@xinshen I have managed to reproduce your issue with the mesh you sent me.
The full error message is:
Succesfully load mesh with 845815 cells
/home/remidm/FESTIM/festim/stepsize.py:54: DeprecationWarning: stepsize_stop_max and t_stop attributes will be deprecated in a future release, please use max_stepsize instead
warnings.warn(
/home/remidm/FESTIM/festim/exports/derived_quantities/derived_quantities.py:64: DeprecationWarning: The derived_quantities attribute will be deprecated in a future release, please use festim.DerivedQuantities as a list instead
warnings.warn(
Calling FFC just-in-time (JIT) compiler, this may take some time.
/home/remidm/FESTIM/festim/materials/materials.py:151: UserWarning: rho key will be ignored
warnings.warn(key + " key will be ignored", UserWarning)
/home/remidm/FESTIM/festim/materials/materials.py:151: UserWarning: heat_capacity key will be ignored
warnings.warn(key + " key will be ignored", UserWarning)
/home/remidm/FESTIM/festim/materials/materials.py:169: UserWarning: thermal_cond key will be ignored
warnings.warn("thermal_cond key will be ignored", UserWarning)
Calling FFC just-in-time (JIT) compiler, this may take some time.
No Jacobian form specified for nonlinear variational problem.
Differentiating residual form F to obtain Jacobian J = F'.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Solving nonlinear variational problem.
Newton iteration 0: r (abs) = 0.000e+00 (tol = 1.000e-10) r (rel) = -nan (tol = 1.000e-09)
Newton solver finished in 0 iterations and 0 linear solver iterations.
No Jacobian form specified for nonlinear variational problem.
Differentiating residual form F to obtain Jacobian J = F'.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Solving nonlinear variational problem.
Newton iteration 0: r (abs) = 1.930e-08 (tol = 1.000e-10) r (rel) = 1.000e+00 (tol = 1.000e-09)
Newton iteration 1: r (abs) = 0.000e+00 (tol = 1.000e-10) r (rel) = 0.000e+00 (tol = 1.000e-09)
Newton solver finished in 1 iterations and 1 linear solver iterations.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Defining initial values
Defining variational problem
Defining source terms
Defining boundary conditions
Time stepping...
Calling FFC just-in-time (JIT) compiler, this may take some time.
WARNING: The number of integration points for each cell will be: 125
Consider using the option 'quadrature_degree' to reduce the number of points
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
Calling FFC just-in-time (JIT) compiler, this may take some time.
WARNING: The number of integration points for each cell will be: 125
Consider using the option 'quadrature_degree' to reduce the number of points
Solving nonlinear variational problem.
Newton iteration 0: r (abs) = 4.491e+25 (tol = 1.000e+11) r (rel) = 1.000e+00 (tol = 1.000e-10)
UMFPACK V5.7.9 (Oct 20, 2019): ERROR: out of memory
Traceback (most recent call last):
File "/home/remidm/FESTIM/xin.py", line 185, in <module>
my_model.run()
File "/home/remidm/FESTIM/festim/generic_simulation.py", line 365, in run
self.run_transient()
File "/home/remidm/FESTIM/festim/generic_simulation.py", line 388, in run_transient
self.iterate()
File "/home/remidm/FESTIM/festim/generic_simulation.py", line 416, in iterate
self.h_transport_problem.update(self.t, self.dt)
File "/home/remidm/FESTIM/festim/h_transport_problem.py", line 250, in update
nb_it, converged = self.solve_once()
^^^^^^^^^^^^^^^^^
File "/home/remidm/FESTIM/festim/h_transport_problem.py", line 288, in solve_once
nb_it, converged = solver.solve()
^^^^^^^^^^^^^^
RuntimeError:
*** -------------------------------------------------------------------------
*** DOLFIN encountered an error. If you are not able to resolve this issue
*** using the information listed below, you can ask for help at
***
*** fenics-support@googlegroups.com
***
*** Remember to include the error message listed below and, if possible,
*** include a *minimal* running example to reproduce the error.
***
*** -------------------------------------------------------------------------
*** Error: Unable to successfully call PETSc function 'KSPSolve'.
*** Reason: PETSc error code is: 76 (Error in external library).
*** Where: This error was encountered inside /home/conda/feedstock_root/build_artifacts/fenics-pkgs_1696906506503/work/dolfin/dolfin/la/PETScKrylovSolver.cpp.
*** Process: 0
***
*** DOLFIN version: 2019.1.0
*** Git changeset: 2e001bd1aae8e14d758264f77382245e6eed04b0
*** -------------------------------------------------------------------------
As indicated by the error message UMFPACK V5.7.9 (Oct 20, 2019): ERROR: out of memory it is a memory issue.
Several things you can try:
- using MUMPS as a linear solver
my_model.settings = F.Settings(
absolute_tolerance=1e11,
relative_tolerance=1e-10,
maximum_iterations=20,
linear_solver="mumps",
traps_element_type="DG",
)
- grouping traps 1 2 3 into one trap. This will greatly reduce the number of degrees of freedom ( see this for more details)
- running the script in parallel with
mpirun -np 4 python your_script.py
Here 4 is the number of cores.
I’ve used MUMPS and grouped the traps and was able to have a few Newton iterations (although the model is struggling to converge, maybe due to the fairly low temperature, but that’s another problem)