1:~/build/pylith/tests/axial_incomp$ pylith poro_test.cfg >> /home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/problems/Problem.py:136:preinitialize -- timedependent(info) -- Performing minimal initialization before verifying configuration. >> ../../../pylith/libsrc/pylith/problems/Problem.cc:97:void pylith::problems::Problem::setSolverType(pylith::problems::Problem::SolverTypeEnum) -- timedependent(debug) -- Component 'problem': Problem::setSolverType(value=1) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:115:void pylith::problems::Problem::setNormalizer(const spatialdata::units::Nondimensional&) -- timedependent(debug) -- Component 'problem': Problem::setNormalizer(dim=N11spatialdata5units14NondimensionalE) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:129:void pylith::problems::Problem::setGravityField(spatialdata::spatialdb::GravityField*) -- timedependent(debug) -- Component 'problem': Problem::setGravityField(g=PN11spatialdata9spatialdb12GravityFieldE) >> /home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/problems/Solution.py:66:preinitialize -- solution(info) -- Performing minimal initialization of solution. >> /home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/problems/Solution.py:77:preinitialize -- solution(debug) -- Adding subfield 'displacement' as 'displacement' with components ['displacement_x', 'displacement_y'] to solution. >> /home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/problems/Solution.py:77:preinitialize -- solution(debug) -- Adding subfield 'pressure' as 'pressure' with components ['pressure'] to solution. >> /home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/problems/Solution.py:77:preinitialize -- solution(debug) -- Adding subfield 'trace_strain' as 'trace_strain' with components ['trace_strain'] to solution. >> ../../../pylith/libsrc/pylith/problems/Problem.cc:169:void pylith::problems::Problem::setSolution(pylith::topology::Field*) -- timedependent(debug) -- Component 'problem': Problem::setSolution(field=N6pylith8topology5FieldE) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:181:void pylith::problems::Problem::setMaterials(pylith::materials::Material**, int) -- timedependent(debug) -- Component 'problem': Problem::setMaterials(0x560534801420, numMaterials=1) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:200:void pylith::problems::Problem::setBoundaryConditions(pylith::bc::BoundaryCondition**, int) -- timedependent(debug) -- Component 'problem': Problem::setBoundaryConditions(0, numBC=0) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:219:void pylith::problems::Problem::setInterfaces(pylith::faults::FaultCohesive**, int) -- timedependent(debug) -- Component 'problem': Problem::setInterfaces(0, numInterfaces=0) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:140:void pylith::problems::Problem::registerObserver(pylith::problems::ObserverSoln*) -- timedependent(debug) -- Component 'problem': registerObserver(observer=PN6pylith8problems12ObserverSolnE) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:237:virtual void pylith::problems::Problem::preinitialize(const pylith::topology::Mesh&) -- timedependent(debug) -- Component 'problem': Problem::preinitialzie(mesh=N6pylith8topology4MeshE) >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:95:void pylith::problems::TimeDependent::setStartTime(double) -- timedependent(debug) -- Component 'problem': startTime(value=-1) >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:166:void pylith::problems::TimeDependent::setInitialTimeStep(double) -- timedependent(debug) -- Component 'problem': setInitialTimeStep(value=1) >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:114:void pylith::problems::TimeDependent::setTotalTime(double) -- timedependent(debug) -- Component 'problem': totalTime(value=0) >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:140:void pylith::problems::TimeDependent::setMaxTimeSteps(size_t) -- timedependent(debug) -- Component 'problem': maxTimeSteps(value=20000) >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:193:void pylith::problems::TimeDependent::setInitialCondition(pylith::problems::InitialCondition**, int) -- timedependent(debug) -- Component 'problem': setInitialCondition(ic=0, numIC=0) >> /home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/problems/Problem.py:185:verifyConfiguration -- timedependent(info) -- Verifying compatibility of problem configuration. >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:256:virtual void pylith::problems::TimeDependent::verifyConfiguration() const -- timedependent(debug) -- Component 'problem': Problem::verifyConfiguration(void) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:269:virtual void pylith::problems::Problem::verifyConfiguration() const -- timedependent(debug) -- Component 'problem': Problem::verifyConfiguration(void) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:606:void pylith::problems::Problem::_checkMaterialIds() const -- timedependent(debug) -- Component 'problem': Problem::_checkMaterialIds() >> /home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/problems/Problem.py:241:_printInfo -- timedependent(info) -- Scales for nondimensionalization: Length scale: 1000*m Time scale: 1*s Pressure scale: 3e+10*m**-1*kg*s**-2 Density scale: 30000*m**-3*kg Temperature scale: 1*K >> /home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/problems/Problem.py:199:initialize -- timedependent(info) -- Initializing problem. >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:278:virtual void pylith::problems::TimeDependent::initialize() -- timedependent(debug) -- Component 'problem': initialize() >> ../../../pylith/libsrc/pylith/problems/Problem.cc:308:virtual void pylith::problems::Problem::initialize() -- timedependent(debug) -- Component 'problem': Problem::initialize() >> ../../../pylith/libsrc/pylith/problems/Problem.cc:633:void pylith::problems::Problem::_createIntegrators() -- timedependent(debug) -- Component 'problem': Problem::_createIntegrators() >> ../../../pylith/libsrc/pylith/problems/Problem.cc:676:void pylith::problems::Problem::_createConstraints() -- timedependent(debug) -- Component 'problem': Problem::_createConstraints() >> ../../../pylith/libsrc/pylith/problems/Problem.cc:344:virtual void pylith::problems::Problem::initialize() -- timedependent(debug) -- Component 'problem': Displaying solution field layout Viewing field 'solution' Solution field. Subfields: Subfield displacement, index: 0, components: displacement_x displacement_y, scale: 1000, basisOrder: 1, quadOrder: 2, dimension: -1 Subfield pressure, index: 1, components: pressure, scale: 3e+10, basisOrder: 1, quadOrder: 2, dimension: -1 Subfield trace_strain, index: 2, components: trace_strain, scale: 1, basisOrder: 1, quadOrder: 2, dimension: -1 dimensionalize flag: 0 DM Object: solution_global 1 MPI processes type: plex solution_global in 2 dimensions: 0-cells: 20 1-cells: 31 2-cells: 12 Labels: depth: 3 strata with value/size (0 (20), 1 (31), 2 (12)) material-id: 1 strata with value/size (0 (12)) boundary_xneg: 1 strata with value/size (1 (9)) boundary_yneg: 1 strata with value/size (1 (7)) boundary_xpos: 1 strata with value/size (1 (9)) boundary_ypos: 1 strata with value/size (1 (7)) Field displacement: adjacency FEM Field pressure: adjacency FEM Field trace_strain: adjacency FEM PetscSection Object: 1 MPI processes type not yet set 3 fields field 0 with 2 components Process 0: ( 0) dim 0 offset 0 ( 1) dim 0 offset 0 ( 2) dim 0 offset 0 ( 3) dim 0 offset 0 ( 4) dim 0 offset 0 ( 5) dim 0 offset 0 ( 6) dim 0 offset 0 ( 7) dim 0 offset 0 ( 8) dim 0 offset 0 ( 9) dim 0 offset 0 ( 10) dim 0 offset 0 ( 11) dim 0 offset 0 ( 12) dim 2 offset 0 ( 13) dim 2 offset 4 ( 14) dim 2 offset 8 ( 15) dim 2 offset 12 ( 16) dim 2 offset 16 ( 17) dim 2 offset 20 ( 18) dim 2 offset 24 ( 19) dim 2 offset 28 ( 20) dim 2 offset 32 ( 21) dim 2 offset 36 ( 22) dim 2 offset 40 ( 23) dim 2 offset 44 ( 24) dim 2 offset 48 ( 25) dim 2 offset 52 ( 26) dim 2 offset 56 ( 27) dim 2 offset 60 ( 28) dim 2 offset 64 ( 29) dim 2 offset 68 ( 30) dim 2 offset 72 ( 31) dim 2 offset 76 ( 32) dim 0 offset 80 ( 33) dim 0 offset 80 ( 34) dim 0 offset 80 ( 35) dim 0 offset 80 ( 36) dim 0 offset 80 ( 37) dim 0 offset 80 ( 38) dim 0 offset 80 ( 39) dim 0 offset 80 ( 40) dim 0 offset 80 ( 41) dim 0 offset 80 ( 42) dim 0 offset 80 ( 43) dim 0 offset 80 ( 44) dim 0 offset 80 ( 45) dim 0 offset 80 ( 46) dim 0 offset 80 ( 47) dim 0 offset 80 ( 48) dim 0 offset 80 ( 49) dim 0 offset 80 ( 50) dim 0 offset 80 ( 51) dim 0 offset 80 ( 52) dim 0 offset 80 ( 53) dim 0 offset 80 ( 54) dim 0 offset 80 ( 55) dim 0 offset 80 ( 56) dim 0 offset 80 ( 57) dim 0 offset 80 ( 58) dim 0 offset 80 ( 59) dim 0 offset 80 ( 60) dim 0 offset 80 ( 61) dim 0 offset 80 ( 62) dim 0 offset 80 field 1 with 1 components Process 0: ( 0) dim 0 offset 0 ( 1) dim 0 offset 0 ( 2) dim 0 offset 0 ( 3) dim 0 offset 0 ( 4) dim 0 offset 0 ( 5) dim 0 offset 0 ( 6) dim 0 offset 0 ( 7) dim 0 offset 0 ( 8) dim 0 offset 0 ( 9) dim 0 offset 0 ( 10) dim 0 offset 0 ( 11) dim 0 offset 0 ( 12) dim 1 offset 2 ( 13) dim 1 offset 6 ( 14) dim 1 offset 10 ( 15) dim 1 offset 14 ( 16) dim 1 offset 18 ( 17) dim 1 offset 22 ( 18) dim 1 offset 26 ( 19) dim 1 offset 30 ( 20) dim 1 offset 34 ( 21) dim 1 offset 38 ( 22) dim 1 offset 42 ( 23) dim 1 offset 46 ( 24) dim 1 offset 50 ( 25) dim 1 offset 54 ( 26) dim 1 offset 58 ( 27) dim 1 offset 62 ( 28) dim 1 offset 66 ( 29) dim 1 offset 70 ( 30) dim 1 offset 74 ( 31) dim 1 offset 78 ( 32) dim 0 offset 80 ( 33) dim 0 offset 80 ( 34) dim 0 offset 80 ( 35) dim 0 offset 80 ( 36) dim 0 offset 80 ( 37) dim 0 offset 80 ( 38) dim 0 offset 80 ( 39) dim 0 offset 80 ( 40) dim 0 offset 80 ( 41) dim 0 offset 80 ( 42) dim 0 offset 80 ( 43) dim 0 offset 80 ( 44) dim 0 offset 80 ( 45) dim 0 offset 80 ( 46) dim 0 offset 80 ( 47) dim 0 offset 80 ( 48) dim 0 offset 80 ( 49) dim 0 offset 80 ( 50) dim 0 offset 80 ( 51) dim 0 offset 80 ( 52) dim 0 offset 80 ( 53) dim 0 offset 80 ( 54) dim 0 offset 80 ( 55) dim 0 offset 80 ( 56) dim 0 offset 80 ( 57) dim 0 offset 80 ( 58) dim 0 offset 80 ( 59) dim 0 offset 80 ( 60) dim 0 offset 80 ( 61) dim 0 offset 80 ( 62) dim 0 offset 80 field 2 with 1 components Process 0: ( 0) dim 0 offset 0 ( 1) dim 0 offset 0 ( 2) dim 0 offset 0 ( 3) dim 0 offset 0 ( 4) dim 0 offset 0 ( 5) dim 0 offset 0 ( 6) dim 0 offset 0 ( 7) dim 0 offset 0 ( 8) dim 0 offset 0 ( 9) dim 0 offset 0 ( 10) dim 0 offset 0 ( 11) dim 0 offset 0 ( 12) dim 1 offset 3 ( 13) dim 1 offset 7 ( 14) dim 1 offset 11 ( 15) dim 1 offset 15 ( 16) dim 1 offset 19 ( 17) dim 1 offset 23 ( 18) dim 1 offset 27 ( 19) dim 1 offset 31 ( 20) dim 1 offset 35 ( 21) dim 1 offset 39 ( 22) dim 1 offset 43 ( 23) dim 1 offset 47 ( 24) dim 1 offset 51 ( 25) dim 1 offset 55 ( 26) dim 1 offset 59 ( 27) dim 1 offset 63 ( 28) dim 1 offset 67 ( 29) dim 1 offset 71 ( 30) dim 1 offset 75 ( 31) dim 1 offset 79 ( 32) dim 0 offset 80 ( 33) dim 0 offset 80 ( 34) dim 0 offset 80 ( 35) dim 0 offset 80 ( 36) dim 0 offset 80 ( 37) dim 0 offset 80 ( 38) dim 0 offset 80 ( 39) dim 0 offset 80 ( 40) dim 0 offset 80 ( 41) dim 0 offset 80 ( 42) dim 0 offset 80 ( 43) dim 0 offset 80 ( 44) dim 0 offset 80 ( 45) dim 0 offset 80 ( 46) dim 0 offset 80 ( 47) dim 0 offset 80 ( 48) dim 0 offset 80 ( 49) dim 0 offset 80 ( 50) dim 0 offset 80 ( 51) dim 0 offset 80 ( 52) dim 0 offset 80 ( 53) dim 0 offset 80 ( 54) dim 0 offset 80 ( 55) dim 0 offset 80 ( 56) dim 0 offset 80 ( 57) dim 0 offset 80 ( 58) dim 0 offset 80 ( 59) dim 0 offset 80 ( 60) dim 0 offset 80 ( 61) dim 0 offset 80 ( 62) dim 0 offset 80 >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:316:virtual void pylith::problems::TimeDependent::initialize() -- timedependent(debug) -- Component 'problem': Recognized PetscTS as implicit time stepping. >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:331:virtual void pylith::problems::TimeDependent::initialize() -- timedependent(debug) -- Component 'problem': Setting PetscTS problem type to 'nonlinear'. >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:341:virtual void pylith::problems::TimeDependent::initialize() -- timedependent(debug) -- Component 'problem': Setting PetscTS parameters: dtInitial=1, startTime=-1, maxTimeSteps=20000, totalTime=0 >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:352:virtual void pylith::problems::TimeDependent::initialize() -- timedependent(debug) -- Component 'problem': Setting PetscTS initial conditions using global vector for solution. >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:365:virtual void pylith::problems::TimeDependent::initialize() -- timedependent(debug) -- Component 'problem': Setting PetscTS callbacks prestep(), poststep(), computeRHSJacobian(), and computeRHSFunction(). >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:372:virtual void pylith::problems::TimeDependent::initialize() -- timedependent(debug) -- Component 'problem': Setting PetscTS callbacks computeLHSJacobian(), and computeLHSFunction(). >> /home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:129:run -- timedependent(info) -- Solving problem. >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:405:void pylith::problems::TimeDependent::solve() -- timedependent(debug) -- Component 'problem': solve() 0 TS dt 1. time -1. >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:607:static PetscErrorCode pylith::problems::TimeDependent::prestep(PetscTS) -- timedependent(debug) -- prestep(ts=0x560535d21780) >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:418:void pylith::problems::TimeDependent::prestep() -- timedependent(debug) -- Component 'problem': prestep() >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:559:static PetscErrorCode pylith::problems::TimeDependent::computeLHSResidual(PetscTS, PetscReal, PetscVec, PetscVec, PetscVec, void*) -- timedependent(debug) -- computeLHSResidual(ts=0x560535d21780, t=0, solutionVec=0x560535d58ab0, solutionDotVec=0x560535d5cab0, residualVec=0x560535e09ed0, context=0x5605347857a0) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:481:void pylith::problems::Problem::computeLHSResidual(PetscVec, PylithReal, PylithReal, PetscVec, PetscVec) -- timedependent(debug) -- Component 'problem': Problem::computeLHSResidual(t=0, dt=1, solutionVec=0x560535d58ab0, solutionDotVec=0x560535d5cab0, residualVec=0x560535e09ed0) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:364:void pylith::problems::Problem::setSolutionLocal(PylithReal, PetscVec, PetscVec) -- timedependent(debug) -- Component 'problem': setSolutionLocal(t=0, solutionVec=0x560535d58ab0, solutionDotVec=0x560535d5cab0) >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:500:static PetscErrorCode pylith::problems::TimeDependent::computeRHSResidual(PetscTS, PetscReal, PetscVec, PetscVec, void*) -- timedependent(debug) -- computeRHSResidual(ts=0x560535d21780, t=0, solutionVec=0x560535d58ab0, residualVec=0x560535fbd2c0, context=0x5605347857a0) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:398:void pylith::problems::Problem::computeRHSResidual(PetscVec, PylithReal, PylithReal, PetscVec) -- timedependent(debug) -- Component 'problem': Problem::computeRHSResidual(t=0, dt=1, solutionVec=0x560535d58ab0, residualVec=0x560535fbd2c0) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:364:void pylith::problems::Problem::setSolutionLocal(PylithReal, PetscVec, PetscVec) -- timedependent(debug) -- Component 'problem': setSolutionLocal(t=0, solutionVec=0x560535d58ab0, solutionDotVec=0) 0 SNES Function norm 3.635727225120e-02 >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:586:static PetscErrorCode pylith::problems::TimeDependent::computeLHSJacobian(PetscTS, PetscReal, PetscVec, PetscVec, PetscReal, PetscMat, PetscMat, void*) -- timedependent(debug) -- computeLHSJacobian(ts=0x560535d21780, t=0, solutionVec=0x560535d58ab0, solutionDotVec=0x560535d5cab0, s_tshift=1, jacobianMat=0x560535e0d570, precondMat=0x560535e0d570, context=0x5605347857a0) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:518:void pylith::problems::Problem::computeLHSJacobian(PetscMat, PetscMat, PylithReal, PylithReal, PylithReal, PetscVec, PetscVec) -- timedependent(debug) -- Component 'problem': Problem::computeLHSJacobian(t=0, dt=1, s_tshift=1, solutionVec=0x560535d58ab0, solutionDotVec=0x560535d5cab0, jacobianMat=0x560535e0d570, precondMat=0x560535e0d570) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:364:void pylith::problems::Problem::setSolutionLocal(PylithReal, PetscVec, PetscVec) -- timedependent(debug) -- Component 'problem': setSolutionLocal(t=0, solutionVec=0x560535d58ab0, solutionDotVec=0x560535d5cab0) >> ../../../pylith/libsrc/pylith/problems/TimeDependent.cc:534:static PetscErrorCode pylith::problems::TimeDependent::computeRHSJacobian(PetscTS, PetscReal, PetscVec, PetscMat, PetscMat, void*) -- timedependent(debug) -- computeRHSJacobian(ts=0x560535d21780, t=0, solutionVec=0x560535d58ab0, jacobianMat=0x560535fce120, precondMat=0x560535fce120, context=0x5605347857a0) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:433:void pylith::problems::Problem::computeRHSJacobian(PetscMat, PetscMat, PylithReal, PylithReal, PetscVec) -- timedependent(debug) -- Component 'problem': Problem::computeRHSJacobian(t=0, dt=1, solutionVec=0x560535d58ab0, jacobianMat=0x560535fce120, precondMat=0x560535fce120) >> ../../../pylith/libsrc/pylith/problems/Problem.cc:364:void pylith::problems::Problem::setSolutionLocal(PylithReal, PetscVec, PetscVec) -- timedependent(debug) -- Component 'problem': setSolutionLocal(t=0, solutionVec=0x560535d58ab0, solutionDotVec=0) Fatal error. Calling MPI_Abort() to abort PyLith application. Traceback (most recent call last): File "/home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 74, in onComputeNodes self.main(*args, **kwds) File "/home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 129, in main self.problem.run(self) File "/home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/problems/TimeDependent.py", line 131, in run ModuleTimeDependent.solve(self) File "/home/dockimble/build/pylith/lib/python2.7/site-packages/pylith/problems/problems.py", line 184, in solve def solve(self): return _problems.TimeDependent_solve(self) RuntimeError: Could not find subfield '' in field 'solution'. Available subfields: 'displacement' 'pressure' 'trace_strain' application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=-1 : system msg for write_line failure : Bad file descriptor ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[27249,1],0] Exit code: 255 -------------------------------------------------------------------------- /home/dockimble/build/pylith/bin/nemesis: mpirun: exit 255 /home/dockimble/build/pylith/bin/pylith: /home/dockimble/build/pylith/bin/nemesis: exit 1