FAILED test/base/test_roadrunner.py::test_petab_case[0018-sbml-v1.0.0]

[dweindl]

test/base/test_roadrunner.py::test_petab_case[0018-sbml-v1.0.0] fails with:

RuntimeError: SteadyStateSolver failed to solve presimulation program: Jacobian matrix singular in NLEQ. Failed to converge to steady state. Check if Jacobian matrix is non-invertible or steady state solution does not exist.

@PaulJonasJost Can we use simulation-based pre-equilibration with roadrunner by default?

[dweindl]

Can we use simulation-based pre-equilibration with roadrunner by default?

Apparently we can't (at least not without implementing our own steady-state checks):

https://libroadrunner.readthedocs.io/en/latest/tutorial/solvers.html:

Currently, RoadRunner only has a single steady state solver (NLEQ).

https://libroadrunner.readthedocs.io/en/latest/PythonAPIReference/cls_SteadyStateSolver.html#nleq2:

NLEQ2 is a non-linear equation solver which uses a global Newton method with adaptive damping strategies

[PaulJonasJost]

roadrunner uses presimulation. It also uses a different steady state solver than amicis newton. I changed the presimulation times and the solver and locally it worked now (see #1604)

[dweindl]

roadrunner uses presimulation. It also uses a different steady state solver than amicis newton. I changed the presimulation times and the solver and locally it worked now (see #1604)

This test still fails on macos-latest (https://github.com/ICB-DCM/pyPESTO/actions/runs/18831360344/job/53723290667?pr=1629, #1629), but now with a different error:

ERROR    test.base.test_roadrunner:test_roadrunner.py:99 LLH: simulated: -4.35823840888611, expected: -6.3898204385477, match = False
ERROR    test.base.test_roadrunner:test_roadrunner.py:103 Simulations: match = False
ERROR    test.base.test_roadrunner:test_roadrunner.py:109 Case v1.0.0/sbml/0018 failed.