0]Got new tag 2147483504 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' viewing Section : Parallel Section' [0]: 2 dim 1 offset 0 0 [0]: 4 dim 1 offset 1 0 viewing Section x_pos : Serial Section' [0]: 3 dim 1 offset 0 0 [0]: 5 dim 1 offset 1 0 [0]Got new tag 2147483504 [0]Got new tag 2147483503 [0]Got new tag 2147483503 [0]Got new tag 2147483502 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' viewing Section : Parallel Section' [0]: 3 dim 1 offset 0 0 [0]: 5 dim 1 offset 1 0 viewing UniformSection 'Serial ArrowSection' [0]: empty [0]Got new tag 2147483502 [0]Got new tag 2147483501 [0]Got new tag 2147483501 [0]Got new tag 2147483500 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' viewing UniformSection 'Parallel ArrowSection' [0]: empty viewing Mesh 'Parallel Mesh' viewing a Sieve, comm = 1140850688, commRank = 0 viewing Sieve :'mesh sieve' cap --> base: [0]: 2--(0)-->0 [0]: 3--(0)-->1 [0]: 3--(1)-->0 [0]: 4--(2)-->0 [0]: 4--(2)-->1 [0]: 5--(1)-->1 base --> cap: [0]: 0<--(0)--2 [0]: 0<--(1)--3 [0]: 0<--(2)--4 [0]: 1<--(0)--3 [0]: 1<--(1)--5 [0]: 1<--(2)--4 cap : [0]: [ <2, 0, 0, 0, 0> <3, 0, 0, 0, 0> <4, 0, 0, 0, 0> <5, 0, 0, 0, 0> ] base : [0]: [ <0,0, 0, 0, 0> <1,0, 0, 0, 0> ] viewing GeneralSection 'coordinates' Fields: 0 [0]: 2 dim 2 offset 0 -0.5 -0.5 [0]: 3 dim 2 offset 2 0.5 -0.5 [0]: 4 dim 2 offset 4 -0.5 0.5 [0]: 5 dim 2 offset 6 0.5 0.5 viewing Section : end points' [0]: 2 dim 1 offset 0 0 [0]: 5 dim 1 offset 1 0 viewing Section : fault' [0]: 3 dim 1 offset 0 0 [0]: 4 dim 1 offset 1 0 viewing Section : x_neg' [0]: 2 dim 1 offset 0 0 [0]: 4 dim 1 offset 1 0 viewing Section : x_pos' [0]: 3 dim 1 offset 0 0 [0]: 5 dim 1 offset 1 0 viewing UniformSection 'orientation' [0]: empty >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/TimeDependent.py:92:initialize -- timedependent(info) -- Initializing problem. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Formulation.py:89:initialize -- implicit(info) -- Initializing materials. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/feassemble/quadrature/Quadrature.py:78:initialize -- quadrature2d(info) -- Initializing reference cell. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/feassemble/FIATSimplex.py:138:initialize -- fiatsimplex(info) -- Cell geometry: -- -- Vertices: -- [[-1. -1.] [ 1. -1.] [-1. 1.]] -- Quad pts: -- [[-0.64288254 -0.68989795] [-0.84993778 0.28989795] [ 0.33278049 -0.68989795] [-0.43996017 0.28989795]] -- Quad wts: -- [ 0.63608276 0.36391724 0.63608276 0.36391724] -- Basis fns @ quad pts ): -- [[ 0.66639025 0.17855873 0.15505103] [ 0.28001992 0.07503111 0.64494897] [ 0.17855873 0.66639025 0.15505103] [ 0.07503111 0.28001992 0.64494897]] -- Basis fn derivatives @ quad pts: -- [[[ -5.00000000e-01 -5.00000000e-01] [ 5.00000000e-01 1.88464537e-17] [ 0.00000000e+00 5.00000000e-01]] [[ -5.00000000e-01 -5.00000000e-01] [ 5.00000000e-01 3.87306122e-17] [ 0.00000000e+00 5.00000000e-01]] [[ -5.00000000e-01 -5.00000000e-01] [ 5.00000000e-01 8.74038606e-17] [ 0.00000000e+00 5.00000000e-01]] [[ -5.00000000e-01 -5.00000000e-01] [ 5.00000000e-01 6.75387159e-17] [ 0.00000000e+00 5.00000000e-01]]] >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/feassemble/quadrature/Quadrature.py:88:initialize -- quadrature2d(info) -- Initializing C++ quadrature. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Formulation.py:106:initialize -- implicit(info) -- Added elasticity integrator for material 'elastic material'. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Formulation.py:108:initialize -- implicit(info) -- Initializing boundary conditions. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Formulation.py:121:initialize -- implicit(info) -- Added boundary condition 'end points' as a constraint. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Formulation.py:127:initialize -- implicit(info) -- Initializing interior interfaces. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Formulation.py:146:initialize -- implicit(info) -- Setting up solution output. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Formulation.py:151:initialize -- implicit(info) -- Creating solution field. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Implicit.py:92:initialize -- implicit(info) -- Creating other fields and matrices. viewing a Sifter, comm = 1140850688, PETSC_COMM_SELF = 1140850689, commRank = 0 viewing Sifter: 'Send overlap' cap --> base: [0]: empty cap: [0]: [ ] base: [0]: [ ] viewing a Sifter, comm = 1140850688, PETSC_COMM_SELF = 1140850689, commRank = 0 viewing Sifter: 'Receive overlap' cap --> base: [0]: empty cap: [0]: [ ] base: [0]: [ ] [0]Got new tag 2147483519 [0]Got new tag 2147483500 [0]Got new tag 2147483499 [0]Got new tag 2147483498 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' Creating new global order: name default [0]Got new tag 2147483499 [0]Got new tag 2147483518 [0]Got new tag 2147483498 [0]Got new tag 2147483497 [0]Got new tag 2147483496 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' [0]: dnz[0]: 4 onz[0]: 0 [0]: dnz[1]: 4 onz[1]: 0 [0]: dnz[2]: 4 onz[2]: 0 [0]: dnz[3]: 4 onz[3]: 0 [0]Got new tag 2147483519 [0]Got new tag 2147483519 [0]Got new tag 2147483519 [0]Got new tag 2147483518 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' Creating new global order: name viewing UniformSection 'Global Order' [0]: 2 dim 1 (0, 0) [0]: 3 dim 1 (0, 2) [0]: 4 dim 1 (2, 2) [0]: 5 dim 1 (4, 0) [0] localIndex[0]: 2 globalIndex[0]: 0 [0] localIndex[1]: 3 globalIndex[1]: 1 [0] localIndex[2]: 4 globalIndex[2]: 2 [0] localIndex[3]: 5 globalIndex[3]: 3 >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/TimeDependent.py:109:run -- timedependent(info) -- Solving problem. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Implicit.py:118:stableTimeStep -- implicit(info) -- WARNING: Implicit::stableTimeStep() not implemented. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/TimeDependent.py:117:run -- timedependent(info) -- Main time loop, current time is t=-1*s >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Implicit.py:118:stableTimeStep -- implicit(info) -- WARNING: Implicit::stableTimeStep() not implemented. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/TimeDependent.py:183:_prestep -- timedependent(info) -- Preparing to advance solution from time t=-1*s. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Implicit.py:130:prestep -- implicit(info) -- Setting constraints. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Formulation.py:204:_reformJacobian -- implicit(info) -- Reforming Jacobian of operator. [0]mat for element 0 [0]mat indices[0] = -1 [0]mat indices[1] = -2 [0]mat indices[2] = 0 [0]mat indices[3] = 1 [0]mat indices[4] = 2 [0]mat indices[5] = 3 [0] 6e+10 3e+10 -4.5e+10 -1.5e+10 -1.5e+10 -1.5e+10 [0] 3e+10 6e+10 -1.5e+10 -1.5e+10 -1.5e+10 -4.5e+10 [0] -4.5e+10 -1.5e+10 4.5e+10 9.92737e-07 4.96369e-07 1.5e+10 [0] -1.5e+10 -1.5e+10 9.92737e-07 1.5e+10 1.5e+10 1.48911e-06 [0] -1.5e+10 -1.5e+10 4.96369e-07 1.5e+10 1.5e+10 0 [0] -1.5e+10 -4.5e+10 1.5e+10 1.48911e-06 0 4.5e+10 [0]mat for element 1 [0]mat indices[0] = 0 [0]mat indices[1] = 1 [0]mat indices[2] = -1 [0]mat indices[3] = -2 [0]mat indices[4] = 2 [0]mat indices[5] = 3 [0] 1.5e+10 1.21209e-06 -1.5e+10 -1.5e+10 1.81813e-06 1.5e+10 [0] 1.21209e-06 4.5e+10 -1.5e+10 -4.5e+10 1.5e+10 6.06044e-07 [0] -1.5e+10 -1.5e+10 6e+10 3e+10 -4.5e+10 -1.5e+10 [0] -1.5e+10 -4.5e+10 3e+10 6e+10 -1.5e+10 -1.5e+10 [0] 1.81813e-06 1.5e+10 -4.5e+10 -1.5e+10 4.5e+10 0 [0] 1.5e+10 6.06044e-07 -1.5e+10 -1.5e+10 0 1.5e+10 >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/TimeDependent.py:192:_step -- timedependent(info) -- Advancing solution from t=-1*s to t=0*s. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Implicit.py:148:step -- implicit(info) -- Integrating residual term in operator. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Implicit.py:158:step -- implicit(info) -- Completing residual. [0]Got new tag 2147483518 [0]Got new tag 2147483497 [0]Got new tag 2147483495 [0]Got new tag 2147483494 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Implicit.py:161:step -- implicit(info) -- Solving equations. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/solver/SolverLinear.py:67:solve -- solverlinear(info) -- Solving linear equations. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/TimeDependent.py:201:_poststep -- timedependent(info) -- Finishing advancing solution to t=0*s. >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/problems/Implicit.py:180:poststep -- implicit(info) -- Updating integrators states. [0]Got new tag 2147483519 [0]Got new tag 2147483518 [0]Got new tag 2147483519 [0]Got new tag 2147483518 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' Creating new numbering: depth 0 Creating new ParallelFactory [0]Got new tag 2147483517 [0]Got new tag 2147483516 [0]Got new tag 2147483517 [0]Got new tag 2147483516 viewing Field 'Send Sizer in Completion' viewing Field 'Receive Sizer in Completion' viewing Field 'Send Section in Completion' viewing Field 'Receive Section in Completion' Creating new numbering: depth 1 >> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/utils/PetscManager.py:63:finalize -- petsc(info) -- Finalizing PETSc.